May 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Display line errors in data table registry display encountered when loading a location file.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d963b05c497c/ Changeset: d963b05c497c User: dan Date: 2014-05-13 22:10:27 Summary: Display line errors in data table registry display encountered when loading a location file. Affected #: 2 files diff -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 -r d963b05c497cc17d36a16696077e5a0f3158e52b lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -285,8 +285,9 @@ filename = corrected_filename found = True + errors = [] if found: - self.data.extend( self.parse_file_fields( open( filename ) ) ) + self.data.extend( self.parse_file_fields( open( filename ), errors=errors ) ) self._update_version() else: self.missing_index_file = filename @@ -294,7 +295,7 @@ if filename not in self.filenames or not self.filenames[ filename ][ 'found' ]: self.filenames[ filename ] = dict( found=found, filename=filename, from_shed_config=from_shed_config, tool_data_path=tool_data_path, - config_element=config_element, tool_shed_repository=repo_info ) + config_element=config_element, tool_shed_repository=repo_info, errors=errors ) else: log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() ) @@ -353,7 +354,7 @@ if 'name' not in self.columns: self.columns['name'] = self.columns['value'] - def parse_file_fields( self, reader ): + def parse_file_fields( self, reader, errors=None ): """ Parse separated lines from file and return a list of tuples. @@ -371,9 +372,10 @@ if self.largest_index < len( fields ): rval.append( fields ) else: - log.warn( "Line %i in tool data table '%s' is invalid (HINT: " - "'%s' characters must be used to separate fields):\n%s" - % ( ( i + 1 ), self.name, separator_char, line ) ) + line_error = "Line %i in tool data table '%s' is invalid (HINT: '%s' characters must be used to separate fields):\n%s" % ( ( i + 1 ), self.name, separator_char, line ) + if errors is not None: + errors.append( line_error ) + log.warn( line_error ) return rval def get_column_name_list( self ): diff -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 -r d963b05c497cc17d36a16696077e5a0f3158e52b templates/admin/view_data_tables_registry.mako --- a/templates/admin/view_data_tables_registry.mako +++ b/templates/admin/view_data_tables_registry.mako @@ -18,7 +18,7 @@ <th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Filename</th><th bgcolor="#D8D8D8">Tool data path</th> - <th bgcolor="#D8D8D8">Missing index file</th> + <th bgcolor="#D8D8D8">Errors</th></tr> %for data_table_elem_name, data_table in sorted_data_tables: %if ctr % 2 == 1: @@ -35,8 +35,11 @@ <td>${ file_dict.get( 'tool_data_path' ) | h }</td><td> %if not file_dict.get( 'found' ): - missing + file missing %endif + %for error in file_dict.get( 'errors', [] ): + ${ error | h } <br/> + %endfor </td></tr> %endfor 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: More Data Manager UI fixes. Fix for viewing data manager job info when dataset has been deleted.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d0ab4f31e0e0/ Changeset: d0ab4f31e0e0 User: dan Date: 2014-05-13 21:47:54 Summary: More Data Manager UI fixes. Fix for viewing data manager job info when dataset has been deleted. Affected #: 5 files diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -55,13 +55,18 @@ data_manager = trans.app.data_managers.get_manager( data_manager_id ) hdas = [ assoc.dataset for assoc in job.get_output_datasets() ] data_manager_output = [] + error_messages = [] for hda in hdas: - data_manager_json = from_json_string( open( hda.get_file_name() ).read() ) + try: + data_manager_json = from_json_string( open( hda.get_file_name() ).read() ) + except Exception, e: + data_manager_json = {} + error_messages.append( "Unable to obtain data_table info for hda (%s): %s" % ( hda.id, e ) ) values = [] for key, value in data_manager_json.get( 'data_tables', {} ).iteritems(): values.append( ( key, value ) ) data_manager_output.append( values ) - return trans.fill_template( "data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status ) + return trans.fill_template( "data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status, error_messages=error_messages ) @web.expose def manage_data_table( self, trans, **kwd ): diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 templates/webapps/galaxy/data_manager/index.mako --- a/templates/webapps/galaxy/data_manager/index.mako +++ b/templates/webapps/galaxy/data_manager/index.mako @@ -51,11 +51,10 @@ <li><a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main"> %if table_name in managed_table_names: - <strong>${ table_name | h }</strong> + </span><strong>${ table_name | h }</strong></a><span class="fa fa-exchange"> %else: - ${ table_name | h } + ${ table_name | h }</a> %endif - </a></li><p/> %endfor diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 templates/webapps/galaxy/data_manager/manage_data_manager.mako --- a/templates/webapps/galaxy/data_manager/manage_data_manager.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_manager.mako @@ -28,7 +28,11 @@ <td>PID/Cluster ID</td></tr> %for job in jobs: - <td><a class="icon-btn" href="${ h.url_for( controller="data_manager", action="view_job", id=trans.security.encode_id( job.id ) ) }" title="View info"><span class="fa fa-info"></span></a></td> + <td> + <div class="icon-btn-group"> + <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="view_job", id=trans.security.encode_id( job.id ) ) }" title="View info"><span class="fa fa-info-circle"></span></a><a class="icon-btn" href="${ h.url_for( controller="tool_runner", action="rerun", job_id=trans.security.encode_id( job.id ) ) }" title="Rerun"><span class="fa fa-refresh"></span></a> + </div> + </td><td>${ job.id | h }</td> %if job.history and job.history.user: <td>${job.history.user.email | h}</td> diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 templates/webapps/galaxy/data_manager/manage_data_table.mako --- a/templates/webapps/galaxy/data_manager/manage_data_table.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_table.mako @@ -1,7 +1,7 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%def name="title()">Data Table Manager: ${ data_table.name | h }</%def> +<%def name="title()">Tool Data Table: ${ data_table.name | h }</%def> %if message: ${render_msg( message, status )} diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 templates/webapps/galaxy/data_manager/view_job.mako --- a/templates/webapps/galaxy/data_manager/view_job.mako +++ b/templates/webapps/galaxy/data_manager/view_job.mako @@ -8,6 +8,12 @@ ${render_msg( message, status )} %endif +%if error_messages: + %for error_message in error_messages: + ${ render_msg( error_message, 'error' ) } + %endfor +%endif + %if view_only: <p>Not implemented</p> %else: @@ -15,7 +21,7 @@ <table class="tabletip"><thead><tr><th colspan="2" style="font-size: 120%;"> - Data Manager: ${ data_manager.name | h } - ${ data_manager.description | h } + Data Manager: <a href="${ h.url_for( controller='tool_runner', action='index', tool_id=data_manager.tool.id ) }">${ data_manager.name | h }</a> - ${ data_manager.description | h } <a class="icon-btn" href="${ h.url_for( controller="tool_runner", action="rerun", job_id=trans.security.encode_id( job.id ) ) }" title="Rerun" data-placement="bottom"><span class="fa fa-refresh"></span></a></th></tr></thead><tbody> 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 tool_runner rerun to accept a job_id instead of a dataset_id.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc74a95853b6/ Changeset: dc74a95853b6 User: dan Date: 2014-05-13 21:12:25 Summary: Allow tool_runner rerun to accept a job_id instead of a dataset_id. Affected #: 1 file diff -r f7de39159497fbcffb3f0ed785f26ecf56b40155 -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -106,33 +106,41 @@ **vars ) @web.expose - def rerun( self, trans, id=None, from_noframe=None, **kwd ): + def rerun( self, trans, id=None, from_noframe=None, job_id=None, **kwd ): """ Given a HistoryDatasetAssociation id, find the job and that created the dataset, extract the parameters, and display the appropriate tool form with parameters already filled in. """ - if not id: - error( "'id' parameter is required" ); - try: - id = int( id ) - - except: - # it's not an un-encoded id, try to parse as encoded + if job_id: try: - id = trans.security.decode_id( id ) + job_id = trans.security.decode_id( job_id ) + job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) except: - error( "Invalid value for 'id' parameter" ) - - # Get the dataset object - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id ) - #only allow rerunning if user is allowed access to the dataset. - if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ): - error( "You are not allowed to access this dataset" ) - # Get the associated job, if any. - job = data.creating_job - if not job: - raise Exception("Failed to get job information for dataset hid %d" % data.hid) + error( "Invalid value for 'job_id' parameter" ) + param_error_text = "Failed to get parameters for job id %d " % job_id + else: + if not id: + error( "'id' parameter is required" ); + try: + id = int( id ) + except: + # it's not an un-encoded id, try to parse as encoded + try: + id = trans.security.decode_id( id ) + except: + error( "Invalid value for 'id' parameter" ) + + # Get the dataset object + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id ) + #only allow rerunning if user is allowed access to the dataset. + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ): + error( "You are not allowed to access this dataset" ) + # Get the associated job, if any. + job = data.creating_job + if not job: + raise Exception("Failed to get job information for dataset hid %d" % data.hid) + param_error_text = "Failed to get parameters for dataset id %d " % data.id # Get the tool object tool_id = job.tool_id tool_version = job.tool_version @@ -172,7 +180,7 @@ try: params_objects = job.get_param_values( trans.app, ignore_errors = True ) except: - raise Exception( "Failed to get parameters for dataset id %d " % data.id ) + raise Exception( param_error_text ) upgrade_messages = tool.check_and_update_param_values( params_objects, trans, update_values=False ) # Need to remap dataset parameters. Job parameters point to original # dataset used; parameter should be the analygous dataset in the 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: More Data Manager UI tweaks.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7de39159497/ Changeset: f7de39159497 User: dan Date: 2014-05-13 20:34:57 Summary: More Data Manager UI tweaks. Affected #: 1 file diff -r 1c913c980053c4ce2dc6425cdf102298488242ec -r f7de39159497fbcffb3f0ed785f26ecf56b40155 templates/webapps/galaxy/data_manager/index.mako --- a/templates/webapps/galaxy/data_manager/index.mako +++ b/templates/webapps/galaxy/data_manager/index.mako @@ -12,11 +12,11 @@ %if view_only: <p>Not implemented</p> %elif not data_managers.data_managers: - ${render_msg( "You do not currently have any Data Managers installed.", "warning" ) } + ${ render_msg( 'You do not currently have any Data Managers installed. You can install some from a <a href="%s">ToolShed</a>.' % ( h.url_for( controller="admin_toolshed", action="browse_tool_sheds" ) ), "warning" ) } %else: - <p>Choose your data managing option from below.</p> + <p>Choose your data managing option from below. You may install additional Data Managers from a <a href="${ h.url_for( controller='admin_toolshed', action='browse_tool_sheds' ) }">ToolShed</a>.</p><ul> - <li><strong>Run Data Manager Tools</strong> + <li><h3>Run Data Manager Tools</h3><div style="margin-left:1em"><ul> %for data_manager_id, data_manager in sorted( data_managers.data_managers.iteritems(), key=lambda x:x[1].name ): @@ -29,12 +29,12 @@ </div></li><p/> - <li><strong>View Data Manager Jobs</strong> + <li><h3>View Data Manager Jobs</h3><div style="margin-left:1em"><ul> %for data_manager_id, data_manager in sorted( data_managers.data_managers.iteritems(), key=lambda x:x[1].name ): <li> - <a href="${h.url_for( controller='data_manager', action='manage_data_manager', id=data_manager_id)}" target="galaxy_main"><strong>${ data_manager.name | h }</strong></a> - ${ data_manager.description | h }</a> + <a href="${ h.url_for( controller='data_manager', action='manage_data_manager', id=data_manager_id)}" target="galaxy_main"><strong>${ data_manager.name | h }</strong></a> - ${ data_manager.description | h }</a></li><p/> %endfor @@ -43,7 +43,7 @@ </li><p/><p/> - <li><strong>View Tool Data Table Entries</strong> + <li><h3>View Tool Data Table Entries</h3><div style="margin-left:1em"><ul><% managed_table_names = data_managers.managed_data_tables.keys() %> 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: Alphabetize lists of Data Manager elements on index page.