Changeset 554

Timestamp:

Jan 25, 2008, 4:38:19 PM (15 years ago)

Author:

Martin Svensson

Message:

References #89 Illumina items are now created by the installation plug-in but there are still some checks and testings that need to be done befor this plug-in is finished.

File:

• trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/install/Install.java (modified) (12 diffs)

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

@@ -24 +24 @@
 */
 package net.sf.basedb.illumina.install;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.EnumSet;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
 
 import net.sf.basedb.core.BaseException;
@@ -42 +32 @@
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemAlreadyExistsException;
+import net.sf.basedb.core.ItemNotFoundException;
 import net.sf.basedb.core.Permission;
 import net.sf.basedb.core.Platform;
@@ -61 +52 @@
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.EnumSet;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
 
 /**
@@ -202 +203 @@
         if (installExp2) expressionTypes.add(2);
         
-        installIlluminaItems(installSnp, expressionTypes, alreadyExistingItem.equals(SKIP_OPTION));
+        installIlluminaItems(installSnp, expressionTypes, alreadyExistingItem.equals(SKIP_OPTION), progress);
       }
       catch(Throwable ex)
@@ -296 +297 @@
     @throws ItemAlreadyExistsException If ignoreInstalledItems = FALSE and one of the
    */
-  public void installIlluminaItems(boolean installSNP, HashSet<Integer> expressionTypes, boolean ignoreExistingItems)
+  public void installIlluminaItems(boolean installSNP, HashSet<Integer> expressionTypes, boolean ignoreExistingItems, ProgressReporter progress)
     throws ItemAlreadyExistsException
   {
@@ -319 +320 @@
       dc = sc.newDbControl();
   
-      List<DataFileType> dataFileTypes = new ArrayList<DataFileType>();
-      dataFileTypes.add(createDataFileType(dc, bgxFileTypeId, "BGX file", Item.ARRAYDESIGN, BGX_FILEYTPE_EXTENSION, ignoreExistingItems));
+      List<DataFileType> expressionDataFileTypes = new ArrayList<DataFileType>();
+      DataFileType dft = createDataFileType(dc, bgxFileTypeId, "BGX file", Item.ARRAYDESIGN, BGX_FILEYTPE_EXTENSION, ignoreExistingItems);
+      dft.setDescription("Illumina BGX file");
+      expressionDataFileTypes.add(dft);
 
