Changeset 3848

Timestamp:

Sep 14, 2010, 12:22:53 PM (13 years ago)

Author:

Fredrik Levander

Message:

Refs #701. Refs #405. Only exporting PRIDE files for the selected sample or gel.

File:

• trunk/client/servlet/src/org/proteios/action/hit/CreatePrideExportJob.java (modified) (13 diffs)

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

@@ -28 +28 @@
 package org.proteios.action.hit;
 
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.GregorianCalendar;
-import java.util.List;
 import org.proteios.action.ProteiosAction;
 import org.proteios.action.job.ListJobs;
@@ -53 +49 @@
 import org.proteios.core.query.Hql;
 import org.proteios.core.query.Restrictions;
-import org.proteios.gui.form.*;
-import org.proteios.plugins.PrideExportPlugin;
+import org.proteios.gui.form.ExternalGelIdField;
+import org.proteios.gui.form.FormFactory;
+import org.proteios.gui.form.LocalSampleSelect;
+
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
@@ -62 +60 @@
 import se.lu.thep.waf.constraints.VString;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * @author gregory
@@ -68 +69 @@
     extends ProteiosAction<CreatePrideExportJob>
 {
-  public static final VBoolean VEXTRAPREFIX = new VBoolean("appendPrefix", false);
+  public static final VBoolean VEXTRAPREFIX = new VBoolean("appendPrefix",
+    false);
   public static final VFloat VCUTOFF = new VFloat("cutOff", true);
-  public static final VString VCUTOFFSTRING = new VString("cutOffString", 0, 256, false);
+  public static final VString VCUTOFFSTRING = new VString("cutOffString", 0,
+    256, false);
   public static final VInteger VPRIDEPROTOCOLFILEID = new VInteger(
     "prideProtocolFileId", 0, false);
-  public static final VString VEXPERIMENTTITLE = new VString("expTitle",0,256,false);
-  public static final VString VCONTACTNAME = new VString("contactName",0,256,false);
-  public static final VString VCONTACTINST = new VString("contactInst",0,256,false);
-  public static final VString VCONTACTINFO = new VString("contactInfo",0,256,false);
-  public static final VString VCONTACTEMAIL = new VString("contactEmail",0,256,false);
-  public static final VString VCONTACTURL = new VString("contactURL",0,256,false);
+  public static final VString VEXPERIMENTTITLE = new VString("expTitle", 0,
+    256, false);
+  public static final VString VCONTACTNAME = new VString("contactName", 0,
+    256, false);
+  public static final VString VCONTACTINST = new VString("contactInst", 0,
+    256, false);
+  public static final VString VCONTACTINFO = new VString("contactInfo", 0,
+    256, false);
+  public static final VString VCONTACTEMAIL = new VString("contactEmail", 0,
+    256, false);
+  public static final VString VCONTACTURL = new VString("contactURL", 0, 256,
+    false);
   public static final VBoolean VADDCONTACT = new VBoolean("addContact", false);
-  public static final VBoolean VADDSAMPLENAME = new VBoolean("addSampleName", false);
+  public static final VBoolean VADDSAMPLENAME = new VBoolean("addSampleName",
+    false);
+
 
