October 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Add basic UI for managng tool shed repositories installed into a local Galaxy instance from a tool shed. Add the ability to view the list of tools and workflows included in installed tool shed repositories. Ad the ability to import a workflow from an installed tool shed repository into the local Galaxy instance.
by Bitbucket 28 Oct '11

28 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c3582a9913fa/ changeset: c3582a9913fa user: greg date: 2011-10-28 20:05:14 summary: Add basic UI for managng tool shed repositories installed into a local Galaxy instance from a tool shed. Add the ability to view the list of tools and workflows included in installed tool shed repositories. Ad the ability to import a workflow from an installed tool shed repository into the local Galaxy instance. affected #: 7 files diff -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2443,13 +2443,6 @@ id = trans.security.decode_id( id ) quota = trans.sa_session.query( trans.model.Quota ).get( id ) return quota -def get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ): - return trans.sa_session.query( trans.model.ToolShedRepository ) \ - .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed, - trans.model.ToolShedRepository.table.c.name == name, - trans.model.ToolShedRepository.table.c.owner == owner, - trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ - .first() def handle_sample_tool_data_table_conf_file( trans, filename ): """ Parse the incoming filename and add new entries to the in-memory diff -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -410,7 +410,8 @@ columns = [ NameColumn( "Name", key="name", - attach_popup=True ), + link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ), + attach_popup=False ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), RevisionColumn( "Revision" ), @@ -426,17 +427,14 @@ key="free-text-search", visible=False, filterable="standard" ) ) - operations = [ grids.GridOperation( "Get updates", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] standard_filters = [] default_filter = dict( deleted="False" ) num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ) \ + .filter( self.model_class.table.c.deleted == False ) class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): @@ -678,11 +676,88 @@ return quota, params @web.expose @web.require_admin - def browse_repositories( self, trans, **kwd ): + def browse_tool_shed_repository( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = get_repository( trans, kwd[ 'id' ] ) + relative_install_dir = self.__get_relative_install_dir( trans, repository ) + repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + tool_dicts = [] + workflow_dicts = [] + for root, dirs, files in os.walk( repo_files_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories. + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files. + files.remove( 'hgrc' ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + tool = trans.app.toolbox.load_tool( full_path ) + if tool is not None: + tool_config = os.path.join( root, name ) + # Handle tool.requirements. + tool_requirements = [] + for tr in tool.requirements: + name=tr.name + type=tr.type + if type == 'fabfile': + version = None + fabfile = tr.fabfile + method = tr.method + else: + version = tr.version + fabfile = None + method = None + requirement_dict = dict( name=name, + type=type, + version=version, + fabfile=fabfile, + method=method ) + tool_requirements.append( requirement_dict ) + tool_dict = dict( id=tool.id, + old_id=tool.old_id, + name=tool.name, + version=tool.version, + description=tool.description, + requirements=tool_requirements, + tool_config=tool_config ) + tool_dicts.append( tool_dict ) + except Exception, e: + # The file is not a Galaxy tool config. + pass + # Find all exported workflows + elif name.endswith( '.ga' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + # Convert workflow data from json + fp = open( full_path, 'rb' ) + workflow_text = fp.read() + fp.close() + workflow_dict = from_json_string( workflow_text ) + if workflow_dict[ 'a_galaxy_workflow' ] == 'true': + workflow_dicts.append( dict( full_path=full_path, workflow_dict=workflow_dict ) ) + except Exception, e: + # The file is not a Galaxy workflow. + pass + return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako', + repository=repository, + tool_dicts=tool_dicts, + workflow_dicts=workflow_dicts, + message=message, + status=status ) + @web.expose + @web.require_admin + def browse_tool_shed_repositories( self, trans, **kwd ): if 'operation' in kwd: - operation = kwd.pop('operation').lower() - if operation == "get updates": - return self.check_for_updates( trans, **kwd ) + operation = kwd.pop( 'operation' ).lower() + if operation == "manage_repository": + return self.manage_tool_shed_repository( trans, **kwd ) # Render the list view return self.repository_list_grid( trans, **kwd ) @web.expose @@ -850,10 +925,35 @@ status=status ) @web.expose @web.require_admin + def manage_tool_shed_repository( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository_id = params.get( 'id', None ) + repository = get_repository( trans, repository_id ) + description = util.restore_text( params.get( 'description', repository.description ) ) + if params.get( 'edit_repository_button', False ): + if description != repository.description: + repository.description = description + trans.sa_session.add( repository ) + trans.sa_session.flush() + message = "The repository information has been updated." + relative_install_dir = self.__get_relative_install_dir( trans, repository ) + if relative_install_dir: + repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + else: + repo_files_dir = 'unknown' + return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', + repository=repository, + description=description, + repo_files_dir=repo_files_dir, + message=message, + status=status ) + @web.expose + @web.require_admin def check_for_updates( self, trans, **kwd ): params = util.Params( kwd ) - repository_id = params.get( 'id', None ) - repository = get_repository( trans, repository_id ) + repository = get_repository( trans, kwd[ 'id' ] ) galaxy_url = trans.request.host # Send a request to the relevant tool shed to see if there are any updates. # TODO: support https in the following url. @@ -872,26 +972,16 @@ owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) latest_changeset_revision = params.get( 'latest_changeset_revision', None ) + repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed_url, name, owner, changeset_revision ) if changeset_revision and latest_changeset_revision: if changeset_revision == latest_changeset_revision: message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name else: - repository = get_repository_by_name_owner_changeset_revision( trans, name, owner, changeset_revision ) current_working_dir = os.getcwd() - # Get the directory where the repository is cloned. - cleaned_tool_shed_url = self.__clean_tool_shed_url( tool_shed_url ) - partial_cloned_dir = '%s/repos/%s/%s/%s' % ( cleaned_tool_shed_url, owner, name, changeset_revision ) - # Get the relative tool installation paths from each of the shed tool configs. - shed_tool_confs = trans.app.toolbox.shed_tool_confs - relative_cloned_dir = None - # The shed_tool_confs dictionary contains shed_conf_filename : tool_path pairs. - for shed_conf_filename, tool_path in shed_tool_confs.items(): - relative_cloned_dir = os.path.join( tool_path, partial_cloned_dir ) - if os.path.isdir( relative_cloned_dir ): - break - if relative_cloned_dir: + relative_install_dir = self.__get_relative_install_dir( trans, repository ) + if relative_install_dir: # Update the cloned repository to changeset_revision. - repo_files_dir = os.path.join( relative_cloned_dir, name ) + repo_files_dir = os.path.join( relative_install_dir, name ) log.debug( "Updating cloned repository named '%s' from revision '%s' to revision '%s'..." % \ ( name, changeset_revision, latest_changeset_revision ) ) cmd = 'hg pull' @@ -935,9 +1025,23 @@ message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name status = 'error' return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_repositories', + action='manage_tool_shed_repository', + id=trans.security.encode_id( repository.id ), message=message, status=status ) ) + def __get_relative_install_dir( self, trans, repository ): + # Get the directory where the repository is install. + tool_shed = self.__clean_tool_shed_url( repository.tool_shed ) + partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.changeset_revision ) + # Get the relative tool installation paths from each of the shed tool configs. + shed_tool_confs = trans.app.toolbox.shed_tool_confs + relative_install_dir = None + # The shed_tool_confs dictionary contains { shed_conf_filename : tool_path } pairs. + for shed_conf_filename, tool_path in shed_tool_confs.items(): + relative_install_dir = os.path.join( tool_path, partial_install_dir ) + if os.path.isdir( relative_install_dir ): + break + return relative_install_dir def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ): # Inspect each tool to see if any have input parameters that are dynamically # generated select lists that require entries in the tool_data_table_conf.xml file. @@ -1057,7 +1161,7 @@ tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) owner = self.