Changeset 3586

Timestamp:

Jul 20, 2007, 2:40:10 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

References #326: Mass annotation plug-in

Major features in place. Code needs to be polished up and documented. Need to add permissions.
User documentation (docbook) should be checked if it needs to be updated.

Location:

trunk/src

Files:

• core/net/sf/basedb/core/AnnotationType.java (modified) (1 diff)
• core/net/sf/basedb/core/DisallowedValueException.java (added)
• core/net/sf/basedb/core/Install.java (modified) (1 diff)
• core/net/sf/basedb/core/PluginRequest.java (modified) (4 diffs)
• core/net/sf/basedb/core/plugin/ParameterValuesWrapper.java (added)
• plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java (modified) (1 diff)
• plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java (added)
• test/TestAll.java (modified) (2 diffs)
• test/TestAnnotation.java (modified) (5 diffs)
• test/TestAnnotationFlatFileImporter.java (added)
• test/TestAnnotationType.java (modified) (5 diffs)
• test/TestAnnotationTypeCategory.java (modified) (1 diff)
• test/TestAnyToAny.java (modified) (1 diff)
• test/TestExtract.java (modified) (1 diff)
• test/TestSample.java (modified) (3 diffs)
• test/data/test.annotation.import.txt (added)

trunk/src/core/net/sf/basedb/core/AnnotationType.java

@@ -1094 +1094 @@
       if (pv == null || !pv.getValues().contains(value))
       {
-        throw new InvalidDataException("Value '"+value+"' is not among the list of allowed values: "+(pv == null ? "" : pv.getValues()));
+        throw new DisallowedValueException("Value '"+value+"' is not among the list of allowed values " +
+          "for annotation type: "+getName());
       }
     }

trunk/src/core/net/sf/basedb/core/Install.java

@@ -606 +606 @@
       createPluginDefinition("net.sf.basedb.plugins.CdfFileReporterImporter", null, null, true, null, false);
       createPluginDefinition("net.sf.basedb.plugins.PackedFileExporter", null, keyEveryoneUse, true, null, true);
+      createPluginDefinition("net.sf.basedb.plugins.AnnotationFlatFileImporter", null, keyEveryoneUse, true, null, false);
       
       // Plugin configurations

trunk/src/core/net/sf/basedb/core/PluginRequest.java

@@ -146 +146 @@
   }
   
+  /**
+    Get the values that are currently stored in the job or plugin configuration
+    related to this request. This method will first check the job and then the
+    plugin configuration.
+    @param name The name of the parameter
+    @return The parameter values, or null if no parameter with the given name
+      exists
+  */
   public List<?> getCurrentParameterValues(String name)
   {
@@ -153 +161 @@
       values = jobParameters.getValues(name);
     }
-    else if (configurationParameters != null)
+    if (values == null && configurationParameters != null)
     {
       values = configurationParameters.getValues(name);
@@ -161 +169 @@
   
   
+  /**
+    Get the values that are currently stored in the plugin configuration
+    related to this request.
+    @param name The name of the parameter
+    @return The parameter values, or null if no parameter with the given name
+      exists or if this request isn't associated with a plugin configuration
+  */
   public List<?> getCurrentConfigurationParameterValues(String name)
   {
@@ -171 +186 @@
   }
   
+  /**
+    Get the values that are currently stored in the job related to this
+    request.
+    @param name The name of the parameter
+    @return The parameter values, or null if no parameter with the given name
+      exists or if this request isn't associated with a job
+  */
   public List<?> getCurrentJobParameterValues(String name)
   {

trunk/src/plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java

@@ -953 +953 @@
     return mapper;
   }
-    
+  
+  /**
+    Get the value for an error handling parameter. If no value
+    is found for the specified parameter the value for the 'defaultError' parameter
+    is returned.
+    @param parameterName The name of the error parameter
+    @return The error option or null if no option has been set
+    @since 2.4
+  */
+  protected String getErrorOption(String parameterName)
+  {
+    Object option = null;
+    option = job.getValue(parameterName);
+    if (option == null) option = job.getValue("defaultError");
+    return option == null ? null : option.toString();
+  }
+  
   protected ErrorHandler getErrorHandler(String method, ErrorHandler defaultErrorHandler)
   {

trunk/src/test/TestAll.java

@@ -72 +72 @@
     results.put("TestProtocol", TestProtocol.test_all());
 
