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commit/galaxy-central: dannon: Missed .hgignore change, reverted.
by Bitbucket 29 Aug '12

29 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/36591da93d40/ changeset: 36591da93d40 user: dannon date: 2012-08-29 16:20:49 summary: Missed .hgignore change, reverted. affected #: 1 file diff -r 07045f4895170a154c955f48291f2b5e6feb94c2 -r 36591da93d40a924a6276aefa49edcf8a675437c .hgignore --- a/.hgignore +++ b/.hgignore @@ -78,7 +78,3 @@ *.rej *~ -syntax: regexp -^database$ -syntax: regexp -^scripts/api/spp_submodule\.ga$ 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: 10 new changesets
by Bitbucket 29 Aug '12

29 Aug '12

10 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/849e1713f613/ changeset: 849e1713f613 user: rpark37 date: 2012-02-01 22:21:38 summary: Updated scripts for API workflow enhancements and changing wor= kflow parameters programatically affected #: 6 files diff -r 90aa7ae565d60d38c90f444322a68b55fc895701 -r 849e1713f613a1932595b82= fcd0e65a19bf5e366 .hgignore --- a/.hgignore +++ b/.hgignore @@ -78,3 +78,7 @@ *.rej *~ =20 +syntax: regexp +^database$ +syntax: regexp +^scripts/api/spp_submodule\.ga$ diff -r 90aa7ae565d60d38c90f444322a68b55fc895701 -r 849e1713f613a1932595b82= fcd0e65a19bf5e366 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -84,6 +84,20 @@ =20 However, we will import them if installed_repository_file is speci= fied """ + + # ----------------------------------------------------------------= --------------- # =20 + ### RPARK: dictionary containing which workflows to change and edi= t ### + param_map =3D {}; + if (payload.has_key('parameters') ): + #if (payload['parameters']): + param_map =3D payload['parameters']; + print("PARAMETER MAP:"); + print(param_map); + # ----------------------------------------------------------------= --------------- # =20 + =20 + + =20 + =20 if 'workflow_id' not in payload: # create new if 'installed_repository_file' in payload: @@ -168,6 +182,30 @@ # are not persisted so we need to do it every time) step.module.add_dummy_datasets( connections=3Dstep.input_c= onnections ) step.state =3D step.module.state + =20 + #################################################### + #################################################### + #print("CHECKING WORKFLOW STEPS:") + #print(step.tool_id); + #print(step.state.inputs); + #print("upgard messages"); + #print(step.state); + #print("\n"); + # RPARK: IF TOOL_NAME IN PARAMETER MAP # + if step.tool_id in param_map: + #print("-------------------------FOUND IN PARAMETER DI= CTIONARY") + #print(param_map[step.tool_id]); + change_param =3D param_map[step.tool_id]['param']; + change_value =3D param_map[step.tool_id]['value']; + #step.state.inputs['refGenomeSource']['index'] =3D "cr= apolo"; + #print(step.state.inputs[change_param]); + step.state.inputs[change_param] =3D change_value; + #print(step.state.inputs[change_param]); + #print(param_map[step.tool_id][change_value]); + #print("----------------------------------------------= ----") + #################################################### + #################################################### + =20 if step.tool_errors: trans.response.status =3D 400 return "Workflow cannot be run because of validation e= rrors in some steps: %s" % step_errors @@ -220,3 +258,343 @@ trans.sa_session.flush() return rval =20 + # --------------------------------------------------------------------= -------------------------- # + # --------------------------------------------------------------------= -------------------------- # + # ---- RPARK EDITS ---- # + # --------------------------------------------------------------------= -------------------------- # + # --------------------------------------------------------------------= -------------------------- # + @web.expose_api + @web.json + def workflow_dict( self, trans, workflow_id, **kwd ): + """ + GET /api/workflows/{encoded_workflow_id}/download + Returns a selected workflow as a json dictionary.=20 + """ + print "workflow controller: workflow dict called" + print workflow_id + =20 + try: + stored_workflow =3D trans.sa_session.query(self.app.model.Stor= edWorkflow).get(trans.security.decode_id(workflow_id)) + except Exception,e: + return ("Workflow with ID=3D'%s' can not be found\n Exception:= %s") % (workflow_id, str( e )) + =20 + # check to see if user has permissions to selected workflow=20 + if stored_workflow.user !=3D trans.user and not trans.user_is_admi= n(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserSh= areAssociation).filter_by(user=3Dtrans.user, stored_workflow=3Dstored_workf= low).count() =3D=3D 0: + trans.response.status =3D 400 + return("Workflow is not owned by or shared with current us= er") + =20 + return self._workflow_to_dict( trans, stored_workflow ) + =20 + @web.expose_api + def delete( self, trans, id, **kwd ): =20 + """ + DELETE /api/workflows/{encoded_workflow_id} + Deletes a specified workflow + Author: rpark + =20 + copied from galaxy.web.controllers.workflows.py (delete) + """ + workflow_id =3D id; + =20 + try: + stored_workflow =3D trans.sa_session.query(self.app.model.Stor= edWorkflow).get(trans.security.decode_id(workflow_id)) + except Exception,e: + return ("Workflow with ID=3D'%s' can not be found\n Exception:= %s") % (workflow_id, str( e )) + =20 + # check to see if user has permissions to selected workflow=20 + if stored_workflow.user !=3D trans.user and not trans.user_is_admi= n(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserSh= areAssociation).filter_by(user=3Dtrans.user, stored_workflow=3Dstored_workf= low).count() =3D=3D 0: + trans.response.status =3D 400 + return("Workflow is not owned by or shared with current us= er") + + #Mark a workflow as deleted + stored_workflow.deleted =3D True + trans.sa_session.flush() + =20 + # Python Debugger + #import pdb; pdb.set_trace() + =20 + # TODO: Unsure of response message to let api know that a workflow= was successfully deleted + #return 'OK' + return ( "Workflow '%s' successfully deleted" % stored_workflow.na= me ) + =20 + @web.expose_api + def import_new_workflow(self, trans, payload, **kwd): + """ + POST /api/workflows + Importing dynamic workflows from the api. Return newly generated w= orkflow id. + Author: rpark=20 + =20 + # currently assumes payload['workflow'] is a json representation o= f a workflow to be inserted into the database + """ + =20 + #import pdb; pdb.set_trace() + =20 + data =3D payload['workflow']; + workflow, missing_tool_tups =3D self._workflow_from_dict( trans, d= ata, source=3D"API" ) + =20 + # galaxy workflow newly created id =20 + workflow_id =3D workflow.id; + # api encoded, id=20 + encoded_id =3D trans.security.encode_id(workflow_id); + =20 + =20 + =20 + # return list + rval=3D []; + =20 + item =3D workflow.get_api_value(value_mapper=3D{'id':trans.securit= y.encode_id}) + item['url'] =3D url_for('workflow', id=3Dencoded_id) + =20 + rval.append(item); =20 + =20 + return rval; + =20 + + def _workflow_from_dict( self, trans, data, source=3DNone ): + """ + RPARK: copied from galaxy.web.controllers.workflows.py + Creates a workflow from a dict. Created workflow is stored in the = database and returned. + """ + # Put parameters in workflow mode + trans.workflow_building_mode =3D True + # Create new workflow from incoming dict + workflow =3D model.Workflow() + # If there's a source, put it in the workflow name. + if source: + name =3D "%s (imported from %s)" % ( data['name'], source ) + else: + name =3D data['name'] + workflow.name =3D name + # Assume no errors until we find a step that has some + workflow.has_errors =3D False + # Create each step + steps =3D [] + # The editor will provide ids for each step that we don't need to = save, + # but do need to use to make connections + steps_by_external_id =3D {} + # Keep track of tools required by the workflow that are not availa= ble in + # the local Galaxy instance. Each tuple in the list of missing_to= ol_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups =3D [] + # First pass to build step objects and populate basic values + for key, step_dict in data[ 'steps' ].iteritems(): + # Create the model class for the step + step =3D model.WorkflowStep() + steps.append( step ) + steps_by_external_id[ step_dict['id' ] ] =3D step + # FIXME: Position should be handled inside module + step.position =3D step_dict['position'] + module =3D module_factory.from_dict( trans, step_dict, secure= =3DFalse ) + if module.type =3D=3D 'tool' and module.tool is None: + # A required tool is not available in the local Galaxy ins= tance. + missing_tool_tup =3D ( step_dict[ 'tool_id' ], step_dict[ = 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) + module.save_to_step( step ) + if step.tool_errors: + workflow.has_errors =3D True + # Stick this in the step temporarily + step.temp_input_connections =3D step_dict['input_connections'] + =20 + # Save step annotation. + annotation =3D step_dict[ 'annotation' ] + if annotation: + annotation =3D sanitize_html( annotation, 'utf-8', 'text/h= tml' ) + # ------------------------------------------ # + # RPARK REMOVING: user annotation b/c of API + #self.add_item_annotation( trans.sa_session, trans.get_use= r(), step, annotation ) + # ------------------------------------------ # + =20 + # Unpack and add post-job actions. + post_job_actions =3D step_dict.get( 'post_job_actions', {} ) + for name, pja_dict in post_job_actions.items(): + pja =3D PostJobAction( pja_dict[ 'action_type' ],=20 + step, pja_dict[ 'output_name' ],=20 + pja_dict[ 'action_arguments' ] ) + # Second pass to deal with connections between steps + for step in steps: + # Input connections + for input_name, conn_dict in step.temp_input_connections.iteri= tems(): + if conn_dict: + conn =3D model.WorkflowStepConnection() + conn.input_step =3D step + conn.input_name =3D input_name + conn.output_name =3D conn_dict['output_name'] + conn.output_step =3D steps_by_external_id[ conn_dict['= id'] ] + del step.temp_input_connections + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + # Connect up + stored =3D model.StoredWorkflow() + stored.name =3D workflow.name + workflow.stored_workflow =3D stored + stored.latest_workflow =3D workflow + stored.user =3D trans.user + # Persist + trans.sa_session.add( stored ) + trans.sa_session.flush() + return stored, missing_tool_tups + =20 + def _workflow_to_dict( self, trans, stored ): + """ + RPARK: copied from galaxy.web.controllers.workflows.py + Converts a workflow to a dict of attributes suitable for exporting. + """ + workflow =3D stored.latest_workflow + =20 + ### ----------------------------------- ### + ## RPARK EDIT ## + workflow_annotation =3D self.get_item_annotation_obj( trans.sa_ses= sion, trans.user, stored ) + annotation_str =3D "" + if workflow_annotation: + annotation_str =3D workflow_annotation.annotation + ### ----------------------------------- ### + =20 + =20 + # Pack workflow data into a dictionary and return + data =3D {} + data['a_galaxy_workflow'] =3D 'true' # Placeholder for identifying= galaxy workflow + data['format-version'] =3D "0.1" + data['name'] =3D workflow.name + ### ----------------------------------- ### + ## RPARK EDIT ## + data['annotation'] =3D annotation_str + ### ----------------------------------- ### + =20 + data['steps'] =3D {} + # For each step, rebuild the form and encode the state + for step in workflow.steps: + # Load from database representation + module =3D module_factory.from_workflow_step( trans, step ) + =20 + ### ----------------------------------- ### + ## RPARK EDIT ## + # Get user annotation. + step_annotation =3D self.get_item_annotation_obj(trans.sa_sess= ion, trans.user, step ) + annotation_str =3D "" + if step_annotation: + annotation_str =3D step_annotation.annotation =20 + ### ----------------------------------- ### + =20 + # Step info + step_dict =3D { + 'id': step.order_index, + 'type': module.type, + 'tool_id': module.get_tool_id(), + 'tool_version' : step.tool_version, + 'name': module.get_name(), + 'tool_state': module.get_state( secure=3DFalse ), + 'tool_errors': module.get_errors(), + ## 'data_inputs': module.get_data_inputs(), + ## 'data_outputs': module.get_data_outputs(), + =20 + ### ----------------------------------- ### + ## RPARK EDIT ## + 'annotation' : annotation_str + ### ----------------------------------- ### + =20 + } + # Add post-job actions to step dict. + if module.type =3D=3D 'tool': + pja_dict =3D {} + for pja in step.post_job_actions: + pja_dict[pja.action_type+pja.output_name] =3D dict( ac= tion_type =3D pja.action_type,=20 + outp= ut_name =3D pja.output_name, + acti= on_arguments =3D pja.action_arguments ) + step_dict[ 'post_job_actions' ] =3D pja_dict + # Data inputs + step_dict['inputs'] =3D [] + if module.type =3D=3D "data_input": + # Get input dataset name; default to 'Input Dataset' + name =3D module.state.get( 'name', 'Input Dataset') + step_dict['inputs'].append( { "name" : name, "description"= : annotation_str } ) + else: + # Step is a tool and may have runtime inputs. + for name, val in module.state.inputs.items(): + input_type =3D type( val ) + if input_type =3D=3D RuntimeValue: + step_dict['inputs'].append( { "name" : name, "desc= ription" : "runtime parameter for tool %s" % module.get_name() } ) + elif input_type =3D=3D dict: + # Input type is described by a dict, e.g. indexed = parameters. + for partname, partval in val.items(): + if type( partval ) =3D=3D RuntimeValue: + step_dict['inputs'].append( { "name" : nam= e, "description" : "runtime parameter for tool %s" % module.get_name() } ) + # User outputs + step_dict['user_outputs'] =3D [] + """ + module_outputs =3D module.get_data_outputs() + step_outputs =3D trans.sa_session.query( WorkflowOutput ).filt= er( step=3Dstep ) + for output in step_outputs: + name =3D output.output_name + annotation =3D "" + for module_output in module_outputs: + if module_output.get( 'name', None ) =3D=3D name: + output_type =3D module_output.get( 'extension', ''= ) + break + data['outputs'][name] =3D { 'name' : name, 'annotation' : = annotation, 'type' : output_type } + """ + + # All step outputs + step_dict['outputs'] =3D [] + if type( module ) is ToolModule: + for output in module.get_data_outputs(): + step_dict['outputs'].append( { 'name' : output['name']= , 'type' : output['extensions'][0] } ) + # Connections + input_connections =3D step.input_connections + if step.type is None or step.type =3D=3D 'tool': + # Determine full (prefixed) names of valid input datasets + data_input_names =3D {} + def callback( input, value, prefixed_name, prefixed_label = ): + if isinstance( input, DataToolParameter ): + data_input_names[ prefixed_name ] =3D True + visit_input_values( module.tool.inputs, module.state.input= s, callback ) + # Filter + # FIXME: this removes connection without displaying a mess= age currently! + input_connections =3D [ conn for conn in input_connections= if conn.input_name in data_input_names ] + # Encode input connections as dictionary + input_conn_dict =3D {} + for conn in input_connections: + input_conn_dict[ conn.input_name ] =3D \ + dict( id=3Dconn.output_step.order_index, output_name= =3Dconn.output_name ) + step_dict['input_connections'] =3D input_conn_dict + # Position + step_dict['position'] =3D step.position + # Add to return value + data['steps'][step.order_index] =3D step_dict + return data + =20 + def get_item_annotation_obj( self, db_session, user, item ): + """=20 + RPARK: copied from galaxy.model.item_attr.py + Returns a user's annotation object for an item. """ + # Get annotation association class. + annotation_assoc_class =3D self._get_annotation_assoc_class( item ) + if not annotation_assoc_class: + return None + =20 + # Get annotation association object. + annotation_assoc =3D db_session.query( annotation_assoc_class ).fi= lter_by( user=3Duser ) + =20 + # TODO: use filtering like that in _get_item_id_filter_str() + if item.__class__ =3D=3D galaxy.model.History: + annotation_assoc =3D annotation_assoc.filter_by( history=3Dite= m ) + elif item.__class__ =3D=3D galaxy.model.HistoryDatasetAssociation: + annotation_assoc =3D annotation_assoc.filter_by( hda=3Ditem ) + elif item.__class__ =3D=3D galaxy.model.StoredWorkflow: + annotation_assoc =3D annotation_assoc.filter_by( stored_workfl= ow=3Ditem ) + elif item.__class__ =3D=3D galaxy.model.WorkflowStep: + annotation_assoc =3D annotation_assoc.filter_by( workflow_step= =3Ditem ) + elif item.__class__ =3D=3D galaxy.model.Page: + annotation_assoc =3D annotation_assoc.filter_by( page=3Ditem ) + elif item.__class__ =3D=3D galaxy.model.Visualization: + annotation_assoc =3D annotation_assoc.filter_by( visualization= =3Ditem ) + return annotation_assoc.first() + =20 + def _get_annotation_assoc_class( self, item ): + """=20 + RPARK: copied from galaxy.model.item_attr.py + Returns an item's item-annotation association class. """ + class_name =3D '%sAnnotationAssociation' % item.__class__.__name__ + return getattr( galaxy.model, class_name, None ) diff -r 90aa7ae565d60d38c90f444322a68b55fc895701 -r 849e1713f613a1932595b82= fcd0e65a19bf5e366 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -151,6 +151,20 @@ webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_= prefix=3D'/api' ) #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_i= d}/library/{library_id}', controller=3D'workflows', action=3D'run', workflo= w_id=3DNone, library_id=3DNone, conditions=3Ddict(method=3D["GET"]) ) =20 + # ---------------------------------------------- # + # ---------------------------------------------- # + # RPARK EDIT=20 + =20 + # How to extend API: url_mapping=20 + # "POST /api/workflows/import" =3D> ``workflows.import_workflow(= )``. + # Defines a named route "import_workflow". + webapp.api_mapper.connect("import_workflow", "/api/workflows/uploa= d", controller=3D"workflows", action=3D"import_new_workflow", conditions=3D= dict(method=3D["POST"])) + webapp.api_mapper.connect("workflow_dict", '/api/workflows/downloa= d/{workflow_id}', controller=3D'workflows', action=3D'workflow_dict', condi= tions=3Ddict(method=3D['GET'])) + =20 + #import pdb; pdb.set_trace() =20 + # ---------------------------------------------- # + # ---------------------------------------------- # + =20 webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r 90aa7ae565d60d38c90f444322a68b55fc895701 -r 849e1713f613a1932595b82= fcd0e65a19bf5e366 scripts/api/workflow_delete_workflow_rpark.py --- /dev/null +++ b/scripts/api/workflow_delete_workflow_rpark.py @@ -0,0 +1,22 @@ +#!/usr/bin/env python +""" +# Author: RPARK +API script for deleting workflows=20 +""" + +import os, sys +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import delete + +try: + assert sys.argv[2] +except IndexError: + print 'usage: %s key url [purge (true/false)] ' % os.path.basename( sy= s.argv[0] ) + sys.exit( 1 ) +try: + data =3D {} + data[ 'purge' ] =3D sys.argv[3] +except IndexError: + pass + +delete( sys.argv[1], sys.argv[2], data ) diff -r 90aa7ae565d60d38c90f444322a68b55fc895701 -r 849e1713f613a1932595b82= fcd0e65a19bf5e366 scripts/api/workflow_execute_rpark.py --- /dev/null +++ b/scripts/api/workflow_execute_rpark.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python +""" +Execute workflows from the command line. +Example calls: +python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'Test API History' '38=3Dldda=3D0qr350234d2d192f' +python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'hist_id=3Da912e9e5d84530d4' '38=3Dhda=3D03501d7626bd192f' +""" + +""" +python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'hist_id=3Da912e9e5d84530d4' '38=3Dhda=3D03501d7626bd192f' 'param=3Dt= ool=3Dname=3Dvalue'=20 + +'param=3Dtool=3Dname=3Dvalue' + +Example=20 +python workflow_execute_rpark.py 35a24ae2643785ff3d046c98ea362c7f http://l= ocalhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da799d386= 79e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Daligner= =3Dbwa'=20 + +python workflow_execute_rpark.py 35a24ae2643785ff3d046c98ea362c7f http://l= ocalhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da799d386= 79e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Daligner= =3Darachne' 'param=3Dbowtie_wrapper=3DsuppressHeader=3DTrue' + +python workflow_execute_rpark.py 35a24ae2643785ff3d046c98ea362c7f http://l= ocalhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da799d386= 79e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Daligner= =3Dbowtie' 'param=3Dbowtie_wrapper=3DsuppressHeader=3DTrue' 'param=3Dpeakca= lling_spp=3Dwindow_size=3D1000'=20 + +""" + +import os, sys +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import submit + + +def main(): + try: + print("workflow_execute:py:"); + data =3D {} + data['workflow_id'] =3D sys.argv[3] + data['history'] =3D sys.argv[4] + data['ds_map'] =3D {} + + ######################################################### + ### MY EDITS ############################################ + ### Trying to pass in parameter for my own dictionary ### + data['parameters'] =3D {}; + + # DBTODO If only one input is given, don't require a step + # mapping, just use it for everything? + for v in sys.argv[5:]: + print("Multiple arguments "); + print(v); + + try: + step, src, ds_id =3D v.split('=3D'); + data['ds_map'][step] =3D {'src':src, 'id':ds_id}; + + except ValueError: + print("VALUE ERROR:"); + wtype, wtool, wparam, wvalue =3D v.split('=3D'); + data['parameters'][wtool] =3D {'param':wparam, 'value':wva= lue} + + + ######################################################### + ### MY EDITS ############################################ + ### Trying to pass in parameter for my own dictionary ### + #data['parameters']['bowtie'] =3D {'param':'stepSize', 'value':100} + #data['parameters']['sam_to_bam'] =3D {'param':'genome', 'value':'= hg18'} + + except IndexError: + print 'usage: %s key url workflow_id history step=3Dsrc=3Ddataset_= id' % os.path.basename(sys.argv[0]) + sys.exit(1) + submit( sys.argv[1], sys.argv[2], data ) + +if __name__ =3D=3D '__main__': + main() + diff -r 90aa7ae565d60d38c90f444322a68b55fc895701 -r 849e1713f613a1932595b82= fcd0e65a19bf5e366 scripts/api/workflow_import_from_file_rpark.py --- /dev/null +++ b/scripts/api/workflow_import_from_file_rpark.py @@ -0,0 +1,39 @@ +#!