__get_repository_owner( tmp_url ) flush_needed = False - tool_shed_repository = get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ) + tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ) if tool_shed_repository: if tool_shed_repository.deleted: tool_shed_repository.deleted = False @@ -1200,3 +1304,11 @@ trans.model.ToolShedRepository.table.c.owner == owner, trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ .first() +def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ): + return trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed, + trans.model.ToolShedRepository.table.c.name == name, + trans.model.ToolShedRepository.table.c.owner == owner, + trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ + .first() + diff -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1095,8 +1095,8 @@ @web.expose def import_workflow( self, trans, **kwd ): """ - Import a workflow by reading an url, uploading a file, or receiving the textual - representation of a workflow. + Import a workflow by reading an url, uploading a file, opening and reading the contents + of a local file, or receiving the textual representation of a workflow via http. """ url = kwd.get( 'url', '' ) workflow_text = kwd.get( 'workflow_text', '' ) @@ -1104,6 +1104,8 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) import_button = kwd.get( 'import_button', False ) + # The following parameters will have values only if the workflow + # id being imported from a Galaxy tool shed repository. tool_shed_url = kwd.get( 'tool_shed_url', '' ) repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) # The workflow_name parameter is in the request only if the import originated @@ -1111,6 +1113,15 @@ workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: workflow_name = tool_shed_decode( workflow_name ) + # The following parameters will have a value only if the import originated + # from a tool shed repository installed locally. + local_file = kwd.get( 'local_file', '' ) + repository_id = kwd.get( 'repository_id', '' ) + if local_file and not import_button: + workflow_file = open( local_file, 'rb' ) + workflow_text = workflow_file.read() + workflow_file.close() + import_button = True if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. workflow_url = 'http://%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ @@ -1118,7 +1129,6 @@ response = urllib2.urlopen( workflow_url ) workflow_text = response.read() response.close() - workflow_text = workflow_text import_button = True if import_button: workflow_data = None @@ -1131,6 +1141,7 @@ message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) ) status = 'error' elif workflow_text: + # This case occurs when the workflow_text was sent via http from the tool shed. workflow_data = workflow_text else: # Load workflow from browsed file. @@ -1170,7 +1181,7 @@ message += "Imported, but this workflow contains cycles. " status = "error" else: - message += "Workflow '%s' imported successfully. " % workflow.name + message += "Workflow <b>%s</b> imported successfully. " % workflow.name if missing_tool_tups: if trans.user_is_admin(): # A required tool is not available in the local Galaxy instance. @@ -1201,11 +1212,19 @@ pass if tool_shed_url: # We've received the textual representation of a workflow from a Galaxy tool shed. - message = "This workflow has been successfully imported into your local Galaxy instance." + message = "Workflow <b>%s</b> imported successfully." % workflow.name # TODO: support https in the following url. url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) return trans.response.send_redirect( url ) + elif local_file: + # The workflow was read from a file included with an installed tool shed repository. + message = "Workflow <b>%s</b> imported successfully." % workflow.name + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tool_shed_repository', + id=repository_id, + message=message, + status=status ) ) return self.list( trans ) return trans.fill_template( "workflow/import.mako", url=url, diff -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -361,8 +361,9 @@ workflow_text = fp.read() fp.close() exported_workflow_dict = from_json_string( workflow_text ) - # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) + if exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + # Update the list of metadata dictionaries for workflows in metadata_dict. + metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) else: diff -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 templates/admin/tool_shed_repository/browse_repository.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -0,0 +1,127 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% from galaxy.web.base.controller import tool_shed_encode, tool_shed_decode %> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='manage_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='admin', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Installed tool shed repository '${repository.name}'</div> + <div class="toolFormBody"> + + %if tool_dicts: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Tools</b></td> + </tr> + </table> + </div> + <div class="form-row"> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> + %for tool_dict in tool_dicts: + <tr> + <td>${tool_dict[ 'name' ]}</div> + </td> + <td>${tool_dict[ 'description' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if workflow_dicts: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Workflows</b></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>steps</b></td> + <td><b>format-version</b></td> + <td><b>annotation</b></td> + </tr> + <% index = 0 %> + %for wf_dict in workflow_dicts: + <% + full_path = wf_dict[ 'full_path' ] + workflow_dict = wf_dict[ 'workflow_dict' ] + workflow_name = workflow_dict[ 'name' ] + if 'steps' in workflow_dict: + ## Initially steps were not stored in the metadata record. + steps = workflow_dict[ 'steps' ] + else: + steps = [] + format_version = workflow_dict[ 'format-version' ] + annotation = workflow_dict[ 'annotation' ] + %> + <tr> + <td> + <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> + ${workflow_name} + <div popupmenu="workflow-${index}-popup"> + <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', local_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> + </div> + </div> + </td> + <td> + %if 'steps' in workflow_dict: + ${len( steps )} + %else: + unknown + %endif + </td> + <td>${format_version}</td> + <td>${annotation}</td> + </tr> + <% index += 1 %> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + </div> +</div> diff -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 templates/admin/tool_shed_repository/manage_repository.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -0,0 +1,57 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='admin', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <form name="edit_repository" id="edit_repository" action="${h.url_for( controller='admin', action='manage_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Tool shed:</label> + ${repository.tool_shed} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Name:</label> + ${repository.name} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <input name="description" type="textfield" value="${description}" size="80"/> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Revision:</label> + ${repository.changeset_revision} + </div> + <div class="form-row"> + <label>Owner:</label> + ${repository.owner} + </div> + <div class="form-row"> + <label>Location:</label> + ${repo_files_dir} + </div> + <div class="form-row"> + <label>Deleted:</label> + ${repository.deleted} + </div> + <div class="form-row"> + <input type="submit" name="edit_repository_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 -r c3582a9913fad4d41b7b7e151163fa4a45371bc1 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -64,7 +64,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div> %if cloned_repositories: - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_shed_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div> %endif </div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for refresh on change in workflow run interface triggering actual running of workflow.
by Bitbucket 28 Oct '11

28 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/07f3f601d645/ changeset: 07f3f601d645 user: dan date: 2011-10-28 17:38:55 summary: Fix for refresh on change in workflow run interface triggering actual running of workflow. affected #: 1 file diff -r 9a6e51c4efeb1b901cb4cc5b2c494577b5f11ad8 -r 07f3f601d645f07b76b196879ecd6d1c68c5b5d4 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1480,10 +1480,10 @@ trans.sa_session.add( workflow_invocation ) invocations.append({'outputs': outputs, 'new_history': new_history}) - trans.sa_session.flush() - return trans.fill_template( "workflow/run_complete.mako", - workflow=stored, - invocations=invocations ) + trans.sa_session.flush() + return trans.fill_template( "workflow/run_complete.mako", + workflow=stored, + invocations=invocations ) else: # Prepare each step missing_tools = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Create a new ToolShedRepository record only if necessary - if one already exists for the installed repository but is marked deleted, mark the exisint record undeleted.
