galaxy-commits January 2015

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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset ff6e36d7a238
by commits-noreply＠bitbucket.org 06 Jan '15

06 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c25df9f3d31e/ Changeset: c25df9f3d31e Branch: stable User: natefoo Date: 2015-01-06 14:00:16+00:00 Summary: Update tag latest_2014.10.06 for changeset ff6e36d7a238 Affected #: 1 file diff -r ff6e36d7a2388214fe7636c43d30838c07246907 -r c25df9f3d31effd9c4abdbbffd40381f23fc6dc8 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -793d9cd5f9dec66ceafb36bc38f53453457056e6 latest_2014.10.06 +ff6e36d7a2388214fe7636c43d30838c07246907 latest_2014.10.06 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: martenson: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #620)
by commits-noreply＠bitbucket.org 05 Jan '15

05 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff6e36d7a238/ Changeset: ff6e36d7a238 Branch: stable User: martenson Date: 2015-01-05 21:53:57+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #620) [STABLE] Don't choke on tool versions switches with significant parameter changes. Affected #: 1 file diff -r dff4071c13f9b2908556583227766c65fcfb8a29 -r ff6e36d7a2388214fe7636c43d30838c07246907 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 @@ -80,14 +80,28 @@ message=message, status=status, redirect=redirect ) ) - params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers - #do param translation here, used by datasource tools - if tool.input_translator: - tool.input_translator.translate( params ) + + def _validated_params_for( kwd ): + params = galaxy.util.Params( kwd, sanitize=False ) # Sanitize parameters when substituting into command line via input wrappers + #do param translation here, used by datasource tools + if tool.input_translator: + tool.input_translator.translate( params ) + return params + + params = _validated_params_for( kwd ) # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. history = tool.get_default_history_by_trans( trans, create=True ) - template, vars = tool.handle_input( trans, params.__dict__ ) + try: + template, vars = tool.handle_input( trans, params.__dict__ ) + except KeyError: + # This error indicates (or at least can indicate) there was a + # problem with the stored tool_state - it is incompatible with + # this variant of the tool - possibly because the tool changed + # or because the tool version changed. + del kwd[ "tool_state" ] + params = _validated_params_for( kwd ) + template, vars = tool.handle_input( trans, params.__dict__ ) if len( params ) > 0: trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) add_frame = AddFrameData() 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 05 Jan '15

05 Jan '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/24c62137d466/ Changeset: 24c62137d466 Branch: stable User: jmchilton Date: 2014-12-18 14:47:08+00:00 Summary: Don't choke on tool versions switches with significant parameter changes. Just regenerate the tool state from the supplied parameters instead - seems to still perserve parameters on the tool form that are common between the versions because they are coming in throuh kwd. Affected #: 1 file diff -r 7197e949d3ab990ceb76c193ebc940d90aa04cad -r 24c62137d46629f9200b43612485799cf39600d5 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 @@ -80,14 +80,28 @@ message=message, status=status, redirect=redirect ) ) - params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers - #do param translation here, used by datasource tools - if tool.input_translator: - tool.input_translator.translate( params ) + + def _validated_params_for( kwd ): + params = galaxy.util.Params( kwd, sanitize=False ) # Sanitize parameters when substituting into command line via input wrappers + #do param translation here, used by datasource tools + if tool.input_translator: + tool.input_translator.translate( params ) + return params + + params = _validated_params_for( kwd ) # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. history = tool.get_default_history_by_trans( trans, create=True ) - template, vars = tool.handle_input( trans, params.__dict__ ) + try: + template, vars = tool.handle_input( trans, params.__dict__ ) + except KeyError: + # This error indicates (or at least can indicate) there was a + # problem with the stored tool_state - it is incompatible with + # this variant of the tool - possibly because the tool changed + # or because the tool version changed. + del kwd[ "tool_state" ] + params = _validated_params_for( kwd ) + template, vars = tool.handle_input( trans, params.__dict__ ) if len( params ) > 0: trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) add_frame = AddFrameData() https://bitbucket.org/galaxy/galaxy-central/commits/ff6e36d7a238/ Changeset: ff6e36d7a238 Branch: stable User: martenson Date: 2015-01-05 21:53:57+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #620) [STABLE] Don't choke on tool versions switches with significant parameter changes. Affected #: 1 file diff -r dff4071c13f9b2908556583227766c65fcfb8a29 -r ff6e36d7a2388214fe7636c43d30838c07246907 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 @@ -80,14 +80,28 @@ message=message, status=status, redirect=redirect ) ) - params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers - #do param translation here, used by datasource tools - if tool.input_translator: - tool.input_translator.translate( params ) + + def _validated_params_for( kwd ): + params = galaxy.util.Params( kwd, sanitize=False ) # Sanitize parameters when substituting into command line via input wrappers + #do param translation here, used by datasource tools + if tool.input_translator: + tool.input_translator.translate( params ) + return params + + params = _validated_params_for( kwd ) # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. history = tool.get_default_history_by_trans( trans, create=True ) - template, vars = tool.handle_input( trans, params.__dict__ ) + try: + template, vars = tool.handle_input( trans, params.__dict__ ) + except KeyError: + # This error indicates (or at least can indicate) there was a + # problem with the stored tool_state - it is incompatible with + # this variant of the tool - possibly because the tool changed + # or because the tool version changed. + del kwd[ "tool_state" ] + params = _validated_params_for( kwd ) + template, vars = tool.handle_input( trans, params.__dict__ ) if len( params ) > 0: trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) add_frame = AddFrameData() 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: jmchilton: Fix for Pull Request #614.