/usr/bin/env python + +""" + +python rpark_import_workflow_from_file.py 35a24ae2643785ff3d046c98ea362c7f= http://localhost:8080/api/workflows/import 'spp_submodule.ga' +python rpark_import_workflow_from_file.py 35a24ae2643785ff3d046c98ea362c7f= http://localhost:8080/api/workflows/import 'spp_submodule.ga' +""" + +import os, sys +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import submit + +### Rpark edit ### +import simplejson + +def openWorkflow(in_file): =20 + with open(in_file) as f: + temp_data =3D simplejson.load(f) + return temp_data; + + + +try: + assert sys.argv[2] +except IndexError: + print 'usage: %s key url [name] ' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) +try: + #data =3D {} + #data[ 'name' ] =3D sys.argv[3] + data =3D {}; + workflow_dict =3D openWorkflow(sys.argv[3]); + data ['workflow'] =3D workflow_dict; + =20 + =20 +except IndexError: + pass + +submit( sys.argv[1], sys.argv[2], data ) https://bitbucket.org/galaxy/galaxy-central/changeset/67e4caf2a34f/ changeset: 67e4caf2a34f user: rpark37 date: 2012-02-01 22:28:00 summary: Updated import statements in workflows api controller affected #: 1 file diff -r 849e1713f613a1932595b82fcd0e65a19bf5e366 -r 67e4caf2a34f4dc6ae37697= 04696b18db98a3540 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -11,6 +11,21 @@ from galaxy.workflow.modules import module_factory from galaxy.jobs.actions.post import ActionBox =20 +# ------------------------------------------------------------------------= ---------------------- # +# ------------------------------------------------------------------------= ---------------------- # +# ---- RPARK EDITS ---- # +import pkg_resources +pkg_resources.require( "simplejson" ) +from galaxy import model +from galaxy.web.controllers.workflow import attach_ordered_steps +from galaxy.util.sanitize_html import sanitize_html +from galaxy.workflow.modules import * +from galaxy.model.item_attrs import * + +# ------------------------------------------------------------------------= ---------------------- # +# ------------------------------------------------------------------------= ---------------------- #=20 + + log =3D logging.getLogger(__name__) =20 class WorkflowsAPIController(BaseAPIController): https://bitbucket.org/galaxy/galaxy-central/changeset/7738795047c6/ changeset: 7738795047c6 user: rpark37 date: 2012-02-01 23:22:50 summary: updated workflow_dict function for returning a selected workfl= ow as a json object via API affected #: 1 file diff -r 67e4caf2a34f4dc6ae3769704696b18db98a3540 -r 7738795047c6a2af15d6b8a= 58173212b95c9f528 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -285,8 +285,6 @@ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary.=20 """ - print "workflow controller: workflow dict called" - print workflow_id =20 try: stored_workflow =3D trans.sa_session.query(self.app.model.Stor= edWorkflow).get(trans.security.decode_id(workflow_id)) https://bitbucket.org/galaxy/galaxy-central/changeset/a81a7e9ef257/ changeset: a81a7e9ef257 user: rpark37 date: 2012-02-08 23:23:58 summary: Updated import new workflow function affected #: 1 file diff -r 7738795047c6a2af15d6b8a58173212b95c9f528 -r a81a7e9ef257d26ee0fdcdc= d124f6205a4692653 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -279,7 +279,7 @@ # --------------------------------------------------------------------= -------------------------- # # --------------------------------------------------------------------= -------------------------- # @web.expose_api - @web.json + #(a)web.json def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download @@ -297,8 +297,9 @@ trans.response.status =3D 400 return("Workflow is not owned by or shared with current us= er") =20 - return self._workflow_to_dict( trans, stored_workflow ) - =20 + ret_dict =3D self._workflow_to_dict( trans, stored_workflow ); + return ret_dict + =20 @web.expose_api def delete( self, trans, id, **kwd ): =20 """ @@ -352,8 +353,6 @@ # api encoded, id=20 encoded_id =3D trans.security.encode_id(workflow_id); =20 - =20 - =20 # return list rval=3D []; =20 @@ -362,8 +361,7 @@ =20 rval.append(item); =20 =20 - return rval; - =20 + return item; =20 def _workflow_from_dict( self, trans, data, source=3DNone ): """ https://bitbucket.org/galaxy/galaxy-central/changeset/edcfb659dc4f/ changeset: edcfb659dc4f user: rpark37 date: 2012-03-16 22:23:15 summary: Updated workflow API affected #: 1 file diff -r a81a7e9ef257d26ee0fdcdcd124f6205a4692653 -r edcfb659dc4fc03e4385d63= e36e5df380a20c898 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -336,7 +336,7 @@ @web.expose_api def import_new_workflow(self, trans, payload, **kwd): """ - POST /api/workflows + POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated w= orkflow id. Author: rpark=20 =20 @@ -344,7 +344,7 @@ """ =20 #import pdb; pdb.set_trace() - =20 + =20 data =3D payload['workflow']; workflow, missing_tool_tups =3D self._workflow_from_dict( trans, d= ata, source=3D"API" ) =20 https://bitbucket.org/galaxy/galaxy-central/changeset/0f3e6e68d8f5/ changeset: 0f3e6e68d8f5 user: rpark37 date: 2012-04-11 05:00:41 summary: Updated notes on how to run api/workflow_execute_parameters.py affected #: 2 files diff -r edcfb659dc4fc03e4385d63e36e5df380a20c898 -r 0f3e6e68d8f53ffdaee2f37= 1cc3d21a0d6a3b3aa scripts/api/workflow_execute_parameters.py --- /dev/null +++ b/scripts/api/workflow_execute_parameters.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python +""" +Execute workflows from the command line. +Example calls: +python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'Test API History' '38=3Dldda=3D0qr350234d2d192f' +python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'hist_id=3Da912e9e5d84530d4' '38=3Dhda=3D03501d7626bd192f' +""" + +""" +python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'hist_id=3Da912e9e5d84530d4' '38=3Dhda=3D03501d7626bd192f' 'param=3Dt= ool=3Dname=3Dvalue'=20 + +'param=3Dtool=3Dname=3Dvalue' + +Example=20 +python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f htt= p://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da79= 9d38679e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Dalig= ner=3Dbwa'=20 + +python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f htt= p://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da79= 9d38679e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Dalig= ner=3Darachne' 'param=3Dbowtie_wrapper=3DsuppressHeader=3DTrue' + +python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f htt= p://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da79= 9d38679e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Dalig= ner=3Dbowtie' 'param=3Dbowtie_wrapper=3DsuppressHeader=3DTrue' 'param=3Dpea= kcalling_spp=3Dwindow_size=3D1000'=20 + +""" + +import os, sys +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import submit + + +def main(): + try: + print("workflow_execute:py:"); + data =3D {} + data['workflow_id'] =3D sys.argv[3] + data['history'] =3D sys.argv[4] + data['ds_map'] =3D {} + + ######################################################### + ### MY EDITS ############################################ + ### Trying to pass in parameter for my own dictionary ### + data['parameters'] =3D {}; + + # DBTODO If only one input is given, don't require a step + # mapping, just use it for everything? + for v in sys.argv[5:]: + print("Multiple arguments "); + print(v); + + try: + step, src, ds_id =3D v.split('=3D'); + data['ds_map'][step] =3D {'src':src, 'id':ds_id}; + + except ValueError: + print("VALUE ERROR:"); + wtype, wtool, wparam, wvalue =3D v.split('=3D'); + data['parameters'][wtool] =3D {'param':wparam, 'value':wva= lue} + + + ######################################################### + ### MY EDITS ############################################ + ### Trying to pass in parameter for my own dictionary ### + #data['parameters']['bowtie'] =3D {'param':'stepSize', 'value':100} + #data['parameters']['sam_to_bam'] =3D {'param':'genome', 'value':'= hg18'} + + except IndexError: + print 'usage: %s key url workflow_id history step=3Dsrc=3Ddataset_= id' % os.path.basename(sys.argv[0]) + sys.exit(1) + submit( sys.argv[1], sys.argv[2], data ) + +if __name__ =3D=3D '__main__': + main() + diff -r edcfb659dc4fc03e4385d63e36e5df380a20c898 -r 0f3e6e68d8f53ffdaee2f37= 1cc3d21a0d6a3b3aa scripts/api/workflow_execute_rpark.py --- a/scripts/api/workflow_execute_rpark.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python -""" -Execute workflows from the command line. -Example calls: -python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'Test API History' '38=3Dldda=3D0qr350234d2d192f' -python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'hist_id=3Da912e9e5d84530d4' '38=3Dhda=3D03501d7626bd192f' -""" - -""" -python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'hist_id=3Da912e9e5d84530d4' '38=3Dhda=3D03501d7626bd192f' 'param=3Dt= ool=3Dname=3Dvalue'=20 - -'param=3Dtool=3Dname=3Dvalue' - -Example=20 -python workflow_execute_rpark.py 35a24ae2643785ff3d046c98ea362c7f http://l= ocalhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da799d386= 79e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Daligner= =3Dbwa'=20 - -python workflow_execute_rpark.py 35a24ae2643785ff3d046c98ea362c7f http://l= ocalhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da799d386= 79e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Daligner= =3Darachne' 'param=3Dbowtie_wrapper=3DsuppressHeader=3DTrue' - -python workflow_execute_rpark.py 35a24ae2643785ff3d046c98ea362c7f http://l= ocalhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da799d386= 79e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Daligner= =3Dbowtie' 'param=3Dbowtie_wrapper=3DsuppressHeader=3DTrue' 'param=3Dpeakca= lling_spp=3Dwindow_size=3D1000'=20 - -""" - -import os, sys -sys.path.insert( 0, os.path.dirname( __file__ ) ) -from common import submit - - -def main(): - try: - print("workflow_execute:py:"); - data =3D {} - data['workflow_id'] =3D sys.argv[3] - data['history'] =3D sys.argv[4] - data['ds_map'] =3D {} - - ######################################################### - ### MY EDITS ############################################ - ### Trying to pass in parameter for my own dictionary ### - data['parameters'] =3D {}; - - # DBTODO If only one input is given, don't require a step - # mapping, just use it for everything? - for v in sys.argv[5:]: - print("Multiple arguments "); - print(v); - - try: - step, src, ds_id =3D v.split('=3D'); - data['ds_map'][step] =3D {'src':src, 'id':ds_id}; - - except ValueError: - print("VALUE ERROR:"); - wtype, wtool, wparam, wvalue =3D v.split('=3D'); - data['parameters'][wtool] =3D {'param':wparam, 'value':wva= lue} - - - ######################################################### - ### MY EDITS ############################################ - ### Trying to pass in parameter for my own dictionary ### - #data['parameters']['bowtie'] =3D {'param':'stepSize', 'value':100} - #data['parameters']['sam_to_bam'] =3D {'param':'genome', 'value':'= hg18'} - - except IndexError: - print 'usage: %s key url workflow_id history step=3Dsrc=3Ddataset_= id' % os.path.basename(sys.argv[0]) - sys.exit(1) - submit( sys.argv[1], sys.argv[2], data ) - -if __name__ =3D=3D '__main__': - main() - https://bitbucket.org/galaxy/galaxy-central/changeset/414b1b3fb029/ changeset: 414b1b3fb029 user: rpark37 date: 2012-04-11 05:05:23 summary: Cleaned up code for api/workflows.py affected #: 1 file diff -r 0f3e6e68d8f53ffdaee2f371cc3d21a0d6a3b3aa -r 414b1b3fb029a1acdd925b5= bef41d2a38415c695 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -104,10 +104,7 @@ ### RPARK: dictionary containing which workflows to change and edi= t ### param_map =3D {}; if (payload.has_key('parameters') ): - #if (payload['parameters']): param_map =3D payload['parameters']; - print("PARAMETER MAP:"); - print(param_map); # ----------------------------------------------------------------= --------------- # =20 =20 =20 @@ -200,24 +197,11 @@ =20 #################################################### #################################################### - #print("CHECKING WORKFLOW STEPS:") - #print(step.tool_id); - #print(step.state.inputs); - #print("upgard messages"); - #print(step.state); - #print("\n"); # RPARK: IF TOOL_NAME IN PARAMETER MAP # if step.tool_id in param_map: - #print("-------------------------FOUND IN PARAMETER DI= CTIONARY") - #print(param_map[step.tool_id]); change_param =3D param_map[step.tool_id]['param']; change_value =3D param_map[step.tool_id]['value']; - #step.state.inputs['refGenomeSource']['index'] =3D "cr= apolo"; - #print(step.state.inputs[change_param]); step.state.inputs[change_param] =3D change_value; - #print(step.state.inputs[change_param]); - #print(param_map[step.tool_id][change_value]); - #print("----------------------------------------------= ----") #################################################### #################################################### =20 https://bitbucket.org/galaxy/galaxy-central/changeset/8c33567aeca5/ changeset: 8c33567aeca5 user: rpark37 date: 2012-08-03 08:09:05 summary: Cleaned up codebase for attempting adding api additions to the= galaxy main branch affected #: 3 files diff -r 414b1b3fb029a1acdd925b5bef41d2a38415c695 -r 8c33567aeca58c4e7306d3b= eef590b82cff90be2 scripts/api/workflow_delete.py --- /dev/null +++ b/scripts/api/workflow_delete.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python +""" +# ---------------------------------------------- # +# PARKLAB, Author: RPARK +API example script for deleting workflows=20 +# ---------------------------------------------- # + +Example calls: +python workflow_delete.py <api_key><galaxy_url>/api/workflows/<workflow id= > True +""" + +import os, sys +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import delete + +try: + assert sys.argv[2] +except IndexError: + print 'usage: %s key url [purge (true/false)] ' % os.path.basename( sy= s.argv[0] ) + sys.exit( 1 ) +try: + data =3D {} + data[ 'purge' ] =3D sys.argv[3] +except IndexError: + pass + +delete( sys.argv[1], sys.argv[2], data ) diff -r 414b1b3fb029a1acdd925b5bef41d2a38415c695 -r 8c33567aeca58c4e7306d3b= eef590b82cff90be2 scripts/api/workflow_delete_workflow_rpark.py --- a/scripts/api/workflow_delete_workflow_rpark.py +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env python -""" -# Author: RPARK -API script for deleting workflows=20 -""" - -import os, sys -sys.path.insert( 0, os.path.dirname( __file__ ) ) -from common import delete - -try: - assert sys.argv[2] -except IndexError: - print 'usage: %s key url [purge (true/false)] ' % os.path.basename( sy= s.argv[0] ) - sys.exit( 1 ) -try: - data =3D {} - data[ 'purge' ] =3D sys.argv[3] -except IndexError: - pass - -delete( sys.argv[1], sys.argv[2], data ) diff -r 414b1b3fb029a1acdd925b5bef41d2a38415c695 -r 8c33567aeca58c4e7306d3b= eef590b82cff90be2 scripts/api/workflow_execute_parameters.py --- a/scripts/api/workflow_execute_parameters.py +++ b/scripts/api/workflow_execute_parameters.py @@ -1,23 +1,13 @@ #!/usr/bin/env python """ +# ---------------------------------------------- # +# PARKLAB, Author: RPARK +# ---------------------------------------------- # + Execute workflows from the command line. Example calls: -python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'Test API History' '38=3Dldda=3D0qr350234d2d192f' -python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'hist_id=3Da912e9e5d84530d4' '38=3Dhda=3D03501d7626bd192f' -""" - -""" -python workflow_execute.py <api_key><galaxy_url>/api/workflows f2db41e1fa3= 31b3e 'hist_id=3Da912e9e5d84530d4' '38=3Dhda=3D03501d7626bd192f' 'param=3Dt= ool=3Dname=3Dvalue'=20 - -'param=3Dtool=3Dname=3Dvalue' - -Example=20 -python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f htt= p://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da79= 9d38679e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Dalig= ner=3Dbwa'=20 - -python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f htt= p://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da79= 9d38679e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Dalig= ner=3Darachne' 'param=3Dbowtie_wrapper=3DsuppressHeader=3DTrue' - -python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f htt= p://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da79= 9d38679e985db' '70=3Dld=3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Dalig= ner=3Dbowtie' 'param=3Dbowtie_wrapper=3DsuppressHeader=3DTrue' 'param=3Dpea= kcalling_spp=3Dwindow_size=3D1000'=20 - +python workflow_execute.py <api_key><galaxy_url>/api/workflows <workflow_i= d> 'hist_id=3D<history_id>' '38=3Dhda=3D<file_id>' 'param=3Dtool=3Dname=3Dv= alue'=20 +python workflow_execute_parameters.py <api_key> http://localhost:8080/api/= workflows 1cd8e2f6b131e891 'Test API' '69=3Dld=3Da799d38679e985db' '70=3Dld= =3D33b43b4e7093c91f' 'param=3Dpeakcalling_spp=3Daligner=3Dbowtie' 'param=3D= bowtie_wrapper=3DsuppressHeader=3DTrue' 'param=3Dpeakcalling_spp=3Dwindow_s= ize=3D1000'=20 """ =20 import os, sys @@ -34,7 +24,6 @@ data['ds_map'] =3D {} =20 ######################################################### - ### MY EDITS ############################################ ### Trying to pass in parameter for my own dictionary ### data['parameters'] =3D {}; =20 @@ -51,14 +40,10 @@ except ValueError: print("VALUE ERROR:"); wtype, wtool, wparam, wvalue =3D v.split('=3D'); - data['parameters'][wtool] =3D {'param':wparam, 'value':wva= lue} - - - ######################################################### - ### MY EDITS ############################################ - ### Trying to pass in parameter for my own dictionary ### - #data['parameters']['bowtie'] =3D {'param':'stepSize', 'value':100} - #data['parameters']['sam_to_bam'] =3D {'param':'genome', 'value':'= hg18'} + try: + data['parameters'][wtool] =3D {'param':wparam, 'value'= :wvalue} + except ValueError: + print("TOOL ID ERROR:"); =20 except IndexError: print 'usage: %s key url workflow_id history step=3Dsrc=3Ddataset_= id' % os.path.basename(sys.argv[0]) https://bitbucket.org/galaxy/galaxy-central/changeset/6a644558eed7/ changeset: 6a644558eed7 user: dannon date: 2012-08-29 16:17:53 summary: Merge of rpark's workflow API changes to support parameter exe= cution and workflow creation. TODO: Refactor copied workflow methods back out. affected #: 2 files diff -r 8c33567aeca58c4e7306d3beef590b82cff90be2 -r 6a644558eed7aba74a74060= ccf0aa4ec211809c2 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -10,25 +10,12 @@ from galaxy.web.base.controller import BaseAPIController, url_for from galaxy.workflow.modules import module_factory from galaxy.jobs.actions.post import ActionBox - -# ------------------------------------------------------------------------= ---------------------- # -# ------------------------------------------------------------------------= ---------------------- # -# ---- RPARK EDITS ---- # -import pkg_resources -pkg_resources.require( "simplejson" ) -from galaxy import model +from galaxy.model.item_attrs import UsesAnnotations from galaxy.web.controllers.workflow import attach_ordered_steps -from galaxy.util.sanitize_html import sanitize_html -from galaxy.workflow.modules import * -from galaxy.model.item_attrs import * - -# ------------------------------------------------------------------------= ---------------------- # -# ------------------------------------------------------------------------= ---------------------- #=20 - =20 log =3D logging.getLogger(__name__) =20 -class WorkflowsAPIController(BaseAPIController): +class WorkflowsAPIController(BaseAPIController, UsesAnnotations): @web.expose_api def index(self, trans, **kwd): """ @@ -100,16 +87,16 @@ However, we will import them if installed_repository_file is speci= fied """ =20 - # ----------------------------------------------------------------= --------------- # =20 + # ----------------------------------------------------------------= --------------- # ### RPARK: dictionary containing which workflows to change and edi= t ### param_map =3D {}; if (payload.has_key('parameters') ): param_map =3D payload['parameters']; - # ----------------------------------------------------------------= --------------- # =20 - =20 + # ----------------------------------------------------------------= --------------- # =20 - =20 - =20 + + + if 'workflow_id' not in payload: # create new if 'installed_repository_file' in payload: @@ -194,7 +181,7 @@ # are not persisted so we need to do it every time) step.module.add_dummy_datasets( connections=3Dstep.input_c= onnections ) step.state =3D step.module.state - =20 + #################################################### #################################################### # RPARK: IF TOOL_NAME IN PARAMETER MAP # @@ -204,7 +191,7 @@ step.state.inputs[change_param] =3D change_value; #################################################### #################################################### - =20 + if step.tool_errors: trans.response.status =3D 400 return "Workflow cannot be run because of validation e= rrors in some steps: %s" % step_errors @@ -267,40 +254,40 @@ def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download - Returns a selected workflow as a json dictionary.