by Bitbucket 27 Oct '11

27 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9a6e51c4efeb/ changeset: 9a6e51c4efeb user: greg date: 2011-10-27 21:08:07 summary: Create a new ToolShedRepository record only if necessary - if one already exists for the installed repository but is marked deleted, mark the exisint record undeleted. affected #: 2 files diff -r 786a5d6c56c77b592598df8e32b227cb6e5cb63f -r 9a6e51c4efeb1b901cb4cc5b2c494577b5f11ad8 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2443,6 +2443,13 @@ id = trans.security.decode_id( id ) quota = trans.sa_session.query( trans.model.Quota ).get( id ) return quota +def get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ): + return trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed, + trans.model.ToolShedRepository.table.c.name == name, + trans.model.ToolShedRepository.table.c.owner == owner, + trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ + .first() def handle_sample_tool_data_table_conf_file( trans, filename ): """ Parse the incoming filename and add new entries to the in-memory diff -r 786a5d6c56c77b592598df8e32b227cb6e5cb63f -r 9a6e51c4efeb1b901cb4cc5b2c494577b5f11ad8 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -766,12 +766,9 @@ os.chdir( current_working_dir ) tmp_stderr.close() if returncode == 0: - # Add a new record to the tool_shed_repository table. - tool_shed_repository = self.__create_tool_shed_repository( trans, - name, - description, - changeset_revision, - repository_clone_url ) + # Add a new record to the tool_shed_repository table if one doesn't + # already exist. If one exists but is marked deleted, undelete it. + self.__create_or_undelete_tool_shed_repository( trans, name, description, changeset_revision, repository_clone_url ) # Update the cloned repository to changeset_revision. repo_files_dir = os.path.join( clone_dir, name ) log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision ) @@ -1055,17 +1052,26 @@ # We have an invalid .xml file, so not a tool config. log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) return sample_files, repository_tools_tups - def __create_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ): + def __create_or_undelete_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ): tmp_url = self.__clean_repository_clone_url( repository_clone_url ) tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) owner = self.__get_repository_owner( tmp_url ) - tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed, - name=name, - description=description, - owner=owner, - changeset_revision=changeset_revision ) - trans.sa_session.add( tool_shed_repository ) - trans.sa_session.flush() + flush_needed = False + tool_shed_repository = get_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ) + if tool_shed_repository: + if tool_shed_repository.deleted: + tool_shed_repository.deleted = False + flush_needed = True + else: + tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed, + name=name, + description=description, + owner=owner, + changeset_revision=changeset_revision ) + flush_needed = True + if flush_needed: + trans.sa_session.add( tool_shed_repository ) + trans.sa_session.flush() def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ): # Add an entry in the shed_tool_conf file. An entry looks something like: # <section name="Filter and Sort" id="filter"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Eliminate forgotten (and not wanted) PostJobAction code when generating a workflow it's dict representation for rendering as an svg image in the tool shed.
by Bitbucket 27 Oct '11

27 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/786a5d6c56c7/ changeset: 786a5d6c56c7 user: greg date: 2011-10-27 19:52:05 summary: Eliminate forgotten (and not wanted) PostJobAction code when generating a workflow it's dict representation for rendering as an svg image in the tool shed. affected #: 1 file diff -r 753196399060239c365040aa6ecb18cba345b69e -r 786a5d6c56c77b592598df8e32b227cb6e5cb63f lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -339,12 +339,6 @@ workflow.has_errors = True # Stick this in the step temporarily. step.temp_input_connections = step_dict[ 'input_connections' ] - # Unpack and add post-job actions. - post_job_actions = step_dict.get( 'post_job_actions', {} ) - for name, pja_dict in post_job_actions.items(): - pja = PostJobAction( pja_dict[ 'action_type' ], - step, pja_dict[ 'output_name' ], - pja_dict[ 'action_arguments' ] ) steps.append( step ) steps_by_external_id[ step_dict[ 'id' ] ] = step # Second pass to deal with connections between steps. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for rendering workflow metadata.
by Bitbucket 27 Oct '11

27 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/753196399060/ changeset: 753196399060 user: greg date: 2011-10-27 19:37:48 summary: Fix for rendering workflow metadata. affected #: 1 file diff -r c528fab7ea8c89ab55cb9977d5916c72e5170546 -r 753196399060239c365040aa6ecb18cba345b69e templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -168,7 +168,11 @@ %for workflow_dict in workflow_dicts: <% workflow_name = workflow_dict[ 'name' ] - steps = workflow_dict[ 'steps' ] + if 'steps' in workflow_dict: + ## Initially steps were not stored in the metadata record. + steps = workflow_dict[ 'steps' ] + else: + steps = [] format_version = workflow_dict[ 'format-version' ] annotation = workflow_dict[ 'annotation' ] %> @@ -178,7 +182,6 @@ </td><td> %if 'steps' in workflow_dict: - ## Initially steps were not stored in the metadata record. ${len( steps )} %else: unknown Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the ability to search for workflows by name in a Galalxy tool shed, either within the tool shed itself or in a local Galaxy instance configured to communicate with the tool shed.
by Bitbucket 27 Oct '11

27 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c528fab7ea8c/ changeset: c528fab7ea8c user: greg date: 2011-10-27 19:26:43 summary: Add the ability to search for workflows by name in a Galalxy tool shed, either within the tool shed itself or in a local Galaxy instance configured to communicate with the tool shed. affected #: 13 files diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -704,6 +704,13 @@ return trans.response.send_redirect( url ) @web.expose @web.require_admin + def find_workflows_in_tool_shed( self, trans, **kwd ): + tool_shed_url = kwd[ 'tool_shed_url' ] + galaxy_url = trans.request.host + url = '%s/repository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + return trans.response.send_redirect( url ) + @web.expose + @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = trans.request.host diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -231,7 +231,7 @@ return repository_metadata.repository.user.username return 'no user' # Grid definition - title = "Repositories with matching tools" + title = "Matching repositories" model_class = model.RepositoryMetadata template='/webapps/community/repository/grid.mako' default_sort_key = "Repository.name" @@ -375,6 +375,83 @@ # Render the list view return self.valid_repository_list_grid( trans, **kwd ) @web.expose + def find_workflows( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + if 'operation' in kwd: + item_id = kwd.get( 'id', '' ) + if item_id: + operation = kwd[ 'operation' ].lower() + is_admin = trans.user_is_admin() + if operation == "view_or_manage_repository": + # The received id is a RepositoryMetadata id, so we have to get the repository id. + repository_metadata = get_repository_metadata_by_id( trans, item_id ) + repository_id = trans.security.encode_id( repository_metadata.repository.id ) + repository = get_repository( trans, repository_id ) + kwd[ 'id' ] = repository_id + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + if webapp == 'community' and ( is_admin or repository.user == trans.user ): + a = 'manage_repository' + else: + a = 'view_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + action=a, + **kwd ) ) + if operation == "install": + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) + # TODO: support https in the following url. + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ + ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict ) + return trans.response.send_redirect( url ) + else: + # This can only occur when there is a multi-select grid with check boxes and an operation, + # and the user clicked the operation button without checking any of the check boxes. + return trans.show_error_message( "No items were selected." ) + workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ] + exact_matches = params.get( 'exact_matches', '' ) + exact_matches_checked = CheckboxField.is_checked( exact_matches ) + match_tuples = [] + ok = True + if workflow_names: + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) + if ok: + kwd[ 'match_tuples' ] = match_tuples + # Render the list view + if webapp == 'galaxy': + # Our initial request originated from a Galaxy instance. + global_actions = [ grids.GridAction( "Browse valid repositories", + dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + grids.GridAction( "Search for valid tools", + dict( controller='repository', action='find_tools', webapp=webapp ) ), + grids.GridAction( "Search for workflows", + dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + self.install_matched_repository_list_grid.global_actions = global_actions + install_url_args = dict( controller='repository', action='find_workflows', webapp=webapp ) + operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] + self.install_matched_repository_list_grid.operations = operations + return self.install_matched_repository_list_grid( trans, **kwd ) + else: + kwd[ 'message' ] = "workflow name: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ + ( self.__stringify( workflow_names ), str( exact_matches_checked ) ) + self.matched_repository_list_grid.title = "Repositories with matching workflows" + return self.matched_repository_list_grid( trans, **kwd ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + return trans.fill_template( '/webapps/community/repository/find_workflows.mako', + webapp=webapp, + workflow_name=self.