Changeset 6213

Timestamp:

Apr 15, 2021, 8:38:55 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1295: Registration of specimen handled by external lab

Added MergeType and DemuxType annotations to be used on Software/Protocol? items to make it possible to separate the external pipeline from the internal.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/analysis/demux_start.js (modified) (1 diff)
• resources/analysis/import_fastq.js (modified) (4 diffs)
• resources/batch/import-external-specimen.js (modified) (1 diff)
• resources/mipsanalysis/demux_start.js (modified) (1 diff)
• src/net/sf/basedb/reggie/autoconfirm/SequencingRunAutoConfirmer.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/dao/Annotationtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/FastqServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/analysis/demux_start.js

@@ -394 +394 @@
     frm.debug.checked = debug || location.protocol != 'https:';
 
-    Reggie.loadProtocols('DEMUX_PROTOCOL', 'demuxProtocol', 'PIPELINE', pipeline.name);
-    Reggie.loadSoftware('DEMUX_SOFTWARE', 'demuxSoftware', 'PIPELINE,PARAMETER_SET', pipeline.name);
-    Reggie.loadProtocols('MERGE_PROTOCOL', 'mergeProtocol', 'PIPELINE', pipeline.name);
-    Reggie.loadSoftware('MERGE_SOFTWARE', 'mergeSoftware', 'PIPELINE,PARAMETER_SET', pipeline.name);
+    Reggie.loadProtocols('DEMUX_PROTOCOL', 'demuxProtocol', 'PIPELINE,DEMUX_TYPE', pipeline.name+',Picard');
+    Reggie.loadSoftware('DEMUX_SOFTWARE', 'demuxSoftware', 'PIPELINE,DEMUX_TYPE,PARAMETER_SET', pipeline.name+',Picard');
+    Reggie.loadProtocols('MERGE_PROTOCOL', 'mergeProtocol', 'PIPELINE,MERGE_TYPE', pipeline.name+',Default');
+    Reggie.loadSoftware('MERGE_SOFTWARE', 'mergeSoftware', 'PIPELINE,MERGE_TYPE,PARAMETER_SET', pipeline.name+',Default');
 
     // Load open grid clusters

extensions/net.sf.basedb.reggie/trunk/resources/analysis/import_fastq.js

@@ -103 +103 @@
     var numDoNotUse = 0;
     var invalidPipeline = null;
+    var missingRawFastq = null;
     
     Wizard.setInputStatus('mergedSequences');
@@ -117 +118 @@
           invalidPipeline = Strings.encodeTags(ms.name+' ('+ms.pipeline)+') is not intended for the RNAseq pipeline.';
         }
+        if (ms.rawFastq.length == 0)
+        {
+          missingRawFastq = Strings.encodeTags(ms.name+' is missing RawFASTQ information');
+        }
       }
     }
@@ -130 +135 @@
       return;
     }
+    if (missingRawFastq)
+    {
+      Wizard.setInputStatus('mergedSequences', 'invalid', missingRawFastq);
+      return;
+    }
     selectionIsValid = true;
     
@@ -152 +162 @@
     frm.debug.checked = debug || location.protocol != 'https:';
 
-    Reggie.loadProtocols('MERGE_PROTOCOL', 'mergeProtocol', 'PIPELINE', 'RNAseq');
-    Reggie.loadSoftware('MERGE_SOFTWARE', 'mergeSoftware', 'PIPELINE,PARAMETER_SET', 'RNAseq');
+    Reggie.loadProtocols('MERGE_PROTOCOL', 'mergeProtocol', 'PIPELINE,MERGE_TYPE', 'RNAseq,Import');
+    Reggie.loadSoftware('MERGE_SOFTWARE', 'mergeSoftware', 'PIPELINE,MERGE_TYPE,PARAMETER_SET', 'RNAseq,Import');
     
     // Load open grid clusters

extensions/net.sf.basedb.reggie/trunk/resources/batch/import-external-specimen.js

@@ -191 +191 @@
     frm.debug.checked = debug || location.protocol != 'https:';
 
-    Reggie.loadProtocols('MERGE_PROTOCOL', 'mergeProtocol', 'PIPELINE', 'RNAseq');
-    Reggie.loadSoftware('MERGE_SOFTWARE', 'mergeSoftware', 'PIPELINE,PARAMETER_SET', 'RNAseq');
+    Reggie.loadProtocols('MERGE_PROTOCOL', 'mergeProtocol', 'PIPELINE,MERGE_TYPE', 'RNAseq,Import');
+    Reggie.loadSoftware('MERGE_SOFTWARE', 'mergeSoftware', 'PIPELINE,MERGE_TYPE,PARAMETER_SET', 'RNAseq,Import');
 
     // Load open grid clusters

extensions/net.sf.basedb.reggie/trunk/resources/mipsanalysis/demux_start.js

@@ -393 +393 @@
     frm.debug.checked = debug || location.protocol != 'https:';
 
-    Reggie.loadProtocols('DEMUX_PROTOCOL', 'demuxProtocol', 'PIPELINE', pipeline.name);
-    Reggie.loadSoftware('DEMUX_SOFTWARE', 'demuxSoftware', 'PIPELINE,PARAMETER_SET', pipeline.name);
+    Reggie.loadProtocols('DEMUX_PROTOCOL', 'demuxProtocol', 'PIPELINE,DEMUX_TYPE', pipeline.name+',Picard');
+    Reggie.loadSoftware('DEMUX_SOFTWARE', 'demuxSoftware', 'PIPELINE,DEMUX_TYPE,PARAMETER_SET', pipeline.name+',Picard');
 
