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package net.sf.basedb.reggie.servlet; |
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|
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import java.io.IOException; |
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import java.net.URI; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Collections; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Set; |
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|
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import javax.servlet.ServletException; |
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import javax.servlet.http.HttpServlet; |
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import javax.servlet.http.HttpServletRequest; |
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import javax.servlet.http.HttpServletResponse; |
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|
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import org.jdom2.Element; |
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import org.json.simple.JSONArray; |
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import org.json.simple.JSONObject; |
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|
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import net.sf.basedb.core.Annotatable; |
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import net.sf.basedb.core.AnnotationType; |
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import net.sf.basedb.core.AnnotationTypeCategory; |
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import net.sf.basedb.core.Application; |
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import net.sf.basedb.core.BasicItem; |
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import net.sf.basedb.core.ItemList; |
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import net.sf.basedb.core.BioPlateEventType; |
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import net.sf.basedb.core.BioPlateType; |
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import net.sf.basedb.core.Client; |
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import net.sf.basedb.core.DataFileType; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.Directory; |
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import net.sf.basedb.core.Extract; |
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import net.sf.basedb.core.FileServer; |
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import net.sf.basedb.core.Group; |
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import net.sf.basedb.core.Include; |
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import net.sf.basedb.core.Item; |
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import net.sf.basedb.core.ItemKey; |
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import net.sf.basedb.core.ItemNotFoundException; |
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import net.sf.basedb.core.ItemQuery; |
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import net.sf.basedb.core.ItemSubtype; |
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import net.sf.basedb.core.ItemSubtypeFileType; |
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import net.sf.basedb.core.MimeType; |
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import net.sf.basedb.core.MultiPermissions; |
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import net.sf.basedb.core.Nameable; |
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import net.sf.basedb.core.Path; |
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import net.sf.basedb.core.Permission; |
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import net.sf.basedb.core.PlateGeometry; |
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import net.sf.basedb.core.Platform; |
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import net.sf.basedb.core.PlatformFileType; |
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import net.sf.basedb.core.PlatformVariant; |
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import net.sf.basedb.core.PluginConfiguration; |
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import net.sf.basedb.core.PluginDefinition; |
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import net.sf.basedb.core.Project; |
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import net.sf.basedb.core.ProjectKey; |
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import net.sf.basedb.core.RawBioAssay; |
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import net.sf.basedb.core.SessionControl; |
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import net.sf.basedb.core.SharedItem; |
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import net.sf.basedb.core.SystemItems; |
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import net.sf.basedb.core.Tag; |
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import net.sf.basedb.core.Type; |
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import net.sf.basedb.core.query.Expressions; |
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import net.sf.basedb.core.query.Hql; |
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import net.sf.basedb.core.query.Restrictions; |
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import net.sf.basedb.reggie.JsonUtil; |
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import net.sf.basedb.reggie.Reggie; |
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import net.sf.basedb.reggie.Site; |
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import net.sf.basedb.reggie.XmlConfig; |
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import net.sf.basedb.reggie.activity.ActivityDef; |
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import net.sf.basedb.reggie.counter.CounterService; |
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import net.sf.basedb.reggie.dao.Annotationtype; |
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import net.sf.basedb.reggie.dao.BarcodeSet; |
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import net.sf.basedb.reggie.dao.BiomaterialList; |
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import net.sf.basedb.reggie.dao.BioplateEventtype; |
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import net.sf.basedb.reggie.dao.BioplateType; |
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import net.sf.basedb.reggie.dao.ClientApp; |
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import net.sf.basedb.reggie.dao.Consent; |
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import net.sf.basedb.reggie.dao.Datafiletype; |
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import net.sf.basedb.reggie.dao.Dna; |
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import net.sf.basedb.reggie.dao.Fileserver; |
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import net.sf.basedb.reggie.dao.FlowCell; |
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import net.sf.basedb.reggie.dao.Geometry; |
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import net.sf.basedb.reggie.dao.Histology; |
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import net.sf.basedb.reggie.dao.Mimetype; |
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import net.sf.basedb.reggie.dao.Pipeline; |
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import net.sf.basedb.reggie.dao.PooledLibrary; |
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import net.sf.basedb.reggie.dao.Rawdatatype; |
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import net.sf.basedb.reggie.dao.ReactionPlate; |
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import net.sf.basedb.reggie.dao.ReferenceDateSource; |
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import net.sf.basedb.reggie.dao.ReggieRole; |
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import net.sf.basedb.reggie.dao.Rna; |
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import net.sf.basedb.reggie.dao.SequencingRun; |
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import net.sf.basedb.reggie.dao.SpecimenTube; |
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import net.sf.basedb.reggie.dao.Subtype; |
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import net.sf.basedb.reggie.grid.AscatJobCreator.AllelicImbalanceTest; |
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import net.sf.basedb.reggie.grid.DemuxJobCreator; |
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import net.sf.basedb.reggie.grid.TargetedGenotypeJobCreator; |
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import net.sf.basedb.reggie.grid.VariantCallingJobCreator; |
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import net.sf.basedb.reggie.plugins.CaliperLibPrepParametersExporter; |
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import net.sf.basedb.reggie.plugins.CaliperRunParametersExporter; |
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import net.sf.basedb.reggie.plugins.CaliperSampleNameExporter; |
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import net.sf.basedb.reggie.plugins.GeneReportsCombinerPlugin; |
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import net.sf.basedb.reggie.plugins.GeneReportPlugin; |
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import net.sf.basedb.reggie.plugins.QubitSampleNameExporter; |
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import net.sf.basedb.reggie.plugins.SetPermissionsForDeliveryPlugin; |
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import net.sf.basedb.reggie.ssp.SspAnalysis; |
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import net.sf.basedb.reggie.ssp.SspInfoResult; |
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import net.sf.basedb.reggie.ssp.SspAnalysis.Info; |
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import net.sf.basedb.reggie.ssp.SspModel; |
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import net.sf.basedb.util.StaticCache; |
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import net.sf.basedb.util.Values; |
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import net.sf.basedb.util.error.ThrowableUtil; |
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import net.sf.basedb.util.uri.ConnectionManager; |
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import net.sf.basedb.util.uri.ConnectionManagerFactory; |
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import net.sf.basedb.util.uri.ConnectionManagerUtil; |
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import net.sf.basedb.util.uri.ConnectionParameters; |
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import net.sf.basedb.util.uri.UriMetadata; |
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|
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/** |
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Servlet that verify and install items that are required by other Reggie actions. |
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@author nicklas |
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*/ |
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public class InstallServlet |
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extends HttpServlet |
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{ |
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|
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private static final long serialVersionUID = -3216326283682707833L; |
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|
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public InstallServlet() |
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{} |
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|
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@Override |
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protected void doGet(HttpServletRequest req, HttpServletResponse resp) |
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throws ServletException, IOException |
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{ |
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String cmd = req.getParameter("cmd"); |
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JsonUtil.setJsonResponseHeaders(resp); |
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|
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JSONObject json = new JSONObject(); |
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json.put("status", "ok"); |
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|
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final SessionControl sc = Reggie.getSessionControl(req); |
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DbControl dc = null; |
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try |
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{ |
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if ("Validate".equals(cmd) || "Install".equals(cmd)) |
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{ |
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dc = sc.newDbControl(":Installation wizard"); |
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|
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ReggieRole.checkPermission(dc, "'Installation wizard'", ReggieRole.ADMINISTRATOR); |
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|
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boolean createIfMissing = "Install".equals(cmd); |
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JSONArray jsonChecks = new JSONArray(); |
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|
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Reggie.getConfig(); |
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|
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// Project checks |
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jsonChecks.add(checkActiveProject(dc)); |
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|
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// Group checks |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.PATIENT_CURATOR, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.SECONDARY_ANALYSIS, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.MIPS_SECONDARY_ANALYSIS, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.SCANB_DELIVERY, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.SCANB_LAB, createIfMissing)); |
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|
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for (Site s : Site.getAllSites()) |
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{ |
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jsonChecks.add(checkReggieRole(dc, s, createIfMissing)); |
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} |
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|
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// Role checks |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.ADMINISTRATOR, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.SAMPLE_PREP, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.HISTOLOGY, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.LIBRARY_PREP, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.LIBRARY_PLATE_DESIGNER, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.MIPS_LIBRARY_PREP, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.MIPS_PLATE_DESIGNER, createIfMissing)); |
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jsonChecks.add(checkReggieRole(dc, ReggieRole.PREP_CURATOR, createIfMissing)); |
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|
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int projectId = dc.getSessionControl().getActiveProjectId(); |
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Project activeProject = projectId == 0 ? null : Project.getById(dc, projectId); |
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|
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Group patientCurator = ReggieRole.PATIENT_CURATOR.get(dc); |
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PermissionOptions patientCuratorUse = null; |
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PermissionOptions patientCuratorWrite = null; |
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PermissionOptions patientCuratorRead = null; |
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if (patientCurator != null) |
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{ |
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patientCuratorRead = new PermissionOptions(); |
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patientCuratorRead.set(patientCurator, Permission.READ); |
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patientCuratorUse = new PermissionOptions(); |
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patientCuratorUse.set(patientCurator, Permission.USE); |
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patientCuratorWrite = new PermissionOptions(); |
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patientCuratorWrite.set(patientCurator, Permission.WRITE); |
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if (activeProject != null) |
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{ |
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patientCuratorRead.set(activeProject, null); |
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patientCuratorUse.set(activeProject, null); |
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patientCuratorWrite.set(activeProject, null); |
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} |
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} |
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|
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Group secondaryAnalysis = ReggieRole.SECONDARY_ANALYSIS.get(dc); |
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PermissionOptions secondaryAnalysisUse = null; |
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if (secondaryAnalysis != null) |
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{ |
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secondaryAnalysisUse = new PermissionOptions(); |
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secondaryAnalysisUse.set(secondaryAnalysis, Permission.USE); |
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if (activeProject != null) |
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{ |
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secondaryAnalysisUse.set(activeProject, Permission.READ); |
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} |
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} |
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|
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PermissionOptions activeProjectRead = null; |
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PermissionOptions activeProjectUse = null; |
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PermissionOptions activeProjectWrite = null; |
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if (activeProject != null) |
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{ |
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activeProjectRead = new PermissionOptions(); |
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activeProjectRead.set(activeProject, Permission.READ); |
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activeProjectUse = new PermissionOptions(); |
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activeProjectUse.set(activeProject, Permission.USE); |
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10 Dec 13 |
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227 |
activeProjectWrite = new PermissionOptions(); |
| 2168 |
10 Dec 13 |
nicklas |
228 |
activeProjectWrite.set(activeProject, Permission.WRITE); |
| 1310 |
04 Mar 11 |
nicklas |
229 |
} |
| 1310 |
04 Mar 11 |
nicklas |
230 |
|
| 2344 |
09 Apr 14 |
nicklas |
231 |
PermissionOptions effectivePermissionsRead = activeProjectRead == null ? |
| 2344 |
09 Apr 14 |
nicklas |
232 |
patientCuratorRead : activeProjectRead; |
| 2168 |
10 Dec 13 |
nicklas |
233 |
PermissionOptions effectivePermissionsUse = activeProjectUse == null ? |
| 2168 |
10 Dec 13 |
nicklas |
234 |
patientCuratorUse : activeProjectUse; |
| 2168 |
10 Dec 13 |
nicklas |
235 |
PermissionOptions effectivePermissionsWrite = activeProjectWrite == null ? |
| 2168 |
10 Dec 13 |
nicklas |
236 |
patientCuratorWrite : activeProjectWrite; |
| 1463 |
14 Nov 11 |
martin |
237 |
Map<String, Item> subtypeItems = new HashMap<String, Item>(); |
| 2565 |
11 Aug 14 |
nicklas |
238 |
|
| 3986 |
10 Jun 16 |
nicklas |
239 |
Group everyone = Group.getById(dc, SystemItems.getId(Group.EVERYONE)); |
| 3986 |
10 Jun 16 |
nicklas |
240 |
PermissionOptions scanbLabUse = new PermissionOptions();; |
| 3986 |
10 Jun 16 |
nicklas |
241 |
scanbLabUse.set(everyone, null); |
| 3986 |
10 Jun 16 |
nicklas |
242 |
Group scanbLab = ReggieRole.SCANB_LAB.get(dc); |
| 3986 |
10 Jun 16 |
nicklas |
243 |
if (scanbLab != null) |
| 3986 |
10 Jun 16 |
nicklas |
244 |
{ |
| 3986 |
10 Jun 16 |
nicklas |
245 |
scanbLabUse.set(scanbLab, Permission.USE); |
| 3986 |
10 Jun 16 |
nicklas |
246 |
} |
| 3986 |
10 Jun 16 |
nicklas |
247 |
|
| 3986 |
10 Jun 16 |
nicklas |
248 |
PermissionOptions scanbDeliveryUse = new PermissionOptions(); |
| 4001 |
17 Jun 16 |
nicklas |
249 |
PermissionOptions scanbDeliveryRead = new PermissionOptions(); |
| 3986 |
10 Jun 16 |
nicklas |
250 |
scanbDeliveryUse.set(everyone, null); |
| 4001 |
17 Jun 16 |
nicklas |
251 |
scanbDeliveryRead.set(everyone, null); |
| 3986 |
10 Jun 16 |
nicklas |
252 |
Group scanbDelivery = ReggieRole.SCANB_DELIVERY.get(dc); |
| 3986 |
10 Jun 16 |
nicklas |
253 |
if (scanbDelivery != null) |
| 3986 |
10 Jun 16 |
nicklas |
254 |
{ |
| 3986 |
10 Jun 16 |
nicklas |
255 |
scanbDeliveryUse.set(scanbDelivery, Permission.USE); |
| 4001 |
17 Jun 16 |
nicklas |
256 |
scanbDeliveryRead.set(scanbDelivery, Permission.READ); |
| 3986 |
10 Jun 16 |
nicklas |
257 |
} |
| 3986 |
10 Jun 16 |
nicklas |
258 |
|
| 6277 |
03 Jun 21 |
nicklas |
259 |
jsonChecks.add(checkClient(dc, ClientApp.REGGIE, effectivePermissionsUse.merge(patientCuratorWrite), createIfMissing)); |
| 3988 |
10 Jun 16 |
nicklas |
260 |
jsonChecks.add(checkClient(dc, ClientApp.SCANB_DELIVERY, scanbDeliveryUse, createIfMissing)); |
| 3988 |
10 Jun 16 |
nicklas |
261 |
jsonChecks.add(checkClient(dc, ClientApp.WEB_CLIENT, scanbLabUse, createIfMissing)); |
| 3974 |
26 May 16 |
nicklas |
262 |
|
| 2565 |
11 Aug 14 |
nicklas |
// Must check/install some file subtypes first, since they are used by 'data file types' |
| 2565 |
11 Aug 14 |
nicklas |
264 |
JSONObject jsonSubtype_SEQUENCE_DATA = checkSubtype(dc, Subtype.SEQUENCE_DATA, null, createIfMissing); |
| 2565 |
11 Aug 14 |
nicklas |
265 |
JSONObject jsonSubtype_ALIGNED_SEQUENCE_DATA = checkSubtype(dc, Subtype.ALIGNED_SEQUENCE_DATA, null, createIfMissing); |
| 6475 |
05 Nov 21 |
nicklas |
266 |
JSONObject jsonSubtype_GENOTYPE_CALL_FILE = checkSubtype(dc, Subtype.GENOTYPE_CALL_FILE, null, createIfMissing); |
| 6866 |
14 Nov 22 |
nicklas |
267 |
JSONObject jsonSubtype_IDAT_FILE = checkSubtype(dc, Subtype.IDAT, null, createIfMissing); |
| 2565 |
11 Aug 14 |
nicklas |
268 |
|
| 2565 |
11 Aug 14 |
nicklas |
// Data file types |
| 2565 |
11 Aug 14 |
nicklas |
270 |
jsonChecks.add(checkDataFileType(dc, Datafiletype.FASTQ, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
271 |
jsonChecks.add(checkDataFileType(dc, Datafiletype.BAM, createIfMissing)); |
| 2721 |
01 Oct 14 |
nicklas |
272 |
jsonChecks.add(checkDataFileType(dc, Datafiletype.FPKM, createIfMissing)); |
| 5706 |
07 Nov 19 |
nicklas |
273 |
jsonChecks.add(checkDataFileType(dc, Datafiletype.VCF, createIfMissing)); |
| 6542 |
18 Jan 22 |
nicklas |
274 |
jsonChecks.add(checkDataFileType(dc, Datafiletype.VCF_DESIGN, createIfMissing)); |
| 6475 |
05 Nov 21 |
nicklas |
275 |
jsonChecks.add(checkDataFileType(dc, Datafiletype.GTC, createIfMissing)); |
| 6866 |
14 Nov 22 |
nicklas |
276 |
jsonChecks.add(checkDataFileType(dc, Datafiletype.IDAT, createIfMissing)); |
| 1463 |
14 Nov 11 |
martin |
277 |
|
| 4673 |
08 Feb 18 |
nicklas |
// Platforms |
| 4673 |
08 Feb 18 |
nicklas |
279 |
jsonChecks.add(checkPlatform(dc, Rawdatatype.STRINGTIE, createIfMissing, Datafiletype.GENERIC_RAWDATA, Datafiletype.GTF)); |
| 5706 |
07 Nov 19 |
nicklas |
280 |
jsonChecks.add(checkPlatform(dc, Rawdatatype.VARIANT_CALL, createIfMissing, Datafiletype.VCF)); |
| 6542 |
18 Jan 22 |
nicklas |
281 |
jsonChecks.add(checkPlatform(dc, Rawdatatype.ONCOARRAY500K, createIfMissing, Datafiletype.VCF, Datafiletype.VCF_DESIGN)); |
| 4673 |
08 Feb 18 |
nicklas |
282 |
|
| 1463 |
14 Nov 11 |
martin |
// Subtype checks |
| 2565 |
11 Aug 14 |
nicklas |
284 |
jsonChecks.add(checkSubtype(dc, Subtype.PATIENT, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
285 |
jsonChecks.add(checkSubtype(dc, Subtype.NO, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
286 |
jsonChecks.add(checkSubtype(dc, Subtype.NOT_ASKED, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
287 |
jsonChecks.add(checkSubtype(dc, Subtype.CASE, null, createIfMissing, Subtype.PATIENT)); |
| 2565 |
11 Aug 14 |
nicklas |
288 |
jsonChecks.add(checkSubtype(dc, Subtype.BLOOD, null, createIfMissing, Subtype.PATIENT)); |
| 3355 |
28 May 15 |
nicklas |
289 |
jsonChecks.add(checkSubtype(dc, Subtype.BLOOD_DNA, null, createIfMissing, Subtype.BLOOD)); |
| 2565 |
11 Aug 14 |
nicklas |
290 |
jsonChecks.add(checkSubtype(dc, Subtype.SPECIMEN,null, createIfMissing, Subtype.CASE)); |
| 2565 |
11 Aug 14 |
nicklas |
291 |
jsonChecks.add(checkSubtype(dc, Subtype.NO_SPECIMEN,null, createIfMissing, Subtype.CASE)); |
| 5774 |
04 Dec 19 |
nicklas |
292 |
jsonChecks.add(checkSubtype(dc, Subtype.TMA_SPECIMEN,null, createIfMissing, Subtype.CASE)); |
| 2565 |
11 Aug 14 |
nicklas |
293 |
jsonChecks.add(checkSubtype(dc, Subtype.HISTOLOGY_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
294 |
jsonChecks.add(checkSubtype(dc, Subtype.HISTOLOGY, null, createIfMissing, Subtype.SPECIMEN, Subtype.HISTOLOGY_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
295 |
jsonChecks.add(checkSubtype(dc, Subtype.STAINING_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
296 |
jsonChecks.add(checkSubtype(dc, Subtype.STAINED, null, createIfMissing, Subtype.HISTOLOGY, Subtype.STAINING_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
297 |
jsonChecks.add(checkSubtype(dc, Subtype.SAMPLE_HANDLING_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
298 |
jsonChecks.add(checkSubtype(dc, Subtype.EXTRACTION_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
299 |
jsonChecks.add(checkSubtype(dc, Subtype.LYSATE, null, createIfMissing, Subtype.SPECIMEN, Subtype.SAMPLE_HANDLING_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
300 |
jsonChecks.add(checkSubtype(dc, Subtype.DNA, null, createIfMissing, Subtype.LYSATE, Subtype.EXTRACTION_PROTOCOL)); |
| 5359 |
12 Apr 19 |
nicklas |
301 |
jsonChecks.add(checkSubtype(dc, Subtype.DNA_NORMALIZATION_PROTOCOL, null, createIfMissing, Subtype.DNA)); |
| 5359 |
12 Apr 19 |
nicklas |
302 |
jsonChecks.add(checkSubtype(dc, Subtype.DNA_NORMALIZED_ALIQUOT, null, createIfMissing, Subtype.DNA, Subtype.DNA_NORMALIZATION_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
303 |
jsonChecks.add(checkSubtype(dc, Subtype.RNA, null, createIfMissing, Subtype.LYSATE, Subtype.EXTRACTION_PROTOCOL)); |
| 3269 |
23 Apr 15 |
nicklas |
304 |
jsonChecks.add(checkSubtype(dc, Subtype.RNA_NORMALIZATION_PROTOCOL, null, createIfMissing, Subtype.RNA)); |
| 3269 |
23 Apr 15 |
nicklas |
305 |
jsonChecks.add(checkSubtype(dc, Subtype.RNA_NORMALIZED_ALIQUOT, null, createIfMissing, Subtype.RNA, Subtype.RNA_NORMALIZATION_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
306 |
jsonChecks.add(checkSubtype(dc, Subtype.FLOW_THROUGH, null, createIfMissing, Subtype.LYSATE, Subtype.EXTRACTION_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
307 |
jsonChecks.add(checkSubtype(dc, Subtype.QUALITY_CONTROL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
308 |
jsonChecks.add(checkSubtype(dc, Subtype.RNAQC, null, createIfMissing, Subtype.RNA, Subtype.QUALITY_CONTROL)); |
| 2565 |
11 Aug 14 |
nicklas |
309 |
jsonChecks.add(checkSubtype(dc, Subtype.MRNA_PROTOCOL, null, createIfMissing)); |
| 2898 |
05 Nov 14 |
nicklas |
310 |
jsonChecks.add(checkSubtype(dc, Subtype.MRNA, null, createIfMissing, Subtype.RNA_NORMALIZED_ALIQUOT, Subtype.MRNA_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
311 |
jsonChecks.add(checkSubtype(dc, Subtype.CDNA_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
312 |
jsonChecks.add(checkSubtype(dc, Subtype.CDNA, null, createIfMissing, Subtype.MRNA, Subtype.CDNA_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
313 |
jsonChecks.add(checkSubtype(dc, Subtype.LIBRARY_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
314 |
jsonChecks.add(checkSubtype(dc, Subtype.BARCODE, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
315 |
jsonChecks.add(checkSubtype(dc, Subtype.LIBRARY, null, createIfMissing, Subtype.CDNA, Subtype.BARCODE, Subtype.LIBRARY_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
316 |
jsonChecks.add(checkSubtype(dc, Subtype.POOLING_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
317 |
jsonChecks.add(checkSubtype(dc, Subtype.POOLED_LIBRARY, null, createIfMissing, Subtype.LIBRARY, Subtype.POOLING_PROTOCOL)); |
| 2565 |
11 Aug 14 |
nicklas |
318 |
jsonChecks.add(checkSubtype(dc, Subtype.POOLED_LIBRARY_ALIQUOT, null, createIfMissing, Subtype.POOLED_LIBRARY)); |
| 2565 |
11 Aug 14 |
nicklas |
319 |
jsonChecks.add(checkSubtype(dc, Subtype.CLUSTER_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
320 |
jsonChecks.add(checkSubtype(dc, Subtype.CLUSTER_GENERATOR, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
321 |
jsonChecks.add(checkSubtype(dc, Subtype.FLOW_CELL, null, createIfMissing, Subtype.POOLED_LIBRARY_ALIQUOT, Subtype.CLUSTER_GENERATOR, Subtype.CLUSTER_PROTOCOL)); |
| 6461 |
01 Nov 21 |
nicklas |
322 |
jsonChecks.add(checkSubtype(dc, Subtype.BEAD_CHIP, null, createIfMissing, Subtype.BLOOD_DNA)); |
| 6477 |
05 Nov 21 |
nicklas |
323 |
jsonChecks.add(checkSubtype(dc, Subtype.SCANNER, null, createIfMissing)); |
| 6477 |
05 Nov 21 |
nicklas |
324 |
jsonChecks.add(checkSubtype(dc, Subtype.SCAN, null, createIfMissing, Subtype.BEAD_CHIP, Subtype.SCANNER)); |
| 6475 |
05 Nov 21 |
nicklas |
325 |
jsonChecks.add(checkSubtype(dc, Subtype.GENOTYPING_SOFTWARE, null, createIfMissing)); |
| 6475 |
05 Nov 21 |
nicklas |
326 |
jsonChecks.add(jsonSubtype_GENOTYPE_CALL_FILE); |
| 6475 |
05 Nov 21 |
nicklas |
327 |
jsonChecks.add(checkSubtype(dc, Subtype.GENOTYPE_CALL, Datafiletype.GTC, createIfMissing, Subtype.SCAN, Subtype.GENOTYPING_SOFTWARE)); |
| 6866 |
14 Nov 22 |
nicklas |
328 |
jsonChecks.add(checkSubtype(dc, Subtype.METHYLATION_SOFTWARE, null, createIfMissing)); |
| 6866 |
14 Nov 22 |
nicklas |
329 |
jsonChecks.add(jsonSubtype_IDAT_FILE); |
| 6866 |
14 Nov 22 |
nicklas |
330 |
jsonChecks.add(checkSubtype(dc, Subtype.METHYLATION, Datafiletype.IDAT, createIfMissing, Subtype.SCAN, Subtype.METHYLATION_SOFTWARE)); |
| 6870 |
16 Nov 22 |
nicklas |
331 |
jsonChecks.add(checkSubtype(dc, Subtype.METHYLATION_BETA_JOB, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
332 |
jsonChecks.add(checkSubtype(dc, Subtype.BIOANALYZER_PDF, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
333 |
jsonChecks.add(checkSubtype(dc, Subtype.CALIPER_PDF, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
334 |
jsonChecks.add(checkSubtype(dc, Subtype.CALIPER_RAW_DATA, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
335 |
jsonChecks.add(checkSubtype(dc, Subtype.CALIPER_WELL_TABLE, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
336 |
jsonChecks.add(checkSubtype(dc, Subtype.QUBIT_CSV, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
337 |
jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCER, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
338 |
jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCING_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
339 |
jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCING_RUN, null, createIfMissing, Subtype.FLOW_CELL, Subtype.SEQUENCER, Subtype.SEQUENCING_PROTOCOL)); |
| 4325 |
30 Jan 17 |
nicklas |
340 |
jsonChecks.add(checkSubtype(dc, Subtype.SEQUENCING_RUN_JOB, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
341 |
jsonChecks.add(jsonSubtype_SEQUENCE_DATA); |
| 2565 |
11 Aug 14 |
nicklas |
342 |
jsonChecks.add(checkSubtype(dc, Subtype.DEMUX_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
343 |
jsonChecks.add(checkSubtype(dc, Subtype.DEMUX_SOFTWARE, null, createIfMissing)); |
| 7053 |
21 Feb 23 |
nicklas |
344 |
jsonChecks.add(checkSubtype(dc, Subtype.DEMUXED_SEQUENCES, Datafiletype.FASTQ, createIfMissing, Subtype.SEQUENCING_RUN, Subtype.DEMUX_PROTOCOL, Subtype.DEMUX_SOFTWARE)); |
| 2565 |
11 Aug 14 |
nicklas |
345 |
jsonChecks.add(checkSubtype(dc, Subtype.MERGE_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
346 |
jsonChecks.add(checkSubtype(dc, Subtype.MERGE_SOFTWARE, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
347 |
jsonChecks.add(checkSubtype(dc, Subtype.MERGED_SEQUENCES, Datafiletype.FASTQ, createIfMissing, Subtype.DEMUXED_SEQUENCES, Subtype.LIBRARY, Subtype.MERGE_PROTOCOL, Subtype.MERGE_SOFTWARE)); |
| 4325 |
30 Jan 17 |
nicklas |
348 |
jsonChecks.add(checkSubtype(dc, Subtype.DEMUX_MERGE_JOB, null, createIfMissing)); |
| 6181 |
25 Mar 21 |
nicklas |
349 |
jsonChecks.add(checkSubtype(dc, Subtype.FASTQ_IMPORT_JOB, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
350 |
jsonChecks.add(checkSubtype(dc, Subtype.MASKING_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
351 |
jsonChecks.add(checkSubtype(dc, Subtype.MASKING_SOFTWARE, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
352 |
jsonChecks.add(checkSubtype(dc, Subtype.MASKED_SEQUENCES, null, createIfMissing, Subtype.MERGED_SEQUENCES, Subtype.LIBRARY, Subtype.MASKING_PROTOCOL, Subtype.MASKING_SOFTWARE)); |
| 2565 |
11 Aug 14 |
nicklas |
353 |
jsonChecks.add(checkSubtype(dc, Subtype.ALIGNMENT_PROTOCOL, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
354 |
jsonChecks.add(checkSubtype(dc, Subtype.ALIGNMENT_SOFTWARE, null, createIfMissing)); |
| 7268 |
22 Jun 23 |
nicklas |
355 |
jsonChecks.add(checkSubtype(dc, Subtype.COPY_NUMBER, null, createIfMissing, Subtype.ALIGNED_SEQUENCES, Subtype.COPY_NUMBER_SOFTWARE)); |
| 7267 |
21 Jun 23 |
nicklas |
356 |
jsonChecks.add(checkSubtype(dc, Subtype.COPY_NUMBER_SOFTWARE, null, createIfMissing)); |
| 7268 |
22 Jun 23 |
nicklas |
357 |
jsonChecks.add(checkSubtype(dc, Subtype.ASCAT_JOB, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
358 |
jsonChecks.add(checkSubtype(dc, Subtype.ALIGNED_SEQUENCES, Datafiletype.BAM, createIfMissing, Subtype.MASKED_SEQUENCES, Subtype.LIBRARY, Subtype.ALIGNMENT_PROTOCOL, Subtype.ALIGNMENT_SOFTWARE)); |
| 7388 |
31 Oct 23 |
nicklas |
359 |
jsonChecks.add(checkSubtype(dc, Subtype.PANEL_OF_NORMAL, null, createIfMissing, Subtype.ALIGNED_SEQUENCES, Subtype.LIBRARY, Subtype.VARIANT_CALLING_SOFTWARE)); |
| 4325 |
30 Jan 17 |
nicklas |
360 |
jsonChecks.add(checkSubtype(dc, Subtype.MASK_ALIGN_JOB, null, createIfMissing)); |
| 4325 |
30 Jan 17 |
nicklas |
361 |
jsonChecks.add(checkSubtype(dc, Subtype.CUFFLINKS_JOB, null, createIfMissing)); |
| 4543 |
27 Jun 17 |
nicklas |
362 |
jsonChecks.add(checkSubtype(dc, Subtype.TOPHAT_CUFFLINKS_JOB, null, createIfMissing)); |
| 4588 |
25 Sep 17 |
nicklas |
363 |
jsonChecks.add(checkSubtype(dc, Subtype.HISAT_ALIGN_JOB, null, createIfMissing)); |
| 7085 |
31 Mar 23 |
nicklas |
364 |
jsonChecks.add(checkSubtype(dc, Subtype.BWA_MEM2_ALIGN_JOB, null, createIfMissing)); |
| 5826 |
18 Feb 20 |
nicklas |
365 |
jsonChecks.add(checkSubtype(dc, Subtype.MIPS_ALIGN_JOB, null, createIfMissing)); |
| 4664 |
30 Jan 18 |
nicklas |
366 |
jsonChecks.add(checkSubtype(dc, Subtype.STRINGTIE_JOB, null, createIfMissing)); |
| 5057 |
29 Oct 18 |
nicklas |
367 |
jsonChecks.add(checkSubtype(dc, Subtype.VARIANT_CALLING_SOFTWARE, null, createIfMissing)); |
| 5032 |
16 Oct 18 |
nicklas |
368 |
jsonChecks.add(checkSubtype(dc, Subtype.MBAF_JOB, null, createIfMissing)); |
| 5684 |
25 Oct 19 |
nicklas |
369 |
jsonChecks.add(checkSubtype(dc, Subtype.VARIANT_CALLING_JOB, null, createIfMissing)); |
| 5772 |
03 Dec 19 |
nicklas |
370 |
jsonChecks.add(checkSubtype(dc, Subtype.VARIANT_STATISTICS_JOB, null, createIfMissing)); |
| 6387 |
15 Sep 21 |
nicklas |
371 |
jsonChecks.add(checkSubtype(dc, Subtype.TARGETED_GENOTYPING_JOB, null, createIfMissing)); |
| 5922 |
27 Apr 20 |
nicklas |
372 |
jsonChecks.add(checkSubtype(dc, Subtype.SSP_JOB, null, createIfMissing)); |
| 3616 |
23 Nov 15 |
nicklas |
373 |
jsonChecks.add(checkSubtype(dc, Subtype.REPORT_SOFTWARE, null, createIfMissing)); |
| 4325 |
30 Jan 17 |
nicklas |
374 |
jsonChecks.add(checkSubtype(dc, Subtype.REPORT_JOB, null, createIfMissing)); |
| 2839 |
20 Oct 14 |
olle |
375 |
jsonChecks.add(checkSubtype(dc, Subtype.RETRACT, null, createIfMissing)); |
| 2839 |
20 Oct 14 |
olle |
376 |
jsonChecks.add(checkSubtype(dc, Subtype.RETRO_NO, null, createIfMissing)); |
| 2565 |
11 Aug 14 |
nicklas |
377 |
jsonChecks.add(jsonSubtype_ALIGNED_SEQUENCE_DATA); |
| 4619 |
13 Nov 17 |
nicklas |
378 |
jsonChecks.add(checkSubtype(dc, Subtype.VARIANT_CALL_FORMAT, null, createIfMissing)); |
| 2721 |
01 Oct 14 |
nicklas |
379 |
jsonChecks.add(checkSubtype(dc, Subtype.RAW_DATA, null, createIfMissing)); |
| 3640 |
02 Dec 15 |
nicklas |
380 |
jsonChecks.add(checkSubtype(dc, Subtype.FREEZER, null, createIfMissing)); |
| 3640 |
02 Dec 15 |
nicklas |
381 |
|
| 1865 |
19 Feb 13 |
nicklas |
// Plate geometries |
| 1666 |
23 May 12 |
nicklas |
383 |
jsonChecks.add(checkPlateGeometry(dc, Geometry.THREE_BY_TWO, createIfMissing)); |
| 1606 |
19 Apr 12 |
nicklas |
384 |
jsonChecks.add(checkPlateGeometry(dc, Geometry.ONE_BY_TWELVE, createIfMissing)); |
| 6474 |
04 Nov 21 |
nicklas |
385 |
jsonChecks.add(checkPlateGeometry(dc, Geometry.ONE_BY_EIGHT, createIfMissing)); |
| 1606 |
19 Apr 12 |
nicklas |
386 |
jsonChecks.add(checkPlateGeometry(dc, Geometry.NINE_BY_NINE, createIfMissing)); |
| 1606 |
19 Apr 12 |
nicklas |
387 |
jsonChecks.add(checkPlateGeometry(dc, Geometry.EIGHT_BY_TWELVE, createIfMissing)); |
| 3284 |
29 Apr 15 |
nicklas |
388 |
jsonChecks.add(checkPlateGeometry(dc, Geometry.EIGHT_BY_TWO, createIfMissing)); |
| 1606 |
19 Apr 12 |
nicklas |
389 |
|
| 1543 |
28 Feb 12 |
nicklas |
// Bioplate types |
| 3640 |
02 Dec 15 |
nicklas |
391 |
jsonChecks.add(checkBioplateType(dc, BioplateType.STORAGE_BOX, createIfMissing)); |
| 1543 |
28 Feb 12 |
nicklas |
392 |
jsonChecks.add(checkBioplateType(dc, BioplateType.BA_RNAQC, createIfMissing)); |
| 1543 |
28 Feb 12 |
nicklas |
393 |
jsonChecks.add(checkBioplateType(dc, BioplateType.CALIPER_RNAQC, createIfMissing)); |
| 5361 |
15 Apr 19 |
nicklas |
394 |
jsonChecks.add(checkBioplateType(dc, BioplateType.PRE_NORMALIZED_DNA, createIfMissing)); |
| 1606 |
19 Apr 12 |
nicklas |
395 |
jsonChecks.add(checkBioplateType(dc, BioplateType.PARAFFIN_BLOCK, createIfMissing)); |
| 1668 |
25 May 12 |
nicklas |
396 |
jsonChecks.add(checkBioplateType(dc, BioplateType.HE_GLASS, createIfMissing)); |
| 1865 |
19 Feb 13 |
nicklas |
397 |
jsonChecks.add(checkBioplateType(dc, BioplateType.MRNA, createIfMissing)); |
| 1865 |
19 Feb 13 |
nicklas |
398 |
jsonChecks.add(checkBioplateType(dc, BioplateType.CDNA, createIfMissing)); |
| 1893 |
04 Mar 13 |
nicklas |
399 |
jsonChecks.add(checkBioplateType(dc, BioplateType.LIBRARY, createIfMissing)); |
| 5867 |
18 Mar 20 |
nicklas |
400 |
jsonChecks.add(checkBioplateType(dc, BioplateType.EXTERNAL_LIBRARY, createIfMissing)); |
| 6474 |
04 Nov 21 |
nicklas |
401 |
jsonChecks.add(checkBioplateType(dc, BioplateType.EXTERNAL_LIBRARY_STRIP, createIfMissing)); |
| 3284 |
29 Apr 15 |
nicklas |
402 |
jsonChecks.add(checkBioplateType(dc, BioplateType.NEOPREP, createIfMissing)); |
| 5390 |
29 Apr 19 |
nicklas |
403 |
jsonChecks.add(checkBioplateType(dc, BioplateType.MIPS, createIfMissing)); |
| 5429 |
16 May 19 |
nicklas |
404 |
jsonChecks.add(checkBioplateType(dc, BioplateType.BARCODE_TEMPLATE, createIfMissing)); |
| 1865 |
19 Feb 13 |
nicklas |
405 |
|
| 1865 |
19 Feb 13 |
nicklas |
// Bioplate event types |
| 1463 |
14 Nov 11 |
martin |
407 |
|
| 1310 |
04 Mar 11 |
nicklas |
// Annotation type checks |
| 1310 |
04 Mar 11 |
nicklas |
// -- the first batch need to be shared to the PatientCurator group |
| 4001 |
17 Jun 16 |
nicklas |
410 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PERSONAL_NUMBER, 1, null, createIfMissing, patientCuratorUse, scanbDeliveryRead)); |
| 4001 |
17 Jun 16 |
nicklas |
411 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FAMILY_NAME, 1, null, createIfMissing, patientCuratorUse, scanbDeliveryRead)); |
| 4001 |
17 Jun 16 |
nicklas |
412 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ALL_FIRST_NAMES, 1, null, createIfMissing, patientCuratorUse, scanbDeliveryRead)); |
| 1310 |
04 Mar 11 |
nicklas |
413 |
|
| 1310 |
04 Mar 11 |
nicklas |
// -- the second batch need only be shared to the active project or to the PatientCurator group |
| 6197 |
06 Apr 21 |
nicklas |
415 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.EXTERNAL_REF, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6926 |
02 Dec 22 |
nicklas |
416 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.IMPORT_WARNINGS, 0, null, createIfMissing, patientCuratorUse)); |
| 7168 |
12 May 23 |
nicklas |
417 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.TRANSPORT_MESSAGES, 0, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
418 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DATE_OF_BIRTH, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
419 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GENDER, 1, new ValueOptions("F", "M"), createIfMissing, effectivePermissionsUse)); |
| 4512 |
31 May 17 |
nicklas |
420 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LIASON_COMMENT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
421 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LATERALITY, 1, new ValueOptions("LEFT", "RIGHT"), createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
422 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.REASON_IF_NO_SPECIMEN, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6574 |
08 Feb 22 |
nicklas |
423 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.EXTERNAL_SPECIMEN_EXISTS, 1, new ValueOptions("Yes", "No"), createIfMissing, effectivePermissionsUse)); |
| 6918 |
01 Dec 22 |
nicklas |
424 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.EXTERNAL_STORAGE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7186 |
22 May 23 |
nicklas |
425 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MOVE_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7186 |
22 May 23 |
nicklas |
426 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MOVE_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4037 |
29 Jul 16 |
nicklas |
427 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PAD, 1, null, createIfMissing, patientCuratorUse, scanbDeliveryRead)); |
| 6990 |
19 Jan 23 |
nicklas |
428 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ALTERNATE_PAD, 1, null, createIfMissing, patientCuratorUse)); |
| 6711 |
27 Apr 22 |
nicklas |
429 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.TUBE_LABEL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 1608 |
20 Apr 12 |
nicklas |
430 |
|
| 4001 |
17 Jun 16 |
nicklas |
431 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_NA_LAB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
432 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_TX_LAB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
433 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_RX_LAB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
