Changeset 4461

Timestamp:

Mar 21, 2013, 12:42:01 PM (11 years ago)

Author:

olle

Message:

Refs #802. Non-gel hits import updated to support replicate ID input from parsing filename of mass spectrum file. The design is based on that for fraction ID input, but with fewer alternatives.

Location:

trunk

Files:

• client/servlet/src/locale/en/dictionary (modified) (3 diffs)
• client/servlet/src/org/proteios/action/hit/ImportHitsNonGelWizardStep1a.java (modified) (2 diffs)
• client/servlet/src/org/proteios/action/hit/ImportHitsNonGelWizardStep1b.java (modified) (5 diffs)
• client/servlet/src/org/proteios/gui/form/ImportHitsNonGelWizardStep1Form.java (modified) (2 diffs)
• client/servlet/src/org/proteios/gui/form/ReplicateIdEntryModeMenu.java (added)
• client/servlet/src/org/proteios/gui/form/ReplicateIdRegexField.java (added)
• plugin/src/org/proteios/plugins/PeakListToHitNonGelPlugin.java (modified) (6 diffs)

trunk/client/servlet/src/locale/en/dictionary

@@ -294 +294 @@
 ImportedPeakLists=Imported Peak Lists
 ImportedSearches=Imported Searches
-ImportHitsNonGelWizardRegexPattern=Regex pattern:
+ImportHitsNonGelWizardRegexPatternFractionId=Regex pattern:
+ImportHitsNonGelWizardRegexPatternReplicateId=Regex pattern:
 ImportHitsNonGelWizardStep1AdditionalParametersDescription=Step 1. Additional Parameters Description
 ImportHitsNonGelWizardStep1FormLegend=Step 1. Register peaklist files for local sample ID
@@ -302 +303 @@
 ImportHitsNonGelWizardStep1FormLegendStep1a=Step 1a. Register peaklist files for local sample ID
 ImportHitsNonGelWizardStep2FormLegend=Step 2. Import protein identification results
-ImportHitsNonGelWizardUseRegexPattern=Use regex pattern to parse fraction ID from filename
+ImportHitsNonGelWizardUseRegexPatternFractionId=Use regex pattern to parse fraction ID from filename
+ImportHitsNonGelWizardUseRegexPatternReplicateId=Use regex pattern to parse replicate ID from filename
 ImportHitsWizardStep1FormLegend=Step 1. Add spots and mapping to plates
 ImportHitsWizardStep2FormLegend=Step 2. Register peaklist files
@@ -836 +838 @@
 SelectProject=Select project
 SelectProtocolFile=Select Protocol File
+SelectReplicateIdEntryMode=Replicate ID input:
 SelectSpectrumFile=Select Spectrum File
 SelectVisibleColumns=Select Visible Columns

trunk/client/servlet/src/org/proteios/action/hit/ImportHitsNonGelWizardStep1a.java

@@ -64 +64 @@
     String selectedLocalSampleId = getString(LocalSampleSelect.VPARAM);
     String fractionIdEntryMode = getString(FractionIdEntryModeMenu.VPARAM);
-    String regexPattern = getValidString(RegexField.VPARAM);
+    String fractionIdRegexPattern = getValidString(RegexField.VPARAM);
+    String replicateIdEntryMode = getString(ReplicateIdEntryModeMenu.VPARAM);
+    String replicateIdRegexPattern = getValidString(ReplicateIdRegexField.VPARAM);
     log.debug("localSampleIdEntryMode = \"" + localSampleIdEntryMode + "\"");
     log.debug("enteredLocalSampleId = \"" + enteredLocalSampleId + "\"");
     log.debug("selectedLocalSampleId = \"" + selectedLocalSampleId + "\"");
     log.debug("fractionIdEntryMode = \"" + fractionIdEntryMode + "\"");
-    log.debug("regexPattern = \"" + regexPattern + "\"");
+    log.debug("fractionIdRegexPattern = \"" + fractionIdRegexPattern + "\"");
+    log.debug("replicateIdEntryMode = \"" + replicateIdEntryMode + "\"");
+    log.debug("replicateIdRegexPattern = \"" + replicateIdRegexPattern + "\"");
   if (localSampleIdEntryMode.equals(LocalSampleIdEntryModeMenu.ENTER_EXPLICIT_LOCAL_SAMPLE_ID))
   {
@@ -93 +97 @@
     saveToSession(FractionIdEntryModeMenu.VPARAM);
     saveToSession(RegexField.VPARAM);
+    saveToSession(ReplicateIdEntryModeMenu.VPARAM);
+    saveToSession(ReplicateIdRegexField.VPARAM);
     saveToSession(ForwardField.VPARAM);
     saveToSession(PluginIdField.VPARAM);

trunk/client/servlet/src/org/proteios/action/hit/ImportHitsNonGelWizardStep1b.java

@@ -74 +74 @@
     List<Integer> fileIds = getValidIntegerList(ItemIdField.VPARAM);
     String fractionIdEntryMode = getSessionAttribute(FractionIdEntryModeMenu.VPARAM);
-    String regexPattern = getSessionAttribute(RegexField.VPARAM);
+    String fractionIdRegexPattern = getSessionAttribute(RegexField.VPARAM);
+    String replicateIdEntryMode = getSessionAttribute(ReplicateIdEntryModeMenu.VPARAM);
+    String replicateIdRegexPattern = getSessionAttribute(ReplicateIdRegexField.VPARAM);
     // Set default value of local sample id entry mode to explicit entry
      log.debug("localSampleIdEntryMode from request = \"" + localSampleIdEntryMode + "\"");
@@ -93 +95 @@
   }
   log.debug("fractionIdEntryMode = \"" + fractionIdEntryMode + "\"");
-    log.debug("regexPattern = \"" + regexPattern + "\"");
+    log.debug("fractionIdRegexPattern = \"" + fractionIdRegexPattern + "\"");
+    // Set default value of replicate id entry mode
+    log.debug("replicateIdEntryMode from request = \"" + replicateIdEntryMode + "\"");
+  if (replicateIdEntryMode == null)
+  {
+    replicateIdEntryMode = new String(ReplicateIdEntryModeMenu.GET_REPLICATE_ID_FROM_PEAKLIST_FILE_ANNOTATION);
+  }
+  log.debug("replicateIdEntryMode = \"" + replicateIdEntryMode + "\"");
+    log.debug("replicateIdRegexPattern = \"" + replicateIdRegexPattern + "\"");
+    //
     log.debug("fileIds = " + fileIds);
     if (fileIds == null || fileIds.size() == 0)
@@ -126 +137 @@
         {
             Job job = createJob(factory, plugin, file,
-            localSampleIdEntryMode, fractionIdEntryMode,
-            localSampleId, project, regexPattern);
+            localSampleIdEntryMode, fractionIdEntryMode, replicateIdEntryMode,
+            localSampleId, project, fractionIdRegexPattern, replicateIdRegexPattern);
             //
             dc.saveItem(job);
@@ -173 +184 @@
    * @param localSampleIdEntryMode String Local sample id entry mode.
    * @param fractionIdEntryMode String Fraction id entry mode.
+   * @param replicateIdEntryMode String Replicate id entry mode.
    * @param localSampleId String Local sample id.
    * @param project Project The project.
-   * @param regexPattern String Optional regular expression pattern to parse fraction id from name of peaklist file.
+   * @param fractionIdRegexPattern String Optional regular expression pattern to parse fraction id from name of peaklist file.
+   * @param replicateIdRegexPattern String Optional regular expression pattern to parse replicate id from name of peaklist file.
    * @return job Job The created non gel-based import job.
    */
   private Job createJob(ItemFactory factory, PluginDefinition plugin,
       File file,
-      String localSampleIdEntryMode, String fractionIdEntryMode,
-      String localSampleId, Project project, String regexPattern)
+      String localSampleIdEntryMode, String fractionIdEntryMode, String replicateIdEntryMode,
+      String localSampleId, Project project, String fractionIdRegexPattern, String replicateIdRegexPattern)
   {
       Job job = factory.createJob(plugin, null);
@@ -205 +218 @@
       job.setParameterValue("fractionIdEntryMode", fractionIdEntryModeParam, fractionIdEntryMode);
       //
-      StringParameterType regexPatternParam = new StringParameterType();
-      job.setParameterValue("regexPattern", regexPatternParam, regexPattern);
+      StringParameterType fractionIdRegexPatternParam = new StringParameterType();
+      job.setParameterValue("fractionIdRegexPattern", fractionIdRegexPatternParam, fractionIdRegexPattern);
+      //
+      StringParameterType replicateIdEntryModeParam = new StringParameterType();
+      job.setParameterValue("replicateIdEntryMode", replicateIdEntryModeParam, replicateIdEntryMode);
+      //
+      StringParameterType replicateIdRegexPatternParam = new StringParameterType();
+      job.setParameterValue("replicateIdRegexPattern", replicateIdRegexPatternParam, replicateIdRegexPattern);
       //
     return job;

