opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-19 02:21:32 +08:00
Code Issues Packages Projects Releases Wiki Activity

Refactor set_peek and move exception handling

Browse Source
This commit is contained in:
mvdbeek
2024-05-27 10:15:54 +02:00
parent 11ae179c9a
commit 3cd64e7861
3 changed files with 12 additions and 14 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/jobs/__init__.py
+1 -6
View File
@@ -1788,12 +1788,7 @@ class MinimalJobWrapper(HasResourceParameters):
)
if final_job_state != job.states.ERROR:
line_count = context.get("line_count", None)
try:
# Certain datatype's set_peek methods contain a line_count argument
dataset.set_peek(line_count=line_count)
except TypeError:
# ... and others don't
dataset.set_peek()
dataset.set_peek(line_count=line_count)
else:
# Handle purged datasets.
dataset.blurb = "empty"
lib/galaxy/metadata/set_metadata.py
+1 -6
View File
@@ -506,12 +506,7 @@ def set_metadata_portable(
dataset.dataset.uuid = context["uuid"]
if not final_job_state == Job.states.ERROR:
line_count = context.get("line_count", None)
try:
# Certain datatype's set_peek methods contain a line_count argument
dataset.set_peek(line_count=line_count)
except TypeError:
# ... and others don't
dataset.set_peek()
dataset.set_peek(line_count=line_count)
for context_key in TOOL_PROVIDED_JOB_METADATA_KEYS:
if context_key in context:
context_value = context[context_key]
lib/galaxy/model/__init__.py
+10 -2
View File
@@ -4652,8 +4652,16 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
# extension is None
return "data"
def set_peek(self, **kwd):
return self.datatype.set_peek(self, **kwd)
def set_peek(self, line_count=None, **kwd):
try:
# Certain datatype's set_peek methods contain a line_count argument
return self.datatype.set_peek(self, line_count=line_count, **kwd)
except TypeError:
# ... and others don't
return self.datatype.set_peek(self, **kwd)
except Exception:
# Never fail peek setting, but do log exception so datatype logic can be fixed
log.exception("Setting peek failed")
def init_meta(self, copy_from=None):
return self.datatype.init_meta(self, copy_from=copy_from)