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1c913c980053/ Changeset: 1c913c980053 User: dan Date: 2014-05-13 20:21:08 Summary: Alphabetize lists of Data Manager elements on index page. Affected #: 1 file diff -r a5a7edbe49055c328960eaa5c622a62ecf83b27d -r 1c913c980053c4ce2dc6425cdf102298488242ec templates/webapps/galaxy/data_manager/index.mako --- a/templates/webapps/galaxy/data_manager/index.mako +++ b/templates/webapps/galaxy/data_manager/index.mako @@ -19,7 +19,7 @@ <li><strong>Run Data Manager Tools</strong><div style="margin-left:1em"><ul> - %for data_manager_id, data_manager in data_managers.data_managers.iteritems(): + %for data_manager_id, data_manager in sorted( data_managers.data_managers.iteritems(), key=lambda x:x[1].name ): <li><a href="${ h.url_for( controller='tool_runner', action='index', tool_id=data_manager.tool.id ) }"><strong>${ data_manager.name | h }</strong></a> - ${ data_manager.description | h } </li> @@ -32,7 +32,7 @@ <li><strong>View Data Manager Jobs</strong><div style="margin-left:1em"><ul> - %for data_manager_id, data_manager in data_managers.data_managers.iteritems(): + %for data_manager_id, data_manager in sorted( data_managers.data_managers.iteritems(), key=lambda x:x[1].name ): <li><a href="${h.url_for( controller='data_manager', action='manage_data_manager', id=data_manager_id)}" target="galaxy_main"><strong>${ data_manager.name | h }</strong></a> - ${ data_manager.description | h }</a></li> @@ -46,20 +46,19 @@ <li><strong>View Tool Data Table Entries</strong><div style="margin-left:1em"><ul> - %for table_name, managers in data_managers.managed_data_tables.iteritems(): + <% managed_table_names = data_managers.managed_data_tables.keys() %> + %for table_name in sorted( tool_data_tables.get_tables().keys() ): <li> - <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main"><strong>${ table_name | h }</strong></a> + <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main"> + %if table_name in managed_table_names: + <strong>${ table_name | h }</strong> + %else: + ${ table_name | h } + %endif + </a></li><p/> %endfor - %for table_name in tool_data_tables.get_tables(): - %if table_name not in data_managers.managed_data_tables: - <li> - <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main">${ table_name | h }</a> - </li> - <p/> - %endif - %endfor </ul></div></li> 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: Data Manager UI enhancements.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a5a7edbe4905/ Changeset: a5a7edbe4905 User: dan Date: 2014-05-13 20:07:07 Summary: Data Manager UI enhancements. Affected #: 5 files diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -19,7 +19,7 @@ raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) message = kwd.get( 'message' ) status = kwd.get( 'status', 'info' ) - return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, view_only=not_is_admin, message=message, status=status ) + return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, tool_data_tables=trans.app.tool_data_tables, view_only=not_is_admin, message=message, status=status ) @web.expose def manage_data_manager( self, trans, **kwd ): @@ -32,7 +32,7 @@ data_manager = trans.app.data_managers.get_manager( data_manager_id ) if data_manager is None: return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data Manager (%s) was requested" % data_manager_id, status="error" ) ) - jobs = reversed( [ assoc.job for assoc in trans.sa_session.query( trans.app.model.DataManagerJobAssociation ).filter_by( data_manager_id=data_manager_id ) ] ) + jobs = list( reversed( [ assoc.job for assoc in trans.sa_session.query( trans.app.model.DataManagerJobAssociation ).filter_by( data_manager_id=data_manager_id ) ] ) ) return trans.fill_template( "data_manager/manage_data_manager.mako", data_manager=data_manager, jobs=jobs, view_only=not_is_admin, message=message, status=status ) @web.expose diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d templates/webapps/galaxy/data_manager/index.mako --- a/templates/webapps/galaxy/data_manager/index.mako +++ b/templates/webapps/galaxy/data_manager/index.mako @@ -11,11 +11,13 @@ %if view_only: <p>Not implemented</p> +%elif not data_managers.data_managers: + ${render_msg( "You do not currently have any Data Managers installed.", "warning" ) } %else: <p>Choose your data managing option from below.