=20 + Returns a selected workflow as a json dictionary. """ - =20 + try: stored_workflow =3D trans.sa_session.query(self.app.model.Stor= edWorkflow).get(trans.security.decode_id(workflow_id)) except Exception,e: return ("Workflow with ID=3D'%s' can not be found\n Exception:= %s") % (workflow_id, str( e )) - =20 - # check to see if user has permissions to selected workflow=20 + + # check to see if user has permissions to selected workflow if stored_workflow.user !=3D trans.user and not trans.user_is_admi= n(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserSh= areAssociation).filter_by(user=3Dtrans.user, stored_workflow=3Dstored_workf= low).count() =3D=3D 0: trans.response.status =3D 400 return("Workflow is not owned by or shared with current us= er") - =20 + ret_dict =3D self._workflow_to_dict( trans, stored_workflow ); return ret_dict - =20 + @web.expose_api - def delete( self, trans, id, **kwd ): =20 + def delete( self, trans, id, **kwd ): """ DELETE /api/workflows/{encoded_workflow_id} Deletes a specified workflow Author: rpark - =20 + copied from galaxy.web.controllers.workflows.py (delete) """ workflow_id =3D id; - =20 + try: stored_workflow =3D trans.sa_session.query(self.app.model.Stor= edWorkflow).get(trans.security.decode_id(workflow_id)) except Exception,e: return ("Workflow with ID=3D'%s' can not be found\n Exception:= %s") % (workflow_id, str( e )) - =20 - # check to see if user has permissions to selected workflow=20 + + # check to see if user has permissions to selected workflow if stored_workflow.user !=3D trans.user and not trans.user_is_admi= n(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserSh= areAssociation).filter_by(user=3Dtrans.user, stored_workflow=3Dstored_workf= low).count() =3D=3D 0: trans.response.status =3D 400 @@ -309,42 +296,37 @@ #Mark a workflow as deleted stored_workflow.deleted =3D True trans.sa_session.flush() - =20 - # Python Debugger - #import pdb; pdb.set_trace() - =20 + # TODO: Unsure of response message to let api know that a workflow= was successfully deleted #return 'OK' return ( "Workflow '%s' successfully deleted" % stored_workflow.na= me ) - =20 + @web.expose_api def import_new_workflow(self, trans, payload, **kwd): """ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated w= orkflow id. - Author: rpark=20 - =20 + Author: rpark + # currently assumes payload['workflow'] is a json representation o= f a workflow to be inserted into the database """ - =20 - #import pdb; pdb.set_trace() - =20 + data =3D payload['workflow']; workflow, missing_tool_tups =3D self._workflow_from_dict( trans, d= ata, source=3D"API" ) - =20 - # galaxy workflow newly created id =20 + + # galaxy workflow newly created id workflow_id =3D workflow.id; - # api encoded, id=20 + # api encoded, id encoded_id =3D trans.security.encode_id(workflow_id); - =20 + # return list rval=3D []; - =20 + item =3D workflow.get_api_value(value_mapper=3D{'id':trans.securit= y.encode_id}) item['url'] =3D url_for('workflow', id=3Dencoded_id) - =20 - rval.append(item); =20 - =20 + + rval.append(item); + return item; =20 def _workflow_from_dict( self, trans, data, source=3DNone ): @@ -392,21 +374,19 @@ workflow.has_errors =3D True # Stick this in the step temporarily step.temp_input_connections =3D step_dict['input_connections'] - =20 # Save step annotation. annotation =3D step_dict[ 'annotation' ] - if annotation: - annotation =3D sanitize_html( annotation, 'utf-8', 'text/h= tml' ) + #if annotation: + #annotation =3D sanitize_html( annotation, 'utf-8', 'text/= html' ) # ------------------------------------------ # # RPARK REMOVING: user annotation b/c of API #self.add_item_annotation( trans.sa_session, trans.get_use= r(), step, annotation ) # ------------------------------------------ # - =20 # Unpack and add post-job actions. post_job_actions =3D step_dict.get( 'post_job_actions', {} ) for name, pja_dict in post_job_actions.items(): - pja =3D PostJobAction( pja_dict[ 'action_type' ],=20 - step, pja_dict[ 'output_name' ],=20 + pja =3D PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps for step in steps: @@ -431,14 +411,14 @@ trans.sa_session.add( stored ) trans.sa_session.flush() return stored, missing_tool_tups - =20 + def _workflow_to_dict( self, trans, stored ): """ RPARK: copied from galaxy.web.controllers.workflows.py Converts a workflow to a dict of attributes suitable for exporting. """ workflow =3D stored.latest_workflow - =20 + ### ----------------------------------- ### ## RPARK EDIT ## workflow_annotation =3D self.get_item_annotation_obj( trans.sa_ses= sion, trans.user, stored ) @@ -446,8 +426,8 @@ if workflow_annotation: annotation_str =3D workflow_annotation.annotation ### ----------------------------------- ### - =20 - =20 + + # Pack workflow data into a dictionary and return data =3D {} data['a_galaxy_workflow'] =3D 'true' # Placeholder for identifying= galaxy workflow @@ -457,22 +437,22 @@ ## RPARK EDIT ## data['annotation'] =3D annotation_str ### ----------------------------------- ### - =20 + data['steps'] =3D {} # For each step, rebuild the form and encode the state for step in workflow.steps: # Load from database representation module =3D module_factory.from_workflow_step( trans, step ) - =20 + ### ----------------------------------- ### ## RPARK EDIT ## # Get user annotation. step_annotation =3D self.get_item_annotation_obj(trans.sa_sess= ion, trans.user, step ) annotation_str =3D "" if step_annotation: - annotation_str =3D step_annotation.annotation =20 + annotation_str =3D step_annotation.annotation ### ----------------------------------- ### - =20 + # Step info step_dict =3D { 'id': step.order_index, @@ -484,18 +464,18 @@ 'tool_errors': module.get_errors(), ## 'data_inputs': module.get_data_inputs(), ## 'data_outputs': module.get_data_outputs(), - =20 + ### ----------------------------------- ### ## RPARK EDIT ## 'annotation' : annotation_str ### ----------------------------------- ### - =20 + } # Add post-job actions to step dict. if module.type =3D=3D 'tool': pja_dict =3D {} for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] =3D dict( ac= tion_type =3D pja.action_type,=20 + pja_dict[pja.action_type+pja.output_name] =3D dict( ac= tion_type =3D pja.action_type, outp= ut_name =3D pja.output_name, acti= on_arguments =3D pja.action_arguments ) step_dict[ 'post_job_actions' ] =3D pja_dict @@ -559,37 +539,4 @@ # Add to return value data['steps'][step.order_index] =3D step_dict return data - =20 - def get_item_annotation_obj( self, db_session, user, item ): - """=20 - RPARK: copied from galaxy.model.item_attr.py - Returns a user's annotation object for an item. """ - # Get annotation association class. - annotation_assoc_class =3D self._get_annotation_assoc_class( item ) - if not annotation_assoc_class: - return None - =20 - # Get annotation association object. - annotation_assoc =3D db_session.query( annotation_assoc_class ).fi= lter_by( user=3Duser ) - =20 - # TODO: use filtering like that in _get_item_id_filter_str() - if item.__class__ =3D=3D galaxy.model.History: - annotation_assoc =3D annotation_assoc.filter_by( history=3Dite= m ) - elif item.__class__ =3D=3D galaxy.model.HistoryDatasetAssociation: - annotation_assoc =3D annotation_assoc.filter_by( hda=3Ditem ) - elif item.__class__ =3D=3D galaxy.model.StoredWorkflow: - annotation_assoc =3D annotation_assoc.filter_by( stored_workfl= ow=3Ditem ) - elif item.__class__ =3D=3D galaxy.model.WorkflowStep: - annotation_assoc =3D annotation_assoc.filter_by( workflow_step= =3Ditem ) - elif item.__class__ =3D=3D galaxy.model.Page: - annotation_assoc =3D annotation_assoc.filter_by( page=3Ditem ) - elif item.__class__ =3D=3D galaxy.model.Visualization: - annotation_assoc =3D annotation_assoc.filter_by( visualization= =3Ditem ) - return annotation_assoc.first() - =20 - def _get_annotation_assoc_class( self, item ): - """=20 - RPARK: copied from galaxy.model.item_attr.py - Returns an item's item-annotation association class. """ - class_name =3D '%sAnnotationAssociation' % item.__class__.__name__ - return getattr( galaxy.model, class_name, None ) + diff -r 8c33567aeca58c4e7306d3beef590b82cff90be2 -r 6a644558eed7aba74a74060= ccf0aa4ec211809c2 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -151,20 +151,11 @@ webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_= prefix=3D'/api' ) #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_i= d}/library/{library_id}', controller=3D'workflows', action=3D'run', workflo= w_id=3DNone, library_id=3DNone, conditions=3Ddict(method=3D["GET"]) ) =20 - # ---------------------------------------------- # - # ---------------------------------------------- # - # RPARK EDIT=20 - =20 - # How to extend API: url_mapping=20 - # "POST /api/workflows/import" =3D> ``workflows.import_workflow(= )``. - # Defines a named route "import_workflow". - webapp.api_mapper.connect("import_workflow", "/api/workflows/uploa= d", controller=3D"workflows", action=3D"import_new_workflow", conditions=3D= dict(method=3D["POST"])) - webapp.api_mapper.connect("workflow_dict", '/api/workflows/downloa= d/{workflow_id}', controller=3D'workflows', action=3D'workflow_dict', condi= tions=3Ddict(method=3D['GET'])) - =20 - #import pdb; pdb.set_trace() =20 - # ---------------------------------------------- # - # ---------------------------------------------- # - =20 + # "POST /api/workflows/import" =3D> ``workflows.import_workflow()``. + # Defines a named route "import_workflow". + webapp.api_mapper.connect("import_workflow", "/api/workflows/upload", = controller=3D"workflows", action=3D"import_new_workflow", conditions=3Ddict= (method=3D["POST"])) + webapp.api_mapper.connect("workflow_dict", '/api/workflows/download/{w= orkflow_id}', controller=3D'workflows', action=3D'workflow_dict', condition= s=3Ddict(method=3D['GET'])) + webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): https://bitbucket.org/galaxy/galaxy-central/changeset/07045f489517/ changeset: 07045f489517 user: dannon date: 2012-08-29 16:18:23 summary: Merge. affected #: 36 files diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -719,7 +719,49 @@ pass =20 class Newick( Text ): - pass + """New Hampshire/Newick Format""" + file_ext =3D "nhx" + + MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu= mns", readonly=3DTrue ) + + def __init__(self, **kwd): + """Initialize foobar datatype""" + Text.__init__(self, **kwd) + + def init_meta( self, dataset, copy_from=3DNone ): + Text.init_meta( self, dataset, copy_from=3Dcopy_from ) + + + def sniff( self, filename ): + """ Returning false as the newick format is too general and cannot= be sniffed.""" + return False + + +class Nexus( Text ): + """Nexus format as used By Paup, Mr Bayes, etc""" + file_ext =3D "nex" + + MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu= mns", readonly=3DTrue ) + + def __init__(self, **kwd): + """Initialize foobar datatype""" + Text.__init__(self, **kwd) + + def init_meta( self, dataset, copy_from=3DNone ): + Text.init_meta( self, dataset, copy_from=3Dcopy_from ) + + + def sniff( self, filename ): + """All Nexus Files Simply puts a '#NEXUS' in its first line""" + f =3D open(filename, "r") + firstline =3D f.readline().upper() + f.close() + + if "#NEXUS" in firstline: + return True + else: + return False + =20 # ------------- Utility methods -------------- =20 diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -6,6 +6,7 @@ from galaxy import util from galaxy.datatypes.checkers import * from galaxy.datatypes.binary import unsniffable_binary_formats +from encodings import search_function as encodings_search_function =20 log =3D logging.getLogger(__name__) =20 @@ -15,7 +16,7 @@ full_path =3D os.path.join(path, 'test', fname) return full_path =20 -def stream_to_open_named_file( stream, fd, filename ): +def stream_to_open_named_file( stream, fd, filename, source_encoding=3DNon= e, source_error=3D'strict', target_encoding=3DNone, target_error=3D'strict'= ): """Writes a stream to the provided file descriptor, returns the file's= name and bool( is_multi_byte ). Closes file descriptor""" #signature and behavor is somewhat odd, due to backwards compatibility= , but this can/should be done better CHUNK_SIZE =3D 1048576 @@ -23,6 +24,10 @@ is_compressed =3D False is_binary =3D False is_multi_byte =3D False + if not target_encoding or not encodings_search_function( target_encodi= ng ): + target_encoding =3D util.DEFAULT_ENCODING #utf-8 + if not source_encoding: + source_encoding =3D util.DEFAULT_ENCODING #sys.getdefaultencoding(= ) would mimic old behavior (defaults to ascii) while 1: chunk =3D stream.read( CHUNK_SIZE ) if not chunk: @@ -42,13 +47,12 @@ chars =3D chunk[:100] is_multi_byte =3D util.is_multi_byte( chars ) if not is_multi_byte: - for char in chars: - if ord( char ) > 128: - is_binary =3D True - break + is_binary =3D util.is_binary( chunk ) data_checked =3D True if not is_compressed and not is_binary: - os.write( fd, chunk.encode( "utf-8" ) ) + if not isinstance( chunk, unicode ): + chunk =3D chunk.decode( source_encoding, source_error ) + os.write( fd, chunk.encode( target_encoding, target_error ) ) else: # Compressed files must be encoded after they are uncompressed= in the upload utility, # while binary files should not be encoded at all. @@ -56,10 +60,10 @@ os.close( fd ) return filename, is_multi_byte =20 -def stream_to_file( stream, suffix=3D'', prefix=3D'', dir=3DNone, text=3DF= alse ): +def stream_to_file( stream, suffix=3D'', prefix=3D'', dir=3DNone, text=3DF= alse, **kwd ): """Writes a stream to a temporary file, returns the temporary file's n= ame""" fd, temp_name =3D tempfile.mkstemp( suffix=3Dsuffix, prefix=3Dprefix, = dir=3Ddir, text=3Dtext ) - return stream_to_open_named_file( stream, fd, temp_name ) + return stream_to_open_named_file( stream, fd, temp_name, **kwd ) =20 def check_newlines( fname, bytes_to_read=3D52428800 ): """ @@ -305,14 +309,9 @@ else: for hdr in headers: for char in hdr: - if len( char ) > 1: - for c in char: - if ord( c ) > 128: - is_binary =3D True - break - elif ord( char ) > 128: - is_binary =3D True - break + #old behavior had 'char' possibly having length > 1, + #need to determine when/if this occurs=20 + is_binary =3D util.is_binary( char ) if is_binary: break if is_binary: diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -76,3 +76,24 @@ dataset.blurb =3D 'file purged from disk' def sniff( self, filename ): return False + +class Phyloxml( GenericXml ): + """Format for defining phyloxml data http://www.phyloxml.org/""" + file_ext =3D "phyloxml" + def set_peek( self, dataset, is_multi_byte=3DFalse ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek =3D data.get_file_peek( dataset.file_name, is_mul= ti_byte=3Dis_multi_byte ) + dataset.blurb =3D 'Phyloxml data' + else: + dataset.peek =3D 'file does not exist' + dataset.blurb =3D 'file purged from disk' + + def sniff( self, filename ): + """"Checking for keyword - 'phyloxml' always in lowercase in the f= irst few lines""" + f =3D open(filename, "r") + firstlines =3D "".join(f.readlines(5)) + f.close() + if "phyloxml" in firstlines: + return True + return False \ No newline at end of file diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -471,7 +471,7 @@ job.user.total_disk_usage +=3D bytes =20 # fix permissions - for path in [ dp.real_path for dp in self.get_output_fnames() ]: + for path in [ dp.real_path for dp in self.get_mutable_output_fname= s() ]: util.umask_fix_perms( path, self.app.config.umask, 0666, self.= app.config.gid ) self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) @@ -679,6 +679,11 @@ self.compute_outputs() return self.output_paths =20 + def get_mutable_output_fnames( self ): + if self.output_paths is None: + self.compute_outputs() + return filter( lambda dsp: dsp.mutable, self.output_paths ) + def get_output_hdas_and_fnames( self ): if self.output_hdas_and_paths is None: self.compute_outputs() @@ -686,10 +691,11 @@ =20 def compute_outputs( self ) : class DatasetPath( object ): - def __init__( self, dataset_id, real_path, false_path =3D None= ): + def __init__( self, dataset_id, real_path, false_path =3D None= , mutable =3D True ): self.dataset_id =3D dataset_id self.real_path =3D real_path self.false_path =3D false_path + self.mutable =3D mutable def __str__( self ): if self.false_path is None: return self.real_path @@ -706,13 +712,13 @@ self.output_hdas_and_paths =3D {} for name, hda in [ ( da.name, da.dataset ) for da in job.outpu= t_datasets + job.output_library_datasets ]: false_path =3D os.path.abspath( os.path.join( self.working= _directory, "galaxy_dataset_%d.dat" % hda.dataset.id ) ) - dsp =3D DatasetPath( hda.dataset.id, hda.dataset.file_name= , false_path ) + dsp =3D DatasetPath( hda.dataset.id, hda.dataset.file_name= , false_path, mutable =3D hda.dataset.external_filename is None ) self.output_paths.append( dsp ) self.output_hdas_and_paths[name] =3D hda, dsp if special: false_path =3D os.path.abspath( os.path.join( self.working= _directory, "galaxy_dataset_%d.dat" % special.dataset.id ) ) else: - results =3D [ ( da.name, da.dataset, DatasetPath( da.dataset.d= ataset.id, da.dataset.file_name ) ) for da in job.output_datasets + job.out= put_library_datasets ] + results =3D [ ( da.name, da.dataset, DatasetPath( da.dataset.d= ataset.id, da.dataset.file_name, mutable =3D da.dataset.dataset.external_fi= lename is None ) ) for da in job.output_datasets + job.output_library_datas= ets ] self.output_paths =3D [t[2] for t in results] self.output_hdas_and_paths =3D dict([(t[0], t[1:]) for t in r= esults]) if special: diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/jobs/deferred/genome_transfer.py --- a/lib/galaxy/jobs/deferred/genome_transfer.py +++ b/lib/galaxy/jobs/deferred/genome_transfer.py @@ -115,15 +115,16 @@ files =3D tar.getmembers() for filename in files: z =3D tar.extractfile(filename) - try: - chunk =3D z.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - log.error( 'Problem decompressing compressed data'= ) - exit() - if not chunk: - break - os.write( fd, chunk ) + while 1: + try: + chunk =3D z.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + log.error( 'Problem decompressing compressed d= ata' ) + exit() + if not chunk: + break + os.write( fd, chunk ) os.write( fd, '\n' ) os.close( fd ) tar.close() diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/model/item_attrs.py --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -95,7 +95,7 @@ """ Returns a user's annotation string for an item. """ annotation_obj =3D self.get_item_annotation_obj( db_session, user,= item ) if annotation_obj: - return annotation_obj.annotation + return galaxy.util.unicodify( annotation_obj.annotation ) return None =20 def get_item_annotation_obj( self, db_session, user, item ): diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -187,7 +187,9 @@ section.elems[ section_key ] =3D workflow log.debug( "Loaded workflow: %s %s" % ( workfl= ow_id, workflow.name ) ) elif section_key.startswith( 'label_' ): - section.elems[ section_key ] =3D section_val + if section_val: + section.elems[ section_key ] =3D section_val + log.debug( "Loaded label: %s" % ( section_val.