__stringify( workflow_names ), + exact_matches_check_box=exact_matches_check_box, + message=message, + status=status ) + @web.expose def find_tools( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -421,7 +498,7 @@ match_tuples = [] ok = True if tool_ids or tool_names or tool_versions: - ok, match_tuples = self.__search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked ) + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions ) if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view @@ -430,7 +507,9 @@ global_actions = [ grids.GridAction( "Browse valid repositories", dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ) ] + dict( controller='repository', action='find_tools', webapp=webapp ) ), + grids.GridAction( "Search for workflows", + dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] self.install_matched_repository_list_grid.global_actions = global_actions install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] @@ -439,6 +518,7 @@ else: kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) ) + self.matched_repository_list_grid.title = "Repositories with matching tools" return self.matched_repository_list_grid( trans, **kwd ) else: message = "No search performed - each field must contain the same number of comma-separated items." @@ -452,62 +532,76 @@ exact_matches_check_box=exact_matches_check_box, message=message, status=status ) - def __search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ): + def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='' ): match_tuples = [] ok = True for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): metadata = repository_metadata.metadata - if 'tools' in metadata: - tools = metadata[ 'tools' ] - else: - tools = [] - for tool_dict in tools: - if tool_ids and not tool_names and not tool_versions: - for tool_id in tool_ids: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + if tool_ids or tool_names or tool_versions: + if 'tools' in metadata: + tools = metadata[ 'tools' ] + else: + tools = [] + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + if workflow_names: + if 'workflows' in metadata: + workflows = metadata[ 'workflows' ] + else: + workflows = [] + for workflow_dict in workflows: + for workflow_name in workflow_names: + if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name=workflow_name ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_names and not tool_ids and not tool_versions: - for tool_name in tool_names: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_versions and not tool_ids and not tool_names: - for tool_version in tool_versions: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_ids and tool_names and not tool_versions: - if len( tool_ids ) == len( tool_names ): - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - elif len( tool_ids ) == 1 or len( tool_names ) == 1: - tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - else: - ok = False - elif tool_ids and tool_versions and not tool_names: - if len( tool_ids ) == len( tool_versions ): - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - elif len( tool_ids ) == 1 or len( tool_versions ) == 1: - tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and not tool_ids: - if len( tool_versions ) == len( tool_names ): - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - elif len( tool_versions ) == 1 or len( tool_names ) == 1: - tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and tool_ids: - if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): - for i, tool_version in enumerate( tool_versions ): - tool_name = tool_names[ i ] - tool_id = tool_ids[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - ok = False return ok, match_tuples + def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name=None ): + workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() + return ( workflow_name == workflow_dict_workflow_name ) or \ + ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): found = False if tool_id and not tool_name and not tool_version: diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -744,7 +744,7 @@ %if grid.global_actions: <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 4: + %if len( grid.global_actions ) < 3: %for action in grid.global_actions: <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a></li> %endfor diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -44,6 +44,20 @@ <div class="page-container" style="padding: 10px;"><div class="toolMenu"><div class="toolSectionList"> + %if repository_metadata: + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + Search + </div> + <div class="toolSectionBody"> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows', webapp='community' )}">Search for workflows</a> + </div> + </div> + %endif <div class="toolSectionPad"></div><div class="toolSectionTitle"> Repositories @@ -61,11 +75,6 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a></div> %endif - %if repository_metadata: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a> - </div> - %endif </div></div><div class="toolSectionBody"> diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/community/repository/find_tools.mako --- a/templates/webapps/community/repository/find_tools.mako +++ b/templates/webapps/community/repository/find_tools.mako @@ -14,6 +14,7 @@ <br/><br/><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></li></ul> %endif diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/community/repository/find_workflows.mako --- /dev/null +++ b/templates/webapps/community/repository/find_workflows.mako @@ -0,0 +1,53 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/community/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +%if webapp == 'galaxy': + <br/><br/> + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </ul> +%endif + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Search repositories for workflows</div> + <div class="toolFormBody"> + <div class="form-row"> + Enter a workflow name to find repositories that contain workflows matching the search criteria.<br/><br/> + Comma-separated strings may be entered to expand search criteria. + </div> + <div style="clear: both"></div> + <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}" method="post" > + <div style="clear: both"></div> + <div class="form-row"> + <label>Workflow name:</label> + <input name="workflow_name" type="textfield" value="${workflow_name}" size="40"/> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Exact matches only:</label> + ${exact_matches_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Check the box to match text exactly (text case doesn't matter as all strings are forced to lower case). + </div> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" value="Search repositories"/> + </div> + </form> + </div> +</div> diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -69,6 +69,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div></ul> diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -116,6 +116,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div> %else: %if is_new: diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -99,6 +99,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div> %endif </ul> diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -39,6 +39,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div> %else: %if is_new: diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/community/repository/view_workflow.mako --- a/templates/webapps/community/repository/view_workflow.mako +++ b/templates/webapps/community/repository/view_workflow.mako @@ -84,6 +84,7 @@ <div popupmenu="toolshed-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div> %endif </ul> @@ -92,10 +93,12 @@ ${render_msg( message, status )} %endif -<br/> -<b>Boxes are red when tools are not available in this repository</b> -<div class="toolParamHelp" style="clear: both;"> - (this page displays SVG graphics) +<div class="toolFormTitle">${workflow_name}</div> +<div class="form-row"> + <b>Boxes are red when tools are not available in this repository</b> + <div class="toolParamHelp" style="clear: both;"> + (this page displays SVG graphics) + </div></div><br clear="left"/> diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -73,7 +73,7 @@ <div class="toolSectionTitle">Tool sheds</div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Browse tool sheds</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Search and browse tool sheds</a></div></div></div> %endif diff -r 216d4f09480468bb01ee56df9a393c5b740fe51d -r c528fab7ea8c89ab55cb9977d5916c72e5170546 templates/webapps/galaxy/admin/tool_sheds.mako --- a/templates/webapps/galaxy/admin/tool_sheds.mako +++ b/templates/webapps/galaxy/admin/tool_sheds.mako @@ -27,6 +27,7 @@ <div popupmenu="dataset-${shed_id}-popup"><a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='admin', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='admin', action='find_workflows_in_tool_shed', tool_shed_url=url )}">Search for workflows</a></div></td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Have Picard MergeSamFiles use return code to determine tool error.
by Bitbucket 27 Oct '11

27 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/216d4f094804/ changeset: 216d4f094804 user: dan date: 2011-10-27 16:54:42 summary: Have Picard MergeSamFiles use return code to determine tool error. affected #: 1 file diff -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec -r 216d4f09480468bb01ee56df9a393c5b740fe51d tools/samtools/sam_merge.xml --- a/tools/samtools/sam_merge.xml +++ b/tools/samtools/sam_merge.xml @@ -9,6 +9,7 @@ I=${i.input} #end for 2> $outlog + || echo "Error running Picard MergeSamFiles" >&2 </command><inputs><param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the ability to view workflows contained in a tool shed repository as svg images. Add the ability to import a specific workflow from a Galaxy tool shed repository to a loacl Galaxy instance. Fix bugs when displaying or running a workflow that requires tools that use the old Galaxy tool id, but the local Galaxy instance uses tools installed from a tool shed.