434 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_NA_BB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
435 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_TX_BB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
436 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_RX_BB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
437 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_NA_FROZEN, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
438 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_TX_FROZEN, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
439 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_RX_FROZEN, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
440 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_NA_RCC_SYD, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
441 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_TX_RCC_SYD, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5637 |
03 Oct 19 |
nicklas |
442 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RETRACT_STATUS, 1, new ValueOptions("ReadyForDestruction", "RetractionCompleted", "Destroyed"), createIfMissing, effectivePermissionsUse)); |
| 3085 |
15 Jan 15 |
olle |
443 |
|
| 4001 |
17 Jun 16 |
nicklas |
444 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BLOOD_SAMPLING_DATETIME, 1,null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
445 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BLOOD_FREEZER_DATETIME, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
446 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BLOOD_SERUM, 1, new ValueOptions("Yes", "No"), createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
447 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BLOOD_SAMPLE, 1, new ValueOptions("PreNeo", "PreOp", "FollowUp06", "FollowUp12", "FollowUp36"), createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
448 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BLOOD_RCCIDNUMBER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6277 |
03 Jun 21 |
nicklas |
449 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BD47_ID, 1, null, createIfMissing, effectivePermissionsUse)); |
| 1614 |
24 Apr 12 |
nicklas |
450 |
|
| 4001 |
17 Jun 16 |
nicklas |
451 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SAMPLING_DATETIME, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
452 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RNALATER_DATETIME, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
453 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CONSENT, 1, new ValueOptions("Yes", "No", "Not asked"), createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
454 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CONSENT_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4458 |
21 Apr 17 |
nicklas |
455 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.REFERENCE_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4458 |
21 Apr 17 |
nicklas |
456 |
|
| 4458 |
21 Apr 17 |
nicklas |
457 |
Object[] refDateSources = new Object[ReferenceDateSource.values().length]; |
| 4458 |
21 Apr 17 |
nicklas |
458 |
for (int i = 0; i < ReferenceDateSource.values().length; i++) |
| 4458 |
21 Apr 17 |
nicklas |
459 |
{ |
| 4458 |
21 Apr 17 |
nicklas |
460 |
refDateSources[i] = ReferenceDateSource.values()[i].getTitle(); |
| 4458 |
21 Apr 17 |
nicklas |
461 |
} |
| 4458 |
21 Apr 17 |
nicklas |
462 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.REFERENCE_DATE_SOURCE, 1, |
| 4458 |
21 Apr 17 |
nicklas |
463 |
new ValueOptions(refDateSources), createIfMissing, effectivePermissionsUse)); |
| 6098 |
11 Jan 21 |
nicklas |
464 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LINKED_CASE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
465 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FROZEN_TISSUE_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
466 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.INCA_EXPORT_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
467 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.INCA_IMPORT_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
468 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ARRIVAL_DATE, 1, null, createIfMissing, effectivePermissionsUse, scanbDeliveryRead)); |
| 4001 |
17 Jun 16 |
nicklas |
469 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NOF_DELIVERED_TUBES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
470 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OPERATOR_DELIVERY_COMMENT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
471 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OTHER_PATH_NOTE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 3602 |
16 Nov 15 |
nicklas |
472 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.YELLOW_LABEL, 1, |
| 3602 |
16 Nov 15 |
nicklas |
473 |
new ValueOptions("yellow"), |
| 4001 |
17 Jun 16 |
nicklas |
474 |
createIfMissing, effectivePermissionsUse, scanbDeliveryRead)); |
| 4040 |
29 Jul 16 |
nicklas |
475 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.COMPLETED_DATE, 1, null, createIfMissing, effectivePermissionsUse, scanbDeliveryRead)); |
| 1610 |
23 Apr 12 |
nicklas |
476 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SPECIMEN_TYPE, 1, |
| 2801 |
13 Oct 14 |
nicklas |
477 |
new ValueOptions("Primary", "LymphnodeRegional", "MetastasisDistant", "RecurrenceLocal", "RecurrenceRegional", "Normal", "Uncertain"), |
| 4001 |
17 Jun 16 |
nicklas |
478 |
createIfMissing, effectivePermissionsUse)); |
| 1610 |
23 Apr 12 |
nicklas |
479 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BIOPSY_TYPE, 1, |
| 2840 |
20 Oct 14 |
nicklas |
480 |
new ValueOptions("SpecimenSurgery", "SpecimenCoreBiopsy", "SpecimenCoreBiopsy2nd", "SpecimenFineNeedleAspiration"), |
| 4001 |
17 Jun 16 |
nicklas |
481 |
createIfMissing, effectivePermissionsUse)); |
| 3394 |
12 Jun 15 |
nicklas |
482 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LINKED_SPECIMEN, 1, |
| 3481 |
09 Sep 15 |
nicklas |
483 |
new ValueOptions("IpsilateralCoreBiopsy", "ContralateralCoreBiopsy", "IpsilateralSample", "ContralateralSample", "MissingDate"), |
| 4001 |
17 Jun 16 |
nicklas |
484 |
createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
485 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NOF_PIECES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
486 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MULTIPLE_PIECES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
487 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OPERATOR_PARTITION_COMMENT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
488 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PARTITION_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 1639 |
09 May 12 |
nicklas |
489 |
|
| 5774 |
04 Dec 19 |
nicklas |
490 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.TMA_BLOCK, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5774 |
04 Dec 19 |
nicklas |
491 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.TMA_BLOCK_POS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5799 |
18 Dec 19 |
nicklas |
492 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PAD_REQUESTED, 1, null, createIfMissing, patientCuratorUse)); |
| 5798 |
18 Dec 19 |
nicklas |
493 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SAMPLE_OWNER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5774 |
04 Dec 19 |
nicklas |
494 |
|
| 4001 |
17 Jun 16 |
nicklas |
495 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RLT_PLUS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
496 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BETA_MERCA, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
497 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.REAGENT_DX, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
498 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QIA_SHREDDER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 2690 |
24 Sep 14 |
nicklas |
499 |
|
| 4001 |
17 Jun 16 |
nicklas |
500 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ALLPREP_MINI_KIT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
501 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ETOH70, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
502 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BUFFER_RW1, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
503 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BUFFER_RPE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
504 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BUFFER_AW1, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
505 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BUFFER_AW2, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
506 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BUFFER_EB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
507 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RNASE_FREE_WATER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
508 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ALLPREP_DNA_COL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
509 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RNEASY_COL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 2690 |
24 Sep 14 |
nicklas |
510 |
|
| 4001 |
17 Jun 16 |
nicklas |
511 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.EMBED_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
512 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GOOD_STAIN, 1, null, createIfMissing, effectivePermissionsUse)); |
| 3121 |
06 Feb 15 |
nicklas |
513 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.IHC, 1, |
| 3121 |
06 Feb 15 |
nicklas |
514 |
new ValueOptions("p63"), |
| 4001 |
17 Jun 16 |
nicklas |
515 |
createIfMissing, effectivePermissionsUse)); |
| 3169 |
06 Mar 15 |
nicklas |
516 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.IHC_QUALITY, 1, |
| 3549 |
19 Oct 15 |
nicklas |
517 |
new ValueOptions("Good", "Fail", "Inconclusive"), |
| 4001 |
17 Jun 16 |
nicklas |
518 |
createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
519 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCORE_COMPLETE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
520 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCORE_INVASIVE_CANCER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
521 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCORE_INSITU_CANCER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
522 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCORE_LYMPHOCYTES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
523 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCORE_NORMAL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
524 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCORE_STROMA, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
525 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCORE_FAT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 1668 |
25 May 12 |
nicklas |
526 |
|
| 4001 |
17 Jun 16 |
nicklas |
527 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RESERVED_BY, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
528 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QIACUBE_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
529 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QIACUBE_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
530 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QIACUBE_POSITION, 1, new ValueOptions(1, 12), createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
531 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QIACUBE_RUN_NO, 1, new ValueOptions(1, null), createIfMissing, effectivePermissionsUse)); |
| 6510 |
03 Dec 21 |
nicklas |
532 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QIACUBE_RUN_ID, 1, null, createIfMissing, effectivePermissionsUse)); |
| 1639 |
09 May 12 |
nicklas |
533 |
|
| 4001 |
17 Jun 16 |
nicklas |
534 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_RUN_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
535 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
536 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_HISENSE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
537 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BA_RIN, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
538 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CA_RQS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
539 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ND_CONC, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
540 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ND_260_BY_280, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
541 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ND_260_BY_230, 1, null, createIfMissing, effectivePermissionsUse)); |
| 1409 |
18 Oct 11 |
martin |
542 |
|
| 4001 |
17 Jun 16 |
nicklas |
543 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RNA_TARGET_AMOUNT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
544 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RNA_MINIMAL_AMOUNT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
545 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RNA_TARGET_VOLUME, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5359 |
12 Apr 19 |
nicklas |
546 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DNA_TARGET_AMOUNT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5359 |
12 Apr 19 |
nicklas |
547 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DNA_MINIMAL_AMOUNT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5359 |
12 Apr 19 |
nicklas |
548 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DNA_TARGET_VOLUME, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5899 |
15 Apr 20 |
nicklas |
549 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LIBPREP_TARGET, 0, |
| 5899 |
15 Apr 20 |
nicklas |
550 |
new ValueOptions("Manual", "NeoPrep", "MIPs", "External"), createIfMissing, effectivePermissionsUse)); |
| 5434 |
17 May 19 |
nicklas |
551 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PIPELINE, 1, |
| 5546 |
07 Aug 19 |
nicklas |
552 |
new ValueOptions(Pipeline.RNA_SEQ.getName(), Pipeline.MIPS.getName(), |
| 5725 |
13 Nov 19 |
nicklas |
553 |
Pipeline.RNASEQ_LEGACY.getName(), Pipeline.RNASEQ_HISAT_STRINGTIE.getName(), |
| 6811 |
25 Aug 22 |
nicklas |
554 |
Pipeline.RNASEQ_HISAT_2023.getName(), Pipeline.RNASEQ_STRINGTIE_2023.getName(), |
| 6865 |
09 Nov 22 |
nicklas |
555 |
Pipeline.RNASEQ_HISAT_VARIANTCALL.getName(), Pipeline.DNA_GENOTYPING.getName(), |
| 7054 |
21 Feb 23 |
nicklas |
556 |
Pipeline.DNA_METHYLATION.getName(), Pipeline.DNA_TUMOR_WGS.getName(), |
| 7411 |
10 Nov 23 |
nicklas |
557 |
Pipeline.DNA_NORMAL_WGS.getName(), Pipeline.DNA_PAIRED_VARIANTCALL.getName()), |
| 5434 |
17 May 19 |
nicklas |
558 |
createIfMissing, effectivePermissionsUse)); |
| 3269 |
23 Apr 15 |
nicklas |
559 |
|
| 5601 |
13 Sep 19 |
nicklas |
560 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MIPS_PANEL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5447 |
24 May 19 |
nicklas |
561 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MIPS_POOL_VOLUME, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5447 |
24 May 19 |
nicklas |
562 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MIPS_NORMAL_TUMOR, 1, |
| 5447 |
24 May 19 |
nicklas |
563 |
new ValueOptions("N", "T"), createIfMissing, effectivePermissionsUse)); |
| 5447 |
24 May 19 |
nicklas |
564 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MIPS_FORM, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5447 |
24 May 19 |
nicklas |
565 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MIPS_VARIANT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5447 |
24 May 19 |
nicklas |
566 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MIPS_VARIANT_LIST, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5447 |
24 May 19 |
nicklas |
567 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MIPS_SCREENING, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5663 |
11 Oct 19 |
nicklas |
568 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BRCA_PATIENTID, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5663 |
11 Oct 19 |
nicklas |
569 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BRCA_PROVNUMMER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5402 |
07 May 19 |
nicklas |
570 |
|
| 4001 |
17 Jun 16 |
nicklas |
571 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.USE_FOR_QC, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
572 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DILUTION_CONC, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
573 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DILUTION_VOLUME, 1, null, createIfMissing, effectivePermissionsUse)); |
| 3303 |
04 May 15 |
nicklas |
574 |
|
| 1889 |
27 Feb 13 |
nicklas |
575 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FLAG, 1, |
| 2077 |
17 Oct 13 |
nicklas |
576 |
new ValueOptions( |
| 2242 |
21 Feb 14 |
nicklas |
577 |
Histology.FLAG_NO_GOOD_STAIN, |
| 2077 |
17 Oct 13 |
nicklas |
578 |
Rna.FLAG_NOT_ENOUGH_REMAINING_QUANTITY, Rna.FLAG_LOW_QUALITY_SCORE, Rna.FLAG_MANUAL, |
| 1987 |
23 May 13 |
nicklas |
579 |
Rna.FLAG_MRNA_PLATE_FAILED, Rna.FLAG_CDNA_PLATE_FAILED, Rna.FLAG_LIB_PLATE_FAILED, |
| 2077 |
17 Oct 13 |
nicklas |
580 |
Rna.FLAG_EXCLUDED_FROM_POOL, |
| 2367 |
17 Apr 14 |
nicklas |
581 |
PooledLibrary.FLAG_CLUSTERING_FAILED, PooledLibrary.FLAG_SEQUENCING_FAILED, |
| 6187 |
26 Mar 21 |
nicklas |
582 |
Rna.FLAG_DEMUX_FAILED, Rna.FLAG_FASTQ_IMPORT_FAILED, Rna.FLAG_ALIGN_FAILED, Rna.FLAG_HIGH_HET, |
| 7186 |
22 May 23 |
nicklas |
583 |
Rna.FLAG_CUFFLINKS_FAILED, Rna.FLAG_STRINGTIE_FAILED, Consent.FLAG_RETRACTED, |
| 7186 |
22 May 23 |
nicklas |
584 |
SpecimenTube.FLAG_MISSING_IN_TRANSPORT_BOX), |
| 4001 |
17 Jun 16 |
nicklas |
585 |
createIfMissing, effectivePermissionsUse)); |
| 1889 |
27 Feb 13 |
nicklas |
586 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.AUTO_PROCESSING, 1, |
| 5356 |
12 Apr 19 |
nicklas |
587 |
new ValueOptions( |
| 5356 |
12 Apr 19 |
nicklas |
588 |
"Disable", "ReProcess", "AutoConfirm", |
| 5356 |
12 Apr 19 |
nicklas |
589 |
Rna.AUTO_PROCESSING_PRE_NORMALIZE, Dna.AUTO_PROCESSING_PRE_NORMALIZE), |
| 4001 |
17 Jun 16 |
nicklas |
590 |
createIfMissing, effectivePermissionsUse)); |
| 5407 |
08 May 19 |
nicklas |
591 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PLATE_PROCESSING, 1, |
| 5417 |
10 May 19 |
nicklas |
592 |
new ValueOptions("AddAliquots", "DesignMIPs", "Disable"), |
| 5407 |
08 May 19 |
nicklas |
593 |
createIfMissing, effectivePermissionsUse)); |
| 1890 |
01 Mar 13 |
nicklas |
594 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PLATE_PROCESS_RESULT, 1, |
| 1890 |
01 Mar 13 |
nicklas |
595 |
new ValueOptions(ReactionPlate.PROCESS_SUCCESSFUL, ReactionPlate.PROCESS_FAILED), |
| 4001 |
17 Jun 16 |
nicklas |
596 |
createIfMissing, effectivePermissionsUse)); |
| 1890 |
01 Mar 13 |
nicklas |
597 |
|
| 1865 |
19 Feb 13 |
nicklas |
598 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_SCHEMA, 1, |
| 5884 |
27 Mar 20 |
nicklas |
599 |
new ValueOptions("1by24offset", "2by24offset", "4by24", "1by16", "1by16offset", "2by16", "2by16offset", |
| 5884 |
27 Mar 20 |
nicklas |
600 |
"3by16", "4by16", "5by16", "NP1by16", "external32", "external64"), |
| 4001 |
17 Jun 16 |
nicklas |
601 |
createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
602 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BARCODE_VARIANT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
603 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QUBIT_CONC, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
604 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QUBIT_CONC_AFTER_SPEEDVAC, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7286 |
15 Aug 23 |
nicklas |
605 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QUANTIT_CONC, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
606 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CA_SIZE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
607 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CA_MOLARITY, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
608 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CA_SIZE_ADPT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
609 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CA_MOLARITY_ADPT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
610 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LIBRARY_MOLARITY_EST, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
611 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LIBRARY_SIZE_EST, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
612 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LIBRARY_CONC_EST, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
613 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LIBRARY_FRAC_ADPT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5870 |
20 Mar 20 |
nicklas |
614 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.EXTERNAL_PLATE_POS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5870 |
20 Mar 20 |
nicklas |
615 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.EXTERNAL_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
616 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_CONC, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
617 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_MOLARITY, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
618 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_TARGET_VOLUME_PER_LIB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
619 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_TARGET_MOLARITY, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
620 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_IS_MANUAL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 2041 |
04 Oct 13 |
nicklas |
621 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_MIXING_STRATEGY, 1, |
| 2041 |
04 Oct 13 |
nicklas |
622 |
new ValueOptions(PooledLibrary.MIXING_STRATEGY_FIXED, PooledLibrary.MIXING_STRATEGY_DYNAMIC), |
| 4001 |
17 Jun 16 |
nicklas |
623 |
createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
624 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
625 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
626 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DILUTION_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
627 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DILUTION_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
628 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PURIFICATION_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
629 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PURIFICATION_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
630 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FRAGMENTATION_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
631 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FRAGMENTATION_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
632 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CLEANUP_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
633 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CLEANUP_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
634 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SYNTHESIS_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
635 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SYNTHESIS_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
636 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.AMPLIFICATION_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
637 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.AMPLIFICATION_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5450 |
27 May 19 |
nicklas |
638 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.HYBRIDIZATION_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5450 |
27 May 19 |
nicklas |
639 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.HYBRIDIZATION_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5450 |
27 May 19 |
nicklas |
640 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PCR_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5450 |
27 May 19 |
nicklas |
641 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PCR_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
642 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NEOPREP_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
643 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NEOPREP_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 1902 |
13 Mar 13 |
nicklas |
644 |
|
| 4001 |
17 Jun 16 |
nicklas |
645 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FLOWCELL_ID, 1, null, createIfMissing, effectivePermissionsUse)); |
| 2412 |
09 May 14 |
nicklas |
646 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FLOWCELL_TYPE, 1, |
| 5855 |
09 Mar 20 |
nicklas |
647 |
new ValueOptions(FlowCell.FLOW_CELL_TYPE_HISEQ, FlowCell.FLOW_CELL_TYPE_NEXTSEQ, FlowCell.FLOW_CELL_TYPE_NOVASEQ), |
| 4001 |
17 Jun 16 |
nicklas |
648 |
createIfMissing, effectivePermissionsUse)); |
| 7101 |
06 Apr 23 |
nicklas |
649 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LANE_NUMBER, 1, new ValueOptions(1, 2, 3, 4, 5, 6, 7, 8), createIfMissing, effectivePermissionsUse)); |
| 7101 |
06 Apr 23 |
nicklas |
650 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_NUMBER, 1, new ValueOptions(new Object[] {1, 2}), createIfMissing, effectivePermissionsUse)); |
| 7108 |
13 Apr 23 |
nicklas |
651 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_LENGTH, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
652 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CLUSTER_START, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
653 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CLUSTER_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
654 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_CYCLES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
655 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FAILED_LANES, 0, null, createIfMissing, effectivePermissionsUse)); |
| 2224 |
12 Feb 14 |
nicklas |
656 |
|
| 6461 |
01 Nov 21 |
nicklas |
657 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_ID, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6461 |
01 Nov 21 |
nicklas |
658 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_TYPE, 1, |
| 6865 |
09 Nov 22 |
nicklas |
659 |
new ValueOptions("OncoArray500K", "Epic850K"), |
| 6461 |
01 Nov 21 |
nicklas |
660 |
createIfMissing, effectivePermissionsUse)); |
| 6461 |
01 Nov 21 |
nicklas |
661 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_POSITION, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6461 |
01 Nov 21 |
nicklas |
662 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCAN_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6476 |
05 Nov 21 |
nicklas |
663 |
|
| 6476 |
05 Nov 21 |
nicklas |
664 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CALL_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6476 |
05 Nov 21 |
nicklas |
665 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_CALLS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6476 |
05 Nov 21 |
nicklas |
666 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_NO_CALLS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6476 |
05 Nov 21 |
nicklas |
667 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CALL_RATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6476 |
05 Nov 21 |
nicklas |
668 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GC10, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6476 |
05 Nov 21 |
nicklas |
669 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GC50, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6476 |
05 Nov 21 |
nicklas |
670 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LOG_R_DEV, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6557 |
31 Jan 22 |
nicklas |
671 |
|
| 6557 |
31 Jan 22 |
nicklas |
672 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GENOTYPE_COUNT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6557 |
31 Jan 22 |
nicklas |
673 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GENOTYPE_REF_PCT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6557 |
31 Jan 22 |
nicklas |
674 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GENOTYPE_HET_PCT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6557 |
31 Jan 22 |
nicklas |
675 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GENOTYPE_ALT_PCT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6461 |
01 Nov 21 |
nicklas |
676 |
|
| 6876 |
18 Nov 22 |
nicklas |
677 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_PROBES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
678 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_PROBES_BAD_PVAL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
679 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_PROBES_I, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
680 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_PROBES_II, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
681 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PROBES_RATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
682 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MEDIAN_METH, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
683 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MEDIAN_UNMETH, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
684 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PEAK_METH_I, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
685 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PEAK_UNMETH_I, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
686 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PEAK_METH_II, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6876 |
18 Nov 22 |
nicklas |
687 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PEAK_UNMETH_II, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6878 |
18 Nov 22 |
nicklas |
688 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ANALYSIS_FLAG, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7287 |
15 Aug 23 |
nicklas |
689 |
|
| 7287 |
15 Aug 23 |
nicklas |
690 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.TAU_MANUAL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7287 |
15 Aug 23 |
nicklas |
691 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RHO_MANUAL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7287 |
15 Aug 23 |
nicklas |
692 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PSI_MANUAL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7341 |
11 Sep 23 |
nicklas |
693 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PENALTY, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7341 |
11 Sep 23 |
nicklas |
694 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MIN_DEPTH, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7341 |
11 Sep 23 |
nicklas |
695 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.IMBALANCE_TEST, 1, |
| 7341 |
11 Sep 23 |
nicklas |
696 |
new ValueOptions(AllelicImbalanceTest.LEGACY.getTitle(), |
| 7341 |
11 Sep 23 |
nicklas |
697 |
AllelicImbalanceTest.MAD_SEGMENT.getTitle(), |
| 7341 |
11 Sep 23 |
nicklas |
698 |
AllelicImbalanceTest.BIMODALITY_COEFFICIENT.getTitle()), createIfMissing, effectivePermissionsUse)); |
| 7287 |
15 Aug 23 |
nicklas |
699 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NORMAL_CONTAMINATION, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7287 |
15 Aug 23 |
nicklas |
700 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PLOIDY, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7287 |
15 Aug 23 |
nicklas |
701 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PURITY, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7287 |
15 Aug 23 |
nicklas |
702 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GOODNESS_OF_FIT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7405 |
08 Nov 23 |
nicklas |
703 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUMBER_OF_SEGMENTS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7405 |
08 Nov 23 |
nicklas |
704 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.LOH_FRACTION, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7405 |
08 Nov 23 |
nicklas |
705 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.GI_SCORE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7341 |
11 Sep 23 |
nicklas |
706 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NON_ABERRANT, 1, |
| 7341 |
11 Sep 23 |
nicklas |
707 |
new ValueOptions("No", "Yes"), createIfMissing, effectivePermissionsUse)); |
| 7293 |
22 Aug 23 |
nicklas |
708 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ASCAT_RESULT, 1, |
| 7293 |
22 Aug 23 |
nicklas |
709 |
new ValueOptions("Accepted", "NotAccepted", "Undecided", "Failed"), createIfMissing, effectivePermissionsUse)); |
| 7287 |
15 Aug 23 |
nicklas |
710 |
|
| 4001 |
17 Jun 16 |
nicklas |
711 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_START, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
712 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_TURN_AROUND, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
713 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_END, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
714 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_RUN_NUMBER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
715 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_OPERATOR, 1, null, createIfMissing, effectivePermissionsUse)); |
| 2224 |
12 Feb 14 |
nicklas |
716 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.HISEQ_POSITION, 1, |
| 2224 |
12 Feb 14 |
nicklas |
717 |
new ValueOptions("A", "B"), |
| 4001 |
17 Jun 16 |
nicklas |
718 |
createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
719 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DATA_FILES_FOLDER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6209 |
13 Apr 21 |
nicklas |
720 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.RAW_FASTQ, 2, null, createIfMissing, effectivePermissionsUse)); |
| 2225 |
13 Feb 14 |
nicklas |
721 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_RESULT, 1, |
| 2225 |
13 Feb 14 |
nicklas |
722 |
new ValueOptions(SequencingRun.SEQUENCING_SUCCESSFUL, SequencingRun.SEQUENCING_FIRST_BASE_REPORT_FAILED, SequencingRun.SEQUENCING_FAILED), |
| 4001 |
17 Jun 16 |
nicklas |
723 |
createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
724 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_CONFIRMED, 1, null, createIfMissing, effectivePermissionsUse)); |
| 2320 |
04 Apr 14 |
nicklas |
725 |
|
| 4001 |
17 Jun 16 |
nicklas |
726 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_STRING, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
727 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OMIT_LANES, 0, null, createIfMissing, effectivePermissionsUse)); |
| 2364 |
15 Apr 14 |
nicklas |
728 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ANALYSIS_RESULT, 1, |
| 3723 |
25 Jan 16 |
nicklas |
729 |
new ValueOptions("Successful", "Partial", "Failed"), |
| 4001 |
17 Jun 16 |
nicklas |
730 |
createIfMissing, effectivePermissionsUse)); |
| 2049 |
07 Oct 13 |
nicklas |
731 |
|
| 4001 |
17 Jun 16 |
nicklas |
732 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
733 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PF_READS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
734 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ADAPTER_READS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
735 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PT_READS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
736 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FRAGMENT_SIZE_AVG, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
737 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FRAGMENT_SIZE_STDEV, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6421 |
23 Sep 21 |
nicklas |
738 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READLENGTH_AVG_R1, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6421 |
23 Sep 21 |
nicklas |
739 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READLENGTH_AVG_R2, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
740 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PF_NNNN_PCT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
741 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PF_UNUSED_PCT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
742 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DEMUX_WARNINGS, 0, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
743 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SKIPPED_TILES, 0, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
744 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PM_READS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
745 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ALIGNED_PAIRS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7113 |
14 Apr 23 |
nicklas |
746 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PF_BASES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7113 |
14 Apr 23 |
nicklas |
747 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PF_Q30_BASES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5843 |
25 Feb 20 |
nicklas |
748 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ALIGNED_BASES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
749 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_PAIRS_EXAMINED, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
750 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_PAIR_DUPLICATES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7104 |
11 Apr 23 |
nicklas |
751 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_PAIR_OPTICAL_DUPLICATES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7106 |
12 Apr 23 |
nicklas |
752 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MEAN_COVERAGE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7106 |
12 Apr 23 |
nicklas |
753 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SD_COVERAGE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
754 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FRACTION_DUPLICATION, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7104 |
11 Apr 23 |
nicklas |
755 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FRACTION_OPTICAL_DUPLICATION, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4620 |
16 Nov 17 |
nicklas |
756 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_GENOTYPE_COUNT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4658 |
26 Jan 18 |
nicklas |
757 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_GENOTYPE_HET_PCT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4642 |
28 Nov 17 |
nicklas |
758 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_GENOTYPE_STATUS, 1, |
| 4642 |
28 Nov 17 |
nicklas |
759 |
new ValueOptions("Checked", "Disabled"), |
| 4642 |
28 Nov 17 |
nicklas |
760 |
createIfMissing, effectivePermissionsUse)); |
| 4710 |
20 Mar 18 |
nicklas |
761 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_GENOTYPE_VERIFIED, 1, |
| 4712 |
22 Mar 18 |
nicklas |
762 |
new ValueOptions("DNA", "Specimen", "Lysate"), // See VerifiedMatch.getTitle() |
| 4710 |
20 Mar 18 |
nicklas |
763 |
createIfMissing, effectivePermissionsUse)); |
| 4648 |
15 Dec 17 |
nicklas |
764 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.QC_GENOTYPE_COMMENT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5046 |
22 Oct 18 |
nicklas |
765 |
|
| 5057 |
29 Oct 18 |
nicklas |
766 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.VARIANT_CALL_TYPE, 1, |
| 7396 |
06 Nov 23 |
nicklas |
767 |
new ValueOptions("mBAF", "VariantCall", "TargetedGenotype", "PanelOfNormal"), |
| 5057 |
29 Oct 18 |
nicklas |
768 |
createIfMissing, effectivePermissionsUse)); |
| 5046 |
22 Oct 18 |
nicklas |
769 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MBAF_SNP_COUNT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5046 |
22 Oct 18 |
nicklas |
770 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MBAF_SNP_COUNT_FILTERED, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5046 |
22 Oct 18 |
nicklas |
771 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MBAF_MIN_PVALUE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5046 |
22 Oct 18 |
nicklas |
772 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MBAF_MIN_PREGION, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5050 |
24 Oct 18 |
nicklas |
773 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MBAF_NUM_REGIONS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5050 |
24 Oct 18 |
nicklas |
774 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MBAF_SIGNIFICANT_REGIONS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 2365 |
16 Apr 14 |
nicklas |
775 |
|
| 5706 |
07 Nov 19 |
nicklas |
776 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.CALLABLE_BASES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 7439 |
16 Nov 23 |
nicklas |
777 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PANEL_OF_NORMALS, 1, |
| 7439 |
16 Nov 23 |
nicklas |
778 |
new ValueOptions("Novogene", "Sanger", "Cegat"), |
| 7439 |
16 Nov 23 |
nicklas |
779 |
createIfMissing, effectivePermissionsUse)); |
| 5721 |
13 Nov 19 |
nicklas |
780 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.VARIANTS_RAW, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5706 |
07 Nov 19 |
nicklas |
781 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.VARIANTS_PASSED_FILTER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6387 |
15 Sep 21 |
nicklas |
782 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.TARGETED_GENOTYPE, 1, |
| 6387 |
15 Sep 21 |
nicklas |
783 |
new ValueOptions((Object[])TargetedGenotypeJobCreator.getConfiguredTargetNames()), |
| 6387 |
15 Sep 21 |
nicklas |
784 |
createIfMissing, effectivePermissionsUse)); |
| 6388 |
15 Sep 21 |
nicklas |
785 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_TARGETED_GENOTYPES, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6388 |
15 Sep 21 |
nicklas |
786 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_TARGETED_VARIANTS, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5706 |
07 Nov 19 |
nicklas |
787 |
|
| 4972 |
20 Sep 18 |
nicklas |
788 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DO_NOT_USE, 1, |
| 5113 |
20 Nov 18 |
nicklas |
789 |
new ValueOptions("Specimen", "Lysate", "RNA", "PreNormalizedRNA", "Library", "Manual"), |
| 4972 |
20 Sep 18 |
nicklas |
790 |
createIfMissing, effectivePermissionsUse)); |
| 4972 |
20 Sep 18 |
nicklas |
791 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DO_NOT_USE_COMMENT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4972 |
20 Sep 18 |
nicklas |
792 |
|
| 5865 |
12 Mar 20 |
nicklas |
793 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BARCODE_SET, 1, |
| 6887 |
24 Nov 22 |
nicklas |
794 |
new ValueOptions(BarcodeSet.TRUSEQ_SINGLE.getName(), BarcodeSet.TRUSEQ_UNIQUE_DUAL.getName(), BarcodeSet.IDT10_UDI.getName()), |
| 5865 |
12 Mar 20 |
nicklas |
795 |
createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
796 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BARCODE_SEQUENCE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5489 |
12 Jun 19 |
nicklas |
797 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.BARCODE_SEQUENCE_2, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4001 |
17 Jun 16 |
nicklas |
798 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.SERIAL_NUMBER, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6010 |
18 Sep 20 |
nicklas |