= text ) ) self.tool_panel[ key ] =3D section def load_integrated_tool_panel_keys( self ): """ @@ -215,12 +217,12 @@ section.elems[ key ] =3D None elif section_elem.tag =3D=3D 'label': key =3D 'label_%s' % section_elem.get( 'id' ) - section.elems[ key ] =3D ToolSectionLabel( section= _elem ) + section.elems[ key ] =3D None key =3D 'section_%s' % elem.get( 'id' ) self.integrated_tool_panel[ key ] =3D section elif elem.tag =3D=3D 'label': key =3D 'label_%s' % elem.get( 'id' ) - self.integrated_tool_panel[ key ] =3D ToolSectionLabel( el= em ) + self.integrated_tool_panel[ key ] =3D None def write_integrated_tool_panel_config_file( self ): """ Write the current in-memory version of the integrated_tool_panel.x= ml file to disk. Since Galaxy administrators=20 @@ -254,10 +256,11 @@ if section_item: os.write( fd, ' <workflow id=3D"%s" />\= n' % section_item.id ) elif section_key.startswith( 'label_' ): - label_id =3D section_item.id or '' - label_text =3D section_item.text or '' - label_version =3D section_item.version or '' - os.write( fd, ' <label id=3D"%s" text=3D"%s= " version=3D"%s" />\n' % ( label_id, label_text, label_version ) ) + if section_item: + label_id =3D section_item.id or '' + label_text =3D section_item.text or '' + label_version =3D section_item.version or '' + os.write( fd, ' <label id=3D"%s" text= =3D"%s" version=3D"%s" />\n' % ( label_id, label_text, label_version ) ) os.write( fd, ' </section>\n' ) os.write( fd, '</toolbox>\n' ) os.close( fd ) diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/tools/genome_index/index_genome.py --- a/lib/galaxy/tools/genome_index/index_genome.py +++ b/lib/galaxy/tools/genome_index/index_genome.py @@ -54,6 +54,7 @@ self._log( self.locations ) self._log( 'Indexer %s completed successfully.' % inde= xer ) self._flush_files() + exit(0) =20 def _check_link( self ): self._log( 'Checking symlink to %s' % self.fafile ) diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -34,6 +34,9 @@ =20 gzip_magic =3D '\037\213' bz2_magic =3D 'BZh' +DEFAULT_ENCODING =3D 'utf-8' +NULL_CHAR =3D '\000' +BINARY_CHARS =3D [ NULL_CHAR ] =20 from inflection import Inflector, English inflector =3D Inflector(English) @@ -57,6 +60,32 @@ return True return False =20 +def is_binary( value, binary_chars=3DNone ): + """ + File is binary if it contains a null-byte by default (e.g. behavior of= grep, etc.). + This may fail for utf-16 files, but so would ASCII encoding. + >>> is_binary( string.printable ) + False + >>> is_binary( '\\xce\\x94' ) + False + >>> is_binary( '\\000' ) + True + """ + if binary_chars is None: + binary_chars =3D BINARY_CHARS + for binary_char in binary_chars: + if binary_char in value: + return True + return False + +def get_charset_from_http_headers( headers, default=3DNone ): + rval =3D headers.get('content-type', None ) + if rval and 'charset=3D' in rval: + rval =3D rval.split('charset=3D')[-1].split(';')[0].strip() + if rval: + return rval + return default + def synchronized(func): """This wrapper will serialize access to 'func' to a single thread. Us= e it as a decorator.""" def caller(*params, **kparams): @@ -333,6 +362,17 @@ else: return amount[0:sfs] + '0'*(len(amount) - sfs) =20 +def unicodify( value, encoding=3DDEFAULT_ENCODING, error=3D'replace', defa= ult=3DNone ): + """ + Returns a unicode string or None + """ + if isinstance( value, unicode ): + return value + try: + return unicode( value, encoding, error ) + except: + return default + def object_to_string( obj ): return binascii.hexlify( pickle.dumps( obj, 2 ) ) =20 @@ -502,7 +542,7 @@ =20 def recursively_stringify_dictionary_keys( d ): if isinstance(d, dict): - return dict([(k.encode('utf-8'), recursively_stringify_dictionary_= keys(v)) for k,v in d.iteritems()]) + return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_= dictionary_keys(v)) for k,v in d.iteritems()]) elif isinstance(d, list): return [recursively_stringify_dictionary_keys(x) for x in d] else: @@ -622,7 +662,7 @@ Sends an email. """ to =3D listify( to ) - msg =3D MIMEText( body ) + msg =3D MIMEText( body.encode( 'ascii', 'replace' ) ) msg[ 'To' ] =3D ', '.join( to ) msg[ 'From' ] =3D frm msg[ 'Subject' ] =3D subject diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -454,7 +454,7 @@ def generate_clone_url( trans, repository ): """Generate the URL for cloning a repository.""" tool_shed_url =3D get_url_from_repository_tool_shed( trans.app, reposi= tory ) - return '%s/repos/%s/%s' % ( tool_shed_url, repository.owner, repositor= y.name ) + return url_join( tool_shed_url, 'repos', repository.owner, repository.= name ) def generate_datatypes_metadata( datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed = datatypes_config.""" tree =3D ElementTree.parse( datatypes_config ) @@ -993,7 +993,7 @@ break return converter_path, display_path def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): - url =3D '%s/repository/get_ctx_rev?name=3D%s&owner=3D%s&changeset_revi= sion=3D%s&webapp=3Dgalaxy' % ( tool_shed_url, name, owner, changeset_revisi= on ) + url =3D url_join( tool_shed_url, 'repository/get_ctx_rev?name=3D%s&own= er=3D%s&changeset_revision=3D%s&webapp=3Dgalaxy' % ( name, owner, changeset= _revision ) ) response =3D urllib2.urlopen( url ) ctx_rev =3D response.read() response.close() @@ -1221,8 +1221,8 @@ def get_update_to_changeset_revision_and_ctx_rev( trans, repository ): """Return the changeset revision hash to which the repository can be u= pdated.""" tool_shed_url =3D get_url_from_repository_tool_shed( trans.app, reposi= tory ) - url =3D '%s/repository/get_changeset_revision_and_ctx_rev?name=3D%s&ow= ner=3D%s&changeset_revision=3D%s' % \ - ( tool_shed_url, repository.name, repository.owner, repository.ins= talled_changeset_revision ) + url =3D url_join( tool_shed_url, 'repository/get_changeset_revision_an= d_ctx_rev?name=3D%s&owner=3D%s&changeset_revision=3D%s' % \ + ( repository.name, repository.owner, repository.installed_changese= t_revision ) ) try: response =3D urllib2.urlopen( url ) encoded_update_dict =3D response.read() @@ -1645,3 +1645,8 @@ tool_shed_repository.status =3D status sa_session.add( tool_shed_repository ) sa_session.flush() +def url_join( *args ): + parts =3D [] + for arg in args: + parts.append( arg.strip( '/' ) ) + return '/'.join( parts ) diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/visualization/phyloviz/__init__.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/__init__.py @@ -0,0 +1,1 @@ +__author__ =3D 'Tomithy' diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/visualization/phyloviz/baseparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/baseparser.py @@ -0,0 +1,125 @@ +import json + +class Node(object): + """Node class of PhyloTree, which represents a CLAUDE in a phylogeneti= c tree""" + def __init__(self, nodeName, **kwargs): + """Creates a node and adds in the typical annotations""" + self.name, self.id =3D nodeName, kwargs.get("id", 0) + self.depth =3D kwargs.get("depth", 0) + self.children =3D [] + + self.isInternal =3D kwargs.get("isInternal", 0) + self.length, self.bootstrap =3D kwargs.get("length", 0), kwargs.ge= t("bootstrap", None) + self.events =3D kwargs.get("events", "") + + # clean up boot strap values + if self.bootstrap =3D=3D -1: + self.bootstrap =3D None + + def addChildNode(self, child): + """Adds a child node to the current node""" + if isinstance(child, Node): + self.children.append(child) + else: + self.children +=3D child + + + def __str__(self): + return self.name + " id:" + str(self.id) + ", depth: " + str(self.= depth) + + + def toJson(self): + """Converts the data in the node to a dict representation of json"= "" + thisJson =3D { + "name" : self.name, + "id" : self.id, + "depth" : self.depth, + "dist" : self.length + } + thisJson =3D self.addChildrenToJson(thisJson) + thisJson =3D self.addMiscToJson(thisJson) + return thisJson + + def addChildrenToJson(self, jsonDict): + """Needs a special method to addChildren, such that the key does n= ot appear in the Jsondict when the children is empty + this requirement is due to the layout algorithm used by d3 layout = for hiding subtree """ + if len(self.children) > 0: + children =3D [ node.toJson() for node in self.children] + jsonDict["children"] =3D children + return jsonDict + + + def addMiscToJson(self, jsonDict): + """Adds other misc attributes to json if they are present""" + if not self.events =3D=3D "": + jsonDict["events"] =3D self.events + if not self.bootstrap =3D=3D None: + jsonDict["bootstrap"] =3D self.bootstrap + return jsonDict + + + +class PhyloTree(object): + """Standardized python based class to represent the phylogenetic tree = parsed from different + phylogenetic file formats.""" + + def __init__(self): + self.root, self.rootAttr =3D None, {} + self.nodes =3D {} + self.title =3D None + self.id =3D 1 + + def addAttributesToRoot(self, attrDict): + """Adds attributes to root, but first we put it in a temp store an= d bind it with root when .toJson is called""" + for key, value in attrDict.items(): + self.rootAttr[key] =3D value + + def makeNode(self, nodeName, **kwargs): + """Called to make a node within PhyloTree, arbitrary kwargs can be= passed to annotate nodes + Tracks the number of nodes via internally incremented id""" + kwargs["id"] =3D self.id + self.id +=3D 1 + return Node(nodeName, **kwargs) + + def addRoot(self, root): + """Creates a root for phyloTree""" + assert isinstance(root, Node) + root.parent =3D None + self.root =3D root + + def generateJsonableDict(self): + """Changes itself into a dictonary by recurssively calling the toj= son on all its nodes. Think of it + as a dict in an array of dict in an array of dict and so on...""" + jsonTree =3D "" + if self.root: + assert isinstance(self.root, Node) + jsonTree =3D self.root.toJson() + for key, value in self.rootAttr.items(): + # transfer temporary stored attr to root + jsonTree[key] =3D value + else: + raise Exception("Root is not assigned!") + return jsonTree + + + +class Base_Parser(object): + """Base parsers contain all the methods to handle phylogeny tree creat= ion and + converting the data to json that all parsers should have""" + + def __init__(self): + self.phyloTrees =3D [] + + def parseFile(self, filePath): + """Base method that all phylogeny file parser should have""" + raise Exception("Base method for phylogeny file parsers is not imp= lemented") + + def toJson(self, jsonDict): + """Convenience method to get a json string from a python json dict= """ + return json.dumps(jsonDict) + + def _writeJsonToFile(self, filepath, json): + """Writes the file out to the system""" + f =3D open(filepath, "w") + f.writelines(json) + f.close() diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/visualization/phyloviz/newickparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/newickparser.py @@ -0,0 +1,185 @@ +from baseparser import Base_Parser, PhyloTree +import re + +class Newick_Parser(Base_Parser): + """For parsing trees stored in the newick format (.nhx) + It is necessarily more complex because this parser is later extended b= y Nexus for parsing newick as well..""" + + + def __init__(self): + super(Newick_Parser, self).__init__() + + + def parseFile(self, filePath): + """Parses a newick file to obtain the string inside. Returns: json= ableDict""" + with open(filePath, "r") as newickFile: + newickString =3D newickFile.read() + newickString =3D newickString.replace("\n", "").replace("\r", = "") + return [self.parseData(newickString)], "Success" + + + def parseData(self, newickString): + """To be called on a newickString directly to parse it. Returns: j= sonableDict""" + return self._parseNewickToJson(newickString) + + + def _parseNewickToJson(self, newickString, treeName=3DNone, nameMap=3D= None): + """parses a newick representation of a tree into a PhyloTree data = structure, + which can be easily converted to json""" + self.phyloTree =3D PhyloTree() + newickString =3D self.cleanNewickString(newickString) + if nameMap: + newickString =3D self._mapName(newickString, nameMap) + + self.phyloTree.root =3D self.parseNode(newickString, 0) + if nameMap: + self.phyloTree.addAttributesToRoot({"treeName": treeName}) + + return self.phyloTree.generateJsonableDict() + + + def cleanNewickString(self, rawNewick): + """removing semi colon, and illegal json characters (\,',") and wh= ite spaces""" + return re.sub(r'\s|;|\"|\'|\\', '', rawNewick) + + + def _makeNodesFromString(self, string, depth): + """elements separated by comma could be empty""" + + if string.find("(") !=3D -1: + raise Exception("Tree is not well form, location: " + string) + + childrenString =3D string.split(",") + childrenNodes =3D [] + + for childString in childrenString: + if len(childString) =3D=3D 0: + continue + nodeInfo =3D childString.split(":") + name, length, bootstrap =3D "", None, -1 + if len(nodeInfo) =3D=3D 2: # has length info + length =3D nodeInfo[1] + # checking for bootstap values + name =3D nodeInfo[0] + try: # Nexus may bootstrap in names position + name =3D float(name) + if 0<=3D name <=3D 1: + bootstrap =3D name + elif 1 <=3D name <=3D 100: + bootstrap =3D name / 100 + name =3D "" + except ValueError: + name =3D nodeInfo[0] + else: + name =3D nodeInfo[0] # string only contains name + node =3D self.phyloTree.makeNode(name, length=3Dlength, depth= =3Ddepth, bootstrap=3D bootstrap) + childrenNodes +=3D [node] + return childrenNodes + + + + def _mapName(self, newickString, nameMap): + """ + Necessary to replace names of terms inside nexus representation + Also, its here because Mailaud's doesnt deal with id_strings outsi= de of quotes(" ") + """ + newString =3D "" + start =3D 0 + end =3D 0 + + for i in xrange(len(newickString)): + if newickString[i] =3D=3D "(" or newickString[i] =3D=3D ",": + if re.match(r"[,(]", newickString[i+1:]): + continue + else: + end =3D i + 1 + # i now refers to the starting position of the term to= be replaced, + # we will next find j which is the ending pos of the t= erm + for j in xrange(i+1, len(newickString)): + enclosingSymbol =3D newickString[j] # the immedi= ate symbol after a common or left bracket which denotes the end of a term + if enclosingSymbol =3D=3D ")" or enclosingSymbol = =3D=3D ":" or enclosingSymbol =3D=3D ",": + termToReplace =3D newickString[end:j] + + newString +=3D newickString[start : end] + na= meMap[termToReplace] #+ "'" "'" + + start =3D j + break + + newString +=3D newickString[start:] + return newString + + + def parseNode(self, string, depth): + """ Recursive method for parsing newick string, works by stripping= down the string into substring + of newick contained with brackers, which is used to call itself. + Eg ... ( A, B, (D, E)C, F, G ) ... + We will make the preceeding nodes first A, B, then the internal no= de C, its children D, E, + and finally the succeeding nodes F, G""" + + # Base case where there is only an empty string + if string =3D=3D "": + return + # Base case there its only an internal claude + if string.find("(") =3D=3D -1: + return self._makeNodesFromString(string, depth) + + nodes, children =3D [], [] # nodes refer to the nodes on this= level, children refers to the child of the + start =3D 0 + lenOfPreceedingInternalNodeString =3D 0 + bracketStack =3D [] + + for j in xrange(len(string)): + if string[j] =3D=3D "(": #finding the positions of all the = open brackets + bracketStack.append(j) + continue + if string[j] =3D=3D ")": #finding the positions of all the = closed brackets to extract claude + i =3D bracketStack.pop() + + if len(bracketStack) =3D=3D 0: # is child of current node + + InternalNode =3D None + + #First flat call to make nodes of the same depth but f= rom the preceeding string. + startSubstring =3D string[start + lenOfPreceedingInter= nalNodeString: i] + preceedingNodes =3D self._makeNodesFromString(startSu= bstring, depth) + nodes +=3D preceedingNodes + + # Then We will try to see if the substring has any int= ernal nodes first, make it then make nodes preceeding it and succeeding it. + if j + 1 < len(string): + stringRightOfBracket =3D string[j+1:] # Eg. '= (b:0.4,a:0.3)c:0.3, stringRightOfBracket =3D c:0.3 + match =3D re.search(r"[\)\,\(]", stringRightOfBrac= ket) + if match: + indexOfNextSymbol =3D match.start() + stringRepOfInternalNode =3D stringRightOfBrack= et[:indexOfNextSymbol] + internalNodes =3D self._makeNodesFromString( s= tringRepOfInternalNode, depth) + if len(internalNodes) > 0: + InternalNode =3D internalNodes[0] + lenOfPreceedingInternalNodeString =3D len(stri= ngRepOfInternalNode) + else: # sometimes the node can be the last eleme= nt of a string + InternalNode =3D self._makeNodesFromString(str= ing[j+1:], depth)[0] + lenOfPreceedingInternalNodeString =3D len(stri= ng) - j + if InternalNode =3D=3D None: #creating a generic= node if it is unnamed + InternalNode =3D self.phyloTree.makeNode( "", dept= h=3Ddepth, isInternal=3DTrue ) #"internal-" + str(depth) + lenOfPreceedingInternalNodeString =3D 0 + + # recussive call to make the internal claude + childSubString =3D string[ i + 1 : j ] + InternalNode.addChildNode(self.parseNode(childSubStrin= g, depth + 1)) + + nodes.append(InternalNode) # we append the internal n= ode later to preserve order + + start =3D j + 1 + continue + + if depth =3D=3D 0: # if its the root node, we do nothing about = it and return + return nodes[0] + + # Adding last most set of children + endString =3D string[start:] + if string[start-1] =3D=3D ")": # if the symbol belongs to an inte= rnal node which is created previously, then we remove it from the string le= ft to parse + match =3D re.search(r"[\)\,\(]", endString) + if match: + endOfNodeName =3D start + match.start() + 1 + endString =3D string[endOfNodeName:] + nodes +=3D self._makeNodesFromString(endString, depth) + + return nodes diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/visualization/phyloviz/nexusparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/nexusparser.py @@ -0,0 +1,107 @@ +from newickparser import Newick_Parser +import re + +MAX_READLINES =3D 200000 + + +class Nexus_Parser(Newick_Parser): + + def __init__(self): + super(Nexus_Parser, self).__init__() + + def parseFile(self, filePath): + """passes a file and extracts its Nexus content.""" + return self.parseNexus(filePath) + + + def parseNexus(self, filename): + """ Nexus data is stored in blocks between a line starting with be= gin and another line starting with end; + Commends inside square brackets are to be ignored, + For more information: http://wiki.christophchamp.com/index.php/NEX= US_file_format + Nexus can store multiple trees + """ + + with open( filename, "rt") as nex_file: + nexlines =3D nex_file.readlines() + + rowCount =3D 0 + inTreeBlock =3D False # sentinel to check if we are in a t= ree block + intranslateBlock =3D False # sentinel to check if we are in the= translate region of the tree. Stores synonyms of the labellings + self.inCommentBlock =3D False + self.nameMapping =3D None # stores mapping representation us= ed in nexus format + treeNames =3D [] + + for line in nexlines: + line =3D line.replace(";\n", "") + lline =3D line.lower() + + if rowCount > MAX_READLINES or (not nex_file) : + break + rowCount +=3D1 + # We are only interested in the tree block. + if "begin" in lline and "tree" in lline and not inTreeBlock: + inTreeBlock =3D True + continue + if inTreeBlock and "end" in lline[:3]: + inTreeBlock, currPhyloTree =3D False, None + continue + + if inTreeBlock: + + if "title" in lline: # Adding title to the tree + titleLoc =3D lline.find("title") + title =3D line[titleLoc + 5:].replace(" ", "") + + continue + + if "translate" in lline: + intranslateBlock =3D True + self.nameMapping =3D {} + continue + + if intranslateBlock: + mappingLine =3D self.splitLinebyWhitespaces(line) + key, value =3D mappingLine[1], mappingLine[2].replace(= ",", "").replace("'","") #replacing illegal json characters + self.nameMapping[key] =3D value + + # Extracting newick Trees + if "tree" in lline: + intranslateBlock =3D False + + treeLineCols =3D self.splitLinebyWhitespaces(line) + treeName, newick =3D treeLineCols[2], treeLineCols[-1] + + if newick =3D=3D "": # Empty lines can be found in = tree blocks + continue + + currPhyloTree =3D self._parseNewickToJson(newick, tree= Name, nameMap=3Dself.nameMapping) + + self.phyloTrees.append(currPhyloTree) + treeIndex =3D len(self.phyloTrees) - 1 + treeNames.append( (treeName, treeIndex) ) # appendi= ng name of tree, and its index + continue + + return self.phyloTrees, treeNames + + + def splitLinebyWhitespaces(self, line): + """replace tabs and write spaces to a single write space, so we ca= n properly split it.""" + return re.split(r"\s+", line) + + + def checkComments(self, line): + """Check to see if the line/lines is a comment.""" + if not self.inCommentBlock: + if "[" in line: + if "]" not in line: + self.inCommentBlock =3D True + else: + return "Nextline" # need to move on to the nextline = after getting out of comment + else : + if "]" in line: + if line.rfind("[") > line.rfind("]"): + pass # a comment block is closed but an= other is open. + else: + self.inCommentBlock =3D False + return "Nextline" # need to move on to the nextline = after getting out of comment + return "" \ No newline at end of file diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py @@ -0,0 +1,35 @@ +from newickparser import Newick_Parser +from nexusparser import Nexus_Parser +from phyloxmlparser import Phyloxml_Parser + +class Phyloviz_DataProvider(object): + + def __init__(self): + pass + + def parseFile(self, filepath, fileExt): + """returns [trees], meta + Trees are actually an array of JsonDicts. It's usually one tre= e, except in the case of Nexus + """ + jsonDicts, meta =3D [], {} + try: + if fileExt =3D=3D "nhx": # parses newick files + newickParser =3D Newick_Parser() + jsonDicts, parseMsg =3D newickParser.parseFile(filepath) + elif fileExt =3D=3D "phyloxml": # parses phyloXML files + phyloxmlParser =3D Phyloxml_Parser() + jsonDicts, parseMsg =3D phyloxmlParser.parseFile(filepath) + elif fileExt =3D=3D "nex": # parses nexus files + nexusParser =3D Nexus_Parser() + jsonDicts, parseMsg =3D nexusParser.parseFile(filepath) + meta["trees"] =3D parseMsg + else: + raise Exception("File type is not supported") + + meta["msg"] =3D parseMsg + + except Exception: + jsonDicts, meta["msg"] =3D [], "Parse failed" + + return jsonDicts, meta + diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/visualization/phyloviz/phyloxmlparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/phyloxmlparser.py @@ -0,0 +1,134 @@ +from baseparser import Base_Parser, PhyloTree, Node +from xml.etree import ElementTree + +class Phyloxml_Parser(Base_Parser): + """Parses a phyloxml file into a json file that will be passed to Phyl= oViz for display""" + + def __init__(self): + super(Phyloxml_Parser, self).