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

Handle invalid repository dependency definitions contained in tool shed repositories.

Browse Source
This commit is contained in:
Greg Von Kuster
2013-01-22 13:24:23 -05:00
parent 487f53657c
commit 39ccc0b9ce
2 changed files with 46 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/util/shed_util_common.py
+31 -6
View File
@@ -1888,6 +1888,7 @@ def get_repository_dependencies_for_changeset_revision( trans, repository, repos
handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies )
elif key_rd_dicts_to_be_processed:
handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies )
all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies )
return all_repository_dependencies
def get_repository_dependency_as_key( repository_dependency ):
return container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ],
@@ -2181,12 +2182,12 @@ def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_d
for key_rd_dict in key_rd_dicts:
key = key_rd_dict.keys()[ 0 ]
repository_dependency = key_rd_dict[ key ]
toolshed, name, owner, changeset_revision = repository_dependency
if tool_shed_is_this_tool_shed( toolshed ):
repository = get_repository_by_name_and_owner( trans, name, owner )
rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_dependency
if tool_shed_is_this_tool_shed( rd_toolshed ):
repository = get_repository_by_name_and_owner( trans, rd_name, rd_owner )
repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans,
trans.security.encode_id( repository.id ),
changeset_revision )
rd_changeset_revision )
if repository_metadata:
# The repository changeset_revision is installable, so no updates are available.
new_key_rd_dict = {}
@@ -2196,15 +2197,20 @@ def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_d
# The repository changeset_revision is no longer installable, so see if there's been an update.
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( get_configured_ui(), repo_dir )
changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
changeset_revision = get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision )
repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans,
trans.security.encode_id( repository.id ),
changeset_revision )
if repository_metadata:
new_key_rd_dict = {}
new_key_rd_dict[ key ] = [ toolshed, name, owner, repository_metadata.changeset_revision ]
new_key_rd_dict[ key ] = [ rd_toolshed, rd_name, rd_owner, repository_metadata.changeset_revision ]
# We have the updated changset revision.
updated_key_rd_dicts.append( new_key_rd_dict )
else:
toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key )
message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \
( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) )
log.debug( message )
return updated_key_rd_dicts
def get_url_from_repository_tool_shed( app, repository ):
"""
@@ -2816,6 +2822,25 @@ def populate_repository_dependency_objects_for_processing( trans, current_reposi
new_key_rd_dict[ current_repository_key ] = repository_dependency
key_rd_dicts_to_be_processed.append( new_key_rd_dict )
return filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies
def prune_invalid_repository_dependencies( repository_dependencies ):
"""
Eliminate all invalid entries in the received repository_dependencies dictionary. An entry is invalid if if the value_list of the key/value pair is
empty. This occurs when an invalid combination of tool shed, name , owner, changeset_revision is used and a repository_metadata reocrd is not found.
"""
valid_repository_dependencies = {}
description = repository_dependencies.get( 'description', None )
root_key = repository_dependencies.get( 'root_key', None )
if root_key is None:
return valid_repository_dependencies
for key, value in repository_dependencies.items():
if key in [ 'description', 'root_key' ]:
continue
if value:
valid_repository_dependencies[ key ] = value
if valid_repository_dependencies:
valid_repository_dependencies[ 'description' ] = description
valid_repository_dependencies[ 'root_key' ] = root_key
return valid_repository_dependencies
def remove_dir( dir ):
if os.path.exists( dir ):
try:
lib/galaxy/webapps/community/controllers/repository.py
+15
View File
@@ -1909,6 +1909,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
metadata = repository_metadata.metadata
is_malicious = repository_metadata.malicious
if repository_metadata:
metadata = repository_metadata.metadata
# Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
repository=repository,
@@ -1917,6 +1918,12 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
key_rd_dicts_to_be_processed=None,
all_repository_dependencies=None,
handled_key_rd_dicts=None )
if metadata:
if 'repository_dependencies' in metadata and not repository_dependencies:
message += 'The repository dependency definitions for this repository are invalid and will be ignored. Make sure valid <b>toolshed</b>, '
message += '<b>name</b>, <b>owner</b> and <b>changeset_revision</b> values are defined in the contained <b>repository_dependencies.xml</b> '
message += 'file to correct this problem.'
status = 'error'
if is_malicious:
if trans.app.security_agent.can_push( trans.app, trans.user, repository ):
message += malicious_error_can_push
@@ -2029,6 +2036,10 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
key_rd_dicts_to_be_processed=None,
all_repository_dependencies=None,
handled_key_rd_dicts=None )
if metadata:
if 'repository_dependencies' in metadata and not repository_dependencies:
message += 'The repository dependency definitions for this repository are invalid and will be ignored.'
status = 'error'
else:
repository_metadata_id = None
metadata = None
@@ -2550,6 +2561,10 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
key_rd_dicts_to_be_processed=None,
all_repository_dependencies=None,
handled_key_rd_dicts=None )
if metadata:
if 'repository_dependencies' in metadata and not repository_dependencies:
message += 'The repository dependency definitions for this repository are invalid and will be ignored.'
status = 'error'
else:
repository_metadata_id = None
metadata = None