</p><ul> - <li><strong>Access data managers</strong> - get data, build indexes, etc - <p/> + <li><strong>Run Data Manager Tools</strong> + <div style="margin-left:1em"><ul> %for data_manager_id, data_manager in data_managers.data_managers.iteritems(): <li> @@ -24,10 +26,11 @@ <p/> %endfor </ul> + </div></li><p/> - <li><strong>View managed data by manager</strong> - <p/> + <li><strong>View Data Manager Jobs</strong> + <div style="margin-left:1em"><ul> %for data_manager_id, data_manager in data_managers.data_managers.iteritems(): <li> @@ -36,11 +39,12 @@ <p/> %endfor </ul> + </div></li><p/><p/> - <li><strong>View managed data by Tool Data Table</strong> - <p/> + <li><strong>View Tool Data Table Entries</strong> + <div style="margin-left:1em"><ul> %for table_name, managers in data_managers.managed_data_tables.iteritems(): <li> @@ -48,10 +52,21 @@ </li><p/> %endfor + %for table_name in tool_data_tables.get_tables(): + %if table_name not in data_managers.managed_data_tables: + <li> + <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main">${ table_name | h }</a> + </li> + <p/> + %endif + %endfor </ul> + </div></li><p/></ul><p/><br/> %endif + +${render_msg( 'To find out more information about Data Managers, please visit the <a href="https://wiki.galaxyproject.org/Admin/Tools/DataManagers" target="_blank">wiki.</a>', "info" ) } diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d templates/webapps/galaxy/data_manager/manage_data_manager.mako --- a/templates/webapps/galaxy/data_manager/manage_data_manager.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_manager.mako @@ -18,6 +18,7 @@ <div><table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"><tr class="header"> + <td>Actions</td><td>Job ID</td><td>User</td><td>Last Update</td> @@ -27,7 +28,8 @@ <td>PID/Cluster ID</td></tr> %for job in jobs: - <td><a href="${ h.url_for( controller="data_manager", action="view_job", id=trans.security.encode_id( job.id ) ) }">${ job.id | h }</a></td> + <td><a class="icon-btn" href="${ h.url_for( controller="data_manager", action="view_job", id=trans.security.encode_id( job.id ) ) }" title="View info"><span class="fa fa-info"></span></a></td> + <td>${ job.id | h }</td> %if job.history and job.history.user: <td>${job.history.user.email | h}</td> %else: diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d templates/webapps/galaxy/data_manager/manage_data_table.mako --- a/templates/webapps/galaxy/data_manager/manage_data_table.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_table.mako @@ -10,30 +10,36 @@ %if view_only: <p>Not implemented</p> %else: -<% column_name_list = data_table.get_column_name_list() %> -<table class="tabletip"> - <thead> - <tr><th colspan="${len (column_name_list) }" style="font-size: 120%;"> - Data Manager: ${ data_table.name | h } - <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name} tool data table" data-placement="bottom"> - <span class="fa fa-refresh"></span> - </a> - </th></tr> - <tr> - - %for name in column_name_list: - <th>${name | h}</th> - %endfor - </tr> - </thead> - <tbody> - %for table_row in data_table.data: - <tr> - %for field in table_row: - <td>${field | h}</td> - %endfor - </tr> - %endfor -</table> + <p> + <% column_name_list = data_table.get_column_name_list() %> + <table class="tabletip"> + <thead> + <tr><th colspan="${len (column_name_list) }" style="font-size: 120%;"> + Data Manager: ${ data_table.name | h } + <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name} tool data table" data-placement="bottom"> + <span class="fa fa-refresh"></span> + </a> + </th></tr> + <tr> + + %for name in column_name_list: + <th>${name | h}</th> + %endfor + </tr> + </thead> + <tbody> + %for table_row in data_table.data: + <tr> + %for field in table_row: + <td>${field | h}</td> + %endfor + </tr> + %endfor + </tbody> + </table> + </p> + %if not data_table.data: + ${render_msg( "There are currently no entries in this Tool Data Table.", "warning" ) } + %endif %endif diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r a5a7edbe49055c328960eaa5c622a62ecf83b27d templates/webapps/galaxy/data_manager/view_job.mako --- a/templates/webapps/galaxy/data_manager/view_job.mako +++ b/templates/webapps/galaxy/data_manager/view_job.mako @@ -34,7 +34,7 @@ <table class="tabletip"><thead><tr><th colspan="2" style="font-size: 120%;"> - Data Table: ${ table_name | h } + Data Table: <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}">${ table_name | h }</a></th></tr></thead><% len_json_table = len( json_table ) %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add the ability for Admins to reload tool data table entries from disk without restarting the Galaxy server. This does not look for new <table> entries or contained new <file>s within XML files, but will e.g. make any changes to a .loc file become live immediately without restart.