-    // Annotation types and annotations
-    results.put("TestAnnotationType", TestAnnotationType.test_all());
-    results.put("TestAnnotationTypeCategory", TestAnnotationTypeCategory.test_all());
-    results.put("TestAnnotation", TestAnnotation.test_all());
-
+    // File parsing
+    results.put("TestFlatFileParser", TestFlatFileParser.test_all());
+    
     // Biomaterials
     results.put("TestBioSource", TestBioSource.test_all());
@@ -84 +82 @@
     results.put("TestLabeledExtract", TestLabeledExtract.test_all());
 
-    // File parsing
-    results.put("TestFlatFileParser", TestFlatFileParser.test_all());
-
+    // Annotation types and annotations
+    results.put("TestAnnotationType", TestAnnotationType.test_all());
+    results.put("TestAnnotationTypeCategory", TestAnnotationTypeCategory.test_all());
+    results.put("TestAnnotation", TestAnnotation.test_all());
+    results.put("TestAnnotationFlatFileImporter", TestAnnotationFlatFileImporter.test_all());
+    
     // Reporters
     results.put("TestReporterType", TestReporterType.test_all());

trunk/src/test/TestAnnotation.java

@@ -48 +48 @@
     // Create annotation types and array design
 
-    int intId = TestAnnotationType.test_create(Type.INT, 10, Item.ARRAYDESIGN, null, true);
-    int longId = TestAnnotationType.test_create(Type.LONG, 1056567756767l, Item.ARRAYDESIGN, null, true);
-    int floatId = TestAnnotationType.test_create(Type.FLOAT, 10.1f, Item.ARRAYDESIGN, null, true);
-    int doubleId = TestAnnotationType.test_create(Type.DOUBLE, 8.13454646d, Item.ARRAYDESIGN, null, true);
-    int dateId = TestAnnotationType.test_create(Type.DATE, new Date(), Item.ARRAYDESIGN, null, true);
-    int textId = TestAnnotationType.test_create(Type.TEXT, "default value", Item.ARRAYDESIGN, null, true);
-    int stringId = TestAnnotationType.test_create(Type.STRING, "default value", Item.ARRAYDESIGN, null, true);
-    int booleanId = TestAnnotationType.test_create(Type.BOOLEAN, true, Item.ARRAYDESIGN, null, true);
-    int enumId = TestAnnotationType.test_create(Type.INT, 3, Item.ARRAYDESIGN, new Object[] { 1, 2, 3, 4, 5 }, false);
+    int intId = TestAnnotationType.test_create(null, Type.INT, 10, null, Item.ARRAYDESIGN, 1, null, true);
+    int longId = TestAnnotationType.test_create(null, Type.LONG, 1056567756767l, null, Item.ARRAYDESIGN, 1, null, true);
+    int floatId = TestAnnotationType.test_create(null, Type.FLOAT, 10.1f, null, Item.ARRAYDESIGN, 1, null, true);
+    int doubleId = TestAnnotationType.test_create(null, Type.DOUBLE, 8.13454646d, null, Item.ARRAYDESIGN, 1, null, true);
+    int dateId = TestAnnotationType.test_create(null, Type.DATE, new Date(), null, Item.ARRAYDESIGN, 1, null, true);
+    int textId = TestAnnotationType.test_create(null, Type.TEXT, "default value", null, Item.ARRAYDESIGN, 1, null, true);
+    int stringId = TestAnnotationType.test_create(null, Type.STRING, "default value", null, Item.ARRAYDESIGN, 1, null, true);
+    int booleanId = TestAnnotationType.test_create(null, Type.BOOLEAN, true, null, Item.ARRAYDESIGN, 1, null, true);
+    int enumId = TestAnnotationType.test_create(null, Type.INT, 3, null, Item.ARRAYDESIGN, 1, new Object[] { 1, 2, 3, 4, 5 }, false);
     int arrayDesignId = TestArrayDesign.test_create(true, false);
 