799 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.HARDWARE_MODEL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 2350 |
10 Apr 14 |
nicklas |
800 |
|
| 4001 |
17 Jun 16 |
nicklas |
801 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PARAMETER_SET, 1, null, createIfMissing, secondaryAnalysisUse)); |
| 3616 |
23 Nov 15 |
nicklas |
802 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.REPORT_TEMPLATE, 1, |
| 5664 |
14 Oct 19 |
nicklas |
803 |
new ValueOptions("GENE_REPORT", "PILOT_REPORT", "SCANB_REPORT"), |
| 4001 |
17 Jun 16 |
nicklas |
804 |
createIfMissing, effectivePermissionsUse)); |
| 6213 |
15 Apr 21 |
nicklas |
805 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.DEMUX_TYPE, 1, |
| 6213 |
15 Apr 21 |
nicklas |
806 |
new ValueOptions("Picard", "bcl2fastq"), |
| 6213 |
15 Apr 21 |
nicklas |
807 |
createIfMissing, effectivePermissionsUse)); |
| 6213 |
15 Apr 21 |
nicklas |
808 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.MERGE_TYPE, 1, |
| 6213 |
15 Apr 21 |
nicklas |
809 |
new ValueOptions("Default", "Import"), |
| 6213 |
15 Apr 21 |
nicklas |
810 |
createIfMissing, effectivePermissionsUse)); |
| 4602 |
29 Sep 17 |
nicklas |
811 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ALIGNMENT_TYPE, 1, |
| 7131 |
24 Apr 23 |
nicklas |
812 |
new ValueOptions("Tophat", "Hisat", "MIPs", "Bwa-mem2"), |
| 4602 |
29 Sep 17 |
nicklas |
813 |
createIfMissing, effectivePermissionsUse)); |
| 4662 |
29 Jan 18 |
nicklas |
814 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.EXPRESSION_TYPE, 1, |
| 4663 |
29 Jan 18 |
nicklas |
815 |
new ValueOptions("Cufflinks", "StringTie"), |
| 4662 |
29 Jan 18 |
nicklas |
816 |
createIfMissing, effectivePermissionsUse)); |
| 2364 |
15 Apr 14 |
nicklas |
817 |
|
| 4138 |
29 Sep 16 |
nicklas |
818 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_COMPLETED_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4138 |
29 Sep 16 |
nicklas |
819 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_DELIVERED_DATE, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4154 |
06 Oct 16 |
nicklas |
820 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_TARGET_AMOUNT, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4154 |
06 Oct 16 |
nicklas |
821 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_TARGET_VOLUME, 1, null, createIfMissing, effectivePermissionsUse)); |
| 6326 |
14 Jun 21 |
nicklas |
822 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_PARENT_TYPE, 1, |
| 7037 |
13 Feb 23 |
nicklas |
823 |
new ValueOptions("DNA", "RNA", "Lysate", "FlowThrough", "BloodDNA"), createIfMissing, effectivePermissionsUse)); |
| 4179 |
27 Oct 16 |
nicklas |
824 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_RESULT, 1, |
| 4179 |
27 Oct 16 |
nicklas |
825 |
new ValueOptions("Successful", "Failed"), |
| 4179 |
27 Oct 16 |
nicklas |
826 |
createIfMissing, effectivePermissionsUse)); |
| 4138 |
29 Sep 16 |
nicklas |
827 |
|
| 6864 |
04 Nov 22 |
nicklas |
828 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.ZIP_PASSWORD, 1, null, createIfMissing, patientCuratorUse)); |
| 7224 |
31 May 23 |
nicklas |
829 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.FILES_TO_IGNORE, 0, null, createIfMissing, effectivePermissionsUse)); |
| 6864 |
04 Nov 22 |
nicklas |
830 |
|
| 4699 |
15 Mar 18 |
nicklas |
831 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.INCA2_a_diag_dat, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4459 |
21 Apr 17 |
nicklas |
832 |
|
| 4536 |
21 Jun 17 |
nicklas |
// Pilot report annotation types |
| 4536 |
21 Jun 17 |
nicklas |
834 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_SUBTYPE, 1, |
| 4568 |
01 Sep 17 |
nicklas |
835 |
new ValueOptions("HER2 enriched", "Luminal B", "Luminal A", "Basal", "Normal-like", "unclassified"), |
| 4536 |
21 Jun 17 |
nicklas |
836 |
createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
837 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_GGI, 1, |
| 4536 |
21 Jun 17 |
nicklas |
838 |
new ValueOptions("High", "Low"), createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
839 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_ER, 1, |
| 4536 |
21 Jun 17 |
nicklas |
840 |
new ValueOptions("Negative", "Positive"), createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
841 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_PGR, 1, |
| 4536 |
21 Jun 17 |
nicklas |
842 |
new ValueOptions("Negative", "Positive"), createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
843 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_HER2, 1, |
| 4536 |
21 Jun 17 |
nicklas |
844 |
new ValueOptions("Negative", "Positive"), createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
845 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_KI67, 1, |
| 4536 |
21 Jun 17 |
nicklas |
846 |
new ValueOptions("High", "Low"), createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
847 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_SCORE_LUMA, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
848 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_SCORE_LUMB, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
849 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_SCORE_HER2, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
850 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_SCORE_BASAL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
851 |
jsonChecks.add(checkAnnotationType(dc, Annotationtype.PILOT_SCORE_NORMAL, 1, null, createIfMissing, effectivePermissionsUse)); |
| 4536 |
21 Jun 17 |
nicklas |
852 |
|
| 5792 |
16 Dec 19 |
nicklas |
// Mutation signatures -- save in array for later AnnotationTypeCategory check |
| 5872 |
23 Mar 20 |
nicklas |
854 |
List<Annotationtype> variantCallAnnotations = new ArrayList<>(); |
| 5792 |
16 Dec 19 |
nicklas |
855 |
for (int index = 0; index < Annotationtype.NUM_MUTATION_SIGNATURES; index++) |
| 5792 |
16 Dec 19 |
nicklas |
856 |
{ |
| 5872 |
23 Mar 20 |
nicklas |
857 |
Annotationtype at = Annotationtype.mutationSignature(index+1); |
| 5872 |
23 Mar 20 |
nicklas |
858 |
jsonChecks.add(checkAnnotationType(dc, at, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5872 |
23 Mar 20 |
nicklas |
859 |
variantCallAnnotations.add(at); |
| 5792 |
16 Dec 19 |
nicklas |
860 |
} |
| 5792 |
16 Dec 19 |
nicklas |
861 |
|
| 5872 |
23 Mar 20 |
nicklas |
// Interesting genes for the variant calling |
| 5872 |
23 Mar 20 |
nicklas |
863 |
for (String gene : new VariantCallingJobCreator.VariantCollector().getGenes()) |
| 5872 |
23 Mar 20 |
nicklas |
864 |
{ |
| 5872 |
23 Mar 20 |
nicklas |
865 |
Annotationtype at = Annotationtype.geneVariantAnnotation(gene); |
| 5872 |
23 Mar 20 |
nicklas |
866 |
jsonChecks.add(checkAnnotationType(dc, at, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5872 |
23 Mar 20 |
nicklas |
867 |
variantCallAnnotations.add(at); |
| 5872 |
23 Mar 20 |
nicklas |
868 |
} |
| 5872 |
23 Mar 20 |
nicklas |
869 |
Annotationtype at = Annotationtype.geneVariantAnnotation("ESR1"); |
| 5872 |
23 Mar 20 |
nicklas |
870 |
jsonChecks.add(checkAnnotationType(dc, at, 1, null, createIfMissing, effectivePermissionsUse)); |
| 5872 |
23 Mar 20 |
nicklas |
871 |
variantCallAnnotations.add(at); |
| 5872 |
23 Mar 20 |
nicklas |
872 |
|
| 5962 |
03 Jun 20 |
nicklas |
// Single Sample Predictor installation |
| 5962 |
03 Jun 20 |
nicklas |
874 |
List<SspModel> validModels = SspModel.getConfiguredModels(); |
| 5962 |
03 Jun 20 |
nicklas |
875 |
Info sspInfo = null; |
| 5962 |
03 Jun 20 |
nicklas |
876 |
try |
| 5962 |
03 Jun 20 |
nicklas |
877 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
878 |
SspAnalysis ssp = new SspAnalysis(); |
| 5962 |
03 Jun 20 |
nicklas |
879 |
Info tmp = ssp.info(dc, validModels); |
| 5962 |
03 Jun 20 |
nicklas |
880 |
if (tmp.getExitStatus() != 0) |
| 5962 |
03 Jun 20 |
nicklas |
881 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
882 |
throw new RuntimeException(tmp.toString(), tmp.getException()); |
| 5962 |
03 Jun 20 |
nicklas |
883 |
} |
| 5962 |
03 Jun 20 |
nicklas |
884 |
sspInfo = tmp; |
| 5962 |
03 Jun 20 |
nicklas |
885 |
} |
| 5962 |
03 Jun 20 |
nicklas |
886 |
catch (Exception ex) |
| 5962 |
03 Jun 20 |
nicklas |
887 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
888 |
ex.printStackTrace(System.out); |
| 5962 |
03 Jun 20 |
nicklas |
889 |
JSONObject jsonSsp = new JSONObject(); |
| 5962 |
03 Jun 20 |
nicklas |
890 |
jsonSsp.put("itemType", "SSP"); |
| 5962 |
03 Jun 20 |
nicklas |
891 |
jsonSsp.put("name", "SSP R script"); |
| 5962 |
03 Jun 20 |
nicklas |
892 |
jsonSsp.put("status", "warning"); |
| 5962 |
03 Jun 20 |
nicklas |
893 |
JSONArray jsonMessages = new JSONArray(); |
| 5962 |
03 Jun 20 |
nicklas |
894 |
jsonMessages.add("The SSP R script failed"); |
| 5962 |
03 Jun 20 |
nicklas |
895 |
jsonSsp.put("stderr", ex.getMessage()); |
| 5962 |
03 Jun 20 |
nicklas |
896 |
jsonSsp.put("messages", jsonMessages); |
| 5962 |
03 Jun 20 |
nicklas |
897 |
jsonChecks.add(jsonSsp); |
| 5962 |
03 Jun 20 |
nicklas |
898 |
} |
| 5962 |
03 Jun 20 |
nicklas |
899 |
|
| 5962 |
03 Jun 20 |
nicklas |
900 |
List<Annotationtype> sspAnnotations = new ArrayList<>(); |
| 5962 |
03 Jun 20 |
nicklas |
901 |
if (sspInfo != null) |
| 5962 |
03 Jun 20 |
nicklas |
902 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
903 |
for (SspInfoResult info : sspInfo.getInfoResults()) |
| 5962 |
03 Jun 20 |
nicklas |
904 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
905 |
jsonChecks.addAll(checkSspInfo(dc, info, sspAnnotations, createIfMissing, effectivePermissionsUse)); |
| 5962 |
03 Jun 20 |
nicklas |
906 |
} |
| 5962 |
03 Jun 20 |
nicklas |
907 |
} |
| 5962 |
03 Jun 20 |
nicklas |
908 |
|
| 1463 |
14 Nov 11 |
martin |
// Annotation type categories |
| 1463 |
14 Nov 11 |
martin |
910 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.PATIENT, createIfMissing, |
| 1610 |
23 Apr 12 |
nicklas |
911 |
Annotationtype.ALL_FIRST_NAMES, Annotationtype.DATE_OF_BIRTH, |
| 1610 |
23 Apr 12 |
nicklas |
912 |
Annotationtype.FAMILY_NAME, Annotationtype.GENDER, Annotationtype.PERSONAL_NUMBER)); |
| 1516 |
19 Jan 12 |
nicklas |
913 |
|
| 3085 |
15 Jan 15 |
olle |
914 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RETRACT, createIfMissing, |
| 3756 |
18 Feb 16 |
olle |
915 |
Annotationtype.RETRACT_NA_LAB, |
| 3091 |
15 Jan 15 |
olle |
916 |
Annotationtype.RETRACT_TX_LAB, |
| 3091 |
15 Jan 15 |
olle |
917 |
Annotationtype.RETRACT_RX_LAB, |
| 3756 |
18 Feb 16 |
olle |
918 |
Annotationtype.RETRACT_NA_BB, |
| 3091 |
15 Jan 15 |
olle |
919 |
Annotationtype.RETRACT_TX_BB, |
| 3091 |
15 Jan 15 |
olle |
920 |
Annotationtype.RETRACT_RX_BB, |
| 3756 |
18 Feb 16 |
olle |
921 |
Annotationtype.RETRACT_NA_FROZEN, |
| 3091 |
15 Jan 15 |
olle |
922 |
Annotationtype.RETRACT_TX_FROZEN, |
| 3091 |
15 Jan 15 |
olle |
923 |
Annotationtype.RETRACT_RX_FROZEN, |
| 3756 |
18 Feb 16 |
olle |
924 |
Annotationtype.RETRACT_NA_RCC_SYD, |
| 3265 |
21 Apr 15 |
olle |
925 |
Annotationtype.RETRACT_TX_RCC_SYD, |
| 3085 |
15 Jan 15 |
olle |
926 |
Annotationtype.RETRACT_STATUS)); |
| 3085 |
15 Jan 15 |
olle |
927 |
|
| 3085 |
15 Jan 15 |
olle |
928 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RETRO_NO, createIfMissing, |
| 3756 |
18 Feb 16 |
olle |
929 |
Annotationtype.RETRACT_NA_LAB, |
| 3091 |
15 Jan 15 |
olle |
930 |
Annotationtype.RETRACT_TX_LAB, |
| 3091 |
15 Jan 15 |
olle |
931 |
Annotationtype.RETRACT_RX_LAB, |
| 3756 |
18 Feb 16 |
olle |
932 |
Annotationtype.RETRACT_NA_BB, |
| 3091 |
15 Jan 15 |
olle |
933 |
Annotationtype.RETRACT_TX_BB, |
| 3091 |
15 Jan 15 |
olle |
934 |
Annotationtype.RETRACT_RX_BB, |
| 3756 |
18 Feb 16 |
olle |
935 |
Annotationtype.RETRACT_NA_FROZEN, |
| 3091 |
15 Jan 15 |
olle |
936 |
Annotationtype.RETRACT_TX_FROZEN, |
| 3091 |
15 Jan 15 |
olle |
937 |
Annotationtype.RETRACT_RX_FROZEN, |
| 3756 |
18 Feb 16 |
olle |
938 |
Annotationtype.RETRACT_NA_RCC_SYD, |
| 3265 |
21 Apr 15 |
olle |
939 |
Annotationtype.RETRACT_TX_RCC_SYD, |
| 3085 |
15 Jan 15 |
olle |
940 |
Annotationtype.RETRACT_STATUS)); |
| 3085 |
15 Jan 15 |
olle |
941 |
|
| 1463 |
14 Nov 11 |
martin |
942 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.CASE, createIfMissing, |
| 3484 |
14 Sep 15 |
nicklas |
943 |
Annotationtype.CONSENT, Annotationtype.CONSENT_DATE, Annotationtype.FROZEN_TISSUE_DATE, |
| 4458 |
21 Apr 17 |
nicklas |
944 |
Annotationtype.LATERALITY, Annotationtype.REFERENCE_DATE, Annotationtype.REFERENCE_DATE_SOURCE, |
| 6098 |
11 Jan 21 |
nicklas |
945 |
Annotationtype.LINKED_CASE, |
| 5141 |
22 Nov 18 |
nicklas |
946 |
Annotationtype.INCA_EXPORT_DATE, Annotationtype.INCA_IMPORT_DATE, |
| 5141 |
22 Nov 18 |
nicklas |
947 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT)); |
| 1516 |
19 Jan 12 |
nicklas |
948 |
|
| 1515 |
19 Jan 12 |
nicklas |
949 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BLOOD, createIfMissing, |
| 1610 |
23 Apr 12 |
nicklas |
950 |
Annotationtype.CONSENT, Annotationtype.CONSENT_DATE, |
| 1610 |
23 Apr 12 |
nicklas |
951 |
Annotationtype.BLOOD_SAMPLING_DATETIME, Annotationtype.BLOOD_FREEZER_DATETIME, |
| 1775 |
11 Dec 12 |
olle |
952 |
Annotationtype.BLOOD_SERUM, Annotationtype.BLOOD_SAMPLE, |
| 5141 |
22 Nov 18 |
nicklas |
953 |
Annotationtype.BLOOD_RCCIDNUMBER, Annotationtype.OTHER_PATH_NOTE, |
| 6277 |
03 Jun 21 |
nicklas |
954 |
Annotationtype.BD47_ID, |
| 5141 |
22 Nov 18 |
nicklas |
955 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT)); |
| 3355 |
28 May 15 |
nicklas |
956 |
|
| 3355 |
28 May 15 |
nicklas |
957 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BLOOD_DNA, createIfMissing, |
| 6461 |
01 Nov 21 |
nicklas |
958 |
Annotationtype.ND_CONC, Annotationtype.BEADCHIP_POSITION, |
| 6461 |
01 Nov 21 |
nicklas |
959 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT)); |
| 3355 |
28 May 15 |
nicklas |
960 |
|
| 1463 |
14 Nov 11 |
martin |
961 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SPECIMEN, createIfMissing, |
| 1610 |
23 Apr 12 |
nicklas |
962 |
Annotationtype.ARRIVAL_DATE, Annotationtype.BIOPSY_TYPE, |
| 1610 |
23 Apr 12 |
nicklas |
963 |
Annotationtype.LATERALITY, Annotationtype.NOF_DELIVERED_TUBES, |
| 1610 |
23 Apr 12 |
nicklas |
964 |
Annotationtype.NOF_PIECES, Annotationtype.OPERATOR_DELIVERY_COMMENT, |
| 1610 |
23 Apr 12 |
nicklas |
965 |
Annotationtype.OPERATOR_PARTITION_COMMENT, Annotationtype.OTHER_PATH_NOTE, |
| 6994 |
20 Jan 23 |
nicklas |
966 |
Annotationtype.PAD, Annotationtype.ALTERNATE_PAD, |
| 6995 |
20 Jan 23 |
nicklas |
967 |
Annotationtype.EXTERNAL_OPERATOR, Annotationtype.EXTERNAL_SPECIMEN_EXISTS, |
| 6990 |
19 Jan 23 |
nicklas |
968 |
Annotationtype.RNALATER_DATETIME, Annotationtype.SAMPLING_DATETIME, |
| 6990 |
19 Jan 23 |
nicklas |
969 |
Annotationtype.SPECIMEN_TYPE, |
| 6711 |
27 Apr 22 |
nicklas |
970 |
Annotationtype.EXTERNAL_REF, Annotationtype.TUBE_LABEL, |
| 3784 |
16 Mar 16 |
nicklas |
971 |
Annotationtype.LINKED_SPECIMEN, Annotationtype.YELLOW_LABEL, |
| 6910 |
30 Nov 22 |
nicklas |
972 |
Annotationtype.COMPLETED_DATE, Annotationtype.IMPORT_WARNINGS, |
| 6918 |
01 Dec 22 |
nicklas |
973 |
Annotationtype.EXTERNAL_STORAGE, |
| 4972 |
20 Sep 18 |
nicklas |
974 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 3144 |
24 Feb 15 |
nicklas |
975 |
Annotationtype.AUTO_PROCESSING)); |
| 1608 |
20 Apr 12 |
nicklas |
976 |
|
| 1608 |
20 Apr 12 |
nicklas |
977 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.NO_SPECIMEN, createIfMissing, |
| 1677 |
31 May 12 |
nicklas |
978 |
Annotationtype.LATERALITY, |
| 6990 |
19 Jan 23 |
nicklas |
979 |
Annotationtype.PAD, Annotationtype.ALTERNATE_PAD, |
| 6990 |
19 Jan 23 |
nicklas |
980 |
Annotationtype.REASON_IF_NO_SPECIMEN, |
| 6574 |
08 Feb 22 |
nicklas |
981 |
Annotationtype.SAMPLING_DATETIME, Annotationtype.RNALATER_DATETIME, |
| 6574 |
08 Feb 22 |
nicklas |
982 |
Annotationtype.BIOPSY_TYPE, Annotationtype.OTHER_PATH_NOTE, |
| 6574 |
08 Feb 22 |
nicklas |
983 |
Annotationtype.EXTERNAL_SPECIMEN_EXISTS, Annotationtype.EXTERNAL_OPERATOR, |
| 6918 |
01 Dec 22 |
nicklas |
984 |
Annotationtype.EXTERNAL_STORAGE, |
| 6574 |
08 Feb 22 |
nicklas |
985 |
Annotationtype.LIASON_COMMENT, Annotationtype.LINKED_SPECIMEN, |
| 6574 |
08 Feb 22 |
nicklas |
986 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT |
| 1608 |
20 Apr 12 |
nicklas |
987 |
)); |
| 6151 |
26 Feb 21 |
nicklas |
988 |
|
| 5774 |
04 Dec 19 |
nicklas |
989 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.TMA_SPECIMEN, createIfMissing, |
| 5774 |
04 Dec 19 |
nicklas |
990 |
Annotationtype.TMA_BLOCK, Annotationtype.TMA_BLOCK_POS, |
| 5799 |
18 Dec 19 |
nicklas |
991 |
Annotationtype.PAD, Annotationtype.PAD_REQUESTED, Annotationtype.SAMPLE_OWNER |
| 5774 |
04 Dec 19 |
nicklas |
992 |
)); |
| 1608 |
20 Apr 12 |
nicklas |
993 |
|
| 2242 |
21 Feb 14 |
nicklas |
994 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.HISTOLOGY, createIfMissing, |
| 5141 |
22 Nov 18 |
nicklas |
995 |
Annotationtype.AUTO_PROCESSING, Annotationtype.FLAG, |
| 5141 |
22 Nov 18 |
nicklas |
996 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT)); |
| 2242 |
21 Feb 14 |
nicklas |
997 |
|
| 1668 |
25 May 12 |
nicklas |
998 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.STAINED, createIfMissing, |
| 3169 |
06 Mar 15 |
nicklas |
999 |
Annotationtype.IHC, Annotationtype.IHC_QUALITY, |
| 2134 |
11 Nov 13 |
nicklas |
1000 |
Annotationtype.GOOD_STAIN, Annotationtype.SCORE_COMPLETE, Annotationtype.SCORE_INVASIVE_CANCER, |
| 2134 |
11 Nov 13 |
nicklas |
1001 |
Annotationtype.SCORE_INSITU_CANCER, Annotationtype.SCORE_LYMPHOCYTES, Annotationtype.SCORE_NORMAL, |
| 2134 |
11 Nov 13 |
nicklas |
1002 |
Annotationtype.SCORE_STROMA, Annotationtype.SCORE_FAT)); |
| 1668 |
25 May 12 |
nicklas |
1003 |
|
| 6221 |
23 Apr 21 |
nicklas |
1004 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SAMPLE_HANDLING_PROTOCOL, createIfMissing, |
| 6221 |
23 Apr 21 |
nicklas |
1005 |
Annotationtype.EXTERNAL_REF |
| 6221 |
23 Apr 21 |
nicklas |
1006 |
)); |
| 6221 |
23 Apr 21 |
nicklas |
1007 |
|
| 1463 |
14 Nov 11 |
martin |
1008 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.LYSATE, createIfMissing, |
| 2690 |
24 Sep 14 |
nicklas |
1009 |
Annotationtype.PARTITION_DATE, Annotationtype.MULTIPLE_PIECES, |
| 2690 |
24 Sep 14 |
nicklas |
1010 |
Annotationtype.RLT_PLUS, Annotationtype.BETA_MERCA, |
| 3469 |
27 Aug 15 |
nicklas |
1011 |
Annotationtype.REAGENT_DX, Annotationtype.QIA_SHREDDER, |
| 6711 |
27 Apr 22 |
nicklas |
1012 |
Annotationtype.RESERVED_BY, Annotationtype.TUBE_LABEL, |
| 6918 |
01 Dec 22 |
nicklas |
1013 |
Annotationtype.EXTERNAL_STORAGE, |
| 4972 |
20 Sep 18 |
nicklas |
1014 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 4972 |
20 Sep 18 |
nicklas |
1015 |
Annotationtype.AUTO_PROCESSING |
| 2690 |
24 Sep 14 |
nicklas |
1016 |
)); |
| 1463 |
14 Nov 11 |
martin |
1017 |
|
| 6221 |
23 Apr 21 |
nicklas |
1018 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.EXTRACTION_PROTOCOL, createIfMissing, |
| 6221 |
23 Apr 21 |
nicklas |
1019 |
Annotationtype.EXTERNAL_REF |
| 6221 |
23 Apr 21 |
nicklas |
1020 |
)); |
| 6221 |
23 Apr 21 |
nicklas |
1021 |
|
| 1543 |
28 Feb 12 |
nicklas |
1022 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RNA, createIfMissing, |
| 1639 |
09 May 12 |
nicklas |
1023 |
Annotationtype.QIACUBE_DATE, Annotationtype.QIACUBE_OPERATOR, |
| 6510 |
03 Dec 21 |
nicklas |
1024 |
Annotationtype.QIACUBE_POSITION, Annotationtype.QIACUBE_RUN_NO, Annotationtype.QIACUBE_RUN_ID, |
| 1865 |
19 Feb 13 |
nicklas |
1025 |
Annotationtype.ND_CONC, Annotationtype.ND_260_BY_280, Annotationtype.ND_260_BY_230, |
| 6711 |
27 Apr 22 |
nicklas |
1026 |
Annotationtype.QUBIT_CONC, Annotationtype.TUBE_LABEL, |
| 2690 |
24 Sep 14 |
nicklas |
1027 |
Annotationtype.ALLPREP_MINI_KIT, Annotationtype.ETOH70, |
| 2690 |
24 Sep 14 |
nicklas |
1028 |
Annotationtype.BUFFER_RW1, Annotationtype.BUFFER_RPE, |
| 2690 |
24 Sep 14 |
nicklas |
1029 |
Annotationtype.BUFFER_AW1, Annotationtype.BUFFER_AW2, |
| 2690 |
24 Sep 14 |
nicklas |
1030 |
Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER, |
| 2690 |
24 Sep 14 |
nicklas |
1031 |
Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL, |
| 6918 |
01 Dec 22 |
nicklas |
1032 |
Annotationtype.IMPORT_WARNINGS, Annotationtype.EXTERNAL_STORAGE, |
| 4972 |
20 Sep 18 |
nicklas |
1033 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 1889 |
27 Feb 13 |
nicklas |
1034 |
Annotationtype.AUTO_PROCESSING, Annotationtype.FLAG)); |
| 1543 |
28 Feb 12 |
nicklas |
1035 |
|
| 2898 |
05 Nov 14 |
nicklas |
1036 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RNA_NORMALIZED_ALIQUOT, createIfMissing, |
| 2898 |
05 Nov 14 |
nicklas |
1037 |
Annotationtype.DILUTION_DATE, Annotationtype.DILUTION_OPERATOR, |
| 6219 |
20 Apr 21 |
nicklas |
1038 |
Annotationtype.ND_CONC, Annotationtype.QUBIT_CONC, |
| 2909 |
07 Nov 14 |
nicklas |
1039 |
Annotationtype.AUTO_PROCESSING, Annotationtype.FLAG |
| 2898 |
05 Nov 14 |
nicklas |
1040 |
)); |
| 2898 |
05 Nov 14 |
nicklas |
1041 |
|
| 3269 |
23 Apr 15 |
nicklas |
1042 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RNA_NORMALIZATION_PROTOCOL, createIfMissing, |
| 3829 |
06 Apr 16 |
nicklas |
1043 |
Annotationtype.RNA_TARGET_VOLUME, Annotationtype.RNA_TARGET_AMOUNT, |
| 3833 |
08 Apr 16 |
nicklas |
1044 |
Annotationtype.RNA_MINIMAL_AMOUNT, Annotationtype.LIBPREP_TARGET |
| 3269 |
23 Apr 15 |
nicklas |
1045 |
)); |
| 3269 |
23 Apr 15 |
nicklas |
1046 |
|
| 1549 |
06 Mar 12 |
nicklas |
1047 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DNA, createIfMissing, |
| 1639 |
09 May 12 |
nicklas |
1048 |
Annotationtype.QIACUBE_DATE, Annotationtype.QIACUBE_OPERATOR, |
| 6510 |
03 Dec 21 |
nicklas |
1049 |
Annotationtype.QIACUBE_POSITION, Annotationtype.QIACUBE_RUN_NO, Annotationtype.QIACUBE_RUN_ID, |
| 2690 |
24 Sep 14 |
nicklas |
1050 |
Annotationtype.ND_CONC, Annotationtype.ND_260_BY_280, Annotationtype.ND_260_BY_230, |
| 6711 |
27 Apr 22 |
nicklas |
1051 |
Annotationtype.QUBIT_CONC, Annotationtype.TUBE_LABEL, |
| 2690 |
24 Sep 14 |
nicklas |
1052 |
Annotationtype.ALLPREP_MINI_KIT, Annotationtype.ETOH70, |
| 2690 |
24 Sep 14 |
nicklas |
1053 |
Annotationtype.BUFFER_RW1, Annotationtype.BUFFER_RPE, |
| 2690 |
24 Sep 14 |
nicklas |
1054 |
Annotationtype.BUFFER_AW1, Annotationtype.BUFFER_AW2, |
| 2690 |
24 Sep 14 |
nicklas |
1055 |
Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER, |
| 4972 |
20 Sep 18 |
nicklas |
1056 |
Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL, |
| 5356 |
12 Apr 19 |
nicklas |
1057 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 6918 |
01 Dec 22 |
nicklas |
1058 |
Annotationtype.EXTERNAL_STORAGE, |
| 5356 |
12 Apr 19 |
nicklas |
1059 |
Annotationtype.AUTO_PROCESSING, Annotationtype.FLAG |
| 2690 |
24 Sep 14 |
nicklas |
1060 |
)); |
| 1639 |
09 May 12 |
nicklas |
1061 |
|
| 5359 |
12 Apr 19 |
nicklas |
1062 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DNA_NORMALIZED_ALIQUOT, createIfMissing, |
| 5359 |
12 Apr 19 |
nicklas |
1063 |
Annotationtype.DILUTION_DATE, Annotationtype.DILUTION_OPERATOR, |
| 6219 |
20 Apr 21 |
nicklas |
1064 |
Annotationtype.ND_CONC, Annotationtype.QUBIT_CONC, |
| 5601 |
13 Sep 19 |
nicklas |
1065 |
Annotationtype.MIPS_PANEL, Annotationtype.MIPS_POOL_VOLUME, |
| 5447 |
24 May 19 |
nicklas |
1066 |
Annotationtype.MIPS_NORMAL_TUMOR, Annotationtype.MIPS_FORM, |
| 5447 |
24 May 19 |
nicklas |
1067 |
Annotationtype.MIPS_VARIANT, Annotationtype.MIPS_VARIANT_LIST, Annotationtype.MIPS_SCREENING, |
| 5407 |
08 May 19 |
nicklas |
1068 |
Annotationtype.AUTO_PROCESSING, Annotationtype.FLAG, |
| 5407 |
08 May 19 |
nicklas |
1069 |
Annotationtype.PLATE_PROCESSING |
| 5359 |
12 Apr 19 |
nicklas |
1070 |
)); |
| 5359 |
12 Apr 19 |
nicklas |
1071 |
|
| 5359 |
12 Apr 19 |
nicklas |
1072 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DNA_NORMALIZATION_PROTOCOL, createIfMissing, |
| 5359 |
12 Apr 19 |
nicklas |
1073 |
Annotationtype.DNA_TARGET_VOLUME, Annotationtype.DNA_TARGET_AMOUNT, |
| 5449 |
27 May 19 |
nicklas |
1074 |
Annotationtype.DNA_MINIMAL_AMOUNT, Annotationtype.LIBPREP_TARGET, |
| 5601 |
13 Sep 19 |
nicklas |
1075 |
Annotationtype.MIPS_PANEL |
| 5359 |
12 Apr 19 |
nicklas |
1076 |
)); |
| 5359 |
12 Apr 19 |
nicklas |
1077 |
|
| 2095 |
23 Oct 13 |
nicklas |
1078 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.FLOW_THROUGH, createIfMissing, |
| 2095 |
23 Oct 13 |
nicklas |
1079 |
Annotationtype.QIACUBE_DATE, Annotationtype.QIACUBE_OPERATOR, |
| 6510 |
03 Dec 21 |
nicklas |
1080 |
Annotationtype.QIACUBE_POSITION, Annotationtype.QIACUBE_RUN_NO, Annotationtype.QIACUBE_RUN_ID, |
| 6918 |
01 Dec 22 |
nicklas |
1081 |
Annotationtype.TUBE_LABEL, Annotationtype.EXTERNAL_STORAGE, |
| 2690 |
24 Sep 14 |
nicklas |
1082 |
Annotationtype.ALLPREP_MINI_KIT, Annotationtype.ETOH70, |
| 2690 |
24 Sep 14 |
nicklas |
1083 |
Annotationtype.BUFFER_RW1, Annotationtype.BUFFER_RPE, |
| 2690 |
24 Sep 14 |
nicklas |
1084 |
Annotationtype.BUFFER_AW1, Annotationtype.BUFFER_AW2, |
| 2690 |
24 Sep 14 |
nicklas |
1085 |
Annotationtype.BUFFER_EB, Annotationtype.RNASE_FREE_WATER, |
| 4972 |
20 Sep 18 |
nicklas |
1086 |
Annotationtype.ALLPREP_DNA_COL, Annotationtype.RNEASY_COL, |
| 4972 |
20 Sep 18 |
nicklas |
1087 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT |
| 2690 |
24 Sep 14 |
nicklas |
1088 |
)); |
| 1543 |
28 Feb 12 |
nicklas |
1089 |
|
| 1546 |
02 Mar 12 |
nicklas |
1090 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RNAQC, createIfMissing, |
| 5141 |
22 Nov 18 |
nicklas |
1091 |
Annotationtype.BA_RIN, Annotationtype.CA_RQS, Annotationtype.QC_HISENSE, |
| 5141 |
22 Nov 18 |
nicklas |
1092 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT)); |
| 1865 |
19 Feb 13 |
nicklas |
1093 |
|
| 2004 |
29 May 13 |
nicklas |
1094 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MRNA, createIfMissing, |
| 2004 |
29 May 13 |
nicklas |
1095 |
Annotationtype.POOL_SCHEMA, Annotationtype.PLATE_PROCESS_RESULT, |
| 2004 |
29 May 13 |
nicklas |
1096 |
Annotationtype.DILUTION_DATE, Annotationtype.DILUTION_OPERATOR, |
| 3832 |
07 Apr 16 |
nicklas |
1097 |
Annotationtype.DILUTION_CONC, Annotationtype.DILUTION_VOLUME, |
| 3832 |
07 Apr 16 |
nicklas |
1098 |
Annotationtype.USE_FOR_QC, |
| 2004 |
29 May 13 |
nicklas |
1099 |
Annotationtype.PURIFICATION_DATE, Annotationtype.PURIFICATION_OPERATOR, |
| 2004 |
29 May 13 |
nicklas |
1100 |
Annotationtype.FRAGMENTATION_DATE, Annotationtype.FRAGMENTATION_OPERATOR, |
| 2906 |
07 Nov 14 |
nicklas |
1101 |
Annotationtype.AUTO_PROCESSING, |
| 5141 |
22 Nov 18 |
nicklas |
1102 |
Annotationtype.CLEANUP_DATE, Annotationtype.CLEANUP_OPERATOR, |
| 5891 |
07 Apr 20 |
nicklas |
1103 |
Annotationtype.RNA_TARGET_VOLUME, Annotationtype.RNA_TARGET_AMOUNT, |
| 5436 |
17 May 19 |
nicklas |
1104 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 5436 |
17 May 19 |
nicklas |
1105 |
Annotationtype.PIPELINE)); |
| 2004 |
29 May 13 |
nicklas |
1106 |
|
| 2004 |
29 May 13 |
nicklas |
1107 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.CDNA, createIfMissing, |
| 2004 |
29 May 13 |
nicklas |
1108 |
Annotationtype.SYNTHESIS_DATE, Annotationtype.SYNTHESIS_OPERATOR, |
| 5141 |
22 Nov 18 |
nicklas |
1109 |
Annotationtype.POOL_SCHEMA, Annotationtype.BARCODE_VARIANT, Annotationtype.PLATE_PROCESS_RESULT, |
| 5436 |
17 May 19 |
nicklas |
1110 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 5436 |
17 May 19 |
nicklas |
1111 |
Annotationtype.PIPELINE)); |
| 2004 |
29 May 13 |
nicklas |
1112 |
|
| 1902 |
13 Mar 13 |
nicklas |
1113 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.LIBRARY, createIfMissing, |
| 3832 |
07 Apr 16 |
nicklas |
1114 |
Annotationtype.DILUTION_CONC, Annotationtype.DILUTION_VOLUME, |
| 1987 |
23 May 13 |
nicklas |
1115 |
Annotationtype.QUBIT_CONC, Annotationtype.QUBIT_CONC_AFTER_SPEEDVAC, |
| 7286 |
15 Aug 23 |
nicklas |
1116 |
Annotationtype.QUANTIT_CONC, |
| 1987 |
23 May 13 |
nicklas |
1117 |
Annotationtype.CA_SIZE, Annotationtype.CA_MOLARITY, |
| 2454 |
23 May 14 |
nicklas |
1118 |
Annotationtype.CA_SIZE_ADPT, Annotationtype.CA_MOLARITY_ADPT, |
| 2454 |
23 May 14 |
nicklas |
1119 |
Annotationtype.LIBRARY_MOLARITY_EST, Annotationtype.LIBRARY_SIZE_EST, |
| 3309 |
06 May 15 |
nicklas |
1120 |
Annotationtype.LIBRARY_CONC_EST, Annotationtype.LIBRARY_FRAC_ADPT, |
| 2004 |
29 May 13 |
nicklas |
1121 |
Annotationtype.FLAG, |
| 2004 |
29 May 13 |
nicklas |
1122 |
Annotationtype.AMPLIFICATION_DATE, Annotationtype.AMPLIFICATION_OPERATOR, |
| 5450 |
27 May 19 |
nicklas |
1123 |
Annotationtype.HYBRIDIZATION_DATE, Annotationtype.HYBRIDIZATION_OPERATOR, |
| 5450 |
27 May 19 |
nicklas |
1124 |
Annotationtype.PCR_DATE, Annotationtype.PCR_OPERATOR, |
| 2004 |
29 May 13 |
nicklas |
1125 |
Annotationtype.CLEANUP_DATE, Annotationtype.CLEANUP_OPERATOR, |
| 3319 |
11 May 15 |
nicklas |
1126 |
Annotationtype.DILUTION_DATE, Annotationtype.DILUTION_OPERATOR, |
| 3319 |
11 May 15 |
nicklas |
1127 |
Annotationtype.NEOPREP_DATE, Annotationtype.NEOPREP_DATE, |
| 4972 |
20 Sep 18 |
nicklas |
1128 |
Annotationtype.POOL_SCHEMA, Annotationtype.BARCODE_VARIANT, |
| 5427 |
14 May 19 |
nicklas |
1129 |
Annotationtype.POOL_DATE, Annotationtype.POOL_OPERATOR, |
| 4972 |
20 Sep 18 |
nicklas |
1130 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 5870 |
20 Mar 20 |
nicklas |
1131 |
Annotationtype.PIPELINE, Annotationtype.EXTERNAL_PLATE_POS, |
| 6197 |
06 Apr 21 |
nicklas |
1132 |
Annotationtype.EXTERNAL_OPERATOR, Annotationtype.EXTERNAL_REF, |
| 5891 |
07 Apr 20 |
nicklas |
1133 |
Annotationtype.RNA_TARGET_VOLUME, Annotationtype.RNA_TARGET_AMOUNT, |
| 4972 |
20 Sep 18 |
nicklas |
1134 |
Annotationtype.PLATE_PROCESS_RESULT)); |
| 1865 |
19 Feb 13 |
nicklas |
1135 |
|
| 5425 |
14 May 19 |
nicklas |
1136 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.LIBRARY_PROTOCOL, createIfMissing, |
| 6221 |
23 Apr 21 |
nicklas |
1137 |
Annotationtype.LIBPREP_TARGET, Annotationtype.EXTERNAL_REF |
| 5425 |
14 May 19 |
nicklas |
1138 |
)); |
| 5425 |
14 May 19 |
nicklas |
1139 |
|
| 1959 |
03 May 13 |
nicklas |
1140 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.POOLED_LIBRARY, createIfMissing, |
| 2027 |
30 Sep 13 |
nicklas |
1141 |
Annotationtype.POOL_MOLARITY, Annotationtype.POOL_CONC, Annotationtype.POOL_TARGET_VOLUME_PER_LIB, |
| 2141 |
18 Nov 13 |
nicklas |
1142 |
Annotationtype.POOL_TARGET_MOLARITY, Annotationtype.POOL_IS_MANUAL, |
| 2191 |
13 Jan 14 |
nicklas |
1143 |
Annotationtype.POOL_MIXING_STRATEGY, Annotationtype.POOL_DATE, Annotationtype.POOL_OPERATOR, |
| 6197 |
06 Apr 21 |
nicklas |
1144 |
Annotationtype.PIPELINE, Annotationtype.EXTERNAL_REF, |
| 2077 |
17 Oct 13 |
nicklas |
1145 |
Annotationtype.FLAG, Annotationtype.AUTO_PROCESSING)); |
| 1959 |
03 May 13 |
nicklas |
1146 |
|
| 2021 |
17 Sep 13 |
nicklas |
1147 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.FLOW_CELL, createIfMissing, |
| 2412 |
09 May 14 |
nicklas |
1148 |
Annotationtype.FLOWCELL_ID, Annotationtype.FLOWCELL_TYPE, |
| 2412 |
09 May 14 |
nicklas |
1149 |
Annotationtype.CLUSTER_START, Annotationtype.CLUSTER_OPERATOR, |
| 2226 |
13 Feb 14 |
nicklas |
1150 |
Annotationtype.SEQUENCING_CYCLES, Annotationtype.FAILED_LANES, |
| 6203 |
09 Apr 21 |
nicklas |
1151 |
Annotationtype.PIPELINE, |
| 2226 |
13 Feb 14 |
nicklas |
1152 |
Annotationtype.PLATE_PROCESS_RESULT, Annotationtype.SEQUENCING_RESULT)); |
| 2021 |
17 Sep 13 |
nicklas |
1153 |
|
| 6461 |
01 Nov 21 |
nicklas |
1154 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BEAD_CHIP, createIfMissing, |
| 6461 |
01 Nov 21 |
nicklas |
1155 |
Annotationtype.BEADCHIP_ID, Annotationtype.BEADCHIP_TYPE, |
| 6461 |
01 Nov 21 |
nicklas |
1156 |
Annotationtype.PLATE_PROCESS_RESULT, Annotationtype.PIPELINE |
| 6461 |
01 Nov 21 |
nicklas |
1157 |
)); |
| 6461 |
01 Nov 21 |
nicklas |
1158 |
|
| 6461 |
01 Nov 21 |
nicklas |
1159 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SCAN, createIfMissing, |
| 6461 |
01 Nov 21 |
nicklas |
1160 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.SCAN_DATE, |
| 6461 |
01 Nov 21 |
nicklas |
1161 |
Annotationtype.ANALYSIS_RESULT, |
| 6461 |
01 Nov 21 |
nicklas |
1162 |
Annotationtype.PIPELINE |
| 6461 |
01 Nov 21 |
nicklas |
1163 |
)); |
| 6477 |
05 Nov 21 |
nicklas |
1164 |
|
| 6477 |
05 Nov 21 |
nicklas |
1165 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SCANNER, createIfMissing, |
| 7017 |
27 Jan 23 |
nicklas |
1166 |
Annotationtype.SERIAL_NUMBER, Annotationtype.HARDWARE_MODEL |
| 6477 |
05 Nov 21 |
nicklas |
1167 |
)); |
| 6475 |
05 Nov 21 |
nicklas |
1168 |
|
| 6475 |
05 Nov 21 |
nicklas |
1169 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.GENOTYPE_CALL, createIfMissing, |
| 6476 |
05 Nov 21 |
nicklas |
1170 |
Annotationtype.CALL_DATE, Annotationtype.NUM_CALLS, Annotationtype.NUM_NO_CALLS, |
| 6476 |
05 Nov 21 |
nicklas |
1171 |
Annotationtype.CALL_RATE, Annotationtype.GC10, Annotationtype.GC50, |
| 6476 |
05 Nov 21 |
nicklas |
1172 |
Annotationtype.LOG_R_DEV, Annotationtype.DATA_FILES_FOLDER, |
| 6512 |
06 Dec 21 |
nicklas |
1173 |
Annotationtype.QC_GENOTYPE_COUNT, Annotationtype.QC_GENOTYPE_HET_PCT, |
| 6512 |
06 Dec 21 |
nicklas |
1174 |
Annotationtype.QC_GENOTYPE_STATUS, |
| 6476 |
05 Nov 21 |
nicklas |
1175 |
Annotationtype.ANALYSIS_RESULT, Annotationtype.PIPELINE |
| 6475 |
05 Nov 21 |
nicklas |
1176 |
)); |
| 6865 |
09 Nov 22 |
nicklas |
1177 |
|
| 6865 |
09 Nov 22 |
nicklas |
1178 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.METHYLATION, createIfMissing, |
| 6880 |
22 Nov 22 |
nicklas |
1179 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.AUTO_PROCESSING, |
| 6876 |
18 Nov 22 |
nicklas |
1180 |
Annotationtype.ANALYSIS_RESULT, Annotationtype.PIPELINE, |
| 6876 |
18 Nov 22 |
nicklas |
1181 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 6876 |
18 Nov 22 |
nicklas |
1182 |
Annotationtype.NUM_PROBES, Annotationtype.NUM_PROBES_BAD_PVAL, |
| 6876 |
18 Nov 22 |
nicklas |
1183 |
Annotationtype.NUM_PROBES_I, Annotationtype.NUM_PROBES_II, |
| 6876 |
18 Nov 22 |
nicklas |
1184 |
Annotationtype.PROBES_RATE, |
| 6876 |
18 Nov 22 |
nicklas |
1185 |
Annotationtype.MEDIAN_METH, Annotationtype.MEDIAN_UNMETH, |
| 6876 |
18 Nov 22 |
nicklas |
1186 |
Annotationtype.PEAK_METH_I, Annotationtype.PEAK_UNMETH_I, |
| 6878 |
18 Nov 22 |
nicklas |
1187 |
Annotationtype.PEAK_METH_II, Annotationtype.PEAK_UNMETH_II, |
| 6878 |
18 Nov 22 |
nicklas |
1188 |
Annotationtype.ANALYSIS_FLAG |
| 6876 |
18 Nov 22 |
nicklas |
1189 |
)); |
| 6865 |
09 Nov 22 |
nicklas |
1190 |
|
| 6461 |
01 Nov 21 |
nicklas |
1191 |
|
| 2049 |
07 Oct 13 |
nicklas |
1192 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCING_RUN, createIfMissing, |
| 2196 |
13 Jan 14 |
nicklas |
1193 |
Annotationtype.SEQUENCING_START, Annotationtype.SEQUENCING_TURN_AROUND, Annotationtype.SEQUENCING_END, |
| 2224 |
12 Feb 14 |
nicklas |
1194 |
Annotationtype.SEQUENCING_OPERATOR, Annotationtype.SEQUENCING_RUN_NUMBER, Annotationtype.SEQUENCING_CYCLES, |
| 2228 |
14 Feb 14 |
nicklas |
1195 |
Annotationtype.HISEQ_POSITION, Annotationtype.DATA_FILES_FOLDER, Annotationtype.SEQUENCING_RESULT, |
| 5470 |
05 Jun 19 |
nicklas |
1196 |
Annotationtype.SEQUENCING_CONFIRMED, Annotationtype.AUTO_PROCESSING, |
| 6203 |
09 Apr 21 |
nicklas |
1197 |
Annotationtype.PIPELINE |
| 2049 |
07 Oct 13 |
nicklas |
1198 |
)); |
| 2049 |
07 Oct 13 |
nicklas |
1199 |
|
| 7099 |
06 Apr 23 |
nicklas |
1200 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCE_DATA, createIfMissing, |
| 7099 |
06 Apr 23 |
nicklas |
1201 |
Annotationtype.READS, Annotationtype.SERIAL_NUMBER, Annotationtype.SEQUENCING_RUN_NUMBER, |
| 7107 |
12 Apr 23 |
nicklas |
1202 |
Annotationtype.FLOWCELL_ID, Annotationtype.LANE_NUMBER, Annotationtype.READ_NUMBER, |
| 7108 |
13 Apr 23 |
nicklas |
1203 |
Annotationtype.FLOWCELL_TYPE, Annotationtype.READ_LENGTH |
| 7099 |
06 Apr 23 |
nicklas |
1204 |
)); |
| 7099 |
06 Apr 23 |
nicklas |
1205 |
|
| 7099 |
06 Apr 23 |
nicklas |
1206 |
|
| 2320 |
04 Apr 14 |
nicklas |
1207 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DEMUXED_SEQUENCES, createIfMissing, |
| 3032 |
12 Dec 14 |
nicklas |
1208 |
Annotationtype.READ_STRING, Annotationtype.OMIT_LANES, |
| 3032 |
12 Dec 14 |
nicklas |
1209 |
Annotationtype.ANALYSIS_RESULT, Annotationtype.AUTO_PROCESSING, |
| 6215 |
16 Apr 21 |
nicklas |
1210 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.RAW_FASTQ, |
| 2434 |
19 May 14 |
nicklas |
1211 |
Annotationtype.READS, Annotationtype.PF_READS, Annotationtype.PF_NNNN_PCT, |
| 5480 |
10 Jun 19 |
nicklas |
1212 |
Annotationtype.PF_UNUSED_PCT, Annotationtype.DEMUX_WARNINGS, Annotationtype.SKIPPED_TILES, |
| 5480 |
10 Jun 19 |
nicklas |
1213 |
Annotationtype.PIPELINE |
| 2320 |
04 Apr 14 |
nicklas |
1214 |
)); |
| 2364 |
15 Apr 14 |
nicklas |
1215 |
|
| 2364 |
15 Apr 14 |
nicklas |
1216 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MERGED_SEQUENCES, createIfMissing, |
| 2497 |
05 Jun 14 |
nicklas |
1217 |
Annotationtype.ANALYSIS_RESULT, |
| 2689 |
23 Sep 14 |
nicklas |
1218 |
Annotationtype.READS, Annotationtype.PF_READS, Annotationtype.ADAPTER_READS, Annotationtype.PT_READS, |
| 2680 |
18 Sep 14 |
nicklas |
1219 |
Annotationtype.FRAGMENT_SIZE_AVG, Annotationtype.FRAGMENT_SIZE_STDEV, |
| 6421 |
23 Sep 21 |
nicklas |
1220 |
Annotationtype.READLENGTH_AVG_R1, Annotationtype.READLENGTH_AVG_R2, |
| 6215 |
16 Apr 21 |
nicklas |
1221 |
Annotationtype.DATA_FILES_FOLDER, |
| 4972 |
20 Sep 18 |
nicklas |
1222 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 5480 |
10 Jun 19 |
nicklas |
1223 |
Annotationtype.AUTO_PROCESSING, |
| 5480 |
10 Jun 19 |
nicklas |
1224 |
Annotationtype.PIPELINE |
| 2364 |
15 Apr 14 |
nicklas |
1225 |
)); |
| 2320 |
04 Apr 14 |
nicklas |
1226 |
|
| 2420 |
13 May 14 |
nicklas |
1227 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MASKED_SEQUENCES, createIfMissing, |
| 5546 |
07 Aug 19 |
nicklas |
1228 |
Annotationtype.PM_READS, Annotationtype.PIPELINE, |
| 5141 |
22 Nov 18 |
nicklas |
1229 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT |
| 2399 |
05 May 14 |
nicklas |
1230 |
)); |
| 2399 |
05 May 14 |
nicklas |
1231 |
|
| 2399 |
05 May 14 |
nicklas |
1232 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.ALIGNED_SEQUENCES, createIfMissing, |
| 2706 |
29 Sep 14 |
nicklas |
1233 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.ALIGNED_PAIRS, |
| 7113 |
14 Apr 23 |
nicklas |
1234 |
Annotationtype.PF_BASES, Annotationtype.PF_Q30_BASES, |
| 7104 |
11 Apr 23 |
nicklas |
1235 |
Annotationtype.ALIGNED_BASES, Annotationtype.READ_PAIRS_EXAMINED, |
| 7106 |
12 Apr 23 |
nicklas |
1236 |
Annotationtype.READ_PAIR_DUPLICATES, Annotationtype.READ_PAIR_OPTICAL_DUPLICATES, |
| 7106 |
12 Apr 23 |
nicklas |
1237 |
Annotationtype.MEAN_COVERAGE, Annotationtype.SD_COVERAGE, |
| 7104 |
11 Apr 23 |
nicklas |
1238 |
Annotationtype.FRACTION_DUPLICATION, Annotationtype.FRACTION_OPTICAL_DUPLICATION, |
| 7104 |
11 Apr 23 |
nicklas |
1239 |
Annotationtype.FRAGMENT_SIZE_AVG, Annotationtype.FRAGMENT_SIZE_STDEV, |
| 7104 |
11 Apr 23 |
nicklas |
1240 |
Annotationtype.ANALYSIS_RESULT, |
| 4658 |
26 Jan 18 |
nicklas |
1241 |
Annotationtype.QC_GENOTYPE_COUNT, Annotationtype.QC_GENOTYPE_HET_PCT, |
| 4710 |
20 Mar 18 |
nicklas |
1242 |
Annotationtype.QC_GENOTYPE_STATUS, Annotationtype.QC_GENOTYPE_VERIFIED, |
| 5546 |
07 Aug 19 |
nicklas |
1243 |
Annotationtype.QC_GENOTYPE_COMMENT, Annotationtype.PIPELINE, |
| 5721 |
13 Nov 19 |
nicklas |
1244 |
Annotationtype.CALLABLE_BASES, Annotationtype.VARIANTS_RAW, |
| 4972 |
20 Sep 18 |
nicklas |
1245 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 5046 |
22 Oct 18 |
nicklas |
1246 |
Annotationtype.MBAF_SNP_COUNT, Annotationtype.MBAF_SNP_COUNT_FILTERED, |
| 5046 |
22 Oct 18 |
nicklas |
1247 |
Annotationtype.MBAF_MIN_PVALUE, Annotationtype.MBAF_MIN_PREGION, |
| 5050 |
24 Oct 18 |
nicklas |
1248 |
Annotationtype.MBAF_NUM_REGIONS, Annotationtype.MBAF_SIGNIFICANT_REGIONS, |
| 4972 |
20 Sep 18 |
nicklas |
1249 |
Annotationtype.AUTO_PROCESSING |
| 2399 |
05 May 14 |
nicklas |
1250 |
)); |
| 2399 |
05 May 14 |
nicklas |
1251 |
|
| 7388 |
31 Oct 23 |
nicklas |
1252 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.PANEL_OF_NORMAL, createIfMissing, |
| 7389 |
01 Nov 23 |
nicklas |
1253 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.VARIANTS_RAW, |
| 7439 |
16 Nov 23 |
nicklas |
1254 |
Annotationtype.CALLABLE_BASES, Annotationtype.PANEL_OF_NORMALS, |
| 7388 |
31 Oct 23 |
nicklas |
1255 |
Annotationtype.PIPELINE, Annotationtype.ANALYSIS_RESULT, |
| 7388 |
31 Oct 23 |
nicklas |
1256 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 7388 |
31 Oct 23 |
nicklas |
1257 |
Annotationtype.AUTO_PROCESSING |
| 7388 |
31 Oct 23 |
nicklas |
1258 |
)); |
| 7388 |
31 Oct 23 |
nicklas |
1259 |
|
| 2350 |
10 Apr 14 |
nicklas |
1260 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.BARCODE, createIfMissing, |
| 5489 |
12 Jun 19 |
nicklas |
1261 |
Annotationtype.BARCODE_SEQUENCE, Annotationtype.BARCODE_SEQUENCE_2, |
| 5865 |
12 Mar 20 |
nicklas |
1262 |
Annotationtype.PIPELINE, Annotationtype.BARCODE_SET |
| 2350 |
10 Apr 14 |
nicklas |
1263 |
)); |
| 2350 |
10 Apr 14 |
nicklas |
1264 |
|
| 5880 |
25 Mar 20 |
nicklas |
1265 |
jsonChecks.add(checkAnnotationTypeCategory(dc, "BarcodeTemplate", null, createIfMissing, |
| 5438 |
17 May 19 |
nicklas |
1266 |
Annotationtype.PIPELINE |
| 5438 |
17 May 19 |
nicklas |
1267 |
)); |
| 5438 |
17 May 19 |
nicklas |
1268 |
|
| 2368 |
17 Apr 14 |
nicklas |
1269 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCER, createIfMissing, |
| 6010 |
18 Sep 20 |
nicklas |
1270 |
Annotationtype.SERIAL_NUMBER, Annotationtype.HARDWARE_MODEL, Annotationtype.FLOWCELL_TYPE |
| 2368 |
17 Apr 14 |
nicklas |
1271 |
)); |
| 2368 |
17 Apr 14 |
nicklas |
1272 |
|
| 3114 |
05 Feb 15 |
nicklas |
1273 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DEMUX_SOFTWARE, createIfMissing, |
| 6213 |
15 Apr 21 |
nicklas |
1274 |
Annotationtype.PARAMETER_SET, Annotationtype.PIPELINE, Annotationtype.EXTERNAL_REF, |
| 6213 |
15 Apr 21 |
nicklas |
1275 |
Annotationtype.DEMUX_TYPE |
| 3114 |
05 Feb 15 |
nicklas |
1276 |
)); |
| 6213 |
15 Apr 21 |
nicklas |
1277 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DEMUX_PROTOCOL, createIfMissing, |
| 6213 |
15 Apr 21 |
nicklas |
1278 |
Annotationtype.PIPELINE, Annotationtype.DEMUX_TYPE |
| 6213 |
15 Apr 21 |
nicklas |
1279 |
)); |
| 3114 |
05 Feb 15 |
nicklas |
1280 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MERGE_SOFTWARE, createIfMissing, |
| 6213 |
15 Apr 21 |
nicklas |
1281 |
Annotationtype.PARAMETER_SET, Annotationtype.PIPELINE, Annotationtype.MERGE_TYPE |
| 3114 |
05 Feb 15 |
nicklas |
1282 |
)); |
| 6213 |
15 Apr 21 |
nicklas |
1283 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MERGE_PROTOCOL, createIfMissing, |
| 6213 |
15 Apr 21 |
nicklas |
1284 |
Annotationtype.PIPELINE, Annotationtype.MERGE_TYPE |
| 6213 |
15 Apr 21 |
nicklas |
1285 |
)); |
| 3114 |
05 Feb 15 |
nicklas |
1286 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MASKING_SOFTWARE, createIfMissing, |
| 6811 |
25 Aug 22 |
nicklas |
1287 |
Annotationtype.PARAMETER_SET, Annotationtype.PIPELINE |
| 3114 |
05 Feb 15 |
nicklas |
1288 |
)); |
| 3114 |
05 Feb 15 |
nicklas |
1289 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.ALIGNMENT_SOFTWARE, createIfMissing, |
| 6811 |
25 Aug 22 |
nicklas |
1290 |
Annotationtype.PARAMETER_SET, Annotationtype.ALIGNMENT_TYPE, Annotationtype.PIPELINE |
| 3114 |
05 Feb 15 |
nicklas |
1291 |
)); |
| 4602 |
29 Sep 17 |
nicklas |
1292 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.ALIGNMENT_PROTOCOL, createIfMissing, |
| 6811 |
25 Aug 22 |
nicklas |
1293 |
Annotationtype.ALIGNMENT_TYPE, Annotationtype.PIPELINE |
| 4602 |
29 Sep 17 |
nicklas |
1294 |
)); |
| 5057 |
29 Oct 18 |
nicklas |
1295 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.VARIANT_CALLING_SOFTWARE, createIfMissing, |
| 6811 |
25 Aug 22 |
nicklas |
1296 |
Annotationtype.PARAMETER_SET, Annotationtype.VARIANT_CALL_TYPE, Annotationtype.PIPELINE |
| 5057 |
29 Oct 18 |
nicklas |
1297 |
)); |
