3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/23afd47845fe/ Changeset: 23afd47845fe User: jmchilton Date: 2013-11-20 23:44:09 Summary: Add stderr and stdout to provenance information. Affected #: 1 file diff -r ef45d85b1f579c5bb4b07284dd96ad8403003c03 -r 23afd47845fec9b8169712d0e78ee8d2baf0d96d lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -48,6 +48,8 @@ "uuid": ( lambda uuid: str( uuid ) if uuid else None )( item.dataset.uuid), "tool_id": job.tool_id, "parameters": self._get_job_record(trans, job, follow), + "stderr": job.stderr, + "stdout": job.stdout, } return None https://bitbucket.org/galaxy/galaxy-central/commits/bd8b3e2a9938/ Changeset: bd8b3e2a9938 User: jmchilton Date: 2013-11-20 23:44:09 Summary: Allow raw display of composite files via API. Affected #: 1 file diff -r 23afd47845fec9b8169712d0e78ee8d2baf0d96d -r bd8b3e2a99389f0564a1ff0dbfb9e3d56e56f990 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -265,7 +265,12 @@ except KeyError: pass if raw: - rval = open( hda.file_name ) + if filename and filename != 'index': + file_path = trans.app.object_store.get_filename(hda.dataset, extra_dir='dataset_%s_files' % hda.dataset.id, alt_name=filename) + else: + file_path = hda.file_name + rval = open( file_path ) + else: rval = hda.datatype.display_data( trans, hda, preview, filename, to_ext, chunk, **display_kwd ) https://bitbucket.org/galaxy/galaxy-central/commits/7a882c5fdd34/ Changeset: 7a882c5fdd34 User: jmchilton Date: 2013-11-20 23:44:09 Summary: Allow simple use of multi-page tools via API. In tools module, when process_state=='populate' (i.e. coming from tool API without existing tool_state specified), populate and validate state of all pages of tools. Affected #: 1 file diff -r bd8b3e2a99389f0564a1ff0dbfb9e3d56e56f990 -r 7a882c5fdd34636ae5ca98f63709c13a6648c3cf lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1811,7 +1811,8 @@ from API). May want an incremental version of the API also at some point, that is why this is not just called for_api. """ - state, state_new = self.__fetch_state( trans, incoming, history ) + all_pages = ( process_state == "populate" ) # If process_state = update, handle all pages at once. + state, state_new = self.__fetch_state( trans, incoming, history, all_pages=all_pages ) if state_new: # This feels a bit like a hack. It allows forcing full processing # of inputs even when there is no state in the incoming dictionary @@ -1837,7 +1838,7 @@ error_message = "One or more errors were found in the input you provided. The specific errors are marked below." return "tool_form.mako", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message ) # If we've completed the last page we can execute the tool - elif state.page == self.last_page: + elif all_pages or state.page == self.last_page: return self.__handle_tool_execute( trans, incoming, params, history ) # Otherwise move on to the next page else: @@ -1891,7 +1892,7 @@ return 'message.mako', dict( status='info', message="The interface for this tool cannot be displayed", refresh_frames=['everything'] ) return 'tool_form.mako', dict( errors=errors, tool_state=state ) - def __fetch_state( self, trans, incoming, history ): + def __fetch_state( self, trans, incoming, history, all_pages ): # Get the state or create if not found if "tool_state" in incoming: encoded_state = string_to_object( incoming["tool_state"] ) @@ -1899,7 +1900,7 @@ state.decode( encoded_state, self, trans.app ) new = False else: - state = self.new_state( trans, history=history ) + state = self.new_state( trans, history=history, all_pages=all_pages ) new = True return state, new @@ -1917,15 +1918,17 @@ # Update state for all inputs on the current page taking new # values from `incoming`. if process_state == "update": - errors = self.update_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, old_errors=old_errors or {}, source=source ) + inputs = self.inputs_by_page[state.page] + errors = self.update_state( trans, inputs, state.inputs, incoming, old_errors=old_errors or {}, source=source ) elif process_state == "populate": - errors = self.populate_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, history, source=source ) + inputs = self.inputs + errors = self.populate_state( trans, inputs, state.inputs, incoming, history, source=source ) else: raise Exception("Unknown process_state type %s" % process_state) # If the tool provides a `validate_input` hook, call it. validate_input = self.get_hook( 'validate_input' ) if validate_input: - validate_input( trans, errors, state.inputs, self.inputs_by_page[state.page] ) + validate_input( trans, errors, state.inputs, inputs ) params = state.inputs return errors, params Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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