galaxy-commits April 2014

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commit/galaxy-central: jmchilton: More refactoring of tools API test case.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0fee9a84cec6/ Changeset: 0fee9a84cec6 User: jmchilton Date: 2014-04-29 20:53:06 Summary: More refactoring of tools API test case. Affected #: 1 file diff -r 43cf1476a77405f9890a6b97fe9993c2936650a5 -r 0fee9a84cec6dd78774f30bd60ab7d41d2efc619 test/functional/api/test_tools.py --- a/test/functional/api/test_tools.py +++ b/test/functional/api/test_tools.py @@ -82,15 +82,23 @@ self.assertEqual( output1_content.strip(), "Cat1Test\nCat2Test" ) def _cat1_outputs( self, history_id, inputs ): - create_response = self._run_cat1( history_id, inputs ) + return self._run_outputs( self._run_cat1( history_id, inputs ) ) + + def _run_and_get_outputs( self, tool_id, history_id, inputs ): + return self._run_outputs( self._run( tool_id, history_id, inputs ) ) + + def _run_outputs( self, create_response ): self._assert_status_code_is( create_response, 200 ) create = create_response.json() self._assert_has_keys( create, 'outputs' ) return create[ 'outputs' ] def _run_cat1( self, history_id, inputs ): + return self._run( 'cat1', history_id, inputs ) + + def _run( self, tool_id, history_id, inputs ): payload = self.dataset_populator.run_tool_payload( - tool_id='cat1', + tool_id=tool_id, inputs=inputs, history_id=history_id, ) 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: davebgx: Fix sample tracking functional tests.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43cf1476a774/ Changeset: 43cf1476a774 User: davebgx Date: 2014-04-29 19:21:28 Summary: Fix sample tracking functional tests. Affected #: 3 files diff -r b67a59a2beca5072eb19ad7c7e20beb40adda8da -r 43cf1476a77405f9890a6b97fe9993c2936650a5 templates/webapps/galaxy/requests/common/edit_samples.mako --- a/templates/webapps/galaxy/requests/common/edit_samples.mako +++ b/templates/webapps/galaxy/requests/common/edit_samples.mako @@ -78,7 +78,7 @@ grid_header = '<h3>Edit Current Samples of Sequencing Request "%s"</h3>' % request.name %> ${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )} - %if len( sample_operation_select_field.options ) > 1 and not is_unsubmitted: + %if len( sample_operation_select_field.options ) >= 1 and not is_unsubmitted: <div class="form-row" style="background-color:#FAFAFA;"> For selected samples: ${sample_operation_select_field.get_html()} diff -r b67a59a2beca5072eb19ad7c7e20beb40adda8da -r 43cf1476a77405f9890a6b97fe9993c2936650a5 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1633,7 +1633,7 @@ tc.submit( "create_form_button" ) if form_type == "Sequencing Sample Form": tc.submit( "add_layout_grid" ) - tc.fv( "create_form_definition", "grid_layout0", form_layout_name ) + tc.fv( "edit_form_definition", "grid_layout0", form_layout_name ) # if not adding any fields at this time, remove the default empty field if num_fields == 0: tc.submit( "remove_button" ) @@ -1677,9 +1677,9 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) if new_form_name: - tc.fv( "1", "name", new_form_name ) + tc.fv( "edit_form_definition", "name", new_form_name ) if new_form_desc: - tc.fv( "1", "description", new_form_desc ) + tc.fv( "edit_form_definition", "description", new_form_desc ) for i, field_dict in enumerate( field_dicts ): index = i + field_index tc.submit( "add_field_button" ) @@ -1693,18 +1693,18 @@ field_required_value = field_dict[ 'required' ] field_name = "field_name_%i" % index field_name_value = field_dict.get( 'name', '%i_field_name' % index ) - tc.fv( "1", field_label, field_label_value ) - tc.fv( "1", field_help, field_help_value ) - tc.fv( "1", field_required, field_required_value ) - tc.fv( "1", field_name, field_name_value ) + tc.fv( "edit_form_definition", field_label, field_label_value ) + tc.fv( "edit_form_definition", field_help, field_help_value ) + tc.fv( "edit_form_definition", field_required, field_required_value ) + tc.fv( "edit_form_definition", field_name, field_name_value ) if field_type_value.lower() == 'selectfield': # SelectFields require a refresh_on_change self.refresh_form( field_type, field_type_value ) for option_index, option in enumerate( field_dict[ 'selectlist' ] ): tc.submit( "addoption_%i" % index ) - tc.fv( "1", "field_%i_option_%i" % ( index, option_index ), option ) + tc.fv( "edit_form_definition", "field_%i_option_%i" % ( index, option_index ), option ) else: - tc.fv( "1", field_type, field_type_value ) + tc.fv( "edit_form_definition", field_type, field_type_value ) tc.submit( "save_changes_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) @@ -1892,20 +1892,22 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) for sample_index, ( sample_name, target_library_info, sample_field_values ) in enumerate( sample_value_tuples ): - tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) - tc.fv( "1", "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) - self.refresh_form( "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) + tc.fv( "add_samples", "sample_%i_name" % sample_index, sample_name ) + if target_library_info[ 'library' ] is not None: + tc.fv( "add_samples", "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) + self.refresh_form( "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) # check if the folder selectfield has been correctly populated for check_str in folder_options: self.check_page_for_string( check_str ) - tc.fv( "1", "sample_%i_folder_id" % sample_index, target_library_info[ 'folder' ] ) + if target_library_info[ 'folder' ] is not None: + tc.fv( "add_samples", "sample_%i_folder_id" % sample_index, target_library_info[ 'folder' ] ) for field_index, field_value in enumerate( sample_field_values ): - tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) + tc.fv( "add_samples", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) # Do not click on Add sample button when all the sample have been added if sample_index < len( sample_value_tuples ) - 1: tc.submit( "add_sample_button" ) # select the correct form before submitting it - tc.fv( "1", "copy_sample_index", "-1" ) + tc.fv( "add_samples", "copy_sample_index", "-1" ) tc.submit( "save_samples_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) diff -r b67a59a2beca5072eb19ad7c7e20beb40adda8da -r 43cf1476a77405f9890a6b97fe9993c2936650a5 test/functional/test_sample_tracking.py --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -722,7 +722,7 @@ % ( request2.name, request2.states.NEW ) def test_0100_add_samples_to_request( self ): - target_library_info = dict( library='none', folder='none' ) + target_library_info = dict( library=None, folder=None ) # Sample fields - the tuple represents a sample name and a list of sample form field values sample_value_tuples = \ [ ( 'Sample1', target_library_info, [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ), @@ -741,12 +741,10 @@ '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # Submit the request - select_target_library_message = "Select a target data library and folder for a sample before selecting its datasets to transfer from the external service" self.submit_request( cntrller='requests_admin', request_id=self.security.encode_id( request2.id ), request_name=request2.name, - strings_displayed_after_submit=[ select_target_library_message, - 'The sequencing request has been submitted.' ] ) + strings_displayed_after_submit=[ 'The sequencing request has been submitted.' ] ) refresh( request2 ) # Make sure the request is showing in the 'submitted' filter self.check_request_grid( cntrller='requests_admin', @@ -776,7 +774,8 @@ strings_displayed_count = [] strings_displayed_count.append( ( library2.name, len( request1.samples ) ) ) strings_displayed_count.append( ( library2_folder1.name, len( request1.samples ) ) ) - strings_displayed = [ 'Sequencing request "%s"' % name, regular_user1.email, request2.states.SUBMITTED ] + strings_displayed = [ 'Sequencing request "%s"' % request2.name, regular_user1.email, request2.states.SUBMITTED ] + select_target_library_message = "Select a target data library and folder for a sample before selecting its datasets to transfer from the external service" self.view_request( cntrller='requests', request_id=self.security.encode_id( request2.id ), strings_displayed=strings_displayed, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History options: have 'Purge deleted datasets' update the user disk size
