Changeset 4514

Timestamp:

Aug 20, 2013, 3:09:43 PM (10 years ago)

Author:

Fredrik Levander

Message:

Refs #807. Added some new required fields to the generated PRIDE XML. Parsing database version.

File:

• trunk/plugin/src/org/proteios/plugins/PrideExportPlugin.java (modified) (12 diffs)

trunk/plugin/src/org/proteios/plugins/PrideExportPlugin.java

@@ -1167 +1167 @@
       }
       // Write PRIDE XML generator info
-      writePrideXmlGeneratorInfo(xmlCrudeWriter);
+      writePrideXmlGeneratorInfo(xmlCrudeWriter, project);
       // Write PRIDE XML end part
       writePrideXmlEnd(xmlCrudeWriter);
@@ -1677 +1677 @@
         currentHit);
       log.debug("database from SpectrumSearch = \"" + database + "\"");
+      String databaseVersion = "";
       if (database == null || database.equals(""))
       {
         // Otherwise get database info from accession number
         database = getDatabaseFromAccessionNumber(externalIds[0]);
+      }
+      else if (database.contains("_"))
+      {
+        databaseVersion = database
+          .substring(database.lastIndexOf("_") + 1);
+        database = database.substring(0, database.lastIndexOf("_"));
       }
       log.debug("database = \"" + database + "\"");
@@ -1692 +1699 @@
         // writeEndTag("Database");
         xmlCrudeWriterImpl.writeEndElement("Database");
+        xmlCrudeWriterImpl.writeStartElement("DatabaseVersion");
+        xmlCrudeWriterImpl.writeStartElementEnd();
+        xmlCrudeWriterImpl.writeCharacters(databaseVersion);
+        // writeEndTag("Database");
+        xmlCrudeWriterImpl.writeEndElement("DatabaseVersion");
+
       }
     }
@@ -1885 +1898 @@
   {
     // Get score types from Hit query
-    List<String> scoreTypeList = Hit.getUniqueScoreTypesWithCombinedFDR(project, dc);
+    List<String> scoreTypeList = Hit.getUniqueScoreTypesWithCombinedFDR(
+      project, dc);
     log.debug("scoreTypeList = " + scoreTypeList);
     List<String> usedScoreTypeList = new ArrayList<String>();
@@ -2268 +2282 @@
    *        XMLCrudeWriterImpl to use.
    */
-  private void writePrideXmlGeneratorInfo(XMLCrudeWriter xmlCrudeWriterImpl)
+  private void writePrideXmlGeneratorInfo(XMLCrudeWriter xmlCrudeWriterImpl, Project project)
   {
     try
@@ -2287 +2301 @@
       xmlCrudeWriterImpl.writeStartElement(cvParamStr);
       xmlCrudeWriterImpl.writeSingleElementEnd();
+      cvParamStr = new String(
+        "cvParam cvLabel=\"PRIDE\" accession=\"PRIDE:0000218\" name=\"Original MS data file format\" value=\"Proteios\" ");
+      xmlCrudeWriterImpl.writeStartElement(cvParamStr);
+      xmlCrudeWriterImpl.writeSingleElementEnd();
+      cvParamStr = new String(
+        "cvParam cvLabel=\"PRIDE\" accession=\"PRIDE:0000097\" name=\"Project\" value=\"" + project.getName() + "\" ");
+      xmlCrudeWriterImpl.writeStartElement(cvParamStr);
+      xmlCrudeWriterImpl.writeSingleElementEnd();
+      cvParamStr = new String(
+        "cvParam cvLabel=\"PRIDE\" accession=\"PRIDE:0000040\" name=\"Experiment description\" value=\"" + project.getDescription() + "\" ");
+      xmlCrudeWriterImpl.writeStartElement(cvParamStr);
+      xmlCrudeWriterImpl.writeSingleElementEnd();
+  
       //
       // writeEndTag("additional");
@@ -2402 +2429 @@
 
 
-
-
-
   private List<SearchModification> fetchSearchModifications(Hit currentHit,
       DbControl dc)
@@ -2423 +2447 @@
     }
   }
-
-
 
 
@@ -2560 +2582 @@
 
 
-
-
   /**
    * Appends a new string to an input base string, after an optional separator
@@ -2593 +2613 @@
     return newStr;
   }
-
-
 
 
@@ -3022 +3040 @@
       selectedXmlTagName, selectedXMLEndTag, convertPsiToMsOntology, 0);
   }
-
 
 
@@ -3253 +3270 @@
     return line;
   }
-
-