mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fixes for getting updates to installed tool shed repositories.
This commit is contained in:
Greg Von Kuster
@@ -174,6 +174,40 @@ class AdminToolshed( AdminGalaxy ):
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return trans.response.send_redirect( url )
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@web.expose
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@web.require_admin
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def check_installed_tool_dependencies( self, trans, repository_id, relative_install_dir ):
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"""See if any tool dependencies need to be installed."""
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tool_dependencies_missing = False
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repository = get_repository( trans, repository_id )
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if repository.includes_tool_dependencies:
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# Get the tool_dependencies.xml file from the repository.
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work_dir = make_tmp_directory()
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tool_dependencies_config = get_config_from_repository( trans.app,
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'tool_dependencies.xml',
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repository,
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repository.changeset_revision,
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work_dir,
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install_dir=relative_install_dir )
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# Parse the tool_dependencies.xml config.
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tree = ElementTree.parse( tool_dependencies_config )
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root = tree.getroot()
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ElementInclude.include( root )
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fabric_version_checked = False
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for elem in root:
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if elem.tag == 'package':
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package_name = elem.get( 'name', None )
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package_version = elem.get( 'version', None )
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if package_name and package_version:
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install_dir = get_install_dir( trans.app, repository, repository.installed_changeset_revision, package_name, package_version )
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if not_installed( install_dir ):
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tool_dependencies_missing = True
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break
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try:
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shutil.rmtree( work_dir )
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except:
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pass
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return tool_dependencies_missing
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@web.expose
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@web.require_admin
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def deactivate_or_uninstall_repository( self, trans, **kwd ):
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params = util.Params( kwd )
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message = util.restore_text( params.get( 'message', '' ) )
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@@ -540,7 +574,8 @@ class AdminToolshed( AdminGalaxy ):
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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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repository = get_repository( trans, kwd[ 'id' ] )
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repository_id = kwd[ 'id' ]
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repository = get_repository( trans, repository_id )
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description = util.restore_text( params.get( 'description', repository.description ) )
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shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository )
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repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
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@@ -558,34 +593,7 @@ class AdminToolshed( AdminGalaxy ):
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trans.sa_session.add( repository )
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trans.sa_session.flush()
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message = "Repository metadata has been reset."
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tool_dependencies_missing = False
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if repository.includes_tool_dependencies:
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# See if any tool dependencies need to be installed, get the tool_dependencies.xml file from the repository.
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work_dir = make_tmp_directory()
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tool_dependencies_config = get_config_from_repository( trans.app,
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'tool_dependencies.xml',
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repository,
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repository.changeset_revision,
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work_dir,
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install_dir=relative_install_dir )
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# Parse the tool_dependencies.xml config.
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tree = ElementTree.parse( tool_dependencies_config )
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root = tree.getroot()
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ElementInclude.include( root )
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fabric_version_checked = False
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for elem in root:
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if elem.tag == 'package':
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package_name = elem.get( 'name', None )
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package_version = elem.get( 'version', None )
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if package_name and package_version:
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install_dir = get_install_dir( trans.app, repository, repository.installed_changeset_revision, package_name, package_version )
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if not_installed( install_dir ):
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tool_dependencies_missing = True
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break
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try:
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shutil.rmtree( work_dir )
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except:
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pass
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tool_dependencies_missing = self.check_installed_tool_dependencies( trans, repository_id, relative_install_dir )
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return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
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repository=repository,
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description=description,
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@@ -782,7 +790,7 @@ class AdminToolshed( AdminGalaxy ):
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repository = get_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision )
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if changeset_revision and latest_changeset_revision and latest_ctx_rev:
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if changeset_revision == latest_changeset_revision:
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message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name
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message = "The installed repository named '%s' is current, there are no updates available. " % name
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else:
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shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository )
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if relative_install_dir:
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@@ -801,13 +809,17 @@ class AdminToolshed( AdminGalaxy ):
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repository.update_available = False
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trans.sa_session.add( repository )
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trans.sa_session.flush()
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message = "The cloned repository named '%s' has been updated to change set revision '%s'." % \
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( name, latest_changeset_revision )
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message = "The installed repository named '%s' has been updated to change set revision '%s'. " % ( name, latest_changeset_revision )
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# See if any tool dependencies can be installed.
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shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository )
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tool_dependencies_missing = self.check_installed_tool_dependencies( trans, trans.security.encode_id( repository.id ), relative_install_dir )
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if tool_dependencies_missing:
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message += "Select <b>Install tool dependencies</b> from the repository's pop-up menu to install tool dependencies."