by commits-noreply＠bitbucket.org 05 Jan '15

05 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d50ee9520583/ Changeset: d50ee9520583 User: jmchilton Date: 2015-01-05 21:09:45+00:00 Summary: Fix for Pull Request #614. Affected #: 1 file diff -r 2aa2f508c50864b3d309d384137e53f5750aed2d -r d50ee9520583c225e48c577ab977f18fd6cb7d6a config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -299,7 +299,7 @@ <sniffer type="galaxy.datatypes.data:Newick"/><sniffer type="galaxy.datatypes.data:Nexus"/><sniffer type="galaxy.datatypes.text:Obo"/> - <sniffer type="galaxy.datatypes.text.Arff"/> + <sniffer type="galaxy.datatypes.text:Arff"/><sniffer type="galaxy.datatypes.text:Ipynb"/><sniffer type="galaxy.datatypes.text:Json"/><sniffer type="galaxy.datatypes.images:Jpg"/> 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: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #621)
by commits-noreply＠bitbucket.org 05 Jan '15

05 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2aa2f508c508/ Changeset: 2aa2f508c508 User: jmchilton Date: 2015-01-05 20:59:02+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #621) Workflow API: Replace preferred usage terminology in the API (s/usage/invocation) Affected #: 2 files diff -r 03955af117563248e950ec97d151c4a4615eaa58 -r 2aa2f508c50864b3d309d384137e53f5750aed2d lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -372,9 +372,9 @@ return item @expose_api - def workflow_request( self, trans, workflow_id, payload, **kwd ): + def invoke( self, trans, workflow_id, payload, **kwd ): """ - POST /api/workflows/{encoded_workflow_id}/usage + POST /api/workflows/{encoded_workflow_id}/invocations Schedule the workflow specified by `workflow_id` to run. """ @@ -398,10 +398,11 @@ return self.encode_all_ids( trans, workflow_invocation.to_dict(), recursive=True ) @expose_api - def workflow_usage(self, trans, workflow_id, **kwd): + def index_invocations(self, trans, workflow_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage - Get the list of the workflow usage + GET /api/workflows/{workflow_id}/invocations + + Get the list of the workflow invocations :param workflow_id: the workflow id (required) :type workflow_id: str @@ -416,53 +417,53 @@ return out @expose_api - def workflow_usage_contents(self, trans, workflow_id, usage_id, **kwd): + def show_invocation(self, trans, workflow_id, invocation_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage/{usage_id} - Get detailed description of workflow usage + GET /api/workflows/{workflow_id}/invocation/{invocation_id} + Get detailed description of workflow invocation - :param workflow_id: the workflow id (required) - :type workflow_id: str + :param workflow_id: the workflow id (required) + :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the invocation id (required) + :type invocation_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ - decoded_workflow_invocation_id = self.__decode_id( trans, usage_id ) + decoded_workflow_invocation_id = self.__decode_id( trans, invocation_id ) workflow_invocation = self.workflow_manager.get_invocation( trans, decoded_workflow_invocation_id ) if workflow_invocation: return self.__encode_invocation( trans, workflow_invocation ) return None @expose_api - def cancel_workflow_invocation(self, trans, workflow_id, usage_id, **kwd): + def cancel_invocation(self, trans, workflow_id, invocation_id, **kwd): """ - DELETE /api/workflows/{workflow_id}/usage/{usage_id} + DELETE /api/workflows/{workflow_id}/invocation/{invocation_id} Cancel the specified workflow invocation. :param workflow_id: the workflow id (required) :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the usage id (required) + :type invocation_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ - decoded_workflow_invocation_id = self.__decode_id( trans, usage_id ) + decoded_workflow_invocation_id = self.__decode_id( trans, invocation_id ) workflow_invocation = self.workflow_manager.cancel_invocation( trans, decoded_workflow_invocation_id ) return self.__encode_invocation( trans, workflow_invocation ) @expose_api - def workflow_invocation_step(self, trans, workflow_id, usage_id, step_id, **kwd): + def invocation_step(self, trans, workflow_id, invocation_id, step_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id} + GET /api/workflows/{workflow_id}/invocation/{invocation_id}/steps/{step_id} - :param workflow_id: the workflow id (required) - :type workflow_id: str + :param workflow_id: the workflow id (required) + :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the invocation id (required) + :type invocation_id: str :param step_id: encoded id of the WorkflowInvocationStep (required) :type step_id: str @@ -480,9 +481,9 @@ return self.__encode_invocation_step( trans, invocation_step ) @expose_api - def workflow_invocation_step_update(self, trans, workflow_id, usage_id, step_id, payload, **kwd): + def update_invocation_step(self, trans, workflow_id, invocation_id, step_id, payload, **kwd): """ - PUT /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id} + PUT /api/workflows/{workflow_id}/invocation/{invocation_id}/steps/{step_id} Update state of running workflow step invocation - still very nebulous but this would be for stuff like confirming paused steps can proceed etc.... @@ -491,8 +492,8 @@ :param workflow_id: the workflow id (required) :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the usage id (required) + :type invocation_id: str :param step_id: encoded id of the WorkflowInvocationStep (required) :type step_id: str diff -r 03955af117563248e950ec97d151c4a4615eaa58 -r 2aa2f508c50864b3d309d384137e53f5750aed2d lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -227,14 +227,62 @@ webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) - webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'cancel_workflow_invocation', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='cancel_workflow_invocation', conditions=dict(method=['DELETE'])) - webapp.mapper.connect( 'workflow_invocation_step', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'workflow_invocation_step_update', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step_update', conditions=dict(method=['PUT'])) + # API refers to usages and invocations - these mean the same thing but the + # usage routes should be considered deprecated. + invoke_names = { + "invocations": "", + "usage": "_deprecated", + } + for noun, suffix in invoke_names.iteritems(): + name = "%s%s" % (noun, suffix) + webapp.mapper.connect( + 'list_workflow_%s' % name, + '/api/workflows/{workflow_id}/%s' % noun, + controller='workflows', + action='index_invocations', + conditions=dict(method=['GET']) + ) - webapp.mapper.connect( 'workflow_request', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_request', conditions=dict( method=['POST'] ) ) + webapp.mapper.connect( + 'workflow_%s_contents' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}' % noun, + controller='workflows', + action='show_invocation', + conditions=dict(method=['GET']) + ) + + webapp.mapper.connect( + 'cancel_workflow_%s' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}' % noun, + controller='workflows', + action='cancel_invocation', + conditions=dict(method=['DELETE']) + ) + + webapp.mapper.connect( + 'workflow_%s_step' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun, + controller='workflows', + action='invocation_step', + conditions=dict(method=['GET']) + ) + + webapp.mapper.connect( + 'workflow_%s_step_update' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun, + controller='workflows', + action='update_invocation_step', + conditions=dict(method=['PUT']) + ) + + webapp.mapper.connect( + 'workflow_%s' % name, + '/api/workflows/{workflow_id}/%s' % noun, + controller='workflows', + action='invoke', + conditions=dict( method=['POST'] ) + ) # ============================ # ===== AUTHENTICATE API ===== # ============================ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 05 Jan '15

05 Jan '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ddcb4c7e2957/ Changeset: ddcb4c7e2957 User: jmchilton Date: 2014-12-19 14:15:27+00:00 Summary: Replace preferred workflow usage terminology in the API (s/usage/invocation) `GET /api/workflows/<workflow_id>/usage` made sense for read-only operations - but now for instance `POST /api/workflows/<workflow_id>/usage` is the preferred method for invoking workflows and `PUT /api/workflows/<workflow_id>/usage/<usage_id>/steps/<step_id>` can be used to interact with steps while the workflow is running. I think the term is a little awkward in that sense and is incongruous with the rest of Galaxy which uses the terminology "invocations". In a backward compatible way this replaces the usage terminology with invocation terminology (and uses the plural in the route which is more consistent with the rest of the API - `POST /api/histories` for instance). Affected #: 2 files diff -r 815d38c48a5639d47eed92806ef4c196406f58f1 -r ddcb4c7e29574f8605e6a9cd99b039b25300eee9 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -372,9 +372,9 @@ return item @expose_api - def workflow_request( self, trans, workflow_id, payload, **kwd ): + def invoke( self, trans, workflow_id, payload, **kwd ): """ - POST /api/workflows/{encoded_workflow_id}/usage + POST /api/workflows/{encoded_workflow_id}/invocations Schedule the workflow specified by `workflow_id` to run. """ @@ -398,10 +398,11 @@ return self.encode_all_ids( trans, workflow_invocation.to_dict(), recursive=True ) @expose_api - def workflow_usage(self, trans, workflow_id, **kwd): + def index_invocations(self, trans, workflow_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage - Get the list of the workflow usage + GET /api/workflows/{workflow_id}/invocations + + Get the list of the workflow invocations :param workflow_id: the workflow id (required) :type workflow_id: str @@ -416,53 +417,53 @@ return out @expose_api - def workflow_usage_contents(self, trans, workflow_id, usage_id, **kwd): + def show_invocation(self, trans, workflow_id, invocation_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage/{usage_id} - Get detailed description of workflow usage + GET /api/workflows/{workflow_id}/invocation/{invocation_id} + Get detailed description of workflow invocation - :param workflow_id: the workflow id (required) - :type workflow_id: str + :param workflow_id: the workflow id (required) + :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the invocation id (required) + :type invocation_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ - decoded_workflow_invocation_id = self.__decode_id( trans, usage_id ) + decoded_workflow_invocation_id = self.__decode_id( trans, invocation_id ) workflow_invocation = self.workflow_manager.get_invocation( trans, decoded_workflow_invocation_id ) if workflow_invocation: return self.__encode_invocation( trans, workflow_invocation ) return None @expose_api - def cancel_workflow_invocation(self, trans, workflow_id, usage_id, **kwd): + def cancel_invocation(self, trans, workflow_id, invocation_id, **kwd): """ - DELETE /api/workflows/{workflow_id}/usage/{usage_id} + DELETE /api/workflows/{workflow_id}/invocation/{invocation_id} Cancel the specified workflow invocation. :param workflow_id: the workflow id (required) :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the usage id (required) + :type invocation_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ - decoded_workflow_invocation_id = self.