| 3114 |
05 Feb 15 |
nicklas |
1298 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.FEATURE_EXTRACTION_SOFTWARE, createIfMissing, |
| 6811 |
25 Aug 22 |
nicklas |
1299 |
Annotationtype.PARAMETER_SET, Annotationtype.EXPRESSION_TYPE, Annotationtype.PIPELINE |
| 3114 |
05 Feb 15 |
nicklas |
1300 |
)); |
| 4662 |
29 Jan 18 |
nicklas |
1301 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.FEATURE_EXTRACTION_PROTOCOL, createIfMissing, |
| 6811 |
25 Aug 22 |
nicklas |
1302 |
Annotationtype.EXPRESSION_TYPE, Annotationtype.PIPELINE |
| 4662 |
29 Jan 18 |
nicklas |
1303 |
)); |
| 4662 |
29 Jan 18 |
nicklas |
1304 |
|
| 3616 |
23 Nov 15 |
nicklas |
1305 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.REPORT_SOFTWARE, createIfMissing, |
| 3616 |
23 Nov 15 |
nicklas |
1306 |
Annotationtype.PARAMETER_SET, Annotationtype.REPORT_TEMPLATE |
| 3616 |
23 Nov 15 |
nicklas |
1307 |
)); |
| 5230 |
15 Jan 19 |
nicklas |
1308 |
|
| 5230 |
15 Jan 19 |
nicklas |
1309 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Rawdatatype.STRINGTIE, createIfMissing, |
| 5546 |
07 Aug 19 |
nicklas |
1310 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.PIPELINE, |
| 5230 |
15 Jan 19 |
nicklas |
1311 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 5230 |
15 Jan 19 |
nicklas |
1312 |
Annotationtype.ANALYSIS_RESULT, Annotationtype.AUTO_PROCESSING |
| 5230 |
15 Jan 19 |
nicklas |
1313 |
)); |
| 5962 |
03 Jun 20 |
nicklas |
1314 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Rawdatatype.STRINGTIE, createIfMissing, |
| 5962 |
03 Jun 20 |
nicklas |
1315 |
sspAnnotations.toArray(new Annotationtype[sspAnnotations.size()]) |
| 5962 |
03 Jun 20 |
nicklas |
1316 |
)); |
| 3114 |
05 Feb 15 |
nicklas |
1317 |
|
| 5706 |
07 Nov 19 |
nicklas |
1318 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Rawdatatype.VARIANT_CALL, createIfMissing, |
| 5706 |
07 Nov 19 |
nicklas |
1319 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.PIPELINE, |
| 7439 |
16 Nov 23 |
nicklas |
1320 |
Annotationtype.CALLABLE_BASES, Annotationtype.PANEL_OF_NORMALS, |
| 7410 |
10 Nov 23 |
nicklas |
1321 |
Annotationtype.VARIANTS_PASSED_FILTER, Annotationtype.VARIANTS_RAW, |
| 5706 |
07 Nov 19 |
nicklas |
1322 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 5706 |
07 Nov 19 |
nicklas |
1323 |
Annotationtype.ANALYSIS_RESULT, Annotationtype.AUTO_PROCESSING |
| 5706 |
07 Nov 19 |
nicklas |
1324 |
)); |
| 5792 |
16 Dec 19 |
nicklas |
1325 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Rawdatatype.VARIANT_CALL, createIfMissing, |
| 5872 |
23 Mar 20 |
nicklas |
1326 |
variantCallAnnotations.toArray(new Annotationtype[variantCallAnnotations.size()]) |
| 5792 |
16 Dec 19 |
nicklas |
1327 |
)); |
| 5706 |
07 Nov 19 |
nicklas |
1328 |
|
| 6538 |
13 Jan 22 |
nicklas |
1329 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Rawdatatype.ONCOARRAY500K, createIfMissing, |
| 6538 |
13 Jan 22 |
nicklas |
1330 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.PIPELINE, |
| 6557 |
31 Jan 22 |
nicklas |
1331 |
Annotationtype.GENOTYPE_COUNT, Annotationtype.GENOTYPE_REF_PCT, |
| 6557 |
31 Jan 22 |
nicklas |
1332 |
Annotationtype.GENOTYPE_HET_PCT, Annotationtype.GENOTYPE_ALT_PCT, |
| 6538 |
13 Jan 22 |
nicklas |
1333 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 6538 |
13 Jan 22 |
nicklas |
1334 |
Annotationtype.ANALYSIS_RESULT, Annotationtype.AUTO_PROCESSING |
| 6538 |
13 Jan 22 |
nicklas |
1335 |
)); |
| 6538 |
13 Jan 22 |
nicklas |
1336 |
|
| 7287 |
15 Aug 23 |
nicklas |
1337 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.COPY_NUMBER, createIfMissing, |
| 7287 |
15 Aug 23 |
nicklas |
1338 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.PIPELINE, |
| 7287 |
15 Aug 23 |
nicklas |
1339 |
Annotationtype.TAU_MANUAL, Annotationtype.RHO_MANUAL, |
| 7341 |
11 Sep 23 |
nicklas |
1340 |
Annotationtype.PSI_MANUAL, Annotationtype.PENALTY, |
| 7341 |
11 Sep 23 |
nicklas |
1341 |
Annotationtype.MIN_DEPTH, Annotationtype.IMBALANCE_TEST, |
| 7287 |
15 Aug 23 |
nicklas |
1342 |
Annotationtype.NORMAL_CONTAMINATION, Annotationtype.PLOIDY, |
| 7287 |
15 Aug 23 |
nicklas |
1343 |
Annotationtype.PURITY, Annotationtype.GOODNESS_OF_FIT, |
| 7405 |
08 Nov 23 |
nicklas |
1344 |
Annotationtype.NUMBER_OF_SEGMENTS, Annotationtype.LOH_FRACTION, |
| 7405 |
08 Nov 23 |
nicklas |
1345 |
Annotationtype.GI_SCORE, |
| 7341 |
11 Sep 23 |
nicklas |
1346 |
Annotationtype.NON_ABERRANT, Annotationtype.ASCAT_RESULT, |
| 7287 |
15 Aug 23 |
nicklas |
1347 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 7287 |
15 Aug 23 |
nicklas |
1348 |
Annotationtype.ANALYSIS_RESULT, Annotationtype.AUTO_PROCESSING |
| 7287 |
15 Aug 23 |
nicklas |
1349 |
)); |
| 7287 |
15 Aug 23 |
nicklas |
1350 |
|
| 6387 |
15 Sep 21 |
nicklas |
1351 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.VARIANT_CALL_FORMAT, createIfMissing, |
| 6388 |
15 Sep 21 |
nicklas |
1352 |
Annotationtype.TARGETED_GENOTYPE, Annotationtype.NUM_TARGETED_GENOTYPES, |
| 6388 |
15 Sep 21 |
nicklas |
1353 |
Annotationtype.NUM_TARGETED_VARIANTS |
| 6387 |
15 Sep 21 |
nicklas |
1354 |
)); |
| 6387 |
15 Sep 21 |
nicklas |
1355 |
|
| 5230 |
15 Jan 19 |
nicklas |
1356 |
jsonChecks.add(checkAnnotationTypeCategory(dc, Rawdatatype.CUFFLINKS, createIfMissing, |
| 5546 |
07 Aug 19 |
nicklas |
1357 |
Annotationtype.DATA_FILES_FOLDER, Annotationtype.PIPELINE, |
| 5230 |
15 Jan 19 |
nicklas |
1358 |
Annotationtype.DO_NOT_USE, Annotationtype.DO_NOT_USE_COMMENT, |
| 5230 |
15 Jan 19 |
nicklas |
1359 |
Annotationtype.ANALYSIS_RESULT, Annotationtype.AUTO_PROCESSING, |
| 6864 |
04 Nov 22 |
nicklas |
1360 |
Annotationtype.PILOT_SUBTYPE, |
| 5230 |
15 Jan 19 |
nicklas |
1361 |
Annotationtype.PILOT_ER, Annotationtype.PILOT_GGI, Annotationtype.PILOT_HER2, |
| 5230 |
15 Jan 19 |
nicklas |
1362 |
Annotationtype.PILOT_KI67, Annotationtype.PILOT_PGR, |
| 5230 |
15 Jan 19 |
nicklas |
1363 |
Annotationtype.PILOT_SCORE_BASAL, Annotationtype.PILOT_SCORE_HER2, |
| 5230 |
15 Jan 19 |
nicklas |
1364 |
Annotationtype.PILOT_SCORE_LUMA, Annotationtype.PILOT_SCORE_LUMB, |
| 5230 |
15 Jan 19 |
nicklas |
1365 |
Annotationtype.PILOT_SCORE_NORMAL, Annotationtype.PILOT_SCORE_NORMAL |
| 5230 |
15 Jan 19 |
nicklas |
1366 |
)); |
| 5230 |
15 Jan 19 |
nicklas |
1367 |
|
| 5880 |
25 Mar 20 |
nicklas |
1368 |
jsonChecks.add(checkAnnotationTypeCategory(dc, "INCA", "Annotation type category for INCA annotations used on Case items. Used by INCA import wizard.", createIfMissing)); |
| 5880 |
25 Mar 20 |
nicklas |
1369 |
jsonChecks.add(checkAnnotationTypeCategory(dc, "INCA_Release", "This category is for INCA annotations that should be included in data releases.", createIfMissing)); |
| 5880 |
25 Mar 20 |
nicklas |
1370 |
jsonChecks.add(checkAnnotationTypeCategory(dc, "GEX_Release", "This category is for Cufflinks annotations that should be included in data releases.", createIfMissing)); |
| 5880 |
25 Mar 20 |
nicklas |
1371 |
jsonChecks.add(checkAnnotationTypeCategory(dc, "VCALL_Release", "This category is for VariantCall annotations that should be included in data releases.", createIfMissing)); |
| 5928 |
29 Apr 20 |
nicklas |
1372 |
jsonChecks.add(checkAnnotationTypeCategory(dc, "STRINGTIE_Release", "This category is for StringTie annotations that should be included in data releases.", createIfMissing)); |
| 4475 |
27 Apr 17 |
nicklas |
1373 |
|
| 2565 |
11 Aug 14 |
nicklas |
// File servers |
| 3772 |
04 Mar 16 |
nicklas |
1375 |
jsonChecks.add(checkFileServer(dc, Fileserver.PROJECT_ARCHIVE, effectivePermissionsUse, createIfMissing)); |
| 3772 |
04 Mar 16 |
nicklas |
1376 |
jsonChecks.add(checkFileServer(dc, Fileserver.EXTERNAL_ARCHIVE, effectivePermissionsUse, createIfMissing)); |
| 7046 |
14 Feb 23 |
nicklas |
1377 |
jsonChecks.add(checkFileServer(dc, Fileserver.PROJECT_ARCHIVE_DNA, effectivePermissionsUse, createIfMissing)); |
| 4431 |
29 Mar 17 |
nicklas |
1378 |
jsonChecks.add(checkFileServer(dc, Fileserver.RELEASE_ARCHIVE, effectivePermissionsUse, createIfMissing)); |
| 6209 |
13 Apr 21 |
nicklas |
1379 |
jsonChecks.add(checkFileServer(dc, Fileserver.IMPORT_GATEWAY, effectivePermissionsUse, createIfMissing)); |
| 6177 |
23 Mar 21 |
nicklas |
1380 |
jsonChecks.add(checkFileServer(dc, Fileserver.IMPORT_ARCHIVE, effectivePermissionsUse, createIfMissing)); |
| 2562 |
08 Aug 14 |
nicklas |
1381 |
|
| 3600 |
13 Nov 15 |
nicklas |
// Directories |
| 4028 |
26 Jul 16 |
nicklas |
1383 |
jsonChecks.add(checkDirectory(dc, Histology.IMAGE_DIR, createIfMissing, effectivePermissionsUse)); |
| 5784 |
12 Dec 19 |
nicklas |
1384 |
jsonChecks.add(checkDirectory(dc, Histology.EXTERNAL_IMAGE_DIR, createIfMissing, effectivePermissionsUse)); |
| 4028 |
26 Jul 16 |
nicklas |
1385 |
jsonChecks.add(checkDirectory(dc, DemuxJobCreator.DEMULTIPLEX_METRICS_DIR, createIfMissing, effectivePermissionsUse)); |
| 4512 |
31 May 17 |
nicklas |
1386 |
jsonChecks.add(checkDirectory(dc, Reggie.FROZEN_TISSUE_FILES, createIfMissing, patientCuratorUse)); |
| 5397 |
03 May 19 |
nicklas |
1387 |
jsonChecks.add(checkDirectory(dc, Reggie.MIPS_IMPORT_FILES, createIfMissing, effectivePermissionsUse)); |
| 4028 |
26 Jul 16 |
nicklas |
1388 |
jsonChecks.add(checkDirectory(dc, Reggie.SECONDARY_ANALYSIS_DIR, createIfMissing, effectivePermissionsUse)); |
| 4028 |
26 Jul 16 |
nicklas |
1389 |
jsonChecks.add(checkDirectory(dc, Reggie.EXTERNAL_ANALYSIS_DIR, createIfMissing, effectivePermissionsUse)); |
| 4028 |
26 Jul 16 |
nicklas |
1390 |
jsonChecks.add(checkDirectory(dc, Reggie.DELIVERY_DIR, createIfMissing, patientCuratorUse, scanbDeliveryRead)); |
| 5889 |
06 Apr 20 |
nicklas |
1391 |
jsonChecks.add(checkDirectory(dc, Reggie.TEMPLATES_DIR, createIfMissing, effectivePermissionsUse)); |
| 6277 |
03 Jun 21 |
nicklas |
1392 |
jsonChecks.add(checkDirectory(dc, Reggie.REFERRAL_LOGS_DIR, createIfMissing, effectivePermissionsUse)); |
| 5892 |
07 Apr 20 |
nicklas |
1393 |
jsonChecks.add(checkDirectory(dc, Reggie.EXTERNAL_LIB_PLATES_DIR, createIfMissing, effectivePermissionsUse)); |
| 6960 |
13 Dec 22 |
nicklas |
1394 |
jsonChecks.add(checkDirectory(dc, Reggie.EXTERNAL_JSON_IMPORT_DIR, createIfMissing, patientCuratorUse)); |
| 7139 |
27 Apr 23 |
nicklas |
1395 |
jsonChecks.add(checkDirectory(dc, Reggie.TRANSPORT_BOX_IMPORT_FILES, createIfMissing, effectivePermissionsUse)); |
| 3600 |
13 Nov 15 |
nicklas |
1396 |
|
| 1865 |
19 Feb 13 |
nicklas |
// Plugin definitions and configurations |
| 2724 |
02 Oct 14 |
nicklas |
1398 |
jsonChecks.add(checkPlugin(dc, CaliperSampleNameExporter.class.getName(), effectivePermissionsUse, createIfMissing)); |
| 2022 |
17 Sep 13 |
nicklas |
1399 |
|
| 2724 |
02 Oct 14 |
nicklas |
1400 |
jsonChecks.add(checkPlugin(dc, CaliperRunParametersExporter.class.getName(), effectivePermissionsUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1401 |
jsonChecks.add(checkPluginConfiguration(dc, CaliperRunParametersExporter.class.getName(), "Standard sensitivity", effectivePermissionsUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1402 |
jsonChecks.add(checkPluginConfiguration(dc, CaliperRunParametersExporter.class.getName(), "High sensitivity", effectivePermissionsUse, createIfMissing)); |
| 2022 |
17 Sep 13 |
nicklas |
1403 |
|
| 2724 |
02 Oct 14 |
nicklas |
1404 |
jsonChecks.add(checkPlugin(dc, CaliperLibPrepParametersExporter.class.getName(), effectivePermissionsUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1405 |
jsonChecks.add(checkPluginConfiguration(dc, CaliperLibPrepParametersExporter.class.getName(), "HT DNA 1K Ver2 (96)", effectivePermissionsRead, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1406 |
jsonChecks.add(checkPluginConfiguration(dc, CaliperLibPrepParametersExporter.class.getName(), "HT DNA High Sensitivity (96)", effectivePermissionsUse, createIfMissing)); |
| 2021 |
17 Sep 13 |
nicklas |
1407 |
|
| 2724 |
02 Oct 14 |
nicklas |
1408 |
jsonChecks.add(checkPlugin(dc, QubitSampleNameExporter.class.getName(), effectivePermissionsUse, createIfMissing)); |
| 2022 |
17 Sep 13 |
nicklas |
1409 |
|
| 2724 |
02 Oct 14 |
nicklas |
1410 |
jsonChecks.add(checkPlugin(dc, "net.sf.basedb.plugins.gtf.GtfReporterImporter", secondaryAnalysisUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1411 |
jsonChecks.add(checkPluginConfiguration(dc, "net.sf.basedb.plugins.gtf.GtfReporterImporter", "SCAN-B (transcript_id)", secondaryAnalysisUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1412 |
jsonChecks.add(checkPlugin(dc, "net.sf.basedb.plugins.gtf.GtfReporterMapImporter", effectivePermissionsUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1413 |
jsonChecks.add(checkPluginConfiguration(dc, "net.sf.basedb.plugins.gtf.GtfReporterMapImporter", "SCAN-B (transcript_id)", secondaryAnalysisUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1414 |
jsonChecks.add(checkPlugin(dc, "net.sf.basedb.plugins.RawDataFlatFileImporter", effectivePermissionsUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1415 |
jsonChecks.add(checkPluginConfiguration(dc, "net.sf.basedb.plugins.RawDataFlatFileImporter", "SCAN-B (transcript_id)", secondaryAnalysisUse, createIfMissing)); |
| 2724 |
02 Oct 14 |
nicklas |
1416 |
|
| 2911 |
10 Nov 14 |
nicklas |
1417 |
jsonChecks.add(checkPlugin(dc, GeneReportPlugin.class.getName(), secondaryAnalysisUse, createIfMissing)); |
| 3499 |
21 Sep 15 |
nicklas |
1418 |
jsonChecks.add(checkPluginConfiguration(dc, GeneReportPlugin.class.getName(), "Gene report", secondaryAnalysisUse, createIfMissing)); |
| 3499 |
21 Sep 15 |
nicklas |
1419 |
jsonChecks.add(checkPluginConfiguration(dc, GeneReportPlugin.class.getName(), "Pilot report", secondaryAnalysisUse, createIfMissing)); |
| 6087 |
26 Nov 20 |
nicklas |
1420 |
jsonChecks.add(checkPluginConfiguration(dc, GeneReportPlugin.class.getName(), "SCAN-B report", secondaryAnalysisUse, createIfMissing)); |
| 2911 |
10 Nov 14 |
nicklas |
1421 |
jsonChecks.add(checkPlugin(dc, GeneReportsCombinerPlugin.class.getName(), effectivePermissionsUse, createIfMissing)); |
| 3500 |
21 Sep 15 |
nicklas |
1422 |
jsonChecks.add(checkPluginConfiguration(dc, GeneReportsCombinerPlugin.class.getName(), "Gene report", secondaryAnalysisUse, createIfMissing)); |
| 3500 |
21 Sep 15 |
nicklas |
1423 |
jsonChecks.add(checkPluginConfiguration(dc, GeneReportsCombinerPlugin.class.getName(), "Pilot report", secondaryAnalysisUse, createIfMissing)); |
| 6087 |
26 Nov 20 |
nicklas |
1424 |
jsonChecks.add(checkPluginConfiguration(dc, GeneReportsCombinerPlugin.class.getName(), "SCAN-B report", secondaryAnalysisUse, createIfMissing)); |
| 4034 |
29 Jul 16 |
nicklas |
1425 |
|
| 4034 |
29 Jul 16 |
nicklas |
1426 |
jsonChecks.add(checkPlugin(dc, SetPermissionsForDeliveryPlugin.class.getName(), patientCuratorUse, createIfMissing)); |
| 4034 |
29 Jul 16 |
nicklas |
1427 |
|
| 1865 |
19 Feb 13 |
nicklas |
// Biomaterial lists |
| 5962 |
03 Jun 20 |
nicklas |
1429 |
jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_RNA, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1430 |
jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_DNA, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1431 |
jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_POOL, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1432 |
jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_HISTOLOGY, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1433 |
jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_SPECIMEN, true, effectivePermissionsWrite, createIfMissing)); |
| 7164 |
12 May 23 |
nicklas |
1434 |
jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_EXERNAL_SPECIMEN, false, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1435 |
jsonChecks.add(checkItemList(dc, BiomaterialList.RNA_AUTO_DESIGN_1, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1436 |
jsonChecks.add(checkItemList(dc, BiomaterialList.RNA_AUTO_DESIGN_2, true, effectivePermissionsWrite, createIfMissing)); |
| 6179 |
24 Mar 21 |
nicklas |
1437 |
jsonChecks.add(checkItemList(dc, BiomaterialList.FASTQ_IMPORT_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1438 |
jsonChecks.add(checkItemList(dc, BiomaterialList.HISAT_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 6811 |
25 Aug 22 |
nicklas |
1439 |
jsonChecks.add(checkItemList(dc, BiomaterialList.HISAT_2023_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 7083 |
28 Mar 23 |
nicklas |
1440 |
jsonChecks.add(checkItemList(dc, BiomaterialList.BWA_MEM2_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1441 |
jsonChecks.add(checkItemList(dc, BiomaterialList.LEGACY_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1442 |
jsonChecks.add(checkItemList(dc, BiomaterialList.STRINGTIE_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 6815 |
26 Aug 22 |
nicklas |
1443 |
jsonChecks.add(checkItemList(dc, BiomaterialList.STRINGTIE_2023_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 6868 |
15 Nov 22 |
nicklas |
1444 |
jsonChecks.add(checkItemList(dc, BiomaterialList.METHYLATION_PIPELINE, false, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1445 |
jsonChecks.add(checkItemList(dc, BiomaterialList.MBAF_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1446 |
jsonChecks.add(checkItemList(dc, BiomaterialList.VARIANT_CALLING_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1447 |
jsonChecks.add(checkItemList(dc, BiomaterialList.MIPS_ALIGN_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1448 |
jsonChecks.add(checkItemList(dc, BiomaterialList.FLAGGED_ALIGNMENT, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1449 |
jsonChecks.add(checkItemList(dc, BiomaterialList.VARIANT_IMPORT_TMP, false, effectivePermissionsWrite, createIfMissing)); |
| 6023 |
26 Oct 20 |
nicklas |
1450 |
jsonChecks.add(checkItemList(dc, BiomaterialList.GENE_REPORT_CREATE, true, effectivePermissionsWrite, createIfMissing)); |
| 6023 |
26 Oct 20 |
nicklas |
1451 |
jsonChecks.add(checkItemList(dc, BiomaterialList.PILOT_REPORT_CREATE, true, effectivePermissionsWrite, createIfMissing)); |
| 6023 |
26 Oct 20 |
nicklas |
1452 |
jsonChecks.add(checkItemList(dc, BiomaterialList.SCANB_REPORT_CREATE, true, effectivePermissionsWrite, createIfMissing)); |
| 5962 |
03 Jun 20 |
nicklas |
1453 |
jsonChecks.add(checkItemList(dc, BiomaterialList.SSP_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 6387 |
15 Sep 21 |
nicklas |
1454 |
jsonChecks.add(checkItemList(dc, BiomaterialList.TARGETED_GENOTYPE_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 6387 |
15 Sep 21 |
nicklas |
1455 |
jsonChecks.add(checkItemList(dc, BiomaterialList.VARIANT_INDEX_ALL, true, effectivePermissionsWrite, createIfMissing)); |
| 6387 |
15 Sep 21 |
nicklas |
1456 |
jsonChecks.add(checkItemList(dc, BiomaterialList.VARIANT_INDEX_FILTERED, true, effectivePermissionsWrite, createIfMissing)); |
| 6387 |
15 Sep 21 |
nicklas |
1457 |
jsonChecks.add(checkItemList(dc, BiomaterialList.VARIANT_INDEX_TARGETED, true, effectivePermissionsWrite, createIfMissing)); |
| 7266 |
19 Jun 23 |
nicklas |
1458 |
jsonChecks.add(checkItemList(dc, BiomaterialList.ASCAT_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 7398 |
07 Nov 23 |
nicklas |
1459 |
jsonChecks.add(checkItemList(dc, BiomaterialList.WGS_VARIANT_CALLING_PIPELINE, true, effectivePermissionsWrite, createIfMissing)); |
| 1865 |
19 Feb 13 |
nicklas |
1460 |
|
| 1865 |
19 Feb 13 |
nicklas |
// MIME types |
| 1865 |
19 Feb 13 |
nicklas |
1462 |
jsonChecks.add(checkMimeType(dc, Mimetype.GDX, createIfMissing)); |
| 4619 |
13 Nov 17 |
nicklas |
1463 |
jsonChecks.add(checkMimeType(dc, Mimetype.VCF, createIfMissing)); |
| 6475 |
05 Nov 21 |
nicklas |
1464 |
jsonChecks.add(checkMimeType(dc, Mimetype.GTC, createIfMissing)); |
| 6866 |
14 Nov 22 |
nicklas |
1465 |
jsonChecks.add(checkMimeType(dc, Mimetype.IDAT, createIfMissing)); |
| 1865 |
19 Feb 13 |
nicklas |
1466 |
|
| 1865 |
19 Feb 13 |
nicklas |
// Special items |
| 2168 |
10 Dec 13 |
nicklas |
1468 |
jsonChecks.add(checkExtract(dc, Rna.STRATAGENE, Subtype.RNA, null, effectivePermissionsUse, createIfMissing)); |
| 1890 |
01 Mar 13 |
nicklas |
1469 |
jsonChecks.add(checkExtract(dc, Rna.EXTERNAL, Subtype.RNA, |
| 2168 |
10 Dec 13 |
nicklas |
1470 |
"This RNA is used to indicate that a bioplate location is taken by RNA not registered in BASE.", effectivePermissionsUse, createIfMissing)); |
| 1865 |
19 Feb 13 |
nicklas |
1471 |
|
| 1865 |
19 Feb 13 |
nicklas |
// Tags |
| 5865 |
12 Mar 20 |
nicklas |
// TruSeq single indexes |
| 1865 |
19 Feb 13 |
nicklas |
1474 |
for (int i = 1; i <= 27; i++) |
| 1865 |
19 Feb 13 |
nicklas |
1475 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
// Skip 17, 24 and 26 since those are not present in our kits |
| 1865 |
19 Feb 13 |
nicklas |
1477 |
if (i == 17 || i == 24 || i == 26) continue; |
| 5437 |
17 May 19 |
nicklas |
1478 |
jsonChecks.add(checkTag(dc, "AD"+(i < 10 ? "00" : "0")+i, Subtype.BARCODE, Pipeline.RNA_SEQ, |
| 5865 |
12 Mar 20 |
nicklas |
1479 |
BarcodeSet.TRUSEQ_SINGLE, "TruSeq Adapter Index " + i, |
| 2168 |
10 Dec 13 |
nicklas |
1480 |
effectivePermissionsUse, createIfMissing)); |
| 1865 |
19 Feb 13 |
nicklas |
1481 |
} |
| 5865 |
12 Mar 20 |
nicklas |
// TruSeq Unique Dual indexes |
| 5893 |
07 Apr 20 |
nicklas |
1483 |
for (int i = 1; i <= 96; i++) |
| 5865 |
12 Mar 20 |
nicklas |
1484 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
1485 |
jsonChecks.add(checkTag(dc, "UDI"+(i < 10 ? "000" : "00")+i, Subtype.BARCODE, Pipeline.RNA_SEQ, |
| 5865 |
12 Mar 20 |
nicklas |
1486 |
BarcodeSet.TRUSEQ_UNIQUE_DUAL, "TruSeq Unique Dual Index " + i, |
| 5865 |
12 Mar 20 |
nicklas |
1487 |
effectivePermissionsUse, createIfMissing)); |
| 5865 |
12 Mar 20 |
nicklas |
1488 |
} |
| 1865 |
19 Feb 13 |
nicklas |
1489 |
|
| 1284 |
08 Feb 11 |
nicklas |
1490 |
json.put("checks", jsonChecks); |
| 6713 |
28 Apr 22 |
nicklas |
1491 |
StaticCache cache = Application.getStaticCache(); |
| 5384 |
26 Apr 19 |
nicklas |
1492 |
|
| 3059 |
19 Dec 14 |
nicklas |
1493 |
if (createIfMissing) |
| 3059 |
19 Dec 14 |
nicklas |
1494 |
{ |
| 5421 |
13 May 19 |
nicklas |
1495 |
ActivityDef.UPDATED_REGGIE.merge(dc, Reggie.VERSION, 1); |
| 3059 |
19 Dec 14 |
nicklas |
1496 |
dc.commit(); |
| 6713 |
28 Apr 22 |
nicklas |
1497 |
cache.store("reggie/installed-version", Reggie.VERSION, 5); |
| 3059 |
19 Dec 14 |
nicklas |
1498 |
CounterService.getInstance().setForceCount(); |
| 3059 |
19 Dec 14 |
nicklas |
1499 |
} |
| 6713 |
28 Apr 22 |
nicklas |
1500 |
|
| 6713 |
28 Apr 22 |
nicklas |
1501 |
String installedVersion = cache.load("reggie/installed-version", 5); |
| 6713 |
28 Apr 22 |
nicklas |
1502 |
if (installedVersion == null) installedVersion = Reggie.VERSION; |
| 6713 |
28 Apr 22 |
nicklas |
1503 |
json.put("installedVersion", installedVersion); |
| 1284 |
08 Feb 11 |
nicklas |
1504 |
} |
| 2157 |
05 Dec 13 |
nicklas |
1505 |
|
| 2157 |
05 Dec 13 |
nicklas |
1506 |
else if ("GetPermissions".equals(cmd)) |
| 2157 |
05 Dec 13 |
nicklas |
1507 |
{ |
| 6328 |
14 Jun 21 |
nicklas |
1508 |
dc = sc.newDbControl(":Installation wizard"); |
| 3787 |
17 Mar 16 |
nicklas |
1509 |
json.put("permissions", JsonUtil.getPermissions(dc)); |
| 3743 |
12 Feb 16 |
nicklas |
1510 |
json.put("experimentalFeatures", JsonUtil.getExperimentalFeatures()); |
| 6684 |
20 Apr 22 |
nicklas |
1511 |
json.put("configIsModified", Reggie.configIsModified()); |
| 4624 |
17 Nov 17 |
nicklas |
1512 |
|
| 6836 |
05 Sep 22 |
nicklas |
1513 |
StaticCache cache = Application.getStaticCache(); |
| 6836 |
05 Sep 22 |
nicklas |
1514 |
if (!cache.exists("reggie/installed-version")) |
| 6836 |
05 Sep 22 |
nicklas |
1515 |
{ |
| 6836 |
05 Sep 22 |
nicklas |
1516 |
cache.store("reggie/installed-version", Reggie.VERSION, 5); |
| 6836 |
05 Sep 22 |
nicklas |
1517 |
} |
| 4624 |
17 Nov 17 |
nicklas |
1518 |
AnnotationType autoProc = Annotationtype.AUTO_PROCESSING.get(dc); |
| 7399 |
07 Nov 23 |
nicklas |
1519 |
JSONArray jsonAutoProcessingDisabled = new JSONArray(); |
| 7399 |
07 Nov 23 |
nicklas |
1520 |
json.put("autoProcessingDisabled", jsonAutoProcessingDisabled); |
| 4624 |
17 Nov 17 |
nicklas |
1521 |
if (autoProc != null) |
| 4624 |
17 Nov 17 |
nicklas |
1522 |
{ |
| 7399 |
07 Nov 23 |
nicklas |
1523 |
if (isDisabled(dc, BiomaterialList.FASTQ_IMPORT_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("fastq-import-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1524 |
if (isDisabled(dc, Fileserver.IMPORT_GATEWAY.get(dc))) jsonAutoProcessingDisabled.add("json-auto-import-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1525 |
if (isDisabled(dc, BiomaterialList.HISAT_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("hisat-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1526 |
if (isDisabled(dc, BiomaterialList.HISAT_2023_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("hisat2023-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1527 |
if (isDisabled(dc, BiomaterialList.BWA_MEM2_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("bwamem2-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1528 |
if (isDisabled(dc, BiomaterialList.LEGACY_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("legacy-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1529 |
if (isDisabled(dc, BiomaterialList.STRINGTIE_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("stringtie-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1530 |
if (isDisabled(dc, BiomaterialList.STRINGTIE_2023_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("stringtie2023-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1531 |
if (isDisabled(dc, BiomaterialList.MBAF_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("mbaf-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1532 |
if (isDisabled(dc, BiomaterialList.VARIANT_CALLING_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("variant-calling-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1533 |
if (isDisabled(dc, BiomaterialList.TARGETED_GENOTYPE_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("targeted-genotype-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1534 |
if (isDisabled(dc, BiomaterialList.SSP_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("ssp-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1535 |
if (isDisabled(dc, BiomaterialList.GENE_REPORT_CREATE.get(dc))) jsonAutoProcessingDisabled.add("gene-report-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1536 |
if (isDisabled(dc, BiomaterialList.PILOT_REPORT_CREATE.get(dc))) jsonAutoProcessingDisabled.add("pilot-report-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1537 |
if (isDisabled(dc, BiomaterialList.SCANB_REPORT_CREATE.get(dc))) jsonAutoProcessingDisabled.add("scanb-report-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1538 |
if (isDisabled(dc, BiomaterialList.MIPS_ALIGN_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("mips-align-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1539 |
if (isDisabled(dc, BiomaterialList.ASCAT_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("ascat-pipeline-disabled"); |
| 7399 |
07 Nov 23 |
nicklas |
1540 |
if (isDisabled(dc, BiomaterialList.WGS_VARIANT_CALLING_PIPELINE.get(dc))) jsonAutoProcessingDisabled.add("wgs-variant-calling-pipeline-disabled"); |
| 4624 |
17 Nov 17 |
nicklas |
1541 |
} |
| 7399 |
07 Nov 23 |
nicklas |
1542 |
JSONArray jsonHiddenWizards = new JSONArray(); |
| 7399 |
07 Nov 23 |
nicklas |
1543 |
json.put("hiddenWizards", jsonHiddenWizards); |
| 7399 |
07 Nov 23 |
nicklas |
1544 |
ItemList variantImport = BiomaterialList.VARIANT_IMPORT_TMP.get(dc); |
| 7399 |
07 Nov 23 |
nicklas |
1545 |
if (variantImport == null || variantImport.getSize() == 0) jsonHiddenWizards.add("variant-import-wizard"); |
| 2157 |
05 Dec 13 |
nicklas |
1546 |
dc.close(); |
| 2157 |
05 Dec 13 |
nicklas |
1547 |
} |
| 3116 |
06 Feb 15 |
nicklas |
1548 |
|
| 3116 |
06 Feb 15 |
nicklas |
1549 |
else if ("GetParameterSetInfo".equals(cmd)) |
| 3116 |
06 Feb 15 |
nicklas |
1550 |
{ |
| 3116 |
06 Feb 15 |
nicklas |
1551 |
String parameterSet = Values.getStringOrNull(req.getParameter("parameterSet")); |
| 3116 |
06 Feb 15 |
nicklas |
1552 |
String targetId = Values.getStringOrNull(req.getParameter("targetId")); |
| 3116 |
06 Feb 15 |
nicklas |
1553 |
|
| 3116 |
06 Feb 15 |
nicklas |
1554 |
XmlConfig cfg = Reggie.getConfig(); |
| 3116 |
06 Feb 15 |
nicklas |
1555 |
JSONArray jsonParameters = new JSONArray(); |
| 3116 |
06 Feb 15 |
nicklas |
1556 |
json.put("parameterSet", parameterSet); |
| 3116 |
06 Feb 15 |
nicklas |
1557 |
json.put("parameters", jsonParameters); |
| 3116 |
06 Feb 15 |
nicklas |
1558 |
json.put("targetId", targetId); |
| 3116 |
06 Feb 15 |
nicklas |
1559 |
|
| 3116 |
06 Feb 15 |
nicklas |
1560 |
for (Element e : cfg.getAllInParameterSet(parameterSet)) |
| 3116 |
06 Feb 15 |
nicklas |
1561 |
{ |
| 3116 |
06 Feb 15 |
nicklas |
1562 |
JSONObject jsonElement = new JSONObject(); |
| 3116 |
06 Feb 15 |
nicklas |
1563 |
jsonElement.put("value", e.getTextTrim()); |
| 3116 |
06 Feb 15 |
nicklas |
1564 |
List<String> fullName = new ArrayList<String>(); |
| 3116 |
06 Feb 15 |
nicklas |
1565 |
while (e != null) |
| 3116 |
06 Feb 15 |
nicklas |
1566 |
{ |
| 3117 |
06 Feb 15 |
nicklas |
1567 |
String name = e.getName(); |
| 3117 |
06 Feb 15 |
nicklas |
1568 |
if ("host".equals(name)) |
| 3117 |
06 Feb 15 |
nicklas |
1569 |
{ |
| 3117 |
06 Feb 15 |
nicklas |
1570 |
name += "[" + e.getAttributeValue("address") + ":" + e.getAttributeValue("port") + "]"; |
| 3117 |
06 Feb 15 |
nicklas |
1571 |
} |
| 3117 |
06 Feb 15 |
nicklas |
1572 |
fullName.add(0, name); |
| 3116 |
06 Feb 15 |
nicklas |
1573 |
e = e.getParentElement(); |
| 3116 |
06 Feb 15 |
nicklas |
1574 |
} |
| 3116 |
06 Feb 15 |
nicklas |
1575 |
jsonElement.put("name", Values.getString(fullName, "/", true)); |
| 3116 |
06 Feb 15 |
nicklas |
1576 |
jsonParameters.add(jsonElement); |
| 3116 |
06 Feb 15 |
nicklas |
1577 |
} |
| 3116 |
06 Feb 15 |
nicklas |
1578 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1579 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1580 |
catch (Throwable t) |
| 1284 |
08 Feb 11 |
nicklas |
1581 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1582 |
t.printStackTrace(); |
| 1284 |
08 Feb 11 |
nicklas |
1583 |
json.clear(); |
| 1284 |
08 Feb 11 |
nicklas |
1584 |
json.put("status", "error"); |
| 1284 |
08 Feb 11 |
nicklas |
1585 |
json.put("message", t.getMessage()); |
| 1284 |
08 Feb 11 |
nicklas |
1586 |
json.put("stacktrace", ThrowableUtil.stackTraceToString(t)); |
| 1284 |
08 Feb 11 |
nicklas |
1587 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1588 |
finally |
| 1284 |
08 Feb 11 |
nicklas |
1589 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1590 |
if (dc != null) dc.close(); |
| 1284 |
08 Feb 11 |
nicklas |
1591 |
json.writeJSONString(resp.getWriter()); |
| 1284 |
08 Feb 11 |
nicklas |
1592 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1593 |
|
| 1284 |
08 Feb 11 |
nicklas |
1594 |
|
| 1284 |
08 Feb 11 |
nicklas |
1595 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1596 |
|
| 7399 |
07 Nov 23 |
nicklas |
1597 |
private boolean isDisabled(DbControl dc, Annotatable item) |
| 7399 |
07 Nov 23 |
nicklas |
1598 |
{ |
| 7399 |
07 Nov 23 |
nicklas |
1599 |
return "Disable".equals(Annotationtype.AUTO_PROCESSING.getAnnotationValue(dc, item)); |
| 7399 |
07 Nov 23 |
nicklas |
1600 |
} |
| 2157 |
05 Dec 13 |
nicklas |
1601 |
|
| 7399 |
07 Nov 23 |
nicklas |
1602 |
|
| 5962 |
03 Jun 20 |
nicklas |
1603 |
public List<JSONObject> checkSspInfo(DbControl dc, SspInfoResult info, List<Annotationtype> sspAnnotations, |
| 5962 |
03 Jun 20 |
nicklas |
1604 |
boolean createIfMissing, PermissionOptions... permissions) |
| 5962 |
03 Jun 20 |
nicklas |
1605 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
1606 |
SspModel model = info.getModel(); |
| 5962 |
03 Jun 20 |
nicklas |
1607 |
|
| 5962 |
03 Jun 20 |
nicklas |
1608 |
List<JSONObject> jsonChecks = new ArrayList<>(); |
| 5962 |
03 Jun 20 |
nicklas |
1609 |
JSONObject json = new JSONObject(); |
| 5962 |
03 Jun 20 |
nicklas |
1610 |
JSONArray jsonMessages = new JSONArray(); |
| 5962 |
03 Jun 20 |
nicklas |
1611 |
json.put("itemType", "SSP"); |
| 5962 |
03 Jun 20 |
nicklas |
1612 |
json.put("name", model.getName()); |
| 5962 |
03 Jun 20 |
nicklas |
1613 |
json.put("status", "ok"); |
| 5962 |
03 Jun 20 |
nicklas |
1614 |
|
| 5962 |
03 Jun 20 |
nicklas |
1615 |
if (model.modelDataExists()) |
| 5962 |
03 Jun 20 |
nicklas |
1616 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
1617 |
Annotationtype sspResult = Annotationtype.sspResultAnnotation(model); |
| 5962 |
03 Jun 20 |
nicklas |
1618 |
jsonChecks.add(checkAnnotationType(dc, sspResult, 1, |
| 5962 |
03 Jun 20 |
nicklas |
1619 |
new ValueOptions((Object[])info.getTranslatedClasses()), createIfMissing, permissions)); |
| 5962 |
03 Jun 20 |
nicklas |
1620 |
sspAnnotations.add(sspResult); |
| 5962 |
03 Jun 20 |
nicklas |
1621 |
Annotationtype sspScore = Annotationtype.sspScoreAnnotation(model); |
| 5962 |
03 Jun 20 |
nicklas |
1622 |
if (sspScore != null) |
| 5962 |
03 Jun 20 |
nicklas |
1623 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
1624 |
jsonChecks.add(checkAnnotationType(dc, sspScore, 1, null, createIfMissing, permissions)); |
| 5962 |
03 Jun 20 |
nicklas |
1625 |
sspAnnotations.add(sspScore); |
| 5962 |
03 Jun 20 |
nicklas |
1626 |
} |
| 5962 |
03 Jun 20 |
nicklas |
1627 |
} |
| 5962 |
03 Jun 20 |
nicklas |
1628 |
else |
| 5962 |
03 Jun 20 |
nicklas |
1629 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
1630 |
json.put("status", "warning"); |
| 5962 |
03 Jun 20 |
nicklas |
1631 |
jsonMessages.add("File '"+model.getModelData()+"' not found. This SSP will be disabled."); |
| 5962 |
03 Jun 20 |
nicklas |
1632 |
} |
| 5962 |
03 Jun 20 |
nicklas |
1633 |
|
| 5962 |
03 Jun 20 |
nicklas |
1634 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 5962 |
03 Jun 20 |
nicklas |
1635 |
json.put("messages", jsonMessages); |
| 5962 |
03 Jun 20 |
nicklas |
1636 |
jsonChecks.add(json); |
| 5962 |
03 Jun 20 |
nicklas |
1637 |
|
| 5962 |
03 Jun 20 |
nicklas |
1638 |
return jsonChecks; |
| 5962 |
03 Jun 20 |
nicklas |
1639 |
} |
| 5962 |
03 Jun 20 |
nicklas |
1640 |
|
| 1284 |
08 Feb 11 |
nicklas |
1641 |
/** |
| 1409 |
18 Oct 11 |
martin |
Creates an annotation type with the given options. The annotation |
| 1409 |
18 Oct 11 |
martin |
type is created in a separate transaction. The annotation can be enabled for |
| 1409 |
18 Oct 11 |
martin |
one or more item-types. |
| 1409 |
18 Oct 11 |
martin |
1645 |
|
| 1610 |
23 Apr 12 |
nicklas |
@since 2.5 |
| 1409 |
18 Oct 11 |
martin |
1647 |
*/ |
| 1610 |
23 Apr 12 |
nicklas |
1648 |
public AnnotationType createAnnotationType(SessionControl sc, Annotationtype annotationType, |
| 4001 |
17 Jun 16 |
nicklas |
1649 |
int multiplicity, ValueOptions valueOptions, PermissionOptions... permissions) |
| 1409 |
18 Oct 11 |
martin |
1650 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1651 |
AnnotationType at = null; |
| 6328 |
14 Jun 21 |
nicklas |
1652 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1284 |
08 Feb 11 |
nicklas |
1653 |
try |
| 1284 |
08 Feb 11 |
nicklas |
1654 |
{ |
| 1610 |
23 Apr 12 |
nicklas |
1655 |
at = AnnotationType.getNew(dc, annotationType.getValueType()); |
| 1610 |
23 Apr 12 |
nicklas |
1656 |
at.setName(annotationType.getName()); |
| 5962 |
03 Jun 20 |
nicklas |
1657 |
at.setDescription(annotationType.getDescription()); |
| 1610 |
23 Apr 12 |
nicklas |
1658 |
for (Item it : annotationType.getMainType()) |
| 1409 |
18 Oct 11 |
martin |
1659 |
{ |
| 1409 |
18 Oct 11 |
martin |
1660 |
at.enableForItem(it); |
| 1409 |
18 Oct 11 |
martin |
1661 |
} |
| 1285 |
08 Feb 11 |
nicklas |
1662 |
at.setMultiplicity(multiplicity); |
| 5799 |
18 Dec 19 |
nicklas |
1663 |
at.setDisableLogOfValues(annotationType.getDisableChangeHistoryLog()); |
| 1639 |
09 May 12 |
nicklas |
1664 |
if (valueOptions != null) |
| 1284 |
08 Feb 11 |
nicklas |
1665 |
{ |
| 1639 |
09 May 12 |
nicklas |
1666 |
if (valueOptions.isEnumeration()) |
| 1639 |
09 May 12 |
nicklas |
1667 |
{ |
| 1639 |
09 May 12 |
nicklas |
1668 |
at.setEnumeration(true); |
| 1639 |
09 May 12 |
nicklas |
1669 |
at.setDisplayAsList(false); |
| 1639 |
09 May 12 |
nicklas |
1670 |
at.setValues(valueOptions.getList()); |
| 1639 |
09 May 12 |
nicklas |
1671 |
} |
| 1639 |
09 May 12 |
nicklas |
1672 |
else if (at.getValueType().isNumerical()) |
| 1639 |
09 May 12 |
nicklas |
1673 |
{ |
| 1639 |
09 May 12 |
nicklas |
1674 |
Integer max = valueOptions.getMax(); |
| 1639 |
09 May 12 |
nicklas |
1675 |
if (max != null) |
| 1639 |
09 May 12 |
nicklas |
1676 |
{ |
| 1639 |
09 May 12 |
nicklas |
1677 |
at.setMaxValueLong(max.longValue()); |
| 1639 |
09 May 12 |
nicklas |
1678 |
} |
| 1639 |
09 May 12 |
nicklas |
1679 |
Integer min = valueOptions.getMin(); |
| 1639 |
09 May 12 |
nicklas |
1680 |
if (min != null) |
| 1639 |
09 May 12 |
nicklas |
1681 |
{ |
| 1639 |
09 May 12 |
nicklas |
1682 |
at.setMinValueLong(min.longValue()); |
| 1639 |
09 May 12 |
nicklas |
1683 |
} |
| 1639 |
09 May 12 |
nicklas |
1684 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1685 |
} |
| 4001 |
17 Jun 16 |
nicklas |
1686 |
if (permissions != null) |
| 4001 |
17 Jun 16 |
nicklas |
1687 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1688 |
for (PermissionOptions p : permissions) |
| 4001 |
17 Jun 16 |
nicklas |
1689 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1690 |
p.applyPermissions(at); |
| 4001 |
17 Jun 16 |
nicklas |
1691 |
} |
| 4001 |
17 Jun 16 |
nicklas |
1692 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1693 |
dc.saveItem(at); |
| 1284 |
08 Feb 11 |
nicklas |
1694 |
dc.commit(); |
| 1284 |
08 Feb 11 |
nicklas |
1695 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1696 |
finally |
| 1284 |
08 Feb 11 |
nicklas |
1697 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1698 |
if (dc != null) dc.close(); |
| 1284 |
08 Feb 11 |
nicklas |
1699 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1700 |
return at; |
| 1284 |
08 Feb 11 |
nicklas |
1701 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1702 |
|
| 1284 |
08 Feb 11 |
nicklas |
1703 |
/** |
| 1284 |
08 Feb 11 |
nicklas |
Check for an existing annotation type with the given options. A JSONObject is returned |
| 1284 |
08 Feb 11 |
nicklas |
with the result. The following keys are used: |
| 1284 |
08 Feb 11 |
nicklas |
<ul> |
| 1284 |
08 Feb 11 |
nicklas |
<li>itemType: ANNOTATIONTYPE |
| 1284 |
08 Feb 11 |
nicklas |
<li>name: The name of the annotation type |
| 1284 |
08 Feb 11 |
nicklas |
<li>id: The id of the annotation type if it exists |
| 1284 |
08 Feb 11 |
nicklas |
<li>status: ok, error, or missing |
| 1284 |
08 Feb 11 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1284 |
08 Feb 11 |
nicklas |
</ul> |
| 1409 |
18 Oct 11 |
martin |
1713 |
|
| 1610 |
23 Apr 12 |
nicklas |
@since 2.5 |
| 1409 |
18 Oct 11 |
martin |
1715 |
*/ |
| 1610 |
23 Apr 12 |
nicklas |
1716 |
public JSONObject checkAnnotationType(DbControl dc, Annotationtype annotationType, |
| 4001 |
17 Jun 16 |
nicklas |
1717 |
int multiplicity, ValueOptions valueOptions, boolean createIfMissing, |
| 4001 |
17 Jun 16 |
nicklas |
1718 |
PermissionOptions... permissions) |
| 1409 |
18 Oct 11 |
martin |
1719 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1720 |
JSONObject json = new JSONObject(); |
| 1309 |
04 Mar 11 |
nicklas |
1721 |
JSONArray jsonMessages = new JSONArray(); |
| 1284 |
08 Feb 11 |
nicklas |
1722 |
json.put("itemType", Item.ANNOTATIONTYPE.name()); |
| 1610 |
23 Apr 12 |
nicklas |
1723 |
json.put("name", annotationType.getName()); |
| 1284 |
08 Feb 11 |
nicklas |
1724 |
|
| 1610 |
23 Apr 12 |
nicklas |
1725 |
List<AnnotationType> result = annotationType.list(dc); |
| 1284 |
08 Feb 11 |
nicklas |
1726 |
if (result.size() == 0) |
| 1284 |
08 Feb 11 |
nicklas |
1727 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1728 |
if (createIfMissing) |
| 1284 |
08 Feb 11 |
nicklas |
1729 |
{ |
| 1610 |
23 Apr 12 |
nicklas |
1730 |
AnnotationType at = createAnnotationType(dc.getSessionControl(), annotationType, |
| 1639 |
09 May 12 |
nicklas |
1731 |
multiplicity, valueOptions, permissions); |
| 1284 |
08 Feb 11 |
nicklas |
1732 |
json.put("id", at.getId()); |
| 1284 |
08 Feb 11 |
nicklas |
1733 |
json.put("status", "ok"); |
| 1309 |
04 Mar 11 |
nicklas |
1734 |
jsonMessages.add("Created"); |
| 1284 |
08 Feb 11 |
nicklas |
1735 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1736 |
else |
| 1284 |
08 Feb 11 |
nicklas |
1737 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1738 |
json.put("status", "missing"); |
| 1309 |
04 Mar 11 |
nicklas |
1739 |
jsonMessages.add("Not found"); |
| 1284 |
08 Feb 11 |
nicklas |
1740 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1741 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1742 |
else if (result.size() > 1) |
| 1284 |
08 Feb 11 |
nicklas |
1743 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1744 |
json.put("status", "error"); |
| 1309 |
04 Mar 11 |
nicklas |
1745 |
jsonMessages.add("Found > 1 annotation type"); |
| 1284 |
08 Feb 11 |
nicklas |
1746 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1747 |
else |
| 1284 |
08 Feb 11 |
nicklas |
1748 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1749 |
AnnotationType at = result.get(0); |
| 1284 |
08 Feb 11 |
nicklas |
1750 |
json.put("id", at.getId()); |
| 1309 |
04 Mar 11 |
nicklas |
1751 |
json.put("status", "ok");// For now -- more checks below |
| 4001 |
17 Jun 16 |
nicklas |
1752 |
if (permissions != null) |
| 1284 |
08 Feb 11 |
nicklas |
1753 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1754 |
String permissionCheck = null; |
| 4001 |
17 Jun 16 |
nicklas |
1755 |
for (PermissionOptions p : permissions) |
| 1570 |
16 Mar 12 |
nicklas |
1756 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1757 |
if (!p.checkPermissions(at)) |
| 4001 |
17 Jun 16 |
nicklas |
1758 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1759 |
permissionCheck = p.getMessage(); |
| 4001 |
17 Jun 16 |
nicklas |
1760 |
break; |
| 4001 |
17 Jun 16 |
nicklas |
1761 |
} |
| 1570 |
16 Mar 12 |
nicklas |
1762 |
} |
| 4001 |
17 Jun 16 |
nicklas |
1763 |
|
| 4001 |
17 Jun 16 |
nicklas |
1764 |
if (permissionCheck != null) |
| 1570 |
16 Mar 12 |
nicklas |
1765 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1766 |
if (createIfMissing) |
| 4001 |
17 Jun 16 |
nicklas |
1767 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1768 |
for (PermissionOptions p : permissions) |
| 4001 |
17 Jun 16 |
nicklas |
1769 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1770 |
p.applyPermissions(at); |
| 4001 |
17 Jun 16 |
nicklas |
1771 |
} |
| 4001 |
17 Jun 16 |
nicklas |
1772 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 4001 |
17 Jun 16 |
nicklas |
1773 |
} |
| 4001 |
17 Jun 16 |
nicklas |
1774 |
else |
| 4001 |
17 Jun 16 |
nicklas |
1775 |
{ |
| 4001 |
17 Jun 16 |
nicklas |
1776 |
json.put("status", "incomplete"); |
| 4001 |
17 Jun 16 |
nicklas |
1777 |
jsonMessages.add(permissionCheck); |
| 4001 |
17 Jun 16 |
nicklas |
1778 |
} |
| 1570 |
16 Mar 12 |
nicklas |
1779 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1780 |
} |
| 1985 |
21 May 13 |
nicklas |
1781 |
boolean allTypesOk = true; |
| 1985 |
21 May 13 |
nicklas |
1782 |
boolean fixedTypes = false; |
| 1610 |
23 Apr 12 |
nicklas |
1783 |
for (Item it : annotationType.getMainType()) |
| 1284 |
08 Feb 11 |
nicklas |
1784 |
{ |
| 1409 |
18 Oct 11 |
martin |
1785 |
if (!at.isEnabledForItem(it)) |
| 1409 |
18 Oct 11 |
martin |
1786 |
{ |
| 1985 |
21 May 13 |
nicklas |
1787 |
allTypesOk = false; |
| 1985 |
21 May 13 |
nicklas |
1788 |
if (createIfMissing) |
| 1985 |
21 May 13 |
nicklas |
1789 |
{ |
| 1985 |
21 May 13 |
nicklas |
1790 |
at.enableForItem(it); |
| 1985 |
21 May 13 |
nicklas |
1791 |
fixedTypes = true; |
| 1985 |
21 May 13 |
nicklas |
1792 |
} |
| 1985 |
21 May 13 |
nicklas |
1793 |
else |
| 1985 |
21 May 13 |
nicklas |
1794 |
{ |
| 1985 |
21 May 13 |
nicklas |
1795 |
json.put("status", "incomplete"); |
| 1985 |
21 May 13 |
