Changeset 555

Timestamp:

Jan 28, 2008, 11:48:07 AM (15 years ago)

Author:

Martin Svensson

Message:

References #89 Added more property checks when an item already exists and changed some exception messages. Now await some comments on names, ids etc. according to our meeting 25/1.

File:

• trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/install/Install.java (modified) (16 diffs)

trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/install/Install.java

@@ -29 +29 @@
 import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.FileType;
 import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.Item;
@@ -43 +44 @@
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.StringParameterType;
+import net.sf.basedb.core.SystemItems;
 import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.core.plugin.AboutImpl;
@@ -111 +113 @@
     (
       "installSnp",
-      "Install SNP variant",
-      "The SNP variant of Illumina should be installed?",
+      "SNP variant",
+      "TRUE if he SNP variant of Illumina should be installed, FALSE otherwise.",
       new BooleanParameterType(true, true)
     );    
@@ -118 +120 @@
   (
     "installExp1",
-    "Install Expression1 variant",
-    "The Expression1 variant of Illumina should be installed?",
+    "Expression 1",
+    "TRUE if the Expression 1 variant of Illumina should be installed, FALSE otherwise.",
     new BooleanParameterType(true, true)
   );  
@@ -125 +127 @@
   (
     "installExp2",
-    "Install Expression2 variant",
-    "The Expression2 variant of Illumina should be installed?",
+    "Expression2",
+    "TRUE if the Expression 2 variant of Illumina should be installed, FALSE otherwise",
     new BooleanParameterType(true, true)
   );
@@ -134 +136 @@
   
   private static final String BGX_FILEYTPE_EXTENSION = "bgx";
-  private static final String SCANDATA_FILETYPE_EXTENSION = "";
-  private static final String SNP_FILETYPE_EXTENSION = "";
+  private static final String SCANDATA_FILETYPE_EXTENSION = ""; //TODO
+  private static final String SNP_FILETYPE_EXTENSION = ""; //TODO
   
   private static final PluginParameter<String> alreadyInstalledErrorParameter = new PluginParameter<String>(
     "alreadyInstalledError",
-    "Platform or any of the selected variants is already installed",
-    "How to situations where the platform or any of the selected variants " +
-    "already exists in the database." +
-    "If not specified, default value will be used.\n\n" +
+    "Item already exists.",
+    "How to act when an external id is taken for either the platform or any of the selected variants." +
+    "If not specified, default value(skip) will be used.\n\n" +
     "abort = Abort the installation, nothing will be created.\n" +
-    "skip = Installation of the already existing item will be skipped " +
-    "and the installation tries to proceed with rest of the items.",
+    "skip = The installation will skip the existing item " +
+    "and try to proceed.",
     new StringParameterType(255, SKIP_OPTION, true, 1, 0, 0, 
       Arrays.asList( new String[] { ABORT_OPTION, SKIP_OPTION}))
@@ -198 +199 @@
         boolean installExp2 = (Boolean)job.getValue("installExp2");
         String alreadyExistingItem = (String)job.getValue("alreadyInstalledError");
-        
+
         HashSet<Integer> expressionTypes = new HashSet<Integer>();
         if (installExp1) expressionTypes.add(1);
@@ -299 +300 @@
   public void installIlluminaItems(boolean installSNP, HashSet<Integer> expressionTypes, boolean ignoreExistingItems, ProgressReporter progress)
     throws ItemAlreadyExistsException
-  {
+  {   
+    RawDataType illuminaRawDataType = RawDataTypes.getRawDataType("illumina_scandata");
+    if (illuminaRawDataType == null) 
+    {
+      throw new InvalidDataException("Raw data type[illumina.scandata] is missing. " +
+          "This must exist before the items can be installed, see the Illumina plug-in manual.");
+    }
     DbControl dc = null;
     int largestNumOfStrips = 0;
@@ -309 +316 @@
     String bgxFileTypeId = "illumina.bgx";
     
+    FileType reporterMapType = null;
+    FileType rawDataType = null;
+    
     Iterator<Integer> expressionTypeIterator = expressionTypes.iterator();
     while(expressionTypeIterator.hasNext())
@@ -320 +330 @@
       dc = sc.newDbControl();
   
+      reporterMapType = FileType.getById(dc, SystemItems.getId("net.sf.basedb.core.FileType.REPORTER_MAP"));
+      rawDataType = FileType.getById(dc, SystemItems.getId("net.sf.basedb.core.FileType.RAW_DATA"));
+      
       List<DataFileType> expressionDataFileTypes = new ArrayList<DataFileType>();
       DataFileType dft = createDataFileType(dc, bgxFileTypeId, "BGX file", Item.ARRAYDESIGN, BGX_FILEYTPE_EXTENSION, ignoreExistingItems);
-      dft.setDescription("Illumina BGX file");
+      if (dft.getDescription() == null || dft.getDescription().equals(""))dft.setDescription("Illumina BGX file");
+      if (dft.getGenericType() == null) dft.setGenericType(reporterMapType);
       expressionDataFileTypes.add(dft);
 
