Changeset 22711

Timestamp:

03/09/10 16:20:02 (17 months ago)

Author:

contrino

Message:

modmine meta: added experiment category and now experiment type is set by experiment prop if present.

Location:

trunk

Files:

• bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/ModEncodeMetaDataProcessor.java (modified) (11 diffs)
• modmine/dbmodel/resources/modencode-metadata_additions.xml (modified) (1 diff)

trunk/bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/ModEncodeMetaDataProcessor.java

@@ -42 +42 @@
 import org.intermine.xml.full.ReferenceList;
 
+
 /**
  * Create items from the modENCODE metadata extensions to the chado schema.
@@ -103 +104 @@
     private Map<String, List<Integer>> expSubMap = new HashMap<String, List<Integer>>();
 
+
     // ...we need a further map to link to submission
     private Map<Integer, String> submissionProjectMap = new HashMap<Integer, String>();
     private Map<Integer, String> submissionLabMap = new HashMap<Integer, String>();
 
+    // to store the category in experiment
+    private Map<Integer, String> submissionExpCatMap = new HashMap<Integer, String>();
+    // to check if experiment type is set
+    private Set<Integer> submissionWithExpTypeSet = new HashSet<Integer>();
 
     // submission/applied_protocol/protocol maps
@@ -901 +907 @@
             exp.setAttribute("name", name);
 
+            // find experiment category from map (take first available)
+            String category =  null;
+            for (Integer ii : expSubMap.get(name)) {
+                category = submissionExpCatMap.get(ii);
+                if (category != null) {
+                    exp.setAttribute("category", category);
+                    break;
+                }
+            }
+
             String project = expProMap.get(name);
             exp.setReference("project", projectIdRefMap.get(project));
@@ -1071 +1087 @@
             }
 
+            if (fieldName.equals("category")) { // Data Type
+                submissionExpCatMap.put(submissionId, value);
+                continue;
+            }
+
+            if (fieldName.equals("experimentType")) { // Assay Type
+                submissionWithExpTypeSet.add(submissionId);
+            }
+
             if (fieldName.equals("pubMedId")) {
                 // sometime in the form PMID:16938558
@@ -1091 +1116 @@
         LOG.info("created " + count + " submission properties");
         res.close();
-        LOG.info("PROCESS TIME submission properties: " + (System.currentTimeMillis() - bT) + " ms");
+        LOG.info("PROCESS TIME submission properties: "
+                + (System.currentTimeMillis() - bT) + " ms");
     }
 
@@ -1846 +1872 @@
             }
         }
-        LOG.info("PROCESS TIME submission properties: " + (System.currentTimeMillis() - bT) + " ms");
+        LOG.info("PROCESS TIME submission properties: "
+                + (System.currentTimeMillis() - bT) + " ms");
     }
 
@@ -2722 +2749 @@
             }
         }
-        LOG.info("TIME setting submission-data references: " + (System.currentTimeMillis() - bT) + " ms");
+        LOG.info("TIME setting submission-data references: "
+                + (System.currentTimeMillis() - bT) + " ms");
     }
 
@@ -2751 +2779 @@
             }
         }
-        LOG.info("TIME creating DatabaseRecord objects: " + (System.currentTimeMillis() - bT) + " ms");
+        LOG.info("TIME creating DatabaseRecord objects: "
+                + (System.currentTimeMillis() - bT) + " ms");
     }
 
@@ -2928 +2957 @@
             getChadoDBConverter().store(collection, storedSubmissionId);
 
-            // may need protocols from referenced submissions to work out experiment type
-            protocolChadoIds.addAll(findProtocolIdsFromReferencedSubmissions(thisSubmissionId));
-
-            String piName = submissionProjectMap.get(thisSubmissionId);
-            setSubmissionExperimentType(storedSubmissionId, protocolChadoIds, piName);
+            // TODO use Item?
+            if (!submissionWithExpTypeSet.contains(thisSubmissionId)) {
+                // may need protocols from referenced submissions to work out experiment type
+                protocolChadoIds.addAll(findProtocolIdsFromReferencedSubmissions(thisSubmissionId));
+
+                String piName = submissionProjectMap.get(thisSubmissionId);
+                setSubmissionExperimentType(storedSubmissionId, protocolChadoIds, piName);
+            }
         }
         LOG.info("TIME setting submission-protocol references: "
@@ -2974 +3006 @@
     /**
      * Work out an experiment type give the combination of protocols used for the
-     * submussion.  e.g. *immunoprecipitation + hybridization = chIP-chip
-     * @param protocolTypes the protocal types
+     * submission.  e.g. *immunoprecipitation + hybridization = chIP-chip
+     * @param protocolTypes the protocol types
      * @param piName name of PI
      * @return a short experiment type
@@ -3196 +3228 @@
         FIELD_NAME_MAP.put("Person Roles", NOT_TO_BE_LOADED);
 
+        FIELD_NAME_MAP.put("Data Type", "category");
+        FIELD_NAME_MAP.put("Assay Type", "experimentType");
+
         // data: parameter values
         FIELD_NAME_MAP.put("Array Data File", "arrayDataFile");

trunk/modmine/dbmodel/resources/modencode-metadata_additions.xml

@@ -166 +166 @@
 <class name="Experiment" is-interface="true">
   <attribute name="name" type="java.lang.String" />
+  <attribute name="category" type="java.lang.String" />
   <reference name="project" referenced-type="Project" reverse-reference="experiments" />
   <collection name="submissions" referenced-type="Submission" reverse-reference="experiment" />