__init__() + self.phyloTree =3D PhyloTree() + self.tagsOfInterest =3D { + "clade": "", + "name" : "name", + "branch_length" : "length", + "confidence" : "bootstrap", + "events" : "events" + } + + def parseFile(self, filePath): + """passes a file and extracts its Phylogeny Tree content.""" + phyloXmlFile =3D open(filePath, "r") + + xmlTree =3D ElementTree.parse(phyloXmlFile) + xmlRoot =3D xmlTree.getroot()[0] + self.nameSpaceIndex =3D xmlRoot.tag.rfind("}") + 1 # used later by= the clean tag method to remove the name space in every element.tag + + phyloRoot =3D None + for child in xmlRoot: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + phyloRoot =3D child + elif childTag =3D=3D "name": + self.phyloTree.title =3D child.text + + self.phyloTree.root =3D self.parseNode(phyloRoot, 0) + jsonDict =3D self.phyloTree.generateJsonableDict() + return [jsonDict], "Success" + + + def parseNode(self, node, depth): + """Parses any node within a phyloxml tree and looks out for claude= , which signals the creation of + nodes - internal OR leaf""" + assert isinstance(node, etree._Element) + + tag =3D self.cleanTag(node.tag) + if not tag =3D=3D "clade": + return None + hasInnerClade =3D False + + # peeking once for parent and once for child to check if the node = is internal + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + hasInnerClade =3D True + break + + if hasInnerClade: # this node is an internal node + currentNode =3D self._makeInternalNode(node, depth=3D depth) + for child in node: + child =3D self.parseNode(child, depth + 1) + if isinstance(child, Node): + currentNode.addChildNode(child) + + else: # this node is a leaf node + currentNode =3D self._makeLeafNode(node, depth=3Ddepth+1) + + return currentNode + + + def _makeLeafNode(self, leafNode, depth =3D 0 ): + """Makes leaf nodes by calling Phylotree methods""" + node =3D {} + for child in leafNode: + childTag =3D self.cleanTag(child.tag) + if childTag in self.tagsOfInterest: + key =3D self.tagsOfInterest[childTag] # need to map phy= loxml terms to ours + node[key] =3D child.text + + node["depth"] =3D depth + return self.phyloTree.makeNode(self._getNodeName(leafNode), **node) + + def _getNodeName(self, node, depth=3D-1): + """Gets the name of a claude. It handles the case where a taxonomy= node is involved""" + + def getTagFromTaxonomyNode(node): + """Returns the name of a taxonomy node. A taxonomy node have t= o be treated differently as the name + is embedded one level deeper""" + phyloxmlTaxoNames =3D { + "common_name" : "", + "scientific_name" : "", + "code" : "" + } + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag in phyloxmlTaxoNames: + return child.text + return "" + + nodeName =3D "" + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "name" : + nodeName =3D child.text + break + elif childTag =3D=3D "taxonomy": + nodeName =3D getTagFromTaxonomyNode(child) + break + + return nodeName + + + def _makeInternalNode(self, internalNode, depth=3D0): + """ Makes an internal node from an element object that is gurantee= d to be a parent node. + Gets the value of interests like events and appends it to a custom= node object that will be passed to PhyloTree to make nodes + """ + node =3D {} + for child in internalNode: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + continue + elif childTag in self.tagsOfInterest: + if childTag =3D=3D "events": # events is nested 1 more = level deeper than others + key, text =3D "events", self.cleanTag(child[0].tag) + else: + key =3D self.tagsOfInterest[childTag] + text =3D child.text + node[key] =3D text + + + return self.phyloTree.makeNode(self._getNodeName(internalNode, dep= th), **node) + + + def cleanTag(self, tagString): + return tagString[self.nameSpaceIndex:] + =20 \ No newline at end of file diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -374,7 +374,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url =3D kwd[ 'tool_shed_url' ] galaxy_url =3D url_for( '/', qualified=3DTrue ) - url =3D '%srepository/browse_valid_categories?galaxy_url=3D%s&weba= pp=3Dgalaxy' % ( tool_shed_url, galaxy_url ) + url =3D url_join( tool_shed_url, 'repository/browse_valid_categori= es?galaxy_url=3D%s&webapp=3Dgalaxy' % ( galaxy_url ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -392,8 +392,9 @@ # Send a request to the relevant tool shed to see if there are any= updates. repository =3D get_repository( trans, kwd[ 'id' ] ) tool_shed_url =3D get_url_from_repository_tool_shed( trans.app, re= pository ) - url =3D '%s/repository/check_for_updates?galaxy_url=3D%s&name=3D%s= &owner=3D%s&changeset_revision=3D%s&webapp=3Dgalaxy' % \ - ( tool_shed_url, url_for( '/', qualified=3DTrue ), repository.= name, repository.owner, repository.changeset_revision ) + url =3D url_join( tool_shed_url, + 'repository/check_for_updates?galaxy_url=3D%s&name= =3D%s&owner=3D%s&changeset_revision=3D%s&webapp=3Dgalaxy' % \ + ( url_for( '/', qualified=3DTrue ), repository.nam= e, repository.owner, repository.changeset_revision ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -467,14 +468,14 @@ def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url =3D kwd[ 'tool_shed_url' ] galaxy_url =3D url_for( '/', qualified=3DTrue ) - url =3D '%srepository/find_tools?galaxy_url=3D%s&webapp=3Dgalaxy' = % ( tool_shed_url, galaxy_url ) + url =3D url_join( tool_shed_url, 'repository/find_tools?galaxy_url= =3D%s&webapp=3Dgalaxy' % galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url =3D kwd[ 'tool_shed_url' ] galaxy_url =3D url_for( '/', qualified=3DTrue ) - url =3D '%srepository/find_workflows?galaxy_url=3D%s&webapp=3Dgala= xy' % ( tool_shed_url, galaxy_url ) + url =3D url_join( tool_shed_url, 'repository/find_workflows?galaxy= _url=3D%s&webapp=3Dgalaxy' % galaxy_url ) return trans.response.send_redirect( url ) def generate_tool_path( self, repository_clone_url, changeset_revision= ): """ @@ -489,7 +490,7 @@ tool_shed_url =3D items[ 0 ] repo_path =3D items[ 1 ] tool_shed_url =3D clean_tool_shed_url( tool_shed_url ) - return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_rev= ision ) + return url_join( tool_shed_url, 'repos', repo_path, changeset_revi= sion ) @web.json @web.require_admin def get_file_contents( self, trans, file_path ): @@ -634,8 +635,9 @@ tool_shed_repository, trans.model.ToolShedRe= pository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url =3D get_url_from_repository_tool_shed( trans= .app, tool_shed_repository ) - url =3D '%s/repository/get_tool_versions?name=3D%s&owner= =3D%s&changeset_revision=3D%s&webapp=3Dgalaxy' % \ - ( tool_shed_url, tool_shed_repository.name, tool_shed_= repository.owner, tool_shed_repository.changeset_revision ) + url =3D url_join( tool_shed_url, + '/repository/get_tool_versions?name=3D%s&o= wner=3D%s&changeset_revision=3D%s&webapp=3Dgalaxy' % \ + ( tool_shed_repository.name, tool_shed_rep= ository.owner, tool_shed_repository.changeset_revision ) ) response =3D urllib2.urlopen( url ) text =3D response.read() response.close() @@ -954,7 +956,9 @@ repository_ids =3D kwd.get( 'repository_ids', None ) changeset_revisions =3D kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. - url =3D '%srepository/get_repository_information?repository_id= s=3D%s&changeset_revisions=3D%s&webapp=3Dgalaxy' % ( tool_shed_url, reposit= ory_ids, changeset_revisions ) + url =3D url_join( tool_shed_url, + 'repository/get_repository_information?reposit= ory_ids=3D%s&changeset_revisions=3D%s&webapp=3Dgalaxy' % \ + ( repository_ids, changeset_revisions ) ) response =3D urllib2.urlopen( url ) raw_text =3D response.read() response.close() @@ -1097,8 +1101,9 @@ name =3D repo_info_dict.keys()[ 0 ] repo_info_tuple =3D repo_info_dict[ name ] description, repository_clone_url, changeset_revision, ctx_rev= , repository_owner, tool_dependencies =3D repo_info_tuple - url =3D '%srepository/get_readme?name=3D%s&owner=3D%s&changese= t_revision=3D%s&webapp=3Dgalaxy' % \ - ( tool_shed_url, name, repository_owner, changeset_revisio= n ) + url =3D url_join( tool_shed_url, + 'repository/get_readme?name=3D%s&owner=3D%s&ch= angeset_revision=3D%s&webapp=3Dgalaxy' % \ + ( name, repository_owner, changeset_revision )= ) response =3D urllib2.urlopen( url ) raw_text =3D response.read() response.close() @@ -1273,8 +1278,9 @@ tool_shed =3D get_tool_shed_from_clone_url( repository_clone_url ) # Get all previous change set revisions from the tool shed for the= repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. - url =3D '%s/repository/previous_changeset_revisions?galaxy_url=3D%= s&name=3D%s&owner=3D%s&changeset_revision=3D%s&webapp=3Dgalaxy' % \ - ( tool_shed_url, url_for( '/', qualified=3DTrue ), repository_= name, repository_owner, changeset_revision ) + url =3D url_join( tool_shed_url, + 'repository/previous_changeset_revisions?galaxy_ur= l=3D%s&name=3D%s&owner=3D%s&changeset_revision=3D%s&webapp=3Dgalaxy' % \ + ( url_for( '/', qualified=3DTrue ), repository_nam= e, repository_owner, changeset_revision ) ) response =3D urllib2.urlopen( url ) text =3D response.read() response.close() @@ -1350,8 +1356,9 @@ # Get the tool_versions from the tool shed for each tool in the in= stalled change set. repository =3D get_repository( trans, kwd[ 'id' ] ) tool_shed_url =3D get_url_from_repository_tool_shed( trans.app, re= pository ) - url =3D '%s/repository/get_tool_versions?name=3D%s&owner=3D%s&chan= geset_revision=3D%s&webapp=3Dgalaxy' % \ - ( tool_shed_url, repository.name, repository.owner, repository= .changeset_revision ) + url =3D url_join( tool_shed_url, + 'repository/get_tool_versions?name=3D%s&owner=3D%s= &changeset_revision=3D%s&webapp=3Dgalaxy' % \ + ( repository.name, repository.owner, repository.ch= angeset_revision ) ) response =3D urllib2.urlopen( url ) text =3D response.read() response.close() @@ -1522,7 +1529,7 @@ def __generate_clone_url( self, trans, repository ): """Generate the URL for cloning a repository.""" tool_shed_url =3D get_url_from_repository_tool_shed( trans.app, re= pository ) - return '%s/repos/%s/%s' % ( tool_shed_url, repository.owner, repos= itory.name ) + return url_join( tool_shed_url, 'repos', repository.owner, reposit= ory.name ) =20 ## ---- Utility methods --------------------------------------------------= ----- =20 diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -148,7 +148,8 @@ dbkey =3D build[0] longname =3D build[1] break =20 - assert dbkey is not '?', 'That build was not found' + if dbkey =3D=3D '?': + return trans.fill_template( '/admin/data_admin/generic_err= or.mako', message=3D'An invalid build was specified.' ) ftp =3D ftplib.FTP('hgdownload.cse.ucsc.edu') ftp.login('anonymous', trans.get_user().email) checker =3D [] @@ -189,7 +190,8 @@ dbkeys=3Dtrans.ucsc_builds ) elif source =3D=3D 'Ensembl': dbkey =3D params.get( 'ensembl_dbkey', None ) - assert dbkey is not '?', 'That build was not found' + if dbkey =3D=3D '?': + return trans.fill_template( '/admin/data_admin/generic_err= or.mako', message=3D'An invalid build was specified.' ) for build in trans.ensembl_builds: if build[ 'dbkey' ] =3D=3D dbkey: dbkey =3D build[ 'dbkey' ] @@ -199,7 +201,7 @@ break url =3D 'ftp://ftp.ensembl.org/pub/release-%s/fasta/%s/dna/%s.= %s.%s.dna.toplevel.fa.gz' % ( release, pathname.lower(), pathname, dbkey, r= elease ) else: - return trans.fill_template( '/admin/data_admin/generic_error.m= ako', message=3D'Somehow an invalid data source was specified.' ) + return trans.fill_template( '/admin/data_admin/generic_error.m= ako', message=3D'An invalid data source was specified.' ) if url is None: return trans.fill_template( '/admin/data_admin/generic_error.m= ako', message=3D'Unable to generate a valid URL with the specified paramete= rs.' ) params =3D dict( protocol=3D'http', name=3Ddbkey, datatype=3D'fast= a', url=3Durl, user=3Dtrans.user.id ) @@ -248,7 +250,8 @@ sa =3D trans.app.model.context.current if jobtype =3D=3D 'liftover': job =3D sa.query( model.TransferJob ).filter_by( id=3Djobid ).= first() - joblabel =3D 'Download liftOver' + liftover =3D trans.app.job_manager.deferred_job_queue.plugins[= 'LiftOverTransferPlugin'].get_job_status( jobid ) + joblabel =3D 'Download liftOver (%s to %s)' % ( liftover.param= s[ 'from_genome' ], liftover.params[ 'to_genome' ] ) elif jobtype =3D=3D 'transfer': job =3D sa.query( model.TransferJob ).filter_by( id=3Djobid ).= first() joblabel =3D 'Download Genome' diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -203,12 +203,12 @@ job_id=3Djob.id, job_tool_id=3Djob.tool_id, job_command_line=3Djob.command_line, - job_stderr=3Djob.stderr, - job_stdout=3Djob.stdout, - job_info=3Djob.info, - job_traceback=3Djob.traceback, + job_stderr=3Dutil.unicodify( job.stderr ), + job_stdout=3Dutil.unicodify( job.stdout ), + job_info=3Dutil.unicodify( job.info ), + job_traceback=3Dutil.unicodify( job.tracebac= k ), email=3Demail, - message=3Dmessage ) + message=3Dutil.unicodify( message ) ) frm =3D to_address # Check email a bit email =3D email.strip() @@ -644,7 +644,10 @@ dataset =3D self.get_dataset( trans, id, False, True ) if not dataset: web.httpexceptions.HTTPNotFound() - return self.get_item_annotation_str( trans.sa_session, trans.user,= dataset ) + annotation =3D self.get_item_annotation_str( trans.sa_session, tra= ns.user, dataset ) + if annotation and isinstance( annotation, unicode ): + annotation =3D annotation.encode( 'ascii', 'replace' ) #paste = needs ascii here + return annotation =20 @web.expose def display_at( self, trans, dataset_id, filename=3DNone, **kwd ): diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/web/controllers/phyloviz.py --- /dev/null +++ b/lib/galaxy/web/controllers/phyloviz.py @@ -0,0 +1,97 @@ +import pkg_resources +pkg_resources.require( "bx-python" ) + +from galaxy.util.json import to_json_string, from_json_string +from galaxy.web.base.controller import * +from galaxy.visualization.phyloviz.phyloviz_dataprovider import Phyloviz_D= ataProvider + + +class PhyloVizController( BaseUIController, UsesVisualizationMixin, UsesHi= storyDatasetAssociationMixin, SharableMixin ): + """ + Controller for phyloViz browser interface. + """ + def __init__(self, app ): + BaseUIController.__init__( self, app ) + + @web.expose + @web.require_login() + def index( self, trans, dataset_id =3D None, **kwargs ): + """ + The index method is called using phyloviz/ with a dataset id passe= d in. + The relevant data set is then retrieved via get_json_from_datasetI= d which interfaces with the parser + The json representation of the phylogenetic tree along with the co= nfig is then written in the .mako template and passed back to the user + """ + json, config =3D self.get_json_from_datasetId(trans, dataset_id) + config["saved_visualization"] =3D False + return trans.fill_template( "visualization/phyloviz.mako", data = =3D json, config=3Dconfig) + + + @web.expose + def visualization(self, trans, id): + """ + Called using a viz_id (id) to retrieved stored visualization data = (in json format) and all the viz_config + """ + viz =3D self.get_visualization(trans, id) + config =3D self.get_visualization_config(trans, viz) + config["saved_visualization"] =3D True + data =3D config["root"] + + return trans.fill_template( "visualization/phyloviz.mako", data = =3D data, config=3Dconfig) + + + @web.expose + @web.json + def load_visualization_json(self, trans, viz_id): + """ + Though not used in current implementation, this provides user with= a convenient method to retrieve the viz_data & viz_config via json. + """ + viz =3D self.get_visualization(trans, viz_id) + viz_config =3D self.get_visualization_config(trans, viz) + viz_config["saved_visualization"] =3D True + return { + "data" : viz_config["root"], + "config" : viz_config + } + + + @web.expose + @web.json + def getJsonData(self, trans, dataset_id, treeIndex=3D0): + """ + Method to retrieve data asynchronously via json format. Retriving = from here rather than + making a direct datasets/ call allows for some processing and even= t capturing + """ + treeIndex =3D int(treeIndex) + json, config =3D self.get_json_from_datasetId(trans, dataset_id, t= reeIndex) + packedJson =3D { + "data" : json, + "config" : config + } + + return packedJson + + + def get_json_from_datasetId(self, trans, dataset_id, treeIndex=3D0): + """ + For interfacing phyloviz controllers with phyloviz visualization d= ata provider (parsers) + """ + dataset =3D self.get_dataset(trans, dataset_id) + fileExt, filepath =3D dataset.ext, dataset.file_name # .name= stores the name of the dataset from the orginal upload + json, config =3D "", {} # config contains propertie= s of the tree and file + + if fileExt =3D=3D "json": + something, json =3D self.get_data(dataset) + else: + try: + pd =3D Phyloviz_DataProvider() + json, config =3D pd.parseFile(filepath, fileExt) + json =3D json[treeIndex] + except Exception: + pass + + config["title"] =3D dataset.display_name() + config["ext"] =3D fileExt + config["dataset_id"] =3D dataset_id + config["treeIndex"] =3D treeIndex + + return json, config diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -16,6 +16,10 @@ action =3D "paramamonster" elif item.type =3D=3D "circster": action =3D "circster" + elif item.type =3D=3D "phyloviz": + # Support phyloviz + controller =3D "phyloviz" + action =3D "visualization" return dict( controller=3Dcontroller, action=3Daction, id=3Ditem.i= d ) =20 # Grid definition diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -11,7 +11,7 @@ from galaxy.model.orm import * from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for= _changeset, get_configured_ui, get_repository_file_contents, NOT_TOOL_CONFI= GS from galaxy.util.shed_util import open_repository_files_folder, reversed_l= ower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path -from galaxy.util.shed_util import to_html_escaped, update_repository +from galaxy.util.shed_util import to_html_escaped, update_repository, url_= join from galaxy.tool_shed.encoding_util import * from common import * =20 @@ -246,6 +246,25 @@ grids.GridAction( "User preferences", dict( controller=3D'user= ', action=3D'index', cntrller=3D'repository', webapp=3D'community' ) ) ] =20 +class WritableRepositoryListGrid( RepositoryListGrid ): + def build_initial_query( self, trans, **kwd ): + # TODO: improve performance by adding a db table associating users= with repositories for which they have write access. + username =3D kwd[ 'username' ] + clause_list =3D [] + for repository in trans.sa_session.query( self.model_class ): + allow_push_usernames =3D repository.allow_push.split( ',' ) + if username in allow_push_usernames: + clause_list.append( self.model_class.table.c.id =3D=3D rep= ository.id ) + if clause_list: + return trans.sa_session.query( self.model_class ) \ + .filter( or_( *clause_list ) ) \ + .join( model.User.table ) \ + .outerjoin( model.RepositoryCategoryAss= ociation.table ) \ + .outerjoin( model.Category.table ) + # Return an empty query. + return trans.sa_session.query( self.model_class ) \ + .filter( self.model_class.table.c.id < 0 ) + class ValidRepositoryListGrid( RepositoryListGrid ): class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): @@ -393,6 +412,7 @@ email_alerts_repository_list_grid =3D EmailAlertsRepositoryListGrid() category_list_grid =3D CategoryListGrid() valid_category_list_grid =3D ValidCategoryListGrid() + writable_repository_list_grid =3D WritableRepositoryListGrid() =20 def __add_hgweb_config_entry( self, trans, repository, repository_path= ): # Add an entry in the hgweb.config file for a new repository. An = entry looks something like: @@ -519,12 +539,15 @@ repository_id =3D kwd.get( 'id', None ) repository =3D get_repository( trans, repository_id ) kwd[ 'f-email' ] =3D repository.user.email - elif operation =3D=3D "my_repositories": + elif operation =3D=3D "repositories_i_own": # Eliminate the current filters if any exist. for k, v in kwd.items(): if k.startswith( 'f-' ): del kwd[ k ] kwd[ 'f-email' ] =3D trans.user.email + elif operation =3D=3D "writable_repositories": + kwd[ 'username' ] =3D trans.user.username + return self.writable_repository_list_grid( trans, **kwd ) elif operation =3D=3D "repositories_by_category": # Eliminate the current filters if any exist. for k, v in kwd.items(): @@ -726,9 +749,10 @@ update =3D 'true' no_update =3D 'false' else: - # Start building up the url to redirect back to the calling Ga= laxy instance. - url =3D '%sadmin_toolshed/update_to_changeset_revision?tool_sh= ed_url=3D%s' % ( galaxy_url, url_for( '/', qualified=3DTrue ) ) - url +=3D '&name=3D%s&owner=3D%s&changeset_revision=3D%s&latest= _changeset_revision=3D' % ( repository.name, repository.user.username, chan= geset_revision ) + # Start building up the url to redirect back to the calling Ga= laxy instance. =20 + url =3D url_join( galaxy_url, + 'admin_toolshed/update_to_changeset_revision?t= ool_shed_url=3D%s&name=3D%s&owner=3D%s&changeset_revision=3D%s&latest_chang= eset_revision=3D' % \ + ( url_for( '/', qualified=3DTrue ), repository= .name, repository.user.username, changeset_revision ) ) if changeset_revision =3D=3D repository.tip: # If changeset_revision is the repository tip, there are no ad= ditional updates. if from_update_manager: @@ -1372,10 +1396,9 @@ """Send the list of repository_ids and changeset_revisions to Gala= xy so it can begin the installation process.""" galaxy_url =3D trans.get_cookie( name=3D'toolshedgalaxyurl' ) # Redirect back to local Galaxy to perform install. - url =3D '%sadmin_toolshed/prepare_for_install' % galaxy_url - url +=3D '?tool_shed_url=3D%s' % url_for( '/', qualified=3DTrue ) - url +=3D '&repository_ids=3D%s' % ','.join( util.listify( reposito= ry_ids ) ) - url +=3D '&changeset_revisions=3D%s' % ','.join( util.listify( cha= ngeset_revisions ) ) + url =3D url_join( galaxy_url, + 'admin_toolshed/prepare_for_install?tool_shed_url= =3D%s&repository_ids=3D%s&changeset_revisions=3D%s' % \ + ( url_for( '/', qualified=3DTrue ), ','.join( util= .listify( repository_ids ) ), ','.join( util.listify( changeset_revisions )= ) ) ) return trans.response.send_redirect( url ) @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, change= set_revision, **kwd ): diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 static/scripts/viz/phyloviz.js --- /dev/null +++ b/static/scripts/viz/phyloviz.js @@ -0,0 +1,955 @@ +var UserMenuBase =3D Backbone.View.extend({ + /** + * Base class of any menus that takes in user interaction. Contains ch= ecking methods. + */ + + className: 'UserMenuBase', + + isAcceptableValue : function ($inputKey, min, max) { + /** + * Check if an input value is a number and falls within max min. + */ + var self =3D this, + value =3D $inputKey.val(), + fieldName =3D $inputKey.attr("displayLabel") || $inputKey.attr= ("id").replace("phyloViz", ""); + + function isNumeric(n) { + return !isNaN(parseFloat(n)) && isFinite(n); + } + + if (!isNumeric(value)){ + alert(fieldName + " is not a number!"); + return false; + } + + if ( value > max){ + alert(fieldName + " is too large."); + return false; + } else if ( value < min) { + alert(fieldName + " is too small."); + return false; + } + return true; + }, + + hasIllegalJsonCharacters : function($inputKey) { + /** + * Check if any user string inputs has illegal characters that jso= n cannot accept + */ + if ($inputKey.val().search(/"|'|\\/) !