Fixed #545. A third parameter is returned, specifying whether a file …

…as been skipped or not.
refinery-platform · Jun 29, 2015 · 345a341 · 345a341
1 parent 951f9cc
commit 345a341
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Showing 3 changed files with 10 additions and 9 deletions.
diff --git a/refinery/data_set_manager/management/commands/process_isatab.py b/refinery/data_set_manager/management/commands/process_isatab.py
@@ -127,9 +127,9 @@ def handle(self, username, base_isa_dir, **options):
 
         task_num = 1
         total = len(isatab_dict)
-        for (i, filename) in result.iterate():
+        for (i, filename, skipped) in result.iterate():
             try:
-                if i:
+                if !skipped:
                     print (
                         "{num} / {total}: Successfully parsed {file} into "
                         "DataSet with UUID {uuid}".format(
@@ -142,10 +142,11 @@ def handle(self, username, base_isa_dir, **options):
                 else:
                     print (
                         "{num} / {total}: Skipped {file} as it has been "
-                        "successfully parsed already".format(
+                        "successfully parsed already. UUID {uuid}".format(
                             num=task_num,
                             total=total,
-                            file=filename
+                            file=filename,
+                            uuid=i
                         )
                     )
                 task_num += 1

diff --git a/refinery/data_set_manager/tasks.py b/refinery/data_set_manager/tasks.py
@@ -578,15 +578,15 @@ def parse_isatab(
                     'The checksum of both files is the same: %s',
                     checksum
                 )
-                return (None, os.path.basename(path))
+                return (investigation.isarchive_file, os.path.basename(path), True)
 
     try:
         investigation = p.run(
             path,
             isa_archive=isa_archive,
             preisa_archive=pre_isa_archive)
         data_uuid = create_dataset(investigation.uuid, username, public=public)
-        return (data_uuid, os.path.basename(path))
+        return (data_uuid, os.path.basename(path), False)
     except:  # prints the error message without breaking things
         logger.error("*** print_tb:")
         exc_type, exc_value, exc_traceback = sys.exc_info()
@@ -600,4 +600,4 @@ def parse_isatab(
                 file=sys.stdout
             )
         )
-    return (None, os.path.basename(path))
+    return (None, os.path.basename(path), False)
diff --git a/refinery/data_set_manager/views.py b/refinery/data_set_manager/views.py
@@ -145,7 +145,7 @@ def get(self, request, *args, **kwargs):
             response.delete_cookie(self.isa_tab_cookie_name)
             return response
         logger.debug("Temp file name: '%s'", temp_file_path)
-        dataset_uuid, _ = parse_isatab.delay(request.user.username,
+        dataset_uuid, _, _ = parse_isatab.delay(request.user.username,
                                           False,
                                           temp_file_path).get()
         #TODO: exception handling
@@ -247,7 +247,7 @@ def post(self, request, *args, **kwargs):
                     return render_to_response(self.template_name,
                                               context_instance=context)
             logger.debug("Temp file name: '%s'", temp_file_path)
-            dataset_uuid, _ = parse_isatab.delay(request.user.username,
+            dataset_uuid, _, _ = parse_isatab.delay(request.user.username,
                                               False, temp_file_path).get()
             #TODO: exception handling (OSError)
             os.unlink(temp_file_path)