trunk/client/servlet/src/org/proteios/gui/form/ImportHitsNonGelWizardStep1Form.java

@@ -48 +48 @@
   public final Select<VString> fractionIdEntryModeMenu;
   public final TextField<String> regexPatternF;
+  public final Select<VString> replicateIdEntryModeMenu;
+  public final TextField<String> regexPatternR;
 
 
@@ -114 +116 @@
     // Optional regex pattern entry field
     regexPatternF = new RegexField();
-    regexPatternF.setLabel("ImportHitsNonGelWizardRegexPattern");
+    regexPatternF.setLabel("ImportHitsNonGelWizardRegexPatternFractionId");
     regexPatternF.setValue(".+\\_(.+)\\..+"); 
     properties.add(regexPatternF);
+    // Replicate id entry mode menu
+    String replicateIdEntryModeDefault = new String(ReplicateIdEntryModeMenu.GET_REPLICATE_ID_FROM_PEAKLIST_FILE_ANNOTATION);
+    replicateIdEntryModeMenu = new ReplicateIdEntryModeMenu(replicateIdEntryModeDefault);
+    replicateIdEntryModeMenu.setLabel("SelectReplicateIdEntryMode");
+    properties.add(replicateIdEntryModeMenu);
+    // Optional regex pattern entry field
+    regexPatternR = new ReplicateIdRegexField();
+    regexPatternR.setLabel("ImportHitsNonGelWizardRegexPatternReplicateId");
+    regexPatternR.setValue(".+\\_(.+)\\..+"); 
+    properties.add(regexPatternR);
     /*
      * Hidden text fields with data

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

@@ -82 +82 @@
   public static final String GET_FRACTION_ID_FROM_PEAKLIST_FILE_NAME = "getFractionIdFromPeaklistFileName";
   public static final String NO_FRACTION_ID = "noFractionId";
+  public static final String GET_REPLICATE_ID_FROM_PEAKLIST_FILE_ANNOTATION = "getReplicateIdFromPeaklistFileAnnotation";
+  public static final String GET_REPLICATE_ID_FROM_PEAKLIST_FILE_NAME = "getReplicateIdFromPeaklistFileName";
 