@@ -69 +69 @@
     int booleanAnnotationId = test_annotatate(arrayDesignId, booleanId, false);
     int enumAnnotationId = test_annotatate(arrayDesignId, enumId, 4);
-    test_list_annotations(arrayDesignId, 9);
+    test_list_annotations(Item.ARRAYDESIGN, arrayDesignId, 9);
 
     // Test: inherit annotations
@@ -95 +95 @@
     test_remove_annotation(arrayDesignId, booleanId);
     test_remove_annotation(arrayDesignId, enumId);
-    test_list_annotations(arrayDesignId, 0);
+    test_list_annotations(Item.ARRAYDESIGN, arrayDesignId, 0);
 
     // Delete annotation types and array design
@@ -176 +176 @@
   }
 
-  static void test_list_annotations(int arrayDesignId, int expectedResults)
-  {
-    DbControl dc = null;
-    try
-    {
-      dc = TestUtil.getDbControl();
-      ArrayDesign ad = ArrayDesign.getById(dc, arrayDesignId);
-      AnnotationSet as = ad.getAnnotationSet();
+  static void test_list_annotations(Item itemType, int itemId, int expectedResults)
+  {
+    DbControl dc = null;
+    Annotatable at = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      at = (Annotatable)itemType.getById(dc, itemId);
+      AnnotationSet as = at.getAnnotationSet();
       ItemResultList<Annotation> l = as.getAnnotations().list(dc);
       for (int i = 0; i<l.size(); i++)
@@ -193 +194 @@
         throw new BaseException("Expected "+expectedResults+" results, not "+l.size());
       }
-      write("--List annotations OK ("+l.size()+")");
-    }
-    catch (Throwable ex)
-    {
-      write("--List annotations FAILED");
+      write("--List annotations for " + at + " OK ("+l.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List annotations for " + at + " FAILED");
       ex.printStackTrace();
       ok = false;

trunk/src/test/TestAnnotationType.java

@@ -45 +45 @@
     write_header();
     // Standard tests: create, load, list
-    int id_int = test_create(Type.INT, 10, Item.SAMPLE, null, true);
-    int id_long = test_create(Type.LONG, 123456789123456l, Item.SAMPLE, null, true);
-    int id_float = test_create(Type.FLOAT, 10.1, Item.SAMPLE, null, false);
-    int id_double = test_create(Type.DOUBLE, 8.13459187745, Item.SAMPLE, null, false);
-    int id_date = test_create(Type.DATE, new Date(), Item.SAMPLE, null, false);
-    int id_text = test_create(Type.TEXT, "default value", Item.SAMPLE, null, false);
-    int id_string = test_create(Type.STRING, "default value", Item.SAMPLE, null, false);
-    int id_boolean = test_create(Type.BOOLEAN, true, Item.SAMPLE, null, false);
-    int id_enum = test_create(Type.INT, 3, Item.SAMPLE, new Object[] { 1, 2, 3, 4, 5 }, false);
-    int id2_enum = test_create(Type.STRING, "one", Item.SAMPLE, new String[] { "one", "two ", "three" }, false);
+    int id_int = test_create(null, Type.INT, 10, null, Item.SAMPLE, 1, null, true);
+    int id_long = test_create(null, Type.LONG, 123456789123456l, null, Item.SAMPLE, 1, null, true);
+    int id_float = test_create(null, Type.FLOAT, 10.1, null, Item.SAMPLE, 1, null, false);
+    int id_double = test_create(null, Type.DOUBLE, 8.13459187745, null, Item.SAMPLE, 1, null, false);
+    int id_date = test_create(null, Type.DATE, new Date(), null, Item.SAMPLE, 1, null, false);
+    int id_text = test_create(null, Type.TEXT, "default value", null, Item.SAMPLE, 1, null, false);
+    int id_string = test_create(null, Type.STRING, "default value", null, Item.SAMPLE, 1, null, false);
+    int id_boolean = test_create(null, Type.BOOLEAN, true, null, Item.SAMPLE, 1, null, false);
+    int id_enum = test_create(null, Type.INT, 3, null, Item.SAMPLE, 1, new Object[] { 1, 2, 3, 4, 5 }, false);
+    int id2_enum = test_create(null, Type.STRING, "one", null, Item.SAMPLE, 1, new String[] { "one", "two ", "three" }, false);
     test_load(id_int);
     test_load(id_long);
@@ -99 +99 @@
   }
   
