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Update Buggy Code in Advance of Python 3 Update #3457

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merged 25 commits into from
Oct 10, 2019
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ea9ea10
save changes to model so that they propagate to tests
ilan-gold Sep 23, 2019
83ebc9a
remove uniquify in favor of list of set
ilan-gold Sep 23, 2019
7af0804
add travis debugging
ilan-gold Sep 24, 2019
c043529
revert travis debugging
ilan-gold Sep 24, 2019
4235b78
add more travis debugging
ilan-gold Sep 24, 2019
339852a
fix formatting issue
ilan-gold Sep 24, 2019
297e650
convert logger arguments
ilan-gold Sep 24, 2019
f71f036
format code properly
ilan-gold Sep 24, 2019
68382fd
app more debugging on default_app
ilan-gold Sep 24, 2019
c294e2e
final formatting change for logging
ilan-gold Sep 24, 2019
7470c9d
remove flake from tavis.yml
ilan-gold Sep 24, 2019
92a9ef4
update sorting to be specified by rank field is solr
ilan-gold Sep 25, 2019
a14f5bb
Merge branches 'develop' and 'ilan-gold/fix_problematic_python2_code'…
ilan-gold Oct 1, 2019
1812fa6
pass request in to the ToolSerializer for getting ownership
ilan-gold Oct 2, 2019
8a8aef2
revert debugging changes for celery
ilan-gold Oct 2, 2019
8a20abb
revert debugging changes for celery
ilan-gold Oct 2, 2019
f000d91
update user logout handling for data sets
ilan-gold Oct 2, 2019
4d15b37
test bam indexing for python3 package update
ilan-gold Oct 2, 2019
e682be6
test bam indexing for python3 package update
ilan-gold Oct 2, 2019
d9485e9
fix formatting issues
ilan-gold Oct 3, 2019
6adcad8
remove pysam testing
ilan-gold Oct 3, 2019
ad1d0cd
revert uniquify change
ilan-gold Oct 3, 2019
c209f97
remove sorting
ilan-gold Oct 3, 2019
eb4917f
remove try-catch on has_perm
ilan-gold Oct 10, 2019
c8ee5bc
re-insert space
ilan-gold Oct 10, 2019
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2 changes: 2 additions & 0 deletions refinery/analysis_manager/test_tasks.py
Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,7 @@ def test__check_galaxy_history_state_progress_less_than_percent_complete(
galaxy_progress_mock
):
self.analysis_status.galaxy_history_progress = 25
self.analysis_status.save()
_check_galaxy_history_state(self.analysis.uuid)

analysis_status = AnalysisStatus.objects.get(analysis=self.analysis)
Expand All @@ -128,6 +129,7 @@ def test__check_galaxy_history_state_percent_complete_is_100(
galaxy_progress_mock
):
self.analysis_status.galaxy_history_progress = 100
self.analysis_status.save()
_check_galaxy_history_state(self.analysis.uuid)

analysis_status = AnalysisStatus.objects.get(analysis=self.analysis)
Expand Down
8 changes: 6 additions & 2 deletions refinery/tool_manager/views.py
Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,9 @@ def create(self, request, *args, **kwargs):
with transaction.atomic():
tool = create_tool(tool_launch_configuration, request.user)
tool.launch()
serializer = ToolSerializer(tool)
serializer = ToolSerializer(
tool, context={'request': request}
)
except Exception as e:
logger.error(e)
return HttpResponseBadRequest(e)
Expand Down Expand Up @@ -181,7 +183,9 @@ def relaunch(self, request, *args, **kwargs):
"currently running")
try:
visualization_tool.launch()
serializer = ToolSerializer(visualization_tool)
serializer = ToolSerializer(
visualization_tool, context={'request': request}
)
return JsonResponse(serializer.data)
except Exception as e:
logger.error(e)
Expand Down