commit/galaxy-central: 3 new changesets
3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce24adaae994/ Changeset: ce24adaae994 Branch: federation_ids User: kellrott Date: 2014-08-14 22:19:43 Summary: Adding method for workflows to use input with 'src' set as 'uuid', it will then scan datasets for a matching uuid. Affected #: 2 files diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r ce24adaae9941568a414f80b5f16da37e55fa192 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -188,6 +188,15 @@ content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get( trans.security.decode_id(input_id)) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif input_source == 'uuid': + dataset = trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid==input_id).first() + if dataset is None: + #this will need to be changed later. If federation code is avalible, then a missing UUID + #could be found amoung fereration partners + message = "Input cannot find UUID: %s." % input_id + raise exceptions.RequestParameterInvalidException( message ) + content = history.add_dataset(dataset) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) elif input_source == 'hdca': content = app.dataset_collections_service.get_dataset_collection_instance( trans, diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r ce24adaae9941568a414f80b5f16da37e55fa192 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -23,7 +23,7 @@ ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } %endfor %elif input.type == "conditional": - <% + <% try: current_case = param_values[input.name]['__current_case__'] is_valid = True @@ -53,7 +53,7 @@ <td></td></tr> %elif input.visible: - <% + <% if hasattr( input, "label" ) and input.label: label = input.label else: @@ -70,7 +70,7 @@ ## Parameter does not have a stored value. <tr><% - # Get parameter label. + # Get parameter label. if input.type == "conditional": label = input.test_param.label elif input.type == "repeat": @@ -83,7 +83,7 @@ <td></td></tr> %endif - + %endfor </%def> @@ -91,7 +91,7 @@ <%def name="inputs_recursive_indent( text, depth )"><td style="padding-left: ${ ( depth - 1 ) * 10 }px"> ${text | h} - </td> + </td></%def><table class="tabletip"> @@ -120,6 +120,9 @@ <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr', dataset_id=encoded_hda_id )}">stderr</a></td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr><tr><td>API ID:</td><td>${encoded_hda_id}</td></tr> + %if hda.dataset.uuid: + <tr><td>UUID:</td><td>${hda.dataset.uuid}</td></tr> + %endif %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif @@ -168,4 +171,3 @@ '${dep[0].name | h}' in ${dep[1]}<br/></div> % endfor - https://bitbucket.org/galaxy/galaxy-central/commits/9440196009e1/ Changeset: 9440196009e1 Branch: federation_ids User: kellrott Date: 2014-08-14 22:38:55 Summary: Checking security before creating the HDA Affected #: 1 file diff -r ce24adaae9941568a414f80b5f16da37e55fa192 -r 9440196009e1efdd69df90a406e49a4fc6d7655b lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -195,8 +195,8 @@ #could be found amoung fereration partners message = "Input cannot find UUID: %s." % input_id raise exceptions.RequestParameterInvalidException( message ) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset ) content = history.add_dataset(dataset) - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) elif input_source == 'hdca': content = app.dataset_collections_service.get_dataset_collection_instance( trans, https://bitbucket.org/galaxy/galaxy-central/commits/0d06d852093f/ Changeset: 0d06d852093f User: dannon Date: 2014-08-18 19:38:24 Summary: Merged in kellrott/galaxy-farm/federation_ids (pull request #462) UUIDs as valid inputs for workflows Affected #: 2 files diff -r eaf8920f999bab18a44c938565b643e0612f6e15 -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -188,6 +188,15 @@ content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get( trans.security.decode_id(input_id)) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif input_source == 'uuid': + dataset = trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid==input_id).first() + if dataset is None: + #this will need to be changed later. If federation code is avalible, then a missing UUID + #could be found amoung fereration partners + message = "Input cannot find UUID: %s." % input_id + raise exceptions.RequestParameterInvalidException( message ) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset ) + content = history.add_dataset(dataset) elif input_source == 'hdca': content = app.dataset_collections_service.get_dataset_collection_instance( trans, diff -r eaf8920f999bab18a44c938565b643e0612f6e15 -r 0d06d852093fcca94adc1a93a0fb9b7efc2880c4 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -23,7 +23,7 @@ ${ inputs_recursive(input.inputs, param_values[input.name][i], depth=depth+1) } %endfor %elif input.type == "conditional": - <% + <% try: current_case = param_values[input.name]['__current_case__'] is_valid = True @@ -53,7 +53,7 @@ <td></td></tr> %elif input.visible: - <% + <% if hasattr( input, "label" ) and input.label: label = input.label else: @@ -70,7 +70,7 @@ ## Parameter does not have a stored value. <tr><% - # Get parameter label. + # Get parameter label. if input.type == "conditional": label = input.test_param.label elif input.type == "repeat": @@ -83,7 +83,7 @@ <td></td></tr> %endif - + %endfor </%def> @@ -91,7 +91,7 @@ <%def name="inputs_recursive_indent( text, depth )"><td style="padding-left: ${ ( depth - 1 ) * 10 }px"> ${text | h} - </td> + </td></%def><table class="tabletip"> @@ -120,6 +120,9 @@ <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr', dataset_id=encoded_hda_id )}">stderr</a></td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr><tr><td>API ID:</td><td>${encoded_hda_id}</td></tr> + %if hda.dataset.uuid: + <tr><td>UUID:</td><td>${hda.dataset.uuid}</td></tr> + %endif %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif @@ -168,4 +171,3 @@ '${dep[0].name | h}' in ${dep[1]}<br/></div> % endfor - Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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