__decode_id( trans, usage_id ) + decoded_workflow_invocation_id = self.__decode_id( trans, invocation_id ) workflow_invocation = self.workflow_manager.cancel_invocation( trans, decoded_workflow_invocation_id ) return self.__encode_invocation( trans, workflow_invocation ) @expose_api - def workflow_invocation_step(self, trans, workflow_id, usage_id, step_id, **kwd): + def invocation_step(self, trans, workflow_id, invocation_id, step_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id} + GET /api/workflows/{workflow_id}/invocation/{invocation_id}/steps/{step_id} - :param workflow_id: the workflow id (required) - :type workflow_id: str + :param workflow_id: the workflow id (required) + :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the invocation id (required) + :type invocation_id: str :param step_id: encoded id of the WorkflowInvocationStep (required) :type step_id: str @@ -480,9 +481,9 @@ return self.__encode_invocation_step( trans, invocation_step ) @expose_api - def workflow_invocation_step_update(self, trans, workflow_id, usage_id, step_id, payload, **kwd): + def update_invocation_step(self, trans, workflow_id, invocation_id, step_id, payload, **kwd): """ - PUT /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id} + PUT /api/workflows/{workflow_id}/invocation/{invocation_id}/steps/{step_id} Update state of running workflow step invocation - still very nebulous but this would be for stuff like confirming paused steps can proceed etc.... @@ -491,8 +492,8 @@ :param workflow_id: the workflow id (required) :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the usage id (required) + :type invocation_id: str :param step_id: encoded id of the WorkflowInvocationStep (required) :type step_id: str diff -r 815d38c48a5639d47eed92806ef4c196406f58f1 -r ddcb4c7e29574f8605e6a9cd99b039b25300eee9 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -227,14 +227,62 @@ webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) - webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'cancel_workflow_invocation', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='cancel_workflow_invocation', conditions=dict(method=['DELETE'])) - webapp.mapper.connect( 'workflow_invocation_step', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'workflow_invocation_step_update', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step_update', conditions=dict(method=['PUT'])) + # API refers to usages and invocations - these mean the same thing but the + # usage routes should be considered deprecated. + invoke_names = { + "invocations": "", + "usage": "_deprecated", + } + for noun, suffix in invoke_names.iteritems(): + name = "%s%s" % (noun, suffix) + webapp.mapper.connect( + 'list_workflow_%s' % name, + '/api/workflows/{workflow_id}/%s' % noun, + controller='workflows', + action='index_invocations', + conditions=dict(method=['GET']) + ) - webapp.mapper.connect( 'workflow_request', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_request', conditions=dict( method=['POST'] ) ) + webapp.mapper.connect( + 'workflow_%s_contents' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}' % noun, + controller='workflows', + action='show_invocation', + conditions=dict(method=['GET']) + ) + + webapp.mapper.connect( + 'cancel_workflow_%s' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}' % noun, + controller='workflows', + action='cancel_invocation', + conditions=dict(method=['DELETE']) + ) + + webapp.mapper.connect( + 'workflow_%s_step' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun, + controller='workflows', + action='invocation_step', + conditions=dict(method=['GET']) + ) + + webapp.mapper.connect( + 'workflow_%s_step_update' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun, + controller='workflows', + action='update_invocation_step', + conditions=dict(method=['PUT']) + ) + + webapp.mapper.connect( + 'workflow_%s' % name, + '/api/workflows/{workflow_id}/%s' % noun, + controller='workflows', + action='invoke', + conditions=dict( method=['POST'] ) + ) # ============================ # ===== AUTHENTICATE API ===== # ============================ https://bitbucket.org/galaxy/galaxy-central/commits/2aa2f508c508/ Changeset: 2aa2f508c508 User: jmchilton Date: 2015-01-05 20:59:02+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #621) Workflow API: Replace preferred usage terminology in the API (s/usage/invocation) Affected #: 2 files diff -r 03955af117563248e950ec97d151c4a4615eaa58 -r 2aa2f508c50864b3d309d384137e53f5750aed2d lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -372,9 +372,9 @@ return item @expose_api - def workflow_request( self, trans, workflow_id, payload, **kwd ): + def invoke( self, trans, workflow_id, payload, **kwd ): """ - POST /api/workflows/{encoded_workflow_id}/usage + POST /api/workflows/{encoded_workflow_id}/invocations Schedule the workflow specified by `workflow_id` to run. """ @@ -398,10 +398,11 @@ return self.encode_all_ids( trans, workflow_invocation.to_dict(), recursive=True ) @expose_api - def workflow_usage(self, trans, workflow_id, **kwd): + def index_invocations(self, trans, workflow_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage - Get the list of the workflow usage + GET /api/workflows/{workflow_id}/invocations + + Get the list of the workflow invocations :param workflow_id: the workflow id (required) :type workflow_id: str @@ -416,53 +417,53 @@ return out @expose_api - def workflow_usage_contents(self, trans, workflow_id, usage_id, **kwd): + def show_invocation(self, trans, workflow_id, invocation_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage/{usage_id} - Get detailed description of workflow usage + GET /api/workflows/{workflow_id}/invocation/{invocation_id} + Get detailed description of workflow invocation - :param workflow_id: the workflow id (required) - :type workflow_id: str + :param workflow_id: the workflow id (required) + :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the invocation id (required) + :type invocation_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ - decoded_workflow_invocation_id = self.