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e5b545b85b83/ Changeset: e5b545b85b83 User: dan Date: 2014-05-13 19:01:47 Summary: Add the ability for Admins to reload tool data table entries from disk without restarting the Galaxy server. This does not look for new <table> entries or contained new <file>s within XML files, but will e.g. make any changes to a .loc file become live immediately without restart. Affected #: 3 files diff -r c74989f7cafe0605af12af8dc2303689fa674bde -r e5b545b85b836b6f1be76164543d7e4613f25d87 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -141,6 +141,18 @@ out.write( '</tables>\n' ) os.chmod( full_path, 0644 ) + def reload_tables( self, table_names=None ): + tables = self.get_tables() + if not table_names: + table_names = tables.keys() + elif not isinstance( table_names, list ): + table_names = [ table_names ] + for table_name in table_names: + tables[ table_name ].reload_from_files() + log.debug( "Reloaded tool data table '%s' from files.", table_name ) + return table_names + + class ToolDataTable( object ): @classmethod @@ -160,9 +172,14 @@ # increment this variable any time a new entry is added, or when the table is totally reloaded # This value has no external meaning, and does not represent an abstract version of the underlying data self._loaded_content_version = 1 + self._load_info = ( [ config_element, tool_data_path ], { 'from_shed_config':from_shed_config } ) + self._merged_load_info = [] - def _update_version( self ): - self._loaded_content_version += 1 + def _update_version( self, version=None ): + if version is not None: + self._loaded_content_version = version + else: + self._loaded_content_version += 1 return self._loaded_content_version def get_empty_field_by_name( self, name ): @@ -187,6 +204,16 @@ def merge_tool_data_table( self, other_table, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): raise NotImplementedError( "Abstract method" ) + def reload_from_files( self ): + new_version = self._update_version() + merged_info = self._merged_load_info + self.__init__( *self._load_info[0], **self._load_info[1] ) + self._update_version( version=new_version ) + for ( tool_data_table_class, load_info ) in merged_info: + self.merge_tool_data_table( tool_data_table_class( *load_info[0], **load_info[1] ), allow_duplicates=False ) + return self._update_version() + + class TabularToolDataTable( ToolDataTable ): """ Data stored in a tabular / separated value format on disk, allows multiple @@ -278,6 +305,8 @@ for filename, info in other_table.filenames.iteritems(): if filename not in self.filenames: self.filenames[ filename ] = info + #save info about table + self._merged_load_info.append( ( other_table.__class__, other_table._load_info ) ) #add data entries and return current data table version return self.add_entries( other_table.data, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd ) diff -r c74989f7cafe0605af12af8dc2303689fa674bde -r e5b545b85b836b6f1be76164543d7e4613f25d87 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -77,3 +77,33 @@ if data_table is None: return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data table (%s) was requested" % data_table_name, status="error" ) ) return trans.fill_template( "data_manager/manage_data_table.mako", data_table=data_table, view_only=not_is_admin, message=message, status=status ) + + @web.expose + @web.require_admin + def reload_tool_data_tables( self, trans, table_name=None, **kwd ): + if table_name and isinstance( table_name, basestring ): + table_name = table_name.split( "," ) + # Reload the tool data tables + table_names = self.app.tool_data_tables.reload_tables( table_names=table_name ) + redirect_url = None + if table_names: + status = 'done' + if len( table_names ) == 1: + message = "The data table '%s' has been reloaded." % table_names[0] + redirect_url = web.url_for( controller='data_manager', + action='manage_data_table', + table_name=table_names[0], + message=message, + status=status ) + else: + message = "The data tables '%s' have been reloaded." % ', '.join( table_names ) + else: + message = "No data tables have been reloaded." + status = 'error' + if redirect_url is None: + redirect_url = web.url_for( controller='admin', + action='view_tool_data_tables', + message=message, + status=status ) + return trans.response.send_redirect( redirect_url ) + diff -r c74989f7cafe0605af12af8dc2303689fa674bde -r e5b545b85b836b6f1be76164543d7e4613f25d87 templates/webapps/galaxy/data_manager/manage_data_table.mako --- a/templates/webapps/galaxy/data_manager/manage_data_table.