=3D=3D -1){ + alert("Named fields cannot contain these illegal characters: d= ouble quote(\"), single guote(\'), or back slash(\\). "); + return true; + } + return false; + } +}); + + +function PhyloTreeLayout() { + /** + * -- Custom Layout call for phyloViz to suit the needs of a phylogene= tic tree. + * -- Specifically: 1) Nodes have a display display of (=3D evo dist X= depth separation) from their parent + * 2) Nodes must appear in other after they have expa= nd and contracted + */ + + var self =3D this, + hierarchy =3D d3.layout.hierarchy().sort(null).value(null), + height =3D 360, // ! represents both the layout angle and the heig= ht of the layout, in px + layoutMode =3D "Linear", + leafHeight =3D 18, // height of each individual leaf node + depthSeparation =3D 200, // separation between nodes of different = depth, in px + leafIndex =3D 0, // change to recurssive call + defaultDist =3D 0.5, // tree defaults to 0.5 dist if no dist is sp= ecified + maxTextWidth =3D 50; // maximum length of the text labels + + + self.leafHeight =3D function(inputLeafHeight){ + if (typeof inputLeafHeight =3D=3D=3D "undefined"){ return leafHeig= ht; } + else { leafHeight =3D inputLeafHeight; return self;} + }; + + self.layoutMode =3D function(mode){ + if (typeof mode =3D=3D=3D "undefined"){ return layoutMode; } + else { layoutMode =3D mode; return self;} + }; + + self.layoutAngle =3D function(angle) { // changes the layout angle = of the display, which is really changing the height + if (typeof angle =3D=3D=3D "undefined"){ return height; } + if (isNaN(angle) || angle < 0 || angle > 360) { return self; } // = to use default if the user puts in strange values + else { height =3D angle; return self;} + }; + + self.separation =3D function(dist){ // changes the dist between the = nodes of different depth + if (typeof dist =3D=3D=3D "undefined"){ return depthSeparation; } + else { depthSeparation =3D dist; return self;} + }; + + self.links =3D function (nodes) { // uses d3 native method to gene= rate links. Done. + return d3.layout.tree().links(nodes); + }; + + // -- Custom method for laying out phylogeny tree in a linear fashion + self.nodes =3D function (d, i) { + var _nodes =3D hierarchy.call(self, d, i), // self is to f= ind the depth of all the nodes, assumes root is passed in + nodes =3D [], + maxDepth =3D 0, + numLeaves =3D 0; + + // changing from hierarchy's custom format for data to usable form= at + _nodes.forEach(function (_node){ + var node =3D _node.data; + node.depth =3D _node.depth; + maxDepth =3D node.depth > maxDepth ? node.depth : maxDepth; /= /finding max depth of tree + nodes.push(node); + }); + // counting the number of leaf nodes and assigning max depth to no= des that do not have children to flush all the leave nodes + nodes.forEach(function(node){ + if ( !node.children ) { //&& !node._children + numLeaves +=3D 1; + node.depth =3D maxDepth; // if a leaf has no child it woul= d be assigned max depth + } + }); + + leafHeight =3D layoutMode =3D=3D=3D "Circular" ? height / numLeave= s : leafHeight; + leafIndex =3D 0; + layout(nodes[0], maxDepth, leafHeight, null); + + return nodes; + }; + + + function layout (node, maxDepth, vertSeparation, parent) { + /** + * -- Function with side effect of adding x0, y0 to all child; tak= e in the root as starting point + * assuming that the leave nodes would be sorted in presented ord= er + * horizontal(y0) is calculated according to (=3D evo dis= t X depth separation) from their parent + * vertical (x0) - if leave node: find its order in all o= f the leave node =3D=3D=3D node.id, then multiply by verticalSeparation + * - if parent node: is place in the mid point al= l of its children nodes + * -- The layout will first calculate the y0 field going towards t= he leaves, and x0 when returning + */ + var children =3D node.children, + sumChildVertSeparation =3D 0; + + // calculation of node's dist from parents, going down. + var dist =3D node.dist || defaultDist; + dist =3D dist > 1 ? 1 : dist; // We constrain all dist to be l= ess than one + node.dist =3D dist; + if (parent !=3D=3D null){ + node.y0 =3D parent.y0 + dist * depthSeparation; + } else { //root node + node.y0 =3D maxTextWidth; + } + + + // if a node have no children, we will treat it as a leaf and star= t laying it out first + if (!children) { + node.x0 =3D leafIndex++ * vertSeparation; + } else { + // if it has children, we will visit all its children and calc= ulate its position from its children + children.forEach( function (child) { + child.parent =3D node; + sumChildVertSeparation +=3D layout(child, maxDepth, vertSe= paration, node); + }); + node.x0 =3D sumChildVertSeparation / children.length; + } + + // adding properties to the newly created node + node.x =3D node.x0; + node.y =3D node.y0; + return node.x0; + } + return self; +} + + +/** + * -- PhyloTree Model -- + */ +var PhyloTree =3D Visualization.extend({ + defaults : { + layout: "Linear", + separation : 250, // px dist between nodes of different depth t= o represent 1 evolutionary until + leafHeight: 18, + type : "phyloviz", // visualization type + title : "Title", + scaleFactor: 1, + translate: [0,0], + fontSize: 12, //fontSize of node label + selectedNode : null, + nodeAttrChangedTime : 0 + }, + + root : {}, // Root has to be its own independent object because it is = not part of the viz_config + + toggle : function (d) { + /** + * Mechanism to expand or contract a single node. Expanded nodes h= ave a children list, while for + * contracted nodes the list is stored in _children. Nodes with th= eir children data stored in _children will not have their + * children rendered. + */ + if(typeof d =3D=3D=3D "undefined") {return ;} + if (d.children ) { + d._children =3D d.children; + d.children =3D null; + } else { + d.children =3D d._children; + d._children =3D null; + } + }, + + toggleAll : function(d) { + /** + * Contracts the phylotree to a single node by repeatedly calling= itself to place all the list + * of children under _children. + */ + if (d.children && d.children.length !=3D=3D 0) { + d.children.forEach(this.toggleAll); + toggle(d); + } + }, + + getData : function (){ + /** + * Return the data of the tree. Used for preserving state. + */ + return this.root; + }, + + save: function() { + /** + * Overriding the default save mechanism to do some clean of circu= lar reference of the + * phyloTree and to include phyloTree in the saved json + */ + var root =3D this.root; + cleanTree(root); + this.set("root", root); + + function cleanTree(node){ + // we need to remove parent to delete circular reference + delete node.parent; + + // removing unnecessary attributes + if (node._selected){ delete node._selected;} + + node.children ? node.children.forEach(cleanTree) : 0; + node._children ? node._children.forEach(cleanTree) : 0; + } + + var config =3D jQuery.extend(true, {}, this.attributes); + config["selectedNode"] =3D null; + + show_message("Saving to Galaxy", "progress"); + + return $.ajax({ + url: this.url(), + type: "POST", + dataType: "json", + data: { + vis_json: JSON.stringify(config) + }, + success: function(res){ + var viz_id =3D res.url.split("id=3D")[1].split("&")[0], + viz_url =3D "/phyloviz/visualization?id=3D" + viz_id; + window.history.pushState({}, "", viz_url + window.location= .hash); + hide_modal(); + } + }); + } +}); + + + +/** + * -- Views -- + */ +var PhylovizLayoutBase =3D Backbone.View.extend({ + /** + * Stores the default variable for setting up the visualization + */ + defaults : { + nodeRadius : 4.5 // radius of each node in the diagram + }, + + + stdInit : function (options) { + /** + * Common initialization in layouts + */ + + var self =3D this; + self.model.on("change:separation change:leafHeight change:fontSize= change:nodeAttrChangedTime", self.updateAndRender, self); + + self.vis =3D options.vis; + self.i =3D 0; + self.maxDepth =3D -1; // stores the max depth of the tree + + self.width =3D options.width; + self.height =3D options.height; + }, + + + updateAndRender : function(source) { + /** + * Updates the visualization whenever there are changes in the ex= pansion and contraction of nodes + * AND possibly when the tree is edited. + */ + var vis =3D d3.select(".vis"), + self =3D this; + source =3D source || self.model.root; + + self.renderNodes(source); + self.renderLinks(source); + self.addTooltips(); + }, + + + renderLinks : function(source) { + /** + * Renders the links for the visualization. + */ + var self =3D this; + var diagonal =3D self.diagonal; + var duration =3D self.duration; + var layoutMode =3D self.layoutMode; + var link =3D self.vis.selectAll("g.completeLink") + .data(self.tree.links(self.nodes), function(d) { return d.targ= et.id; }); + + var calcalateLinePos =3D function(d) { + d.pos0 =3D d.source.y0 + " " + d.source.x0; // position of t= he source node <=3D> starting location of the line drawn + d.pos1 =3D d.source.y0 + " " + d.target.x0; // position where= the line makes a right angle bend + d.pos2 =3D d.target.y0 + " " + d.target.x0; // point where= the horizontal line becomes a dotted line + }; + + var linkEnter =3D link.enter().insert("svg:g","g.node") + .attr("class", "completeLink"); + + + linkEnter.append("svg:path") + .attr("class", "link") + .attr("d", function(d) { + calcalateLinePos(d); + return "M " + d.pos0 + " L " + d.pos1; + }); + + var linkUpdate =3D link.transition().duration(500); + + linkUpdate.select("path.link") + .attr("d", function(d) { + calcalateLinePos(d); + return "M " + d.pos0 + " L " + d.pos1 + " L " + d.pos2; + }); + + var linkExit =3D link.exit().remove(); + + }, + + // User Interaction methods below + + selectNode : function(node){ + /** + * Displays the information for editting + */ + var self =3D this; + d3.selectAll("g.node") + .classed("selectedHighlight", function(d){ + if (node.id =3D=3D=3D d.id){ + if(node._selected) { // for de=3Dselecting node. + delete node._selected; + return false; + } else { + node._selected =3D true; + return true; + } + } + return false; + }); + + self.model.set("selectedNode", node); + $("#phyloVizSelectedNodeName").val(node.name); + $("#phyloVizSelectedNodeDist").val(node.dist); + $("#phyloVizSelectedNodeAnnotation").val(node.annotation || ""); + }, + + addTooltips : function (){ + /** + * Creates bootstrap tooltip for the visualization. Has to be cal= led repeatedly due to newly generated + * enterNodes + */ + $(".bs-tooltip").remove(); //clean up tooltip, just in case i= ts listeners are removed by d3 + $(".node") + .attr("data-original-title", function(){ + var d =3D this.__data__, + annotation =3D d.annotation || "None" ; + return d ? (d.name ? d.name + "<br/>" : "") + "Dist: " + d= .dist + " <br/>Annotation: " + annotation: ""; + }) + .tooltip({'placement':'top', 'trigger' : 'hover'}); + + } +}); + + + + +var PhylovizLinearView =3D PhylovizLayoutBase.extend({ + /** + * Linea layout class of Phyloviz, is responsible for rendering the no= des + * calls PhyloTreeLayout to determine the positions of the nodes + */ + initialize : function(options){ + // Default values of linear layout + var self =3D this; + self.margins =3D options.margins; + self.layoutMode =3D "Linear"; + + self.stdInit(options); + + self.layout(); + self.updateAndRender(self.model.root); + }, + + layout : function() { + /** + * Creates the basic layout of a linear tree by precalculating fix= ed values. + * One of calculations are also made here + */ + + var self =3D this; + + self.tree =3D new PhyloTreeLayout().layoutMode("Linear"); + self.diagonal =3D d3.svg.diagonal() + .projection(function(d) { return [d.y, d.x ]; }); + }, + + renderNodes : function (source) { + /** + * Renders the nodes base on Linear layout. + */ + var self =3D this, + fontSize =3D self.model.get("fontSize") + "px"; + + // assigning properties from models + self.tree.separation(self.model.get("separation")).leafHeight(self= .model.get("leafHeight")); + + var duration =3D 500, + nodes =3D self.tree.separation(self.model.get("separation")).n= odes(self.model.root); + + var node =3D self.vis.selectAll("g.node") + .data(nodes, function(d) { return d.name + d.id || (d.id =3D += +self.i); }); + + // These variables has to be passed into update links which are in= the base methods + self.nodes =3D nodes; + self.duration =3D duration; + + // ------- D3 ENTRY -------- + // Enter any new nodes at the parent's previous position. + var nodeEnter =3D node.enter().append("svg:g") + .attr("class", "node") + .on("dblclick", function(){ d3.event.stopPropagation(); }) + .on("click", function(d) { + if (d3.event.altKey) { + self.selectNode(d); // display info if alt is p= ressed + } else { + if(d.children && d.children.length =3D=3D=3D 0){ retur= n;} // there is no need to toggle leaves + self.model.toggle(d); // contract/expand nodes at da= ta level + self.updateAndRender(d); // re-render the tree + } + }); + + nodeEnter.attr("transform", function(d) { return "translate(" + so= urce.y0 + "," + source.x0 + ")"; }); + + nodeEnter.append("svg:circle") + .attr("r", 1e-6) + .style("fill", function(d) { return d._children ? "lightsteelb= lue" : "#fff"; }); + + nodeEnter.append("svg:text") + .attr("class", "nodeLabel") + .attr("x", function(d) { return d.children || d._children ? -1= 0 : 10; }) + .attr("dy", ".35em") + .attr("text-anchor", function(d) { return d.children || d._chi= ldren ? "end" : "start"; }) + .style("fill-opacity", 1e-6); + + // ------- D3 TRANSITION -------- + // Transition nodes to their new position. + var nodeUpdate =3D node.transition() + .duration(duration); + + nodeUpdate.attr("transform", function(d) { + return "translate(" + d.y + "," + d.x + ")"; }); + + nodeUpdate.select("circle") + .attr("r", self.defaults.nodeRadius) + .style("fill", function(d) { return d._children ? "lightsteelb= lue" : "#fff"; }); + + nodeUpdate.select("text") + .style("fill-opacity", 1) + .style("font-size", fontSize) + .text(function(d) { return d.name; }); + + // ------- D3 EXIT -------- + // Transition exiting nodes to the parent's new position. + var nodeExit =3Dnode.exit().transition() + .duration(duration) + .remove(); + + nodeExit.select("circle") + .attr("r", 1e-6); + + nodeExit.select("text") + .style("fill-opacity", 1e-6); + + // Stash the old positions for transition. + nodes.forEach(function(d) { + d.x0 =3D d.x; // we need the x0, y0 for parents with children + d.y0 =3D d.y; + }); + } + +}); + +var PhylovizView =3D Backbone.View.extend({ + + className: 'phyloviz', + + initialize: function(options) { + var self =3D this; + // -- Default values of the vis + self.MIN_SCALE =3D 0.05; //for zooming + self.MAX_SCALE =3D 5; + self.MAX_DISPLACEMENT =3D 500; + self.margins =3D [10, 60, 10, 80]; + + self.width =3D $("#PhyloViz").width(); + self.height =3D $("#PhyloViz").height(); + self.radius =3D self.width; + self.data =3D options.data; + + // -- Events Phyloviz view responses to + $(window).resize(function(){ + self.width =3D $("#PhyloViz").width(); + self.height =3D $("#PhyloViz").height(); + self.render(); + }); + + // -- Create phyloTree model + self.phyloTree =3D new PhyloTree(options.config); + self.phyloTree.root =3D self.data; + + // -- Set up UI functions of main view + self.zoomFunc =3D d3.behavior.zoom().scaleExtent([self.MIN_SCALE, = self.MAX_SCALE]); + self.zoomFunc.translate(self.phyloTree.get("translate")); + self.zoomFunc.scale(self.phyloTree.get("scaleFactor")); + + // -- set up header buttons, search and settings menu + self.navMenu =3D new HeaderButtons(self); + self.settingsMenu =3D new SettingsMenu({phyloTree : self.phyloTree= }); + self.nodeSelectionView =3D new NodeSelectionView({phyloTree : self= .phyloTree}); + self.search =3D new PhyloVizSearch(); + + + setTimeout(function(){ // using settimeout to call the zoomAn= dPan function according to the stored attributes in viz_config + self.zoomAndPan(); + }, 1000); + }, + + render: function(){ + // -- Creating helper function for vis. -- + var self =3D this; + $("#PhyloViz").empty(); + + // -- Layout viz. -- + self.mainSVG =3D d3.select("#PhyloViz").append("svg:svg") + .attr("width", self.width) + .attr("height", self.height) + .attr("pointer-events", "all") + .call(self.zoomFunc.on("zoom", function(){ + self.zoomAndPan(); + })); + + self.boundingRect =3D self.mainSVG.append("svg:rect") + .attr("class", "boundingRect") + .attr("width", self.width) + .attr("height", self.height) + .attr("stroke", "black") + .attr("fill", "white"); + + self.vis =3D self.mainSVG + .append("svg:g") + .attr("class", "vis"); + + self.layoutOptions =3D { + model : self.phyloTree, + width : self.width, + height : self.height, + vis: self.vis, + margins: self.margins + }; + + // -- Creating Title + $("#title").text("Phylogenetic Tree from " + self.phyloTree.get("t= itle") + ":"); + + // -- Create Linear view instance -- + var linearView =3D new PhylovizLinearView(self.layoutOptions) + }, + + zoomAndPan : function(event){ + /** + * Function to zoom and pan the svg element which the entire tree = is contained within + * Uses d3.zoom events, and extend them to allow manual updates an= d keeping states in model + */ + if (typeof event !=3D=3D "undefined") { + var zoomParams =3D event.zoom, + translateParams =3D event.translate; + } + + var self =3D this, + scaleFactor =3D self.zoomFunc.scale(), + translationCoor =3D self.zoomFunc.translate(), + zoomStatement =3D "", + translateStatement =3D ""; + + // Do manual scaling. + switch (zoomParams) { + case "reset": + scaleFactor =3D 1.0; + translationCoor =3D [0,0]; break; + case "+": + scaleFactor *=3D 1.1; break; + case "-": + scaleFactor *=3D 0.9; break; + default: + if (typeof zoomParams =3D=3D=3D "number") { + scaleFactor =3D zoomParams; + } else if (d3.event !=3D=3D null) { + scaleFactor =3D d3.event.scale; + } + } + if (scaleFactor < self.MIN_SCALE || scaleFactor > self.MAX_SCALE) = { return;} + self.zoomFunc.scale(scaleFactor); //update scale Factor + zoomStatement =3D "translate(" + self.margins[3] + "," + self.mar= gins[0] + ")" + + " scale(" + scaleFactor + ")"; + + // Do manual translation. + if( d3.event !=3D=3D null) { + translateStatement =3D "translate(" + d3.event.translate + ")"; + } else { + if(typeof translateParams !