by Bitbucket 26 Oct '11

26 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0ba260ea43c4/ changeset: 0ba260ea43c4 user: greg date: 2011-10-26 22:11:49 summary: Add the ability to view workflows contained in a tool shed repository as svg images. Add the ability to import a specific workflow from a Galaxy tool shed repository to a loacl Galaxy instance. Fix bugs when displaying or running a workflow that requires tools that use the old Galaxy tool id, but the local Galaxy instance uses tools installed from a tool shed. affected #: 17 files diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1,10 +1,11 @@ """ Contains functionality needed in every web interface """ -import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess +import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess, binascii from datetime import date, datetime, timedelta from time import strftime from galaxy import config, tools, web, util +from galaxy.util.hash_util import * from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.workflow.modules import * @@ -2484,3 +2485,32 @@ message = "The required file named tool_data_table_conf.xml does not exist in the Galaxy install directory." error = True return error, message +def tool_shed_encode( val ): + if isinstance( val, dict ): + value = simplejson.dumps( val ) + else: + value = val + a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + b = binascii.hexlify( value ) + return "%s:%s" % ( a, b ) +def tool_shed_decode( value ): + # Extract and verify hash + a, b = value.split( ":" ) + value = binascii.unhexlify( b ) + test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + assert a == test + # Restore from string + values = None + try: + values = simplejson.loads( value ) + except Exception, e: + log.debug( "Decoding json value from tool shed threw exception: %s" % str( e ) ) + if values is not None: + try: + return json_fix( values ) + except Exception, e: + log.debug( "Fixing decoded json value from tool shed threw exception: %s" % str( e ) ) + fixed_values = values + if values is None: + values = value + return values diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -4,8 +4,7 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.tools.search import ToolBoxSearch from galaxy.tools import json_fix -from galaxy.util.hash_util import * -import simplejson, binascii, logging +import logging log = logging.getLogger( __name__ ) from galaxy.actions.admin import AdminActions @@ -736,7 +735,7 @@ section_key = 'section_%s' % kwd[ 'tool_panel_section' ] tool_section = trans.app.toolbox.tool_panel[ section_key ] # Decode the encoded repo_info_dict param value. - repo_info_dict = self.__decode( repo_info_dict ) + repo_info_dict = tool_shed_decode( repo_info_dict ) # Clone the repository to the configured location. current_working_dir = os.getcwd() for name, repo_info_tuple in repo_info_dict.items(): @@ -1157,15 +1156,6 @@ section_str += ' </tool>\n' section_str += ' </section>\n' return section_str - def __decode( self, value ): - # Extract and verify hash - a, b = value.split( ":" ) - value = binascii.unhexlify( b ) - test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) - assert a == test - # Restore from string - values = json_fix( simplejson.loads( value ) ) - return values ## ---- Utility methods ------------------------------------------------------- diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -4,7 +4,7 @@ pkg_resources.require( "simplejson" ) pkg_resources.require( "SVGFig" ) import simplejson -import base64, httplib, urllib2, sgmllib, svgfig +import base64, httplib, urllib2, sgmllib, svgfig, urllib, urllib2 import math from galaxy.web.framework.helpers import time_ago, grids from galaxy.tools.parameters import * @@ -1092,13 +1092,35 @@ trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-Workflow-%s.ga" % ( sname ) trans.response.set_content_type( 'application/galaxy-archive' ) return stored_dict - @web.expose def import_workflow( self, trans, **kwd ): + """ + Import a workflow by reading an url, uploading a file, or receiving the textual + representation of a workflow. + """ url = kwd.get( 'url', '' ) + workflow_text = kwd.get( 'workflow_text', '' ) + webapp = kwd.get( 'webapp', 'galaxy' ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - if kwd.get( 'import_button', False ): + import_button = kwd.get( 'import_button', False ) + tool_shed_url = kwd.get( 'tool_shed_url', '' ) + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + # The workflow_name parameter is in the request only if the import originated + # from a Galaxy tool shed, in which case the value was encoded. + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = tool_shed_decode( workflow_name ) + if tool_shed_url and not import_button: + # Use urllib (send another request to the tool shed) to retrieve the workflow. + workflow_url = 'http://%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + response = urllib2.urlopen( workflow_url ) + workflow_text = response.read() + response.close() + workflow_text = workflow_text + import_button = True + if import_button: workflow_data = None if url: # Load workflow from external URL @@ -1108,6 +1130,8 @@ except Exception, e: message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) ) status = 'error' + elif workflow_text: + workflow_data = workflow_text else: # Load workflow from browsed file. file_data = kwd.get( 'file_data', '' ) @@ -1175,6 +1199,13 @@ else: # TODO: Figure out what to do here... pass + if tool_shed_url: + # We've received the textual representation of a workflow from a Galaxy tool shed. + message = "This workflow has been successfully imported into your local Galaxy instance." + # TODO: support https in the following url. + url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) + return trans.response.send_redirect( url ) return self.list( trans ) return trans.fill_template( "workflow/import.mako", url=url, diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -35,6 +35,8 @@ self.tag_handler = CommunityTagHandler() # Tool data tables self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) + # The tool shed has no toolbox, but this attribute is still required. + self.toolbox = None # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -332,13 +332,13 @@ if 'tools' in metadata: metadata_str += '<b>Tools:</b><br/>' for tool_metadata_dict in metadata[ 'tools' ]: - metadata_str += '%s <b>%s</b><br/>' % \ - ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + metadata_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], + tool_metadata_dict[ 'version' ] ) if 'workflows' in metadata: metadata_str += '<b>Workflows:</b><br/>' for workflow_metadata_dict in metadata[ 'workflows' ]: - metadata_str += '%s <b>%s</b><br/>' % \ - ( workflow_metadata_dict[ 'name' ], workflow_metadata_dict[ 'format-version' ] ) + metadata_str += '%s <b>%s</b><br/>' % ( workflow_metadata_dict[ 'name' ], + workflow_metadata_dict[ 'format-version' ] ) return metadata_str class MaliciousColumn( grids.BooleanColumn ): def get_value( self, trans, grid, repository_metadata ): diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,8 +1,9 @@ -import os, string, socket, logging +import os, string, socket, logging, simplejson, binascii from time import strftime from datetime import * from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.hash_util import * from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -126,23 +127,18 @@ def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): """ Update the received metadata_dict with changes that have been applied - to the received exported_workflow_dict. Store everything except the - workflow steps in the database. + to the received exported_workflow_dict. Store everything in the database. """ - workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ], - 'name' :exported_workflow_dict[ 'name' ], - 'annotation' : exported_workflow_dict[ 'annotation' ], - 'format-version' : exported_workflow_dict[ 'format-version' ] } if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( workflow_dict ) + metadata_dict[ 'workflows' ].append( exported_workflow_dict ) else: - metadata_dict[ 'workflows' ] = [ workflow_dict ] + metadata_dict[ 'workflows' ] = [ exported_workflow_dict ] return metadata_dict def new_workflow_metadata_required( trans, id, metadata_dict ): """ - TODO: Currently everything about an exported workflow except the name is hard-coded, so - there's no real way to differentiate versions of exported workflows. If this changes at - some future time, this method should be enhanced accordingly... + Currently everything about an exported workflow except the name is hard-coded, so there's + no real way to differentiate versions of exported workflows. If this changes at some future + time, this method should be enhanced accordingly. """ if 'workflows' in metadata_dict: repository_metadata = get_latest_repository_metadata( trans, id ) @@ -425,18 +421,20 @@ trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: - message = "Change set revision '%s' includes no tools or exported workflows for which metadata can be set." % str( changeset_revision ) + message = "Revision '%s' includes no tools or exported workflows for which metadata can be defined " % str( changeset_revision ) + message += "so this revision cannot be automatically installed into a local Galaxy instance." status = "error" else: # change_set is None - message = "Repository does not include change set revision '%s'." % str( changeset_revision ) + message = "This repository does not include revision '%s'." % str( changeset_revision ) status = 'error' if invalid_files: if metadata_dict: - message = "Metadata was defined for some items in change set revision '%s'. " % str( changeset_revision ) + message = "Metadata was defined for some items in revision '%s'. " % str( changeset_revision ) message += "Correct the following problems if necessary and reset metadata.<br/>" else: - message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( changeset_revision ) + message = "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( changeset_revision ) + message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.