nicklas |
1796 |
jsonMessages.add("Not enabled for " + it.name()); |
| 1985 |
21 May 13 |
nicklas |
1797 |
} |
| 1409 |
18 Oct 11 |
martin |
1798 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1799 |
} |
| 1985 |
21 May 13 |
nicklas |
1800 |
if (fixedTypes && jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 1610 |
23 Apr 12 |
nicklas |
1801 |
if (at.getValueType() != annotationType.getValueType()) |
| 1284 |
08 Feb 11 |
nicklas |
1802 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1803 |
json.put("status", "error"); |
| 1610 |
23 Apr 12 |
nicklas |
1804 |
jsonMessages.add("Is not a " + annotationType.getValueType().name() + " type"); |
| 1284 |
08 Feb 11 |
nicklas |
1805 |
} |
| 1309 |
04 Mar 11 |
nicklas |
1806 |
if (at.getMultiplicity() != multiplicity) |
| 1285 |
08 Feb 11 |
nicklas |
1807 |
{ |
| 5899 |
15 Apr 20 |
nicklas |
1808 |
if (createIfMissing) |
| 5899 |
15 Apr 20 |
nicklas |
1809 |
{ |
| 5899 |
15 Apr 20 |
nicklas |
1810 |
at.setMultiplicity(multiplicity); |
| 5899 |
15 Apr 20 |
nicklas |
1811 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 5899 |
15 Apr 20 |
nicklas |
1812 |
} |
| 5899 |
15 Apr 20 |
nicklas |
1813 |
else |
| 5899 |
15 Apr 20 |
nicklas |
1814 |
{ |
| 5899 |
15 Apr 20 |
nicklas |
1815 |
json.put("status", "incomplete"); |
| 5899 |
15 Apr 20 |
nicklas |
1816 |
jsonMessages.add("Should have multiplicity=" + (multiplicity == 0 ? "unlimited" : multiplicity)); |
| 5899 |
15 Apr 20 |
nicklas |
1817 |
} |
| 1285 |
08 Feb 11 |
nicklas |
1818 |
} |
| 2351 |
10 Apr 14 |
nicklas |
1819 |
if (at.getDisableLogOfValues() != annotationType.getDisableChangeHistoryLog()) |
| 2351 |
10 Apr 14 |
nicklas |
1820 |
{ |
| 2351 |
10 Apr 14 |
nicklas |
1821 |
if (createIfMissing) |
| 2351 |
10 Apr 14 |
nicklas |
1822 |
{ |
| 2351 |
10 Apr 14 |
nicklas |
1823 |
at.setDisableLogOfValues(annotationType.getDisableChangeHistoryLog()); |
| 2351 |
10 Apr 14 |
nicklas |
1824 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 2351 |
10 Apr 14 |
nicklas |
1825 |
} |
| 2351 |
10 Apr 14 |
nicklas |
1826 |
else |
| 2351 |
10 Apr 14 |
nicklas |
1827 |
{ |
| 2351 |
10 Apr 14 |
nicklas |
1828 |
json.put("status", "incomplete"); |
| 2351 |
10 Apr 14 |
nicklas |
1829 |
if (annotationType.getDisableChangeHistoryLog()) |
| 2351 |
10 Apr 14 |
nicklas |
1830 |
{ |
| 2351 |
10 Apr 14 |
nicklas |
1831 |
jsonMessages.add("Should disable change log"); |
| 2351 |
10 Apr 14 |
nicklas |
1832 |
} |
| 2351 |
10 Apr 14 |
nicklas |
1833 |
else |
| 2351 |
10 Apr 14 |
nicklas |
1834 |
{ |
| 2351 |
10 Apr 14 |
nicklas |
1835 |
jsonMessages.add("Should not disable change log"); |
| 2351 |
10 Apr 14 |
nicklas |
1836 |
} |
| 2351 |
10 Apr 14 |
nicklas |
1837 |
} |
| 2351 |
10 Apr 14 |
nicklas |
1838 |
} |
| 1639 |
09 May 12 |
nicklas |
1839 |
if (at.isEnumeration() && (valueOptions == null || !valueOptions.isEnumeration())) |
| 1284 |
08 Feb 11 |
nicklas |
1840 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1841 |
json.put("status", "error"); |
| 1309 |
04 Mar 11 |
nicklas |
1842 |
jsonMessages.add("Should not be an enumeration"); |
| 1284 |
08 Feb 11 |
nicklas |
1843 |
} |
| 1639 |
09 May 12 |
nicklas |
1844 |
if (valueOptions != null) |
| 1284 |
08 Feb 11 |
nicklas |
1845 |
{ |
| 1639 |
09 May 12 |
nicklas |
1846 |
if (valueOptions.isEnumeration()) |
| 1284 |
08 Feb 11 |
nicklas |
1847 |
{ |
| 1639 |
09 May 12 |
nicklas |
1848 |
if (!at.isEnumeration()) |
| 1639 |
09 May 12 |
nicklas |
1849 |
{ |
| 1639 |
09 May 12 |
nicklas |
1850 |
json.put("status", "error"); |
| 1639 |
09 May 12 |
nicklas |
1851 |
jsonMessages.add("Is not enumeration of: " + valueOptions.getList()); |
| 1639 |
09 May 12 |
nicklas |
1852 |
} |
| 5894 |
08 Apr 20 |
nicklas |
1853 |
else |
| 1639 |
09 May 12 |
nicklas |
1854 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
1855 |
List<Object> missing = valueOptions.getMissingOptions(at); |
| 5894 |
08 Apr 20 |
nicklas |
1856 |
List<Object> extraOptions = valueOptions.getExtraOptions(at); |
| 5894 |
08 Apr 20 |
nicklas |
1857 |
if (missing.size() > 0) |
| 1889 |
27 Feb 13 |
nicklas |
1858 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
1859 |
if (createIfMissing) |
| 5894 |
08 Apr 20 |
nicklas |
1860 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
1861 |
valueOptions.applyEnumeration(at); |
| 5894 |
08 Apr 20 |
nicklas |
1862 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 5894 |
08 Apr 20 |
nicklas |
1863 |
} |
| 5894 |
08 Apr 20 |
nicklas |
1864 |
else |
| 5894 |
08 Apr 20 |
nicklas |
1865 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
1866 |
json.put("status", "incomplete"); |
| 5894 |
08 Apr 20 |
nicklas |
1867 |
jsonMessages.add(missing.size() + " missing option(s): " + Values.getString(missing, ", ", true)); |
| 5894 |
08 Apr 20 |
nicklas |
1868 |
} |
| 1889 |
27 Feb 13 |
nicklas |
1869 |
} |
| 5894 |
08 Apr 20 |
nicklas |
1870 |
else if (extraOptions.size() > 0) |
| 1889 |
27 Feb 13 |
nicklas |
1871 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
1872 |
json.put("status", "warning"); |
| 5894 |
08 Apr 20 |
nicklas |
1873 |
jsonMessages.add(extraOptions.size() + " extra option(s): " + Values.getString(extraOptions, ", ", true)); |
| 1889 |
27 Feb 13 |
nicklas |
1874 |
} |
| 5894 |
08 Apr 20 |
nicklas |
1875 |
|
| 1639 |
09 May 12 |
nicklas |
1876 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1877 |
} |
| 1639 |
09 May 12 |
nicklas |
1878 |
if (valueOptions.getMax() != null) |
| 1284 |
08 Feb 11 |
nicklas |
1879 |
{ |
| 1639 |
09 May 12 |
nicklas |
1880 |
if (at.getMaxValueLong() == null || at.getMaxValueLong().longValue() != valueOptions.getMax().longValue()) |
| 1639 |
09 May 12 |
nicklas |
1881 |
{ |
| 1639 |
09 May 12 |
nicklas |
1882 |
json.put("status", "error"); |
| 1639 |
09 May 12 |
nicklas |
1883 |
jsonMessages.add("Should have max allowed value=" + valueOptions.getMax()); |
| 1639 |
09 May 12 |
nicklas |
1884 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1885 |
} |
| 1639 |
09 May 12 |
nicklas |
1886 |
if (valueOptions.getMin() != null) |
| 1639 |
09 May 12 |
nicklas |
1887 |
{ |
| 1639 |
09 May 12 |
nicklas |
1888 |
if (at.getMinValueLong() == null || at.getMinValueLong().longValue() != valueOptions.getMin().longValue()) |
| 1639 |
09 May 12 |
nicklas |
1889 |
{ |
| 1639 |
09 May 12 |
nicklas |
1890 |
json.put("status", "error"); |
| 1639 |
09 May 12 |
nicklas |
1891 |
jsonMessages.add("Should have min allowed value=" + valueOptions.getMin()); |
| 1639 |
09 May 12 |
nicklas |
1892 |
} |
| 1639 |
09 May 12 |
nicklas |
1893 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1894 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1895 |
} |
| 1309 |
04 Mar 11 |
nicklas |
1896 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1309 |
04 Mar 11 |
nicklas |
1897 |
json.put("messages", jsonMessages); |
| 1284 |
08 Feb 11 |
nicklas |
1898 |
return json; |
| 1284 |
08 Feb 11 |
nicklas |
1899 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1900 |
|
| 1284 |
08 Feb 11 |
nicklas |
1901 |
/** |
| 2157 |
05 Dec 13 |
nicklas |
Create a group or role with the given options. The item is created in |
| 1284 |
08 Feb 11 |
nicklas |
a separate transaction. |
| 1284 |
08 Feb 11 |
nicklas |
1904 |
*/ |
| 3571 |
30 Oct 15 |
nicklas |
1905 |
public <T extends BasicItem & Nameable> T createReggieRole(SessionControl sc, ReggieRole<T> role) |
| 1284 |
08 Feb 11 |
nicklas |
1906 |
{ |
| 2157 |
05 Dec 13 |
nicklas |
1907 |
T r = null; |
| 6328 |
14 Jun 21 |
nicklas |
1908 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1284 |
08 Feb 11 |
nicklas |
1909 |
try |
| 1284 |
08 Feb 11 |
nicklas |
1910 |
{ |
| 2157 |
05 Dec 13 |
nicklas |
1911 |
r = role.create(dc); |
| 2157 |
05 Dec 13 |
nicklas |
1912 |
r.setName(role.getName()); |
| 3987 |
10 Jun 16 |
nicklas |
1913 |
if (role.getActualType() == Item.GROUP) |
| 3987 |
10 Jun 16 |
nicklas |
1914 |
{ |
| 3987 |
10 Jun 16 |
nicklas |
1915 |
Group g = (Group)r; |
| 3987 |
10 Jun 16 |
nicklas |
1916 |
g.setHiddenMembers(role.hasHiddenMembers()); |
| 3987 |
10 Jun 16 |
nicklas |
1917 |
} |
| 2157 |
05 Dec 13 |
nicklas |
1918 |
dc.saveItem(r); |
| 1284 |
08 Feb 11 |
nicklas |
1919 |
dc.commit(); |
| 1284 |
08 Feb 11 |
nicklas |
1920 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1921 |
finally |
| 1284 |
08 Feb 11 |
nicklas |
1922 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1923 |
if (dc != null) dc.close(); |
| 1284 |
08 Feb 11 |
nicklas |
1924 |
} |
| 2157 |
05 Dec 13 |
nicklas |
1925 |
return r; |
| 1284 |
08 Feb 11 |
nicklas |
1926 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1927 |
|
| 1284 |
08 Feb 11 |
nicklas |
1928 |
/** |
| 2157 |
05 Dec 13 |
nicklas |
Check for an existing reggie role (a BASE role or group) with the given options. |
| 2157 |
05 Dec 13 |
nicklas |
A JSONObject is returned with the result. The following keys are used: |
| 1284 |
08 Feb 11 |
nicklas |
<ul> |
| 2157 |
05 Dec 13 |
nicklas |
<li>itemType: GROUP or ROLE |
| 2157 |
05 Dec 13 |
nicklas |
<li>name: The name of the item |
| 2157 |
05 Dec 13 |
nicklas |
<li>id: The id of the item if it exists |
| 1284 |
08 Feb 11 |
nicklas |
<li>status: ok, error, or missing |
| 1284 |
08 Feb 11 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1284 |
08 Feb 11 |
nicklas |
</ul> |
| 1284 |
08 Feb 11 |
nicklas |
1938 |
*/ |
| 2157 |
05 Dec 13 |
nicklas |
1939 |
public JSONObject checkReggieRole(DbControl dc, ReggieRole<? extends BasicItem> role, boolean createIfMissing) |
| 1284 |
08 Feb 11 |
nicklas |
1940 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1941 |
JSONObject json = new JSONObject(); |
| 1309 |
04 Mar 11 |
nicklas |
1942 |
JSONArray jsonMessages = new JSONArray(); |
| 2157 |
05 Dec 13 |
nicklas |
1943 |
json.put("itemType", role.getActualType().name()); |
| 2157 |
05 Dec 13 |
nicklas |
1944 |
json.put("name", role.getName()); |
| 1309 |
04 Mar 11 |
nicklas |
1945 |
|
| 2157 |
05 Dec 13 |
nicklas |
1946 |
List<? extends BasicItem> result = role.list(dc); |
| 1284 |
08 Feb 11 |
nicklas |
1947 |
if (result.size() == 0) |
| 1284 |
08 Feb 11 |
nicklas |
1948 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1949 |
if (createIfMissing) |
| 1284 |
08 Feb 11 |
nicklas |
1950 |
{ |
| 2157 |
05 Dec 13 |
nicklas |
1951 |
BasicItem g = createReggieRole(dc.getSessionControl(), role); |
| 1284 |
08 Feb 11 |
nicklas |
1952 |
json.put("id", g.getId()); |
| 1284 |
08 Feb 11 |
nicklas |
1953 |
json.put("status", "ok"); |
| 1309 |
04 Mar 11 |
nicklas |
1954 |
jsonMessages.add("Created"); |
| 1284 |
08 Feb 11 |
nicklas |
1955 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1956 |
else |
| 1284 |
08 Feb 11 |
nicklas |
1957 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1958 |
json.put("status", "missing"); |
| 1309 |
04 Mar 11 |
nicklas |
1959 |
jsonMessages.add("Not found"); |
| 1284 |
08 Feb 11 |
nicklas |
1960 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1961 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1962 |
else if (result.size() > 1) |
| 1284 |
08 Feb 11 |
nicklas |
1963 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
1964 |
json.put("status", "error"); |
| 2157 |
05 Dec 13 |
nicklas |
1965 |
jsonMessages.add("Found > 1 " + role.getActualType().toString()); |
| 1284 |
08 Feb 11 |
nicklas |
1966 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1967 |
else |
| 1284 |
08 Feb 11 |
nicklas |
1968 |
{ |
| 3987 |
10 Jun 16 |
nicklas |
1969 |
BasicItem r = result.get(0); |
| 3987 |
10 Jun 16 |
nicklas |
1970 |
json.put("id", r.getId()); |
| 3987 |
10 Jun 16 |
nicklas |
1971 |
json.put("status", "ok"); // For now -- more checks below |
| 3987 |
10 Jun 16 |
nicklas |
1972 |
|
| 3987 |
10 Jun 16 |
nicklas |
1973 |
if (role.getActualType() == Item.GROUP) |
| 3987 |
10 Jun 16 |
nicklas |
1974 |
{ |
| 3987 |
10 Jun 16 |
nicklas |
1975 |
Group g = (Group)r; |
| 3987 |
10 Jun 16 |
nicklas |
1976 |
if (role.hasHiddenMembers()) |
| 3987 |
10 Jun 16 |
nicklas |
1977 |
{ |
| 3987 |
10 Jun 16 |
nicklas |
1978 |
if (!g.hasHiddenMembers()) |
| 3987 |
10 Jun 16 |
nicklas |
1979 |
{ |
| 3987 |
10 Jun 16 |
nicklas |
1980 |
if (createIfMissing) |
| 3987 |
10 Jun 16 |
nicklas |
1981 |
{ |
| 3987 |
10 Jun 16 |
nicklas |
1982 |
g.setHiddenMembers(true); |
| 3987 |
10 Jun 16 |
nicklas |
1983 |
jsonMessages.add("Fixed"); |
| 3987 |
10 Jun 16 |
nicklas |
1984 |
} |
| 3987 |
10 Jun 16 |
nicklas |
1985 |
else |
| 3987 |
10 Jun 16 |
nicklas |
1986 |
{ |
| 3987 |
10 Jun 16 |
nicklas |
1987 |
json.put("status", "incomplete"); |
| 3987 |
10 Jun 16 |
nicklas |
1988 |
jsonMessages.add("Should have hidden members"); |
| 3987 |
10 Jun 16 |
nicklas |
1989 |
} |
| 3987 |
10 Jun 16 |
nicklas |
1990 |
} |
| 3987 |
10 Jun 16 |
nicklas |
1991 |
} |
| 3987 |
10 Jun 16 |
nicklas |
1992 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1993 |
} |
| 1309 |
04 Mar 11 |
nicklas |
1994 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1309 |
04 Mar 11 |
nicklas |
1995 |
json.put("messages", jsonMessages); |
| 1284 |
08 Feb 11 |
nicklas |
1996 |
return json; |
| 1309 |
04 Mar 11 |
nicklas |
1997 |
} |
| 1284 |
08 Feb 11 |
nicklas |
1998 |
|
| 1309 |
04 Mar 11 |
nicklas |
1999 |
public JSONObject checkActiveProject(DbControl dc) |
| 1309 |
04 Mar 11 |
nicklas |
2000 |
{ |
| 1309 |
04 Mar 11 |
nicklas |
2001 |
JSONObject json = new JSONObject(); |
| 1309 |
04 Mar 11 |
nicklas |
2002 |
JSONArray jsonMessages = new JSONArray(); |
| 1309 |
04 Mar 11 |
nicklas |
2003 |
json.put("itemType", Item.PROJECT.name()); |
| 1309 |
04 Mar 11 |
nicklas |
2004 |
|
| 1309 |
04 Mar 11 |
nicklas |
2005 |
int projectId = dc.getSessionControl().getActiveProjectId(); |
| 1309 |
04 Mar 11 |
nicklas |
2006 |
if (projectId == 0) |
| 1309 |
04 Mar 11 |
nicklas |
2007 |
{ |
| 1309 |
04 Mar 11 |
nicklas |
2008 |
json.put("status", "warning"); |
| 1309 |
04 Mar 11 |
nicklas |
2009 |
json.put("name", "not selected"); |
| 1309 |
04 Mar 11 |
nicklas |
2010 |
jsonMessages.add("No active project"); |
| 1309 |
04 Mar 11 |
nicklas |
2011 |
} |
| 1309 |
04 Mar 11 |
nicklas |
2012 |
else |
| 1309 |
04 Mar 11 |
nicklas |
2013 |
{ |
| 1309 |
04 Mar 11 |
nicklas |
2014 |
Project p = Project.getById(dc, projectId); |
| 1309 |
04 Mar 11 |
nicklas |
2015 |
json.put("name", p.getName()); |
| 1309 |
04 Mar 11 |
nicklas |
2016 |
json.put("id", projectId); |
| 1309 |
04 Mar 11 |
nicklas |
2017 |
json.put("status", "ok"); |
| 1309 |
04 Mar 11 |
nicklas |
2018 |
} |
| 1309 |
04 Mar 11 |
nicklas |
2019 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1309 |
04 Mar 11 |
nicklas |
2020 |
json.put("messages", jsonMessages); |
| 1309 |
04 Mar 11 |
nicklas |
2021 |
return json; |
| 1284 |
08 Feb 11 |
nicklas |
2022 |
} |
| 1284 |
08 Feb 11 |
nicklas |
2023 |
|
| 1463 |
14 Nov 11 |
martin |
2024 |
/** |
| 1463 |
14 Nov 11 |
martin |
Create a subtype with the given options. The subtype is created in |
| 1463 |
14 Nov 11 |
martin |
a separate transaction. |
| 1463 |
14 Nov 11 |
martin |
@since 2.0 |
| 1463 |
14 Nov 11 |
martin |
2028 |
*/ |
| 2565 |
11 Aug 14 |
nicklas |
2029 |
public ItemSubtype createSubtype(SessionControl sc, Subtype def, Datafiletype fileType, Subtype... relatedTo) |
| 1463 |
14 Nov 11 |
martin |
2030 |
{ |
| 1463 |
14 Nov 11 |
martin |
2031 |
ItemSubtype subtype = null; |
| 6328 |
14 Jun 21 |
nicklas |
2032 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1463 |
14 Nov 11 |
martin |
2033 |
try |
| 1463 |
14 Nov 11 |
martin |
2034 |
{ |
| 1463 |
14 Nov 11 |
martin |
2035 |
subtype = ItemSubtype.getNew(dc, def.getMainType()); |
| 1463 |
14 Nov 11 |
martin |
2036 |
subtype.setName(def.getName()); |
| 1644 |
15 May 12 |
nicklas |
2037 |
subtype.setPushAnnotations(def.getPushAnnotations()); |
| 1463 |
14 Nov 11 |
martin |
2038 |
|
| 2565 |
11 Aug 14 |
nicklas |
2039 |
if (fileType != null) |
| 2565 |
11 Aug 14 |
nicklas |
2040 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
2041 |
ItemSubtypeFileType ft = subtype.getAssociatedDataFileType(fileType.load(dc), true); |
| 2565 |
11 Aug 14 |
nicklas |
2042 |
ft.setRequired(fileType.isRequired()); |
| 2565 |
11 Aug 14 |
nicklas |
2043 |
ft.setAllowMultiple(fileType.getAllowMultiple()); |
| 2565 |
11 Aug 14 |
nicklas |
2044 |
} |
| 2565 |
11 Aug 14 |
nicklas |
2045 |
|
| 1463 |
14 Nov 11 |
martin |
2046 |
if (relatedTo != null) |
| 1463 |
14 Nov 11 |
martin |
2047 |
{ |
| 1463 |
14 Nov 11 |
martin |
2048 |
for (Subtype related : relatedTo) |
| 1463 |
14 Nov 11 |
martin |
2049 |
{ |
| 1644 |
15 May 12 |
nicklas |
2050 |
ItemSubtype r = related.get(dc); |
| 1644 |
15 May 12 |
nicklas |
2051 |
if (r != null) subtype.setRelatedSubtype(r); |
| 1463 |
14 Nov 11 |
martin |
2052 |
} |
| 1463 |
14 Nov 11 |
martin |
2053 |
} |
| 1463 |
14 Nov 11 |
martin |
2054 |
|
| 1463 |
14 Nov 11 |
martin |
2055 |
dc.saveItem(subtype); |
| 1463 |
14 Nov 11 |
martin |
2056 |
dc.commit(); |
| 1463 |
14 Nov 11 |
martin |
2057 |
} |
| 1463 |
14 Nov 11 |
martin |
2058 |
finally |
| 1463 |
14 Nov 11 |
martin |
2059 |
{ |
| 1463 |
14 Nov 11 |
martin |
2060 |
if (dc != null) dc.close(); |
| 1463 |
14 Nov 11 |
martin |
2061 |
} |
| 1463 |
14 Nov 11 |
martin |
2062 |
return subtype; |
| 1463 |
14 Nov 11 |
martin |
2063 |
} |
| 1309 |
04 Mar 11 |
nicklas |
2064 |
|
| 1284 |
08 Feb 11 |
nicklas |
2065 |
/** |
| 1463 |
14 Nov 11 |
martin |
Check for an existing item subtype with the given options. |
| 1463 |
14 Nov 11 |
martin |
A JSONObject is returned with the result. The following |
| 1463 |
14 Nov 11 |
martin |
keys are used: |
| 1463 |
14 Nov 11 |
martin |
<ul> |
| 1463 |
14 Nov 11 |
martin |
<li>itemType: ITEMSUBTYPE |
| 1463 |
14 Nov 11 |
martin |
<li>name: The name of the subtype |
| 1463 |
14 Nov 11 |
martin |
<li>id: The id of the subtype if it exists |
| 1463 |
14 Nov 11 |
martin |
<li>mainType: The main item type that the subtype applies to |
| 1463 |
14 Nov 11 |
martin |
<li>status: ok, error, or missing |
| 1463 |
14 Nov 11 |
martin |
<li>message: A descriptive message in case of an error |
| 2565 |
11 Aug 14 |
nicklas |
</ul |
| 1463 |
14 Nov 11 |
martin |
@since 2.0 |
| 1463 |
14 Nov 11 |
martin |
2078 |
*/ |
| 1463 |
14 Nov 11 |
martin |
2079 |
public JSONObject checkSubtype(DbControl dc, Subtype subtype, |
| 2565 |
11 Aug 14 |
nicklas |
2080 |
Datafiletype fileType, boolean createIfMissing, Subtype... relatedTo) |
| 1463 |
14 Nov 11 |
martin |
2081 |
{ |
| 1463 |
14 Nov 11 |
martin |
2082 |
|
| 1463 |
14 Nov 11 |
martin |
2083 |
JSONObject json = new JSONObject(); |
| 1463 |
14 Nov 11 |
martin |
2084 |
JSONArray jsonMessages = new JSONArray(); |
| 1463 |
14 Nov 11 |
martin |
2085 |
json.put("itemType", Item.ITEMSUBTYPE.name()); |
| 1463 |
14 Nov 11 |
martin |
2086 |
json.put("name", subtype.getName()); |
| 1463 |
14 Nov 11 |
martin |
2087 |
json.put("mainType", subtype.getMainType().name()); |
| 1463 |
14 Nov 11 |
martin |
2088 |
|
| 1610 |
23 Apr 12 |
nicklas |
2089 |
List<ItemSubtype> result = subtype.list(dc); |
| 1463 |
14 Nov 11 |
martin |
2090 |
if (result.size() == 0) |
| 1463 |
14 Nov 11 |
martin |
2091 |
{ |
| 1463 |
14 Nov 11 |
martin |
2092 |
if (createIfMissing) |
| 1463 |
14 Nov 11 |
martin |
2093 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
2094 |
ItemSubtype s = createSubtype(dc.getSessionControl(), subtype, fileType, relatedTo); |
| 1463 |
14 Nov 11 |
martin |
2095 |
json.put("id", s.getId()); |
| 1463 |
14 Nov 11 |
martin |
2096 |
json.put("status", "ok"); |
| 1463 |
14 Nov 11 |
martin |
2097 |
jsonMessages.add("Created"); |
| 1463 |
14 Nov 11 |
martin |
2098 |
} |
| 1463 |
14 Nov 11 |
martin |
2099 |
else |
| 1463 |
14 Nov 11 |
martin |
2100 |
{ |
| 1463 |
14 Nov 11 |
martin |
2101 |
json.put("status", "missing"); |
| 1463 |
14 Nov 11 |
martin |
2102 |
jsonMessages.add("Not found"); |
| 1463 |
14 Nov 11 |
martin |
2103 |
} |
| 1463 |
14 Nov 11 |
martin |
2104 |
} |
| 1463 |
14 Nov 11 |
martin |
2105 |
else if (result.size() > 1) |
| 1463 |
14 Nov 11 |
martin |
2106 |
{ |
| 1463 |
14 Nov 11 |
martin |
2107 |
json.put("status", "error"); |
| 1463 |
14 Nov 11 |
martin |
2108 |
jsonMessages.add("Found > 1 subtype"); |
| 1463 |
14 Nov 11 |
martin |
2109 |
} |
| 1463 |
14 Nov 11 |
martin |
2110 |
else |
| 1463 |
14 Nov 11 |
martin |
2111 |
{ |
| 1463 |
14 Nov 11 |
martin |
2112 |
ItemSubtype s = result.get(0); |
| 1463 |
14 Nov 11 |
martin |
2113 |
json.put("id", s.getId()); |
| 1463 |
14 Nov 11 |
martin |
2114 |
json.put("status", "ok"); // For now -- more checks below |
| 1463 |
14 Nov 11 |
martin |
2115 |
|
| 1627 |
27 Apr 12 |
nicklas |
2116 |
if (subtype.getPushAnnotations() != s.getPushAnnotations()) |
| 1627 |
27 Apr 12 |
nicklas |
2117 |
{ |
| 4361 |
16 Feb 17 |
nicklas |
2118 |
if (createIfMissing) |
| 4361 |
16 Feb 17 |
nicklas |
2119 |
{ |
| 4361 |
16 Feb 17 |
nicklas |
2120 |
s.setPushAnnotations(subtype.getPushAnnotations()); |
| 4361 |
16 Feb 17 |
nicklas |
2121 |
jsonMessages.add("Fixed"); |
| 4361 |
16 Feb 17 |
nicklas |
2122 |
} |
| 4361 |
16 Feb 17 |
nicklas |
2123 |
else |
| 4361 |
16 Feb 17 |
nicklas |
2124 |
{ |
| 4361 |
16 Feb 17 |
nicklas |
2125 |
json.put("status", "incomplete"); |
| 4361 |
16 Feb 17 |
nicklas |
2126 |
jsonMessages.add("Should have 'Push annotations to parent'="+subtype.getPushAnnotations()); |
| 4361 |
16 Feb 17 |
nicklas |
2127 |
} |
| 1627 |
27 Apr 12 |
nicklas |
2128 |
} |
| 1627 |
27 Apr 12 |
nicklas |
2129 |
|
| 2565 |
11 Aug 14 |
nicklas |
2130 |
if (fileType != null) |
| 2565 |
11 Aug 14 |
nicklas |
2131 |
{ |
| 2709 |
30 Sep 14 |
nicklas |
2132 |
DataFileType dft = fileType.get(dc); |
| 2709 |
30 Sep 14 |
nicklas |
2133 |
if (dft != null && !s.isAssociatedDataFileType(dft)) |
| 2565 |
11 Aug 14 |
nicklas |
2134 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
2135 |
if (createIfMissing) |
| 2565 |
11 Aug 14 |
nicklas |
2136 |
{ |
| 2709 |
30 Sep 14 |
nicklas |
2137 |
ItemSubtypeFileType ft = s.getAssociatedDataFileType(dft, true); |
| 2565 |
11 Aug 14 |
nicklas |
2138 |
ft.setRequired(fileType.isRequired()); |
| 2565 |
11 Aug 14 |
nicklas |
2139 |
ft.setAllowMultiple(fileType.getAllowMultiple()); |
| 2565 |
11 Aug 14 |
nicklas |
2140 |
jsonMessages.add("Fixed"); |
| 2565 |
11 Aug 14 |
nicklas |
2141 |
} |
| 2565 |
11 Aug 14 |
nicklas |
2142 |
else |
| 2565 |
11 Aug 14 |
nicklas |
2143 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
2144 |
json.put("status", "incomplete"); |
| 2565 |
11 Aug 14 |
nicklas |
2145 |
jsonMessages.add("Should be related to '" + fileType.getName() + " file type"); |
| 2565 |
11 Aug 14 |
nicklas |
2146 |
} |
| 2565 |
11 Aug 14 |
nicklas |
2147 |
} |
| 2565 |
11 Aug 14 |
nicklas |
2148 |
} |
| 2565 |
11 Aug 14 |
nicklas |
2149 |
|
| 1463 |
14 Nov 11 |
martin |
2150 |
if (relatedTo != null) |
| 1463 |
14 Nov 11 |
martin |
2151 |
{ |
| 1463 |
14 Nov 11 |
martin |
2152 |
for (Subtype related : relatedTo) |
| 1463 |
14 Nov 11 |
martin |
2153 |
{ |
| 1463 |
14 Nov 11 |
martin |
2154 |
ItemSubtype r = s.getRelatedSubtype(related.getMainType()); |
| 1463 |
14 Nov 11 |
martin |
2155 |
if (r == null) |
| 1463 |
14 Nov 11 |
martin |
2156 |
{ |
| 1644 |
15 May 12 |
nicklas |
2157 |
r = related.get(dc); |
| 1639 |
09 May 12 |
nicklas |
2158 |
if (createIfMissing && r != null) |
| 1639 |
09 May 12 |
nicklas |
2159 |
{ |
| 1639 |
09 May 12 |
nicklas |
2160 |
s.setRelatedSubtype(r); |
| 1639 |
09 May 12 |
nicklas |
2161 |
jsonMessages.add("Fixed"); |
| 1639 |
09 May 12 |
nicklas |
2162 |
} |
| 1639 |
09 May 12 |
nicklas |
2163 |
else |
| 1639 |
09 May 12 |
nicklas |
2164 |
{ |
| 1639 |
09 May 12 |
nicklas |
2165 |
json.put("status", "incomplete"); |
| 2059 |
11 Oct 13 |
nicklas |
2166 |
jsonMessages.add("Should be related to '" + related.getName() + "' [" + related.getMainType().name() + "]"); |
| 1639 |
09 May 12 |
nicklas |
2167 |
} |
| 1463 |
14 Nov 11 |
martin |
2168 |
} |
| 1463 |
14 Nov 11 |
martin |
2169 |
else if (!r.getName().equals(related.getName())) |
| 1463 |
14 Nov 11 |
martin |
2170 |
{ |
| 2109 |
29 Oct 13 |
nicklas |
2171 |
if (createIfMissing) |
| 2109 |
29 Oct 13 |
nicklas |
2172 |
{ |
| 2109 |
29 Oct 13 |
nicklas |
2173 |
s.setRelatedSubtype(related.get(dc)); |
| 2109 |
29 Oct 13 |
nicklas |
2174 |
jsonMessages.add("Fixed"); |
| 2109 |
29 Oct 13 |
nicklas |
2175 |
} |
| 2109 |
29 Oct 13 |
nicklas |
2176 |
else |
| 2109 |
29 Oct 13 |
nicklas |
2177 |
{ |
| 2109 |
29 Oct 13 |
nicklas |
2178 |
json.put("status", "incomplete"); |
| 2109 |
29 Oct 13 |
nicklas |
2179 |
jsonMessages.add("Should be related to: '" + |
| 2109 |
29 Oct 13 |
nicklas |
2180 |
related.getName() + "' not '" + r.getName() + "'"); |
| 2109 |
29 Oct 13 |
nicklas |
2181 |
} |
| 1463 |
14 Nov 11 |
martin |
2182 |
} |
| 1463 |
14 Nov 11 |
martin |
2183 |
} |
| 1463 |
14 Nov 11 |
martin |
2184 |
} |
| 1463 |
14 Nov 11 |
martin |
2185 |
|
| 1463 |
14 Nov 11 |
martin |
2186 |
} |
| 1463 |
14 Nov 11 |
martin |
2187 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1463 |
14 Nov 11 |
martin |
2188 |
json.put("messages", jsonMessages); |
| 1463 |
14 Nov 11 |
martin |
2189 |
return json; |
| 1463 |
14 Nov 11 |
martin |
2190 |
|
| 1463 |
14 Nov 11 |
martin |
2191 |
} |
| 1463 |
14 Nov 11 |
martin |
2192 |
|
| 1463 |
14 Nov 11 |
martin |
2193 |
/** |
| 3974 |
26 May 16 |
nicklas |
Create a Client with the given options. The client is created in |
| 3974 |
26 May 16 |
nicklas |
a separate transaction. |
| 3974 |
26 May 16 |
nicklas |
@since 4.5 |
| 3974 |
26 May 16 |
nicklas |
2197 |
*/ |
| 3988 |
10 Jun 16 |
nicklas |
2198 |
public Client createClient(SessionControl sc, ClientApp client, PermissionOptions permissions) |
| 3974 |
26 May 16 |
nicklas |
2199 |
{ |
| 3974 |
26 May 16 |
nicklas |
2200 |
Client c = null; |
| 6328 |
14 Jun 21 |
nicklas |
2201 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 3974 |
26 May 16 |
nicklas |
2202 |
try |
| 3974 |
26 May 16 |
nicklas |
2203 |
{ |
| 3988 |
10 Jun 16 |
nicklas |
2204 |
c = Client.getNew(dc, client.getExternalId()); |
| 3988 |
10 Jun 16 |
nicklas |
2205 |
c.setName(client.getName()); |
| 3974 |
26 May 16 |
nicklas |
2206 |
if (permissions != null) permissions.applyPermissions(c); |
| 3974 |
26 May 16 |
nicklas |
2207 |
dc.saveItem(c); |
| 3974 |
26 May 16 |
nicklas |
2208 |
dc.commit(); |
| 3974 |
26 May 16 |
nicklas |
2209 |
} |
| 3974 |
26 May 16 |
nicklas |
2210 |
finally |
| 3974 |
26 May 16 |
nicklas |
2211 |
{ |
| 3974 |
26 May 16 |
nicklas |
2212 |
if (dc != null) dc.close(); |
| 3974 |
26 May 16 |
nicklas |
2213 |
} |
| 3974 |
26 May 16 |
nicklas |
2214 |
return c; |
| 3974 |
26 May 16 |
nicklas |
2215 |
} |
| 3974 |
26 May 16 |
nicklas |
2216 |
|
| 3974 |
26 May 16 |
nicklas |
2217 |
|
| 3974 |
26 May 16 |
nicklas |
2218 |
/** |
| 3974 |
26 May 16 |
nicklas |
Check for an existing client with the given options. |
| 3974 |
26 May 16 |
nicklas |
A JSONObject is returned with the result. The following |
| 3974 |
26 May 16 |
nicklas |
keys are used: |
| 3974 |
26 May 16 |
nicklas |
<ul> |
| 3974 |
26 May 16 |
nicklas |
<li>itemType: CLIENT |
| 3974 |
26 May 16 |
nicklas |
<li>name: The name of the client |
| 3974 |
26 May 16 |
nicklas |
<li>id: The id of the client if it exists |
| 3974 |
26 May 16 |
nicklas |
<li>status: ok, error, or missing |
| 3974 |
26 May 16 |
nicklas |
<li>message: A descriptive message in case of an error |
| 3974 |
26 May 16 |
nicklas |
</ul> |
| 3974 |
26 May 16 |
nicklas |
@since 4.5 |
| 3974 |
26 May 16 |
nicklas |
2230 |
*/ |
| 3988 |
10 Jun 16 |
nicklas |
2231 |
public JSONObject checkClient(DbControl dc, ClientApp client, PermissionOptions permissions, boolean createIfMissing) |
| 3974 |
26 May 16 |
nicklas |
2232 |
{ |
| 3974 |
26 May 16 |
nicklas |
2233 |
JSONObject json = new JSONObject(); |
| 3974 |
26 May 16 |
nicklas |
2234 |
JSONArray jsonMessages = new JSONArray(); |
| 3974 |
26 May 16 |
nicklas |
2235 |
json.put("itemType", Item.CLIENT.name()); |
| 3988 |
10 Jun 16 |
nicklas |
2236 |
json.put("name", client.getName()); |
| 3974 |
26 May 16 |
nicklas |
2237 |
|
| 3988 |
10 Jun 16 |
nicklas |
2238 |
List<Client> result = client.list(dc); |
| 3974 |
26 May 16 |
nicklas |
2239 |
if (result.size() == 0) |
| 3974 |
26 May 16 |
nicklas |
2240 |
{ |
| 3974 |
26 May 16 |
nicklas |
2241 |
if (createIfMissing) |
| 3974 |
26 May 16 |
nicklas |
2242 |
{ |
| 3988 |
10 Jun 16 |
nicklas |
2243 |
Client c = createClient(dc.getSessionControl(), client, permissions); |
| 3974 |
26 May 16 |
nicklas |
2244 |
json.put("id", c.getId()); |
| 3974 |
26 May 16 |
nicklas |
2245 |
json.put("status", "ok"); |
| 3974 |
26 May 16 |
nicklas |
2246 |
jsonMessages.add("Created"); |
| 3974 |
26 May 16 |
nicklas |
2247 |
} |
| 3974 |
26 May 16 |
nicklas |
2248 |
else |
| 3974 |
26 May 16 |
nicklas |
2249 |
{ |
| 3974 |
26 May 16 |
nicklas |
2250 |
json.put("status", "missing"); |
| 3974 |
26 May 16 |
nicklas |
2251 |
jsonMessages.add("Not found"); |
| 3974 |
26 May 16 |
nicklas |
2252 |
} |
| 3974 |
26 May 16 |
nicklas |
2253 |
} |
| 3974 |
26 May 16 |
nicklas |
2254 |
else if (result.size() > 1) |
| 3974 |
26 May 16 |
nicklas |
2255 |
{ |
| 3974 |
26 May 16 |
nicklas |
2256 |
json.put("status", "error"); |
| 3974 |
26 May 16 |
nicklas |
2257 |
jsonMessages.add("Found > 1 client"); |
| 3974 |
26 May 16 |
nicklas |
2258 |
} |
| 3974 |
26 May 16 |
nicklas |
2259 |
else |
| 3974 |
26 May 16 |
nicklas |
2260 |
{ |
| 3974 |
26 May 16 |
nicklas |
2261 |
Client c = result.get(0); |
| 3974 |
26 May 16 |
nicklas |
2262 |
json.put("id", c.getId()); |
| 3974 |
26 May 16 |
nicklas |
2263 |
json.put("status", "ok"); // For now -- more checks below |
| 3974 |
26 May 16 |
nicklas |
2264 |
|
| 3974 |
26 May 16 |
nicklas |
2265 |
if (permissions != null && !permissions.checkPermissions(c)) |
| 3974 |
26 May 16 |
nicklas |
2266 |
{ |
| 3974 |
26 May 16 |
nicklas |
2267 |
if (createIfMissing) |
| 3974 |
26 May 16 |
nicklas |
2268 |
{ |
| 3974 |
26 May 16 |
nicklas |
2269 |
permissions.applyPermissions(c); |
| 3974 |
26 May 16 |
nicklas |
2270 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 3974 |
26 May 16 |
nicklas |
2271 |
} |
| 3974 |
26 May 16 |
nicklas |
2272 |
else |
| 3974 |
26 May 16 |
nicklas |
2273 |
{ |
| 3974 |
26 May 16 |
nicklas |
2274 |
json.put("status", "incomplete"); |
| 3974 |
26 May 16 |
nicklas |
2275 |
jsonMessages.add(permissions.getMessage()); |
| 3974 |
26 May 16 |
nicklas |
2276 |
} |
| 3974 |
26 May 16 |
nicklas |
2277 |
} |
| 3974 |
26 May 16 |
nicklas |
2278 |
} |
| 3974 |
26 May 16 |
nicklas |
2279 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 3974 |
26 May 16 |
nicklas |
2280 |
json.put("messages", jsonMessages); |
| 3974 |
26 May 16 |
nicklas |
2281 |
return json; |
| 3974 |
26 May 16 |
nicklas |
2282 |
} |
| 3974 |
26 May 16 |
nicklas |
2283 |
|
| 3974 |
26 May 16 |
nicklas |
2284 |
|
| 3974 |
26 May 16 |
nicklas |
2285 |
/** |
| 1865 |
19 Feb 13 |
nicklas |
Create a Tag with the given options. The tag is created in |
| 1865 |
19 Feb 13 |
nicklas |
a separate transaction. |
| 1867 |
19 Feb 13 |
nicklas |
@since 2.12 |
| 1865 |
19 Feb 13 |
nicklas |
2289 |
*/ |
| 5865 |
12 Mar 20 |
nicklas |
2290 |
public Tag createTag(SessionControl sc, String name, Subtype subtype, Pipeline pipeline, BarcodeSet barcodeSet, String description, PermissionOptions permissions) |
| 1865 |
19 Feb 13 |
nicklas |
2291 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2292 |
Tag tag = null; |
| 6328 |
14 Jun 21 |
nicklas |
2293 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1865 |
19 Feb 13 |
nicklas |
2294 |
try |
| 1865 |
19 Feb 13 |
nicklas |
2295 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2296 |
tag = Tag.getNew(dc); |
| 1865 |
19 Feb 13 |
nicklas |
2297 |
tag.setName(name); |
| 1865 |
19 Feb 13 |
nicklas |
2298 |
tag.setItemSubtype(subtype.get(dc)); |
| 1865 |
19 Feb 13 |
nicklas |
2299 |
tag.setDescription(description); |
| 1865 |
19 Feb 13 |
nicklas |
2300 |
if (permissions != null) permissions.applyPermissions(tag); |
| 5437 |
17 May 19 |
nicklas |
2301 |
if (pipeline != null) pipeline.setAnnotation(dc, tag); |
| 5865 |
12 Mar 20 |
nicklas |
2302 |
if (barcodeSet != null) Annotationtype.BARCODE_SET.setAnnotationValue(dc, tag, barcodeSet.getName()); |
| 5865 |
12 Mar 20 |
nicklas |
2303 |
String seq1 = lookupSequence(name); |
| 5865 |
12 Mar 20 |
nicklas |
2304 |
String seq2 = lookupSequence2(name); |
| 5865 |
12 Mar 20 |
nicklas |
2305 |
if (seq1 != null) Annotationtype.BARCODE_SEQUENCE.setAnnotationValue(dc, tag, seq1); |
| 5865 |
12 Mar 20 |
nicklas |
2306 |
if (seq2 != null) Annotationtype.BARCODE_SEQUENCE_2.setAnnotationValue(dc, tag, seq2); |
| 1865 |
19 Feb 13 |
nicklas |
2307 |
dc.saveItem(tag); |
| 1865 |
19 Feb 13 |
nicklas |
2308 |
dc.commit(); |
| 1865 |
19 Feb 13 |
nicklas |
2309 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2310 |
finally |
| 1865 |
19 Feb 13 |
nicklas |
2311 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2312 |
if (dc != null) dc.close(); |
| 1865 |
19 Feb 13 |
nicklas |
2313 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2314 |
return tag; |
| 1865 |
19 Feb 13 |
nicklas |
2315 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2316 |
|
| 1865 |
19 Feb 13 |
nicklas |
2317 |
|
| 1865 |
19 Feb 13 |
nicklas |
2318 |
/** |
| 1865 |
19 Feb 13 |
nicklas |
Check for an existing tag with the given options. |
| 1865 |
19 Feb 13 |
nicklas |
A JSONObject is returned with the result. The following |
| 1865 |
19 Feb 13 |
nicklas |
keys are used: |
| 1865 |
19 Feb 13 |
nicklas |
<ul> |
| 1865 |
19 Feb 13 |
nicklas |
<li>itemType: TAG |
| 1865 |
19 Feb 13 |
nicklas |
<li>name: The name of the tag |
| 1865 |
19 Feb 13 |
nicklas |
<li>id: The id of the subtype if it exists |
| 1865 |
19 Feb 13 |
nicklas |
<li>status: ok, error, or missing |
| 1865 |
19 Feb 13 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1865 |
19 Feb 13 |
nicklas |
</ul> |
| 1867 |
19 Feb 13 |
nicklas |
@since 2.12 |
| 1865 |
19 Feb 13 |
nicklas |
2330 |
*/ |
| 5865 |
12 Mar 20 |
nicklas |
2331 |
public JSONObject checkTag(DbControl dc, String name, Subtype subtype, Pipeline pipeline, BarcodeSet barcodeSet, String description, PermissionOptions permissions, boolean createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
2332 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2333 |
|
| 1865 |
19 Feb 13 |
nicklas |
2334 |
JSONObject json = new JSONObject(); |
| 1865 |
19 Feb 13 |
nicklas |
2335 |
JSONArray jsonMessages = new JSONArray(); |
| 1865 |
19 Feb 13 |
nicklas |
2336 |
json.put("itemType", Item.TAG.name()); |
| 1865 |
19 Feb 13 |
nicklas |
2337 |
json.put("name", name); |
| 1865 |
19 Feb 13 |
nicklas |
2338 |
|
| 1865 |
19 Feb 13 |
nicklas |
2339 |
ItemQuery<Tag> query = Tag.getQuery(); |
| 1865 |
19 Feb 13 |
nicklas |
2340 |
query.restrict( |
| 1865 |
19 Feb 13 |
nicklas |
2341 |
Restrictions.eq( |
| 1865 |
19 Feb 13 |
nicklas |
2342 |
Hql.property("name"), |
| 1865 |
19 Feb 13 |
nicklas |
2343 |
Expressions.parameter("name", name, Type.STRING) |
| 1865 |
19 Feb 13 |
nicklas |
2344 |
)); |
| 1865 |
19 Feb 13 |
nicklas |
2345 |
query.include(Include.ALL); |
| 1865 |
19 Feb 13 |
nicklas |
2346 |
List<Tag> result = query.list(dc); |
| 1865 |
19 Feb 13 |
nicklas |
2347 |
if (result.size() == 0) |
| 1865 |
19 Feb 13 |
nicklas |
2348 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2349 |
if (createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
2350 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2351 |
Tag t = createTag(dc.getSessionControl(), name, subtype, pipeline, barcodeSet, description, permissions); |
| 1865 |
19 Feb 13 |
nicklas |
2352 |
json.put("id", t.getId()); |
| 1865 |
19 Feb 13 |
nicklas |
2353 |
json.put("status", "ok"); |
| 1865 |
19 Feb 13 |
nicklas |
2354 |
jsonMessages.add("Created"); |
| 1865 |
19 Feb 13 |
nicklas |
2355 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2356 |
else |
| 1865 |
19 Feb 13 |
nicklas |
2357 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2358 |
json.put("status", "missing"); |
| 1865 |
19 Feb 13 |
nicklas |
2359 |
jsonMessages.add("Not found"); |
| 1865 |
19 Feb 13 |
nicklas |
2360 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2361 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2362 |
else if (result.size() > 1) |
| 1865 |
19 Feb 13 |
nicklas |
2363 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2364 |
json.put("status", "error"); |
| 1865 |
19 Feb 13 |
nicklas |
2365 |
jsonMessages.add("Found > 1 tag"); |
| 1865 |
19 Feb 13 |
nicklas |
2366 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2367 |
else |
| 1865 |
19 Feb 13 |
nicklas |
2368 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2369 |
Tag t = result.get(0); |
| 1865 |
19 Feb 13 |
nicklas |
2370 |
json.put("id", t.getId()); |
| 1865 |
19 Feb 13 |
nicklas |
2371 |
json.put("status", "ok"); // For now -- more checks below |
| 1865 |
19 Feb 13 |
nicklas |
2372 |
|
| 1865 |
19 Feb 13 |
nicklas |
2373 |
if (!subtype.load(dc).equals(t.getItemSubtype())) |
| 1865 |
19 Feb 13 |
nicklas |
2374 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2375 |
json.put("status", "error"); |
| 1865 |
19 Feb 13 |
nicklas |
2376 |
jsonMessages.add("Should have '" + subtype.getName() + "' as subtype."); |
| 1865 |
19 Feb 13 |
nicklas |
2377 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2378 |
|
| 1865 |
19 Feb 13 |
nicklas |
2379 |
if (permissions != null && !permissions.checkPermissions(t)) |
| 1865 |
19 Feb 13 |
nicklas |
2380 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2381 |
if (createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
2382 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2383 |
permissions.applyPermissions(t); |
| 1865 |
19 Feb 13 |
nicklas |
2384 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 1865 |
19 Feb 13 |
nicklas |
2385 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2386 |
else |
| 1865 |
19 Feb 13 |
nicklas |
2387 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2388 |
json.put("status", "incomplete"); |
| 1865 |
19 Feb 13 |
nicklas |
2389 |
jsonMessages.add(permissions.getMessage()); |
| 1865 |
19 Feb 13 |
nicklas |
2390 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2391 |
} |
| 2350 |
10 Apr 14 |
nicklas |
2392 |
AnnotationType barcodeSequenceType = Annotationtype.BARCODE_SEQUENCE.get(dc); |
| 5865 |
12 Mar 20 |
nicklas |
2393 |
AnnotationType barcodeSequence2Type = Annotationtype.BARCODE_SEQUENCE_2.get(dc); |
| 5865 |
12 Mar 20 |
nicklas |
2394 |
if (barcodeSequenceType != null && barcodeSequence2Type != null) |
| 2350 |
10 Apr 14 |
nicklas |
2395 |
{ |
| 2350 |
10 Apr 14 |
nicklas |
2396 |
String barcodeSequence = (String)Annotationtype.BARCODE_SEQUENCE.getAnnotationValue(dc, t); |
| 5865 |
12 Mar 20 |
nicklas |
2397 |
String barcodeSequence2 = (String)Annotationtype.BARCODE_SEQUENCE_2.getAnnotationValue(dc, t); |
| 2350 |
10 Apr 14 |
nicklas |
2398 |
if (barcodeSequence == null) |
| 2350 |
10 Apr 14 |
nicklas |
2399 |
{ |
| 2350 |
10 Apr 14 |
nicklas |
2400 |
if (createIfMissing) |
| 2350 |
10 Apr 14 |
nicklas |
2401 |
{ |
| 2350 |
10 Apr 14 |
nicklas |
2402 |
barcodeSequence = lookupSequence(name); |
| 2350 |
10 Apr 14 |
nicklas |
2403 |
Annotationtype.BARCODE_SEQUENCE.setAnnotationValue(dc, t, barcodeSequence); |
| 2350 |
10 Apr 14 |
nicklas |
2404 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 2350 |
10 Apr 14 |
nicklas |
2405 |
} |
| 2350 |
10 Apr 14 |
nicklas |
2406 |
else |
| 2350 |
10 Apr 14 |
nicklas |
2407 |
{ |
| 2350 |
10 Apr 14 |
nicklas |
2408 |
json.put("status", "incomplete"); |
| 2350 |
10 Apr 14 |
nicklas |
2409 |
jsonMessages.add("Missing BarcodeSequence annotation"); |
| 2350 |
10 Apr 14 |
nicklas |
2410 |
} |
| 2350 |
10 Apr 14 |
nicklas |
2411 |
} |
| 5865 |
12 Mar 20 |
nicklas |
2412 |
if (barcodeSequence2 == null) |
| 5865 |
12 Mar 20 |
nicklas |
2413 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2414 |
barcodeSequence2 = lookupSequence2(name); |
| 5865 |
12 Mar 20 |
nicklas |
2415 |
if (barcodeSequence2 != null) |
| 5865 |
12 Mar 20 |
nicklas |
2416 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2417 |
if (createIfMissing) |
| 5865 |
12 Mar 20 |
nicklas |
2418 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2419 |
Annotationtype.BARCODE_SEQUENCE_2.setAnnotationValue(dc, t, barcodeSequence2); |
| 5865 |
12 Mar 20 |
nicklas |
2420 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 5865 |
12 Mar 20 |
nicklas |
2421 |
} |
| 5865 |
12 Mar 20 |
nicklas |
2422 |
else |
| 5865 |
12 Mar 20 |
nicklas |
2423 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2424 |
json.put("status", "incomplete"); |
| 5865 |
12 Mar 20 |
nicklas |
2425 |
jsonMessages.add("Missing BarcodeSequence2 annotation"); |
| 5865 |
12 Mar 20 |
nicklas |
2426 |
} |
| 5865 |
12 Mar 20 |
nicklas |
2427 |
} |
| 5865 |
12 Mar 20 |
nicklas |
2428 |
} |
| 2350 |
10 Apr 14 |
nicklas |
2429 |
} |
| 5437 |
17 May 19 |
nicklas |
2430 |
AnnotationType pipelineType = Annotationtype.PIPELINE.get(dc); |
| 5437 |
17 May 19 |
nicklas |
2431 |
if (pipelineType != null && pipeline != null) |
| 5437 |
17 May 19 |
nicklas |
2432 |
{ |
| 5437 |
17 May 19 |
nicklas |
2433 |
String existing = (String)Annotationtype.PIPELINE.getAnnotationValue(dc, t); |
| 5437 |
17 May 19 |
nicklas |
2434 |
if (existing == null || !existing.equals(pipeline.getName())) |
| 5437 |
17 May 19 |
nicklas |
2435 |
{ |
| 5437 |
17 May 19 |
nicklas |
2436 |
if (createIfMissing) |
| 5437 |
17 May 19 |
nicklas |
2437 |
{ |
| 5437 |
17 May 19 |
nicklas |
2438 |
pipeline.setAnnotation(dc, t); |
| 5437 |
17 May 19 |
nicklas |
2439 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 5437 |
17 May 19 |
nicklas |
2440 |
} |
| 5437 |
17 May 19 |
nicklas |
2441 |
else |
| 5437 |
17 May 19 |
nicklas |
2442 |
{ |
| 5437 |
17 May 19 |
nicklas |
2443 |
json.put("status", "incomplete"); |
| 5437 |
17 May 19 |
nicklas |
2444 |
jsonMessages.add(existing == null ? "Missing Pipeline annotation" : "Pipeline annotation: expected " + pipeline.getName() + "; found " + existing); |
| 5437 |
17 May 19 |
nicklas |
2445 |
} |
| 5437 |
17 May 19 |
nicklas |
2446 |
} |
| 5437 |
17 May 19 |
nicklas |
2447 |
} |
| 5865 |
12 Mar 20 |
nicklas |
2448 |
AnnotationType barcodeSetType = Annotationtype.BARCODE_SET.get(dc); |
| 5865 |
12 Mar 20 |
nicklas |
2449 |
if (barcodeSetType != null && barcodeSet != null) |
| 5865 |
12 Mar 20 |
nicklas |
2450 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2451 |
String existing = (String)Annotationtype.BARCODE_SET.getAnnotationValue(dc, t); |
| 5865 |
12 Mar 20 |
nicklas |
2452 |
if (existing == null || !existing.equals(barcodeSet.getName())) |
| 5865 |
12 Mar 20 |
nicklas |
2453 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2454 |
if (createIfMissing) |
| 5865 |
12 Mar 20 |
nicklas |
2455 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2456 |
Annotationtype.BARCODE_SET.setAnnotationValue(dc, t, barcodeSet.getName()); |
| 5865 |
12 Mar 20 |
nicklas |
2457 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 5865 |
12 Mar 20 |
nicklas |
2458 |
} |
| 5865 |
12 Mar 20 |
nicklas |
2459 |
else |
| 5865 |
12 Mar 20 |
nicklas |
2460 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
2461 |
json.put("status", "incomplete"); |
| 5865 |
12 Mar 20 |
nicklas |
2462 |
jsonMessages.add(existing == null ? "Missing BarcodeSet annotation" : "BarcodeSet annotation: expected " + barcodeSet.getName() + "; found " + existing); |
| 5865 |
12 Mar 20 |
nicklas |
2463 |
} |
| 5865 |
12 Mar 20 |
nicklas |
2464 |
} |
| 5865 |
12 Mar 20 |
nicklas |
2465 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2466 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2467 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1865 |
19 Feb 13 |
nicklas |
2468 |
json.put("messages", jsonMessages); |
| 1865 |
19 Feb 13 |
nicklas |
2469 |
return json; |
| 1865 |
19 Feb 13 |
nicklas |
2470 |
|
| 1865 |
19 Feb 13 |
nicklas |
2471 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2472 |
|
| 1865 |
19 Feb 13 |
nicklas |
2473 |
|
| 1865 |
19 Feb 13 |
nicklas |
2474 |
/** |
| 1463 |
14 Nov 11 |
martin |