   /*
    * (non-Javadoc)
-   * 
    * @see org.proteios.action.ProteiosAction#runMe()
    */
@@ -118 +128 @@
     log.debug("filenamePrefix = \"" + filenamePrefix + "\"");
     //
-    // Check if extra prefix (gel external id or local sample id) should be used
-    //Boolean appendExtraPrefix = getValidBoolean(VEXTRAPREFIX);
+    // Check if extra prefix (gel external id or local sample id) should be
+    // used
+    // Boolean appendExtraPrefix = getValidBoolean(VEXTRAPREFIX);
     Boolean appendExtraPrefix = getSessionAttribute(VEXTRAPREFIX);
     log.debug("appendExtraPrefix from request = " + appendExtraPrefix);
@@ -157 +168 @@
       if (extraPrefix != null && !extraPrefix.equals(""))
       {
-        if (!filenamePrefix.equals("") &&
-            !filenamePrefix.endsWith("_") &&
-            !filenamePrefix.endsWith("-") &&
-            !filenamePrefix.endsWith("."))
+        if (!filenamePrefix.equals("") && !filenamePrefix.endsWith("_") && !filenamePrefix
+          .endsWith("-") && !filenamePrefix.endsWith("."))
         {
           // Add underscore between original prefix and extra prefix
@@ -194 +203 @@
     // Find spectrum files in hits list
     ItemQuery<Hit> hitQuery = Hit.getQuery();
-    hitQuery.restrictPermanent(Restrictions.eq(Hql.property("project"),
-      Hql.entity(project)));
-    hitQuery.restrict(Restrictions.eq(Hql.property("protein"),
-      Expressions.parameter("protein")));
+    hitQuery.restrictPermanent(Restrictions.eq(Hql.property("project"), Hql
+      .entity(project)));
+    hitQuery.restrict(Restrictions.eq(Hql.property("protein"), Expressions
+      .parameter("protein")));
     hitQuery.setParameter("protein", false, null);
+
     ItemResultList<Hit> hitlist = hitQuery.list(dc);
     List<File> peakListFileList = new ArrayList<File>(0);
-    for (Hit hit: hitlist)
+    for (Hit hit : hitlist)
     {
       File file = hit.getPeakListFile();
@@ -231 +241 @@
       {
         dc.close();
-        throw new ActionException("Couldn't find plugin PrideExportPlugin.");
+        throw new ActionException(
+          "Couldn't find plugin PrideExportPlugin.");
       }
     }
@@ -237 +248 @@
     {
       throw new ActionException(
-        "PRIDE Export plugin is not installed. " + e
-          .getMessage());
+        "PRIDE Export plugin is not installed. " + e.getMessage());
     }
     log.debug("pluginDef = " + pluginDef);
@@ -245 +255 @@
     // Create one job per spectrum file in hits list
     int total = peakListFileList.size();
-    int i=0;
-    for (File file: peakListFileList)
+    int i = 0;
+    for (File file : peakListFileList)
     {
       i++;
-      String part = "("+i+"/"+total+")"; 
+      String part = "(" + i + "/" + total + ")";
       log.debug("file = " + file);
       String outputFilename = filenamePrefix + file.getName();
@@ -267 +277 @@
       else
       {
-        job.setName(plugin.getName() + " sample: " + localSampleId + ", title: " + expTitle + " "+part);
+        job
+          .setName(plugin.getName() + " sample: " + localSampleId + ", title: " + expTitle + " " + part);
       }
       //
       Integer fileId = file.getId();
-      job.setParameterValue("peakListFileId", new IntegerParameterType(), fileId);
+      job.setParameterValue("peakListFileId", new IntegerParameterType(),
+        fileId);
       //
       job.setParameterValue("filenamePrefix", new StringParameterType(),
@@ -282 +294 @@
       job.setParameterValue("localSampleId", new StringParameterType(),
         localSampleId);
-      job.setParameterValue("experimentTitle", new StringParameterType(), expTitle);
+      job.setParameterValue("experimentTitle", new StringParameterType(),
+        expTitle);
       job.setParameterValue("details", new StringParameterType(), part);
-      job.setParameterValue("addContact", new BooleanParameterType(), addContact);
-      job.setParameterValue("addSampleName", new BooleanParameterType(), addSampleName);
-      job.setParameterValue("contactName", new StringParameterType(), contactName);
-      job.setParameterValue("contactInst", new StringParameterType(), contactInst);
-      job.setParameterValue("contactInfo", new StringParameterType(), contactInfo);
-      job.setParameterValue("prideProtocolFileId", new IntegerParameterType(),
-        prideProtocolFileId);
+      job.setParameterValue("addContact", new BooleanParameterType(),
+        addContact);
+      job.setParameterValue("addSampleName", new BooleanParameterType(),
+        addSampleName);
+      job.setParameterValue("contactName", new StringParameterType(),
+        contactName);
+      job.setParameterValue("contactInst", new StringParameterType(),
+        contactInst);
+      job.setParameterValue("contactInfo", new StringParameterType(),
+        contactInfo);
+      job.setParameterValue("prideProtocolFileId",
+        new IntegerParameterType(), prideProtocolFileId);
       //
       ItemParameterType<Project> projectParam = new ItemParameterType<Project>(
@@ -304 +322 @@
       job.setParameterValue("directory", dirParam, dir);
       job
-        .setDescription("Output file: " + dir.getName() + "/" + outputFilename + ", FDR upper cutoff: " + fdrCutoff );
+        .setDescription("Output file: " + dir.getName() + "/" + outputFilename + ", FDR upper cutoff: " + fdrCutoff);
       dc.saveItem(job);
       dc.commit();