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_table.mako @@ -15,6 +15,9 @@ <thead><tr><th colspan="${len (column_name_list) }" style="font-size: 120%;"> Data Manager: ${ data_table.name | h } + <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name} tool data table" data-placement="bottom"> + <span class="fa fa-refresh"></span> + </a></th></tr><tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: When viewing tool data table registry in admin interface, provide link to manage data table interface for each tool data table.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c74989f7cafe/ Changeset: c74989f7cafe User: dan Date: 2014-05-13 18:35:35 Summary: When viewing tool data table registry in admin interface, provide link to manage data table interface for each tool data table. Affected #: 1 file diff -r a4bdf116d532cf18560ed2a4f1b94e84d7d9cc8b -r c74989f7cafe0605af12af8dc2303689fa674bde templates/admin/view_data_tables_registry.mako --- a/templates/admin/view_data_tables_registry.mako +++ b/templates/admin/view_data_tables_registry.mako @@ -26,7 +26,7 @@ %else: <tr class="tr"> %endif - <td>${data_table.name}</td> + <td><a href="${ h.url_for( controller="data_manager", action="manage_data_table", table_name=data_table.name ) }">${data_table.name}</a></td> %for i, ( filename, file_dict ) in enumerate( data_table.filenames.iteritems() ): %if i > 0: <tr><td></td> 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: 2 new changesets
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e13610643216/ Changeset: e13610643216 User: jmchilton Date: 2014-05-13 17:20:06 Summary: Remove no longer valid log message. Affected #: 1 file diff -r 953baebbd9d9f7757691b73eee3bc954570b2bbd -r e13610643216c4d59b41722516e9d4aa9b4466b8 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -210,7 +210,6 @@ destination = job_wrapper.get_output_destination( output_paths[ dataset.dataset_id ] ) if in_directory( source_file, job_working_directory ): output_pairs.append( ( source_file, destination ) ) - log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) ) else: # Security violation. log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) https://bitbucket.org/galaxy/galaxy-central/commits/a4bdf116d532/ Changeset: a4bdf116d532 User: jmchilton Date: 2014-05-13 17:20:06 Summary: Optimize/correct LWR remote metadata generation for working directory outputs. Previously I was attempting to mimic Galaxy's behavior of copying these files to a fixed output location after execution on the remote server before setting metadata. This was an un-needed copy since it appears to easier to just send the metadata generation code the expected path on the working directory. Affected #: 1 file diff -r e13610643216c4d59b41722516e9d4aa9b4466b8 -r a4bdf116d532cf18560ed2a4f1b94e84d7d9cc8b lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -172,7 +172,6 @@ job_wrapper.prepare( **prepare_kwds ) self.__prepare_input_files_locally(job_wrapper) remote_metadata = LwrJobRunner.__remote_metadata( client ) - remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) dependency_resolution = LwrJobRunner.__dependency_resolution( client ) metadata_kwds = self.__build_metadata_configuration(client, job_wrapper, remote_metadata, remote_job_config) remote_command_params = dict( @@ -184,7 +183,7 @@ self, job_wrapper=job_wrapper, include_metadata=remote_metadata, - include_work_dir_outputs=remote_work_dir_copy, + include_work_dir_outputs=False, remote_command_params=remote_command_params, ) except Exception: @@ -358,13 +357,7 @@ self.client_manager.shutdown() def __client_outputs( self, client, job_wrapper ): - remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) - if not remote_work_dir_copy: - work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) - else: - # They have already been copied over to look like regular outputs remotely, - # no need to handle them differently here. - work_dir_outputs = [] + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) output_files = self.get_output_files( job_wrapper ) client_outputs = ClientOutputs( working_directory=job_wrapper.working_directory, @@ -400,16 +393,6 @@ return remote_metadata @staticmethod - def __remote_work_dir_copy( lwr_client ): - # Right now remote metadata handling assumes from_work_dir outputs - # have been copied over before it runs. So do that remotely. This is - # not the default though because adding it to the command line is not - # cross-platform (no cp on Windows) and it's un-needed work outside - # the context of metadata settting (just as easy to download from - # either place.) - return LwrJobRunner.