Changeset 5977 for extensions/net.sf.basedb.relax/trunk/src

Timestamp:

Jun 24, 2020, 8:46:34 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1257: Remove the one-time-fix implemented for inserting lysate items between specimen and RNA

Location:

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

Files:

• fixit (deleted)
• servlet/InstallServlet.java (modified) (4 diffs)

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

@@ -43 +43 @@
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.SharedItem;
-import net.sf.basedb.core.SimpleProgressReporter;
 import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.Type;
@@ -56 +55 @@
 import net.sf.basedb.relax.dao.Rawdatatype;
 import net.sf.basedb.relax.dao.Subtype;
-import net.sf.basedb.relax.fixit.AddLysateFix;
 import net.sf.basedb.util.error.ThrowableUtil;
 import net.sf.basedb.util.uri.ConnectionManager;
@@ -126 +124 @@
         jsonChecks.add(checkSubtype(dc, Subtype.BLOOD, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.BLOOD_DNA, createIfMissing));
-        JSONObject jsonLysate = checkSubtype(dc, Subtype.LYSATE, createIfMissing);
-        jsonChecks.add(jsonLysate);
+        jsonChecks.add(checkSubtype(dc, Subtype.LYSATE, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.RNA, createIfMissing));
         jsonChecks.add(checkSubtype(dc, Subtype.DNA, createIfMissing));
@@ -186 +183 @@
         json.put("checks", jsonChecks);
         
-        if (jsonLysate.get("id") != null)
-        {
-          json.put("rnaToSpecimenCount", AddLysateFix.countRNAWithLinkToSpecimen(dc));
-        }
-        
         if (createIfMissing) 
         {
           dc.commit();
         }
-      }
-      else if ("FixRNALinkToLysate".equals(cmd))
-      {
-        Relax.checkIsAdmin(sc, "'" + cmd + "' wizard");
-        JSONArray jsonMessages = new JSONArray();
-        
-        SimpleProgressReporter progress = new SimpleProgressReporter(null);
-        progressId = "relink-rna-progress";
-        sc.setSessionSetting(progressId, progress);
-
-        progress.display(5, "Loading items...");
-
-        dc = sc.newDbControl();
-        
-        AddLysateFix fix = new AddLysateFix(jsonMessages);
-        fix.checkAndFixLysateAnnotationTypeCategory(dc);
-        fix.createLysateItems(dc, progress);
-
-        json.put("messages", jsonMessages);
-        progress.display(95, "Saving all changes to the database...");
-        dc.commit();
       }
     }