=3D=3D "undefined") { + var x =3D translateParams.split(",")[0]; + var y =3D translateParams.split(",")[1]; + if (!isNaN(x) && !isNaN(y)){ + translationCoor =3D [translationCoor[0] + parseFloat(x= ), translationCoor[1] + parseFloat(y)]; + } + } + self.zoomFunc.translate(translationCoor); // update zoomFunc + translateStatement =3D "translate(" + translationCoor + ")"; + } + + self.phyloTree.set("scaleFactor", scaleFactor); + self.phyloTree.set("translate", translationCoor); + self.vis.attr("transform", translateStatement + zoomStatement); //= refers to the view that we are actually zooming + }, + + + reloadViz : function() { + /** + * Primes the Ajax URL to load another Nexus tree + */ + var self =3D this, + treeIndex =3D $("#phylovizNexSelector :selected").val(), + dataset_id =3D self.phyloTree.get("dataset_id"), + url =3D "phyloviz/getJsonData?dataset_id=3D" + dataset_id + "&= treeIndex=3D" + String(treeIndex); + $.getJSON(url, function(packedJson){ + window.initPhyloViz(packedJson.data, packedJson.config); + }); + } +}); + + +var HeaderButtons =3D Backbone.View.extend({ + + initialize : function(phylovizView){ + var self =3D this; + self.phylovizView =3D phylovizView; + + // Clean up code - if the class initialized more than once + $("#panelHeaderRightBtns").empty(); + $("#phyloVizNavBtns").empty(); + $("#phylovizNexSelector").off(); + + self.initNavBtns(); + self.initRightHeaderBtns(); + + // Initial a tree selector in the case of nexus + $("#phylovizNexSelector").off().on("change", function() {self.phy= lovizView.reloadViz();} ); + + }, + + initRightHeaderBtns : function(){ + var self =3D this; + + rightMenu =3D create_icon_buttons_menu([ + { icon_class: 'gear', title: 'PhyloViz Settings', on_click: fu= nction(){ + $("#SettingsMenu").show(); + self.settingsMenu.updateUI(); + } }, + { icon_class: 'disk', title: 'Save visualization', on_click: f= unction() { + var nexSelected =3D $("#phylovizNexSelector option:selecte= d").text(); + if(nexSelected) { + self.phylovizView.phyloTree.set("title", nexSelected); + } + self.phylovizView.phyloTree.save(); + } }, + { icon_class: 'chevron-expand', title: 'Search / Edit Nodes', = on_click: function() { + $("#nodeSelectionView").show(); + } }, + { icon_class: 'information', title: 'Phyloviz Help', on_click:= function() { + window.open('http://wiki.g2.bx.psu.edu/Learn/Visualization= /PhylogeneticTree'); + // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs= 3EyMe1B1X_KFPouzIgrCz3zk/edit + } } + ], + { + tooltip_config: { placement: 'bottom' } + }); + $("#panelHeaderRightBtns").append(rightMenu.$el); + }, + + initNavBtns: function() { + var self =3D this, + navMenu =3D create_icon_buttons_menu([ + { icon_class: 'zoom-in', title: 'Zoom in', on_click: funct= ion() { + self.phylovizView.zoomAndPan({ zoom : "+"}); + } }, + { icon_class: 'zoom-out', title: 'Zoom out', on_click: fun= ction() { + self.phylovizView.zoomAndPan({ zoom : "-"}); + } }, + { icon_class: 'arrow-circle', title: 'Reset Zoom/Pan', on_= click: function() { + self.phylovizView.zoomAndPan({ zoom : "reset"}); + } } + ], + { + tooltip_config: { placement: 'bottom' } + }); + $("#phyloVizNavBtns").append(navMenu.$el); + } +}); + + +var SettingsMenu =3D UserMenuBase.extend({ + + className: 'Settings', + + initialize: function(options){ + // settings needs to directly interact with the phyloviz model so = it will get access to it. + var self =3D this; + self.phyloTree =3D options.phyloTree; + self.el =3D $("#SettingsMenu"); + self.inputs =3D { + separation : $("#phyloVizTreeSeparation"), + leafHeight : $("#phyloVizTreeLeafHeight"), + fontSize : $("#phyloVizTreeFontSize") + }; + + //init all buttons of settings + $("#settingsCloseBtn").off().on("click", function() { self.el.hide= (); }); + $("#phylovizResetSettingsBtn").off().on("click", function() { self= .resetToDefaults(); }); + $("#phylovizApplySettingsBtn").off().on("click", function() { self= .apply(); }); + }, + + apply : function(){ + /** + * Applying user values to phylotree model. + */ + var self =3D this; + if (!self.isAcceptableValue(self.inputs["separation"], 50, 2500) || + !self.isAcceptableValue(self.inputs["leafHeight"], 5, 30) || + !self.isAcceptableValue(self.inputs["fontSize"], 5, 20)){ + return; + } + $.each(self.inputs, function(key, $input){ + self.phyloTree.set(key, $input.val()); + }); + }, + updateUI : function(){ + /** + * Called to update the values input to that stored in the model + */ + var self =3D this; + $.each(self.inputs, function(key, $input){ + $input.val(self.phyloTree.get(key)); + }); + }, + resetToDefaults : function(){ + /** + * Resets the value of the phyloTree model to its default + */ + $(".bs-tooltip").remove(); // just in case the tool tip was n= ot removed + var self =3D this; + $.each(self.phyloTree.defaults, function(key, value) { + self.phyloTree.set(key, value); + }); + self.updateUI(); + }, + + render: function(){ + + } + +}); + + +var NodeSelectionView =3D UserMenuBase.extend({ + /** + * View for inspecting node properties and editing them + */ + className: 'Settings', + + initialize : function (options){ + var self =3D this; + self.el =3D $("#nodeSelectionView"); + self.phyloTree =3D options.phyloTree; + + self.UI =3D { + enableEdit : $('#phylovizEditNodesCheck'), + saveChanges : $('#phylovizNodeSaveChanges'), + cancelChanges : $("#phylovizNodeCancelChanges"), + name : $("#phyloVizSelectedNodeName"), + dist : $("#phyloVizSelectedNodeDist"), + annotation : $("#phyloVizSelectedNodeAnnotation") + }; + + self.valuesOfConcern =3D { + name : null, + dist : null, + annotation : null + }; // temporarily stores the values in case user change their mind + + //init UI buttons + $("#nodeSelCloseBtn").off().on("click", function() { self.el.hide(= ); }); + self.UI.saveChanges.off().on("click", function(){ self.updateNodes= (); }); + self.UI.cancelChanges.off().on("click", function(){ self.cancelCha= nges(); }); + + (function ($) { + // extending jquery fxn for enabling and disabling nodes. + $.fn.enable =3D function (isEnabled) { + return $(this).each(function () { + if(isEnabled){ + $(this).removeAttr('disabled'); + } else { + $(this).attr('disabled', 'disabled'); + } + }); + }; + })(jQuery); + + self.UI.enableEdit.off().on("click", function () { + self.toggleUI(); + }); + }, + + toggleUI : function(){ + /** + * For turning on and off the child elements + */ + var self =3D this, + checked =3D self.UI.enableEdit.is(':checked'); + + !checked ? self.cancelChanges() : ""; + + $.each(self.valuesOfConcern, function(key, value) { + self.UI[key].enable(checked); + }); + if(checked){ + self.UI.saveChanges.show(); + self.UI.cancelChanges.show(); + } else { + self.UI.saveChanges.hide(); + self.UI.cancelChanges.hide(); + } + + }, + + cancelChanges : function() { + /** + * Reverting to previous values in case user change their minds + */ + var self =3D this, + node =3D self.phyloTree.get("selectedNode"); + if (node){ + $.each(self.valuesOfConcern, function(key, value) { + self.UI[key].val(node[key]); + }); + } + }, + + updateNodes : function (){ + /** + * Changing the data in the underlying tree with user-specified va= lues + */ + var self =3D this, + node =3D self.phyloTree.get("selectedNode"); + if (node){ + if (!self.isAcceptableValue(self.UI.dist, 0, 1) || + self.hasIllegalJsonCharacters(self.UI.name) || + self.hasIllegalJsonCharacters(self.UI.annotation) ) { + return; + } + $.each(self.valuesOfConcern, function(key, value) { + (node[key]) =3D self.UI[key].val(); + }); + self.phyloTree.set("nodeAttrChangedTime", new Date()); + } else { + alert("No node selected"); + } + } + + +}); + + + +var PhyloVizSearch =3D UserMenuBase.extend({ + /** + * Initializes the search panel on phyloviz and handles its user inter= action + * It allows user to search the entire free based on some qualifer, li= ke dist <=3D val. + */ + initialize : function () { + var self =3D this; + + $("#phyloVizSearchBtn").on("click", function(){ + var searchTerm =3D $("#phyloVizSearchTerm"), + searchConditionVal =3D $("#phyloVizSearchCondition").val()= .split("-"), + attr =3D searchConditionVal[0], + condition =3D searchConditionVal[1]; + self.hasIllegalJsonCharacters(searchTerm); + + if (attr =3D=3D=3D "dist"){ + self.isAcceptableValue(searchTerm, 0, 1); + } + self.searchTree(attr, condition, searchTerm.val()); + }); + }, + + searchTree : function (attr, condition, val){ + /** + * Searches the entire tree and will highlight the nodes that matc= h the condition in green + */ + d3.selectAll("g.node") + .classed("searchHighlight", function(d){ + var attrVal =3D d[attr]; + if (typeof attrVal !=3D=3D "undefined" && attrVal !=3D=3D = null){ + if (attr =3D=3D=3D "dist"){ + switch (condition) { + case "greaterEqual": + return attrVal >=3D +val; + case "lesserEqual": + return attrVal <=3D +val; + default: + return; + } + + } else if (attr =3D=3D=3D "name" || attr =3D=3D=3D "an= notation") { + return attrVal.toLowerCase().indexOf(val.toLowerCa= se()) !=3D=3D -1; + } + } + }); + } +}); \ No newline at end of file diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -58,7 +58,7 @@ Info: </label><div style=3D"float: left; width: 250px; margin-ri= ght: 10px;"> - <textarea name=3D"info" cols=3D"40" rows=3D"2">${data.= info | h}</textarea> + <textarea name=3D"info" cols=3D"40" rows=3D"2">${ util= .unicodify( data.info ) | h}</textarea></div><div style=3D"clear: both"></d= iv></div> diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 templates/dataset/errors.mako --- a/templates/dataset/errors.mako +++ b/templates/dataset/errors.mako @@ -24,21 +24,21 @@ <% job =3D hda.creating_job_associations[0].job %> %if job.traceback: The Galaxy framework encountered the following error while= attempting to run the tool: - <pre>${job.traceback | h}</pre> + <pre>${ util.unicodify( job.traceback ) | h}</pre> %endif %if job.stderr or job.info: Tool execution generated the following error message: %if job.stderr: - <pre>${job.stderr | h}</pre> + <pre>${ util.unicodify( job.stderr ) | h}</pre> %elif job.info: - <pre>${job.info | h}</pre> + <pre>${ util.unicodify( job.info ) | h}</pre> %endif %else: Tool execution did not generate any error messages. %endif %if job.stdout: The tool produced the following additional output: - <pre>${job.stdout | h}</pre> + <pre>${ util.unicodify( job.stdout ) | h}</pre> %endif %else: The tool did not create any additional job / error info. diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -272,6 +272,17 @@ } =20 init_trackster_links(); + + function init_phyloviz_links() { + // PhyloViz links + // Add to trackster browser functionality + $(".phyloviz-add").live("click", function() { + var dataset =3D this, + dataset_jquery =3D $(this); + window.parent.location =3D dataset_jquery.attr("new-url"); + }); + } + init_phyloviz_links(); =20 // History rename functionality. async_save_text("history-name-container", "history-name", "${h.url_for= ( controller=3D"/history", action=3D"rename_async", id=3Dtrans.security.enc= ode_id(history.id) )}", "new_name", 18); diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -29,6 +29,9 @@ ## Render the dataset `data` as history item, using `hid` as the displayed= id <%def name=3D"render_dataset( data, hid, show_deleted_on_refresh =3D False= , for_editing =3D True, display_structured =3D False )"><% + + from galaxy.datatypes.xml import Phyloxml + from galaxy.datatypes.data import Newick, Nexus dataset_id =3D trans.security.encode_id( data.id ) =20 if data.state in ['no state','',None]: @@ -230,6 +233,14 @@ action-url=3D"${h.url_for( controller=3D't= racks', action=3D'browser', dataset_id=3Ddataset_id)}" new-url=3D"${h.url_for( controller=3D'trac= ks', action=3D'index', dataset_id=3Ddataset_id, default_dbkey=3Ddata.dbkey)= }" title=3D"View in Trackster"></a> %endif + <% + isPhylogenyData =3D isinstance(data.datatype, = (Phyloxml, Nexus, Newick)) + %> + %if isPhylogenyData: + <a href=3D"javascript:void(0)" class=3D"i= con-button chart_curve phyloviz-add" + action-url=3D"${h.url_for( controller= =3D'phyloviz', action=3D'-', dataset_id=3Ddataset_id)}" + new-url=3D"${h.url_for( controller=3D'p= hyloviz', action=3D'index', dataset_id=3Ddataset_id)}" title=3D"View in Phy= loviz"></a> + %endif %if trans.user: %if not display_structured: <div style=3D"float: right"> diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 templates/visualization/phyloviz.mako --- /dev/null +++ b/templates/visualization/phyloviz.mako @@ -0,0 +1,320 @@ +<%inherit file=3D"/webapps/galaxy/base_panels.mako"/> +## +<%def name=3D"init()"> + <% + self.has_left_panel=3DFalse + self.has_right_panel=3DFalse + self.active_view=3D"visualization" + self.message_box_visible=3DFalse + %> +</%def> + +<%def name=3D"stylesheets()"> + ${parent.stylesheets()} + <style> + + .node circle { + cursor: pointer; + fill: #fff; + stroke: steelblue; + stroke-width: 1.5px; + } + + .node.searchHighlight circle { + stroke-width: 3px; + stroke: #7adc26; + } + + .node.selectedHighlight circle { + stroke-width: 3px; + stroke: #dc143c; + } + + path.link { + fill: none; + stroke: #B5BBFF; + stroke-width: 4.0px; + } + + + div #phyloVizNavContainer{ + text-align: center; + width: 100%; + height: 0px; + } + + div #phyloVizNav{ + font-weight: bold; + display: inline-block; + background: transparent; + top: -2em; + position: relative; + } + + div .navControl{ + float: left; + } + + div#FloatingMenu { + left: 0; + top: 15%; + width:20%; + z-index:100; + padding: 5px; + + } + + div#SettingsMenu { + width: 25%; + top: 350px; + + } + + div#nodeSelectionView { + width: 25%; + top:70px; + } + + .Panel { + right: 0%; + z-index: 101; + position: fixed; + + ## Borrowed from galaxy modal_dialogues + background-color: white; + border: 1px solid #999; + border: 1px solid rgba(0, 0, 0, 0.3); + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; + } + + span.PhylovizCloseBtn{ + cursor: pointer; + float : right; + } + + #PhyloViz{ + width: 100%; + height: 95%; + } + + h2.PhyloVizMenuTitle{ + color: white; + } + + ## Settings Menu + .SettingMenuRows{ + margin: 2px 0 2px 0; + } + + + ## Helper Styles + .PhyloVizFloatLeft{ + float : left; + } + .icon-button.zoom-in,.icon-button.zoom-out{display:inline-block;he= ight:16px;width:16px;margin-bottom:-3px;cursor:pointer;} + .icon-button.zoom-out{background:transparent url(../images/fugue/m= agnifier-zoom-out.png) center center no-repeat;} + .icon-button.zoom-in{margin-left:10px;background:transparent url(.= ./images/fugue/magnifier-zoom.png) center center no-repeat;} + + </style> +</%def> + + +<%def name=3D"javascripts()"> + ${parent.javascripts()} + ${h.js( "galaxy.panels", "libs/d3", "mvc/data", "viz/visualization", "= viz/phyloviz")} +</%def> + + + +<%def name=3D"center_panel()"> + + <div class=3D"unified-panel-header" unselectable=3D"on"> + <div class=3D"unified-panel-header-inner"> + <div style=3D"float:left;" id=3D"title"></div> + <div style=3D"float:right;" id=3D"panelHeaderRightBtns"></div> + </div> + <div style=3D"clear: both"></div> + </div> + + + <div id=3D"phyloVizNavContainer"> + <div id=3D"phyloVizNav"> + %if config["ext"] =3D=3D "nex" and not config["saved_visualiza= tion"]: + <div id =3D "phylovizNexInfo" class=3D"navControl"> + <p>Select a tree to view:    + <select id=3D"phylovizNexSelector"> + % for tree, index in config["trees"]: + <option value=3D"${index}">${tree}</option> + % endfor + </select> + </p> + </div> + %endif + <div id=3D"phyloVizNavBtns" class=3D"navControl"> + </div> + <div class=3D"navControl"> + <p> | Alt+click to select nodes</p> + </div> + + + </div> + + </div> + + ## Node Selection Menu + <div id=3D"nodeSelectionView" class=3D"Panel"> + <div class=3D"modal-header"> + <h3 class=3D"PhyloVizMenuTitle">Search / Edit Nodes : + <span class=3D"PhylovizCloseBtn" id=3D"nodeSelCloseBtn"> X= </span> + </h3> + </div> + + <div class=3D"modal-body"> + + <div class=3D"SettingMenuRows"> + Search for nodes with: + <select id=3D"phyloVizSearchCondition" style=3D"width: 55%= "> + <option value=3D"name-containing">Name (containing)</o= ption> + <option value=3D"annotation-containing">Annotation (co= ntaining)</option> + <option value=3D"dist-greaterEqual">Distance (>=3D)</o= ption> + <option value=3D"dist-lesserEqual">Distance (<=3D)</op= tion> + </select> + <input type=3D"text" id=3D"phyloVizSearchTerm" value=3D"N= one" size=3D"15" displayLabel=3D"Distance"> + + <div class=3D"SettingMenuRows" style=3D"text-align: center= ;"> + <button id=3D"phyloVizSearchBtn" > Search! </button> + </div> + </div> + + <br/> + + <div class=3D"SettingMenuRows"> + Name: <input type=3D"text" id=3D"phyloVizSelectedNodeName"= value=3D"None" size=3D"15" disabled=3D"disabled" > + </div> + <div class=3D"SettingMenuRows"> + Dist: <input type=3D"text" id=3D"phyloVizSelectedNodeDist"= value=3D"None" size=3D"15" disabled=3D"disabled" displayLabel=3D"Distance"> + </div> + <div class=3D"SettingMenuRows"> + Annotation: + <textarea id=3D"phyloVizSelectedNodeAnnotation" disabled= =3D"disabled" ></textarea> + </div> + <div class=3D"SettingMenuRows"> + Edit: <input type=3D"checkbox" id=3D"phylovizEditNodesChec= k" value=3D"You can put custom annotations here and it will be saved"> + <button id=3D"phylovizNodeSaveChanges" style=3D"display: n= one;"> Save edits</button> + <button id=3D"phylovizNodeCancelChanges" style=3D"display:= none;"> Cancel</button> + </div> + </div> + </div> + + ## Settings Menus + <div id=3D"SettingsMenu" class=3D"Panel"> + <div class=3D"modal-header"> + <h3 class=3D"PhyloVizMenuTitle">Phyloviz Settings: + <span class=3D"PhylovizCloseBtn" id=3D"settingsCloseBtn"> = X </span> + </h3> + </div> + <div class=3D"modal-body"> + <div class=3D"SettingMenuRows"> + Phylogenetic Spacing (px per unit): <input id=3D"phyloVizT= reeSeparation" type=3D"text" value=3D"250" size=3D"10" displayLabel=3D"Phyl= ogenetic Separation"> (50-2500) + </div> + <div class=3D"SettingMenuRows"> + Vertical Spacing (px): <input type=3D"text" id=3D"phyloViz= TreeLeafHeight" value=3D"18" size=3D"10" displayLabel=3D"Vertical Spacing">= (5-30) + </div> + <div class=3D"SettingMenuRows"> + Font Size (px): <input type=3D"text" id=3D"phyloVizTreeFon= tSize" value=3D"12" size=3D"4" displayLabel=3D"Font Size"> (5-20) + </div> + + </div> + <div class=3D"modal-footer"> + <button id=3D"phylovizResetSettingsBtn" class=3D"PhyloVizFloat= Left" > Reset </button> + <button id=3D"phylovizApplySettingsBtn" class=3D"PhyloVizFloat= Right" > Apply </button> + </div> + </div> + + + + + + + <div class=3D"Panel" id=3D"FloatingMenu" style=3D"display: None;"> + + <h2>PhyloViz (<a onclick=3D"displayHelp()" href=3D"javascript:void= (0);">?</a>)</h2> + <div style=3D"display: none;"> + <h2>Summary of Interactions and Functions:</h2> + <div class=3D"hint">1. Expansion of Nodes: click or option-cli= ck to expand or collapse</div> + <div class=3D"hint">2. Zooming and translation: mousewheel, bu= ttons, click and drag, double click. Reset</div> + <div class=3D"hint">3. Tooltip: Displays "Name and Size" on mo= useOver on nodes</div> + <div class=3D"hint">4. Minimap: Currently displays an exact bu= t scaled down replicate of the tree, orange bounding box is correct for lin= ear only<br/> + Can be switched on or off</div> + <div class=3D"hint">5. Changing Layouts: Able to change betwee= n circular and linear layouts.