Changeset 4269

Timestamp:

Dec 22, 2011, 4:50:55 PM (12 years ago)

Author:

Fredrik Levander

Message:

Refs #772. Updated info reader and hits import.

Location:

trunk

Files:

• api/core/src/org/proteios/core/Hit.java (modified) (1 diff)
• api/core/src/org/proteios/core/data/HitData.java (modified) (2 diffs)
• client/servlet/src/locale/en/dictionary (modified) (1 diff)
• client/servlet/src/org/proteios/action/file/InfoFileHandler.java (modified) (1 diff)
• plugin/src/org/proteios/plugins/PeakListToHitNonGelPlugin.java (modified) (14 diffs)
• plugin/src/org/proteios/plugins/SearchResultsImporter.java (modified) (1 diff)

trunk/api/core/src/org/proteios/core/Hit.java

@@ -266 +266 @@
   {
     getData().setFractionId(fractionId);
+  }
+
+  /**
+   * The maximum length of the replicate ID that can be stored in the database.
+   * 
+   * @see #setReplicateId(String)
+   */
+  public static final int MAX_RELICATE_ID_LENGTH = HitData.MAX_REPLICATE_ID_LENGTH;
+
+
+  public String getReplicateId()
+  {
+    return getData().getReplicateId();
+  }
+
+
+  public void setReplicateId(String replicateId)
+  {
+    getData().setReplicateId(replicateId);
   }
 

trunk/api/core/src/org/proteios/core/data/HitData.java

@@ -48 +48 @@
   private String localSampleId = null;
   private String fractionId = null;
+  private String replicateId = null;
   private Boolean microPlate = null;
   private Date searchDate = null;
@@ -222 +223 @@
   }
 
+  /**
+   * The maximum length of the replicate ID that can be stored in the database.
+   * 
+   * @see #setFractionId(String)
+   */
+  public static final int MAX_REPLICATE_ID_LENGTH = 10;
+
+  
+  /**
+   * A replicate id, e.g. a serial number like 01. Constrained to 10 characters.
+   * 
+   * @hibernate.property column="`replicateId`" length="16" type="string"
+   *                     not-null="false"
+   */
+  public String getReplicateId()
+  {
+    return replicateId;
+  }
+
+
+  public void setReplicateId(String replicateId)
+  {
+    this.replicateId = replicateId;
+  }
+
 
   /**

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

@@ -742 +742 @@
 Remaining=Remaining
 RemainingSampleQuantityInMicroLiters=Remaining Sample Quantity (µl)
+ReplicateId=Replicate ID
 Removed=Removed
 Reports=Reports

trunk/client/servlet/src/org/proteios/action/file/InfoFileHandler.java

@@ -298 +298 @@
           annotationName = "fraction";
         }
+        // To make sure replicate annotation is always lower case
+        else if (annotationName.equalsIgnoreCase("replicate"))
+        {
+          annotationName = "replicate";
+        }
         AnnotationType at = annotator.getAnnotationType(annotationName,
           Type.STRING, file.getType());