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else:
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message = "The directory containing the cloned repository named '%s' cannot be found." % name
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message = "The directory containing the installed repository named '%s' cannot be found. " % name
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status = 'error'
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else:
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message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name
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message = "The latest changeset revision could not be retrieved for the installed repository named '%s'. " % name
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status = 'error'
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return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
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action='manage_repository',
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@@ -599,6 +599,9 @@ class RepositoryController( BaseUIController, ItemRatings ):
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repository = get_repository_by_name_and_owner( trans, name, owner )
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repo_dir = repository.repo_path
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repo = hg.repository( get_configured_ui(), repo_dir )
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# Default to the current changeset revision.
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update_to_ctx = get_changectx_for_changeset( repo, changeset_revision )
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latest_changeset_revision = changeset_revision
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from_update_manager = webapp == 'update_manager'
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if from_update_manager:
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update = 'true'
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@@ -608,80 +611,45 @@ class RepositoryController( BaseUIController, ItemRatings ):
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url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) )
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url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % ( repository.name, repository.user.username, changeset_revision )
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if changeset_revision == repository.tip:
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# If changeset_revision is the repository tip, we know there are no additional updates for the tools.
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# If changeset_revision is the repository tip, there are no additional updates.
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if from_update_manager:
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return no_update
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# Return the same value for changeset_revision and latest_changeset_revision.
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url += repository.tip
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url += latest_changeset_revision
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else:
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repository_metadata = 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, then we know there are no additional updates
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# for the tools.
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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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if from_update_manager:
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return no_update
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else:
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# Return the same value for changeset_revision and latest_changeset_revision.
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url += changeset_revision
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url += latest_changeset_revision
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else:
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# TODO: Re-engineer this to define the change set for update to be the one just before the next change set in the repository_metadata
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# table for this repository.
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# The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the
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# repository was cloned. Load each tool in the repository's changeset_revision to generate a list of tool guids, since guids
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# differentiate tools by id and version.
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ctx = get_changectx_for_changeset( repo, changeset_revision )
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if ctx is not None:
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work_dir = make_tmp_directory()
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tool_guids = []
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for filename in ctx:
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# Find all tool configs in this repository changeset_revision.
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if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ):
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is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans,
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repo,
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repo_dir,
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ctx,
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filename,
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work_dir )
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if valid and tool is not None:
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tool_guids.append( generate_tool_guid( trans, repository, tool ) )
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tool_guids.sort()
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if tool_guids:
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# Compare our list of tool guids against those in each repository_metadata record for the repository to find the
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# repository_metadata record with the changeset_revision value we want to pass back to the caller.
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found = False
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for repository_metadata in get_repository_metadata_by_repository_id( trans, trans.security.encode_id( repository.id ) ):
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metadata = repository_metadata.metadata
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metadata_tool_guids = []
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for tool_dict in metadata[ 'tools' ]:
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metadata_tool_guids.append( tool_dict[ 'guid' ] )
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metadata_tool_guids.sort()
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if tool_guids == metadata_tool_guids:
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# We've found the repository_metadata record whose changeset_revision value has been updated.
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if from_update_manager:
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return update
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url += repository_metadata.changeset_revision
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# Get the ctx_rev for the discovered changeset_revision.
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latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
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found = True
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break
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if not found:
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# There must be a problem in the data, so we'll just send back the received changeset_revision.
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log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id )
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if from_update_manager:
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return no_update
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url += changeset_revision
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else:
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# There are no tools in the changeset_revision, so no tool updates are possible.
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if from_update_manager:
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return no_update
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url += changeset_revision
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try:
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shutil.rmtree( work_dir )
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except:
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pass
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url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
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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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changeset_hash = str( repo.changectx( changeset ) )
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ctx = get_changectx_for_changeset( repo, changeset_hash )
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if update_to_changeset_hash:
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if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ):
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# We found a RepositoryMetadata record.
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if changeset_hash == repository.tip:
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# The current ctx is the repository tip, so use it.
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update_to_ctx = get_changectx_for_changeset( repo, changeset_hash )
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latest_changeset_revision = changeset_hash
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else:
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update_to_ctx = get_changectx_for_changeset( repo, update_to_changeset_hash )
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latest_changeset_revision = update_to_changeset_hash
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break
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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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url += str( latest_changeset_revision )
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url += '&latest_ctx_rev=%s' % str( update_to_ctx.rev() )
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return trans.response.send_redirect( url )
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@web.expose
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def contact_owner( self, trans, id, **kwd ):
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