changeset 45:31838e0ecf45 default tip

Fixes.

--- a/TrustStoreGalaxyBrowse.py	Thu Jun 25 11:11:15 2015 +1000
+++ b/TrustStoreGalaxyBrowse.py	Fri Jun 26 10:24:40 2015 +1000
@@ -72,14 +72,20 @@
         os.close(file_handle)
         gzipped_file.close()
 
-        shutil.copy(uncompressed, outputFile)
+        try:
+            shutil.copy(uncompressed, outputFile)
+        except shutil.Error:
+            pass # If the file is already in the right location, move along.
         try:
             os.remove(uncompressed)
             os.remove(download)
         except OSError:
             pass
     else:
-        shutil.copy(download, outputFile)
+        try:
+            shutil.copy(download, outputFile)
+        except shutil.Error:
+            pass # If the file is already in the right location, move along.
 
 def construct_multi_filename(id, name, file_type):
     """ Implementation of *Number of Output datasets cannot be determined until
@@ -90,12 +96,15 @@
     filename = "%s_%s_%s_%s_%s" % ('primary', id, name, 'visible', file_type)
     return filename
 
-def metadata_to_json(dataset_id, filename, name, extesion, ds_type='dataset', primary=False):
+def metadata_to_json(dataset_id, filename, name, extension, ds_type='dataset', primary=False):
     """ Return line separated JSON
     From https://github.com/mdshw5/galaxy-json-data-source/blob/master/json_data_source.py
     """
+    ext = extension
+    if ext == 'fa':
+        ext = 'fasta'
     meta_dict = dict(type=ds_type,
-                     ext=extesion,
+                     ext=ext,
                      filename=filename,
                      name=name,
                      metadata={})
@@ -190,22 +199,21 @@
                     name = construct_multi_filename(hda_id, filename, extension)
                     target_output_filename = None
                     data_type = "new_primary_dataset"
-                    # if first:
-                    #     target_output_filename = file_name
-                    #     dataset = "new_primary_dataset"
-                    #     first = False
-                    # else:
                     target_output_filename = os.path.normpath(os.path.join(extra_files_path, name))
                     download = truststore.getFile(store, location)
+                    primary = not first
                     if download is None:
                         print("File %s not found." % location.name)
                         sys.exit(4)
+                    if first:
+                        first = False
+                        target_output_filename = file_name
+                        data_type = "dataset"
                     ungzip(download, target_output_filename)
+                    metadata_file.write(
+                        metadata_to_json(dataset_id, target_output_filename, name, extension, data_type, primary=primary))
                     # ext = sniff.handle_uploaded_dataset_file(target_output_filename, datatypes_registry, ext=ext)
                     # print("Guessed file type: " + ext)
-                    print("in file: " + properties_file)
-                    metadata_file.write(
-                        metadata_to_json(dataset_id, target_output_filename, name, extension, data_type))
     else:
         print("Store is damaged or we don't have sufficient access.")
         sys.exit(4)