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Remove transaction helper #19407

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merged 39 commits into from
Jan 24, 2025
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f0de72b
Remove transaction helper from test.unit.job_execution
jdavcs Jan 14, 2025
f39702b
Remove transaction helper from test.unit.workflows
jdavcs Jan 14, 2025
6f47682
Remove transaction helper from test.unit.data
jdavcs Jan 14, 2025
a26cd0f
Remove transaction helper from test.unit.app.jobs
jdavcs Jan 14, 2025
1ce27e3
Remove transaction helper from test.unit.app.managers
jdavcs Jan 14, 2025
dee8804
Remove transaction helper from test.unit.app.tools
jdavcs Jan 14, 2025
62155b9
Remove transaction helper from test.integration
jdavcs Jan 14, 2025
896d084
Remove transaction helper from scripts
jdavcs Jan 14, 2025
7886de0
Fix typo
jdavcs Jan 14, 2025
79f44a2
Remove transaction helper from galaxy.security
jdavcs Jan 14, 2025
6575666
Remove transaction helper from galaxy.model
jdavcs Jan 14, 2025
dd221af
Remove transaction helper from galaxy.tools
jdavcs Jan 14, 2025
cf4f7f9
Remove transaction helper from galaxy.job_execution
jdavcs Jan 14, 2025
87bb447
Remove transaction helper from galaxy.managers
jdavcs Jan 14, 2025
74e4c97
Remove transaction helper from galaxy.quota
jdavcs Jan 14, 2025
bc13d78
Remove transaction helper from galaxy.celery
jdavcs Jan 14, 2025
6125c2e
Remove transaction helper from galaxy.app_unittest_utils
jdavcs Jan 14, 2025
8af74a8
Remove transaction helper from galaxy.work
jdavcs Jan 14, 2025
e65045e
Remove transaction helper from galaxy.authnz
jdavcs Jan 14, 2025
7275332
Remove transaction helper from galaxy.workflow
jdavcs Jan 14, 2025
85b9697
Remove transaction helper from galaxy.actions
jdavcs Jan 14, 2025
b8fe28d
Remove transaction helper from galaxy.jobs
jdavcs Jan 14, 2025
70aa1d6
Remove transaction helper from galaxy.web_stack
jdavcs Jan 14, 2025
2f60482
Remove transaction helper from galaxy.webapps.base
jdavcs Jan 14, 2025
226e00d
Remove transaction helper from galaxy.webapps.galaxy.api
jdavcs Jan 14, 2025
c995c36
Remove transaction helper from galaxy.webapps.galaxy.services
jdavcs Jan 14, 2025
17ebf87
Remove transaction helper from galaxy.webapps.galaxy.controllers
jdavcs Jan 14, 2025
5b79724
Remove transaction helper from galaxy.tool_shed
jdavcs Jan 14, 2025
f279c2e
Remove transaction helper from galaxy_test
jdavcs Jan 14, 2025
9cc45fc
Remove transaction helper from tool_shed.webapp.security
jdavcs Jan 14, 2025
4da662b
Remove transaction helper from tool_shed.webapp.api2
jdavcs Jan 14, 2025
7b1a9aa
Remove transaction helper from tool_shed.webapp.util
jdavcs Jan 14, 2025
1b31616
Remove transaction helper from tool_shed.webapp.api
jdavcs Jan 14, 2025
cee6daa
Remove transaction helper from tool_shed.webapp.controllers
jdavcs Jan 14, 2025
416bb33
Remove transaction helper from tool_shed.managers
jdavcs Jan 14, 2025
0ca0c3b
Remove transaction helper from tool_shed.metadata
jdavcs Jan 14, 2025
c060806
Remove transaction helper from tool_shed.util
jdavcs Jan 14, 2025
ef1aa62
Remove transaction helper from test/unit.test_galaxy_transactions
jdavcs Jan 14, 2025
1bd861a
Remove transaction helper
jdavcs Jan 14, 2025
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Remove transaction helper from tool_shed.metadata
  • Loading branch information
jdavcs committed Jan 23, 2025

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commit 0ca0c3b3e8c3ff8516aaf4dcfcac7e6a739258ce
16 changes: 5 additions & 11 deletions lib/tool_shed/metadata/repository_metadata_manager.py
Original file line number Diff line number Diff line change
@@ -13,7 +13,6 @@
)

from galaxy import util
from galaxy.model.base import transaction
from galaxy.tool_shed.metadata.metadata_generator import (
BaseMetadataGenerator,
HandleResultT,
@@ -270,8 +269,7 @@ def _add_tool_versions(self, id: int, repository_metadata, changeset_revisions):
repository_metadata.tool_versions = tool_versions_dict
self.sa_session.add(repository_metadata)
session = self.sa_session()
with transaction(session):
session.commit()
session.commit()

def build_repository_ids_select_field(
self, name="repository_ids", multiple=True, display="checkboxes", my_writable=False
@@ -297,8 +295,7 @@ def _clean_repository_metadata(self, changeset_revisions):
if changeset_revision not in changeset_revisions:
self.sa_session.delete(repository_metadata)
session = self.sa_session()
with transaction(session):
session.commit()
session.commit()

def compare_changeset_revisions(self, ancestor_changeset_revision, ancestor_metadata_dict):
"""
@@ -524,8 +521,7 @@ def create_or_update_repository_metadata(self, changeset_revision, metadata_dict
repository_metadata.missing_test_components = False
self.sa_session.add(repository_metadata)
session = self.sa_session()
with transaction(session):
session.commit()
session.commit()

return repository_metadata

@@ -908,8 +904,7 @@ def _reset_all_tool_versions(self, repo):
repository_metadata.tool_versions = tool_versions_dict
self.sa_session.add(repository_metadata)
session = self.sa_session()
with transaction(session):
session.commit()
session.commit()

def reset_metadata_on_selected_repositories(self, **kwd):
"""
@@ -1021,8 +1016,7 @@ def set_repository_metadata(self, host, content_alert_str="", **kwd):
repository_metadata.missing_test_components = False
self.sa_session.add(repository_metadata)
session = self.sa_session()
with transaction(session):
session.commit()
session.commit()
else:
# There are no metadata records associated with the repository.
repository_metadata = self.create_or_update_repository_metadata(