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package net.sf.basedb.reggie.plugins.release; |
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import java.util.List; |
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import org.json.simple.JSONArray; |
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import org.json.simple.JSONObject; |
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import net.sf.basedb.core.BioSource; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.Item; |
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import net.sf.basedb.core.ItemSubtype; |
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import net.sf.basedb.reggie.JsonUtil; |
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import net.sf.basedb.reggie.dao.Annotationtype; |
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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.NotNullFilter; |
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/** |
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Cohort writer implementation for the Patient items. |
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@since 4.5 |
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*/ |
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public class PatientWriter |
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extends CohortWriter |
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{ |
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private final ItemSubtype patientType; |
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public PatientWriter(DbControl dc, ReleaseWriterOptions options) |
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{ |
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super(dc, options); |
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this.patientType = Subtype.PATIENT.get(dc); |
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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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BioSource patient = item.getPatient().getItem(); |
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ItemSubtype type = patient.getItemSubtype(); |
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if (!patientType.equals(type)) return null; |
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JSONObject json = new JSONObject(); |
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json.put("name", patient.getExternalId()); |
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json.put("type", patient.getType().name()); |
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json.put("subtype", patientType.getName()); |
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JSONArray jsonAnnotations = new FilteredJSONArray(new NotNullFilter<>(false)); |
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jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.GENDER, patient, null)); |
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json.put("annotations", jsonAnnotations); |
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return JsonUtil.asArray(json); |
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} |
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@Override |
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public List<CohortTypeDef> getTypeDefsInJSON() |
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{ |
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DbControl dc = getDbControl(); |
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CohortTypeDefFactory patFactory = new CohortTypeDefFactory(dc, Item.BIOSOURCE, "Patient"); |
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patFactory.createAnnotationType(Annotationtype.GENDER); |
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return patFactory.allCreated(); |
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} |
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} |