<br/>" for itc_tup in invalid_files: tool_file, exception_msg = itc_tup if exception_msg.find( 'No such file or directory' ) >= 0: @@ -619,3 +617,24 @@ selected = selected_value and option_tup[1] == selected_value select_field.add_option( option_tup[0], option_tup[1], selected=selected ) return select_field +def encode( val ): + if isinstance( val, dict ): + value = simplejson.dumps( val ) + else: + value = val + a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + b = binascii.hexlify( value ) + return "%s:%s" % ( a, b ) +def decode( value ): + # Extract and verify hash + a, b = value.split( ":" ) + value = binascii.unhexlify( b ) + test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + assert a == test + # Restore from string + try: + values = json_fix( simplejson.loads( value ) ) + except Exception, e: + # We do not have a json string + values = value + return values diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,7 +9,6 @@ from galaxy.webapps.community.model import directory_hash_id from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string -from galaxy.util.hash_util import * from galaxy.model.orm import * from common import * from mercurial import hg, ui, patch, commands @@ -458,7 +457,10 @@ ok = True for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): metadata = repository_metadata.metadata - tools = metadata[ 'tools' ] + if 'tools' in metadata: + tools = metadata[ 'tools' ] + else: + tools = [] for tool_dict in tools: if tool_ids and not tool_names and not tool_versions: for tool_id in tool_ids: @@ -588,15 +590,7 @@ changeset_revision = repository_metadata.changeset_revision repository_clone_url = generate_clone_url( trans, repository_id ) repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - return self.__encode( repo_info_dict ) - def __encode( self, val ): - if isinstance( val, dict ): - value = simplejson.dumps( val ) - else: - value = val - a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) - b = binascii.hexlify( value ) - return "%s:%s" % ( a, b ) + return encode( repo_info_dict ) @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) @@ -607,8 +601,10 @@ changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata else: + repository_metadata_id = None metadata = None revision_label = get_revision_label( trans, repository, changeset_revision ) changeset_revision_select_field = build_changeset_revision_select_field( trans, @@ -617,6 +613,7 @@ add_id_to_name=False ) return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', repository=repository, + repository_metadata_id=repository_metadata_id, changeset_revision=changeset_revision, revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, @@ -636,7 +633,7 @@ changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repo_info_dict = {} repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - encoded_repo_info_dict = self.__encode( repo_info_dict ) + encoded_repo_info_dict = encode( repo_info_dict ) # Redirect back to local Galaxy to perform install. # TODO: support https in the following url. url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \ @@ -1159,8 +1156,10 @@ revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata else: + repository_metadata_id = None metadata = None is_malicious = change_set_is_malicious( trans, id, repository.tip ) if is_malicious: @@ -1172,6 +1171,7 @@ return trans.fill_template( '/webapps/community/repository/view_repository.mako', repo=repo, repository=repository, + repository_metadata_id=repository_metadata_id, metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, @@ -1299,9 +1299,11 @@ revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious else: + repository_metadata_id = None metadata = None is_malicious = False if is_malicious: @@ -1321,6 +1323,7 @@ allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, + repository_metadata_id=repository_metadata_id, changeset_revision=changeset_revision, changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/webapps/community/controllers/workflow.py --- /dev/null +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -0,0 +1,395 @@ +import pkg_resources +pkg_resources.require( "simplejson" ) +pkg_resources.require( "SVGFig" ) +import os, logging, ConfigParser, tempfile, shutil, svgfig +from galaxy.webapps.community import model +from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.util.json import from_json_string, to_json_string +from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory +from galaxy.tools import DefaultToolState +from galaxy.web.controllers.workflow import attach_ordered_steps +from galaxy.model.orm import * +from common import * + +class RepoInputDataModule( InputDataModule ): + + type = "data_input" + name = "Input dataset" + + @classmethod + def new( Class, trans, tools_metadata=None, tool_id=None ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + return module + @classmethod + def from_dict( Class, trans, d, tools_metadata=None, secure=True ): + module = Class( trans ) + state = from_json_string( d[ "tool_state" ] ) + module.state = dict( name=state.get( "name", "Input Dataset" ) ) + return module + @classmethod + def from_workflow_step( Class, trans, tools_metadata, step ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + if step.tool_inputs and "name" in step.tool_inputs: + module.state[ 'name' ] = step.tool_inputs[ 'name' ] + return module + +class RepoToolModule( ToolModule ): + + type = "tool" + + def __init__( self, trans, tools_metadata, tool_id ): + self.trans = trans + self.tools_metadata = tools_metadata + self.tool_id = tool_id + self.tool = None + for tool_dict in tools_metadata: + if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: + self.tool = load_tool( trans, os.path.abspath( tool_dict[ 'tool_config' ] ) ) + self.post_job_actions = {} + self.workflow_outputs = [] + self.state = None + self.errors = None + @classmethod + def new( Class, trans, tools_metadata, tool_id=None ): + module = Class( trans, tools_metadata, tool_id ) + module.state = module.tool.new_state( trans, all_pages=True ) + return module + @classmethod + def from_dict( Class, trans, d, tools_metadata, secure=True ): + tool_id = d[ 'tool_id' ] + module = Class( trans, tools_metadata, tool_id ) + module.state = DefaultToolState() + if module.tool is not None: + module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) + module.errors = d.get( "tool_errors", None ) + return module + @classmethod + def from_workflow_step( Class, trans, tools_metadata, step ): + module = Class( trans, tools_metadata, step.tool_id ) + module.state = DefaultToolState() + if module.tool: + module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) + else: + module.state.inputs = {} + module.errors = step.tool_errors + return module + def get_data_inputs( self ): + data_inputs = [] + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + data_inputs.append( dict( name=prefixed_name, + label=prefixed_label, + extensions=input.extensions ) ) + if self.tool: + visit_input_values( self.tool.inputs, self.state.inputs, callback ) + return data_inputs + def get_data_outputs( self ): + data_outputs = [] + if self.tool: + data_inputs = None + for name, tool_output in self.tool.outputs.iteritems(): + if tool_output.format_source != None: + # Default to special name "input" which remove restrictions on connections + formats = [ 'input' ] + if data_inputs == None: + data_inputs = self.get_data_inputs() + # Find the input parameter referenced by format_source + for di in data_inputs: + # Input names come prefixed with conditional and repeat names separated by '|', + # so remove prefixes when comparing with format_source. + if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: + formats = di[ 'extensions' ] + else: + formats = [ tool_output.format ] + for change_elem in tool_output.change_format: + for when_elem in change_elem.findall( 'when' ): + format = when_elem.get( 'format', None ) + if format and format not in formats: + formats.append( format ) + data_outputs.append( dict( name=name, extensions=formats ) ) + return data_outputs + +class RepoWorkflowModuleFactory( WorkflowModuleFactory ): + def __init__( self, module_types ): + self.module_types = module_types + def new( self, trans, type, tools_metadata=None, tool_id=None ): + """Return module for type and (optional) tool_id intialized with new / default state.""" + assert type in self.module_types + return self.module_types[type].new( trans, tool_id ) + def from_dict( self, trans, d, **kwargs ): + """Return module initialized from the data in dictionary `d`.""" + type = d[ 'type' ] + assert type in self.module_types + return self.module_types[ type ].from_dict( trans, d, **kwargs ) + def from_workflow_step( self, trans, tools_metadata, step ): + """Return module initialized from the WorkflowStep object `step`.""" + type = step.type + return self.module_types[ type ].from_workflow_step( trans, tools_metadata, step ) + +module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) + +class WorkflowController( BaseUIController ): + @web.expose + def view_workflow( self, trans, **kwd ): + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = decode( workflow_name ) + webapp = kwd.get( 'webapp', 'community' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + return trans.fill_template( "/webapps/community/repository/view_workflow.mako", + repository=repository, + changeset_revision=repository_metadata.changeset_revision, + repository_metadata_id=repository_metadata_id, + workflow_name=workflow_name, + webapp=webapp, + message=message, + status=status ) + @web.expose + def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ): + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + metadata = repository_metadata.metadata + workflow_name = decode( workflow_name ) + for workflow_dict in metadata[ 'workflows' ]: + if workflow_dict[ 'name' ] == workflow_name: + break + if 'tools' in metadata: + tools_metadata = metadata[ 'tools' ] + else: + tools_metadata = [] + workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata ) + data = [] + canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) + text = svgfig.SVG( "g" ) + connectors = svgfig.SVG( "g" ) + boxes = svgfig.SVG( "g" ) + svgfig.Text.defaults[ "font-size" ] = "10px" + in_pos = {} + out_pos = {} + margin = 5 + # Spacing between input/outputs. + line_px = 16 + # Store px width for boxes of each step. + widths = {} + max_width, max_x, max_y = 0, 0, 0 + for step in workflow.steps: + step.upgrade_messages = {} + module = module_factory.from_workflow_step( trans, tools_metadata, step ) + tool_errors = module.type == 'tool' and not module.tool + module_data_inputs = self.