Changeset 5765

Timestamp:

Sep 27, 2011, 3:38:36 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #1613: Extend the 'roles' test case with some sequence-related tests

• Added GTF reporter importer test (in admin test)
• Added GTF file and GTF feature importer test (in power user test)

Location:

trunk/src/test/net/sf/basedb/test

Files:

• PluginUtil.java (modified) (2 diffs)
• SequenceData.java (added)
• roles/AdminTest.java (modified) (3 diffs)
• roles/PowerUserTest.java (modified) (10 diffs)
• roles/Util.java (modified) (1 diff)

trunk/src/test/net/sf/basedb/test/PluginUtil.java

@@ -75 +75 @@
       ParameterType stringType = new StringParameterType();
       ParameterType intType = new IntegerParameterType();
+      ParameterType boolType = new BooleanParameterType();
       for (Map.Entry<String, Object> param : parameters.entrySet())
       {
@@ -86 +87 @@
         {
           config.setParameterValues(param.getKey(), intType, values);
+        }
+        else if (value instanceof Boolean)
+        {
+          config.setParameterValues(param.getKey(), boolType, values);
         }
         else

trunk/src/test/net/sf/basedb/test/roles/AdminTest.java

@@ -52 +52 @@
 import net.sf.basedb.test.MouseData;
 import net.sf.basedb.test.PluginUtil;
+import net.sf.basedb.test.SequenceData;
 import net.sf.basedb.test.TestUtil;
 
@@ -118 +119 @@
           "Reporters from Affymetrix annotations file",
           "net.sf.basedb.plugins.ReporterFlatFileImporter", AffymetrixData.getReporterParameters());
+      
+      PluginConfiguration gtfReporterImporter = PluginUtil.createPluginConfiguration(dc, 
+          "Reporters from GTF file",
+          "net.sf.basedb.plugins.gtf.GtfReporterImporter", SequenceData.getGtfReporterParameters());
       dc.commit();
       
@@ -124 +129 @@
       File reporters = FileUtil.uploadFile(dc, "/mouse", "plates_and_reporters.mouse.v4.37k.txt", File.PLATE);
       File affyReporters = FileUtil.uploadFile(dc, "/affymetrix/annotations", "MG_U74Av2_annot.csv.tar.bz2", File.REPORTER);
+      File gtfReporters = FileUtil.uploadFile(dc, "/sequencing", "refseq_CDS_fasta-hg19.gtf.tar.bz2", File.REPORTER);
       dc.commit();
       
       //Import reporters
       PluginUtil.importReporters(reporterImporter, reporters, "Importing reporters for project A");
-      PluginUtil.importReporters(affyReporterImporter, affyReporters, "Importing Affymetrix reporter for project A");
+      PluginUtil.importReporters(affyReporterImporter, affyReporters, "Importing Affymetrix reporters for project A");
+      PluginUtil.importReporters(gtfReporterImporter, gtfReporters, "Importing GTF reporters for project A");
       TestUtil.logout();
     }

trunk/src/test/net/sf/basedb/test/roles/PowerUserTest.java

@@ -49 +49 @@
 import net.sf.basedb.core.PlateType;
 import net.sf.basedb.core.Platform;
+import net.sf.basedb.core.PlatformVariant;
 import net.sf.basedb.core.PluginConfiguration;
 import net.sf.basedb.core.PluginDefinition;
@@ -64 +65 @@
 import net.sf.basedb.test.MouseData;
 import net.sf.basedb.test.PluginUtil;
+import net.sf.basedb.test.SequenceData;
 import net.sf.basedb.test.TestUtil;
 
@@ -171 +173 @@
       PluginDefinition printMapImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.PrintMapFlatFileImporter");
 
