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package net.sf.basedb.reggie.plugins.release; |
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import java.util.Arrays; |
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import java.util.HashSet; |
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import java.util.List; |
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|
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import org.json.simple.JSONArray; |
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|
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.DerivedBioAssay; |
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import net.sf.basedb.core.File; |
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import net.sf.basedb.core.ItemSubtype; |
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import net.sf.basedb.core.Job; |
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import net.sf.basedb.core.Location; |
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import net.sf.basedb.reggie.dao.AlignedSequences; |
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import net.sf.basedb.reggie.dao.Annotationtype; |
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import net.sf.basedb.reggie.dao.Datafiletype; |
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import net.sf.basedb.reggie.dao.Subtype; |
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import net.sf.basedb.reggie.json.FilteredJSONArray; |
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import net.sf.basedb.util.filter.Filter; |
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import net.sf.basedb.util.filter.NotNullFilter; |
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/** |
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Cohort writer implementation for the aligned sequences data table. |
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@since 4.5 |
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*/ |
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public class AlignedWriter |
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extends CohortWriter |
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{ |
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|
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private final ScriptWriter scriptWriter; |
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private final ItemSubtype hisatType; |
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private final Filter<File> fileFilterHisat; |
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public AlignedWriter(DbControl dc, ReleaseWriterOptions options, ScriptWriter scriptWriter) |
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{ |
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super(dc, options); |
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this.scriptWriter = scriptWriter; |
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this.hisatType = Subtype.HISAT_ALIGN_JOB.get(dc); |
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this.fileFilterHisat = new FileListFilter(new HashSet<String>(Arrays.asList( |
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"alignment.bai", "alignment.bam", "splicesites.tsv" |
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)), true, new FileLocationFilter(Location.EXTERNAL, true)); |
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} |
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|
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@Override |
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public JSONArray toJSONObjects(CohortItem item) |
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{ |
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if (scriptWriter == null) return null; |
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|
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List<AlignedSequences> alignments = item.getAlignedSequences(); |
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if (alignments.size() == 0) return null; |
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|
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for (AlignedSequences a : alignments) |
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{ |
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DerivedBioAssay aligned = a.getItem(); |
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Job job = aligned.getJob(); |
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if (job != null && hisatType.equals(job.getItemSubtype())) |
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{ |
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JSONArray jsonFiles = new FilteredJSONArray(new NotNullFilter<>(false)); |
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jsonFiles.addAll(item.getDataFilesJSON(Datafiletype.BAM, aligned, fileFilterHisat, false)); |
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jsonFiles.addAll(item.getLinkedFilesJSON(aligned, fileFilterHisat, false)); |
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if (jsonFiles.size() > 0) |
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{ |
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String dataFilesFolder = (String)item.getAnnotationValue(Annotationtype.DATA_FILES_FOLDER, aligned); |
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String releaseDataFilesFolder = item.toReleaseFolder(dataFilesFolder); |
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scriptWriter.addFiles(releaseDataFilesFolder, dataFilesFolder, null, jsonFiles); |
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} |
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} |
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} |
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|
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return null; |
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} |
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|
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} |