__decode_id( trans, usage_id ) + decoded_workflow_invocation_id = self.__decode_id( trans, invocation_id ) workflow_invocation = self.workflow_manager.get_invocation( trans, decoded_workflow_invocation_id ) if workflow_invocation: return self.__encode_invocation( trans, workflow_invocation ) return None @expose_api - def cancel_workflow_invocation(self, trans, workflow_id, usage_id, **kwd): + def cancel_invocation(self, trans, workflow_id, invocation_id, **kwd): """ - DELETE /api/workflows/{workflow_id}/usage/{usage_id} + DELETE /api/workflows/{workflow_id}/invocation/{invocation_id} Cancel the specified workflow invocation. :param workflow_id: the workflow id (required) :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the usage id (required) + :type invocation_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ - decoded_workflow_invocation_id = self.__decode_id( trans, usage_id ) + decoded_workflow_invocation_id = self.__decode_id( trans, invocation_id ) workflow_invocation = self.workflow_manager.cancel_invocation( trans, decoded_workflow_invocation_id ) return self.__encode_invocation( trans, workflow_invocation ) @expose_api - def workflow_invocation_step(self, trans, workflow_id, usage_id, step_id, **kwd): + def invocation_step(self, trans, workflow_id, invocation_id, step_id, **kwd): """ - GET /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id} + GET /api/workflows/{workflow_id}/invocation/{invocation_id}/steps/{step_id} - :param workflow_id: the workflow id (required) - :type workflow_id: str + :param workflow_id: the workflow id (required) + :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the invocation id (required) + :type invocation_id: str :param step_id: encoded id of the WorkflowInvocationStep (required) :type step_id: str @@ -480,9 +481,9 @@ return self.__encode_invocation_step( trans, invocation_step ) @expose_api - def workflow_invocation_step_update(self, trans, workflow_id, usage_id, step_id, payload, **kwd): + def update_invocation_step(self, trans, workflow_id, invocation_id, step_id, payload, **kwd): """ - PUT /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id} + PUT /api/workflows/{workflow_id}/invocation/{invocation_id}/steps/{step_id} Update state of running workflow step invocation - still very nebulous but this would be for stuff like confirming paused steps can proceed etc.... @@ -491,8 +492,8 @@ :param workflow_id: the workflow id (required) :type workflow_id: str - :param usage_id: the usage id (required) - :type usage_id: str + :param invocation_id: the usage id (required) + :type invocation_id: str :param step_id: encoded id of the WorkflowInvocationStep (required) :type step_id: str diff -r 03955af117563248e950ec97d151c4a4615eaa58 -r 2aa2f508c50864b3d309d384137e53f5750aed2d lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -227,14 +227,62 @@ webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) - webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'cancel_workflow_invocation', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='cancel_workflow_invocation', conditions=dict(method=['DELETE'])) - webapp.mapper.connect( 'workflow_invocation_step', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step', conditions=dict(method=['GET'])) - webapp.mapper.connect( 'workflow_invocation_step_update', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step_update', conditions=dict(method=['PUT'])) + # API refers to usages and invocations - these mean the same thing but the + # usage routes should be considered deprecated. + invoke_names = { + "invocations": "", + "usage": "_deprecated", + } + for noun, suffix in invoke_names.iteritems(): + name = "%s%s" % (noun, suffix) + webapp.mapper.connect( + 'list_workflow_%s' % name, + '/api/workflows/{workflow_id}/%s' % noun, + controller='workflows', + action='index_invocations', + conditions=dict(method=['GET']) + ) - webapp.mapper.connect( 'workflow_request', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_request', conditions=dict( method=['POST'] ) ) + webapp.mapper.connect( + 'workflow_%s_contents' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}' % noun, + controller='workflows', + action='show_invocation', + conditions=dict(method=['GET']) + ) + + webapp.mapper.connect( + 'cancel_workflow_%s' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}' % noun, + controller='workflows', + action='cancel_invocation', + conditions=dict(method=['DELETE']) + ) + + webapp.mapper.connect( + 'workflow_%s_step' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun, + controller='workflows', + action='invocation_step', + conditions=dict(method=['GET']) + ) + + webapp.mapper.connect( + 'workflow_%s_step_update' % name, + '/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun, + controller='workflows', + action='update_invocation_step', + conditions=dict(method=['PUT']) + ) + + webapp.mapper.connect( + 'workflow_%s' % name, + '/api/workflows/{workflow_id}/%s' % noun, + controller='workflows', + action='invoke', + conditions=dict( method=['POST'] ) + ) # ============================ # ===== AUTHENTICATE API ===== # ============================ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Allow specification of post job actions at workflow invocation.