       for (int i = 1; i <= largestNumOfStrips; i++ )
       {
-        String name = "Scandata filetype" + i;        
-        dataFileTypes.add(createDataFileType(dc, scandataFileTypePrefix + i, name, Item.RAWBIOASSAY, SCANDATA_FILETYPE_EXTENSION, ignoreExistingItems));
+        String name = "Scandata filetype" + i;  
+        dft = createDataFileType(dc, scandataFileTypePrefix + i, name, Item.RAWBIOASSAY, SCANDATA_FILETYPE_EXTENSION, ignoreExistingItems);
+        dft.setDescription("Illumina scandata file");
+        expressionDataFileTypes.add(dft);
       }
       //TODO Create data file type for SNP filer.
-  
-//
-//      Platform illuminaPlatform = createPlatform(dc, illuminaPlatformExternalId, "Illumina", ignoreExistingItems);
-//            
-//      List<PlatformVariant> platformVariants = new ArrayList<PlatformVariant>();      
-//      String namePrefix = "Illumina expression";
-//      for (int type : expressionTypes)
-//      {
-//        PlatformVariant pfv = createPlatformVariant(dc, expExternalIdPrefix + type, 
-//            illuminaPlatform, RawDataTypes.getRawDataType("illumina.scandata"), ignoreExistingItems);
-//        pfv.setName(namePrefix + type);
-//        pfv.setDescription("Platform variant to use with Illumina expression");
-//        //TODO Add data file types to the expression variants.
-//        platformVariants.add(pfv);        
-//      }
-//      if (installSNP)
-//      {
-//        PlatformVariant pfv = createPlatformVariant(dc, snpVariantExternalId, "Illumina SNP", illuminaPlatform, 2, ignoreExistingItems);
-//        pfv.setName("Illumina SNP");
-//        pfv.setDescription("Platform variant to be used for Illumina SNP data.");
-//        //TODO Add data file types to the SNP variant.
-//        platformVariants.add(pfv);        
-//      }
-      
+      
+      dc.commit();
+      
+      dc = sc.newDbControl();
+      Platform illuminaPlatform = createPlatform(dc, illuminaPlatformExternalId, "Illumina", ignoreExistingItems);
+            
+      List<PlatformVariant> platformVariants = new ArrayList<PlatformVariant>();      
+      String namePrefix = "Illumina 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");
+        pfv.addFileType(DataFileType.getByExternalId(dc, bgxFileTypeId), true);
+        for (int i = 1; i <= type; i++)
+        {
+          pfv.addFileType(DataFileType.getByExternalId(dc, scandataFileTypePrefix+i), true);
+        }
+        platformVariants.add(pfv);        
+      }
+      if (installSNP)
+      {
+        PlatformVariant pfv = createPlatformVariant(dc, snpVariantExternalId, "Illumina SNP", illuminaPlatform, 2, ignoreExistingItems);
+        pfv.setDescription("Platform variant to be used with Illumina SNP data.");
+        //TODO Add data file types to the SNP variant.
+        platformVariants.add(pfv);        
+      }     
       dc.commit();
     }
@@ -393 +401 @@
     try
     {
+      dft = DataFileType.getByExternalId(dc, externalId);
+      String message = null;
+      if (!ignoreExistingItem)
+      {
+        throw new ItemAlreadyExistsException(dft.getExternalId());
+      }
+      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 (message != null) throw new ItemAlreadyExistsException(message);
+      
+    }
+    catch (ItemNotFoundException infe)
+    {
       dft = DataFileType.getNew(dc, externalId, itemType);
       dc.saveItem(dft);
@@ -398 +420 @@
       dft.setExtension(extension);
     }
-    catch (ItemAlreadyExistsException iex)
-    {
-      if (!ignoreExistingItem)
-      {
-        throw iex;
-      }
-      else
-      {
-        dft = DataFileType.getByExternalId(dc, externalId);
-        if (dft.getExtension() != extension) throw new InvalidDataException(dft.getName() + " has invalid extension");
-        if (dft.getItemType() != itemType) throw new InvalidDataException(dft.getName() + " has invalid item type");
-      }
-    }
     return dft;
   }
@@ -419 +428 @@
     try
     {
+      platform = Platform.getByExternalId(dc, externalId);
+      if (!ignoreExistingItem)
+      {
+        throw new ItemAlreadyExistsException(platform.getExternalId());
+      }
+      //TODO Check that existing platform can be used with the rest of the items.
+    }
+    catch (ItemNotFoundException infex)
+    {
       platform = Platform.getNew(dc, externalId, null);
-      //TODO More property to set?
       dc.saveItem(platform);
       platform.setName(name);
-    }
-    catch (ItemAlreadyExistsException iex)
-    {
-      if (!ignoreExistingItem)
-      {
-        throw iex;
-      }
-      else
-      {
-        platform = Platform.getByExternalId(dc, externalId);
-        //TODO Check that existing platform can be used with the rest of the items.
-      }
     }
     return platform;
@@ -442 +447 @@
     Creates variants associated with a raw data type 
    */
-  private PlatformVariant createPlatformVariant(DbControl dc, String extId,
+  private PlatformVariant createPlatformVariant(DbControl dc, String externalId, String name,
       Platform illuminaPlatform, RawDataType rawDataType, boolean ignoreExistingItem)
   {
@@ -448 +453 @@
     try
     {
-      variant = PlatformVariant.getNew(dc, illuminaPlatform, extId, rawDataType);
-      dc.saveItem(variant);     
-    }
-    catch (ItemAlreadyExistsException iex)
-    {
+      variant = PlatformVariant.getByExternalId(dc, externalId);
       if (!ignoreExistingItem)
       {
-        throw iex;
-      }
-      else
-      {
-        variant = PlatformVariant.getByExternalId(dc, extId);
-        if (variant.isFileOnly()) 
-          throw new InvalidDataException ("Platform variant " + variant.getName() + " exists but is not file-only");
-        if (!variant.getRawDataType().equals(rawDataType)) 
-          throw new InvalidDataException ("Platform variant " + variant.getName() + " exists but has not raw data type: " + rawDataType);
-        if (!variant.getPlatform().equals(illuminaPlatform)) 
-          throw new InvalidDataException ("Platform variant " + variant.getName() + " exists but has not platform: " + illuminaPlatform);
-      }
-    }
-    return null;
+        throw new ItemAlreadyExistsException(variant.getExternalId());
+      }
+      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.";
+      if (message != null) throw new ItemAlreadyExistsException(message);
+      
+    }
+    catch (ItemNotFoundException infex)
+    {
+      variant = PlatformVariant.getNew(dc, illuminaPlatform, externalId, rawDataType);
+      dc.saveItem(variant);
+      variant.setName(name);
+    }
+    return variant;
   }
 
@@ -474 +477 @@
     Creates file-only platform variants
    */
-  private PlatformVariant createPlatformVariant(DbControl dc,
-      String snpVariantExternalId, String name, Platform illuminaPlatform,
-      int channels, boolean ignoreExistingItems)
-  {
-    // TODO Auto-generated method stub
-    return null;
+  private PlatformVariant createPlatformVariant(DbControl dc, String externalId, 
+      String name, Platform platform, int channels, boolean ignoreExistingItems)
+  {
+    PlatformVariant variant = null;
+    try
+    {
+      variant = PlatformVariant.getByExternalId(dc, externalId);
+      if (!ignoreExistingItems)
+      {
+        throw new ItemAlreadyExistsException(variant.getExternalId());
+      }
+      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";  
+      if (message != null) throw new InvalidDataException (message);
+    }
+    catch (ItemNotFoundException infex)
+    {
+      variant = PlatformVariant.getNew(dc, platform, externalId, channels);
+      dc.saveItem(variant);
+      variant.setName(name);
+    }
+    return variant;
   }
 }