Create an annotation type category with the given options. The category |
| 1463 |
14 Nov 11 |
martin |
is created in a separate transaction. |
| 4475 |
27 Apr 17 |
nicklas |
@since 2.5, 4.10 |
| 1463 |
14 Nov 11 |
martin |
2478 |
*/ |
| 1610 |
23 Apr 12 |
nicklas |
2479 |
public AnnotationTypeCategory createAnnotationTypeCategory(SessionControl sc, |
| 5880 |
25 Mar 20 |
nicklas |
2480 |
String name, String description) |
| 1463 |
14 Nov 11 |
martin |
2481 |
{ |
| 1463 |
14 Nov 11 |
martin |
2482 |
AnnotationTypeCategory cat = null; |
| 6328 |
14 Jun 21 |
nicklas |
2483 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1463 |
14 Nov 11 |
martin |
2484 |
try |
| 1463 |
14 Nov 11 |
martin |
2485 |
{ |
| 1463 |
14 Nov 11 |
martin |
2486 |
cat = AnnotationTypeCategory.getNew(dc); |
| 4475 |
27 Apr 17 |
nicklas |
2487 |
cat.setName(name); |
| 5880 |
25 Mar 20 |
nicklas |
2488 |
cat.setDescription(description); |
| 1463 |
14 Nov 11 |
martin |
2489 |
dc.saveItem(cat); |
| 1463 |
14 Nov 11 |
martin |
2490 |
dc.commit(); |
| 1463 |
14 Nov 11 |
martin |
2491 |
} |
| 1463 |
14 Nov 11 |
martin |
2492 |
finally |
| 1463 |
14 Nov 11 |
martin |
2493 |
{ |
| 1463 |
14 Nov 11 |
martin |
2494 |
if (dc != null) dc.close(); |
| 1463 |
14 Nov 11 |
martin |
2495 |
} |
| 1463 |
14 Nov 11 |
martin |
2496 |
return cat; |
| 1463 |
14 Nov 11 |
martin |
2497 |
} |
| 5230 |
15 Jan 19 |
nicklas |
2498 |
|
| 5230 |
15 Jan 19 |
nicklas |
2499 |
public JSONObject checkAnnotationTypeCategory(DbControl dc, Rawdatatype rawdatatype, |
| 5230 |
15 Jan 19 |
nicklas |
2500 |
boolean createIfMissing, Annotationtype... annotationTypes) |
| 5230 |
15 Jan 19 |
nicklas |
2501 |
{ |
| 5880 |
25 Mar 20 |
nicklas |
2502 |
return checkAnnotationTypeCategory(dc, rawdatatype.getName(), "Annotations related to rawdata type: " + rawdatatype.getName(), createIfMissing, annotationTypes); |
| 5230 |
15 Jan 19 |
nicklas |
2503 |
} |
| 1463 |
14 Nov 11 |
martin |
2504 |
|
| 4475 |
27 Apr 17 |
nicklas |
2505 |
public JSONObject checkAnnotationTypeCategory(DbControl dc, Subtype subtype, |
| 4475 |
27 Apr 17 |
nicklas |
2506 |
boolean createIfMissing, Annotationtype... annotationTypes) |
| 4475 |
27 Apr 17 |
nicklas |
2507 |
{ |
| 5880 |
25 Mar 20 |
nicklas |
2508 |
return checkAnnotationTypeCategory(dc, subtype.getName(), "Annotations related to subtype: " + subtype.getName(), createIfMissing, annotationTypes); |
| 4475 |
27 Apr 17 |
nicklas |
2509 |
} |
| 4475 |
27 Apr 17 |
nicklas |
2510 |
|
| 1463 |
14 Nov 11 |
martin |
2511 |
/** |
| 1463 |
14 Nov 11 |
martin |
Check for an existing annotation type category. |
| 1463 |
14 Nov 11 |
martin |
A JSONObject is returned with the result. The following |
| 1463 |
14 Nov 11 |
martin |
keys are used: |
| 1463 |
14 Nov 11 |
martin |
<ul> |
| 1463 |
14 Nov 11 |
martin |
<li>itemType: ANNOTATIONTYPECATEGORY |
| 4475 |
27 Apr 17 |
nicklas |
<li>name: The name of the category |
| 4475 |
27 Apr 17 |
nicklas |
<li>id: The id of the category if it exists |
| 1463 |
14 Nov 11 |
martin |
<li>status: ok, error, or missing |
| 1463 |
14 Nov 11 |
martin |
<li>message: A descriptive message in case of an error |
| 1463 |
14 Nov 11 |
martin |
</ul> |
| 4475 |
27 Apr 17 |
nicklas |
@since 4.10 |
| 1463 |
14 Nov 11 |
martin |
2523 |
*/ |
| 4475 |
27 Apr 17 |
nicklas |
2524 |
public JSONObject checkAnnotationTypeCategory(DbControl dc, String name, |
| 5880 |
25 Mar 20 |
nicklas |
2525 |
String description, boolean createIfMissing, Annotationtype... annotationTypes) |
| 1463 |
14 Nov 11 |
martin |
2526 |
{ |
| 1463 |
14 Nov 11 |
martin |
2527 |
|
| 1463 |
14 Nov 11 |
martin |
2528 |
JSONObject json = new JSONObject(); |
| 1463 |
14 Nov 11 |
martin |
2529 |
JSONArray jsonMessages = new JSONArray(); |
| 1463 |
14 Nov 11 |
martin |
2530 |
json.put("itemType", Item.ANNOTATIONTYPECATEGORY.name()); |
| 4475 |
27 Apr 17 |
nicklas |
2531 |
json.put("name", name); |
| 1463 |
14 Nov 11 |
martin |
2532 |
|
| 4475 |
27 Apr 17 |
nicklas |
2533 |
List<AnnotationTypeCategory> result = Reggie.listAnnotationTypeCategories(dc, name); |
| 1463 |
14 Nov 11 |
martin |
2534 |
if (result.size() == 0) |
| 1463 |
14 Nov 11 |
martin |
2535 |
{ |
| 1463 |
14 Nov 11 |
martin |
2536 |
if (createIfMissing) |
| 1463 |
14 Nov 11 |
martin |
2537 |
{ |
| 5880 |
25 Mar 20 |
nicklas |
2538 |
AnnotationTypeCategory cat = createAnnotationTypeCategory(dc.getSessionControl(), name, description); |
| 2080 |
17 Oct 13 |
nicklas |
// Add the category to annotation types in the original transaction |
| 2080 |
17 Oct 13 |
nicklas |
2540 |
if (annotationTypes != null) |
| 2080 |
17 Oct 13 |
nicklas |
2541 |
{ |
| 2080 |
17 Oct 13 |
nicklas |
2542 |
for (Annotationtype annotationType : annotationTypes) |
| 2080 |
17 Oct 13 |
nicklas |
2543 |
{ |
| 2080 |
17 Oct 13 |
nicklas |
2544 |
AnnotationType at = annotationType.load(dc); |
| 2224 |
12 Feb 14 |
nicklas |
2545 |
at.addCategory(cat); |
| 2080 |
17 Oct 13 |
nicklas |
2546 |
} |
| 2080 |
17 Oct 13 |
nicklas |
2547 |
} |
| 2080 |
17 Oct 13 |
nicklas |
2548 |
|
| 1463 |
14 Nov 11 |
martin |
2549 |
json.put("id", cat.getId()); |
| 1463 |
14 Nov 11 |
martin |
2550 |
json.put("status", "ok"); |
| 1463 |
14 Nov 11 |
martin |
2551 |
jsonMessages.add("Created"); |
| 1463 |
14 Nov 11 |
martin |
2552 |
} |
| 1463 |
14 Nov 11 |
martin |
2553 |
else |
| 1463 |
14 Nov 11 |
martin |
2554 |
{ |
| 1463 |
14 Nov 11 |
martin |
2555 |
json.put("status", "missing"); |
| 1463 |
14 Nov 11 |
martin |
2556 |
jsonMessages.add("Not found"); |
| 1463 |
14 Nov 11 |
martin |
2557 |
} |
| 1463 |
14 Nov 11 |
martin |
2558 |
} |
| 1463 |
14 Nov 11 |
martin |
2559 |
else if (result.size() > 1) |
| 1463 |
14 Nov 11 |
martin |
2560 |
{ |
| 1463 |
14 Nov 11 |
martin |
2561 |
json.put("status", "error"); |
| 1463 |
14 Nov 11 |
martin |
2562 |
jsonMessages.add("Found > 1 annotation type category"); |
| 1463 |
14 Nov 11 |
martin |
2563 |
} |
| 1463 |
14 Nov 11 |
martin |
2564 |
else |
| 1463 |
14 Nov 11 |
martin |
2565 |
{ |
| 1463 |
14 Nov 11 |
martin |
2566 |
AnnotationTypeCategory cat = result.get(0); |
| 1463 |
14 Nov 11 |
martin |
2567 |
json.put("id", cat.getId()); |
| 1463 |
14 Nov 11 |
martin |
2568 |
json.put("status", "ok"); // For now -- more checks below |
| 1463 |
14 Nov 11 |
martin |
2569 |
|
| 5880 |
25 Mar 20 |
nicklas |
2570 |
if (createIfMissing && description != null && cat.getDescription() == null) |
| 5880 |
25 Mar 20 |
nicklas |
2571 |
{ |
| 5880 |
25 Mar 20 |
nicklas |
2572 |
cat.setDescription(description); |
| 5880 |
25 Mar 20 |
nicklas |
2573 |
} |
| 5880 |
25 Mar 20 |
nicklas |
2574 |
|
| 1463 |
14 Nov 11 |
martin |
2575 |
if (annotationTypes != null) |
| 1463 |
14 Nov 11 |
martin |
2576 |
{ |
| 1610 |
23 Apr 12 |
nicklas |
2577 |
for (Annotationtype annotationType : annotationTypes) |
| 1463 |
14 Nov 11 |
martin |
2578 |
{ |
| 1610 |
23 Apr 12 |
nicklas |
2579 |
List<AnnotationType> list = annotationType.list(dc); // Use list() to avoid throwing exceptions if the annotation type doesn't exists yet |
| 1610 |
23 Apr 12 |
nicklas |
2580 |
AnnotationType at = list.size() == 1 ? list.get(0) : null; |
| 1463 |
14 Nov 11 |
martin |
2581 |
if (at != null && !at.isMember(cat)) |
| 1463 |
14 Nov 11 |
martin |
2582 |
{ |
| 1463 |
14 Nov 11 |
martin |
2583 |
if (createIfMissing) |
| 1463 |
14 Nov 11 |
martin |
2584 |
{ |
| 2224 |
12 Feb 14 |
nicklas |
2585 |
at.addCategory(cat); |
| 1463 |
14 Nov 11 |
martin |
2586 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 1463 |
14 Nov 11 |
martin |
2587 |
} |
| 1463 |
14 Nov 11 |
martin |
2588 |
else |
| 1463 |
14 Nov 11 |
martin |
2589 |
{ |
| 1463 |
14 Nov 11 |
martin |
2590 |
json.put("status", "incomplete"); |
| 1610 |
23 Apr 12 |
nicklas |
2591 |
jsonMessages.add("Not linked with: " + annotationType.getName()); |
| 1463 |
14 Nov 11 |
martin |
2592 |
} |
| 1463 |
14 Nov 11 |
martin |
2593 |
} |
| 1463 |
14 Nov 11 |
martin |
2594 |
} |
| 1463 |
14 Nov 11 |
martin |
2595 |
} |
| 1463 |
14 Nov 11 |
martin |
2596 |
} |
| 1463 |
14 Nov 11 |
martin |
2597 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1463 |
14 Nov 11 |
martin |
2598 |
json.put("messages", jsonMessages); |
| 1463 |
14 Nov 11 |
martin |
2599 |
return json; |
| 1463 |
14 Nov 11 |
martin |
2600 |
|
| 1463 |
14 Nov 11 |
martin |
2601 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2602 |
|
| 1865 |
19 Feb 13 |
nicklas |
2603 |
|
| 1865 |
19 Feb 13 |
nicklas |
2604 |
/** |
| 1865 |
19 Feb 13 |
nicklas |
Create a bioplate event type with the given options. The bioplate event type is created in |
| 1865 |
19 Feb 13 |
nicklas |
a separate transaction. |
| 1867 |
19 Feb 13 |
nicklas |
@since 2.12 |
| 1865 |
19 Feb 13 |
nicklas |
2608 |
*/ |
| 1865 |
19 Feb 13 |
nicklas |
2609 |
public BioPlateEventType createBioPlateEventType(SessionControl sc, BioplateEventtype def) |
| 1865 |
19 Feb 13 |
nicklas |
2610 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2611 |
BioPlateEventType eventType = null; |
| 6328 |
14 Jun 21 |
nicklas |
2612 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1865 |
19 Feb 13 |
nicklas |
2613 |
try |
| 1865 |
19 Feb 13 |
nicklas |
2614 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2615 |
eventType = BioPlateEventType.getNew(dc, def.getSystemId()); |
| 1865 |
19 Feb 13 |
nicklas |
2616 |
eventType.setName(def.getName()); |
| 1865 |
19 Feb 13 |
nicklas |
2617 |
eventType.setDescription(def.getDescription()); |
| 1865 |
19 Feb 13 |
nicklas |
2618 |
dc.saveItem(eventType); |
| 1865 |
19 Feb 13 |
nicklas |
2619 |
dc.commit(); |
| 1865 |
19 Feb 13 |
nicklas |
2620 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2621 |
finally |
| 1865 |
19 Feb 13 |
nicklas |
2622 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2623 |
if (dc != null) dc.close(); |
| 1865 |
19 Feb 13 |
nicklas |
2624 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2625 |
return eventType; |
| 1865 |
19 Feb 13 |
nicklas |
2626 |
} |
| 1463 |
14 Nov 11 |
martin |
2627 |
|
| 1865 |
19 Feb 13 |
nicklas |
2628 |
|
| 1543 |
28 Feb 12 |
nicklas |
2629 |
/** |
| 1865 |
19 Feb 13 |
nicklas |
Check for an existing bioplate event type with the given options. |
| 1865 |
19 Feb 13 |
nicklas |
A JSONObject is returned with the result. The following |
| 1865 |
19 Feb 13 |
nicklas |
keys are used: |
| 1865 |
19 Feb 13 |
nicklas |
<ul> |
| 1865 |
19 Feb 13 |
nicklas |
<li>itemType: BIOPLATEEVENTTYPE |
| 1865 |
19 Feb 13 |
nicklas |
<li>name: The name of the event type |
| 1865 |
19 Feb 13 |
nicklas |
<li>id: The id of the event type if it exists |
| 1865 |
19 Feb 13 |
nicklas |
<li>status: ok, error, or missing |
| 1865 |
19 Feb 13 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1865 |
19 Feb 13 |
nicklas |
</ul> |
| 1867 |
19 Feb 13 |
nicklas |
@since 2.12 |
| 1865 |
19 Feb 13 |
nicklas |
2641 |
*/ |
| 1865 |
19 Feb 13 |
nicklas |
2642 |
public JSONObject checkBioplateEventtype(DbControl dc, BioplateEventtype eventType, |
| 1865 |
19 Feb 13 |
nicklas |
2643 |
boolean createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
2644 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2645 |
|
| 1865 |
19 Feb 13 |
nicklas |
2646 |
JSONObject json = new JSONObject(); |
| 1865 |
19 Feb 13 |
nicklas |
2647 |
JSONArray jsonMessages = new JSONArray(); |
| 1865 |
19 Feb 13 |
nicklas |
2648 |
json.put("itemType", Item.BIOPLATEEVENTTYPE.name()); |
| 1865 |
19 Feb 13 |
nicklas |
2649 |
json.put("name", eventType.getName()); |
| 1865 |
19 Feb 13 |
nicklas |
2650 |
|
| 1865 |
19 Feb 13 |
nicklas |
2651 |
List<BioPlateEventType> result = eventType.list(dc); |
| 1865 |
19 Feb 13 |
nicklas |
2652 |
if (result.size() == 0) |
| 1865 |
19 Feb 13 |
nicklas |
2653 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2654 |
if (createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
2655 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2656 |
BioPlateEventType t = createBioPlateEventType(dc.getSessionControl(), eventType); |
| 1865 |
19 Feb 13 |
nicklas |
2657 |
json.put("id", t.getId()); |
| 1865 |
19 Feb 13 |
nicklas |
2658 |
json.put("status", "ok"); |
| 1865 |
19 Feb 13 |
nicklas |
2659 |
jsonMessages.add("Created"); |
| 1865 |
19 Feb 13 |
nicklas |
2660 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2661 |
else |
| 1865 |
19 Feb 13 |
nicklas |
2662 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2663 |
json.put("status", "missing"); |
| 1865 |
19 Feb 13 |
nicklas |
2664 |
jsonMessages.add("Not found"); |
| 1865 |
19 Feb 13 |
nicklas |
2665 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2666 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2667 |
else if (result.size() > 1) |
| 1865 |
19 Feb 13 |
nicklas |
2668 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2669 |
json.put("status", "error"); |
| 1865 |
19 Feb 13 |
nicklas |
2670 |
jsonMessages.add("Found > 1 bioplate event type"); |
| 1865 |
19 Feb 13 |
nicklas |
2671 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2672 |
else |
| 1865 |
19 Feb 13 |
nicklas |
2673 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2674 |
BioPlateEventType t = result.get(0); |
| 1865 |
19 Feb 13 |
nicklas |
2675 |
json.put("id", t.getId()); |
| 1865 |
19 Feb 13 |
nicklas |
2676 |
json.put("status", "ok"); // For now -- more checks below |
| 1865 |
19 Feb 13 |
nicklas |
2677 |
|
| 1865 |
19 Feb 13 |
nicklas |
2678 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2679 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1865 |
19 Feb 13 |
nicklas |
2680 |
json.put("messages", jsonMessages); |
| 1865 |
19 Feb 13 |
nicklas |
2681 |
return json; |
| 1865 |
19 Feb 13 |
nicklas |
2682 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2683 |
|
| 1865 |
19 Feb 13 |
nicklas |
2684 |
|
| 1865 |
19 Feb 13 |
nicklas |
2685 |
|
| 1865 |
19 Feb 13 |
nicklas |
2686 |
/** |
| 1543 |
28 Feb 12 |
nicklas |
Create a bioplate type with the given options. The bioplate type is created in |
| 1543 |
28 Feb 12 |
nicklas |
a separate transaction. |
| 1543 |
28 Feb 12 |
nicklas |
@since 2.4 |
| 1543 |
28 Feb 12 |
nicklas |
2690 |
*/ |
| 1543 |
28 Feb 12 |
nicklas |
2691 |
public BioPlateType createBioPlateType(SessionControl sc, BioplateType def) |
| 1543 |
28 Feb 12 |
nicklas |
2692 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2693 |
BioPlateType plateType = null; |
| 6328 |
14 Jun 21 |
nicklas |
2694 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1543 |
28 Feb 12 |
nicklas |
2695 |
try |
| 1543 |
28 Feb 12 |
nicklas |
2696 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2697 |
plateType = BioPlateType.getNew(dc); |
| 1543 |
28 Feb 12 |
nicklas |
2698 |
plateType.setName(def.getName()); |
| 1543 |
28 Feb 12 |
nicklas |
2699 |
plateType.setBioMaterialType(def.getBioMaterialType()); |
| 1543 |
28 Feb 12 |
nicklas |
2700 |
if (def.getSubtype() != null) |
| 1543 |
28 Feb 12 |
nicklas |
2701 |
{ |
| 1644 |
15 May 12 |
nicklas |
2702 |
ItemSubtype subtype = def.getSubtype().get(dc); |
| 1644 |
15 May 12 |
nicklas |
2703 |
if (subtype != null) |
| 1644 |
15 May 12 |
nicklas |
2704 |
{ |
| 1644 |
15 May 12 |
nicklas |
2705 |
plateType.setItemSubtype(subtype); |
| 1644 |
15 May 12 |
nicklas |
2706 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2707 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2708 |
plateType.setLockMode(def.getLockMode()); |
| 1543 |
28 Feb 12 |
nicklas |
2709 |
|
| 1543 |
28 Feb 12 |
nicklas |
2710 |
dc.saveItem(plateType); |
| 1543 |
28 Feb 12 |
nicklas |
2711 |
dc.commit(); |
| 1543 |
28 Feb 12 |
nicklas |
2712 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2713 |
finally |
| 1543 |
28 Feb 12 |
nicklas |
2714 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2715 |
if (dc != null) dc.close(); |
| 1543 |
28 Feb 12 |
nicklas |
2716 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2717 |
return plateType; |
| 1543 |
28 Feb 12 |
nicklas |
2718 |
} |
| 1463 |
14 Nov 11 |
martin |
2719 |
|
| 1543 |
28 Feb 12 |
nicklas |
2720 |
|
| 1463 |
14 Nov 11 |
martin |
2721 |
/** |
| 1543 |
28 Feb 12 |
nicklas |
Check for an existing bioplate type with the given options. |
| 1543 |
28 Feb 12 |
nicklas |
A JSONObject is returned with the result. The following |
| 1543 |
28 Feb 12 |
nicklas |
keys are used: |
| 1543 |
28 Feb 12 |
nicklas |
<ul> |
| 1543 |
28 Feb 12 |
nicklas |
<li>itemType: BIOPLATETYPE |
| 1543 |
28 Feb 12 |
nicklas |
<li>name: The name of the bioplate type |
| 1543 |
28 Feb 12 |
nicklas |
<li>id: The id of the bioplate type if it exists |
| 1543 |
28 Feb 12 |
nicklas |
<li>bioMaterialType: The bioMaterial type that can be used on bioplates with the given type |
| 1543 |
28 Feb 12 |
nicklas |
<li>status: ok, error, or missing |
| 1543 |
28 Feb 12 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1543 |
28 Feb 12 |
nicklas |
</ul> |
| 1543 |
28 Feb 12 |
nicklas |
@since 2.0 |
| 1543 |
28 Feb 12 |
nicklas |
2734 |
*/ |
| 1543 |
28 Feb 12 |
nicklas |
2735 |
public JSONObject checkBioplateType(DbControl dc, BioplateType plateType, |
| 1543 |
28 Feb 12 |
nicklas |
2736 |
boolean createIfMissing) |
| 1543 |
28 Feb 12 |
nicklas |
2737 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2738 |
|
| 1543 |
28 Feb 12 |
nicklas |
2739 |
JSONObject json = new JSONObject(); |
| 1543 |
28 Feb 12 |
nicklas |
2740 |
JSONArray jsonMessages = new JSONArray(); |
| 1543 |
28 Feb 12 |
nicklas |
2741 |
json.put("itemType", Item.BIOPLATETYPE.name()); |
| 1543 |
28 Feb 12 |
nicklas |
2742 |
json.put("name", plateType.getName()); |
| 3640 |
02 Dec 15 |
nicklas |
2743 |
json.put("bioMaterialType", plateType.getBioMaterialType() == null ? null : plateType.getBioMaterialType().name()); |
| 1543 |
28 Feb 12 |
nicklas |
2744 |
|
| 1610 |
23 Apr 12 |
nicklas |
2745 |
List<BioPlateType> result = plateType.list(dc); |
| 1543 |
28 Feb 12 |
nicklas |
2746 |
if (result.size() == 0) |
| 1543 |
28 Feb 12 |
nicklas |
2747 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2748 |
if (createIfMissing) |
| 1543 |
28 Feb 12 |
nicklas |
2749 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2750 |
BioPlateType t = createBioPlateType(dc.getSessionControl(), plateType); |
| 1543 |
28 Feb 12 |
nicklas |
2751 |
json.put("id", t.getId()); |
| 1543 |
28 Feb 12 |
nicklas |
2752 |
json.put("status", "ok"); |
| 1543 |
28 Feb 12 |
nicklas |
2753 |
jsonMessages.add("Created"); |
| 1543 |
28 Feb 12 |
nicklas |
2754 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2755 |
else |
| 1543 |
28 Feb 12 |
nicklas |
2756 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2757 |
json.put("status", "missing"); |
| 1543 |
28 Feb 12 |
nicklas |
2758 |
jsonMessages.add("Not found"); |
| 1543 |
28 Feb 12 |
nicklas |
2759 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2760 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2761 |
else if (result.size() > 1) |
| 1543 |
28 Feb 12 |
nicklas |
2762 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2763 |
json.put("status", "error"); |
| 1543 |
28 Feb 12 |
nicklas |
2764 |
jsonMessages.add("Found > 1 bioplate type"); |
| 1543 |
28 Feb 12 |
nicklas |
2765 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2766 |
else |
| 1543 |
28 Feb 12 |
nicklas |
2767 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2768 |
BioPlateType t = result.get(0); |
| 1543 |
28 Feb 12 |
nicklas |
2769 |
json.put("id", t.getId()); |
| 1543 |
28 Feb 12 |
nicklas |
2770 |
json.put("status", "ok"); // For now -- more checks below |
| 1543 |
28 Feb 12 |
nicklas |
2771 |
|
| 1543 |
28 Feb 12 |
nicklas |
2772 |
if (t.getBioMaterialType() != plateType.getBioMaterialType()) |
| 1543 |
28 Feb 12 |
nicklas |
2773 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2774 |
json.put("status", "error"); |
| 1543 |
28 Feb 12 |
nicklas |
2775 |
jsonMessages.add("Can't be used by '" + plateType.getBioMaterialType() + "' items."); |
| 1543 |
28 Feb 12 |
nicklas |
2776 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2777 |
|
| 1543 |
28 Feb 12 |
nicklas |
2778 |
Subtype subtype = plateType.getSubtype(); |
| 1543 |
28 Feb 12 |
nicklas |
2779 |
if (subtype != null) |
| 1543 |
28 Feb 12 |
nicklas |
2780 |
{ |
| 1644 |
15 May 12 |
nicklas |
2781 |
ItemSubtype st = subtype.get(dc); |
| 1644 |
15 May 12 |
nicklas |
2782 |
if (st == null || !st.equals(t.getItemSubtype())) |
| 1543 |
28 Feb 12 |
nicklas |
2783 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2784 |
json.put("status", "error"); |
| 1543 |
28 Feb 12 |
nicklas |
2785 |
jsonMessages.add("Should be locked to '" + subtype.getName() + "' (" + subtype.getMainType() + ") items."); |
| 1543 |
28 Feb 12 |
nicklas |
2786 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2787 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2788 |
|
| 1543 |
28 Feb 12 |
nicklas |
2789 |
if (t.getLockMode() != plateType.getLockMode()) |
| 1543 |
28 Feb 12 |
nicklas |
2790 |
{ |
| 1543 |
28 Feb 12 |
nicklas |
2791 |
json.put("status", "error"); |
| 1543 |
28 Feb 12 |
nicklas |
2792 |
jsonMessages.add("Should be using '" + plateType.getLockMode().name() + "' well lock mode"); |
| 1543 |
28 Feb 12 |
nicklas |
2793 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2794 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2795 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1543 |
28 Feb 12 |
nicklas |
2796 |
json.put("messages", jsonMessages); |
| 1543 |
28 Feb 12 |
nicklas |
2797 |
return json; |
| 1543 |
28 Feb 12 |
nicklas |
2798 |
|
| 1543 |
28 Feb 12 |
nicklas |
2799 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2800 |
|
| 1546 |
02 Mar 12 |
nicklas |
2801 |
/** |
| 1865 |
19 Feb 13 |
nicklas |
Create a biomaterial list with the given options. The list is created in |
| 1865 |
19 Feb 13 |
nicklas |
a separate transaction. |
| 1867 |
19 Feb 13 |
nicklas |
@since 2.12 |
| 1865 |
19 Feb 13 |
nicklas |
2805 |
*/ |
| 3247 |
14 Apr 15 |
nicklas |
2806 |
public ItemList createItemList(SessionControl sc, BiomaterialList def, PermissionOptions permissions) |
| 1865 |
19 Feb 13 |
nicklas |
2807 |
{ |
| 3247 |
14 Apr 15 |
nicklas |
2808 |
ItemList list = null; |
| 6328 |
14 Jun 21 |
nicklas |
2809 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1865 |
19 Feb 13 |
nicklas |
2810 |
try |
| 1865 |
19 Feb 13 |
nicklas |
2811 |
{ |
| 3247 |
14 Apr 15 |
nicklas |
2812 |
list = ItemList.getNew(dc, def.getBioMaterialType()); |
| 1865 |
19 Feb 13 |
nicklas |
2813 |
list.setName(def.getName()); |
| 1865 |
19 Feb 13 |
nicklas |
2814 |
list.setExternalId(def.getExternalId()); |
| 3659 |
09 Dec 15 |
nicklas |
2815 |
if (def.getSubtype() != null) |
| 3659 |
09 Dec 15 |
nicklas |
2816 |
{ |
| 3659 |
09 Dec 15 |
nicklas |
2817 |
list.setItemSubtype(def.getSubtype().get(dc)); |
| 3659 |
09 Dec 15 |
nicklas |
2818 |
} |
| 5876 |
24 Mar 20 |
nicklas |
2819 |
if (def.getRawdatatype() != null) |
| 5876 |
24 Mar 20 |
nicklas |
2820 |
{ |
| 5876 |
24 Mar 20 |
nicklas |
2821 |
list.setRawDataType(def.getRawdatatype().getRawDataType()); |
| 5876 |
24 Mar 20 |
nicklas |
2822 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2823 |
list.setDescription(def.getDescription()); |
| 2038 |
03 Oct 13 |
olle |
2824 |
if (permissions != null) permissions.applyPermissions(list); |
| 1865 |
19 Feb 13 |
nicklas |
2825 |
|
| 5876 |
24 Mar 20 |
nicklas |
2826 |
if (def == BiomaterialList.VARIANT_IMPORT_TMP) |
| 5876 |
24 Mar 20 |
nicklas |
2827 |
{ |
| 5876 |
24 Mar 20 |
nicklas |
// Fill this list with all existing variant call raw bioassays |
| 5876 |
24 Mar 20 |
nicklas |
2829 |
ItemQuery<RawBioAssay> query = RawBioAssay.getQuery(); |
| 5876 |
24 Mar 20 |
nicklas |
2830 |
query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT); |
| 5876 |
24 Mar 20 |
nicklas |
2831 |
Rawdatatype.VARIANT_CALL.addFilter(dc, query); |
| 5876 |
24 Mar 20 |
nicklas |
2832 |
list.add(query.iterate(dc)); |
| 5876 |
24 Mar 20 |
nicklas |
2833 |
} |
| 5876 |
24 Mar 20 |
nicklas |
2834 |
|
| 1865 |
19 Feb 13 |
nicklas |
2835 |
dc.saveItem(list); |
| 1865 |
19 Feb 13 |
nicklas |
2836 |
dc.commit(); |
| 1865 |
19 Feb 13 |
nicklas |
2837 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2838 |
finally |
| 1865 |
19 Feb 13 |
nicklas |
2839 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2840 |
if (dc != null) dc.close(); |
| 1865 |
19 Feb 13 |
nicklas |
2841 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2842 |
return list; |
| 1865 |
19 Feb 13 |
nicklas |
2843 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2844 |
|
| 1865 |
19 Feb 13 |
nicklas |
2845 |
|
| 1865 |
19 Feb 13 |
nicklas |
2846 |
/** |
| 1865 |
19 Feb 13 |
nicklas |
Check for an existing biomaterial list with the given options. |
| 1865 |
19 Feb 13 |
nicklas |
A JSONObject is returned with the result. The following |
| 1865 |
19 Feb 13 |
nicklas |
keys are used: |
| 1865 |
19 Feb 13 |
nicklas |
<ul> |
| 3247 |
14 Apr 15 |
nicklas |
<li>itemType: ITEMLIST |
| 1865 |
19 Feb 13 |
nicklas |
<li>name: The name of the biomaterial list |
| 1865 |
19 Feb 13 |
nicklas |
<li>id: The id of the biomaterial list if it exists |
| 1865 |
19 Feb 13 |
nicklas |
<li>bioMaterialType: The bioMaterial type that can be stored in the list |
| 1865 |
19 Feb 13 |
nicklas |
<li>status: ok, error, or missing |
| 1865 |
19 Feb 13 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1865 |
19 Feb 13 |
nicklas |
</ul> |
| 1867 |
19 Feb 13 |
nicklas |
@since 2.12 |
| 1865 |
19 Feb 13 |
nicklas |
2859 |
*/ |
| 5962 |
03 Jun 20 |
nicklas |
2860 |
public JSONObject checkItemList(DbControl dc, BiomaterialList list, boolean checkAutoProcessing, |
| 2038 |
03 Oct 13 |
olle |
2861 |
PermissionOptions permissions, boolean createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
2862 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2863 |
|
| 1865 |
19 Feb 13 |
nicklas |
2864 |
JSONObject json = new JSONObject(); |
| 1865 |
19 Feb 13 |
nicklas |
2865 |
JSONArray jsonMessages = new JSONArray(); |
| 3247 |
14 Apr 15 |
nicklas |
2866 |
json.put("itemType", Item.ITEMLIST.name()); |
| 1865 |
19 Feb 13 |
nicklas |
2867 |
json.put("name", list.getName()); |
| 1865 |
19 Feb 13 |
nicklas |
2868 |
json.put("bioMaterialType", list.getBioMaterialType().name()); |
| 1865 |
19 Feb 13 |
nicklas |
2869 |
|
| 3247 |
14 Apr 15 |
nicklas |
2870 |
List<ItemList> result = list.list(dc); |
| 1865 |
19 Feb 13 |
nicklas |
2871 |
if (result.size() == 0) |
| 1865 |
19 Feb 13 |
nicklas |
2872 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2873 |
if (createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
2874 |
{ |
| 3247 |
14 Apr 15 |
nicklas |
2875 |
ItemList l = createItemList(dc.getSessionControl(), list, permissions); |
| 1865 |
19 Feb 13 |
nicklas |
2876 |
json.put("id", l.getId()); |
| 1865 |
19 Feb 13 |
nicklas |
2877 |
json.put("status", "ok"); |
| 1865 |
19 Feb 13 |
nicklas |
2878 |
jsonMessages.add("Created"); |
| 1865 |
19 Feb 13 |
nicklas |
2879 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2880 |
else |
| 1865 |
19 Feb 13 |
nicklas |
2881 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2882 |
json.put("status", "missing"); |
| 1865 |
19 Feb 13 |
nicklas |
2883 |
jsonMessages.add("Not found"); |
| 1865 |
19 Feb 13 |
nicklas |
2884 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2885 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2886 |
else if (result.size() > 1) |
| 1865 |
19 Feb 13 |
nicklas |
2887 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2888 |
json.put("status", "error"); |
| 1865 |
19 Feb 13 |
nicklas |
2889 |
jsonMessages.add("Found > 1 biomaterial list"); |
| 1865 |
19 Feb 13 |
nicklas |
2890 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2891 |
else |
| 1865 |
19 Feb 13 |
nicklas |
2892 |
{ |
| 3247 |
14 Apr 15 |
nicklas |
2893 |
ItemList l = result.get(0); |
| 1865 |
19 Feb 13 |
nicklas |
2894 |
json.put("id", l.getId()); |
| 1865 |
19 Feb 13 |
nicklas |
2895 |
json.put("status", "ok"); // For now -- more checks below |
| 1865 |
19 Feb 13 |
nicklas |
2896 |
|
| 1865 |
19 Feb 13 |
nicklas |
2897 |
if (l.getMemberType() != list.getBioMaterialType()) |
| 1865 |
19 Feb 13 |
nicklas |
2898 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
2899 |
json.put("status", "error"); |
| 1865 |
19 Feb 13 |
nicklas |
2900 |
jsonMessages.add("Can't be used by '" + list.getBioMaterialType() + "' items."); |
| 1865 |
19 Feb 13 |
nicklas |
2901 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2902 |
|
| 3659 |
09 Dec 15 |
nicklas |
2903 |
Subtype subtype = list.getSubtype(); |
| 3659 |
09 Dec 15 |
nicklas |
2904 |
if (subtype != null) |
| 3659 |
09 Dec 15 |
nicklas |
2905 |
{ |
| 3659 |
09 Dec 15 |
nicklas |
2906 |
if (!subtype.get(dc).equals(l.getItemSubtype())) |
| 3659 |
09 Dec 15 |
nicklas |
2907 |
{ |
| 3659 |
09 Dec 15 |
nicklas |
2908 |
if (createIfMissing) |
| 3659 |
09 Dec 15 |
nicklas |
2909 |
{ |
| 3659 |
09 Dec 15 |
nicklas |
2910 |
l.setItemSubtype(subtype.get(dc)); |
| 3659 |
09 Dec 15 |
nicklas |
2911 |
jsonMessages.add("Fixed"); |
| 3659 |
09 Dec 15 |
nicklas |
2912 |
} |
| 3659 |
09 Dec 15 |
nicklas |
2913 |
else |
| 3659 |
09 Dec 15 |
nicklas |
2914 |
{ |
| 3659 |
09 Dec 15 |
nicklas |
2915 |
json.put("status", "incomplete"); |
| 3659 |
09 Dec 15 |
nicklas |
2916 |
jsonMessages.add("Should be be set to '" + subtype.getName() + "'"); |
| 3659 |
09 Dec 15 |
nicklas |
2917 |
} |
| 3659 |
09 Dec 15 |
nicklas |
2918 |
} |
| 3659 |
09 Dec 15 |
nicklas |
2919 |
} |
| 3659 |
09 Dec 15 |
nicklas |
2920 |
|
| 5962 |
03 Jun 20 |
nicklas |
2921 |
if (checkAutoProcessing) |
| 4624 |
17 Nov 17 |
nicklas |
2922 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
2923 |
AnnotationType autoProc = Annotationtype.AUTO_PROCESSING.get(dc); |
| 5962 |
03 Jun 20 |
nicklas |
2924 |
if (autoProc != null) |
| 4624 |
17 Nov 17 |
nicklas |
2925 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
2926 |
boolean disabled = "Disable".equals(Annotationtype.AUTO_PROCESSING.getAnnotationValue(dc, l)); |
| 5962 |
03 Jun 20 |
nicklas |
2927 |
if (disabled) |
| 5962 |
03 Jun 20 |
nicklas |
2928 |
{ |
| 5962 |
03 Jun 20 |
nicklas |
2929 |
json.put("status", "warning"); |
| 5962 |
03 Jun 20 |
nicklas |
2930 |
jsonMessages.add("Auto-processing is disabled. It can be enabled by clearing the AutoProcessing annotation."); |
| 5962 |
03 Jun 20 |
nicklas |
2931 |
} |
| 4624 |
17 Nov 17 |
nicklas |
2932 |
} |
| 4624 |
17 Nov 17 |
nicklas |
2933 |
} |
| 4624 |
17 Nov 17 |
nicklas |
2934 |
|
| 2038 |
03 Oct 13 |
olle |
2935 |
if (permissions != null && !permissions.checkPermissions(l)) |
| 2038 |
03 Oct 13 |
olle |
2936 |
{ |
| 2038 |
03 Oct 13 |
olle |
2937 |
if (createIfMissing) |
| 2038 |
03 Oct 13 |
olle |
2938 |
{ |
| 2038 |
03 Oct 13 |
olle |
2939 |
permissions.applyPermissions(l); |
| 2038 |
03 Oct 13 |
olle |
2940 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 2038 |
03 Oct 13 |
olle |
2941 |
} |
| 2038 |
03 Oct 13 |
olle |
2942 |
else |
| 2038 |
03 Oct 13 |
olle |
2943 |
{ |
| 2038 |
03 Oct 13 |
olle |
2944 |
json.put("status", "incomplete"); |
| 2038 |
03 Oct 13 |
olle |
2945 |
jsonMessages.add(permissions.getMessage()); |
| 2038 |
03 Oct 13 |
olle |
2946 |
} |
| 2038 |
03 Oct 13 |
olle |
2947 |
} |
| 2038 |
03 Oct 13 |
olle |
2948 |
|
| 1865 |
19 Feb 13 |
nicklas |
2949 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2950 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1865 |
19 Feb 13 |
nicklas |
2951 |
json.put("messages", jsonMessages); |
| 1865 |
19 Feb 13 |
nicklas |
2952 |
return json; |
| 1865 |
19 Feb 13 |
nicklas |
2953 |
} |
| 1865 |
19 Feb 13 |
nicklas |
2954 |
|
| 1865 |
19 Feb 13 |
nicklas |
2955 |
|
| 1865 |
19 Feb 13 |
nicklas |
2956 |
/** |
| 1546 |
02 Mar 12 |
nicklas |
Create a MIME type with the given options. The type is created in |
| 1546 |
02 Mar 12 |
nicklas |
a separate transaction. |
| 1546 |
02 Mar 12 |
nicklas |
@since 2.4 |
| 1546 |
02 Mar 12 |
nicklas |
2960 |
*/ |
| 1546 |
02 Mar 12 |
nicklas |
2961 |
public MimeType createMimeType(SessionControl sc, Mimetype def) |
| 1546 |
02 Mar 12 |
nicklas |
2962 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
2963 |
MimeType type = null; |
| 6328 |
14 Jun 21 |
nicklas |
2964 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1546 |
02 Mar 12 |
nicklas |
2965 |
try |
| 1546 |
02 Mar 12 |
nicklas |
2966 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
2967 |
type = MimeType.getNew(dc); |
| 1546 |
02 Mar 12 |
nicklas |
2968 |
type.setName(def.getMimeType()); |
| 1546 |
02 Mar 12 |
nicklas |
2969 |
type.setExtension(def.getExtension()); |
| 1546 |
02 Mar 12 |
nicklas |
2970 |
type.setDescription(def.getDescription()); |
| 1546 |
02 Mar 12 |
nicklas |
2971 |
if (def.getFileType() != null) |
| 1546 |
02 Mar 12 |
nicklas |
2972 |
{ |
| 1644 |
15 May 12 |
nicklas |
2973 |
ItemSubtype subtype = def.getFileType().get(dc); |
| 1644 |
15 May 12 |
nicklas |
2974 |
if (subtype != null) type.setFileType(subtype); |
| 1546 |
02 Mar 12 |
nicklas |
2975 |
} |
| 1546 |
02 Mar 12 |
nicklas |
2976 |
|
| 1546 |
02 Mar 12 |
nicklas |
2977 |
dc.saveItem(type); |
| 1546 |
02 Mar 12 |
nicklas |
2978 |
dc.commit(); |
| 1546 |
02 Mar 12 |
nicklas |
2979 |
} |
| 1546 |
02 Mar 12 |
nicklas |
2980 |
finally |
| 1546 |
02 Mar 12 |
nicklas |
2981 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
2982 |
if (dc != null) dc.close(); |
| 1546 |
02 Mar 12 |
nicklas |
2983 |
} |
| 1546 |
02 Mar 12 |
nicklas |
2984 |
return type; |
| 1546 |
02 Mar 12 |
nicklas |
2985 |
} |
| 1543 |
28 Feb 12 |
nicklas |
2986 |
|
| 1546 |
02 Mar 12 |
nicklas |
2987 |
|
| 1543 |
28 Feb 12 |
nicklas |
2988 |
/** |
| 1546 |
02 Mar 12 |
nicklas |
Check for an existing MIME type with the given options. |
| 1546 |
02 Mar 12 |
nicklas |
A JSONObject is returned with the result. The following |
| 1546 |
02 Mar 12 |
nicklas |
keys are used: |
| 1546 |
02 Mar 12 |
nicklas |
<ul> |
| 1546 |
02 Mar 12 |
nicklas |
<li>itemType: MIMETYPE |
| 1546 |
02 Mar 12 |
nicklas |
<li>name: The name of the subtype |
| 1546 |
02 Mar 12 |
nicklas |
<li>id: The id of the subtype if it exists |
| 1546 |
02 Mar 12 |
nicklas |
<li>mainType: The main item type that the subtype applies to |
| 1546 |
02 Mar 12 |
nicklas |
<li>status: ok, error, or missing |
| 1546 |
02 Mar 12 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1546 |
02 Mar 12 |
nicklas |
</ul> |
| 1546 |
02 Mar 12 |
nicklas |
@since 2.4 |
| 1546 |
02 Mar 12 |
nicklas |
3001 |
*/ |
| 1546 |
02 Mar 12 |
nicklas |
3002 |
public JSONObject checkMimeType(DbControl dc, Mimetype mimeType, |
| 1546 |
02 Mar 12 |
nicklas |
3003 |
boolean createIfMissing) |
| 1546 |
02 Mar 12 |
nicklas |
3004 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
3005 |
|
| 1546 |
02 Mar 12 |
nicklas |
3006 |
JSONObject json = new JSONObject(); |
| 1546 |
02 Mar 12 |
nicklas |
3007 |
JSONArray jsonMessages = new JSONArray(); |
| 1546 |
02 Mar 12 |
nicklas |
3008 |
json.put("itemType", Item.MIMETYPE.name()); |
| 1546 |
02 Mar 12 |
nicklas |
3009 |
json.put("name", mimeType.getDescription()); |
| 1546 |
02 Mar 12 |
nicklas |
3010 |
json.put("mimeType", mimeType.getMimeType()); |
| 1546 |
02 Mar 12 |
nicklas |
3011 |
json.put("extension", mimeType.getExtension()); |
| 1865 |
19 Feb 13 |
nicklas |
3012 |
|
| 1546 |
02 Mar 12 |
nicklas |
3013 |
List<MimeType> result = mimeType.list(dc); |
| 1546 |
02 Mar 12 |
nicklas |
3014 |
if (result.size() == 0) |
| 1546 |
02 Mar 12 |
nicklas |
3015 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
3016 |
if (createIfMissing) |
| 1546 |
02 Mar 12 |
nicklas |
3017 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
3018 |
MimeType type = createMimeType(dc.getSessionControl(), mimeType); |
| 1546 |
02 Mar 12 |
nicklas |
3019 |
json.put("id", type.getId()); |
| 1546 |
02 Mar 12 |
nicklas |
3020 |
json.put("status", "ok"); |
| 1546 |
02 Mar 12 |
nicklas |
3021 |
jsonMessages.add("Created"); |
| 1546 |
02 Mar 12 |
nicklas |
3022 |
} |
| 1546 |
02 Mar 12 |
nicklas |
3023 |
else |
| 1546 |
02 Mar 12 |
nicklas |
3024 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
3025 |
json.put("status", "missing"); |
| 1546 |
02 Mar 12 |
nicklas |
3026 |
jsonMessages.add("Not found"); |
| 1546 |
02 Mar 12 |
nicklas |
3027 |
} |
| 1546 |
02 Mar 12 |
nicklas |
3028 |
} |
| 1546 |
02 Mar 12 |
nicklas |
3029 |
else if (result.size() > 1) |
| 1546 |
02 Mar 12 |
nicklas |
3030 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
3031 |
json.put("status", "error"); |
| 1546 |
02 Mar 12 |
nicklas |
3032 |
jsonMessages.add("Found > 1 MIME type"); |
| 1546 |
02 Mar 12 |
nicklas |
3033 |
} |
| 1546 |
02 Mar 12 |
nicklas |
3034 |
else |
| 1546 |
02 Mar 12 |
nicklas |
3035 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
3036 |
MimeType s = result.get(0); |
| 1546 |
02 Mar 12 |
nicklas |
3037 |
json.put("id", s.getId()); |
| 1546 |
02 Mar 12 |
nicklas |
3038 |
json.put("status", "ok"); // For now -- more checks below |
| 1546 |
02 Mar 12 |
nicklas |
3039 |
|
| 1546 |
02 Mar 12 |
nicklas |
3040 |
if (!s.getName().equals(mimeType.getMimeType())) |
| 1546 |
02 Mar 12 |
nicklas |
3041 |
{ |
| 1546 |
02 Mar 12 |
nicklas |
3042 |
json.put("status", "error"); |
| 1546 |
02 Mar 12 |
nicklas |
3043 |
jsonMessages.add("Should have '" + mimeType.getMimeType() + "' as MIME type."); |
| 1546 |
02 Mar 12 |
nicklas |
3044 |
} |
| 1546 |
02 Mar 12 |
nicklas |
3045 |
|
| 1546 |
02 Mar 12 |
nicklas |
3046 |
} |
| 1546 |
02 Mar 12 |
nicklas |
3047 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1546 |
02 Mar 12 |
nicklas |
3048 |
json.put("messages", jsonMessages); |
| 1546 |
02 Mar 12 |
nicklas |
3049 |
return json; |
| 1546 |
02 Mar 12 |
nicklas |
3050 |
|
| 1546 |
02 Mar 12 |
nicklas |
3051 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3052 |
|
| 1865 |
19 Feb 13 |
nicklas |
3053 |
|
| 1606 |
19 Apr 12 |
nicklas |
3054 |
/** |
| 2562 |
08 Aug 14 |
nicklas |
Create a file server with the given options. The file server is created in |
| 2562 |
08 Aug 14 |
nicklas |
a separate transaction. |
| 2562 |
08 Aug 14 |
nicklas |
@since 2.16 |
| 2562 |
08 Aug 14 |
nicklas |
3058 |
*/ |
| 2562 |
08 Aug 14 |
nicklas |
3059 |
public FileServer createFileServer(SessionControl sc, Fileserver def, PermissionOptions permissions) |
| 2562 |
08 Aug 14 |
nicklas |
3060 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3061 |
FileServer fs = null; |
| 6328 |
14 Jun 21 |
nicklas |
3062 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 2562 |
08 Aug 14 |
nicklas |
3063 |
try |
| 2562 |
08 Aug 14 |
nicklas |
3064 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3065 |
fs = FileServer.getNew(dc); |
| 2562 |
08 Aug 14 |
nicklas |
3066 |
fs.setName(def.getName()); |
| 2562 |
08 Aug 14 |
nicklas |
3067 |
fs.setConnectionManagerFactoryId(def.getConnectionManagerId()); |
| 2562 |
08 Aug 14 |
nicklas |
3068 |
fs.setDescription(def.getDescription()); |
| 2562 |
08 Aug 14 |
nicklas |
3069 |
if (permissions != null) permissions.applyPermissions(fs); |
| 2562 |
08 Aug 14 |
nicklas |
3070 |
|
| 2562 |
08 Aug 14 |
nicklas |
3071 |
dc.saveItem(fs); |
| 2562 |
08 Aug 14 |
nicklas |
3072 |
dc.commit(); |
| 2562 |
08 Aug 14 |
nicklas |
3073 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3074 |
finally |
| 2562 |
08 Aug 14 |
nicklas |
3075 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3076 |
if (dc != null) dc.close(); |
| 2562 |
08 Aug 14 |
nicklas |
3077 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3078 |
return fs; |
| 2562 |
08 Aug 14 |
nicklas |
3079 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3080 |
|
| 2562 |
08 Aug 14 |
nicklas |
3081 |
|
| 2562 |
08 Aug 14 |
nicklas |
3082 |
/** |
| 2562 |
08 Aug 14 |
nicklas |
Check for an existing file server with the given options. |
| 2562 |
08 Aug 14 |
nicklas |
A JSONObject is returned with the result. The following |
| 2562 |
08 Aug 14 |
nicklas |
keys are used: |
| 2562 |
08 Aug 14 |
nicklas |
<ul> |
| 2562 |
08 Aug 14 |
nicklas |
<li>itemType: FILESERVER |
| 2562 |
08 Aug 14 |
nicklas |
<li>name: The name of the fileserver |
| 2562 |
08 Aug 14 |
nicklas |
<li>id: The id of the fileserver if it exists |
| 2562 |
08 Aug 14 |
nicklas |
<li>status: ok, error, or missing |
| 2562 |
08 Aug 14 |
nicklas |
<li>message: A descriptive message in case of an error |
| 2562 |
08 Aug 14 |
nicklas |
</ul> |
| 2562 |
08 Aug 14 |
nicklas |
@since 2.16 |
| 2562 |
08 Aug 14 |
nicklas |
3094 |
*/ |
| 2562 |
08 Aug 14 |
nicklas |
3095 |
public JSONObject checkFileServer(DbControl dc, Fileserver fileServer, |
| 2562 |
08 Aug 14 |
nicklas |
3096 |
PermissionOptions permissions, boolean createIfMissing) |
| 2562 |
08 Aug 14 |
nicklas |
3097 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3098 |
|
| 2562 |
08 Aug 14 |
nicklas |
3099 |
JSONObject json = new JSONObject(); |
| 2562 |
08 Aug 14 |
nicklas |
3100 |
JSONArray jsonMessages = new JSONArray(); |
| 2562 |
08 Aug 14 |
nicklas |
3101 |
json.put("itemType", Item.FILESERVER.name()); |
| 2562 |
08 Aug 14 |
nicklas |
3102 |
json.put("name", fileServer.getName()); |
| 2562 |
08 Aug 14 |
nicklas |
3103 |
|
| 2562 |
08 Aug 14 |
nicklas |
3104 |
FileServer fs = null; |
| 2562 |
08 Aug 14 |
nicklas |
3105 |
List<FileServer> result = fileServer.list(dc); |
| 2562 |
08 Aug 14 |
nicklas |
3106 |
if (result.size() == 0) |
| 2562 |
08 Aug 14 |
nicklas |
3107 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3108 |
if (createIfMissing) |
| 2562 |
08 Aug 14 |
nicklas |
3109 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3110 |
fs = createFileServer(dc.getSessionControl(), fileServer, permissions); |
| 2562 |
08 Aug 14 |
nicklas |
3111 |
fs = FileServer.getById(dc, fs.getId()); |
| 2562 |
08 Aug 14 |
nicklas |
3112 |
json.put("id", fs.getId()); |
| 2562 |
08 Aug 14 |
nicklas |
// Not ok yet, need manual configuration which is checked below |
| 2562 |
08 Aug 14 |
nicklas |
3114 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3115 |
else |
| 2562 |
08 Aug 14 |
nicklas |
3116 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3117 |
json.put("status", "missing"); |
| 2562 |
08 Aug 14 |
nicklas |
3118 |
jsonMessages.add("Not found"); |
| 2562 |
08 Aug 14 |
nicklas |
3119 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3120 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3121 |
else if (result.size() > 1) |
| 2562 |
08 Aug 14 |
nicklas |
3122 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3123 |
json.put("status", "error"); |
| 2562 |
08 Aug 14 |
nicklas |
3124 |
jsonMessages.add("Found > 1 file server"); |
| 2562 |
08 Aug 14 |
nicklas |
3125 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3126 |
else |
| 2562 |
08 Aug 14 |
nicklas |
3127 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3128 |
fs = result.get(0); |
| 2562 |
08 Aug 14 |
nicklas |
3129 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3130 |
|
| 2562 |
08 Aug 14 |
nicklas |
3131 |
if (fs != null) |
| 2562 |
08 Aug 14 |
nicklas |
3132 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3133 |
json.put("id", fs.getId()); |
| 2562 |
08 Aug 14 |
nicklas |
3134 |
json.put("status", "ok"); // For now -- more checks below |
| 2562 |
08 Aug 14 |
nicklas |
3135 |
|
| 2562 |
08 Aug 14 |
nicklas |
3136 |
if (permissions != null && !permissions.checkPermissions(fs)) |
| 2562 |
08 Aug 14 |
nicklas |
3137 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3138 |
if (createIfMissing) |
| 2562 |
08 Aug 14 |
nicklas |
3139 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3140 |
permissions.applyPermissions(fs); |
| 2562 |
08 Aug 14 |
nicklas |
3141 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 2562 |
08 Aug 14 |
nicklas |
3142 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3143 |
else |
| 2562 |
08 Aug 14 |
nicklas |
3144 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3145 |
json.put("status", "incomplete"); |
| 2562 |
08 Aug 14 |
nicklas |
3146 |
jsonMessages.add(permissions.getMessage()); |
| 2562 |
08 Aug 14 |
nicklas |
3147 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3148 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3149 |
|
| 2562 |
08 Aug 14 |
nicklas |
3150 |
if (!fileServer.getConnectionManagerId().equals(fs.getConnectionManagerFactoryId())) |
