opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Fixes for flake8-import-order 0.11

Browse Source 
Also fix Python3 compatibility.
This commit is contained in:
Nicola Soranzo
2016-11-11 15:09:34 +00:00
parent 4b2e875802
commit 9c37c6df89
4 changed files with 44 additions and 16 deletions
Download Patch File Download Diff File Expand all files Collapse all files
scripts/api/filter_failed_datasets_from_collection.py
+14 -9
View File
@@ -6,11 +6,16 @@ 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
from __future__ import print_function
if (len(sys.argv) < 5):
import sys
from bioblend.galaxy import (
dataset_collections as collections,
GalaxyInstance
)
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)
@@ -28,20 +33,20 @@ if (len(historyMatches) > 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)
matchingCollections = [x for x in historyContents if x['hid'] == collectionHistoryId]
if (len(matchingCollections) == 0):
if len(matchingCollections) == 0:
print("Error: no collections matching that id found.")
exit(1)
if (len(matchingCollections) > 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'])
okDatasets = [d for d in failedCollection['elements'] if d['object']['state'] == 'ok' and d['object']['file_size'] > 0]
notOkDatasets = [d for d in failedCollection['elements'] if d['object']['state'] != 'ok' or d['object']['file_size'] == 0]
okCollectionName = failedCollection['name'] + " (ok)"
notOkCollectionName = failedCollection['name'] + " (not ok)"