by commits-noreply＠bitbucket.org 05 Jan '15

05 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/03955af11756/ Changeset: 03955af11756 User: jmchilton Date: 2015-01-05 20:38:27+00:00 Summary: Allow specification of post job actions at workflow invocation. Feature requested by Kyle. Implemented only in the API at this point - not sure it is a feature valuable to UI consumers. Pass in PJAs along with step parameters map but keyed on __POST_JOB_ACTIONS__. JSON definition same as when defining PJA in the workflow definition JSON. Includes test cases for normal use and for use after delayed workflow steps have been evaluated by the new workflow scheduling stuff. Affected #: 3 files diff -r 3fc8ce62285bc3df5b934439e624f2d56cb062cf -r 03955af117563248e950ec97d151c4a4615eaa58 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -29,6 +29,13 @@ log = logging.getLogger( __name__ ) +# Key into Tool state to describe invocation-specific runtime properties. +RUNTIME_STEP_META_STATE_KEY = "__STEP_META_STATE__" +# Key into step runtime state dict describing invocation-specific post job +# actions (i.e. PJA specified at runtime on top of the workflow-wide defined +# ones. +RUNTIME_POST_JOB_ACTIONS_KEY = "__POST_JOB_ACTIONS__" + class WorkflowModule( object ): @@ -472,6 +479,7 @@ self.tool_id = tool_id self.tool = trans.app.toolbox.get_tool( tool_id, tool_version=tool_version ) self.post_job_actions = {} + self.runtime_post_job_actions = {} self.workflow_outputs = [] self.state = None self.version_changes = [] @@ -556,6 +564,9 @@ state = galaxy.tools.DefaultToolState() app = self.trans.app state.decode( runtime_state, self.tool, app, secure=False ) + state_dict = loads( runtime_state ) + if RUNTIME_STEP_META_STATE_KEY in state_dict: + self.__restore_step_meta_runtime_state( loads( state_dict[ RUNTIME_STEP_META_STATE_KEY ] ) ) return state def normalize_runtime_state( self, runtime_state ): @@ -572,16 +583,19 @@ step.tool_inputs = None step.tool_errors = self.errors for k, v in self.post_job_actions.iteritems(): - # Must have action_type, step. output and a_args are optional. - if 'output_name' in v: - output_name = v['output_name'] - else: - output_name = None - if 'action_arguments' in v: - action_arguments = v['action_arguments'] - else: - action_arguments = None - self.trans.sa_session.add(PostJobAction(v['action_type'], step, output_name, action_arguments)) + pja = self.__to_pja( k, v, step ) + self.trans.sa_session.add( pja ) + + def __to_pja( self, key, value, step ): + if 'output_name' in value: + output_name = value['output_name'] + else: + output_name = None + if 'action_arguments' in value: + action_arguments = value['action_arguments'] + else: + action_arguments = None + return PostJobAction(value['action_type'], step, output_name, action_arguments) def get_name( self ): if self.tool: @@ -677,7 +691,8 @@ tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) ) def encode_runtime_state( self, trans, state ): - return state.encode( self.tool, self.trans.app ) + encoded = state.encode( self.tool, self.trans.app ) + return encoded def update_state( self, incoming ): # Build a callback that handles setting an input to be required at @@ -712,26 +727,46 @@ self.errors = errors or None def check_and_update_state( self ): - return self.tool.check_and_update_param_values( self.state.inputs, self.trans, allow_workflow_parameters=True ) + inputs = self.state.inputs + return self.tool.check_and_update_param_values( inputs, self.trans, allow_workflow_parameters=True ) def compute_runtime_state( self, trans, step_updates=None, source="html" ): # Warning: This method destructively modifies existing step state. step_errors = None state = self.state + self.runtime_post_job_actions = {} if step_updates: # Get the tool tool = self.tool # Get old errors old_errors = state.inputs.pop( "__errors__", {} ) # Update the state + self.runtime_post_job_actions = step_updates.get(RUNTIME_POST_JOB_ACTIONS_KEY, {}) step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates, update_only=True, old_errors=old_errors, source=source ) + step_metadata_runtime_state = self.