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b67a59a2beca/ Changeset: b67a59a2beca User: carlfeberhard Date: 2014-04-29 19:21:56 Summary: History options: have 'Purge deleted datasets' update the user disk size Affected #: 1 file diff -r b526afe822e53ce530fabe94dff683818a33b29a -r b67a59a2beca5072eb19ad7c7e20beb40adda8da templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -17,9 +17,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${tool_menu_javascripts()} - ${h.js( - "utils/LazyDataLoader" - )} </%def><%def name="late_javascripts()"> @@ -95,6 +92,10 @@ "${_("Purge Deleted Datasets")}": function() { if ( confirm( "Really delete all deleted datasets permanently? This cannot be undone." ) ) { galaxy_main.location = "${h.url_for( controller='history', action='purge_deleted_datasets' )}"; + // update the user disk size when the purge page loads + $( '#galaxy_main' ).load( function(){ + Galaxy.user.fetch(); + }) } }, "${_("Show Structure")}": function() { 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: carlfeberhard: History: allow admin to use display_structured w/ id, add display_structured link in history/view, allow switching to a history from history/view
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b526afe822e5/ Changeset: b526afe822e5 User: carlfeberhard Date: 2014-04-29 18:34:07 Summary: History: allow admin to use display_structured w/ id, add display_structured link in history/view, allow switching to a history from history/view Affected #: 2 files diff -r 78a2fa5ee8b82011c09a152c5be5334eb14d8ded -r b526afe822e53ce530fabe94dff683818a33b29a lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -456,7 +456,10 @@ eagerload_all( 'active_datasets.children' ) ).get( id ) assert history - assert history.user and ( history.user.id == trans.user.id ) or ( history.id == trans.history.id ) + #TODO: formalize to trans.show_error + assert ( history.user and ( history.user.id == trans.user.id ) + or ( history.id == trans.history.id ) + or ( trans.user_is_admin() ) ) # Resolve jobs and workflow invocations for the datasets in the history # items is filled with items (hdas, jobs, or workflows) that go at the # top level diff -r 78a2fa5ee8b82011c09a152c5be5334eb14d8ded -r b526afe822e53ce530fabe94dff683818a33b29a templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -72,24 +72,37 @@ ## ---------------------------------------------------------------------------- <%def name="center_panel()"><% + imp_with_deleted_url = h.url_for( controller='history', action='imp', id=history[ 'id' ], all_datasets=True ) + imp_without_deleted_url = h.url_for( controller='history', action='imp', id=history[ 'id' ] ) + + structure_url = h.url_for( controller='history', action='display_structured', id=history[ 'id' ] ) + + switch_to_url = h.url_for( controller='history', action='switch_to_history', hist_id=history[ 'id' ] ) + show_deleted = context.get( 'show_deleted', None ) show_hidden = context.get( 'show_hidden', None ) user_is_owner_json = 'true' if user_is_owner else 'false' show_deleted_json = h.to_json_string( show_deleted ) show_hidden_json = h.to_json_string( show_hidden ) - - imp_with_deleted_url = h.url_for( controller='history', action='imp', id=history['id'], all_datasets=True ) - imp_without_deleted_url = h.url_for( controller='history', action='imp', id=history['id'] ) %><div id="header" class="clear"> - <div id="history-view-controls" class="pull-right"> - %if not user_is_owner and not history[ 'purged' ]: - <button id="import" class="btn btn-default"></button> - %endif - <button id="toggle-deleted" class="btn btn-default"></button> - <button id="toggle-hidden" class="btn