   @Override
@@ -112 +114 @@
         .getValue("fractionIdEntryMode");
     log.debug("fractionIdEntryMode = \"" + fractionIdEntryMode + "\"");
-    String regexPattern = (String) job.getValue("regexPattern");
-    log.debug("regexPattern = \"" + regexPattern + "\"");
+    String fractionIdRegexPattern = (String) job.getValue("fractionIdRegexPattern");
+    log.debug("fractionIdRegexPattern = \"" + fractionIdRegexPattern + "\"");
+    String replicateIdEntryMode = (String) job
+        .getValue("replicateIdEntryMode");
+    log.debug("replicateIdEntryMode = \"" + replicateIdEntryMode + "\"");
+    String replicateIdRegexPattern = (String) job.getValue("replicateIdRegexPattern");
+    log.debug("replicateIdRegexPattern = \"" + replicateIdRegexPattern + "\"");
     //
     FilenameParseUtil fpu = new FilenameParseUtil();
@@ -171 +178 @@
     // }
     if (ft != null && (fts.contains(ft))) {
-      // Retrieve replicate ID
-      String replicate = fetchReplicateIdFromFileAnnotation(dc, f);
       // Attempt to obtain fraction ID from file annotation "fraction".
       String fractionIdFromAnnotation = fetchFractionIdFromFileAnnotation(
@@ -178 +183 @@
       // Use regex pattern to parse fraction ID from filename
       String fractionIdFromFilename = null;
-      if (regexPattern != null && !regexPattern.equals("")) {
+      if (fractionIdRegexPattern != null && !fractionIdRegexPattern.equals("")) {
         // Use regex pattern to parse fraction ID from filename
         fractionIdFromFilename = fpu.fetchRegexResult(f.getName(),
-            regexPattern);
+            fractionIdRegexPattern);
       }
       log.debug("fraction id from file annotation = \""
@@ -235 +240 @@
         return;
       }
+      // Attempt to obtain replicate ID from file annotation "replicate".
+      String replicateIdFromAnnotation = fetchReplicateIdFromFileAnnotation(
+          dc, f);
+      // Use regex pattern to parse replicate ID from filename
+      String replicateIdFromFilename = null;
+      if (replicateIdRegexPattern != null && !replicateIdRegexPattern.equals("")) {
+        // Use regex pattern to parse replicate ID from filename
+        replicateIdFromFilename = fpu.fetchRegexResult(f.getName(),
+            replicateIdRegexPattern);
+      }
+      log.debug("replicate id from file annotation = \""
+          + replicateIdFromAnnotation + "\"");
+      log.debug("replicate id from file name = \""
+          + replicateIdFromFilename + "\"");
+      // Get replicate id, if any
+      String replicate = new String("");
+      if (replicateIdEntryMode
+          .equals(GET_REPLICATE_ID_FROM_PEAKLIST_FILE_ANNOTATION)) {
+        if (replicateIdFromAnnotation != null) {
+          replicate = replicateIdFromAnnotation;
+        }
+      } else if (replicateIdEntryMode
+          .equals(GET_REPLICATE_ID_FROM_PEAKLIST_FILE_NAME)) {
+        if (replicateIdFromFilename != null) {
+          replicate = replicateIdFromFilename;
+        }
+      }
+      log.info("peak list, replicate id: \"" + replicate
+          + "\" localsample Id: \"" + localSampleId + "\"");
+      // Check that length of replicate ID is not too long
+      if (replicate != null
+          && replicate.length() > Hit.MAX_REPLICATE_ID_LENGTH) {
+        log.debug("Replicate ID = \"" + replicate + "\" is too long ("
+            + replicate.length() + " characters, "
+            + Hit.MAX_REPLICATE_ID_LENGTH + " allowed).");
+        err.add(new BaseException("Replicate ID = \"" + replicate
+            + "\" is too long (" + replicate.length()
+            + " characters, " + Hit.MAX_REPLICATE_ID_LENGTH
+            + " allowed)."));
+        response.setError("Nothing imported", err);
+        return;
+      }
       // Check if peaklist file already registered for local sample id
       boolean peaklistFileAlreadyRegistered = false;
@@ -306 +353 @@
    * @param File file The file to get the annotation for.
    * 
-   * @return String The found fraction id, or null if none found.
+   * @return String The found replicate id, or null if none found.
    */
   private String fetchReplicateIdFromFileAnnotation(DbControl dc, File file) {