__step_meta_runtime_state() + if step_metadata_runtime_state: + state.inputs[ RUNTIME_STEP_META_STATE_KEY ] = step_metadata_runtime_state return state, step_errors + def __step_meta_runtime_state( self ): + """ Build a dictionary a of meta-step runtime state (state about how + the workflow step - not the tool state) to be serialized with the Tool + state. + """ + return { RUNTIME_POST_JOB_ACTIONS_KEY: self.runtime_post_job_actions } + + def __restore_step_meta_runtime_state( self, step_runtime_state ): + if RUNTIME_POST_JOB_ACTIONS_KEY in step_runtime_state: + self.runtime_post_job_actions = step_runtime_state[ RUNTIME_POST_JOB_ACTIONS_KEY ] + def execute( self, trans, progress, invocation, step ): tool = trans.app.toolbox.get_tool( step.tool_id, tool_version=step.tool_version ) tool_state = step.state - + # Not strictly needed - but keep Tool state clean by stripping runtime + # metadata parameters from it. + if RUNTIME_STEP_META_STATE_KEY in tool_state.inputs: + del tool_state.inputs[ RUNTIME_STEP_META_STATE_KEY ] collections_to_match = self._find_collections_to_match( tool, progress, step ) # Have implicit collections... if collections_to_match.has_collections(): @@ -815,7 +850,10 @@ # Create new PJA associations with the created job, to be run on completion. # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. - for pja in step.post_job_actions: + post_job_actions = step.post_job_actions + for key, value in self.runtime_post_job_actions.iteritems(): + post_job_actions.append( self.__to_pja( key, value, step ) ) + for pja in post_job_actions: if pja.action_type in ActionBox.immediate_actions: ActionBox.execute( self.trans.app, self.trans.sa_session, pja, job, replacement_dict ) else: diff -r 3fc8ce62285bc3df5b934439e624f2d56cb062cf -r 03955af117563248e950ec97d151c4a4615eaa58 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -151,7 +151,7 @@ else: effective_key = key value = param_dict[key] - if isinstance(value, dict) and not ('src' in value and 'id' in value): + if isinstance(value, dict) and (not ('src' in value and 'id' in value) and key != "__POST_JOB_ACTIONS__"): new_params.update(_flatten_step_params( value, effective_key) ) else: new_params[effective_key] = value diff -r 3fc8ce62285bc3df5b934439e624f2d56cb062cf -r 03955af117563248e950ec97d151c4a4615eaa58 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -163,8 +163,7 @@ # Wait for workflow to become fully scheduled and then for all jobs # complete. if wait: - self.wait_for_invocation( workflow_id, invocation_id ) - self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + self._wait_for_workflow( workflow_id, invocation_id, history_id ) jobs = self._history_jobs( history_id ) return RunJobsSummary( history_id=history_id, @@ -180,6 +179,12 @@ def _history_jobs( self, history_id ): return self._get("jobs", { "history_id": history_id, "order_by": "create_time" } ).json() + def _wait_for_workflow( self, workflow_id, invocation_id, history_id, assert_ok=True ): + """ Wait for a workflow invocation to completely schedule and then history + to be complete. """ + self.wait_for_invocation( workflow_id, invocation_id ) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + # Workflow API TODO: # - Allow history_id as param to workflow run action. (hist_id) @@ -743,6 +748,87 @@ content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True ) assert content[ "name" ] == "foo was replaced" + @skip_without_tool( "cat1" ) + def test_run_with_runtime_pja( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_pja_runtime" ) + uuid0, uuid1, uuid2 = str(uuid4()), str(uuid4()), str(uuid4()) + workflow["steps"]["0"]["uuid"] = uuid0 + workflow["steps"]["1"]["uuid"] = uuid1 + workflow["steps"]["2"]["uuid"] = uuid2 + workflow_request, history_id = self._setup_workflow_run( workflow, inputs_by='step_index' ) + workflow_request[ "replacement_params" ] = dumps( dict( replaceme="was replaced" ) ) + + pja_map = { + "RenameDatasetActionout_file1": dict( + action_type="RenameDatasetAction", + output_name="out_file1", + action_arguments=dict( newname="foo ${replaceme}" ), + ) + } + workflow_request[ "parameters" ] = dumps({ + uuid2: { "__POST_JOB_ACTIONS__": pja_map } + }) + + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True ) + assert content[ "name" ] == "foo was replaced", content[ "name" ] + + @skip_without_tool( "cat1" ) + def test_run_with_delayed_runtime_pja( self ): + workflow_id = self._upload_yaml_workflow(""" +- label: test_input + type: input +- label: first_cat + tool_id: cat1 + state: + input1: + $link: test_input +- label: the_pause + type: pause + connect: + input: + - first_cat#out_file1 +- label: second_cat + tool_id: cat1 + state: + input1: + $link: the_pause +""") + downloaded_workflow = self._download_workflow( workflow_id ) + print downloaded_workflow + uuid_dict = dict( map( lambda (index, step): ( int( index ), step["uuid"] ), downloaded_workflow["steps"].iteritems() ) ) + history_id = self.dataset_populator.new_history() + hda = self.dataset_populator.new_dataset( history_id, content="1 2 3" ) + self.dataset_populator.wait_for_history( history_id ) + inputs = { + '0': self._ds_entry( hda ), + } + print inputs + uuid2 = uuid_dict[ 3 ] + workflow_request = {} + workflow_request[ "replacement_params" ] = dumps( dict( replaceme="was replaced" ) ) + pja_map = { + "RenameDatasetActionout_file1": dict( + action_type="RenameDatasetAction", + output_name="out_file1", + action_arguments=dict( newname="foo ${replaceme}" ), + ) + } + workflow_request[ "parameters" ] = dumps({ + uuid2: { "__POST_JOB_ACTIONS__": pja_map } + }) + invocation_id = self.