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Merge pull request #9145 from nsoranzo/misc_fixes

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Misc fixes
This commit is contained in:
Dannon
2019-12-19 09:46:12 -05:00
committed by GitHub
parent b52b022383 66169d099d
commit fc8a31ae77
4 changed files with 6 additions and 6 deletions
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lib/galaxy/tools/__init__.py
+1 -1
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@@ -936,7 +936,7 @@ class Tool(Dictifiable):
if getattr(self, 'tool_shed', None):
tool_dir = Path(self.tool_dir)
for repo_dir in itertools.chain([tool_dir], tool_dir.parents):
if repo_dir.stem == self.repository_name:
if repo_dir.name == self.repository_name:
return str(repo_dir)
else:
log.error("Problem finding repository dir for tool [%s]" % self.id)
lib/galaxy/webapps/galaxy/api/library_contents.py
+1 -1
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@@ -204,7 +204,7 @@ class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
folder to create
* description: (optional, only if create_type is 'folder')
description of the folder to create
* tag_using_filename: (optional)
* tag_using_filenames: (optional)
create tags on datasets using the file's original name
* tags: (optional)
create the given list of tags on datasets
lib/galaxy/webapps/galaxy/api/users.py
+2 -2
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@@ -110,18 +110,18 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
query = query.filter(trans.app.model.User.username.like("%%%s%%" % f_any))
if deleted:
query = query.filter(trans.app.model.User.table.c.deleted == true())
# only admins can see deleted users
if not trans.user_is_admin:
return []
query = query.filter(trans.app.model.User.table.c.deleted == true())
else:
query = query.filter(trans.app.model.User.table.c.deleted == false())
# special case: user can see only their own user
# special case2: if the galaxy admin has specified that other user email/names are
# exposed, we don't want special case #1
if not trans.user_is_admin and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email:
item = trans.user.to_dict(value_mapper={'id': trans.security.encode_id})
return [item]
query = query.filter(trans.app.model.User.table.c.deleted == false())
for user in query:
item = user.to_dict(value_mapper={'id': trans.security.encode_id})
# If NOT configured to expose_email, do not expose email UNLESS the user is self, or
lib/galaxy/webapps/galaxy/api/workflows.py
+2 -2
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@@ -561,7 +561,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
if workflow_dict:
raw_workflow_description = self.__normalize_workflow(trans, workflow_dict)
workflow_dict = raw_workflow_description.as_dict
new_workflow_name = workflow_dict.get('name') or workflow_dict.get('name')
new_workflow_name = workflow_dict.get('name')
if new_workflow_name and new_workflow_name != stored_workflow.name:
sanitized_name = sanitize_html(new_workflow_name)
workflow = stored_workflow.latest_workflow.copy()
@@ -584,7 +584,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
else:
# remove if in list
entries = {x.stored_workflow_id: x for x in trans.get_user().stored_workflow_menu_entries}
if (trans.security.decode_id(id) in entries):
if trans.security.decode_id(id) in entries:
trans.get_user().stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
# set tags
if 'tags' in workflow_dict: