Merge pull request #2358 from chambm/feature/filter_failed_datasets_from_collection

Add filter_failed_datasets_from_collection.py script

scripts/api/filter_failed_datasets_from_collection.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+"""
+Given a history name and a collection integer id in that history, this script will split the collection into the failed/pending/empty
+datasets "(not ok)" and the successfully finished datasets "(ok)".
+
+Sample call:
+python filter_failed_datasets_from_collection.py <GalaxyUrl> <ApiKey> MySpecialHistory 1234
+"""
+import sys
+from bioblend.galaxy import GalaxyInstance
+from bioblend.galaxy import dataset_collections as collections
+
+if (len(sys.argv) < 5):
+    print("Usage: %s <GalaxyUrl> <ApiKey> <HistoryName (must be unique)> <CollectionHistoryId (i.e. the simple integer id)>" % sys.argv[0])
+    exit(0)
+
+galaxyUrl = sys.argv[1]
+galaxyApiKey = sys.argv[2]
+historyName = sys.argv[3]
+collectionHistoryId = int(sys.argv[4])
+
+gi = GalaxyInstance(url=galaxyUrl, key=galaxyApiKey)
+
+historyMatches = gi.histories.get_histories(name=historyName)
+if (len(historyMatches) > 1):
+    print("Error: more than one history matches that name.")
+    exit(1)
+
+historyId = historyMatches[0]['id']
+historyContents = gi.histories.show_history(historyId, contents=True, deleted=False, visible=True, details=False)
+matchingCollections = filter(lambda x: x['hid'] == collectionHistoryId, historyContents)
+
+if (len(matchingCollections) == 0):
+    print("Error: no collections matching that id found.")
+    exit(1)
+
+if (len(matchingCollections) > 1):
+    print("Error: more than one collection matching that id found (WTF?)")
+    exit(1)
+
+collectionId = matchingCollections[0]['id']
+failedCollection = gi.histories.show_dataset_collection(historyId, collectionId)
+okDatasets = filter(lambda d: d['object']['state'] == 'ok' and d['object']['file_size'] > 0, failedCollection['elements'])
+notOkDatasets = filter(lambda d: d['object']['state'] != 'ok' or d['object']['file_size'] == 0, failedCollection['elements'])
+okCollectionName = failedCollection['name'] + " (ok)"
+notOkCollectionName = failedCollection['name'] + " (not ok)"
+
+gi.histories.create_dataset_collection(
+    history_id=historyId,
+    collection_description=collections.CollectionDescription(
+        name=okCollectionName,
+        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in okDatasets]))
+
+gi.histories.create_dataset_collection(
+    history_id=historyId,
+    collection_description=collections.CollectionDescription(
+        name=notOkCollectionName,
+        elements=[collections.HistoryDatasetElement(d['object']['name'], d['object']['id']) for d in notOkDatasets]))