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

@@ -44 +44 @@
 import org.proteios.core.Project;
 import org.proteios.core.SessionControl;
+import org.proteios.core.Type;
 import org.proteios.core.plugin.About;
 import org.proteios.core.plugin.AboutImpl;
@@ -55 +56 @@
 import org.proteios.io.FilenameParseUtil;
 import org.proteios.io.PeakListFileValidationFactory;
+
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
@@ -116 +119 @@
     // Directory d = (Directory) job.getValue("dir");
     ArrayList<Throwable> err = new ArrayList<Throwable>(1);
-    String localSampleIdEntryMode = (String) job.getValue("localSampleIdEntryMode");
-    log.debug("localSampleIdEntryMode = \"" + localSampleIdEntryMode + "\"");
+    String localSampleIdEntryMode = (String) job
+      .getValue("localSampleIdEntryMode");
+    log
+      .debug("localSampleIdEntryMode = \"" + localSampleIdEntryMode + "\"");
     String localSampleId = (String) job.getValue("localSampleId");
-    String fractionIdEntryMode = (String) job.getValue("fractionIdEntryMode");
+    String fractionIdEntryMode = (String) job
+      .getValue("fractionIdEntryMode");
     log.debug("fractionIdEntryMode = \"" + fractionIdEntryMode + "\"");
     String regexPattern = (String) job.getValue("regexPattern");
@@ -128 +134 @@
     DbControl dc = sc.newDbControl();
     Project project = Project.getById(dc, sc.getActiveProjectId());
-    List<FileType> fts = PeakListFileValidationFactory.getPossibleFileTypes(dc); 
+    List<FileType> fts = PeakListFileValidationFactory
+      .getPossibleFileTypes(dc);
     dc.reattachItem(f);
     //
     List<String> localSampleIdStringList = new ArrayList<String>();
     Set<BioMaterial> fileBioMaterialSet = f.getBioMaterials();
-    for (BioMaterial fileBioMaterial: fileBioMaterialSet)
+    for (BioMaterial fileBioMaterial : fileBioMaterialSet)
     {
       String fileBioMaterialName = fileBioMaterial.getName();
@@ -142 +149 @@
         localSampleIdStringList.add(fileBioMaterialName);
       }
-      else if (fileBioMaterialName2 != null && !fileBioMaterialName2.equals(""))
+      else if (fileBioMaterialName2 != null && !fileBioMaterialName2
+        .equals(""))
       {
         // Add name to local sample id string list
@@ -148 +156 @@
       }
     }
-    if (localSampleIdEntryMode.equals(GET_LOCAL_SAMPLE_ID_FROM_FILE_BIOMATERIAL))
-    {
-      if (localSampleIdStringList != null && localSampleIdStringList.size() != 0)
+    if (localSampleIdEntryMode
+      .equals(GET_LOCAL_SAMPLE_ID_FROM_FILE_BIOMATERIAL))
+    {
+      if (localSampleIdStringList != null && localSampleIdStringList
+        .size() != 0)
       {
         // Sort combined list
         Collections.sort(localSampleIdStringList);
         String tmpLocalSampleId = new String("");
-        for (String partStr: localSampleIdStringList)
+        for (String partStr : localSampleIdStringList)
         {
           if (partStr != null && !partStr.equals(""))
@@ -190 +200 @@
     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(dc, f);
+      String fractionIdFromAnnotation = fetchFractionIdFromFileAnnotation(
+        dc, f);
       // Use regex pattern to parse fraction ID from filename
       String fractionIdFromFilename = null;
@@ -197 +210 @@
       {
         // Use regex pattern to parse fraction ID from filename
-        fractionIdFromFilename = fpu.fetchRegexResult(f.getName(), regexPattern);
-      }
-      log.debug("fraction id from file annotation = \"" + fractionIdFromAnnotation + "\"");
-      log.debug("fraction id from file name = \"" + fractionIdFromFilename + "\"");
+        fractionIdFromFilename = fpu.fetchRegexResult(f.getName(),
+          regexPattern);
+      }
+      log
+        .debug("fraction id from file annotation = \"" + fractionIdFromAnnotation + "\"");
+      log
+        .debug("fraction id from file name = \"" + fractionIdFromFilename + "\"");
       // Get fraction id, if any
       String fractionId = new String("");
-      if (fractionIdEntryMode.equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_ANNOTATION)
-          || fractionIdEntryMode.equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_ANNOTATION_OR_NAME))
+      if (fractionIdEntryMode
+        .equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_ANNOTATION) || fractionIdEntryMode
+        .equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_ANNOTATION_OR_NAME))
       {
         if (fractionIdFromAnnotation != null)
         {
-          // First choice, fraction id from annotation for peaklist file
+          // First choice, fraction id from annotation for peaklist
+          // file
           fractionId = fractionIdFromAnnotation;
         }
-        else if (fractionIdEntryMode.equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_ANNOTATION_OR_NAME))
+        else if (fractionIdEntryMode
+          .equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_ANNOTATION_OR_NAME))
         {
           if (fractionIdFromFilename != null)
@@ -220 +239 @@
         }
       }
-      else if (fractionIdEntryMode.equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_NAME)
-          || fractionIdEntryMode.equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_NAME_OR_ANNOTATION))
+      else if (fractionIdEntryMode
+        .equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_NAME) || fractionIdEntryMode
+        .equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_NAME_OR_ANNOTATION))
       {
         if (fractionIdFromFilename != null)
@@ -228 +248 @@
           fractionId = fractionIdFromFilename;
         }
-        else if (fractionIdEntryMode.equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_NAME_OR_ANNOTATION))
+        else if (fractionIdEntryMode
+          .equals(GET_FRACTION_ID_FROM_PEAKLIST_FILE_NAME_OR_ANNOTATION))
         {
           if (fractionIdFromAnnotation != null)
           {
-            // Second choice, fraction id from annotation for peaklist file
+            // Second choice, fraction id from annotation for
+            // peaklist file
             fractionId = fractionIdFromAnnotation;
           }
@@ -242 +264 @@
       if (fractionId != null && fractionId.length() > Hit.MAX_FRACTION_ID_LENGTH)
       {
-        log.debug("Fraction ID = \"" + fractionId + "\" is too long (" + fractionId.length() + " characters, " + Hit.MAX_FRACTION_ID_LENGTH + " allowed).");
-        err.add(new BaseException(
-          "Fraction ID = \"" + fractionId + "\" is too long (" + fractionId.length() + " characters, " + Hit.MAX_FRACTION_ID_LENGTH + " allowed)."));
+        log
+          .debug("Fraction ID = \"" + fractionId + "\" is too long (" + fractionId
+            .length() + " characters, " + Hit.MAX_FRACTION_ID_LENGTH + " allowed).");
+        err
+          .add(new BaseException(
+            "Fraction ID = \"" + fractionId + "\" is too long (" + fractionId
+              .length() + " characters, " + Hit.MAX_FRACTION_ID_LENGTH + " allowed)."));
         response.setError("Nothing imported", err);
         return;
@@ -281 +307 @@
         newhit.setLocalSampleId(localSampleId);
         newhit.setFractionId(fractionId);
+        if (replicate !=null)
+        {
+          newhit.setReplicateId(replicate);
+        }
         dc.saveItem(newhit);
         dc.reattachItem(newhit);
@@ -325 +355 @@
 
