Changeset 5786

Timestamp:

Dec 13, 2019, 9:22:38 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1214: Add support for external specimen

Fixes an issue with generating the secondary analysis top-level folder for external specimen. The old code stopped at the lysate level since it was only considering EXTRACT items. It now moves all the way up to the specimen item and the name of the specimen now becomes the name of the top-level folder.

It seems like all other wizards are working as expected.

Location:

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

Files:

• dao/Library.java (modified) (3 diffs)
• grid/DemuxJobCreator.java (modified) (1 diff)
• grid/MipsDemuxJobCreator.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Library.java

@@ -7 +7 @@
 import org.json.simple.JSONObject;
 
+import net.sf.basedb.core.BioMaterial;
 import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
@@ -15 +16 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemSubtype;
+import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.Tag;
 import net.sf.basedb.core.Type;
@@ -193 +195 @@
 
   /**
-    Load the top-most parent item that is an extract. This method is primarily
-    intended to find the root item (RNA or DNA) for an external library.
-    @since 4.23
-  */
-  public Extract getTopExtract(DbControl dc)
+    Load the top-most parent item that is an extract or sample. This method is primarily
+    intended to find the root item (RNA, DNA or Specimen) for an external library.
+    @since 4.23, 4.25
+  */
+  public BioMaterial getTopExtractOrSample(DbControl dc)
   {
     Extract e = getItem();
+    Sample s = null;
     while (e.getParentType() == Item.EXTRACT)
     {
       e = (Extract)e.getParent();
     }
-    return e;
+    if (e.getParentType() == Item.SAMPLE)
+    {
+      s = (Sample)e.getParent();
+      while (s.getParentType() == Item.SAMPLE)
+      {
+        s = (Sample)s.getParent();
+      }
+    }
+    return s == null ? e : s;
   }
   

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/DemuxJobCreator.java

@@ -269 +269 @@
     
     boolean isExternal = Reggie.isExternalItem(mergeName);
-    String rootName = isExternal ? lib.getTopExtract(dc).getName() : null;
+    String rootName = isExternal ? lib.getTopExtractOrSample(dc).getName() : null;
     
     String dataFilesFolder = ScriptUtil.checkValidPath(MergedSequences.generateDataFilesFolderForProjectArchive(mergeName, rootName, debug), true, true);

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MipsDemuxJobCreator.java

@@ -328 +328 @@
 
         String LB = isExternal ? Reggie.removePrefix(lib.getName()) : lib.getName();
-        String SM = isExternal ? Reggie.removePrefix(lib.getTopExtract(dc).getName()) : LB.replaceFirst("\\.(?!\\d).*", "");
+        String SM = isExternal ? Reggie.removePrefix(lib.getTopExtractOrSample(dc).getName()) : LB.replaceFirst("\\.(?!\\d).*", "");
         
         // Progress between 25-95%