__remote_metadata( lwr_client ) - - @staticmethod def __use_remote_datatypes_conf( lwr_client ): """ When setting remote metadata, use integrated datatypes from this Galaxy instance or use the datatypes config configured via the remote @@ -440,7 +423,21 @@ outputs_directory = remote_job_config['outputs_directory'] configs_directory = remote_job_config['configs_directory'] working_directory = remote_job_config['working_directory'] + # For metadata calculation, we need to build a list of of output + # file objects with real path indicating location on Galaxy server + # and false path indicating location on compute server. Since the + # LWR disables from_work_dir copying as part of the job command + # line we need to take the list of output locations on the LWR + # server (produced by self.get_output_files(job_wrapper)) and for + # each work_dir output substitute the effective path on the LWR + # server relative to the remote working directory as the + # false_path to send the metadata command generation module. + work_dir_outputs = self.get_work_dir_outputs(job_wrapper, job_working_directory=working_directory) outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)] + for output in outputs: + for lwr_workdir_path, real_path in work_dir_outputs: + if real_path == output.real_path: + output.false_path = lwr_workdir_path metadata_kwds['output_fnames'] = outputs metadata_kwds['compute_tmp_dir'] = working_directory metadata_kwds['config_root'] = remote_galaxy_home Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Ensure new_file_path exists before set_metadata.py generates metadata.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/953baebbd9d9/ Changeset: 953baebbd9d9 User: jmchilton Date: 2014-05-13 16:29:41 Summary: Ensure new_file_path exists before set_metadata.py generates metadata. This directory is required to exist but usually unneeded because Galaxy creates this directory on startup. However, when setting metadata remotely with the LWR that remote Galaxy instance may have never been started and this directory may not exist. Affected #: 2 files diff -r f5f6cd1e938304094c9491da10824f93cbfb2d27 -r 953baebbd9d9f7757691b73eee3bc954570b2bbd lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -417,6 +417,16 @@ else: return default + def ensure_tempdir( self ): + self._ensure_directory( self.new_file_path ) + + def _ensure_directory( self, path ): + if path not in [ None, False ] and not os.path.isdir( path ): + try: + os.makedirs( path ) + except Exception, e: + raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) + def check( self ): paths_to_check = [ self.root, self.tool_path, self.tool_data_path, self.template_path ] # Check that required directories exist @@ -440,11 +450,7 @@ self.whoosh_index_dir, \ self.object_store_cache_path, \ os.path.join( self.tool_data_path, 'shared', 'jars' ): - if path not in [ None, False ] and not os.path.isdir( path ): - try: - os.makedirs( path ) - except Exception, e: - raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) + self._ensure_directory( path ) # Check that required files exist tool_configs = self.tool_configs if self.migrated_tools_config not in tool_configs: diff -r f5f6cd1e938304094c9491da10824f93cbfb2d27 -r 953baebbd9d9f7757691b73eee3bc954570b2bbd scripts/set_metadata.py --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -66,6 +66,7 @@ log.debug("Did not load option %s from %s" % (option, config_file_name)) # config object is required by ObjectStore class so create it now universe_config = config.Configuration(**conf_dict) + universe_config.ensure_tempdir() object_store = build_object_store_from_config(universe_config) galaxy.model.Dataset.object_store = object_store 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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