__get_data_inputs( step, module ) + module_data_outputs = self.__get_data_outputs( step, module, workflow.steps ) + step_dict = { + 'id' : step.order_index, + 'data_inputs' : module_data_inputs, + 'data_outputs' : module_data_outputs, + 'position' : step.position, + 'tool_errors' : tool_errors + } + input_conn_dict = {} + for conn in step.input_connections: + input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) + step_dict[ 'input_connections' ] = input_conn_dict + data.append( step_dict ) + x, y = step.position[ 'left' ], step.position[ 'top' ] + count = 0 + module_name = self.__get_name( module, missing_tool_tups ) + max_len = len( module_name ) * 1.5 + text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) + y += 45 + for di in module_data_inputs: + cur_y = y + count * line_px + if step.order_index not in in_pos: + in_pos[ step.order_index ] = {} + in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y ) + text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( di[ 'label' ] ) ) + if len( module.get_data_inputs() ) > 0: + y += 15 + for do in module_data_outputs: + cur_y = y + count * line_px + if step.order_index not in out_pos: + out_pos[ step.order_index ] = {} + out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y ) + text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( do['name' ] ) ) + widths[ step.order_index ] = max_len * 5.5 + max_x = max( max_x, step.position[ 'left' ] ) + max_y = max( max_y, step.position[ 'top' ] ) + max_width = max( max_width, widths[ step.order_index ] ) + for step_dict in data: + tool_unavailable = step_dict[ 'tool_errors' ] + width = widths[ step_dict[ 'id' ] ] + x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ] + if tool_unavailable: + fill = "#EBBCB2" + else: + fill = "#EBD9B2" + boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() ) + box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin + # Draw separator line. + if len( step_dict[ 'data_inputs' ] ) > 0: + box_height += 15 + sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40 + text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() ) + # Define an input/output box. + boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) + for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): + in_coords = in_pos[ step_dict[ 'id' ] ][ conn ] + out_conn_pos = out_pos[ output_dict[ 'id' ] ][ output_dict[ 'output_name' ] ] + adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) + text.append( svgfig.SVG( "circle", + cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin, + cy=out_conn_pos[ 1 ] - margin, + r = 5, + fill="#ffffff" ) ) + connectors.append( svgfig.Line( adjusted[ 0 ], + adjusted[ 1 ] - margin, + in_coords[ 0 ] - 10, + in_coords[ 1 ], + arrow_end = "true" ).SVG() ) + canvas.append( connectors ) + canvas.append( boxes ) + canvas.append( text ) + width, height = ( max_x + max_width + 50 ), max_y + 300 + canvas[ 'width' ] = "%s px" % width + canvas[ 'height' ] = "%s px" % height + canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) + trans.response.set_content_type( "image/svg+xml" ) + return canvas.standalone_xml() + def __get_name( self, module, missing_tool_tups ): + module_name = module.get_name() + if module.type == 'tool' and module_name == 'unavailable': + for missing_tool_tup in missing_tool_tups: + missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup + if missing_tool_id == module.tool_id: + module_name = '%s' % missing_tool_name + return module_name + def __get_data_inputs( self, step, module ): + if module.type == 'tool': + if module.tool: + return module.get_data_inputs() + else: + data_inputs = [] + for wfsc in step.input_connections: + data_inputs_dict = {} + data_inputs_dict[ 'extensions' ] = [ '' ] + data_inputs_dict[ 'name' ] = wfsc.input_name + data_inputs_dict[ 'label' ] = 'Unknown' + data_inputs.append( data_inputs_dict ) + return data_inputs + return module.get_data_inputs() + def __get_data_outputs( self, step, module, steps ): + if module.type == 'tool': + if module.tool: + return module.get_data_outputs() + else: + data_outputs = [] + data_outputs_dict = {} + data_outputs_dict[ 'extensions' ] = [ 'input' ] + found = False + for workflow_step in steps: + for wfsc in workflow_step.input_connections: + if step.name == wfsc.output_step.name: + data_outputs_dict[ 'name' ] = wfsc.output_name + found = True + break + if found: + break + if not found: + # We're at the last step of the workflow. + data_outputs_dict[ 'name' ] = 'output' + data_outputs.append( data_outputs_dict ) + return data_outputs + return module.get_data_outputs() + def __workflow_from_dict( self, trans, data, tools_metadata ): + """Creates and returns workflow object from a dictionary.""" + trans.workflow_building_mode = True + workflow = model.Workflow() + workflow.name = data[ 'name' ] + workflow.has_errors = False + steps = [] + # Keep ids for each step that we need to use to make connections. + steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the tool shed repository. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] + # First pass to build step objects and populate basic values + for key, step_dict in data[ 'steps' ].iteritems(): + # Create the model class for the step + step = model.WorkflowStep() + step.name = step_dict[ 'name' ] + step.position = step_dict[ 'position' ] + module = module_factory.from_dict( trans, step_dict, tools_metadata=tools_metadata, secure=False ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the current repository. + step.tool_errors = 'unavailable' + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) + module.save_to_step( step ) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily. + step.temp_input_connections = step_dict[ 'input_connections' ] + # Unpack and add post-job actions. + post_job_actions = step_dict.get( 'post_job_actions', {} ) + for name, pja_dict in post_job_actions.items(): + pja = PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], + pja_dict[ 'action_arguments' ] ) + steps.append( step ) + steps_by_external_id[ step_dict[ 'id' ] ] = step + # Second pass to deal with connections between steps. + for step in steps: + # Input connections. + for input_name, conn_dict in step.temp_input_connections.iteritems(): + if conn_dict: + output_step = steps_by_external_id[ conn_dict[ 'id' ] ] + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_step = output_step + conn.output_name = conn_dict[ 'output_name' ] + step.input_connections.append( conn ) + del step.temp_input_connections + # Order the steps if possible. + attach_ordered_steps( workflow, steps ) + return workflow, missing_tool_tups + @web.expose + def import_workflow( self, trans, **kwd ): + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = decode( workflow_name ) + webapp = kwd.get( 'webapp', 'community' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + workflows = repository_metadata.metadata[ 'workflows' ] + workflow_data = None + for workflow_data in workflows: + if workflow_data[ 'name' ] == workflow_name: + break + if workflow_data: + if kwd.get( 'open_for_url', False ): + tmp_fd, tmp_fname = tempfile.mkstemp() + to_file = open( tmp_fname, 'wb' ) + to_file.write( to_json_string( workflow_data ) ) + return open( tmp_fname ) + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + # TODO: support https in the following url. + url = 'http://%s/workflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ + ( galaxy_url, trans.request.host, repository_metadata_id, encode( workflow_name ), webapp ) + return trans.response.send_redirect( url ) + return trans.response.send_redirect( web.url_for( controller='workflow', + action='view_workflow', + message=message, + status=status ) ) diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -204,6 +204,34 @@ self.value = None self.user_value = None +class Workflow( object ): + def __init__( self ): + self.user = None + self.name = None + self.has_cycles = None + self.has_errors = None + self.steps = [] + +class WorkflowStep( object ): + def __init__( self ): + self.id = None + self.type = None + self.name = None + self.tool_id = None + self.tool_inputs = None + self.tool_errors = None + self.position = None + self.input_connections = [] + #self.output_connections = [] + self.config = None + +class WorkflowStepConnection( object ): + def __init__( self ): + self.output_step = None + self.output_name = None + self.input_step = None + self.input_name = None + ## ---- Utility methods ------------------------------------------------------- def sort_by_attr( seq, attr ): """ diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -205,14 +205,14 @@ def from_workflow_step( Class, trans, step ): tool_id = step.tool_id install_tool_id = None - if tool_id not in trans.app.toolbox.tools_by_id: + if trans.app.toolbox and tool_id not in trans.app.toolbox.tools_by_id: # The id value of tools installed from a Galaxy tool shed is a guid, but # these tool's old_id attribute should contain what we're looking for. for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): if tool_id == available_tool.old_id: install_tool_id = available_tool_id break - if tool_id in trans.app.toolbox.tools_by_id or install_tool_id: + if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ) or install_tool_id: module = Class( trans, tool_id ) module.state = DefaultToolState() module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) @@ -247,7 +247,9 @@ action_arguments = None n_p = PostJobAction(v['action_type'], step, output_name, action_arguments) def get_name( self ): - return