Scottx611x/auto import of data fix

refinery/analysis_manager/tasks.py

@@ -384,7 +384,7 @@ def get_galaxy_download_tasks(analysis):
                 # TODO: when changing permanent=True, fix update of % download
                 # of file
                 filestore_uuid = create(
-                    source=download_url, filetype=file_type, permanent=False)
+                    source=download_url, filetype=file_type)
                 # adding history files to django model
                 temp_file = AnalysisResult(
                     analysis_uuid=analysis.uuid,

refinery/data_set_manager/isa_tab_parser.py

@@ -1014,19 +1014,16 @@ def run(self, path, isa_archive=None, preisa_archive=None):
             raise Exception()
         # 5. assign ISA-Tab archive and pre-ISA-Tab archive if present
         try:
-            self._current_investigation.isarchive_file = \
-                create(isa_archive, permanent=True)
+            self._current_investigation.isarchive_file = create(isa_archive)
             import_file(self._current_investigation.isarchive_file,
-                        permanent=True,
                         refresh=True)
         except:
             pass
 
         if preisa_archive:
             self._current_investigation.pre_isarchive_file = \
-                create(preisa_archive, permanent=True)
+                create(preisa_archive)
             import_file(self._current_investigation.pre_isarchive_file,
-                        permanent=True,
                         refresh=True)
 
         self._current_investigation.save()

refinery/data_set_manager/single_file_column_parser.py

@@ -183,7 +183,7 @@ def run(self):
         # FIXME: this will not create a FileStoreItem if self.metadata_file
         # does not exist on disk (e.g., a file object like TemporaryFile)
         investigation.pre_isarchive_file = create(
-            self.metadata_file.name, permanent=True)
+            self.metadata_file.name)
         import_file(investigation.pre_isarchive_file, refresh=True)
         investigation.save()
 
@@ -203,14 +203,14 @@ def run(self):
             data_file_path = self.file_source_translator(
                 row[self.file_column_index])
             data_file_uuid = create(
-                source=data_file_path, permanent=self.file_permanent)
+                source=data_file_path)
             data_files.append(data_file_uuid)
             # add auxiliary file to file store
             if self.auxiliary_file_column_index:
                 auxiliary_file_path = self.file_source_translator(
                     row[self.auxiliary_file_column_index])
                 auxiliary_file_uuid = create(
-                    source=auxiliary_file_path, permanent=self.file_permanent)
+                    source=auxiliary_file_path)
                 data_files.append(auxiliary_file_uuid)
             else:
                 auxiliary_file_uuid = None
@@ -259,9 +259,13 @@ def run(self):
                         subtype=self.headers[column_index].strip().lower(),
                         value=row[column_index].strip()
                     )
-        # kick off data file importing tasks
-        for uuid in data_files:
-            import_file.delay(uuid)
+
+        # Start remote file import tasks if `Data File Permanent` flag set
+        # by the user
+        if self.file_permanent:
+            for uuid in data_files:
+                import_file.delay(uuid)
+
         return investigation
 
 

refinery/file_store/tasks.py

@@ -17,19 +17,15 @@
 
 
 @task()
-def create(source, sharename='', filetype='', permanent=False, file_size=1):
+def create(source, sharename='', filetype='', file_size=1):
     """Create a FileStoreItem instance and return its UUID
     Important: source must be either an absolute file system path or a URL
-
     :param source: URL or absolute file system path to a file.
     :type source: str.
     :param sharename: Group share name.
     :type sharename: str.
     :param filetype: File extension
     :type filetype: str.
-    :param permanent: Flag indicating whether to add this instance to the cache
-        or not.
-    :type permanent: bool.
     :param file_size: For cases when the remote site specified by source URL
         doesn't provide file size in the HTTP headers.
     :type file_size: int.
@@ -48,17 +44,12 @@ def create(source, sharename='', filetype='', permanent=False, file_size=1):
 
     logger.info("FileStoreItem created with UUID %s", item.uuid)
 
-    # TODO: don't add to cache if permanent
-
     return item.uuid
 
 
 @task(track_started=True)
-def import_file(uuid, permanent=False, refresh=False, file_size=0):
+def import_file(uuid, refresh=False, file_size=0):
     """Download or copy file specified by UUID.
-
-    :param permanent: Flag for adding the FileStoreItem to cache.
-    :type permanent: bool.
     :param refresh: Flag for forcing update of the file.
     :type refresh: bool.
     :param file_size: size of the remote file.
@@ -195,8 +186,6 @@ def import_file(uuid, permanent=False, refresh=False, file_size=0):
         # save the model instance
         item.save()
 
-    # TODO: if permanent is False then add to cache
-
     return item
 
 

refinery/visualization_manager/views.py

@@ -113,8 +113,8 @@ def createIGVsession(genome, uuids, is_file_uuid=False):
     tempfilename.write(doc.toprettyxml(indent="  "))
     tempfilename.close()
     # getting file_store_uuid
-    filestore_uuid = create(tempfilename.name, permanent=True, filetype="xml")
-    filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)
+    filestore_uuid = create(tempfilename.name, filetype="xml")
+    filestore_item = import_file(filestore_uuid, refresh=True)
     # file to rename
     temp_name = filestore_item.datafile.name.split('/')
     temp_name = temp_name[len(temp_name) - 1] + '.xml'
@@ -358,8 +358,8 @@ def createIGVsessionAnnot(genome, uuids, annot_uuids=None, samp_file=None):
     tempfilename.close()
 
     # getting file_store_uuid
-    filestore_uuid = create(tempfilename.name, permanent=True, filetype="xml")
-    filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)
+    filestore_uuid = create(tempfilename.name, filetype="xml")
+    filestore_item = import_file(filestore_uuid, refresh=True)
 
     # file to rename
     temp_name = filestore_item.datafile.name.split('/')
@@ -449,8 +449,8 @@ def addIGVSamples(fields, results_samp, annot_samples=None):
     tempsampname.close()
 
     # getting file_store_uuid
-    filestore_uuid = create(tempsampname.name, permanent=True, filetype="txt")
-    filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)
+    filestore_uuid = create(tempsampname.name, filetype="txt")
+    filestore_item = import_file(filestore_uuid, refresh=True)
 
     # file to rename
     temp_file = filestore_item.datafile.name.split('/')