Changeset 5928

Timestamp:

Apr 29, 2020, 1:44:13 PM (5 weeks ago)

Author:

Nicklas Nordborg

Message:

Fixes #1240: Release exporter changes due to SSP

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• plugins/release/StringTieWriter.java (modified) (8 diffs)
• servlet/InstallServlet.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/release/StringTieWriter.java

@@ -1 +1 @@
 package net.sf.basedb.reggie.plugins.release;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashSet;
@@ -8 +9 @@
 import org.json.simple.JSONObject;
 
+import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.DerivedBioAssay;
@@ -13 +15 @@
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Location;
 import net.sf.basedb.core.Quantity;
@@ -18 +21 @@
 import net.sf.basedb.core.RawDataType;
 import net.sf.basedb.core.Type;
+import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
+import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.dao.Annotationtype;
 import net.sf.basedb.reggie.dao.Datafiletype;
@@ -37 +45 @@
   private final ScriptWriter scriptWriter;
   private final Filter<File> fileFilterStringTie;
+  private final List<Annotationtype> releaseTypes;
   
   public StringTieWriter(DbControl dc, ReleaseWriterOptions options, ScriptWriter scriptWriter)
@@ -46 +55 @@
       "t_data.ctab", "transcript_covered.gtf"
         )), true, new FileLocationFilter(Location.EXTERNAL, true));
+    
+    // Load all "STRINGTIE_Release" annotation types
+    ItemQuery<AnnotationType> query = AnnotationType.getQuery(Item.RAWBIOASSAY);
+    query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    query.join(Hql.innerJoin("categories", "cat"));
+    query.restrict(Restrictions.eq(Hql.property("cat", "name"), Expressions.string("STRINGTIE_Release")));
+    query.order(Orders.asc(Hql.property("name")));
+    List<AnnotationType> tmp = query.list(dc);
+    
+    releaseTypes = new ArrayList<>(tmp.size());
+    for (AnnotationType at : tmp)
+    {
+      releaseTypes.add(Annotationtype.get(at));
+    }
   }
   
@@ -80 +103 @@
       // From the rawbioassay item
       addCommonRawBioAssayAnnotations(item, rba, jsonAnnotations);
+      for (Annotationtype at : releaseTypes)
+      {
+        jsonAnnotations.add(item.getAnnotationJSON(at, rba, null));
+      }
 
       // From the AlignedSequences item
@@ -136 +163 @@
     rawFactory.createAnnotationType(Annotationtype.DATA_FILES_FOLDER).setProjectSpecificValues(true);
     rawFactory.createFileType(Datafiletype.GENERIC_RAWDATA, Rawdatatype.STRINGTIE.getPlatformId(), Rawdatatype.STRINGTIE.getVariantId());
-    
+
+    for (Annotationtype at : releaseTypes)
+    {
+      CohortAnnotationType cat = rawFactory.createAnnotationType(at);
+    }
+
     return rawFactory.allCreated();
   }

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -1079 +1079 @@
         jsonChecks.add(checkAnnotationTypeCategory(dc, "GEX_Release", "This category is for Cufflinks annotations that should be included in data releases.", createIfMissing));
         jsonChecks.add(checkAnnotationTypeCategory(dc, "VCALL_Release", "This category is for VariantCall annotations that should be included in data releases.", createIfMissing));
+        jsonChecks.add(checkAnnotationTypeCategory(dc, "STRINGTIE_Release", "This category is for StringTie annotations that should be included in data releases.", createIfMissing));
         
         // File servers