| 2562 |
08 Aug 14 |
nicklas |
3151 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3152 |
if (createIfMissing) |
| 2562 |
08 Aug 14 |
nicklas |
3153 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3154 |
fs.setConnectionManagerFactoryId(fileServer.getConnectionManagerId()); |
| 2562 |
08 Aug 14 |
nicklas |
3155 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3156 |
else |
| 2562 |
08 Aug 14 |
nicklas |
3157 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3158 |
json.put("status", "incomplete"); |
| 2562 |
08 Aug 14 |
nicklas |
3159 |
jsonMessages.add("Should use SFTP connection manager"); |
| 2562 |
08 Aug 14 |
nicklas |
3160 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3161 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3162 |
|
| 2562 |
08 Aug 14 |
nicklas |
3163 |
if (fs.getHost() == null) |
| 2562 |
08 Aug 14 |
nicklas |
3164 |
{ |
| 2715 |
30 Sep 14 |
nicklas |
3165 |
json.put("status", "warning"); |
| 2562 |
08 Aug 14 |
nicklas |
3166 |
jsonMessages.add("No host name configured"); |
| 2562 |
08 Aug 14 |
nicklas |
3167 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3168 |
|
| 2562 |
08 Aug 14 |
nicklas |
3169 |
if (fs.getUsername() == null) |
| 2562 |
08 Aug 14 |
nicklas |
3170 |
{ |
| 2715 |
30 Sep 14 |
nicklas |
3171 |
json.put("status", "warning"); |
| 2562 |
08 Aug 14 |
nicklas |
3172 |
jsonMessages.add("No user configured"); |
| 2562 |
08 Aug 14 |
nicklas |
3173 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3174 |
|
| 5577 |
16 Aug 19 |
nicklas |
3175 |
if (!fs.hasPassword() && !fs.hasSshPrivateKey()) |
| 2562 |
08 Aug 14 |
nicklas |
3176 |
{ |
| 2715 |
30 Sep 14 |
nicklas |
3177 |
json.put("status", "warning"); |
| 5577 |
16 Aug 19 |
nicklas |
3178 |
jsonMessages.add("No password or private-key configured"); |
| 2562 |
08 Aug 14 |
nicklas |
3179 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3180 |
|
| 2562 |
08 Aug 14 |
nicklas |
3181 |
if (fs.getRootPath() == null) |
| 2562 |
08 Aug 14 |
nicklas |
3182 |
{ |
| 2715 |
30 Sep 14 |
nicklas |
3183 |
json.put("status", "warning"); |
| 2562 |
08 Aug 14 |
nicklas |
3184 |
jsonMessages.add("No root path configured"); |
| 2562 |
08 Aug 14 |
nicklas |
3185 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3186 |
|
| 2562 |
08 Aug 14 |
nicklas |
3187 |
if (fs.getSshFingerprint() == null) |
| 2562 |
08 Aug 14 |
nicklas |
3188 |
{ |
| 2715 |
30 Sep 14 |
nicklas |
3189 |
json.put("status", "warning"); |
| 2562 |
08 Aug 14 |
nicklas |
3190 |
jsonMessages.add("No SSH fingerprint configured"); |
| 2562 |
08 Aug 14 |
nicklas |
3191 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3192 |
|
| 2562 |
08 Aug 14 |
nicklas |
3193 |
if (json.get("status").equals("ok")) |
| 2562 |
08 Aug 14 |
nicklas |
3194 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3195 |
ConnectionManagerFactory cmf = ConnectionManagerUtil.getFactory(fs.getConnectionManagerFactoryId()); |
| 2562 |
08 Aug 14 |
nicklas |
3196 |
if (cmf == null) |
| 2562 |
08 Aug 14 |
nicklas |
3197 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3198 |
json.put("status", "warning"); |
| 2562 |
08 Aug 14 |
nicklas |
3199 |
jsonMessages.add("SFTP connection manager is not installed"); |
| 2562 |
08 Aug 14 |
nicklas |
3200 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3201 |
else |
| 2562 |
08 Aug 14 |
nicklas |
3202 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3203 |
ConnectionParameters cp = new ConnectionParameters(); |
| 2562 |
08 Aug 14 |
nicklas |
3204 |
cp.setHost(fs.getHost()); |
| 2562 |
08 Aug 14 |
nicklas |
3205 |
cp.setUsername(fs.getUsername()); |
| 2562 |
08 Aug 14 |
nicklas |
3206 |
cp.setPassword(fs.getPassword()); |
| 2562 |
08 Aug 14 |
nicklas |
3207 |
cp.setRootPath(fs.getRootPath()); |
| 2562 |
08 Aug 14 |
nicklas |
3208 |
cp.setSshFingerprint(fs.getSshFingerprint()); |
| 5577 |
16 Aug 19 |
nicklas |
3209 |
byte[] privateKey = fs.getSshPrivateKey(); |
| 5577 |
16 Aug 19 |
nicklas |
3210 |
if (privateKey != null && privateKey.length > 0) |
| 5577 |
16 Aug 19 |
nicklas |
3211 |
{ |
| 5577 |
16 Aug 19 |
nicklas |
3212 |
cp.setSshPrivateKey(privateKey); |
| 5577 |
16 Aug 19 |
nicklas |
3213 |
cp.setSshPrivateKeyPassword(fs.getSshPrivateKeyPassword()); |
| 5577 |
16 Aug 19 |
nicklas |
3214 |
cp.setSshPrivateKeyFormat(fs.getSshPrivateKeyFormat()); |
| 5577 |
16 Aug 19 |
nicklas |
3215 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3216 |
URI uri = cp.changeHost(URI.create("sftp://" + fs.getHost() + "/")); |
| 2562 |
08 Aug 14 |
nicklas |
3217 |
ConnectionManager cm = cmf.createConnectionManager(uri, cp); |
| 2562 |
08 Aug 14 |
nicklas |
3218 |
try |
| 2562 |
08 Aug 14 |
nicklas |
3219 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3220 |
UriMetadata meta = cm.getMetadata(); |
| 2562 |
08 Aug 14 |
nicklas |
3221 |
} |
| 5577 |
16 Aug 19 |
nicklas |
3222 |
catch (Exception ex) |
| 2562 |
08 Aug 14 |
nicklas |
3223 |
{ |
| 2562 |
08 Aug 14 |
nicklas |
3224 |
json.put("status", "warning"); |
| 5577 |
16 Aug 19 |
nicklas |
3225 |
json.put("stacktrace", ThrowableUtil.stackTraceToString(ex)); |
| 2562 |
08 Aug 14 |
nicklas |
3226 |
jsonMessages.add(uri + ": " + ex.getMessage()); |
| 2562 |
08 Aug 14 |
nicklas |
3227 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3228 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3229 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3230 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3231 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 2562 |
08 Aug 14 |
nicklas |
3232 |
json.put("messages", jsonMessages); |
| 2562 |
08 Aug 14 |
nicklas |
3233 |
return json; |
| 2562 |
08 Aug 14 |
nicklas |
3234 |
|
| 2562 |
08 Aug 14 |
nicklas |
3235 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3236 |
|
| 3600 |
13 Nov 15 |
nicklas |
3237 |
/** |
| 3600 |
13 Nov 15 |
nicklas |
Create a directory with the given options. The directory is created in |
| 3600 |
13 Nov 15 |
nicklas |
a separate transaction. |
| 3600 |
13 Nov 15 |
nicklas |
@since 4.0 |
| 3600 |
13 Nov 15 |
nicklas |
3241 |
*/ |
| 4028 |
26 Jul 16 |
nicklas |
3242 |
public Directory createDirectory(SessionControl sc, Path path, PermissionOptions... permissions) |
| 3600 |
13 Nov 15 |
nicklas |
3243 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3244 |
Directory d = null; |
| 6328 |
14 Jun 21 |
nicklas |
3245 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 3600 |
13 Nov 15 |
nicklas |
3246 |
try |
| 3600 |
13 Nov 15 |
nicklas |
3247 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3248 |
d = Directory.getNew(dc, path); |
| 4028 |
26 Jul 16 |
nicklas |
3249 |
if (permissions != null) |
| 4028 |
26 Jul 16 |
nicklas |
3250 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3251 |
for (PermissionOptions p : permissions) |
| 4028 |
26 Jul 16 |
nicklas |
3252 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3253 |
p.applyPermissions(d); |
| 4028 |
26 Jul 16 |
nicklas |
3254 |
} |
| 4028 |
26 Jul 16 |
nicklas |
3255 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3256 |
dc.saveItem(d); |
| 3600 |
13 Nov 15 |
nicklas |
3257 |
dc.commit(); |
| 3600 |
13 Nov 15 |
nicklas |
3258 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3259 |
finally |
| 3600 |
13 Nov 15 |
nicklas |
3260 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3261 |
if (dc != null) dc.close(); |
| 3600 |
13 Nov 15 |
nicklas |
3262 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3263 |
return d; |
| 3600 |
13 Nov 15 |
nicklas |
3264 |
} |
| 2562 |
08 Aug 14 |
nicklas |
3265 |
|
| 2562 |
08 Aug 14 |
nicklas |
3266 |
/** |
| 3600 |
13 Nov 15 |
nicklas |
Check for an existing directory. |
| 3600 |
13 Nov 15 |
nicklas |
A JSONObject is returned with the result. The following |
| 3600 |
13 Nov 15 |
nicklas |
keys are used: |
| 3600 |
13 Nov 15 |
nicklas |
<ul> |
| 3600 |
13 Nov 15 |
nicklas |
<li>itemType: DIRECTORY |
| 3600 |
13 Nov 15 |
nicklas |
<li>name: The full path of the directory |
| 3600 |
13 Nov 15 |
nicklas |
<li>id: The id of the directory if it exists |
| 3600 |
13 Nov 15 |
nicklas |
<li>status: ok, error, or missing |
| 3600 |
13 Nov 15 |
nicklas |
<li>message: A descriptive message in case of an error |
| 3600 |
13 Nov 15 |
nicklas |
</ul> |
| 3600 |
13 Nov 15 |
nicklas |
@since 4.0 |
| 3600 |
13 Nov 15 |
nicklas |
3278 |
*/ |
| 3600 |
13 Nov 15 |
nicklas |
3279 |
public JSONObject checkDirectory(DbControl dc, String name, |
| 4028 |
26 Jul 16 |
nicklas |
3280 |
boolean createIfMissing, PermissionOptions... permissions) |
| 3600 |
13 Nov 15 |
nicklas |
3281 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3282 |
|
| 3600 |
13 Nov 15 |
nicklas |
3283 |
JSONObject json = new JSONObject(); |
| 3600 |
13 Nov 15 |
nicklas |
3284 |
JSONArray jsonMessages = new JSONArray(); |
| 3600 |
13 Nov 15 |
nicklas |
3285 |
json.put("itemType", Item.DIRECTORY.name()); |
| 3600 |
13 Nov 15 |
nicklas |
3286 |
json.put("name", name); |
| 3600 |
13 Nov 15 |
nicklas |
3287 |
|
| 3600 |
13 Nov 15 |
nicklas |
3288 |
Directory d = null; |
| 3600 |
13 Nov 15 |
nicklas |
3289 |
Path path = new Path(name, Path.Type.DIRECTORY); |
| 3600 |
13 Nov 15 |
nicklas |
3290 |
try |
| 3600 |
13 Nov 15 |
nicklas |
3291 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3292 |
d = Directory.getByPath(dc, path); |
| 3600 |
13 Nov 15 |
nicklas |
3293 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3294 |
catch (RuntimeException ex) |
| 3600 |
13 Nov 15 |
nicklas |
3295 |
{} |
| 3600 |
13 Nov 15 |
nicklas |
3296 |
|
| 3600 |
13 Nov 15 |
nicklas |
3297 |
if (d == null) |
| 3600 |
13 Nov 15 |
nicklas |
3298 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3299 |
if (createIfMissing) |
| 3600 |
13 Nov 15 |
nicklas |
3300 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3301 |
d = createDirectory(dc.getSessionControl(), path, permissions); |
| 3600 |
13 Nov 15 |
nicklas |
3302 |
d = Directory.getById(dc, d.getId()); |
| 3600 |
13 Nov 15 |
nicklas |
3303 |
json.put("id", d.getId()); |
| 3600 |
13 Nov 15 |
nicklas |
3304 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3305 |
else |
| 3600 |
13 Nov 15 |
nicklas |
3306 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3307 |
json.put("status", "missing"); |
| 3600 |
13 Nov 15 |
nicklas |
3308 |
jsonMessages.add("Not found"); |
| 3600 |
13 Nov 15 |
nicklas |
3309 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3310 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3311 |
|
| 3600 |
13 Nov 15 |
nicklas |
3312 |
if (d != null) |
| 3600 |
13 Nov 15 |
nicklas |
3313 |
{ |
| 3600 |
13 Nov 15 |
nicklas |
3314 |
json.put("id", d.getId()); |
| 3600 |
13 Nov 15 |
nicklas |
3315 |
json.put("status", "ok"); // For now -- more checks below |
| 3600 |
13 Nov 15 |
nicklas |
3316 |
|
| 4028 |
26 Jul 16 |
nicklas |
3317 |
if (permissions != null) |
| 3600 |
13 Nov 15 |
nicklas |
3318 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3319 |
String permissionCheck = null; |
| 4028 |
26 Jul 16 |
nicklas |
3320 |
for (PermissionOptions p : permissions) |
| 3600 |
13 Nov 15 |
nicklas |
3321 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3322 |
if (!p.checkPermissions(d)) |
| 4028 |
26 Jul 16 |
nicklas |
3323 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3324 |
permissionCheck = p.getMessage(); |
| 4028 |
26 Jul 16 |
nicklas |
3325 |
break; |
| 4028 |
26 Jul 16 |
nicklas |
3326 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3327 |
} |
| 4028 |
26 Jul 16 |
nicklas |
3328 |
|
| 4028 |
26 Jul 16 |
nicklas |
3329 |
if (permissionCheck != null) |
| 3600 |
13 Nov 15 |
nicklas |
3330 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3331 |
if (createIfMissing) |
| 4028 |
26 Jul 16 |
nicklas |
3332 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3333 |
for (PermissionOptions p : permissions) |
| 4028 |
26 Jul 16 |
nicklas |
3334 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3335 |
p.applyPermissions(d); |
| 4028 |
26 Jul 16 |
nicklas |
3336 |
} |
| 4028 |
26 Jul 16 |
nicklas |
3337 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 4028 |
26 Jul 16 |
nicklas |
3338 |
} |
| 4028 |
26 Jul 16 |
nicklas |
3339 |
else |
| 4028 |
26 Jul 16 |
nicklas |
3340 |
{ |
| 4028 |
26 Jul 16 |
nicklas |
3341 |
json.put("status", "incomplete"); |
| 4028 |
26 Jul 16 |
nicklas |
3342 |
jsonMessages.add(permissionCheck); |
| 4028 |
26 Jul 16 |
nicklas |
3343 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3344 |
} |
| 4028 |
26 Jul 16 |
nicklas |
3345 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3346 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3347 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 3600 |
13 Nov 15 |
nicklas |
3348 |
json.put("messages", jsonMessages); |
| 3600 |
13 Nov 15 |
nicklas |
3349 |
return json; |
| 3600 |
13 Nov 15 |
nicklas |
3350 |
} |
| 3600 |
13 Nov 15 |
nicklas |
3351 |
|
| 3600 |
13 Nov 15 |
nicklas |
3352 |
|
| 3600 |
13 Nov 15 |
nicklas |
3353 |
/** |
| 2565 |
11 Aug 14 |
nicklas |
Create a data file type with the given options. The type is created in |
| 2565 |
11 Aug 14 |
nicklas |
a separate transaction. |
| 2565 |
11 Aug 14 |
nicklas |
@since 2.16 |
| 2565 |
11 Aug 14 |
nicklas |
3357 |
*/ |
| 2565 |
11 Aug 14 |
nicklas |
3358 |
public DataFileType createDataFileType(SessionControl sc, Datafiletype def) |
| 2565 |
11 Aug 14 |
nicklas |
3359 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3360 |
DataFileType type = null; |
| 6328 |
14 Jun 21 |
nicklas |
3361 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 2565 |
11 Aug 14 |
nicklas |
3362 |
try |
| 2565 |
11 Aug 14 |
nicklas |
3363 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3364 |
type = DataFileType.getNew(dc, def.getExternalId(), def.getItemType()); |
| 2565 |
11 Aug 14 |
nicklas |
3365 |
type.setName(def.getName()); |
| 2565 |
11 Aug 14 |
nicklas |
3366 |
type.setExtension(def.getExtension()); |
| 2565 |
11 Aug 14 |
nicklas |
3367 |
type.setDescription(def.getDescription()); |
| 2565 |
11 Aug 14 |
nicklas |
3368 |
if (def.getSubtype() != null) |
| 2565 |
11 Aug 14 |
nicklas |
3369 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3370 |
type.setGenericType(def.getSubtype().get(dc)); |
| 2565 |
11 Aug 14 |
nicklas |
3371 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3372 |
dc.saveItem(type); |
| 2565 |
11 Aug 14 |
nicklas |
3373 |
dc.commit(); |
| 2565 |
11 Aug 14 |
nicklas |
3374 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3375 |
finally |
| 2565 |
11 Aug 14 |
nicklas |
3376 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3377 |
if (dc != null) dc.close(); |
| 2565 |
11 Aug 14 |
nicklas |
3378 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3379 |
return type; |
| 2565 |
11 Aug 14 |
nicklas |
3380 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3381 |
|
| 2565 |
11 Aug 14 |
nicklas |
3382 |
|
| 2565 |
11 Aug 14 |
nicklas |
3383 |
/** |
| 2565 |
11 Aug 14 |
nicklas |
Check for an existing data file type with the given options. |
| 2565 |
11 Aug 14 |
nicklas |
A JSONObject is returned with the result. The following |
| 2565 |
11 Aug 14 |
nicklas |
keys are used: |
| 2565 |
11 Aug 14 |
nicklas |
<ul> |
| 2565 |
11 Aug 14 |
nicklas |
<li>itemType: DATAFILETYPE |
| 2565 |
11 Aug 14 |
nicklas |
<li>name: The name of the file type |
| 2565 |
11 Aug 14 |
nicklas |
<li>id: The id of the file type if it exists |
| 2565 |
11 Aug 14 |
nicklas |
<li>status: ok, error, or missing |
| 2565 |
11 Aug 14 |
nicklas |
<li>message: A descriptive message in case of an error |
| 2565 |
11 Aug 14 |
nicklas |
</ul> |
| 2565 |
11 Aug 14 |
nicklas |
@since 2.16 |
| 2565 |
11 Aug 14 |
nicklas |
3395 |
*/ |
| 2565 |
11 Aug 14 |
nicklas |
3396 |
public JSONObject checkDataFileType(DbControl dc, Datafiletype fileType, |
| 2565 |
11 Aug 14 |
nicklas |
3397 |
boolean createIfMissing) |
| 2565 |
11 Aug 14 |
nicklas |
3398 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3399 |
|
| 2565 |
11 Aug 14 |
nicklas |
3400 |
JSONObject json = new JSONObject(); |
| 2565 |
11 Aug 14 |
nicklas |
3401 |
JSONArray jsonMessages = new JSONArray(); |
| 2565 |
11 Aug 14 |
nicklas |
3402 |
json.put("itemType", Item.DATAFILETYPE.name()); |
| 2565 |
11 Aug 14 |
nicklas |
3403 |
json.put("name", fileType.getName()); |
| 2565 |
11 Aug 14 |
nicklas |
3404 |
|
| 2565 |
11 Aug 14 |
nicklas |
3405 |
List<DataFileType> result = fileType.list(dc); |
| 2565 |
11 Aug 14 |
nicklas |
3406 |
if (result.size() == 0) |
| 2565 |
11 Aug 14 |
nicklas |
3407 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3408 |
if (createIfMissing) |
| 2565 |
11 Aug 14 |
nicklas |
3409 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3410 |
DataFileType type = createDataFileType(dc.getSessionControl(), fileType); |
| 2565 |
11 Aug 14 |
nicklas |
3411 |
json.put("id", type.getId()); |
| 2565 |
11 Aug 14 |
nicklas |
3412 |
json.put("status", "ok"); |
| 2565 |
11 Aug 14 |
nicklas |
3413 |
jsonMessages.add("Created"); |
| 2565 |
11 Aug 14 |
nicklas |
3414 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3415 |
else |
| 2565 |
11 Aug 14 |
nicklas |
3416 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3417 |
json.put("status", "missing"); |
| 2565 |
11 Aug 14 |
nicklas |
3418 |
jsonMessages.add("Not found"); |
| 2565 |
11 Aug 14 |
nicklas |
3419 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3420 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3421 |
else if (result.size() > 1) |
| 2565 |
11 Aug 14 |
nicklas |
3422 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3423 |
json.put("status", "error"); |
| 2565 |
11 Aug 14 |
nicklas |
3424 |
jsonMessages.add("Found > 1 MIME type"); |
| 2565 |
11 Aug 14 |
nicklas |
3425 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3426 |
else |
| 2565 |
11 Aug 14 |
nicklas |
3427 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3428 |
DataFileType ft = result.get(0); |
| 2565 |
11 Aug 14 |
nicklas |
3429 |
json.put("id", ft.getId()); |
| 2565 |
11 Aug 14 |
nicklas |
3430 |
json.put("status", "ok"); // For now -- more checks below |
| 2565 |
11 Aug 14 |
nicklas |
3431 |
|
| 2565 |
11 Aug 14 |
nicklas |
3432 |
if (!ft.getExternalId().equals(fileType.getExternalId())) |
| 2565 |
11 Aug 14 |
nicklas |
3433 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3434 |
json.put("status", "error"); |
| 2565 |
11 Aug 14 |
nicklas |
3435 |
jsonMessages.add("Should have '" + fileType.getExternalId() + "' as external id."); |
| 2565 |
11 Aug 14 |
nicklas |
3436 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3437 |
|
| 2565 |
11 Aug 14 |
nicklas |
3438 |
if (!ft.getItemType().equals(fileType.getItemType())) |
| 2565 |
11 Aug 14 |
nicklas |
3439 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3440 |
json.put("status", "error"); |
| 2565 |
11 Aug 14 |
nicklas |
3441 |
jsonMessages.add("Should have '" + fileType.getItemType().name() + "' as item type."); |
| 2565 |
11 Aug 14 |
nicklas |
3442 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3443 |
|
| 2565 |
11 Aug 14 |
nicklas |
3444 |
if (fileType.getSubtype() != null) |
| 2565 |
11 Aug 14 |
nicklas |
3445 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3446 |
ItemSubtype subtype = fileType.getSubtype().get(dc); |
| 2565 |
11 Aug 14 |
nicklas |
3447 |
if (subtype != null && !subtype.equals(ft.getGenericType())) |
| 2565 |
11 Aug 14 |
nicklas |
3448 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3449 |
if (createIfMissing) |
| 2565 |
11 Aug 14 |
nicklas |
3450 |
{ |
| 2565 |
11 Aug 14 |
nicklas |
3451 |
ft.setGenericType(fileType.getSubtype().get(dc)); |
| 2565 |
11 Aug 14 |
nicklas |
3452 |
jsonMessages.add("Fixed"); |
| 2565 |
11 Aug 14 |
nicklas |
3453 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3454 |
else |
| 2565 |
11 Aug 14 |
nicklas |
3455 |
{ |
| 2618 |
01 Sep 14 |
nicklas |
3456 |
json.put("status", "incomplete"); |
| 2565 |
11 Aug 14 |
nicklas |
3457 |
jsonMessages.add("Should be related to '" + fileType.getSubtype().getName() + "' subtype."); |
| 2565 |
11 Aug 14 |
nicklas |
3458 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3459 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3460 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3461 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3462 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 2565 |
11 Aug 14 |
nicklas |
3463 |
json.put("messages", jsonMessages); |
| 2565 |
11 Aug 14 |
nicklas |
3464 |
return json; |
| 2565 |
11 Aug 14 |
nicklas |
3465 |
|
| 2565 |
11 Aug 14 |
nicklas |
3466 |
} |
| 2565 |
11 Aug 14 |
nicklas |
3467 |
|
| 2565 |
11 Aug 14 |
nicklas |
3468 |
|
| 2565 |
11 Aug 14 |
nicklas |
3469 |
/** |
| 4673 |
08 Feb 18 |
nicklas |
Create a platform variant with the given options. The platform is created in |
| 4673 |
08 Feb 18 |
nicklas |
a separate transaction. |
| 4673 |
08 Feb 18 |
nicklas |
@since 4.15 |
| 4673 |
08 Feb 18 |
nicklas |
3473 |
*/ |
| 4673 |
08 Feb 18 |
nicklas |
3474 |
public PlatformVariant createPlatform(SessionControl sc, Rawdatatype rawType, Datafiletype... fileTypes) |
| 4673 |
08 Feb 18 |
nicklas |
3475 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3476 |
PlatformVariant pv = null; |
| 6538 |
13 Jan 22 |
nicklas |
3477 |
Platform p = null; |
| 6328 |
14 Jun 21 |
nicklas |
3478 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 4673 |
08 Feb 18 |
nicklas |
3479 |
try |
| 4673 |
08 Feb 18 |
nicklas |
3480 |
{ |
| 6538 |
13 Jan 22 |
nicklas |
3481 |
try |
| 6538 |
13 Jan 22 |
nicklas |
3482 |
{ |
| 6538 |
13 Jan 22 |
nicklas |
3483 |
p = rawType.getPlatform(dc); |
| 6538 |
13 Jan 22 |
nicklas |
3484 |
} |
| 6538 |
13 Jan 22 |
nicklas |
3485 |
catch (ItemNotFoundException ex) |
| 6538 |
13 Jan 22 |
nicklas |
3486 |
{ |
| 6538 |
13 Jan 22 |
nicklas |
3487 |
p = Platform.getNew(dc, rawType.getPlatformId(), 1); |
| 6538 |
13 Jan 22 |
nicklas |
3488 |
p.setName(rawType.getPlatformName()); |
| 6538 |
13 Jan 22 |
nicklas |
3489 |
dc.saveItem(p); |
| 6538 |
13 Jan 22 |
nicklas |
3490 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3491 |
pv = PlatformVariant.getNew(dc, p, rawType.getVariantId(), 1); |
| 4673 |
08 Feb 18 |
nicklas |
3492 |
pv.setName(rawType.getName()); |
| 4673 |
08 Feb 18 |
nicklas |
3493 |
dc.saveItem(pv); |
| 4673 |
08 Feb 18 |
nicklas |
3494 |
|
| 4673 |
08 Feb 18 |
nicklas |
3495 |
if (fileTypes != null) |
| 4673 |
08 Feb 18 |
nicklas |
3496 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3497 |
for (Datafiletype fileType : fileTypes) |
| 4673 |
08 Feb 18 |
nicklas |
3498 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3499 |
List<DataFileType> list = fileType.list(dc); // Use list() to avoid throwing exceptions if the annotation type doesn't exists yet |
| 4673 |
08 Feb 18 |
nicklas |
3500 |
DataFileType dft = list.size() == 1 ? list.get(0) : null; |
| 4673 |
08 Feb 18 |
nicklas |
3501 |
if (dft != null) |
| 4673 |
08 Feb 18 |
nicklas |
3502 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3503 |
PlatformFileType pft = p.getFileType(dft, pv, true); |
| 4673 |
08 Feb 18 |
nicklas |
3504 |
pft.setAllowMultiple(fileType.getAllowMultiple()); |
| 4673 |
08 Feb 18 |
nicklas |
3505 |
pft.setRequired(fileType.isRequired()); |
| 4673 |
08 Feb 18 |
nicklas |
3506 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3507 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3508 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3509 |
|
| 4673 |
08 Feb 18 |
nicklas |
3510 |
dc.commit(); |
| 4673 |
08 Feb 18 |
nicklas |
3511 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3512 |
finally |
| 4673 |
08 Feb 18 |
nicklas |
3513 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3514 |
if (dc != null) dc.close(); |
| 4673 |
08 Feb 18 |
nicklas |
3515 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3516 |
return pv; |
| 4673 |
08 Feb 18 |
nicklas |
3517 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3518 |
|
| 4673 |
08 Feb 18 |
nicklas |
3519 |
|
| 4673 |
08 Feb 18 |
nicklas |
3520 |
/** |
| 4673 |
08 Feb 18 |
nicklas |
Check for an existing platform (variant) with the given options. |
| 4673 |
08 Feb 18 |
nicklas |
A JSONObject is returned with the result. The following |
| 4673 |
08 Feb 18 |
nicklas |
keys are used: |
| 4673 |
08 Feb 18 |
nicklas |
<ul> |
| 4673 |
08 Feb 18 |
nicklas |
<li>itemType: PLATFORMVARIANT |
| 4673 |
08 Feb 18 |
nicklas |
<li>name: The name of the platform variant |
| 4673 |
08 Feb 18 |
nicklas |
<li>id: The id of the platform variant if it exists |
| 4673 |
08 Feb 18 |
nicklas |
<li>status: ok, error, or missing |
| 4673 |
08 Feb 18 |
nicklas |
<li>message: A descriptive message in case of an error |
| 4673 |
08 Feb 18 |
nicklas |
</ul> |
| 4673 |
08 Feb 18 |
nicklas |
@since 4.15 |
| 4673 |
08 Feb 18 |
nicklas |
3532 |
*/ |
| 4673 |
08 Feb 18 |
nicklas |
3533 |
public JSONObject checkPlatform(DbControl dc, Rawdatatype rawType, |
| 4673 |
08 Feb 18 |
nicklas |
3534 |
boolean createIfMissing, Datafiletype... fileTypes) |
| 4673 |
08 Feb 18 |
nicklas |
3535 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3536 |
|
| 4673 |
08 Feb 18 |
nicklas |
3537 |
JSONObject json = new JSONObject(); |
| 4673 |
08 Feb 18 |
nicklas |
3538 |
JSONArray jsonMessages = new JSONArray(); |
| 4673 |
08 Feb 18 |
nicklas |
3539 |
json.put("itemType", Item.PLATFORMVARIANT.name()); |
| 4673 |
08 Feb 18 |
nicklas |
3540 |
json.put("name", rawType.getName()); |
| 4673 |
08 Feb 18 |
nicklas |
3541 |
|
| 4673 |
08 Feb 18 |
nicklas |
3542 |
List<PlatformVariant> result = rawType.list(dc); |
| 4673 |
08 Feb 18 |
nicklas |
3543 |
if (result.size() == 0) |
| 4673 |
08 Feb 18 |
nicklas |
3544 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3545 |
if (createIfMissing) |
| 4673 |
08 Feb 18 |
nicklas |
3546 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3547 |
PlatformVariant pv = createPlatform(dc.getSessionControl(), rawType, fileTypes); |
| 4673 |
08 Feb 18 |
nicklas |
3548 |
json.put("id", pv.getId()); |
| 4673 |
08 Feb 18 |
nicklas |
3549 |
json.put("status", "ok"); |
| 4673 |
08 Feb 18 |
nicklas |
3550 |
jsonMessages.add("Created"); |
| 4673 |
08 Feb 18 |
nicklas |
3551 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3552 |
else |
| 4673 |
08 Feb 18 |
nicklas |
3553 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3554 |
json.put("status", "missing"); |
| 4673 |
08 Feb 18 |
nicklas |
3555 |
jsonMessages.add("Not found"); |
| 4673 |
08 Feb 18 |
nicklas |
3556 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3557 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3558 |
else if (result.size() > 1) |
| 4673 |
08 Feb 18 |
nicklas |
3559 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3560 |
json.put("status", "error"); |
| 4673 |
08 Feb 18 |
nicklas |
3561 |
jsonMessages.add("Found > 1 platform"); |
| 4673 |
08 Feb 18 |
nicklas |
3562 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3563 |
else |
| 4673 |
08 Feb 18 |
nicklas |
3564 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3565 |
PlatformVariant pv = result.get(0); |
| 4673 |
08 Feb 18 |
nicklas |
3566 |
Platform p = pv.getPlatform(); |
| 4673 |
08 Feb 18 |
nicklas |
3567 |
json.put("id", pv.getId()); |
| 4673 |
08 Feb 18 |
nicklas |
3568 |
json.put("status", "ok"); // For now -- more checks below |
| 4673 |
08 Feb 18 |
nicklas |
3569 |
|
| 4673 |
08 Feb 18 |
nicklas |
3570 |
if (!pv.getExternalId().equals(rawType.getVariantId())) |
| 4673 |
08 Feb 18 |
nicklas |
3571 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3572 |
json.put("status", "error"); |
| 4673 |
08 Feb 18 |
nicklas |
3573 |
jsonMessages.add("Should have '" + rawType.getVariantId() + "' as external id."); |
| 4673 |
08 Feb 18 |
nicklas |
3574 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3575 |
|
| 4673 |
08 Feb 18 |
nicklas |
3576 |
if (fileTypes != null) |
| 4673 |
08 Feb 18 |
nicklas |
3577 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3578 |
for (Datafiletype fileType : fileTypes) |
| 4673 |
08 Feb 18 |
nicklas |
3579 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3580 |
List<DataFileType> list = fileType.list(dc); // Use list() to avoid throwing exceptions if the annotation type doesn't exists yet |
| 4673 |
08 Feb 18 |
nicklas |
3581 |
DataFileType dft = list.size() == 1 ? list.get(0) : null; |
| 4673 |
08 Feb 18 |
nicklas |
3582 |
if (dft != null) |
| 4673 |
08 Feb 18 |
nicklas |
3583 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3584 |
PlatformFileType pft = p.getFileType(dft, pv, createIfMissing); |
| 4673 |
08 Feb 18 |
nicklas |
3585 |
if (pft == null) |
| 4673 |
08 Feb 18 |
nicklas |
3586 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3587 |
json.put("status", "incomplete"); |
| 4673 |
08 Feb 18 |
nicklas |
3588 |
jsonMessages.add("Not linked with: " + fileType.getName()); |
| 4673 |
08 Feb 18 |
nicklas |
3589 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3590 |
else if (!pft.isInDatabase()) |
| 4673 |
08 Feb 18 |
nicklas |
3591 |
{ |
| 4673 |
08 Feb 18 |
nicklas |
3592 |
pft.setAllowMultiple(fileType.getAllowMultiple()); |
| 4673 |
08 Feb 18 |
nicklas |
3593 |
pft.setRequired(fileType.isRequired()); |
| 4673 |
08 Feb 18 |
nicklas |
3594 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 4673 |
08 Feb 18 |
nicklas |
3595 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3596 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3597 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3598 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3599 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3600 |
|
| 4673 |
08 Feb 18 |
nicklas |
3601 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 4673 |
08 Feb 18 |
nicklas |
3602 |
json.put("messages", jsonMessages); |
| 4673 |
08 Feb 18 |
nicklas |
3603 |
return json; |
| 4673 |
08 Feb 18 |
nicklas |
3604 |
|
| 4673 |
08 Feb 18 |
nicklas |
3605 |
} |
| 4673 |
08 Feb 18 |
nicklas |
3606 |
|
| 4673 |
08 Feb 18 |
nicklas |
3607 |
/** |
| 1865 |
19 Feb 13 |
nicklas |
Create a MIME type with the given options. The type is created in |
| 1865 |
19 Feb 13 |
nicklas |
a separate transaction. |
| 1867 |
19 Feb 13 |
nicklas |
@since 2.12 |
| 1865 |
19 Feb 13 |
nicklas |
3611 |
*/ |
| 1865 |
19 Feb 13 |
nicklas |
3612 |
public Extract createExtract(SessionControl sc, String name, Subtype subtype, String description, PermissionOptions permissions) |
| 1865 |
19 Feb 13 |
nicklas |
3613 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3614 |
Extract extract = null; |
| 6328 |
14 Jun 21 |
nicklas |
3615 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1865 |
19 Feb 13 |
nicklas |
3616 |
try |
| 1865 |
19 Feb 13 |
nicklas |
3617 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3618 |
extract = Extract.getNew(dc); |
| 1865 |
19 Feb 13 |
nicklas |
3619 |
extract.setName(name); |
| 1865 |
19 Feb 13 |
nicklas |
3620 |
extract.setItemSubtype(subtype.get(dc)); |
| 1865 |
19 Feb 13 |
nicklas |
3621 |
extract.setDescription(description); |
| 1865 |
19 Feb 13 |
nicklas |
3622 |
if (permissions != null) permissions.applyPermissions(extract); |
| 1865 |
19 Feb 13 |
nicklas |
3623 |
dc.saveItem(extract); |
| 1865 |
19 Feb 13 |
nicklas |
3624 |
dc.commit(); |
| 1865 |
19 Feb 13 |
nicklas |
3625 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3626 |
finally |
| 1865 |
19 Feb 13 |
nicklas |
3627 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3628 |
if (dc != null) dc.close(); |
| 1865 |
19 Feb 13 |
nicklas |
3629 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3630 |
return extract; |
| 1865 |
19 Feb 13 |
nicklas |
3631 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3632 |
|
| 1865 |
19 Feb 13 |
nicklas |
3633 |
/** |
| 1865 |
19 Feb 13 |
nicklas |
Check for an existing Extract type with the given options. |
| 1865 |
19 Feb 13 |
nicklas |
A JSONObject is returned with the result. The following |
| 1865 |
19 Feb 13 |
nicklas |
keys are used: |
| 1865 |
19 Feb 13 |
nicklas |
<ul> |
| 1865 |
19 Feb 13 |
nicklas |
<li>itemType: EXTRACT |
| 1865 |
19 Feb 13 |
nicklas |
<li>name: The name of the extract |
| 1865 |
19 Feb 13 |
nicklas |
<li>id: The id of the extract if it exists |
| 1865 |
19 Feb 13 |
nicklas |
<li>status: ok, error, or missing |
| 1865 |
19 Feb 13 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1865 |
19 Feb 13 |
nicklas |
</ul> |
| 1867 |
19 Feb 13 |
nicklas |
@since 2.12 |
| 1865 |
19 Feb 13 |
nicklas |
3645 |
*/ |
| 1865 |
19 Feb 13 |
nicklas |
3646 |
public JSONObject checkExtract(DbControl dc, String name, Subtype subtype, String description, PermissionOptions permissions, |
| 1865 |
19 Feb 13 |
nicklas |
3647 |
boolean createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
3648 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3649 |
|
| 1865 |
19 Feb 13 |
nicklas |
3650 |
JSONObject json = new JSONObject(); |
| 1865 |
19 Feb 13 |
nicklas |
3651 |
JSONArray jsonMessages = new JSONArray(); |
| 1865 |
19 Feb 13 |
nicklas |
3652 |
json.put("itemType", Item.EXTRACT.name()); |
| 1865 |
19 Feb 13 |
nicklas |
3653 |
json.put("name", name); |
| 1865 |
19 Feb 13 |
nicklas |
3654 |
|
| 1865 |
19 Feb 13 |
nicklas |
3655 |
ItemQuery<Extract> query = Extract.getQuery(); |
| 1865 |
19 Feb 13 |
nicklas |
3656 |
query.setIncludes(Include.ALL); |
| 1865 |
19 Feb 13 |
nicklas |
3657 |
query.restrict( |
| 1865 |
19 Feb 13 |
nicklas |
3658 |
Restrictions.eq( |
| 1865 |
19 Feb 13 |
nicklas |
3659 |
Hql.property("name"), |
| 1865 |
19 Feb 13 |
nicklas |
3660 |
Expressions.parameter("name", name, Type.STRING) |
| 1865 |
19 Feb 13 |
nicklas |
3661 |
)); |
| 1865 |
19 Feb 13 |
nicklas |
3662 |
|
| 1865 |
19 Feb 13 |
nicklas |
3663 |
List<Extract> result = query.list(dc); |
| 1865 |
19 Feb 13 |
nicklas |
3664 |
if (result.size() == 0) |
| 1865 |
19 Feb 13 |
nicklas |
3665 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3666 |
if (createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
3667 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3668 |
Extract extract = createExtract(dc.getSessionControl(), name, subtype, description, permissions); |
| 1865 |
19 Feb 13 |
nicklas |
3669 |
json.put("id", extract.getId()); |
| 1865 |
19 Feb 13 |
nicklas |
3670 |
json.put("status", "ok"); |
| 1865 |
19 Feb 13 |
nicklas |
3671 |
jsonMessages.add("Created"); |
| 1865 |
19 Feb 13 |
nicklas |
3672 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3673 |
else |
| 1865 |
19 Feb 13 |
nicklas |
3674 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3675 |
json.put("status", "missing"); |
| 1865 |
19 Feb 13 |
nicklas |
3676 |
jsonMessages.add("Not found"); |
| 1865 |
19 Feb 13 |
nicklas |
3677 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3678 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3679 |
else if (result.size() > 1) |
| 1865 |
19 Feb 13 |
nicklas |
3680 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3681 |
json.put("status", "error"); |
| 1865 |
19 Feb 13 |
nicklas |
3682 |
jsonMessages.add("Found > 1 Extract [" + name + "]"); |
| 1865 |
19 Feb 13 |
nicklas |
3683 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3684 |
else |
| 1865 |
19 Feb 13 |
nicklas |
3685 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3686 |
Extract e = result.get(0); |
| 1865 |
19 Feb 13 |
nicklas |
3687 |
json.put("id", e.getId()); |
| 1865 |
19 Feb 13 |
nicklas |
3688 |
json.put("status", "ok"); // For now -- more checks below |
| 1865 |
19 Feb 13 |
nicklas |
3689 |
|
| 1865 |
19 Feb 13 |
nicklas |
3690 |
if (!subtype.load(dc).equals(e.getItemSubtype())) |
| 1865 |
19 Feb 13 |
nicklas |
3691 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3692 |
json.put("status", "error"); |
| 1865 |
19 Feb 13 |
nicklas |
3693 |
jsonMessages.add("Should have '" + subtype.getName() + "' as subtype."); |
| 1865 |
19 Feb 13 |
nicklas |
3694 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3695 |
|
| 1865 |
19 Feb 13 |
nicklas |
3696 |
if (permissions != null && !permissions.checkPermissions(e)) |
| 1865 |
19 Feb 13 |
nicklas |
3697 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3698 |
if (createIfMissing) |
| 1865 |
19 Feb 13 |
nicklas |
3699 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3700 |
permissions.applyPermissions(e); |
| 1865 |
19 Feb 13 |
nicklas |
3701 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 1865 |
19 Feb 13 |
nicklas |
3702 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3703 |
else |
| 1865 |
19 Feb 13 |
nicklas |
3704 |
{ |
| 1865 |
19 Feb 13 |
nicklas |
3705 |
json.put("status", "incomplete"); |
| 1865 |
19 Feb 13 |
nicklas |
3706 |
jsonMessages.add(permissions.getMessage()); |
| 1865 |
19 Feb 13 |
nicklas |
3707 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3708 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3709 |
|
| 1865 |
19 Feb 13 |
nicklas |
3710 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3711 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1865 |
19 Feb 13 |
nicklas |
3712 |
json.put("messages", jsonMessages); |
| 1865 |
19 Feb 13 |
nicklas |
3713 |
return json; |
| 1865 |
19 Feb 13 |
nicklas |
3714 |
} |
| 1865 |
19 Feb 13 |
nicklas |
3715 |
|
| 1865 |
19 Feb 13 |
nicklas |
3716 |
|
| 1865 |
19 Feb 13 |
nicklas |
3717 |
/** |
| 1606 |
19 Apr 12 |
nicklas |
Create a Plate geometry with the given options. The geometry is created in |
| 1606 |
19 Apr 12 |
nicklas |
a separate transaction. |
| 1606 |
19 Apr 12 |
nicklas |
@since 2.5 |
| 1606 |
19 Apr 12 |
nicklas |
3721 |
*/ |
| 1606 |
19 Apr 12 |
nicklas |
3722 |
public PlateGeometry createPlateGeometry(SessionControl sc, Geometry def) |
| 1606 |
19 Apr 12 |
nicklas |
3723 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3724 |
PlateGeometry g = null; |
| 6328 |
14 Jun 21 |
nicklas |
3725 |
DbControl dc = sc.newDbControl(":Installation wizard"); |
| 1606 |
19 Apr 12 |
nicklas |
3726 |
try |
| 1606 |
19 Apr 12 |
nicklas |
3727 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3728 |
g = PlateGeometry.getNew(dc, def.getRows(), def.getColumns()); |
| 1606 |
19 Apr 12 |
nicklas |
3729 |
g.setName(def.getName()); |
| 1606 |
19 Apr 12 |
nicklas |
3730 |
dc.saveItem(g); |
| 1606 |
19 Apr 12 |
nicklas |
3731 |
dc.commit(); |
| 1606 |
19 Apr 12 |
nicklas |
3732 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3733 |
finally |
| 1606 |
19 Apr 12 |
nicklas |
3734 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3735 |
if (dc != null) dc.close(); |
| 1606 |
19 Apr 12 |
nicklas |
3736 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3737 |
return g; |
| 1606 |
19 Apr 12 |
nicklas |
3738 |
} |
| 1546 |
02 Mar 12 |
nicklas |
3739 |
|
| 1606 |
19 Apr 12 |
nicklas |
3740 |
|
| 1606 |
19 Apr 12 |
nicklas |
3741 |
/** |
| 1606 |
19 Apr 12 |
nicklas |
Check for an existing Plate geometry type with the given options. |
| 1606 |
19 Apr 12 |
nicklas |
A JSONObject is returned with the result. The following |
| 1606 |
19 Apr 12 |
nicklas |
keys are used: |
| 1606 |
19 Apr 12 |
nicklas |
<ul> |
| 1606 |
19 Apr 12 |
nicklas |
<li>itemType: PLATEGEOMETRY |
| 1606 |
19 Apr 12 |
nicklas |
<li>name: The name of the geometry |
| 1606 |
19 Apr 12 |
nicklas |
<li>id: The id of the geometry if it exists |
| 1606 |
19 Apr 12 |
nicklas |
<li>rows: The number of rows |
| 1606 |
19 Apr 12 |
nicklas |
<li>column: The number of columns |
| 1606 |
19 Apr 12 |
nicklas |
<li>status: ok, error, or missing |
| 1606 |
19 Apr 12 |
nicklas |
<li>message: A descriptive message in case of an error |
| 1606 |
19 Apr 12 |
nicklas |
</ul> |
| 1606 |
19 Apr 12 |
nicklas |
@since 2.5 |
| 1606 |
19 Apr 12 |
nicklas |
3755 |
*/ |
| 1606 |
19 Apr 12 |
nicklas |
3756 |
public JSONObject checkPlateGeometry(DbControl dc, Geometry geometry, boolean createIfMissing) |
| 1606 |
19 Apr 12 |
nicklas |
3757 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3758 |
|
| 1606 |
19 Apr 12 |
nicklas |
3759 |
JSONObject json = new JSONObject(); |
| 1606 |
19 Apr 12 |
nicklas |
3760 |
JSONArray jsonMessages = new JSONArray(); |
| 1606 |
19 Apr 12 |
nicklas |
3761 |
json.put("itemType", Item.PLATEGEOMETRY.name()); |
| 1606 |
19 Apr 12 |
nicklas |
3762 |
json.put("name", geometry.getName()); |
| 1606 |
19 Apr 12 |
nicklas |
3763 |
json.put("rows", geometry.getRows()); |
| 1606 |
19 Apr 12 |
nicklas |
3764 |
json.put("columns", geometry.getColumns()); |
| 1606 |
19 Apr 12 |
nicklas |
3765 |
|
| 1606 |
19 Apr 12 |
nicklas |
3766 |
List<PlateGeometry> result = geometry.list(dc); |
| 1606 |
19 Apr 12 |
nicklas |
3767 |
if (result.size() == 0) |
| 1606 |
19 Apr 12 |
nicklas |
3768 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3769 |
if (createIfMissing) |
| 1606 |
19 Apr 12 |
nicklas |
3770 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3771 |
PlateGeometry g = createPlateGeometry(dc.getSessionControl(), geometry); |
| 1606 |
19 Apr 12 |
nicklas |
3772 |
json.put("id", g.getId()); |
| 1606 |
19 Apr 12 |
nicklas |
3773 |
json.put("status", "ok"); |
| 1606 |
19 Apr 12 |
nicklas |
3774 |
jsonMessages.add("Created"); |
| 1606 |
19 Apr 12 |
nicklas |
3775 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3776 |
else |
| 1606 |
19 Apr 12 |
nicklas |
3777 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3778 |
json.put("status", "missing"); |
| 1606 |
19 Apr 12 |
nicklas |
3779 |
jsonMessages.add("Not found"); |
| 1606 |
19 Apr 12 |
nicklas |
3780 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3781 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3782 |
else if (result.size() > 1) |
| 1606 |
19 Apr 12 |
nicklas |
3783 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3784 |
json.put("status", "error"); |
| 1606 |
19 Apr 12 |
nicklas |
3785 |
jsonMessages.add("Found > 1 geometry"); |
| 1606 |
19 Apr 12 |
nicklas |
3786 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3787 |
else |
| 1606 |
19 Apr 12 |
nicklas |
3788 |
{ |
| 1606 |
19 Apr 12 |
nicklas |
3789 |
PlateGeometry g = result.get(0); |
| 1606 |
19 Apr 12 |
nicklas |
3790 |
json.put("id", g.getId()); |
| 1606 |
19 Apr 12 |
nicklas |
3791 |
json.put("status", "ok"); // For now -- more checks below |
| 1606 |
19 Apr 12 |
nicklas |
3792 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3793 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1606 |
19 Apr 12 |
nicklas |
3794 |
json.put("messages", jsonMessages); |
| 1606 |
19 Apr 12 |
nicklas |
3795 |
return json; |
| 1606 |
19 Apr 12 |
nicklas |
3796 |
|
| 1606 |
19 Apr 12 |
nicklas |
3797 |
} |
| 1606 |
19 Apr 12 |
nicklas |
3798 |
|
| 2724 |
02 Oct 14 |
nicklas |
3799 |
public JSONObject checkPlugin(DbControl dc, String clazz, |
| 1570 |
16 Mar 12 |
nicklas |
3800 |
PermissionOptions permissions, boolean createIfMissing) |
| 1570 |
16 Mar 12 |
nicklas |
3801 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3802 |
JSONObject json = new JSONObject(); |
| 1570 |
16 Mar 12 |
nicklas |
3803 |
JSONArray jsonMessages = new JSONArray(); |
| 1570 |
16 Mar 12 |
nicklas |
3804 |
json.put("itemType", Item.PLUGINDEFINITION.name()); |
| 2724 |
02 Oct 14 |
nicklas |
3805 |
json.put("name", clazz); |
| 1570 |
16 Mar 12 |
nicklas |
3806 |
|
| 1570 |
16 Mar 12 |
nicklas |
3807 |
try |
| 1570 |
16 Mar 12 |
nicklas |
3808 |
{ |
| 2724 |
02 Oct 14 |
nicklas |
3809 |
PluginDefinition plugin = PluginDefinition.getByClassName(dc, clazz); |
| 1570 |
16 Mar 12 |
nicklas |
3810 |
|
| 1570 |
16 Mar 12 |
nicklas |
3811 |
json.put("id", plugin.getId()); |
| 1570 |
16 Mar 12 |
nicklas |
3812 |
json.put("name", plugin.getName()); |
| 1570 |
16 Mar 12 |
nicklas |
3813 |
json.put("status", "ok"); // For now -- more checks below |
| 1570 |
16 Mar 12 |
nicklas |
3814 |
|
| 1570 |
16 Mar 12 |
nicklas |
3815 |
if (permissions != null && !permissions.checkPermissions(plugin)) |
| 1570 |
16 Mar 12 |
nicklas |
3816 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3817 |
if (createIfMissing) |
| 1570 |
16 Mar 12 |
nicklas |
3818 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3819 |
permissions.applyPermissions(plugin); |
| 1570 |
16 Mar 12 |
nicklas |
3820 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 1570 |
16 Mar 12 |
nicklas |
3821 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3822 |