       for (int i = 1; i <= largestNumOfStrips; i++ )
       {
-        String name = "Scandata filetype" + i;  
+        String name = "Scandata " + i;  
         dft = createDataFileType(dc, scandataFileTypePrefix + i, name, Item.RAWBIOASSAY, SCANDATA_FILETYPE_EXTENSION, ignoreExistingItems);
-        dft.setDescription("Illumina scandata file");
+        if (dft.getGenericType() == null) dft.setGenericType(rawDataType);
+        if (dft.getDescription() == null || dft.getDescription().equals("")) dft.setDescription("Illumina scandata file for strip #" + i + " in the array.");
         expressionDataFileTypes.add(dft);
       }
@@ -338 +353 @@
       dc = sc.newDbControl();
       Platform illuminaPlatform = createPlatform(dc, illuminaPlatformExternalId, "Illumina", ignoreExistingItems);
+      if (illuminaPlatform.getDescription() == null || illuminaPlatform.getDescription().equals("")) illuminaPlatform.setDescription("Illumina platform.");
             
       List<PlatformVariant> platformVariants = new ArrayList<PlatformVariant>();      
-      String namePrefix = "Illumina expression";
+      String namePrefix = "Expression ";
       for (int type : expressionTypes)
       {
         PlatformVariant pfv = createPlatformVariant(dc, expExternalIdPrefix + type, namePrefix + type, 
-            illuminaPlatform, RawDataTypes.getRawDataType("illumina.scandata"), ignoreExistingItems);
-        pfv.setDescription("Platform variant to use with Illumina expression containing " + type + " strip(s)/array");
+            illuminaPlatform, illuminaRawDataType, ignoreExistingItems);
+        if (pfv.getDescription() == null || pfv.getDescription().equals("")) pfv.setDescription("Platform variant to use with Illumina expression containing " + type + " strip(s)/array");
         pfv.addFileType(DataFileType.getByExternalId(dc, bgxFileTypeId), true);
         for (int i = 1; i <= type; i++)
@@ -356 +372 @@
       {
         PlatformVariant pfv = createPlatformVariant(dc, snpVariantExternalId, "Illumina SNP", illuminaPlatform, 2, ignoreExistingItems);
-        pfv.setDescription("Platform variant to be used with Illumina SNP data.");
+        if (pfv.getDescription() == null || pfv.getDescription().equals("")) pfv.setDescription("Platform variant to be used with Illumina SNP data.");
         //TODO Add data file types to the SNP variant.
         platformVariants.add(pfv);        
@@ -409 +425 @@
       dft = DataFileType.getByExternalId(dc, externalId);
       if (!dft.getExtension().equals(extension)) message = dft.getName() + " has invalid extension";
-      if (dft.getItemType().equals(itemType)) message = dft.getName() + " has invalid item type";
+      if (!dft.getItemType().equals(itemType)) message = dft.getName() + " has invalid item type";
       if (message != null) throw new ItemAlreadyExistsException(message);
       
@@ -433 +449 @@
         throw new ItemAlreadyExistsException(platform.getExternalId());
       }
+      String message = null;
+      if (platform.getRawDataType() != null) message = "The already existing platform has a raw data type that can't be used with " + name + "[" + externalId + "]";
+      if (message != null) throw new ItemAlreadyExistsException(message);
       //TODO Check that existing platform can be used with the rest of the items.
     }
@@ -460 +479 @@
       String message = null;
       if (variant.isFileOnly()) message = "Platform variant " + variant.getExternalId() + " already exists but is file-only";
-      if (!variant.getRawDataType().equals(rawDataType)) message = "Platform variant " + variant.getExternalId() + " already exists but has not " + rawDataType.getName() + " as raw data type";
-      if (!variant.getPlatform().equals(illuminaPlatform)) message = "Platform variant " + variant.getExternalId() + " already exists for another platform.";
+      else if (variant.getRawDataType() != null && !variant.getRawDataType().equals(rawDataType))
+      {
+        message = "Platform variant " + variant.getExternalId() + " already exists but has not the right raw data type";
+      } 
+      else if (!variant.getPlatform().equals(illuminaPlatform)) message = "Platform variant " + variant.getExternalId() + " already exists for another platform.";
       if (message != null) throw new ItemAlreadyExistsException(message);
       
@@ -490 +512 @@
       String message = null;
       if (!variant.isFileOnly()) message = "Platform variant " + variant.getName() + " exists but is not file-only";
-      if (!variant.getPlatform().equals(platform)) message = "Platform variant " + variant.getName() + " exists but has not platform: " + platform; 
-      if (variant.getRawDataType().getChannels() != channels) message = "Platform variant " + variant.getName() + " exists but not for " + channels + " data";  
+      else if (!variant.getPlatform().equals(platform)) message = "Platform variant " + variant.getName() + " exists but has not platform: " + platform; 
+      else if (variant.getRawDataType().getChannels() != channels) message = "Platform variant " + variant.getName() + " exists but not for " + channels + " data";  
       if (message != null) throw new InvalidDataException (message);
     }