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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fixes for discovering repository dependencies when resinstalling a tool shed repository when the repository dependencies were added to updated revisions of a repository after it was uninstalled.
This commit is contained in:
Greg Von Kuster
@@ -952,12 +952,16 @@ def get_update_to_changeset_revision_and_ctx_rev( trans, repository ):
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update_dict = encoding_util.tool_shed_decode( encoded_update_dict )
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changeset_revision = update_dict[ 'changeset_revision' ]
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ctx_rev = update_dict[ 'ctx_rev' ]
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includes_tools = update_dict.get( 'includes_tools', False )
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has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False )
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response.close()
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except Exception, e:
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log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) )
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includes_tools = False
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has_repository_dependencies = False
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changeset_revision = None
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ctx_rev = None
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return changeset_revision, ctx_rev
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return changeset_revision, ctx_rev, includes_tools, has_repository_dependencies
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def handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ):
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"""
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Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the
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@@ -1256,6 +1256,21 @@ class RepositoryController( BaseUIController, common.ItemRatings ):
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@web.expose
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def get_changeset_revision_and_ctx_rev( self, trans, **kwd ):
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"""Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated."""
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def has_tools_and_repository_dependencies( repository_metadata ):
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includes_tools = False
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has_repository_dependencies = False
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if repository_metadata:
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metadata = repository_metadata.metadata
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if metadata:
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if 'tools' in metadata:
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includes_tools = True
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else:
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includes_tools = False
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if 'repository_dependencies' in metadata:
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has_repository_dependencies = True
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else:
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has_repository_dependencies = False
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return includes_tools, has_repository_dependencies
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params = util.Params( kwd )
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message = util.restore_text( params.get( 'message', '' ) )
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status = params.get( 'status', 'done' )
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@@ -1264,20 +1279,24 @@ class RepositoryController( BaseUIController, common.ItemRatings ):
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owner = params.get( 'owner', None )
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changeset_revision = params.get( 'changeset_revision', None )
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repository = suc.get_repository_by_name_and_owner( trans, name, owner )
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repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
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trans.security.encode_id( repository.id ),
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changeset_revision )
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includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( repository_metadata )
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repo_dir = repository.repo_path( trans.app )
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repo = hg.repository( suc.get_configured_ui(), repo_dir )
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# Default to the received changeset revision and ctx_rev.
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update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
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ctx_rev = str( update_to_ctx.rev() )
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latest_changeset_revision = changeset_revision
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update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev )
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update_dict = dict( changeset_revision=changeset_revision,
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ctx_rev=ctx_rev,
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includes_tools=includes_tools,
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has_repository_dependencies=has_repository_dependencies )
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if changeset_revision == repository.tip( trans.app ):
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# If changeset_revision is the repository tip, there are no additional updates.
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return encoding_util.tool_shed_encode( update_dict )
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else:
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repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
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trans.security.encode_id( repository.id ),
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changeset_revision )
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if repository_metadata:
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# If changeset_revision is in the repository_metadata table for this repository, there are no additional updates.
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return encoding_util.tool_shed_encode( update_dict )
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@@ -1286,10 +1305,16 @@ class RepositoryController( BaseUIController, common.ItemRatings ):
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# repository was installed. We need to find the changeset_revision to which we need to update.
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update_to_changeset_hash = None
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for changeset in repo.changelog:
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includes_tools = False
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has_repository_dependencies = False
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changeset_hash = str( repo.changectx( changeset ) )
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ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
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if update_to_changeset_hash:
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if suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ):
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update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
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trans.security.encode_id( repository.id ),
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changeset_hash )
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if update_to_repository_metadata:
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includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( update_to_repository_metadata )
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# We found a RepositoryMetadata record.
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if changeset_hash == repository.tip( trans.app ):
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# The current ctx is the repository tip, so use it.
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@@ -1302,6 +1327,8 @@ class RepositoryController( BaseUIController, common.ItemRatings ):
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elif not update_to_changeset_hash and changeset_hash == changeset_revision:
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# We've found the changeset in the changelog for which we need to get the next update.
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update_to_changeset_hash = changeset_hash
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update_dict[ 'includes_tools' ] = includes_tools
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update_dict[ 'has_repository_dependencies' ] = has_repository_dependencies
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update_dict[ 'changeset_revision' ] = str( latest_changeset_revision )
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update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() )
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return encoding_util.tool_shed_encode( update_dict )
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@@ -372,27 +372,15 @@ class AdminToolshed( AdminGalaxy ):
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if operation == "activate or reinstall":
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repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
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if repository.uninstalled:
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# Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated so that we
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# Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated so that we
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# can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies
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# will be current.
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current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository )
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if current_ctx_rev != repository.ctx_rev:
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repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( repository.repo_path( trans.app ) ) )
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repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
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shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision )
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suc.update_repository( repo, ctx_rev=current_ctx_rev )
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shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
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shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf )
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metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app,
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repository=repository,
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repository_clone_url=repository_clone_url,
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shed_config_dict=shed_config_dict,
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relative_install_dir=relative_install_dir,
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repository_files_dir=None,
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resetting_all_metadata_on_repository=False,
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updating_installed_repository=True,
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persist=True )
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if repository.includes_tools or repository.has_repository_dependencies:
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current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \
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shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository )
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if current_ctx_rev == repository.ctx_rev:
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includes_tools = repository.includes_tools
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has_repository_dependencies = repository.has_repository_dependencies
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if includes_tools or has_repository_dependencies:
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# Only allow selecting a different section in the tool panel if the repository was uninstalled.
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return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
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action='reselect_tool_panel_section',
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@@ -859,12 +847,12 @@ class AdminToolshed( AdminGalaxy ):
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if cloned_ok:
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if reinstalling:
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# Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated.
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current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository )
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current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \
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shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository )
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if current_ctx_rev != ctx_rev:
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repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) )
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shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision )
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suc.update_repository( repo, ctx_rev=current_ctx_rev )
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self.handle_repository_contents( trans,
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tool_shed_repository=tool_shed_repository,
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tool_path=tool_path,
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