else |
| 1570 |
16 Mar 12 |
nicklas |
3823 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3824 |
json.put("status", "incomplete"); |
| 1570 |
16 Mar 12 |
nicklas |
3825 |
jsonMessages.add(permissions.getMessage()); |
| 1570 |
16 Mar 12 |
nicklas |
3826 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3827 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3828 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3829 |
catch (ItemNotFoundException ex) |
| 1570 |
16 Mar 12 |
nicklas |
3830 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3831 |
jsonMessages.add("Not installed"); |
| 1570 |
16 Mar 12 |
nicklas |
3832 |
json.put("status", "error"); |
| 1570 |
16 Mar 12 |
nicklas |
3833 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3834 |
|
| 1570 |
16 Mar 12 |
nicklas |
3835 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1570 |
16 Mar 12 |
nicklas |
3836 |
json.put("messages", jsonMessages); |
| 1570 |
16 Mar 12 |
nicklas |
3837 |
return json; |
| 1570 |
16 Mar 12 |
nicklas |
3838 |
} |
| 1546 |
02 Mar 12 |
nicklas |
3839 |
|
| 2724 |
02 Oct 14 |
nicklas |
3840 |
public JSONObject checkPluginConfiguration(DbControl dc, String clazz, String configName, |
| 1570 |
16 Mar 12 |
nicklas |
3841 |
PermissionOptions permissions, boolean createIfMissing) |
| 1570 |
16 Mar 12 |
nicklas |
3842 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3843 |
JSONObject json = new JSONObject(); |
| 1570 |
16 Mar 12 |
nicklas |
3844 |
JSONArray jsonMessages = new JSONArray(); |
| 1570 |
16 Mar 12 |
nicklas |
3845 |
json.put("itemType", Item.PLUGINCONFIGURATION.name()); |
| 1570 |
16 Mar 12 |
nicklas |
3846 |
json.put("name", configName); |
| 1570 |
16 Mar 12 |
nicklas |
3847 |
|
| 1570 |
16 Mar 12 |
nicklas |
3848 |
try |
| 1570 |
16 Mar 12 |
nicklas |
3849 |
{ |
| 2724 |
02 Oct 14 |
nicklas |
3850 |
PluginDefinition plugin = PluginDefinition.getByClassName(dc, clazz); |
| 1570 |
16 Mar 12 |
nicklas |
3851 |
|
| 1570 |
16 Mar 12 |
nicklas |
3852 |
ItemQuery<PluginConfiguration> query = plugin.getPluginConfigurations(); |
| 1570 |
16 Mar 12 |
nicklas |
3853 |
query.include(Include.ALL); |
| 1570 |
16 Mar 12 |
nicklas |
3854 |
query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(configName))); |
| 1570 |
16 Mar 12 |
nicklas |
3855 |
|
| 1570 |
16 Mar 12 |
nicklas |
3856 |
List<PluginConfiguration> result = query.list(dc); |
| 1570 |
16 Mar 12 |
nicklas |
3857 |
|
| 1570 |
16 Mar 12 |
nicklas |
3858 |
if (result.size() == 0) |
| 1570 |
16 Mar 12 |
nicklas |
3859 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3860 |
json.put("status", "error"); |
| 1570 |
16 Mar 12 |
nicklas |
3861 |
jsonMessages.add("Not installed"); |
| 1570 |
16 Mar 12 |
nicklas |
3862 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3863 |
else if (result.size() > 1) |
| 1570 |
16 Mar 12 |
nicklas |
3864 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3865 |
json.put("status", "error"); |
| 1570 |
16 Mar 12 |
nicklas |
3866 |
jsonMessages.add("Found > 1 configuration"); |
| 1570 |
16 Mar 12 |
nicklas |
3867 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3868 |
else |
| 1570 |
16 Mar 12 |
nicklas |
3869 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3870 |
PluginConfiguration config = result.get(0); |
| 1570 |
16 Mar 12 |
nicklas |
3871 |
json.put("id", config.getId()); |
| 1570 |
16 Mar 12 |
nicklas |
3872 |
json.put("status", "ok"); // For now -- more checks below |
| 1570 |
16 Mar 12 |
nicklas |
3873 |
|
| 1570 |
16 Mar 12 |
nicklas |
3874 |
if (permissions != null && !permissions.checkPermissions(config)) |
| 1570 |
16 Mar 12 |
nicklas |
3875 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3876 |
if (createIfMissing) |
| 1570 |
16 Mar 12 |
nicklas |
3877 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3878 |
permissions.applyPermissions(config); |
| 1570 |
16 Mar 12 |
nicklas |
3879 |
if (jsonMessages.size() == 0) jsonMessages.add("Fixed"); |
| 1570 |
16 Mar 12 |
nicklas |
3880 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3881 |
else |
| 1570 |
16 Mar 12 |
nicklas |
3882 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3883 |
json.put("status", "incomplete"); |
| 1570 |
16 Mar 12 |
nicklas |
3884 |
jsonMessages.add(permissions.getMessage()); |
| 1570 |
16 Mar 12 |
nicklas |
3885 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3886 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3887 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3888 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3889 |
catch (ItemNotFoundException ex) |
| 1570 |
16 Mar 12 |
nicklas |
3890 |
{ |
| 1570 |
16 Mar 12 |
nicklas |
3891 |
jsonMessages.add("Not installed"); |
| 1570 |
16 Mar 12 |
nicklas |
3892 |
json.put("status", "error"); |
| 1570 |
16 Mar 12 |
nicklas |
3893 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3894 |
|
| 1570 |
16 Mar 12 |
nicklas |
3895 |
if (jsonMessages.size() == 0) jsonMessages.add("Ok"); |
| 1570 |
16 Mar 12 |
nicklas |
3896 |
json.put("messages", jsonMessages); |
| 1570 |
16 Mar 12 |
nicklas |
3897 |
return json; |
| 1570 |
16 Mar 12 |
nicklas |
3898 |
} |
| 1570 |
16 Mar 12 |
nicklas |
3899 |
|
| 2350 |
10 Apr 14 |
nicklas |
3900 |
private Map<String, String> barcodeSequences; |
| 5865 |
12 Mar 20 |
nicklas |
3901 |
private Map<String, String> barcodeSequences2; |
| 2350 |
10 Apr 14 |
nicklas |
3902 |
/** |
| 2350 |
10 Apr 14 |
nicklas |
Maps barcode name (AD001, AD002, ...) to gene sequence. |
| 2350 |
10 Apr 14 |
nicklas |
3904 |
*/ |
| 2350 |
10 Apr 14 |
nicklas |
3905 |
private String lookupSequence(String barcode) |
| 2350 |
10 Apr 14 |
nicklas |
3906 |
{ |
| 2350 |
10 Apr 14 |
nicklas |
3907 |
if (barcodeSequences == null) |
| 2350 |
10 Apr 14 |
nicklas |
3908 |
{ |
| 2350 |
10 Apr 14 |
nicklas |
3909 |
barcodeSequences = new HashMap<String, String>(); |
| 2350 |
10 Apr 14 |
nicklas |
3910 |
barcodeSequences.put("AD001", "ATCACGA"); |
| 2350 |
10 Apr 14 |
nicklas |
3911 |
barcodeSequences.put("AD002", "CGATGTA"); |
| 2350 |
10 Apr 14 |
nicklas |
3912 |
barcodeSequences.put("AD003", "TTAGGCA"); |
| 2350 |
10 Apr 14 |
nicklas |
3913 |
barcodeSequences.put("AD004", "TGACCAA"); |
| 2350 |
10 Apr 14 |
nicklas |
3914 |
barcodeSequences.put("AD005", "ACAGTGA"); |
| 2350 |
10 Apr 14 |
nicklas |
3915 |
barcodeSequences.put("AD006", "GCCAATA"); |
| 2350 |
10 Apr 14 |
nicklas |
3916 |
barcodeSequences.put("AD007", "CAGATCA"); |
| 2350 |
10 Apr 14 |
nicklas |
3917 |
barcodeSequences.put("AD008", "ACTTGAA"); |
| 2350 |
10 Apr 14 |
nicklas |
3918 |
barcodeSequences.put("AD009", "GATCAGA"); |
| 2350 |
10 Apr 14 |
nicklas |
3919 |
barcodeSequences.put("AD010", "TAGCTTA"); |
| 2350 |
10 Apr 14 |
nicklas |
3920 |
barcodeSequences.put("AD011", "GGCTACA"); |
| 2350 |
10 Apr 14 |
nicklas |
3921 |
barcodeSequences.put("AD012", "CTTGTAA"); |
| 2350 |
10 Apr 14 |
nicklas |
3922 |
barcodeSequences.put("AD013", "AGTCAAA"); |
| 2350 |
10 Apr 14 |
nicklas |
3923 |
barcodeSequences.put("AD014", "AGTTCCA"); |
| 2350 |
10 Apr 14 |
nicklas |
3924 |
barcodeSequences.put("AD015", "ATGTCAA"); |
| 2350 |
10 Apr 14 |
nicklas |
3925 |
barcodeSequences.put("AD016", "CCGTCCA"); |
| 2350 |
10 Apr 14 |
nicklas |
3926 |
barcodeSequences.put("AD018", "GTCCGCA"); |
| 2350 |
10 Apr 14 |
nicklas |
3927 |
barcodeSequences.put("AD019", "GTGAAAA"); |
| 2350 |
10 Apr 14 |
nicklas |
3928 |
barcodeSequences.put("AD020", "GTGGCCA"); |
| 2350 |
10 Apr 14 |
nicklas |
3929 |
barcodeSequences.put("AD021", "GTTTCGA"); |
| 2350 |
10 Apr 14 |
nicklas |
3930 |
barcodeSequences.put("AD022", "CGTACGA"); |
| 2350 |
10 Apr 14 |
nicklas |
3931 |
barcodeSequences.put("AD023", "GAGTGGA"); |
| 2350 |
10 Apr 14 |
nicklas |
3932 |
barcodeSequences.put("AD025", "ACTGATA"); |
| 2350 |
10 Apr 14 |
nicklas |
3933 |
barcodeSequences.put("AD027", "ATTCCTA"); |
| 5865 |
12 Mar 20 |
nicklas |
3934 |
|
| 5865 |
12 Mar 20 |
nicklas |
3935 |
barcodeSequences.put("UDI0001", "CCGCGGTT"); |
| 5865 |
12 Mar 20 |
nicklas |
3936 |
barcodeSequences.put("UDI0002", "TTATAACC"); |
| 5865 |
12 Mar 20 |
nicklas |
3937 |
barcodeSequences.put("UDI0003", "GGACTTGG"); |
| 5865 |
12 Mar 20 |
nicklas |
3938 |
barcodeSequences.put("UDI0004", "AAGTCCAA"); |
| 5865 |
12 Mar 20 |
nicklas |
3939 |
barcodeSequences.put("UDI0005", "ATCCACTG"); |
| 5865 |
12 Mar 20 |
nicklas |
3940 |
barcodeSequences.put("UDI0006", "GCTTGTCA"); |
| 5865 |
12 Mar 20 |
nicklas |
3941 |
barcodeSequences.put("UDI0007", "CAAGCTAG"); |
| 5865 |
12 Mar 20 |
nicklas |
3942 |
barcodeSequences.put("UDI0008", "TGGATCGA"); |
| 5865 |
12 Mar 20 |
nicklas |
3943 |
barcodeSequences.put("UDI0009", "AGTTCAGG"); |
| 5865 |
12 Mar 20 |
nicklas |
3944 |
barcodeSequences.put("UDI0010", "GACCTGAA"); |
| 5865 |
12 Mar 20 |
nicklas |
3945 |
barcodeSequences.put("UDI0011", "TCTCTACT"); |
| 5865 |
12 Mar 20 |
nicklas |
3946 |
barcodeSequences.put("UDI0012", "CTCTCGTC"); |
| 5865 |
12 Mar 20 |
nicklas |
3947 |
barcodeSequences.put("UDI0013", "CCAAGTCT"); |
| 5865 |
12 Mar 20 |
nicklas |
3948 |
barcodeSequences.put("UDI0014", "TTGGACTC"); |
| 5865 |
12 Mar 20 |
nicklas |
3949 |
barcodeSequences.put("UDI0015", "GGCTTAAG"); |
| 5865 |
12 Mar 20 |
nicklas |
3950 |
barcodeSequences.put("UDI0016", "AATCCGGA"); |
| 5865 |
12 Mar 20 |
nicklas |
3951 |
barcodeSequences.put("UDI0017", "TAATACAG"); |
| 5865 |
12 Mar 20 |
nicklas |
3952 |
barcodeSequences.put("UDI0018", "CGGCGTGA"); |
| 5865 |
12 Mar 20 |
nicklas |
3953 |
barcodeSequences.put("UDI0019", "ATGTAAGT"); |
| 5865 |
12 Mar 20 |
nicklas |
3954 |
barcodeSequences.put("UDI0020", "GCACGGAC"); |
| 5865 |
12 Mar 20 |
nicklas |
3955 |
barcodeSequences.put("UDI0021", "GGTACCTT"); |
| 5865 |
12 Mar 20 |
nicklas |
3956 |
barcodeSequences.put("UDI0022", "AACGTTCC"); |
| 5865 |
12 Mar 20 |
nicklas |
3957 |
barcodeSequences.put("UDI0023", "GCAGAATT"); |
| 5865 |
12 Mar 20 |
nicklas |
3958 |
barcodeSequences.put("UDI0024", "ATGAGGCC"); |
| 5865 |
12 Mar 20 |
nicklas |
3959 |
barcodeSequences.put("UDI0025", "ACTAAGAT"); |
| 5865 |
12 Mar 20 |
nicklas |
3960 |
barcodeSequences.put("UDI0026", "GTCGGAGC"); |
| 5865 |
12 Mar 20 |
nicklas |
3961 |
barcodeSequences.put("UDI0027", "CTTGGTAT"); |
| 5865 |
12 Mar 20 |
nicklas |
3962 |
barcodeSequences.put("UDI0028", "TCCAACGC"); |
| 5865 |
12 Mar 20 |
nicklas |
3963 |
barcodeSequences.put("UDI0029", "CCGTGAAG"); |
| 5865 |
12 Mar 20 |
nicklas |
3964 |
barcodeSequences.put("UDI0030", "TTACAGGA"); |
| 5865 |
12 Mar 20 |
nicklas |
3965 |
barcodeSequences.put("UDI0031", "GGCATTCT"); |
| 5865 |
12 Mar 20 |
nicklas |
3966 |
barcodeSequences.put("UDI0032", "AATGCCTC"); |
| 5893 |
07 Apr 20 |
nicklas |
3967 |
barcodeSequences.put("UDI0033", "TACCGAGG"); |
| 5893 |
07 Apr 20 |
nicklas |
3968 |
barcodeSequences.put("UDI0034", "CGTTAGAA"); |
| 5893 |
07 Apr 20 |
nicklas |
3969 |
barcodeSequences.put("UDI0035", "AGCCTCAT"); |
| 5893 |
07 Apr 20 |
nicklas |
3970 |
barcodeSequences.put("UDI0036", "GATTCTGC"); |
| 5893 |
07 Apr 20 |
nicklas |
3971 |
barcodeSequences.put("UDI0037", "TCGTAGTG"); |
| 5893 |
07 Apr 20 |
nicklas |
3972 |
barcodeSequences.put("UDI0038", "CTACGACA"); |
| 5893 |
07 Apr 20 |
nicklas |
3973 |
barcodeSequences.put("UDI0039", "TAAGTGGT"); |
| 5893 |
07 Apr 20 |
nicklas |
3974 |
barcodeSequences.put("UDI0040", "CGGACAAC"); |
| 5893 |
07 Apr 20 |
nicklas |
3975 |
barcodeSequences.put("UDI0041", "ATATGGAT"); |
| 5893 |
07 Apr 20 |
nicklas |
3976 |
barcodeSequences.put("UDI0042", "GCGCAAGC"); |
| 5893 |
07 Apr 20 |
nicklas |
3977 |
barcodeSequences.put("UDI0043", "AAGATACT"); |
| 5893 |
07 Apr 20 |
nicklas |
3978 |
barcodeSequences.put("UDI0044", "GGAGCGTC"); |
| 5893 |
07 Apr 20 |
nicklas |
3979 |
barcodeSequences.put("UDI0045", "ATGGCATG"); |
| 5893 |
07 Apr 20 |
nicklas |
3980 |
barcodeSequences.put("UDI0046", "GCAATGCA"); |
| 5893 |
07 Apr 20 |
nicklas |
3981 |
barcodeSequences.put("UDI0047", "GTTCCAAT"); |
| 5893 |
07 Apr 20 |
nicklas |
3982 |
barcodeSequences.put("UDI0048", "ACCTTGGC"); |
| 5893 |
07 Apr 20 |
nicklas |
3983 |
barcodeSequences.put("UDI0049", "ATATCTCG"); |
| 5893 |
07 Apr 20 |
nicklas |
3984 |
barcodeSequences.put("UDI0050", "GCGCTCTA"); |
| 5893 |
07 Apr 20 |
nicklas |
3985 |
barcodeSequences.put("UDI0051", "AACAGGTT"); |
| 5893 |
07 Apr 20 |
nicklas |
3986 |
barcodeSequences.put("UDI0052", "GGTGAACC"); |
| 5893 |
07 Apr 20 |
nicklas |
3987 |
barcodeSequences.put("UDI0053", "CAACAATG"); |
| 5893 |
07 Apr 20 |
nicklas |
3988 |
barcodeSequences.put("UDI0054", "TGGTGGCA"); |
| 5893 |
07 Apr 20 |
nicklas |
3989 |
barcodeSequences.put("UDI0055", "AGGCAGAG"); |
| 5893 |
07 Apr 20 |
nicklas |
3990 |
barcodeSequences.put("UDI0056", "GAATGAGA"); |
| 5893 |
07 Apr 20 |
nicklas |
3991 |
barcodeSequences.put("UDI0057", "TGCGGCGT"); |
| 5893 |
07 Apr 20 |
nicklas |
3992 |
barcodeSequences.put("UDI0058", "CATAATAC"); |
| 5893 |
07 Apr 20 |
nicklas |
3993 |
barcodeSequences.put("UDI0059", "GATCTATC"); |
| 5893 |
07 Apr 20 |
nicklas |
3994 |
barcodeSequences.put("UDI0060", "AGCTCGCT"); |
| 5893 |
07 Apr 20 |
nicklas |
3995 |
barcodeSequences.put("UDI0061", "CGGAACTG"); |
| 5893 |
07 Apr 20 |
nicklas |
3996 |
barcodeSequences.put("UDI0062", "TAAGGTCA"); |
| 5893 |
07 Apr 20 |
nicklas |
3997 |
barcodeSequences.put("UDI0063", "TTGCCTAG"); |
| 5893 |
07 Apr 20 |
nicklas |
3998 |
barcodeSequences.put("UDI0064", "CCATTCGA"); |
| 5893 |
07 Apr 20 |
nicklas |
3999 |
barcodeSequences.put("UDI0065", "ACACTAAG"); |
| 5893 |
07 Apr 20 |
nicklas |
4000 |
barcodeSequences.put("UDI0066", "GTGTCGGA"); |
| 5893 |
07 Apr 20 |
nicklas |
4001 |
barcodeSequences.put("UDI0067", "TTCCTGTT"); |
| 5893 |
07 Apr 20 |
nicklas |
4002 |
barcodeSequences.put("UDI0068", "CCTTCACC"); |
| 5893 |
07 Apr 20 |
nicklas |
4003 |
barcodeSequences.put("UDI0069", "GCCACAGG"); |
| 5893 |
07 Apr 20 |
nicklas |
4004 |
barcodeSequences.put("UDI0070", "ATTGTGAA"); |
| 5893 |
07 Apr 20 |
nicklas |
4005 |
barcodeSequences.put("UDI0071", "ACTCGTGT"); |
| 5893 |
07 Apr 20 |
nicklas |
4006 |
barcodeSequences.put("UDI0072", "GTCTACAC"); |
| 5893 |
07 Apr 20 |
nicklas |
4007 |
barcodeSequences.put("UDI0073", "CAATTAAC"); |
| 5893 |
07 Apr 20 |
nicklas |
4008 |
barcodeSequences.put("UDI0074", "TGGCCGGT"); |
| 5893 |
07 Apr 20 |
nicklas |
4009 |
barcodeSequences.put("UDI0075", "AGTACTCC"); |
| 5893 |
07 Apr 20 |
nicklas |
4010 |
barcodeSequences.put("UDI0076", "GACGTCTT"); |
| 5893 |
07 Apr 20 |
nicklas |
4011 |
barcodeSequences.put("UDI0077", "TGCGAGAC"); |
| 5893 |
07 Apr 20 |
nicklas |
4012 |
barcodeSequences.put("UDI0078", "CATAGAGT"); |
| 5893 |
07 Apr 20 |
nicklas |
4013 |
barcodeSequences.put("UDI0079", "ACAGGCGC"); |
| 5893 |
07 Apr 20 |
nicklas |
4014 |
barcodeSequences.put("UDI0080", "GTGAATAT"); |
| 5893 |
07 Apr 20 |
nicklas |
4015 |
barcodeSequences.put("UDI0081", "AACTGTAG"); |
| 5893 |
07 Apr 20 |
nicklas |
4016 |
barcodeSequences.put("UDI0082", "GGTCACGA"); |
| 5893 |
07 Apr 20 |
nicklas |
4017 |
barcodeSequences.put("UDI0083", "CTGCTTCC"); |
| 5893 |
07 Apr 20 |
nicklas |
4018 |
barcodeSequences.put("UDI0084", "TCATCCTT"); |
| 5893 |
07 Apr 20 |
nicklas |
4019 |
barcodeSequences.put("UDI0085", "AGGTTATA"); |
| 5893 |
07 Apr 20 |
nicklas |
4020 |
barcodeSequences.put("UDI0086", "GAACCGCG"); |
| 5893 |
07 Apr 20 |
nicklas |
4021 |
barcodeSequences.put("UDI0087", "CTCACCAA"); |
| 5893 |
07 Apr 20 |
nicklas |
4022 |
barcodeSequences.put("UDI0088", "TCTGTTGG"); |
| 5893 |
07 Apr 20 |
nicklas |
4023 |
barcodeSequences.put("UDI0089", "TATCGCAC"); |
| 5893 |
07 Apr 20 |
nicklas |
4024 |
barcodeSequences.put("UDI0090", "CGCTATGT"); |
| 5893 |
07 Apr 20 |
nicklas |
4025 |
barcodeSequences.put("UDI0091", "GTATGTTC"); |
| 5893 |
07 Apr 20 |
nicklas |
4026 |
barcodeSequences.put("UDI0092", "ACGCACCT"); |
| 5893 |
07 Apr 20 |
nicklas |
4027 |
barcodeSequences.put("UDI0093", "TACTCATA"); |
| 5893 |
07 Apr 20 |
nicklas |
4028 |
barcodeSequences.put("UDI0094", "CGTCTGCG"); |
| 5893 |
07 Apr 20 |
nicklas |
4029 |
barcodeSequences.put("UDI0095", "TCGATATC"); |
| 5893 |
07 Apr 20 |
nicklas |
4030 |
barcodeSequences.put("UDI0096", "CTAGCGCT"); |
| 2350 |
10 Apr 14 |
nicklas |
4031 |
} |
| 2350 |
10 Apr 14 |
nicklas |
4032 |
|
| 2350 |
10 Apr 14 |
nicklas |
4033 |
return barcodeSequences.get(barcode); |
| 2350 |
10 Apr 14 |
nicklas |
4034 |
} |
| 5865 |
12 Mar 20 |
nicklas |
4035 |
|
| 5865 |
12 Mar 20 |
nicklas |
4036 |
/** |
| 5865 |
12 Mar 20 |
nicklas |
Maps barcode name to gene sequence for second barcode. |
| 5865 |
12 Mar 20 |
nicklas |
4038 |
*/ |
| 5865 |
12 Mar 20 |
nicklas |
4039 |
private String lookupSequence2(String barcode) |
| 5865 |
12 Mar 20 |
nicklas |
4040 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
4041 |
if (barcodeSequences2 == null) |
| 5865 |
12 Mar 20 |
nicklas |
4042 |
{ |
| 5865 |
12 Mar 20 |
nicklas |
4043 |
barcodeSequences2 = new HashMap<String, String>(); |
| 5865 |
12 Mar 20 |
nicklas |
4044 |
|
| 5865 |
12 Mar 20 |
nicklas |
4045 |
barcodeSequences2.put("UDI0001", "AGCGCTAG"); |
| 5865 |
12 Mar 20 |
nicklas |
4046 |
barcodeSequences2.put("UDI0002", "GATATCGA"); |
| 5865 |
12 Mar 20 |
nicklas |
4047 |
barcodeSequences2.put("UDI0003", "CGCAGACG"); |
| 5865 |
12 Mar 20 |
nicklas |
4048 |
barcodeSequences2.put("UDI0004", "TATGAGTA"); |
| 5865 |
12 Mar 20 |
nicklas |
4049 |
barcodeSequences2.put("UDI0005", "AGGTGCGT"); |
| 5865 |
12 Mar 20 |
nicklas |
4050 |
barcodeSequences2.put("UDI0006", "GAACATAC"); |
| 5865 |
12 Mar 20 |
nicklas |
4051 |
barcodeSequences2.put("UDI0007", "ACATAGCG"); |
| 5865 |
12 Mar 20 |
nicklas |
4052 |
barcodeSequences2.put("UDI0008", "GTGCGATA"); |
| 5865 |
12 Mar 20 |
nicklas |
4053 |
barcodeSequences2.put("UDI0009", "CCAACAGA"); |
| 5865 |
12 Mar 20 |
nicklas |
4054 |
barcodeSequences2.put("UDI0010", "TTGGTGAG"); |
| 5865 |
12 Mar 20 |
nicklas |
4055 |
barcodeSequences2.put("UDI0011", "CGCGGTTC"); |
| 5865 |
12 Mar 20 |
nicklas |
4056 |
barcodeSequences2.put("UDI0012", "TATAACCT"); |
| 5865 |
12 Mar 20 |
nicklas |
4057 |
barcodeSequences2.put("UDI0013", "AAGGATGA"); |
| 5865 |
12 Mar 20 |
nicklas |
4058 |
barcodeSequences2.put("UDI0014", "GGAAGCAG"); |
| 5865 |
12 Mar 20 |
nicklas |
4059 |
barcodeSequences2.put("UDI0015", "TCGTGACC"); |
| 5865 |
12 Mar 20 |
nicklas |
4060 |
barcodeSequences2.put("UDI0016", "CTACAGTT"); |
| 5865 |
12 Mar 20 |
nicklas |
4061 |
barcodeSequences2.put("UDI0017", "ATATTCAC"); |
| 5865 |
12 Mar 20 |
nicklas |
4062 |
barcodeSequences2.put("UDI0018", "GCGCCTGT"); |
| 5865 |
12 Mar 20 |
nicklas |
4063 |
barcodeSequences2.put("UDI0019", "ACTCTATG"); |
| 5865 |
12 Mar 20 |
nicklas |
4064 |
barcodeSequences2.put("UDI0020", "GTCTCGCA"); |
| 5865 |
12 Mar 20 |
nicklas |
4065 |
barcodeSequences2.put("UDI0021", "AAGACGTC"); |
| 5865 |
12 Mar 20 |
nicklas |
4066 |
barcodeSequences2.put("UDI0022", "GGAGTACT"); |
| 5865 |
12 Mar 20 |
nicklas |
4067 |
barcodeSequences2.put("UDI0023", "ACCGGCCA"); |
| 5865 |
12 Mar 20 |
nicklas |
4068 |
barcodeSequences2.put("UDI0024", "GTTAATTG"); |
| 5865 |
12 Mar 20 |
nicklas |
4069 |
barcodeSequences2.put("UDI0025", "AACCGCGG"); |
| 5865 |
12 Mar 20 |
nicklas |
4070 |
barcodeSequences2.put("UDI0026", "GGTTATAA"); |
| 5865 |
12 Mar 20 |
nicklas |
4071 |
barcodeSequences2.put("UDI0027", "CCAAGTCC"); |
| 5865 |
12 Mar 20 |
nicklas |
4072 |
barcodeSequences2.put("UDI0028", "TTGGACTT"); |
| 5865 |
12 Mar 20 |
nicklas |
4073 |
barcodeSequences2.put("UDI0029", "CAGTGGAT"); |
| 5865 |
12 Mar 20 |
nicklas |
4074 |
barcodeSequences2.put("UDI0030", "TGACAAGC"); |
| 5865 |
12 Mar 20 |
nicklas |
4075 |
barcodeSequences2.put("UDI0031", "CTAGCTTG"); |
| 5865 |
12 Mar 20 |
nicklas |
4076 |
barcodeSequences2.put("UDI0032", "TCGATCCA"); |
| 5893 |
07 Apr 20 |
nicklas |
4077 |
barcodeSequences2.put("UDI0033", "CCTGAACT"); |
| 5893 |
07 Apr 20 |
nicklas |
4078 |
barcodeSequences2.put("UDI0034", "TTCAGGTC"); |
| 5893 |
07 Apr 20 |
nicklas |
4079 |
barcodeSequences2.put("UDI0035", "AGTAGAGA"); |
| 5893 |
07 Apr 20 |
nicklas |
4080 |
barcodeSequences2.put("UDI0036", "GACGAGAG"); |
| 5893 |
07 Apr 20 |
nicklas |
4081 |
barcodeSequences2.put("UDI0037", "AGACTTGG"); |
| 5893 |
07 Apr 20 |
nicklas |
4082 |
barcodeSequences2.put("UDI0038", "GAGTCCAA"); |
| 5893 |
07 Apr 20 |
nicklas |
4083 |
barcodeSequences2.put("UDI0039", "CTTAAGCC"); |
| 5893 |
07 Apr 20 |
nicklas |
4084 |
barcodeSequences2.put("UDI0040", "TCCGGATT"); |
| 5893 |
07 Apr 20 |
nicklas |
4085 |
barcodeSequences2.put("UDI0041", "CTGTATTA"); |
| 5893 |
07 Apr 20 |
nicklas |
4086 |
barcodeSequences2.put("UDI0042", "TCACGCCG"); |
| 5893 |
07 Apr 20 |
nicklas |
4087 |
barcodeSequences2.put("UDI0043", "ACTTACAT"); |
| 5893 |
07 Apr 20 |
nicklas |
4088 |
barcodeSequences2.put("UDI0044", "GTCCGTGC"); |
| 5893 |
07 Apr 20 |
nicklas |
4089 |
barcodeSequences2.put("UDI0045", "AAGGTACC"); |
| 5893 |
07 Apr 20 |
nicklas |
4090 |
barcodeSequences2.put("UDI0046", "GGAACGTT"); |
| 5893 |
07 Apr 20 |
nicklas |
4091 |
barcodeSequences2.put("UDI0047", "AATTCTGC"); |
| 5893 |
07 Apr 20 |
nicklas |
4092 |
barcodeSequences2.put("UDI0048", "GGCCTCAT"); |
| 5893 |
07 Apr 20 |
nicklas |
4093 |
barcodeSequences2.put("UDI0049", "ATCTTAGT"); |
| 5893 |
07 Apr 20 |
nicklas |
4094 |
barcodeSequences2.put("UDI0050", "GCTCCGAC"); |
| 5893 |
07 Apr 20 |
nicklas |
4095 |
barcodeSequences2.put("UDI0051", "ATACCAAG"); |
| 5893 |
07 Apr 20 |
nicklas |
4096 |
barcodeSequences2.put("UDI0052", "GCGTTGGA"); |
| 5893 |
07 Apr 20 |
nicklas |
4097 |
barcodeSequences2.put("UDI0053", "CTTCACGG"); |
| 5893 |
07 Apr 20 |
nicklas |
4098 |
barcodeSequences2.put("UDI0054", "TCCTGTAA"); |
| 5893 |
07 Apr 20 |
nicklas |
4099 |
barcodeSequences2.put("UDI0055", "AGAATGCC"); |
| 5893 |
07 Apr 20 |
nicklas |
4100 |
barcodeSequences2.put("UDI0056", "GAGGCATT"); |
| 5893 |
07 Apr 20 |
nicklas |
4101 |
barcodeSequences2.put("UDI0057", "CCTCGGTA"); |
| 5893 |
07 Apr 20 |
nicklas |
4102 |
barcodeSequences2.put("UDI0058", "TTCTAACG"); |
| 5893 |
07 Apr 20 |
nicklas |
4103 |
barcodeSequences2.put("UDI0059", "ATGAGGCT"); |
| 5893 |
07 Apr 20 |
nicklas |
4104 |
barcodeSequences2.put("UDI0060", "GCAGAATC"); |
| 5893 |
07 Apr 20 |
nicklas |
4105 |
barcodeSequences2.put("UDI0061", "CACTACGA"); |
| 5893 |
07 Apr 20 |
nicklas |
4106 |
barcodeSequences2.put("UDI0062", "TGTCGTAG"); |
| 5893 |
07 Apr 20 |
nicklas |
4107 |
barcodeSequences2.put("UDI0063", "ACCACTTA"); |
| 5893 |
07 Apr 20 |
nicklas |
4108 |
barcodeSequences2.put("UDI0064", "GTTGTCCG"); |
| 5893 |
07 Apr 20 |
nicklas |
4109 |
barcodeSequences2.put("UDI0065", "ATCCATAT"); |
| 5893 |
07 Apr 20 |
nicklas |
4110 |
barcodeSequences2.put("UDI0066", "GCTTGCGC"); |
| 5893 |
07 Apr 20 |
nicklas |
4111 |
barcodeSequences2.put("UDI0067", "AGTATCTT"); |
| 5893 |
07 Apr 20 |
nicklas |
4112 |
barcodeSequences2.put("UDI0068", "GACGCTCC"); |
| 5893 |
07 Apr 20 |
nicklas |
4113 |
barcodeSequences2.put("UDI0069", "CATGCCAT"); |
| 5893 |
07 Apr 20 |
nicklas |
4114 |
barcodeSequences2.put("UDI0070", "TGCATTGC"); |
| 5893 |
07 Apr 20 |
nicklas |
4115 |
barcodeSequences2.put("UDI0071", "ATTGGAAC"); |
| 5893 |
07 Apr 20 |
nicklas |
4116 |
barcodeSequences2.put("UDI0072", "GCCAAGGT"); |
| 5893 |
07 Apr 20 |
nicklas |
4117 |
barcodeSequences2.put("UDI0073", "CGAGATAT"); |
| 5893 |
07 Apr 20 |
nicklas |
4118 |
barcodeSequences2.put("UDI0074", "TAGAGCGC"); |
| 5893 |
07 Apr 20 |
nicklas |
4119 |
barcodeSequences2.put("UDI0075", "AACCTGTT"); |
| 5893 |
07 Apr 20 |
nicklas |
4120 |
barcodeSequences2.put("UDI0076", "GGTTCACC"); |
| 5893 |
07 Apr 20 |
nicklas |
4121 |
barcodeSequences2.put("UDI0077", "CATTGTTG"); |
| 5893 |
07 Apr 20 |
nicklas |
4122 |
barcodeSequences2.put("UDI0078", "TGCCACCA"); |
| 5893 |
07 Apr 20 |
nicklas |
4123 |
barcodeSequences2.put("UDI0079", "CTCTGCCT"); |
| 5893 |
07 Apr 20 |
nicklas |
4124 |
barcodeSequences2.put("UDI0080", "TCTCATTC"); |
| 5893 |
07 Apr 20 |
nicklas |
4125 |
barcodeSequences2.put("UDI0081", "ACGCCGCA"); |
| 5893 |
07 Apr 20 |
nicklas |
4126 |
barcodeSequences2.put("UDI0082", "GTATTATG"); |
| 5893 |
07 Apr 20 |
nicklas |
4127 |
barcodeSequences2.put("UDI0083", "GATAGATC"); |
| 5893 |
07 Apr 20 |
nicklas |
4128 |
barcodeSequences2.put("UDI0084", "AGCGAGCT"); |
| 5893 |
07 Apr 20 |
nicklas |
4129 |
barcodeSequences2.put("UDI0085", "CAGTTCCG"); |
| 5893 |
07 Apr 20 |
nicklas |
4130 |
barcodeSequences2.put("UDI0086", "TGACCTTA"); |
| 5893 |
07 Apr 20 |
nicklas |
4131 |
barcodeSequences2.put("UDI0087", "CTAGGCAA"); |
| 5893 |
07 Apr 20 |
nicklas |
4132 |
barcodeSequences2.put("UDI0088", "TCGAATGG"); |
| 5893 |
07 Apr 20 |
nicklas |
4133 |
barcodeSequences2.put("UDI0089", "CTTAGTGT"); |
| 5893 |
07 Apr 20 |
nicklas |
4134 |
barcodeSequences2.put("UDI0090", "TCCGACAC"); |
| 5893 |
07 Apr 20 |
nicklas |
4135 |
barcodeSequences2.put("UDI0091", "AACAGGAA"); |
| 5893 |
07 Apr 20 |
nicklas |
4136 |
barcodeSequences2.put("UDI0092", "GGTGAAGG"); |
| 5893 |
07 Apr 20 |
nicklas |
4137 |
barcodeSequences2.put("UDI0093", "CCTGTGGC"); |
| 5893 |
07 Apr 20 |
nicklas |
4138 |
barcodeSequences2.put("UDI0094", "TTCACAAT"); |
| 5893 |
07 Apr 20 |
nicklas |
4139 |
barcodeSequences2.put("UDI0095", "ACACGAGT"); |
| 5893 |
07 Apr 20 |
nicklas |
4140 |
barcodeSequences2.put("UDI0096", "GTGTAGAC"); |
| 5865 |
12 Mar 20 |
nicklas |
4141 |
} |
| 5865 |
12 Mar 20 |
nicklas |
4142 |
|
| 5865 |
12 Mar 20 |
nicklas |
4143 |
return barcodeSequences2.get(barcode); |
| 5865 |
12 Mar 20 |
nicklas |
4144 |
} |
| 2350 |
10 Apr 14 |
nicklas |
4145 |
|
| 1570 |
16 Mar 12 |
nicklas |
4146 |
|
| 1546 |
02 Mar 12 |
nicklas |
4147 |
/** |
| 1639 |
09 May 12 |
nicklas |
Store options for enumerated annotation types and min/max values for numerical annotations. |
| 1284 |
08 Feb 11 |
nicklas |
4149 |
*/ |
| 1639 |
09 May 12 |
nicklas |
4150 |
static class ValueOptions |
| 1284 |
08 Feb 11 |
nicklas |
4151 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4152 |
private final Object[] options; |
| 1639 |
09 May 12 |
nicklas |
4153 |
private final Integer min; |
| 1639 |
09 May 12 |
nicklas |
4154 |
private final Integer max; |
| 1639 |
09 May 12 |
nicklas |
4155 |
|
| 1639 |
09 May 12 |
nicklas |
4156 |
/** |
| 1639 |
09 May 12 |
nicklas |
The annotation type is an enumerated annotation type with the following options. |
| 1639 |
09 May 12 |
nicklas |
4158 |
*/ |
| 1639 |
09 May 12 |
nicklas |
4159 |
ValueOptions(Object... options) |
| 1284 |
08 Feb 11 |
nicklas |
4160 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4161 |
this.options = options; |
| 1639 |
09 May 12 |
nicklas |
4162 |
this.min = null; |
| 1639 |
09 May 12 |
nicklas |
4163 |
this.max = null; |
| 1284 |
08 Feb 11 |
nicklas |
4164 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4165 |
|
| 1284 |
08 Feb 11 |
nicklas |
4166 |
/** |
| 1639 |
09 May 12 |
nicklas |
The annotation type is a numeric annotation type with the following restrictions. |
| 1639 |
09 May 12 |
nicklas |
4168 |
*/ |
| 1639 |
09 May 12 |
nicklas |
4169 |
ValueOptions(Integer min, Integer max) |
| 1639 |
09 May 12 |
nicklas |
4170 |
{ |
| 1639 |
09 May 12 |
nicklas |
4171 |
this.min = min; |
| 1639 |
09 May 12 |
nicklas |
4172 |
this.max = max; |
| 1639 |
09 May 12 |
nicklas |
4173 |
this.options = null; |
| 1639 |
09 May 12 |
nicklas |
4174 |
} |
| 1639 |
09 May 12 |
nicklas |
4175 |
|
| 1639 |
09 May 12 |
nicklas |
4176 |
boolean isEnumeration() |
| 1639 |
09 May 12 |
nicklas |
4177 |
{ |
| 1639 |
09 May 12 |
nicklas |
4178 |
return options != null; |
| 1639 |
09 May 12 |
nicklas |
4179 |
} |
| 1639 |
09 May 12 |
nicklas |
4180 |
|
| 1639 |
09 May 12 |
nicklas |
4181 |
Integer getMin() |
| 1639 |
09 May 12 |
nicklas |
4182 |
{ |
| 1639 |
09 May 12 |
nicklas |
4183 |
return min; |
| 1639 |
09 May 12 |
nicklas |
4184 |
} |
| 1639 |
09 May 12 |
nicklas |
4185 |
|
| 1639 |
09 May 12 |
nicklas |
4186 |
Integer getMax() |
| 1639 |
09 May 12 |
nicklas |
4187 |
{ |
| 1639 |
09 May 12 |
nicklas |
4188 |
return max; |
| 1639 |
09 May 12 |
nicklas |
4189 |
} |
| 1639 |
09 May 12 |
nicklas |
4190 |
|
| 1639 |
09 May 12 |
nicklas |
4191 |
/** |
| 1284 |
08 Feb 11 |
nicklas |
Get the options as a List. |
| 1284 |
08 Feb 11 |
nicklas |
4193 |
*/ |
| 1284 |
08 Feb 11 |
nicklas |
4194 |
List<?> getList() |
| 1284 |
08 Feb 11 |
nicklas |
4195 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4196 |
return Arrays.asList(options); |
| 1284 |
08 Feb 11 |
nicklas |
4197 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4198 |
|
| 1284 |
08 Feb 11 |
nicklas |
4199 |
/** |
| 1284 |
08 Feb 11 |
nicklas |
Get the options as an array. |
| 1284 |
08 Feb 11 |
nicklas |
4201 |
*/ |
| 1284 |
08 Feb 11 |
nicklas |
4202 |
Object[] getArray() |
| 1284 |
08 Feb 11 |
nicklas |
4203 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4204 |
return options; |
| 1284 |
08 Feb 11 |
nicklas |
4205 |
} |
| 1889 |
27 Feb 13 |
nicklas |
4206 |
|
| 1889 |
27 Feb 13 |
nicklas |
4207 |
/** |
| 1889 |
27 Feb 13 |
nicklas |
Add options missing in the current annotation type. |
| 1889 |
27 Feb 13 |
nicklas |
4209 |
*/ |
| 1889 |
27 Feb 13 |
nicklas |
4210 |
void applyEnumeration(AnnotationType at) |
| 1889 |
27 Feb 13 |
nicklas |
4211 |
{ |
| 1889 |
27 Feb 13 |
nicklas |
4212 |
List<Object> values = new ArrayList<Object>(at.getValues()); |
| 1889 |
27 Feb 13 |
nicklas |
4213 |
for (Object opt : options) |
| 1889 |
27 Feb 13 |
nicklas |
4214 |
{ |
| 1889 |
27 Feb 13 |
nicklas |
4215 |
if (!values.contains(opt)) values.add(opt); |
| 1889 |
27 Feb 13 |
nicklas |
4216 |
} |
| 1889 |
27 Feb 13 |
nicklas |
4217 |
at.setValues(values); |
| 1889 |
27 Feb 13 |
nicklas |
4218 |
} |
| 5894 |
08 Apr 20 |
nicklas |
4219 |
|
| 5894 |
08 Apr 20 |
nicklas |
4220 |
/** |
| 5894 |
08 Apr 20 |
nicklas |
Get all required options that are missing in the current |
| 5894 |
08 Apr 20 |
nicklas |
annotation type. |
| 5894 |
08 Apr 20 |
nicklas |
@since 4.26 |
| 5894 |
08 Apr 20 |
nicklas |
4224 |
*/ |
| 5894 |
08 Apr 20 |
nicklas |
4225 |
List<Object> getMissingOptions(AnnotationType at) |
| 5894 |
08 Apr 20 |
nicklas |
4226 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
4227 |
List<Object> missing = new ArrayList<Object>(); |
| 5894 |
08 Apr 20 |
nicklas |
4228 |
List<Object> values = at.getValues(); |
| 5894 |
08 Apr 20 |
nicklas |
4229 |
for (Object opt : options) |
| 5894 |
08 Apr 20 |
nicklas |
4230 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
4231 |
if (!values.contains(opt)) missing.add(opt); |
| 5894 |
08 Apr 20 |
nicklas |
4232 |
} |
| 5894 |
08 Apr 20 |
nicklas |
4233 |
return missing; |
| 5894 |
08 Apr 20 |
nicklas |
4234 |
} |
| 5894 |
08 Apr 20 |
nicklas |
4235 |
|
| 5894 |
08 Apr 20 |
nicklas |
4236 |
|
| 5894 |
08 Apr 20 |
nicklas |
4237 |
/** |
| 5894 |
08 Apr 20 |
nicklas |
Get all extract options that are defined by the current annotation |
| 5894 |
08 Apr 20 |
nicklas |
type. |
| 5894 |
08 Apr 20 |
nicklas |
@since 4.26 |
| 5894 |
08 Apr 20 |
nicklas |
4241 |
*/ |
| 5894 |
08 Apr 20 |
nicklas |
4242 |
List<Object> getExtraOptions(AnnotationType at) |
| 5894 |
08 Apr 20 |
nicklas |
4243 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
4244 |
List<Object> extra = new ArrayList<Object>(); |
| 5894 |
08 Apr 20 |
nicklas |
4245 |
List<?> all = getList(); |
| 5894 |
08 Apr 20 |
nicklas |
4246 |
for (Object v : at.getValues()) |
| 5894 |
08 Apr 20 |
nicklas |
4247 |
{ |
| 5894 |
08 Apr 20 |
nicklas |
4248 |
if (!all.contains(v)) extra.add(v); |
| 5894 |
08 Apr 20 |
nicklas |
4249 |
} |
| 5894 |
08 Apr 20 |
nicklas |
4250 |
return extra; |
| 5894 |
08 Apr 20 |
nicklas |
4251 |
} |
| 5894 |
08 Apr 20 |
nicklas |
4252 |
|
| 1284 |
08 Feb 11 |
nicklas |
4253 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4254 |
|
| 1284 |
08 Feb 11 |
nicklas |
4255 |
/** |
| 1284 |
08 Feb 11 |
nicklas |
Store permissions that can be applied to shareable items. |
| 1284 |
08 Feb 11 |
nicklas |
4257 |
*/ |
| 1284 |
08 Feb 11 |
nicklas |
4258 |
static class PermissionOptions |
| 1284 |
08 Feb 11 |
nicklas |
4259 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4260 |
private Map<Group, Permission> groupPermissions; |
| 1310 |
04 Mar 11 |
nicklas |
4261 |
private Map<Project, Permission> projectPermissions; |
| 1284 |
08 Feb 11 |
nicklas |
4262 |
private String message; |
| 1284 |
08 Feb 11 |
nicklas |
4263 |
|
| 1284 |
08 Feb 11 |
nicklas |
4264 |
PermissionOptions() |
| 1284 |
08 Feb 11 |
nicklas |
4265 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4266 |
groupPermissions = new HashMap<Group, Permission>(); |
| 1310 |
04 Mar 11 |
nicklas |
4267 |
projectPermissions = new HashMap<Project, Permission>(); |
| 1284 |
08 Feb 11 |
nicklas |
4268 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4269 |
|
| 1284 |
08 Feb 11 |
nicklas |
4270 |
/** |
| 6277 |
03 Jun 21 |
nicklas |
Merge the permission options in this instance with |
| 6277 |
03 Jun 21 |
nicklas |
another instance. The merge creates a new instance |
| 6277 |
03 Jun 21 |
nicklas |
and doesn't affect either this nor the other instance. |
| 6277 |
03 Jun 21 |
nicklas |
4274 |
*/ |
| 6277 |
03 Jun 21 |
nicklas |
4275 |
PermissionOptions merge(PermissionOptions other) |
| 6277 |
03 Jun 21 |
nicklas |
4276 |
{ |
| 6277 |
03 Jun 21 |
nicklas |
4277 |
PermissionOptions merged = new PermissionOptions(); |
| 6277 |
03 Jun 21 |
nicklas |
4278 |
merged.groupPermissions.putAll(this.groupPermissions); |
| 6277 |
03 Jun 21 |
nicklas |
4279 |
merged.projectPermissions.putAll(projectPermissions); |
| 6277 |
03 Jun 21 |
nicklas |
4280 |
|
| 6277 |
03 Jun 21 |
nicklas |
4281 |
for (Map.Entry<Project, Permission> entry : other.projectPermissions.entrySet()) |
| 6277 |
03 Jun 21 |
nicklas |
4282 |
{ |
| 6277 |
03 Jun 21 |
nicklas |
4283 |
Project p = entry.getKey(); |
| 6277 |
03 Jun 21 |
nicklas |
4284 |
Permission perm = entry.getValue(); |
| 6277 |
03 Jun 21 |
nicklas |
4285 |
boolean doMerge = true; |
| 6277 |
03 Jun 21 |
nicklas |
4286 |
if (merged.projectPermissions.containsKey(p)) |
| 6277 |
03 Jun 21 |
nicklas |
4287 |
{ |
| 6277 |
03 Jun 21 |
nicklas |
// Should we replace? |
| 6277 |
03 Jun 21 |
nicklas |
4289 |
Permission p1 = merged.projectPermissions.get(p); |
| 6277 |
03 Jun 21 |
nicklas |
4290 |
if (p1 != null) |
| 6277 |
03 Jun 21 |
nicklas |
4291 |
{ |
| 6277 |
03 Jun 21 |
nicklas |
4292 |
if (perm == null || perm.ordinal() < p1.ordinal()) doMerge = false; |
| 6277 |
03 Jun 21 |
nicklas |
4293 |
} |
| 6277 |
03 Jun 21 |
nicklas |
4294 |
} |
| 6277 |
03 Jun 21 |
nicklas |
4295 |
if (doMerge) merged.projectPermissions.put(p, perm); |
| 6277 |
03 Jun 21 |
nicklas |
4296 |
} |
| 6277 |
03 Jun 21 |
nicklas |
4297 |
|
| 6277 |
03 Jun 21 |
nicklas |
4298 |
for (Map.Entry<Group, Permission> entry : other.groupPermissions.entrySet()) |
| 6277 |
03 Jun 21 |
nicklas |
4299 |
{ |
| 6277 |
03 Jun 21 |
nicklas |
4300 |
Group g = entry.getKey(); |
| 6277 |
03 Jun 21 |
nicklas |
4301 |
Permission perm = entry.getValue(); |
| 6277 |
03 Jun 21 |
nicklas |
4302 |
boolean doMerge = true; |
| 6277 |
03 Jun 21 |
nicklas |
4303 |
if (merged.groupPermissions.containsKey(g)) |
| 6277 |
03 Jun 21 |
nicklas |
4304 |
{ |
| 6277 |
03 Jun 21 |
nicklas |
// Should we replace? |
| 6277 |
03 Jun 21 |
nicklas |
4306 |
Permission p1 = merged.groupPermissions.get(g); |
| 6277 |
03 Jun 21 |
nicklas |
4307 |
if (p1 != null) |
| 6277 |
03 Jun 21 |
nicklas |
4308 |
{ |
| 6277 |
03 Jun 21 |
nicklas |
4309 |
if (perm == null || perm.ordinal() < p1.ordinal()) doMerge = false; |
| 6277 |
03 Jun 21 |
nicklas |
4310 |
} |
| 6277 |
03 Jun 21 |
nicklas |
4311 |
} |
| 6277 |
03 Jun 21 |
nicklas |
4312 |
if (doMerge) merged.groupPermissions.put(g, perm); |
| 6277 |
03 Jun 21 |
nicklas |
4313 |
} |
| 6277 |
03 Jun 21 |
nicklas |
4314 |
|
| 6277 |
03 Jun 21 |
nicklas |
4315 |
return merged; |
| 6277 |
03 Jun 21 |
nicklas |
4316 |
} |
| 6277 |
03 Jun 21 |
nicklas |
4317 |
|
| 6277 |
03 Jun 21 |
nicklas |
4318 |
/** |
| 1284 |
08 Feb 11 |
nicklas |
Set a permission for the given group. |
| 1284 |
08 Feb 11 |
nicklas |
4320 |
*/ |
| 1284 |
08 Feb 11 |
nicklas |
4321 |
void set(Group g, Permission p) |
| 1284 |
08 Feb 11 |
nicklas |
4322 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4323 |
groupPermissions.put(g, p); |
| 1284 |
08 Feb 11 |
nicklas |
4324 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4325 |
|
| 1284 |
08 Feb 11 |
nicklas |
4326 |
/** |
| 1310 |
04 Mar 11 |
nicklas |
Set a permission for the given project. |
| 1310 |
04 Mar 11 |
nicklas |
4328 |
*/ |
| 1310 |
04 Mar 11 |
nicklas |
4329 |
void set(Project pr, Permission p) |
| 1310 |
04 Mar 11 |
nicklas |
4330 |
{ |
| 1310 |
04 Mar 11 |
nicklas |
4331 |
projectPermissions.put(pr, p); |
| 1310 |
04 Mar 11 |
nicklas |
4332 |
} |
| 1310 |
04 Mar 11 |
nicklas |
4333 |
|
| 1310 |
04 Mar 11 |
nicklas |
4334 |
/** |
| 1284 |
08 Feb 11 |
nicklas |
Check if the given item includes at least all the required permissions. |
| 1284 |
08 Feb 11 |
nicklas |
@return TRUE if all permissions are ok, FALSE if not (call getMessage()) |
| 1284 |
08 Feb 11 |
nicklas |
to get more information. |
| 1284 |
08 Feb 11 |
nicklas |
4338 |
*/ |
| 1284 |
08 Feb 11 |
nicklas |
4339 |
boolean checkPermissions(SharedItem item) |
| 1284 |
08 Feb 11 |
nicklas |
4340 |
{ |
| 1310 |
04 Mar 11 |
nicklas |
4341 |
ProjectKey pKey = item.getProjectKey(); |
| 1310 |
04 Mar 11 |
nicklas |
4342 |
for (Map.Entry<Project, Permission> entry : projectPermissions.entrySet()) |
| 1310 |
04 Mar 11 |
nicklas |
4343 |
{ |
| 1310 |
04 Mar 11 |
nicklas |
4344 |
Project pr = entry.getKey(); |
| 1310 |
04 Mar 11 |
nicklas |
4345 |
Permission p = entry.getValue(); |
| 2159 |
06 Dec 13 |
nicklas |
4346 |
|
| 2159 |
06 Dec 13 |
nicklas |
4347 |
Set<Permission> permissions = pKey != null ? pKey.getPermissions(pr) : null; |
| 2159 |
06 Dec 13 |
nicklas |
4348 |
if (p == null) |
| 1310 |
04 Mar 11 |
nicklas |
4349 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
// The item should not be shared to project 'pr' |
| 2159 |
06 Dec 13 |
nicklas |
4351 |
if (permissions != null && permissions.size() > 0) |
| 2159 |
06 Dec 13 |
nicklas |
4352 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
4353 |
message = "Should not be shared to project: " + pr.getName() + " (" + permissions + ")"; |
| 2159 |
06 Dec 13 |
nicklas |
4354 |
return false; |
| 2159 |
06 Dec 13 |
nicklas |
4355 |
} |
| 1310 |
04 Mar 11 |
nicklas |
4356 |
} |
| 2159 |
06 Dec 13 |
nicklas |
4357 |
else |
| 2159 |
06 Dec 13 |
nicklas |
4358 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
// The item should be shared to project 'pr' with permission 'p' |
| 2159 |
06 Dec 13 |
nicklas |
4360 |
if (pKey == null || !permissions.contains(p)) |
| 2159 |
06 Dec 13 |
nicklas |
4361 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
4362 |
message = "Not shared to project: " + pr.getName() + " (" + p + ")"; |
| 2159 |
06 Dec 13 |
nicklas |
4363 |
return false; |
| 2159 |
06 Dec 13 |
nicklas |
4364 |
} |
| 2159 |
06 Dec 13 |
nicklas |
4365 |
} |
| 1310 |
04 Mar 11 |
nicklas |
4366 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4367 |
ItemKey key = item.getItemKey(); |
| 1284 |
08 Feb 11 |
nicklas |
4368 |
for (Map.Entry<Group, Permission> entry : groupPermissions.entrySet()) |
| 1284 |
08 Feb 11 |
nicklas |
4369 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4370 |
Group g = entry.getKey(); |
| 1284 |
08 Feb 11 |
nicklas |
4371 |
Permission p = entry.getValue(); |
| 2159 |
06 Dec 13 |
nicklas |
4372 |
|
| 2238 |
20 Feb 14 |
nicklas |
4373 |
Set<Permission> permissions = key != null ? key.getPermissions(g) : null; |
| 2159 |
06 Dec 13 |
nicklas |
4374 |
if (p == null) |
| 1284 |
08 Feb 11 |
nicklas |
4375 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
// The item should not be shared to group 'g' |
| 2159 |
06 Dec 13 |
nicklas |
4377 |
if (permissions != null && permissions.size() > 0) |
| 2159 |
06 Dec 13 |
nicklas |
4378 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
4379 |
message = "Should not be shared to group: " + g.getName() + " (" + permissions + ")"; |
| 2159 |
06 Dec 13 |
nicklas |
4380 |
return false; |
| 2159 |
06 Dec 13 |
nicklas |
4381 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4382 |
} |
| 2159 |
06 Dec 13 |
nicklas |
4383 |
else |
| 2159 |
06 Dec 13 |
nicklas |
4384 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
// The item should be shared to group 'g' with permission 'p' |
| 2159 |
06 Dec 13 |
nicklas |
4386 |
if (key == null || !key.getPermissions(g).contains(p)) |
| 2159 |
06 Dec 13 |
nicklas |
4387 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
4388 |
message = "Not shared to group: " + g.getName() + " (" + p + ")"; |
| 2159 |
06 Dec 13 |
nicklas |
4389 |
return false; |
| 2159 |
06 Dec 13 |
nicklas |
4390 |
} |
| 2159 |
06 Dec 13 |
nicklas |
4391 |
} |
| 2159 |
06 Dec 13 |
nicklas |
4392 |
|
| 1284 |
08 Feb 11 |
nicklas |
4393 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4394 |
return true; |
| 1284 |
08 Feb 11 |
nicklas |
4395 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4396 |
|
| 1284 |
08 Feb 11 |
nicklas |
4397 |
/** |
| 1284 |
08 Feb 11 |
nicklas |
More information about missing permission from the checkPermissions() method. |
| 1284 |
08 Feb 11 |
nicklas |
4399 |
*/ |
| 1284 |
08 Feb 11 |
nicklas |
4400 |
String getMessage() |
| 1284 |
08 Feb 11 |
nicklas |
4401 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4402 |
return message; |
| 1284 |
08 Feb 11 |
nicklas |
4403 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4404 |
|
| 1284 |
08 Feb 11 |
nicklas |
4405 |
/** |
| 1284 |
08 Feb 11 |
nicklas |
Apply all permissions to the given item. |
| 1284 |
08 Feb 11 |
nicklas |
4407 |
*/ |
| 1284 |
08 Feb 11 |
nicklas |
4408 |
void applyPermissions(SharedItem item) |
| 1284 |
08 Feb 11 |
nicklas |
4409 |
{ |
| 6864 |
04 Nov 22 |
nicklas |
4410 |
if (!item.isInDatabase()) |
| 6864 |
04 Nov 22 |
nicklas |
4411 |
{ |
| 6864 |
04 Nov 22 |
nicklas |
// Reset is needed for new items since otherwise BASE may set default values |
| 6864 |
04 Nov 22 |
nicklas |
4413 |
item.setProjectKey(null); |
| 6864 |
04 Nov 22 |
nicklas |
4414 |
item.setItemKey(null); |
| 6864 |
04 Nov 22 |
nicklas |
4415 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4416 |
MultiPermissions mp = new MultiPermissions(Collections.singleton(item)); |
| 1284 |
08 Feb 11 |
nicklas |
4417 |
for (Map.Entry<Group, Permission> entry : groupPermissions.entrySet()) |
| 1284 |
08 Feb 11 |
nicklas |
4418 |
{ |
| 1284 |
08 Feb 11 |
nicklas |
4419 |
Group g = entry.getKey(); |
| 1284 |
08 Feb 11 |
nicklas |
4420 |
Permission p = entry.getValue(); |
| 2159 |
06 Dec 13 |
nicklas |
4421 |
if (p == null) |
| 2159 |
06 Dec 13 |
nicklas |
4422 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
4423 |
mp.setPermissions(g, null); |
| 2159 |
06 Dec 13 |
nicklas |
4424 |
} |
| 2159 |
06 Dec 13 |
nicklas |
4425 |
else |
| 2159 |
06 Dec 13 |
nicklas |
4426 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
4427 |
mp.addPermissions(g, Collections.singleton(p)); |
| 2159 |
06 Dec 13 |
nicklas |
4428 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4429 |
} |
| 1310 |
04 Mar 11 |
nicklas |
4430 |
for (Map.Entry<Project, Permission> entry : projectPermissions.entrySet()) |
| 1310 |
04 Mar 11 |
nicklas |
4431 |
{ |
| 1310 |
04 Mar 11 |
nicklas |
4432 |
Project pr = entry.getKey(); |
| 1310 |
04 Mar 11 |
nicklas |
4433 |
Permission p = entry.getValue(); |
| 2159 |
06 Dec 13 |
nicklas |
4434 |
if (p == null) |
| 2159 |
06 Dec 13 |
nicklas |
4435 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
4436 |
mp.setPermissions(pr, null); |
| 2159 |
06 Dec 13 |
nicklas |
4437 |
} |
| 2159 |
06 Dec 13 |
nicklas |
4438 |
else |
| 2159 |
06 Dec 13 |
nicklas |
4439 |
{ |
| 2159 |
06 Dec 13 |
nicklas |
4440 |
mp.addPermissions(pr, Collections.singleton(p)); |
| 2159 |
06 Dec 13 |
nicklas |
4441 |
} |
| 1310 |
04 Mar 11 |
nicklas |
4442 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4443 |
mp.updateKeys(item.getDbControl()); |
| 1284 |
08 Feb 11 |
nicklas |
4444 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4445 |
} |
| 1284 |
08 Feb 11 |
nicklas |
4446 |
} |