__invoke_workflow( history_id, workflow_id, inputs=inputs, request=workflow_request ) + + time.sleep( 2 ) + self.dataset_populator.wait_for_history( history_id ) + self.__review_paused_steps( workflow_id, invocation_id, order_index=2, action=True ) + + self._wait_for_workflow( workflow_id, invocation_id, history_id ) + time.sleep( 1 ) + content = self.dataset_populator.get_history_dataset_details( history_id ) + assert content[ "name" ] == "foo was replaced", content[ "name" ] + @skip_without_tool( "random_lines1" ) def test_run_replace_params_by_tool( self ): workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" ) @@ -932,15 +1018,13 @@ self._assert_status_code_is( hda_info_response, 200 ) self.assertEquals( hda_info_response.json()[ "metadata_data_lines" ], lines ) - def __invoke_workflow( self, history_id, workflow_id, inputs={}, assert_ok=True ): - workflow_request = dict( - history="hist_id=%s" % history_id, - ) - workflow_request[ "inputs" ] = dumps( inputs ) - workflow_request[ "inputs_by" ] = 'step_index' + def __invoke_workflow( self, history_id, workflow_id, inputs={}, request={}, assert_ok=True ): + request["history"] = "hist_id=%s" % history_id, + if inputs: + request[ "inputs" ] = dumps( inputs ) + request[ "inputs_by" ] = 'step_index' url = "workflows/%s/usage" % ( workflow_id ) - - invocation_response = self._post( url, data=workflow_request ) + invocation_response = self._post( url, data=request ) if assert_ok: self._assert_status_code_is( invocation_response, 200 ) invocation_id = invocation_response.json()[ "id" ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Another hack to fix 08f8850.
by commits-noreply＠bitbucket.org 05 Jan '15

05 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3fc8ce62285b/ Changeset: 3fc8ce62285b User: jmchilton Date: 2015-01-05 17:35:38+00:00 Summary: Another hack to fix 08f8850. Need to figure out when tools are being loaded but don't have lineages defined. Affected #: 1 file diff -r 95189e44b9bfe5adac1841b72d621a99bff6c927 -r 3fc8ce62285bc3df5b934439e624f2d56cb062cf lib/galaxy/tools/toolbox/base.py --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -295,7 +295,10 @@ inserted = True if not inserted: # Check the tool's installed versions. - for tool_lineage_version in tool.lineage.get_versions(): + versions = [] + if hasattr( tool, 'lineage' ): + versions = tool.lineage.get_versions() + for tool_lineage_version in versions: lineage_id = tool_lineage_version.id index = self._integrated_tool_panel.index_of_tool_id( lineage_id ) if index: 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: Browser tests: remove console statements interferring with test json parsing
by commits-noreply＠bitbucket.org 05 Jan '15

05 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95189e44b9bf/ Changeset: 95189e44b9bf User: carlfeberhard Date: 2015-01-05 15:34:05+00:00 Summary: Browser tests: remove console statements interferring with test json parsing Affected #: 2 files diff -r e34bf92384b6a6722657d83833fb52268865126d -r 95189e44b9bfe5adac1841b72d621a99bff6c927 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -355,7 +355,6 @@ // have to attach like GET param - due to body loss in jq url = utils.format( this.urlTpls.update, historyId, id ); if( purge ){ -console.debug( 'adding purge:' + purge ); url += '?purge=True'; } return this.api._ajax( url, { diff -r e34bf92384b6a6722657d83833fb52268865126d -r 95189e44b9bfe5adac1841b72d621a99bff6c927 test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -139,9 +139,6 @@ var hdaOpacity = this.evaluate( function( name ){ // locate the hda by name and return its opacity - console.debug( name ); - console.debug( $( '.name:contains("' + name + '")' ) ); - console.debug( $( '.name:contains("' + name + '")' ).parents( '.hda' ) ); return $( '.name:contains("' + name + '")' ).parents( '.dataset' ).css( 'opacity' ); }, hdaName ); //this.debug( 'fading in: ' + hdaOpacity ); 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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[galaxyproject/usegalaxy-playbook] b5acab: Increase memory for fastq_paired_end_joiner
by GitHub 05 Jan '15

05 Jan '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b5acab82552361587405c1b3140c82fbb709b610 https://github.com/galaxyproject/usegalaxy-playbook/commit/b5acab8255236158… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-01-05 (Mon, 05 Jan 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase memory for fastq_paired_end_joiner

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galaxy-commits January 2015