     // Load open grid clusters

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/SequencingRunAutoConfirmer.java

@@ -7 +7 @@
 import org.slf4j.LoggerFactory;
 
+import net.sf.basedb.core.Annotatable;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.DerivedBioAssay;
@@ -33 +34 @@
 import net.sf.basedb.reggie.servlet.DemuxMergeServlet;
 import net.sf.basedb.reggie.servlet.SequencingRunServlet;
+import net.sf.basedb.util.filter.AllOfFilter;
+import net.sf.basedb.util.filter.Filter;
 
 /**
@@ -159 +162 @@
       Integer priority = (Integer)job.getParameterValue("priority");
       
-      Protocol demuxProtocol = (Protocol)Subtype.DEMUX_PROTOCOL.getLatestProjectDefault(dc, Annotationtype.PIPELINE.createFilter(pipelineName));
-      Software demuxSoftware = (Software)Subtype.DEMUX_SOFTWARE.getLatestProjectDefault(dc, Annotationtype.PIPELINE.createFilter(pipelineName));
-      Protocol mergeProtocol = (Protocol)Subtype.MERGE_PROTOCOL.getLatestProjectDefault(dc, Annotationtype.PIPELINE.createFilter(pipelineName));
-      Software mergeSoftware = (Software)Subtype.MERGE_SOFTWARE.getLatestProjectDefault(dc, Annotationtype.PIPELINE.createFilter(pipelineName));
+      Filter<Annotatable> pipelineFilter = Annotationtype.PIPELINE.createFilter(pipelineName);
+      Filter<Annotatable> demuxFilter = new AllOfFilter<>(Arrays.asList(pipelineFilter, Annotationtype.DEMUX_TYPE.createFilter("Picard")));
+      Filter<Annotatable> mergeFilter = new AllOfFilter<>(Arrays.asList(pipelineFilter, Annotationtype.MERGE_TYPE.createFilter("Default")));
+      Protocol demuxProtocol = (Protocol)Subtype.DEMUX_PROTOCOL.getLatestProjectDefault(dc, demuxFilter);
+      Software demuxSoftware = (Software)Subtype.DEMUX_SOFTWARE.getLatestProjectDefault(dc, demuxFilter);
+      Protocol mergeProtocol = (Protocol)Subtype.MERGE_PROTOCOL.getLatestProjectDefault(dc, mergeFilter);
+      Software mergeSoftware = (Software)Subtype.MERGE_SOFTWARE.getLatestProjectDefault(dc, mergeFilter);
     
       String flowCellType = (String)Annotationtype.FLOWCELL_TYPE.getAnnotationValue(dc, flowCell);

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

@@ -1762 +1762 @@
 
   /**
+    The "DemuxType" annotation, used for software/protocol items
+    of type Demuxing. It is a string enum annotation containing the 
+    name of the merge software used.
+    @since 4.32
+  */
+  public static final Annotationtype DEMUX_TYPE =
+    new Annotationtype("DemuxType", Type.STRING, false, Item.SOFTWARE, Item.PROTOCOL);
+  
+  /**
+    The "MergeType" annotation, used for software/protocol items
+    of type Merging. It is a string enum annotation containing the 
+    name of the merge software used.
+    @since 4.32
+  */
+  public static final Annotationtype MERGE_TYPE =
+    new Annotationtype("MergeType", Type.STRING, false, Item.SOFTWARE, Item.PROTOCOL);
+  
+  /**
     The "AlignmentType" annotation, used for software/protocol items
     of type Alignment. It is a string enum annotation containing the 

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

@@ -98 +98 @@
         {
           ms.loadAnnotations(dc, "pipeline", Annotationtype.PIPELINE, null);
+          ms.loadAnnotations(dc, "rawFastq", Annotationtype.RAW_FASTQ, null);
           Library lib = ms.getLibrary(dc);
           lib.loadBioPlateLocation();

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

@@ -686 +686 @@
             new ValueOptions("GENE_REPORT", "PILOT_REPORT", "SCANB_REPORT"), 
             createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.DEMUX_TYPE, 1, 
+            new ValueOptions("Picard", "bcl2fastq"), 
+            createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.MERGE_TYPE, 1, 
+            new ValueOptions("Default", "Import"), 
+            createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.ALIGNMENT_TYPE, 1, 
             new ValueOptions("Tophat", "Hisat", "MIPs"), 
@@ -1070 +1076 @@
         
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DEMUX_SOFTWARE, createIfMissing,
-            Annotationtype.PARAMETER_SET, Annotationtype.PIPELINE, Annotationtype.EXTERNAL_REF
+            Annotationtype.PARAMETER_SET, Annotationtype.PIPELINE, Annotationtype.EXTERNAL_REF,
+            Annotationtype.DEMUX_TYPE
+          ));
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DEMUX_PROTOCOL, createIfMissing,
+            Annotationtype.PIPELINE, Annotationtype.DEMUX_TYPE
           ));
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MERGE_SOFTWARE, createIfMissing,
-            Annotationtype.PARAMETER_SET, Annotationtype.PIPELINE
+            Annotationtype.PARAMETER_SET, Annotationtype.PIPELINE, Annotationtype.MERGE_TYPE
+          ));
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MERGE_PROTOCOL, createIfMissing,
+            Annotationtype.PIPELINE, Annotationtype.MERGE_TYPE
           ));
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.MASKING_SOFTWARE, createIfMissing,