-  static int test_create(Type type, Object defaultValue, Item itemType, Object[] enumValues, boolean setAll)
+  static int test_create(String name, Type type, Object defaultValue, Number maxValue, Item itemType, int multiplicity, Object[] enumValues, boolean setAll)
   {
     if (!TestUtil.hasPermission(Permission.CREATE, Item.ANNOTATIONTYPE)) return 0;
@@ -110 +110 @@
       if(setAll)
       {
-        at.setName("Test annotation type: "+type);
+        at.setName( "Test annotation type: "+type);
         at.setDescription("Added at "+new Date());
-        at.setMultiplicity(1);
         at.setRequiredForMiame(true);
         at.setHeight(10);
@@ -118 +117 @@
         at.setExternalId("my.external.annotationtype");
       }
+      at.setMultiplicity(multiplicity);
+      if (name != null) at.setName(name);
       if (enumValues != null)
       {
@@ -125 +126 @@
       }
       if (defaultValue != null) at.setDefaultValue(defaultValue.toString());
+      if (maxValue != null)
+      {
+        if (type.isNumerical()) 
+        {
+          at.setMinValueLong(0l);
+          at.setMaxValueLong(maxValue.longValue());
+        }
+        else if (type == Type.STRING) 
+        {
+          at.setMaxLength(maxValue.intValue());
+        }
+      }
       at.enableForItem(itemType);
       dc.saveItem(at);

trunk/src/test/TestAnnotationTypeCategory.java

@@ -59 +59 @@
 
     // extra test: add categories to annotation type
-    int id_int = TestAnnotationType.test_create(Type.INT, 10, Item.SAMPLE, null, true);
+    int id_int = TestAnnotationType.test_create(null, Type.INT, 10, null, Item.SAMPLE, 1, null, true);
     test_add_categories(id_int, id, id2);
     test_list_categories(id_int, 2);

trunk/src/test/TestAnyToAny.java

@@ -48 +48 @@
     write_header();
     // Standard tests: create, load, list
-    int sampleId = TestSample.test_create(0, true);
+    int sampleId = TestSample.test_create(0, null, true);
     int fileId1 = TestFile.test_create("Linked file #1", true);
     int fileId2 = TestFile.test_create("Linked file #2", true);

trunk/src/test/TestExtract.java

@@ -45 +45 @@
     int id2 = test_create(0, false);
     
-    int sampleId = TestSample.test_create(0, true);
+    int sampleId = TestSample.test_create(0, null, true);
     int id3 = test_create(sampleId, false);
     int id4 = test_create_pooled(id, id2, id3);

trunk/src/test/TestSample.java

@@ -42 +42 @@
     write_header();
     // Standard tests: create, load, list
-    int id = test_create(0, true);
-    int id2 = test_create(0, false);
+    int id = test_create(0, null, true);
+    int id2 = test_create(0, null, false);
     
     int bioSourceId = TestBioSource.test_create(false);
-    int id3 = test_create(bioSourceId, false);
+    int id3 = test_create(bioSourceId, null, false);
     int id4 = test_create_pooled(id, id2, id3);
 
@@ -71 +71 @@
   }
 
-  static int test_create(int bioSourceId, boolean setAll)
+  static int test_create(int bioSourceId, String name, boolean setAll)
   {
     if (!TestUtil.hasPermission(Permission.CREATE, Item.SAMPLE)) return 0;
@@ -87 +87 @@
         s.setOriginalQuantity(500.0f);
       }
+      if (name != null) s.setName(name);
       if (bioSourceId != 0)
       {