btn-default"></button> + <div id="history-view-controls"> + <div class="pull-left"> + %if not history[ 'purged' ]: + %if user_is_owner: + <button id="switch" class="btn btn-default">${ _( 'Switch to this history' ) }</button> + %else: + <button id="import" class="btn btn-default"></button> + %endif + <a id="structure" href="${ structure_url }" class="btn btn-default">${ _( 'Show structure' ) }</a> + %endif + </div> + <div class="pull-right"> + <button id="toggle-deleted" class="btn btn-default"></button> + <button id="toggle-hidden" class="btn btn-default"></button> + </div></div></div> @@ -120,6 +133,18 @@ ] }); + $( '#switch' ).click( function( ev ){ + ##HACK:ity hack hack + ##TODO: remove when out of iframe + var hpanel = Galaxy.currHistoryPanel + || ( top.Galaxy && top.Galaxy.currHistoryPanel )? top.Galaxy.currHistoryPanel : null; + if( hpanel ){ + hpanel.switchToHistory( "${ history[ 'id' ] }" ); + } else { + window.location = "${ switch_to_url }"; + } + }); + $( '#import' ).modeButton({ switchModesOnClick : false, initialMode : "${ 'with_deleted' if show_deleted else 'without_deleted' }", @@ -149,11 +174,7 @@ baseUrl : "${h.url_for( '/static/scripts' )}" })([ 'mvc/user/user-model', panelToUse.location, 'utils/localization' ], function( user, panelMod, _l ){ $(function(){ - window._l = _l; setUpBehaviors(); - if( !Galaxy.currUser ){ - Galaxy.currUser = new user.User( ${h.to_json_string( get_user_json() )} ); - } var panelClass = panelMod[ panelToUse.className ], // history module is already in the dpn chain from the panel. We can re-scope it here. 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: Fix for setting environment paths when using setup_virutalenv.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78a2fa5ee8b8/ Changeset: 78a2fa5ee8b8 User: dan Date: 2014-04-29 18:13:01 Summary: Fix for setting environment paths when using setup_virutalenv. Affected #: 1 file diff -r 9469c1d11af520686d6c0e934146dbdab05995a8 -r 78a2fa5ee8b82011c09a152c5be5334eb14d8ded lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1158,20 +1158,15 @@ full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command ) return_code = install_environment.handle_command( app, tool_dependency, install_dir, full_setup_command ) if return_code: + log.error( "Failed to do setup_virtualenv install, exit code='%s'", return_code ) + # would it be better to try to set env variables anway, instead of returning here? return tool_dependency, None, None - # Use raw strings so that python won't automatically unescape the quotes before passing the command - # to subprocess.Popen. - site_packages_command = \ - r"""%s -c 'import os, sys; print os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages")'""" % \ - os.path.join( venv_directory, "bin", "python" ) - output = install_environment.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) - if output.return_code: - return tool_dependency, None, None - if not os.path.exists( output.stdout ): - log.debug( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) - return tool_dependency, None, None - env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=output.stdout ) + site_packages_directory, site_packages_directory_list = self.__get_site_packages_directory( install_environment, app, tool_dependency, install_dir, python_cmd, venv_directory ) env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) + if site_packages_directory is None: + log.error( "virtualenv's site-packages directory '%s' does not exist", site_packages_directory_list ) + else: + env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=site_packages_directory ) # The caller should check the status of the returned tool_dependency since this function does nothing # with the return_code. return_code = env_file_builder.return_code @@ -1203,6 +1198,34 @@ action_dict[ 'python' ] = action_elem.get( 'python', 'python' ) return action_dict + def __get_site_packages_directory( self, install_environment, app, tool_dependency, install_dir, python_cmd, venv_directory ): + lib_dir = os.path.join( venv_directory, "lib" ) + rval = os.path.join( lib_dir, python_cmd, 'site-packages' ) + site_packages_directory_list = [ rval ] + if os.path.exists( rval ): + return ( rval, site_packages_directory_list ) + for ( dirpath, dirnames, filenames ) in os.walk( lib_dir ): + for dirname in dirnames: + rval = os.path.join( lib_dir, dirname, 'site-packages' ) + site_packages_directory_list.append( rval ) + if os.path.exists( rval ): + return ( rval, site_packages_directory_list ) + break + # fall back to python call to get site packages + # FIXME: This is probably more robust?, but there is currently an issue with handling the output.stdout + # preventing the entire path from being included (it gets truncated) + # Use raw strings so that python won't automatically unescape the quotes before passing the command + # to subprocess.Popen. + for site_packages_command in [ r"""%s -c 'import site; site.getsitepackages()[0]'""" % \ + os.path.join( venv_directory, "bin", "python" ), + r"""%s -c 'import os, sys; print os.path.join( sys.prefix, "lib", "python" + sys.version[:3], "site-packages" )'""" % \ + os.path.join( venv_directory, "bin", "python" ) ]: + output = install_environment.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True ) + site_packages_directory_list.append( output.stdout ) + if not output.return_code and os.path.exists( output.stdout ): + return ( output.stdout, site_packages_directory_list ) + return ( None, site_packages_directory_list ) + class ShellCommand( RecipeStep ): def __init__( self ): 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: carlfeberhard: D'oh: fix to ef8ef4ff2e15
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9469c1d11af5/ Changeset: 9469c1d11af5 User: carlfeberhard Date: 2014-04-29 17:41:22 Summary: D'oh: fix to ef8ef4ff2e15 Affected #: 1 file diff -r ef8ef4ff2e1505660871f49b1cfd680f3e5552da -r 9469c1d11af520686d6c0e934146dbdab05995a8 templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -243,7 +243,7 @@ <span class="light">${ _( 'Library' ) + ':' }</span><span class="bold"><a href="${ h.url_for( controller='library', action='list' ) + '#folders/F' + folder_id }"> - ${ library.name } + ${ folder.name } </a></span></div> 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: carlfeberhard: History, structured: wrap copied HDA's in info about library/history they were copied from
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef8ef4ff2e15/ Changeset: ef8ef4ff2e15 User: carlfeberhard Date: 2014-04-29 17:38:20 Summary: History, structured: wrap copied HDA's in info about library/history they were copied from Affected #: 1 file diff -r 828286e70c05a1fcf0eec5c2b7e8c59f98b879ef -r ef8ef4ff2e1505660871f49b1cfd680f3e5552da templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -9,7 +9,7 @@ body { padding: 5px; } - body > .workflow, body > .toolForm { + body > .workflow, body > .toolForm, body > .copied-from { /*width : 80%;*/ margin-bottom : 8px; /*margin-left : auto;*/ @@ -95,6 +95,18 @@ float: right; } + .copied-from { + border: 1px solid lightgrey; + border-width: 1px 1px 0px 1px; + } + .copied-from .header { + border-bottom: 1px solid lightgrey; + padding: 5px; + } + .copied-from .header .bold, .copied-from .header a { + color: #888; + } + .dataset.hda { min-height : 37px; border-width: 0px 0px 1px 0px; @@ -113,6 +125,7 @@ </style></%def> +## ---------------------------------------------------------------------------- <%def name="javascripts()"><% self.js_app = 'display-structured' @@ -174,12 +187,72 @@ %></%def> -<%def name="render_item_hda( hda, children )"> +## ---------------------------------------------------------------------------- hda +<%def name="render_item_hda( hda, children )"> ## render hdas as a id'd stub for js to fill later + + %if hda.copied_from_history_dataset_association: + ${ render_hda_copied_from_history( hda, children ) } + + %elif hda.copied_from_library_dataset_dataset_association: + ${ render_hda_copied_from_library( hda, children ) } + + %else: <% id = trans.security.encode_id( hda.id ) %><div id="hda-${id}" class="dataset hda state-${hda.state}"></div> + %endif </%def> +<%def name="render_hda_copied_from_history( hda, children )"> +## wrap an hda in info about the history from where it was copied + <% id = trans.security.encode_id( hda.id ) %> + <% history_id = trans.security.encode_id( hda.copied_from_history_dataset_association.history_id ) %> + <div class="copied-from copied-from-history"> + <div class="header"> + <div class="copied-from-dataset"> + <span class="light">${ _( 'Copied from history dataset' ) + ':' }</span> + <span class="bold">${ hda.copied_from_history_dataset_association.name }</span> + </div> + <div class="copied-from-source"> + <span class="light">${ _( 'History' ) + ':' }</span> + <span class="bold"> + <a href="${ h.url_for( controller='history', action='view', id=history_id ) }"> + ${ hda.copied_from_history_dataset_association.history.name } + </a> + </span> + </div> + </div> + <div id="hda-${id}" class="dataset hda state-${hda.state}"></div> + </div> +</%def> + +<%def name="render_hda_copied_from_library( hda, children )"> +## wrap an hda in info about the library from where it was copied + <% id = trans.security.encode_id( hda.id ) %> + <% + folder = hda.copied_from_library_dataset_dataset_association.library_dataset.folder + folder_id = 'F' + trans.security.encode_id( folder.id ) + %> + <div class="copied-from copied-from-library"> + <div class="header"> + <div class="copied-from-dataset"> + <span class="light">${ _( 'Copied from library dataset' ) + ':' }</span> + <span class="bold">${ hda.copied_from_library_dataset_dataset_association.name }</span> + </div> + <div class="copied-from-source"> + <span class="light">${ _( 'Library' ) + ':' }</span> + <span class="bold"> + <a href="${ h.url_for( controller='library', action='list' ) + '#folders/F' + folder_id }"> + ${ library.name } + </a> + </span> + </div> + </div> + <div id="hda-${id}" class="dataset hda state-${hda.state}"></div> + </div> +</%def> + +## ---------------------------------------------------------------------------- job (and output hdas) <%def name="render_item_job( job, children )"> ## render a job (as a toolForm) and its children (hdas) <div class="tool toolForm"> @@ -220,6 +293,7 @@ </div></%def> +## ---------------------------------------------------------------------------- workflow (w/ jobs, hdas) <%def name="render_item_wf( wf, children )"> ## render a workflow and its children (jobs/toolForms) <div class="workflow"> @@ -235,7 +309,7 @@ </div></%def> -## ---------------------------------------------------------------------------- +## ---------------------------------------------------------------------------- body ## render all items from a dictionary prov. by history/display_structured %for entity, children in items: ${render_item( entity, children )} 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: carlfeberhard: Fix to 197878e: properly namespace def and use in grid_async
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/828286e70c05/ Changeset: 828286e70c05 User: carlfeberhard Date: 2014-04-29 16:07:40 Summary: Fix to 197878e: properly namespace def and use in grid_async Affected #: 2 files diff -r 5846eb77fc8e7b49fe1cafd986e709974ec1ae87 -r 828286e70c05a1fcf0eec5c2b7e8c59f98b879ef templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -73,13 +73,13 @@ // load grid viewer require(['mvc/grid/grid-view'], function(GridView) { $(function() { - gridView = new GridView( ${ h.to_json_string( self.grid_config() ) } ); + gridView = new GridView( ${ h.to_json_string( self.get_grid_config() ) } ); }); }); </script></%def> -<%def name="grid_config( embedded=False, insert=None )"> +<%def name="get_grid_config( embedded=False, insert=None )"> ## generates dictionary <% self.grid_config = { diff -r 5846eb77fc8e7b49fe1cafd986e709974ec1ae87 -r 828286e70c05a1fcf0eec5c2b7e8c59f98b879ef templates/grid_base_async.mako --- a/templates/grid_base_async.mako +++ b/templates/grid_base_async.mako @@ -1,4 +1,4 @@ <%namespace name="grid_base" file="./grid_base.mako" import="*" /> ${init()} -${h.to_json_string( grid_base.grid_config )} \ No newline at end of file +${h.to_json_string( grid_base.get_grid_config() )} 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: Fix for determining the list of all repository dependency dictionaries when installing a repository into Galaxy that has a deep dependency hierarchy.