self.tool.name + if self.tool: + return self.tool.name + return 'unavailable' def get_tool_id( self ): return self.tool_id def get_tool_version( self ): diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -83,7 +83,8 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def> -<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, webapp='community' )"> +<%def name="render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"> + <% from galaxy.webapps.community.controllers.common import encode, decode %> %if metadata or can_set_metadata: <p/><div class="toolForm"> @@ -160,14 +161,31 @@ <table class="grid"><tr><td><b>name</b></td> + <td><b>steps</b></td><td><b>format-version</b></td><td><b>annotation</b></td></tr> %for workflow_dict in workflow_dicts: + <% + workflow_name = workflow_dict[ 'name' ] + steps = workflow_dict[ 'steps' ] + format_version = workflow_dict[ 'format-version' ] + annotation = workflow_dict[ 'annotation' ] + %><tr> - <td>${workflow_dict[ 'name' ]}</td> - <td>${workflow_dict[ 'format-version' ]}</td> - <td>${workflow_dict[ 'annotation' ]}</td> + <td> + <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">${workflow_name}</a> + </td> + <td> + %if 'steps' in workflow_dict: + ## Initially steps were not stored in the metadata record. + ${len( steps )} + %else: + unknown + %endif + </td> + <td>${format_version}</td> + <td>${annotation}</td></tr> %endfor </table> diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -184,7 +184,7 @@ </form></div></div> -${render_repository_tools_and_workflows( metadata, can_set_metadata=True )} +${render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=True )} <p/><div class="toolForm"><div class="toolFormTitle">Manage categories</div> diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -103,4 +103,4 @@ </div></div><p/> -${render_repository_tools_and_workflows( metadata, webapp=webapp )} +${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )} diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -185,7 +185,7 @@ %endif </div></div> -${render_repository_tools_and_workflows( metadata, webapp=webapp )} +${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )} %if repository.categories: <p/><div class="toolForm"> diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec templates/webapps/community/repository/view_workflow.mako --- /dev/null +++ b/templates/webapps/community/repository/view_workflow.mako @@ -0,0 +1,102 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/webapps/community/common/common.mako" import="*" /> +<%namespace file="/webapps/community/repository/common.mako" import="*" /> + +<% + from galaxy.web.framework.helpers import time_ago + from galaxy.webapps.community.controllers.common import encode + + in_tool_shed = webapp == 'community' + is_admin = trans.user_is_admin() + is_new = repository.is_new + can_manage = is_admin or trans.user == repository.user + can_contact_owner = in_tool_shed and trans.user and trans.user != repository.user + can_push = in_tool_shed and trans.app.security_agent.can_push( trans.user, repository ) + can_upload = can_push + can_download = in_tool_shed and not is_new and ( not is_malicious or can_push ) + can_browse_contents = in_tool_shed and not is_new + can_set_metadata = in_tool_shed and not is_new + can_rate = in_tool_shed and not is_new and trans.user and repository.user != trans.user + can_view_change_log = in_tool_shed and not is_new + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' +%> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/community/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="render_workflow( repository_metadata_id, workflow_name, webapp )"> + <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp ) %> + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> +</%def> + +<br/><br/> +<ul class="manage-table-actions"> + %if in_tool_shed: + %if is_new and can_upload: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + %else: + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + %if can_upload: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + %endif + %if can_manage: + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + %else: + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + %endif + %if can_view_change_log: + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + %endif + %if can_rate: + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> + %endif + %if can_browse_contents: + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + %endif + %if can_contact_owner: + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + %endif + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> + %endif + </div> + %endif + %else: + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">Import workflow to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install repository to local Galaxy</a></li> + </div> + <li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="toolshed-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div> + %endif +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<br/> +<b>Boxes are red when tools are not available in this repository</b> +<div class="toolParamHelp" style="clear: both;"> + (this page displays SVG graphics) +</div> +<br clear="left"/> + +${render_workflow( repository_metadata_id, workflow_name, webapp )} diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec templates/workflow/display.mako --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -1,7 +1,7 @@ <%inherit file="/display_base.mako"/><%namespace file="/display_common.mako" import="render_message" /> -<%! +<% from galaxy.tools.parameters import DataToolParameter, RuntimeValue from galaxy.web import form_builder %> @@ -82,7 +82,17 @@ %for i, step in enumerate( steps ): <tr><td> %if step.type == 'tool' or step.type is None: - <% tool = app.toolbox.tools_by_id[step.tool_id] %> + <% + try: + tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + except KeyError, e: + # The id value of tools installed from a Galaxy tool shed is a guid, but + # these tool's old_id attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if step.tool_id == available_tool.old_id: + tool = available_tool + break + %><div class="toolForm"><div class="toolFormTitle">Step ${int(step.order_index)+1}: ${tool.name}</div><div class="toolFormBody"> diff -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa -r 0ba260ea43c4e9613965e9f32705a118bab7c3ec templates/workflow/run.mako --- a/templates/workflow/run.mako +++ b/templates/workflow/run.mako @@ -363,7 +363,17 @@ %endif %for i, step in enumerate( steps ): %if step.type == 'tool' or step.type is None: - <% tool = app.toolbox.tools_by_id[step.tool_id] %> + <% + try: + tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + except KeyError, e: + # The id value of tools installed from a Galaxy tool shed is a guid, but + # these tool's old_id attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if step.tool_id == available_tool.old_id: + tool = available_tool + break + %><input type="hidden" name="${step.id}|tool_state" value="${step.state.encode( tool, app )}"><div class="toolForm"><div class="toolFormTitle"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Allow Picard based Merge BAM Files tool to work on sam inputs as well as the previously accepted bam.
by Bitbucket 26 Oct '11

26 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/37fb9b1fb62d/ changeset: 37fb9b1fb62d user: dan date: 2011-10-26 22:03:47 summary: Allow Picard based Merge BAM Files tool to work on sam inputs as well as the previously accepted bam. affected #: 1 file diff -r f335b8bbb91f575f1ffac466c53b907e8623a9a8 -r 37fb9b1fb62de6a304c6c500d9610b7eea2cf2aa tools/samtools/sam_merge.xml --- a/tools/samtools/sam_merge.xml +++ b/tools/samtools/sam_merge.xml @@ -16,10 +16,10 @@ <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file" truevalue="true" falsevalue="false" checked="yes" help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" /> - <param name="input1" label="First file" type="data" format="bam" /> - <param name="input2" label="with file" type="data" format="bam" help="Need to add more files? Use controls below." /> + <param name="input1" label="First file" type="data" format="bam,sam" /> + <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." /><repeat name="inputs" title="Input Files"> - <param name="input" label="Add file" type="data" format="bam" /> + <param name="input" label="Add file" type="data" format="bam,sam" /></repeat></inputs><outputs> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: "Merge BAM Files" under SAM Tools section(???) calls Picard MergeSamFiles.jar. Update to new jar location.
by Bitbucket 26 Oct '11

26 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f335b8bbb91f/ changeset: f335b8bbb91f user: dan date: 2011-10-26 19:35:17 summary: "Merge BAM Files" under SAM Tools section(???) calls Picard MergeSamFiles.jar. Update to new jar location. affected #: 1 file diff -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d -r f335b8bbb91f575f1ffac466c53b907e8623a9a8 tools/samtools/sam_merge.xml --- a/tools/samtools/sam_merge.xml +++ b/tools/samtools/sam_merge.xml @@ -4,7 +4,7 @@ <requirement type="package">picard</requirement></requirements><command> -java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 +java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 #for $i in $inputs I=${i.input} #end for @@ -36,7 +36,7 @@ <param name="input1" value="sam_merge_in1.bam" ftype="bam" /><param name="input2" value="sam_merge_in2.bam" ftype="bam" /><output name="output1" file="sam_merge_out1.bam" ftype="bam" /> - <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="10"/> + <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/></test><test><param name="title" value="test2" /> @@ -45,7 +45,7 @@ <param name="input2" value="sam_merge_in2.bam" ftype="bam" /><param name="input" value="sam_merge_in3.bam" ftype="bam" /><output name="output1" file="sam_merge_out2.bam" ftype="bam" /> - <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="10"/> + <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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