+      PluginConfiguration gtfFeatureImporter = PluginUtil.createPluginConfiguration(dc, 
+          "GTF feature for project A", "net.sf.basedb.plugins.gtf.GtfReporterMapImporter", 
+          SequenceData.getGtfFeatureParameters());
+      
       PluginConfiguration rawDataImporter = PluginUtil.createPluginConfiguration(dc, "Raw data for project A", 
           "net.sf.basedb.plugins.RawDataFlatFileImporter", MouseData.getGenePixRawDataParameters(false));
@@ -190 +196 @@
       File printMap = FileUtil.uploadFile(dc, "/mouse", "printmap.mouse.v4.37k.tam", File.PRINT_MAP);
       File cdfFile = FileUtil.uploadFile(dc, "/affymetrix/cdf", "MG_U74Av2.cdf.tar.bz2", File.REPORTER_MAP);
-      // TODO (#1613) - When we have a RefSeq test file
-      // File refSeqFile = FileUtil.uploadFile(dc, "/illumina", "refseq.txt", File.REPORTER_MAP);
+      File refSeqFile = FileUtil.uploadFile(dc, "/sequencing", "refseq_CDS_fasta-hg19.gtf.tar.bz2", File.REPORTER_MAP);
       File batchImportFile_ArrayBatch = null;
       File batchImportFile_ArrayDesign = null;
@@ -211 +216 @@
       Platform genericPlatform = Platform.getByExternalId(dc, Platform.GENERIC);
       Platform affymetrixPlatform = Platform.getByExternalId(dc, Platform.AFFYMETRIX);
+      PlatformVariant seqPlatform = PlatformVariant.getByExternalId(dc, PlatformVariant.SEQUENCING_EXPRESSION);
       if (!useBatchImporters)
       { 
@@ -217 +223 @@
         affyDesign = createArrayDesign(dc, affymetrixPlatform, "Affymetrix A", null);
         FileUtil.addDataFile(dc, affyDesign, DataFileType.AFFYMETRIX_CDF, cdfFile, true);
-        // TODO (#1613) - use different platform when it has been defined by #1153
-        refSeqDesign = createArrayDesign(dc, genericPlatform, "RefSeqDesign A", null);
-        // TODO (#1613) - when a ref-seq file type has been defined by #1153 
-        // and we have a test data set -- DO NOT FORGET TO ADD TO THE BATCH IMPORTER FILES
-        //FileUtil.addDataFile(dc, refSeqDesign, DataFileType.REF_SEQ, refSeqFile, true);
+        refSeqDesign = createArrayDesign(dc, seqPlatform, "RefSeqDesign A", null);
+        FileUtil.addDataFile(dc, refSeqDesign, DataFileType.REF_SEQ_GTF, refSeqFile, true);
       }
       else
@@ -234 +237 @@
       
       importFeatures(printMapImporter, printMap, design);
-      // TODO (#1613) - when we have the importer, data file, etc.
-      // importFeatures(refSeqImporter, refSeqFile, refSeqDesign);
+      importFeatures(gtfFeatureImporter, refSeqFile, refSeqDesign);
       
       dc = TestUtil.getDbControl();
@@ -461 +463 @@
 
   /**
+    Create an array design.
+  */
+  public static ArrayDesign createArrayDesign(DbControl dc, PlatformVariant variant, String name, String linkToPlatesPattern)
+  {
+    TestUtil.write("--Creating array design: " + name + "\n");
+    ArrayDesign design = ArrayDesign.getNew(dc, variant);
+    design.setName(name);
+    
+    if (linkToPlatesPattern != null)
+    {
+      List<Plate> plates = Util.findPlates(dc, linkToPlatesPattern);
+      design.setPlateList(plates);
+    }
+    
+    dc.saveItem(design);
+    return design;
+  }
+
+  /**
     Create an array batch.
   */
@@ -537 +558 @@
     }
   }
+
+  /**
+    Import features.
+  */
+  public static void importFeatures(PluginConfiguration config, File file, ArrayDesign design)
+    throws Exception
+  {
+    TestUtil.write("--Importing features from file: " + file.getName() + "\n");
+    DbControl dc = TestUtil.getDbControl();
+    try
+    {
+      config = PluginConfiguration.getById(dc, config.getId());
+      Job job = Job.getNew(dc, config.getPluginDefinition(), config, null);
+      job.setName("Importing features to array design: " + design.getName());
+      job.setParameterValue("file", new FileParameterType(), file);
+      job.setParameterValue("arrayDesign", 
+        new ItemParameterType<ArrayDesign>(ArrayDesign.class, null), design);
+      dc.saveItem(job);
+      dc.commit();
+      PluginUtil.executeJob(job);
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
   
   public static void importArrayBatches(PluginDefinition batchImporter, File file)
@@ -588 +636 @@
       job.setParameterValue("numArraysColumnMapping", new StringParameterType(), "\\Arrays/slide\\");
       job.setParameterValue("platformColumnMapping", new StringParameterType(), "\\Platform\\");
+      job.setParameterValue("variantColumnMapping", new StringParameterType(), "\\Variant\\");
       job.setParameterValue("fileTypeColumnMapping", new StringParameterType(), "\\File type\\");
       job.setParameterValue("fileColumnMapping", new StringParameterType(), "\\File\\");

trunk/src/test/net/sf/basedb/test/roles/Util.java

@@ -198 +198 @@
     }
     query.order(Orders.asc(Hql.property("name")));
-    System.out.println("Find plates: " + query.toQl(dc));
     return query.list(dc);
   }