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5846eb77fc8e/ Changeset: 5846eb77fc8e User: greg Date: 2014-04-29 15:34:58 Summary: Fix for determining the list of all repository dependency dictionaries when installing a repository into Galaxy that has a deep dependency hierarchy. Affected #: 1 file diff -r e3808d426ef2387a25aa79cbba397a6ec2f0d8f5 -r 5846eb77fc8e7b49fe1cafd986e709974ec1ae87 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -464,7 +464,15 @@ all_required_repo_info_dict[ k ] = v if required_repo_info_dicts: for required_repo_info_dict in required_repo_info_dicts: - if required_repo_info_dict not in all_repo_info_dicts: + # Each required_repo_info_dict has a single entry, and all_repo_info_dicts is a list + # of dictionaries, each of which has a single entry. We'll check keys here rather than + # the entire dictionary because a dictionary entry in all_repo_info_dicts will include + # lists of discovered repository dependencies, but these lists will be empty in the + # required_repo_info_dict since dependency discovery has not yet been performed for these + # dictionaries. + required_repo_infor_dict_key = required_repo_info_dict.keys()[ 0 ] + all_repo_info_dicts_keys = [ d.keys()[ 0 ] for d in all_repo_info_dicts ] + if required_repo_infor_dict_key not in all_repo_info_dicts_keys: all_repo_info_dicts.append( required_repo_info_dict ) all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts return all_required_repo_info_dict 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: Handle changing http protocols in the tool shed registry's password_manager_for_url() function.
by commits-noreply＠bitbucket.org 28 Apr '14

28 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e3808d426ef2/ Changeset: e3808d426ef2 User: greg Date: 2014-04-28 21:58:48 Summary: Handle changing http protocols in the tool shed registry's password_manager_for_url() function. Affected #: 1 file diff -r 04befb2eb25baa347a3f440ed22045d01e75ebc7 -r e3808d426ef2387a25aa79cbba397a6ec2f0d8f5 lib/tool_shed/tool_shed_registry.py --- a/lib/tool_shed/tool_shed_registry.py +++ b/lib/tool_shed/tool_shed_registry.py @@ -2,6 +2,7 @@ import sys import urllib2 from galaxy.util.odict import odict +from tool_shed.util import common_util from tool_shed.util import xml_util log = logging.getLogger( __name__ ) @@ -39,13 +40,17 @@ def password_manager_for_url( self, url ): """ - If the tool shed is using external auth, the client to the tool shed must authenticate to that as well. This provides access to the - urllib2.HTTPPasswordMgrWithdefaultRealm() object for the url passed in. + If the tool shed is using external auth, the client to the tool shed must authenticate to that + as well. This provides access to the urllib2.HTTPPasswordMgrWithdefaultRealm() object for the + url passed in. - Following more what galaxy.demo_sequencer.controllers.common does might be more appropriate at some stage... + Following more what galaxy.demo_sequencer.controllers.common does might be more appropriate at + some stage... """ + url_sans_protocol = common_util.remove_protocol_from_tool_shed_url( url ) for shed_name, shed_url in self.tool_sheds.items(): - if shed_url.find( url ) >= 0: + shed_url_sans_protocol = common_util.remove_protocol_from_tool_shed_url( shed_url ) + if shed_url_sans_protocol.find( url_sans_protocol ) >= 0: return self.tool_sheds_auth[ shed_name ] log.debug( "Invalid url '%s' received by tool shed registry's password_manager_for_url method." % str( url ) ) return None 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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