   /*
+   * Attempts to obtain replicate id from file annotation "replicate".
+   * @param DbControl dc The DbControl to use.
+   * @param File file The file to get the annotation for.
+   * @return String The found fraction id, or null if none found.
+   */
+  private String fetchReplicateIdFromFileAnnotation(DbControl dc, File file)
+  {
+    String replicateId = null;
+    Annotator annotator = new Annotator(new ItemFactory(dc));
+    AnnotationType at = annotator.getAnnotationType(file, "replicate", Type.STRING);
+    Annotation annotation = annotator.getAnnotation(file, at);
+    Iterator<?> it = annotation.getValues().iterator();
+    while (it.hasNext())
+    {
+      replicateId = (String) it.next();
+    }
+    return replicateId;
+  }
+
+
+  /*
    * Attempts to obtain fraction id from file annotation "fraction".
-   * 
    * @param DbControl dc The DbControl to use.
    * @param File file The file to get the anntation for.
@@ -336 +386 @@
     // Try to get fraction id from file annotation "fraction"
     Annotator annotator = new Annotator(new ItemFactory(dc));
-    ItemQuery<Annotation> annotationQuery = annotator.getAnnotationSet(file).getAnnotations();
+    ItemQuery<Annotation> annotationQuery = annotator
+      .getAnnotationSet(file).getAnnotations();
     ItemResultList<Annotation> annotationList = annotationQuery.list(dc);
     if (annotationList != null && annotationList.size() > 0)
     {
-      for (Annotation annotation: annotationList)
+      for (Annotation annotation : annotationList)
       {
         if (annotation != null)
         {
           // Get annotation type
-          AnnotationType annotationType = annotation.getAnnotationType();
+          AnnotationType annotationType = annotation
+            .getAnnotationType();
           if (annotationType != null)
           {
             String annotationTypeName = annotationType.getName();
-            if (annotationTypeName != null && annotationTypeName.equals("fraction"))
+            if (annotationTypeName != null && annotationTypeName
+              .equals("fraction"))
             {
-              List<String> tmpFractionIdList = (List<String>) annotation.getValues();
-              if (tmpFractionIdList != null && tmpFractionIdList.size() > 0)
+              List<String> tmpFractionIdList = (List<String>) annotation
+                .getValues();
+              if (tmpFractionIdList != null && tmpFractionIdList
+                .size() > 0)
               {
-                String tmpFractionId = (String) tmpFractionIdList.get(0);
-                if (tmpFractionId != null && !tmpFractionId.equals(""))
+                String tmpFractionId = (String) tmpFractionIdList
+                  .get(0);
+                if (tmpFractionId != null && !tmpFractionId
+                  .equals(""))
                 {
                   fractionId = tmpFractionId;

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

@@ -221 +221 @@
               hit.setLocalSampleId(emptyHit.getLocalSampleId());
               hit.setFractionId(emptyHit.getFractionId());
+              hit.setReplicateId(emptyHit.getReplicateId());
               hit.setPeakListFile(emptyHit.getPeakListFile());
               dc.saveItem(hit);