</div> + + </div> + + <h5>Scaling & Rotation:</h5> + <button id=3D"phylovizZoomInBtn" class=3D"" > + </button> + <button id=3D"phylovizZoomOutBtn" class=3D"" > - </button> + + + <h5>Translation:</h5> + <button id=3D"phylovizTranslateUpBtn" > Up </button> + <button id=3D"phylovizTranslateDownBtn" > Down </button> + <br/> + <button id=3D"phylovizTranslateLeftBtn" > Left </button> + <button id=3D"phylovizTranslateRightBtn" > Right </button> + + + + <h5>Others:</h5> + <button id=3D"phylovizResetBtn" > Reset Zoom/Translate </button> + <button id=3D"phylovizSaveBtn" > Save vizualization </button> + <button id=3D"phylovizOpenSettingsBtn" > Settings </button> + </div> + + <div id=3D"PhyloViz" > + </div> + + <script type=3D"text/javascript"> + + function initPhyloViz(data, config) { + var phyloviz; + + // -- Initialization code |--> + phyloviz =3D new PhylovizView({ + data: data, + layout : "Linear", + config : config + }); + + // -- Render viz. -- + phyloviz.render(); + + } + + $(function firstVizLoad(){ // calls when viz is loaded for t= he first time + var config =3D JSON.parse( '${ h.to_json_string( config )}'); + var data =3D JSON.parse('${h.to_json_string(data)}'); + initPhyloViz(data, config); + }); + + </script> + +</%def> + + diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -60,34 +60,41 @@ %endif <div class=3D"toolSectionPad"></div><div class=3D"toolSect= ionTitle"> - Repositories + All Repositories </div> - <div class=3D"toolSectionBody"> - <div class=3D"toolSectionBg"> - <div class=3D"toolTitle"> - <a target=3D"galaxy_main" href=3D"${h.url_for(= controller=3D'repository', action=3D'browse_categories', webapp=3D'communi= ty' )}">Browse by category</a> - </div> - %if trans.user: - <div class=3D"toolTitle"> - <a target=3D"galaxy_main" href=3D"${h.url_= for( controller=3D'repository', action=3D'browse_repositories', operation= =3D'my_repositories', webapp=3D'community' )}">Browse my repositories</a> - </div> - <div class=3D"toolTitle"> - <a target=3D"galaxy_main" href=3D"${h.url_= for( controller=3D'repository', action=3D'browse_invalid_tools', cntrller= =3D'repository', webapp=3D'community' )}">Browse my invalid tools</a> - </div> - %endif + <div class=3D"toolTitle"> + <a target=3D"galaxy_main" href=3D"${h.url_for( control= ler=3D'repository', action=3D'browse_categories', webapp=3D'community' )}">= Browse by category</a> + </div> + %if trans.user: + <div class=3D"toolSectionPad"></div> + <div class=3D"toolSectionTitle"> + My Repositories and Tools </div> - </div> - <div class=3D"toolSectionBody"> - <div class=3D"toolSectionBg"> - <div class=3D"toolTitle"> - %if trans.user: - <a target=3D"galaxy_main" href=3D"${h.url_= for( controller=3D'repository', action=3D'create_repository', webapp=3D'com= munity' )}">Create new repository</a> - %else: - <a target=3D"galaxy_main" href=3D"${h.url_= for( controller=3D'/user', action=3D'login', webapp=3D'community' )}">Login= to create a repository</a> - %endif - </div> + <div class=3D"toolTitle"> + <a target=3D"galaxy_main" href=3D"${h.url_for( con= troller=3D'repository', action=3D'browse_repositories', operation=3D'reposi= tories_i_own', webapp=3D'community' )}">Repositories I own</a></div> - </div> + <div class=3D"toolTitle"> + <a target=3D"galaxy_main" href=3D"${h.url_for( con= troller=3D'repository', action=3D'browse_repositories', operation=3D'writab= le_repositories', webapp=3D'community' )}">My writable repositories</a> + </div> + <div class=3D"toolTitle"> + <a target=3D"galaxy_main" href=3D"${h.url_for( con= troller=3D'repository', action=3D'browse_invalid_tools', cntrller=3D'reposi= tory', webapp=3D'community' )}">My invalid tools</a> + </div> + <div class=3D"toolSectionPad"></div> + <div class=3D"toolSectionTitle"> + Available Actions + </div> + <div class=3D"toolTitle"> + <a target=3D"galaxy_main" href=3D"${h.url_for( con= troller=3D'repository', action=3D'create_repository', webapp=3D'community' = )}">Create new repository</a> + </div> + %else: + <div class=3D"toolSectionPad"></div> + <div class=3D"toolSectionTitle"> + Available Actions + </div> + <div class=3D"toolTitle"> + <a target=3D"galaxy_main" href=3D"${h.url_for( con= troller=3D'/user', action=3D'login', webapp=3D'community' )}">Login to crea= te a repository</a> + </div> + %endif </div></div></div> diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 test-data/visualization/phyloviz/1_nexus.nex --- /dev/null +++ b/test-data/visualization/phyloviz/1_nexus.nex @@ -0,0 +1,87 @@ +#NEXUS + +[!This data set was downloaded from TreeBASE, a relational database of phy= logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer= sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl= edgment from the Nexus file. + + +Generated on June 12, 2012; 23:00 GMT + +TreeBASE (cc) 1994-2008 + +Study reference: +Olariaga I., Grebenc T., Salcedo I., & Mart=C3=ADn M.P. 2012. Two new spec= ies of Hydnum +with ovoid basidiospores: H. ovoideisporum and H. vesterholtii. Mycologia,= . + +TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S128= 31] + +BEGIN TREES; + TITLE Hydnum_ITS_result; + LINK TAXA =3D Taxa1; + TRANSLATE + 1 Hydnum_aff_ellipsosporum_RUFHYD1_AJ535304, + 2 Hydnum_albidum_ALB_AY817135, + 3 Hydnum_albidum_ALBHYD1_AJ534974, + 4 Hydnum_albomagnum_ALM_DQ218305, + 5 Hydnum_ellipsosporum_ELL_AY817138, + 6 Hydnum_ellipsosporum_RUFHYD8_AJ547882, + 7 Hydnum_ovoidisporum_12317BIOFungi, + 8 Hydnum_ovoidisporum_12683BIOFungi, + 9 Hydnum_ovoidisporum_12902BIOFungi, + 10 Hydnum_ovoidisporum_14130BIOFungi, + 11 Hydnum_repandum_RE1_REP1_AJ889978, + 12 Hydnum_repandum_RE1_REP2_AJ889949, + 13 Hydnum_repandum_RE1_REP3_AY817136, + 14 Hydnum_repandum_RE1_REP6_UDB000025, + 15 Hydnum_repandum_RE1_REP7_UDB000096, + 16 Hydnum_repandum_RE1_REP8_UDB001479, + 17 Hydnum_repandum_RE1_REPHYD10_AJ547888, + 18 Hydnum_repandum_RE1_REPHYD11_AJ547886, + 19 Hydnum_repandum_RE1_REPHYD1_AJ547871, + 20 Hydnum_repandum_RE1_REPHYD3_AJ547874, + 21 Hydnum_repandum_RE1_REPHYD4_AJ547876, + 22 Hydnum_repandum_RE1_REPHYD5_AJ547875, + 23 Hydnum_repandum_RE1_REPHYD6_AJ547877, + 24 Hydnum_repandum_RE1_REPHYD7_AJ547878, + 25 Hydnum_repandum_RE1_REPHYD8_AJ547881, + 26 Hydnum_repandum_RE1_REPHYD9_AJ547883, + 27 Hydnum_repandum_RE1_RUFHYD10_AJ547866, + 28 Hydnum_repandum_RE1_RUFHYD11_AJ547889, + 29 Hydnum_repandum_RE1_RUFHYD9_AJ535305, + 30 Hydnum_rufescens_RU1_RUFHYD5_AJ547869, + 31 Hydnum_rufescens_RU1_RUFHYD6_AJ547884, + 32 Hydnum_rufescens_RU1_RUFHYD7_AJ547870, + 33 Hydnum_rufescens_RU2_REP5_DQ367902, + 34 Hydnum_rufescens_RU2_RUFHYD2_AJ535301, + 35 Hydnum_rufescens_RU3_12901BIOFungi, + 36 Hydnum_rufescens_RU3_REP4_DQ218306, + 37 Hydnum_rufescens_RU3_RUFHYD3_AJ535303, + 38 Hydnum_rufescens_RU3_RUFHYD4_AJ535302, + 39 Hydnum_rufescens_RU4_RUFHYD12_AJ839969, + 40 Hydnum_rufescens_RU4_RUFHYD16_AJ547868, + 41 Hydnum_rufescens_RU4_RUFHYD17_AJ547885, + 42 Hydnum_rufescens_RU4_UMB1_DQ367903, + 43 Hydnum_rufescens_RU5_12760BIOFungi, + 44 Hydnum_rufescens_RU5_ALBHYD2_AJ534975, + 45 Hydnum_rufescens_RU5_RUF2_DQ658890, + 46 Hydnum_rufescens_RU5_RUF4_UDB001465, + 47 Hydnum_rufescens_RU5_RUF5_UDB002423, + 48 Hydnum_rufescens_RU5_RUFHYD14_AJ547872, + 49 Hydnum_rufescens_RU6_RUF1_AY817137, + 50 Hydnum_rufescens_RU6_RUFHYD15_AJ547867, + 51 Hydnum_rufescens_wrong_taxonomy_RUF3_AM087246, + 52 Hydnum_umbilicatum_UMBHYD1_AJ534972, + 53 Hydnum_umbilicatum_UMBHYD2_AJ534973, + 54 Hydnum_vesterholtii_10429BIOFungi, + 55 Hydnum_vesterholtii_10452BIOFungi, + 56 Hydnum_vesterholtii_12330BIOFungi, + 57 Hydnum_vesterholtii_12904BIOFungi, + 58 Hydnum_vesterholtii_REPHYD12A_AJ547879, + 59 Hydnum_vesterholtii_REPHYD12C_AJ783968, + 60 Hydnum_vesterholtii_REPHYD13_AJ547887, + 61 Sistotrema_muscicola_AJ606040, + 62 Sistotrema_alboluteum_AJ606042; + TREE Fig._2 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66= ,((4:100.0,(2:100.0,3:100.0):100.0):60.639999,(((56:100.0,58:100.0,59:100.0= ):84.639999,(54:100.0,55:100.0,57:100.0,60:100.0):98.330002):92.5,(((30:100= .0,31:100.0,32:100.0):100.0,(11:100.0,12:100.0,13:100.0,14:100.0,15:100.0,1= 6:100.0,17:100.0,18:100.0,19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,24:1= 00.0,25:100.0,26:100.0):99.93):68.690002,(((33:100.0,34:100.0):49.8050005,(= 35:100.0,36:100.0,37:100.0,38:100.0):99.989998):49.8050005,((7:100.0,8:100.= 0,9:100.0,10:100.0):100.0,(42:100.0,(39:100.0,40:100.0,41:100.0):98.449997)= :86.790001,((52:100.0,53:100.0):99.93,(1:100.0,(5:97.47999949999999,6:100.0= ):97.47999949999999):100.0):53.310001,(27:100.0,(28:100.0,29:100.0,49:100.0= ,50:100.0):47.404999):47.404999,(43:100.0,44:100.0,45:100.0,46:100.0,47:100= .0,48:100.0):99.459999):29.245001):29.245001):51.580002):61.540001):49.66); + TREE PAUP_1 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66= ,((4:100.0,(3:100.0,2:100.0):100.0):60.639999,(((58:100.0,59:100.0,56:100.0= ):84.639999,(60:100.0,54:100.0,55:100.0,57:100.0):98.330002):92.5,(((30:100= .0,31:100.0,32:100.0):100.0,(19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,2= 4:100.0,25:100.0,26:100.0,17:100.0,18:100.0,11:100.0,12:100.0,13:100.0,14:1= 00.0,15:100.0,16:100.0):99.93):68.690002,((34:100.0,33:100.0):99.610001,(37= :100.0,38:100.0,35:100.0,36:100.0):99.989998,(42:100.0,(39:100.0,41:100.0,4= 0:100.0):98.449997):86.790001,(8:100.0,7:100.0,9:100.0,10:100.0):100.0,((52= :100.0,53:100.0):99.93,(1:100.0,(5:100.0,6:100.0):94.959999):100.0):53.3100= 01,(29:100.0,27:100.0,28:100.0,50:100.0,49:100.0):94.809998,(44:100.0,43:10= 0.0,48:100.0,45:100.0,46:100.0,47:100.0):99.459999):58.490002):51.580002):6= 1.540001):49.66); + + + +END; diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 test-data/visualization/phyloviz/2_nexus.nex --- /dev/null +++ b/test-data/visualization/phyloviz/2_nexus.nex @@ -0,0 +1,96 @@ +#NEXUS + +[!This data set was downloaded from TreeBASE, a relational database of phy= logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer= sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl= edgment from the Nexus file. + + +Generated on August 18, 2012; 12:14 GMT + +TreeBASE (cc) 1994-2008 + +Study reference: +Naish D., Dyke G., Cau A., & Escuilli=C3=A9 F. 2012. A gigantic bird from = the Upper Cretaceous +of Central Asia. Biology Letters, 8(1): 97-100. + +TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S130= 08] + +BEGIN TREES; + TITLE Imported_trees; + LINK TAXA =3D Taxa1; + TRANSLATE + 1 Herrerasaurus, + 2 Tawa, + 3 Allosaurus, + 4 Alvarezsaurus, + 5 Anchiornis, + 6 Archaeopteryx, + 7 Archaeorhynchus, + 8 Avimimus, + 9 Baryonyx, + 10 Beipiaosaurus, + 11 Caenagnathus, + 12 Caudipteryx, + 13 Ceratosaurus, + 14 Chirostenotes, + 15 Citipati, + 16 Compsognathus, + 17 Confuciusornis, + 18 Dilong, + 19 Dilophosaurus, + 20 Epidendrosaurus, + 21 Epidexipteryx, + 22 Erlicosaurus, + 23 Eustreptospondylus, + 24 Gallimimus, + 25 Garudimimus, + 26 Gobipteryx, + 27 Guanlong, + 28 Haplocheirus, + 29 Harpymimus, + 30 Hebeiornis, + 31 Hongshanornis, + 32 Huoshanornis, + 33 Iberomesornis, + 34 Ichthyornis, + 35 Incisivosaurus, + 36 Jeholornis, + 37 Limusaurus, + 38 Longicrusavis, + 39 Longipteryx, + 40 Longirostravis, + 41 Majungasaurus, + 42 Masiakasaurus, + 43 Monolophosaurus, + 44 Mononykus, + 45 Neornithes, + 46 Ornitholestes, + 47 Ornithomimus, + 48 Patagonykus, + 49 Patagopteryx, + 50 Pelecanimimus, + 51 Pengornis, + 52 Protarchaeopteryx, + 53 Protopteryx, + 54 Rinchenia, + 55 Sapeornis, + 56 Segnosaurus, + 57 Shenzhousaurus, + 58 Shuvuuia, + 59 Sinornithosaurus, + 60 Sinosauropteryx, + 61 Sinovenator, + 62 Sinraptor, + 63 Syntarsus_kayentakatae, + 64 Troodon, + 65 Tyrannosaurus, + 66 Velociraptor, + 67 Yanornis, + 68 Yixianornis, + 69 Zhongjianornis, + 70 Zhongornis, + 71 Zuolong, + 72 Samrukia; + TREE Figure_1A =3D [&R] (1,(2,(((((43,(3,62)),(71,((46,((((28,(4,(48= ,(44,58)))),((((5,(61,(64,(59,66)))),(6,((36,(55,(69,(((7,34,45,49,72,(31,3= 8),(67,68)),(33,((32,((26,30),(39,40))),(51,53)))),(17,70))))),(20,21)))),(= (11,(12,(8,(14,(15,54))))),(35,52))),(10,(22,56)))),(50,(57,(29,(25,(24,47)= ))))),(16,60))),(27,(18,65))))),(9,23)),(13,(41,(37,42)))),(19,63)))); + + + +END; diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 test-data/visualization/phyloviz/3_phyloxml.xml --- /dev/null +++ b/test-data/visualization/phyloviz/3_phyloxml.xml @@ -0,0 +1,257 @@ +<?xml version=3D"1.0" encoding=3D"UTF-8"?> +<phyloxml xmlns:xsi=3D"http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation=3D"http://www.phyloxml.org http://www.phyloxml.org/1= .10/phyloxml.xsd" + xmlns=3D"http://www.phyloxml.org"> + <phylogeny rooted=3D"true"> + <clade> + <clade> + <branch_length>0.18105</branch_length> + <confidence type=3D"unknown">89.0</confidence> + <clade> + <branch_length>0.07466</branch_length> + <confidence type=3D"unknown">32.0</confidence> + <clade> + <branch_length>0.26168</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.22058</branch_length> + <confidence type=3D"unknown">89.0</confidence> + <clade> + <branch_length>0.28901</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.06584</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.02309</branch_length> + <confidence type=3D"unknown">43.0</confidenc= e> + <clade> + <branch_length>0.0746</branch_length> + <confidence type=3D"unknown">100.0</confi= dence> + <clade> + <branch_length>0.02365</branch_length> + <confidence type=3D"unknown">88.0</con= fidence> + <clade> + <name>22_MOUSE</name> + <branch_length>0.05998</branch_leng= th> + <taxonomy> + <code>MOUSE</code> + </taxonomy> + </clade> + <clade> + <name>Apaf-1_HUMAN</name> + <branch_length>0.01825</branch_leng= th> + <taxonomy> + <code>HUMAN</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>12_CANFA</name> + <branch_length>0.04683</branch_length> + <taxonomy> + <code>CANFA</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>11_CHICK</name> + <branch_length>0.15226</branch_length> + <taxonomy> + <code>CHICK</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>16_XENLA</name> + <branch_length>0.4409</branch_length> + <taxonomy> + <code>XENLA</code> + </taxonomy> + </clade> + </clade> + <clade> + <branch_length>0.17031</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.10929</branch_length> + <confidence type=3D"unknown">100.0</confiden= ce> + <clade> + <name>14_FUGRU</name> + <branch_length>0.02255</branch_length> + <taxonomy> + <code>FUGRU</code> + </taxonomy> + </clade> + <clade> + <name>15_TETNG</name> + <branch_length>0.09478</branch_length> + <taxonomy> + <code>TETNG</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>17_BRARE</name> + <branch_length>0.1811</branch_length> + <taxonomy> + <code>BRARE</code> + </taxonomy> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.01594</branch_length> + <confidence type=3D"unknown">53.0</confidence> + <clade> + <branch_length>0.10709</branch_length> + <confidence type=3D"unknown">68.0</confidence> + <clade> + <name>1_BRAFL</name> + <branch_length>0.26131</branch_length> + <taxonomy> + <code>BRAFL</code> + </taxonomy> + </clade> + <clade> + <name>18_NEMVE</name> + <branch_length>0.38014</branch_length> + <taxonomy> + <code>NEMVE</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>23_STRPU</name> + <branch_length>0.48179</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.34475</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>26_STRPU</name> + <branch_length>0.36374</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1319"> + <domain from=3D"18" to=3D"98" confidence=3D"= 3.4E-5">Death</domain> + <domain from=3D"189" to=3D"481" confidence= =3D"1.8E-10">NB-ARC</domain> + <domain from=3D"630" to=3D"668" confidence= =3D"8.2E-5">WD40</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>25_STRPU</name> + <branch_length>0.33137</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1947"> + <domain from=3D"143" to=3D"227" confidence= =3D"7.4E-5">Death</domain> + <domain from=3D"227" to=3D"550" confidence= =3D"2.0E-13">NB-ARC</domain> + <domain from=3D"697" to=3D"736" confidence= =3D"7.9E-4">WD40</domain> + <domain from=3D"745" to=3D"785" confidence= =3D"1.5">WD40</domain> + <domain from=3D"1741" to=3D"1836" confidence= =3D"2.0">Adeno_VII</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + </clade> + <clade> + <branch_length>1.31498</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>CED4_CAEEL</name> + <branch_length>0.13241</branch_length> + <taxonomy> + <code>CAEEL</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"714"> + <domain from=3D"7" to=3D"90" confidence=3D"9.2E= -14">CARD</domain> + <domain from=3D"116" to=3D"442" confidence=3D"5= .8E-151">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>31_CAEBR</name> + <branch_length>0.04777</branch_length> + <taxonomy> + <code>CAEBR</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"554"> + <domain from=3D"1" to=3D"75" confidence=3D"0.00= 46">CARD</domain> + <domain from=3D"101" to=3D"427" confidence=3D"2= .1E-123">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.13172</branch_length> + <confidence type=3D"unknown">45.0</confidence> + <clade> + <branch_length>0.24915</branch_length> + <confidence type=3D"unknown">95.0</confidence> + <clade> + <branch_length>0.76898</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>28_DROPS</name> + <branch_length>0.1732</branch_length> + <taxonomy> + <code>DROPS</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"535"> + <domain from=3D"112" to=3D"399" confidence= =3D"1.4E-5">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>Dark_DROME</name> + <branch_length>0.18863</branch_length> + <taxonomy> + <code>DROME</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1421"> + <domain from=3D"108" to=3D"397" confidence= =3D"2.1E-5">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + <clade> + <name>29_AEDAE</name> + <branch_length>0.86398</branch_length> + <taxonomy> + <code>AEDAE</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"423"> + <domain from=3D"109" to=3D"421" confidence=3D"9= .3E-6">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + <clade> + <name>30_TRICA</name> + <branch_length>0.97698</branch_length> + <taxonomy> + <code>TRICA</code> + </taxonomy> + </clade> + </clade> + </clade> + </clade> + </phylogeny> +</phyloxml> diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 test-data/visualization/phyloviz/4_newick.nhx --- /dev/null +++ b/test-data/visualization/phyloviz/4_newick.nhx @@ -0,0 +1,33 @@ +(((BGIOSIBCA028421_ORYSA:0.423485[&&NHX:S=3DORYSA:O=3DBGIOSIBCA028421.1:G= =3DBGIOSIBCA028421], +At5g41150_ARATH:0.273135[&&NHX:S=3DARATH:O=3DAt5g41150.1:G=3DAt5g41150] +):0.690991[&&NHX:S=3DMagnoliophyta:D=3DN:B=3D100], +(rad16_SCHPO:0.718598[&&NHX:S=3DSCHPO:O=3DSPCC970.01:G=3DSPCC970.01], +RAD1_YEAST:1.05456[&&NHX:S=3DYEAST:O=3DYPL022W.1:G=3DYPL022W] +):0.344838[&&NHX:S=3DAscomycota:D=3DN:B=3D100] +):0.103849[&&NHX:S=3DEukaryota:D=3DN:B=3D61], +((((((((ERCC4_HUMAN:0.067531[&&NHX:S=3DHUMAN:O=3DENST00000311895.3:G=3DENS= G00000175595], +Ercc4_MOUSE:0.17422[&&NHX:S=3DMOUSE:O=3DENSMUST00000023206.5:G=3DENSMUSG00= 000022545] +):0.065513[&&NHX:S=3DEuarchontoglires:D=3DN:B=3D100], +ENSMODT00000006086_MONDO:0.104633[&&NHX:S=3DMONDO:O=3DENSMODT00000006086.2= :G=3DENSMODG00000004840] +):0.083764[&&NHX:S=3DTheria:D=3DN:B=3D100], +Q5ZJP8_CHICK:0.153132[&&NHX:S=3DCHICK:O=3DENSGALT00000004716.2:G=3DENSGALG= 00000002981] +):0.057998[&&NHX:S=3DAmniota:D=3DN:B=3D100], +ENSXETT00000024054_XENTR:0.288632[&&NHX:S=3DXENTR:O=3DENSXETT00000024054.2= :G=3DENSXETG00000010991] +):0.075713[&&NHX:S=3DTetrapoda:D=3DN:B=3D100], +(zgc-63468_BRARE:0.2218[&&NHX:S=3DBRARE:O=3DENSDART00000015780.4:G=3DENSDA= RG00000014161], +NEWSINFRUT00000137921_FUGRU:0.220441[&&NHX:S=3DFUGRU:O=3DNEWSINFRUT0000013= 7921.3:G=3DNEWSINFRUG00000130312] +):0.170605[&&NHX:S=3DClupeocephala:D=3DN:B=3D100] +):0.238713[&&NHX:S=3DEuteleostomi:D=3DN:B=3D100], +ENSCINT00000011737_CIOIN:0.623567[&&NHX:S=3DCIOIN:O=3DENSCINT00000011737.2= :G=3DENSCING00000005673] +):0.07499[&&NHX:S=3DChordata:D=3DN:B=3D100], +(Sm00.scaff00195.0600_SCHMA:0.784609[&&NHX:S=3DSCHMA:O=3DSm00.scaff00195.0= 600:G=3DSm00.scaff00195.0600], +(CBG03141_CAEBR:0.093703[&&NHX:S=3DCAEBR:O=3DCBG03141:G=3DCBG03141], +NP_496498_CAEEL:0.212236[&&NHX:S=3DCAEEL:O=3DC47D12.8.1:G=3DC47D12.8] +):1.47416[&&NHX:S=3DCaenorhabditis:D=3DN:B=3D94] +):0.26906[&&NHX:S=3DBilateria:D=3DN:B=3D97] +):0.071406[&&NHX:S=3DBilateria:D=3DN:B=3D1], +(mei-9-RA_DROME:0.170289[&&NHX:S=3DDROME:O=3DCG3697-RA.3:G=3DCG3697], +GA17620-PA_DROPS:0.154817[&&NHX:S=3DDROPS:O=3DGA17620-PA:G=3DGA17620] +):0.818474[&&NHX:S=3DSophophora:D=3DN:B=3D100] +):0 +)[&&NHX:S=3DEukaryota:D=3DN]; \ No newline at end of file diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 test-data/visualization/phyloviz/5_newick.nhx --- /dev/null +++ b/test-data/visualization/phyloviz/5_newick.nhx @@ -0,0 +1,1 @@ +(CAE_ELE_PORCN:0.303421 ,((((DRO_PER_PORCN:0.001000 ,DRO_PSE_PORCN:0.00100= 0 )67:0.141994 ,(DRO_ANA_PORCN:0.111899 ,(DRO_ERE_PORCN:0.030516 ,(DRO_MEL_= PORCN:0.021127 ,DRO_SEC_PORCN:0.021127 )38:0.030516 )35:0.111899 )18:0.1419= 94 )16:0.162611 ,(DRO_WIL_PORCN:0.152225 ,(DRO_VIR_PORCN:0.085057 ,DRO_MOJ_= PORCN:0.085057 )24:0.152225 )15:0.162611 )13:0.295081 ,(ANO_GAM_PORCN:0.287= 545 ,((CIO_INT_PORCN:0.100686 ,CIO_SAV_PORCN:0.100686 )19:0.275542 ,((LOA_L= OA_PORCN:0.036278 ,BRU_MAL_PORCN:0.036278 )29:0.272631 ,(((((DAN_RER_PORCN:= 0.086499 ,((TAK_RUB_PORCN:0.032609 ,TET_NIG_PORCN:0.032609 )32:0.048864 ,(G= AD_MOR_PORCN:0.039387 ,(ORY_LAT_PORCN:0.031729 ,(GAS_ACU_PORCN:0.021882 ,OR= E_NIL_PORCN:0.021882 )37:0.031729 )34:0.039387 )28:0.048864 )27:0.086499 )2= 3:0.119618 ,(LAT_CHA_PORCN:0.099348 ,((XEN_LAE_PORCN:0.033333 ,XEN_TRO_PORC= N:0.033333 )31:0.091250 ,(ANO_CAR_PORCN:0.086538 ,((MON_DOM_PORCN:0.014100 = ,(MAC_EUG_PORCN:0.005423 ,SAR_HAR_PORCN:0.005423 )57:0.014100 )42:0.062862 = ,(ORN_ANA_PORCN:0.057974 ,(GOR_GOR_PORCN:0.033876 ,(FEL_CAT_PORCN:0.022851 = ,(PRO_CAP_PORCN:0.019716 ,(CAV_POR_PORCN:0.018599 ,(ERI_EUR_PORCN:0.015518 = ,((DIP_ORD_PORCN:0.007231 ,(MUS_MUS_PORCN:0.001085 ,(RAT_NOR_PORCN:0.001000= ,CRI_GRI_PORCN:0.001000 )69:0.001085 )64:0.007231 )53:0.012954 ,(DAS_NOV_P= ORCN:0.011362 ,(LOX_AFR_PORCN:0.010575 ,(CAL_JAC_PORCN:0.010332 ,(OCH_PRI_P= ORCN:0.010063 ,(MIC_MUR_PORCN:0.009123 ,(SUS_SCR_PORCN:0.008880 ,(MYO_LUC_P= ORCN:0.008460 ,((CAN_FAM_PORCN:0.005423 ,AIL_MEL_PORCN:0.005423 )58:0.00809= 3 ,((PTE_VAM_PORCN:0.006508 ,BOS_TAU_PORCN:0.006508 )55:0.007494 ,((SPE_TRI= _PORCN:0.003254 ,TUP_BEL_PORCN:0.003254 )61:0.006929 ,((OTO_GAR_PORCN:0.001= 085 ,(ORY_CUN_PORCN:0.001000 ,TUR_TRU_PORCN:0.001000 )68:0.001085 )65:0.005= 965 ,(EQU_CAB_PORCN:0.003688 ,(MAC_MUL_PORCN:0.002711 ,(PAN_TRO_PORCN:0.001= 446 ,(HOM_SAP_PORCN:0.001085 ,(PON_ABE_PORCN:0.001000 ,NOM_LEU_PORCN:0.0010= 00 )70:0.001085 )66:0.001446 )63:0.002711 )62:0.003688 )60:0.005965 )56:0.0= 06929 )54:0.007494 )52:0.008093 )51:0.008460 )50:0.008880 )49:0.009123 )48:= 0.010063 )47:0.010332 )46:0.010575 )45:0.011362 )44:0.012954 )43:0.015518 )= 41:0.018599 )40:0.019716 )39:0.022851 )36:0.033876 )30:0.057974 )26:0.06286= 2 )25:0.086538 )22:0.091250 )21:0.099348 )20:0.119618 )17:0.214465 ,(BRA_FL= O_PORCN:0.189220 ,SAC_KOW_PORCN:0.189220 )12:0.214465 )11:0.257058 ,(NEM_VE= C_PORCN:0.246631 ,AMP_QUE_PORCN:0.246631 )9:0.257058 )8:0.266904 ,(TRI_CAS_= PORCN:0.259494 ,(PED_HUM_PORCN:0.227009 ,(NAS_VIT_PORCN:0.160241 ,(API_MEL_= PORCN:0.031851 ,(BOM_TER_PORCN:0.004808 ,BOM_IMP_PORCN:0.004808 )59:0.03185= 1 )33:0.160241 )14:0.227009 )10:0.259494 )7:0.266904 )6:0.272631 )5:0.27554= 2 )4:0.287545 )3:0.295081 )2:0.303421 )1:0.0001; diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 tools/data_source/data_source.py --- a/tools/data_source/data_source.py +++ b/tools/data_source/data_source.py @@ -4,6 +4,7 @@ import socket, urllib, sys, os from galaxy import eggs #eggs needs to be imported so that galaxy.util can= find docutils egg... from galaxy.util.json import from_json_string, to_json_string +from galaxy.util import get_charset_from_http_headers import galaxy.model # need to import model before sniff to resolve a circu= lar import dependency from galaxy.datatypes import sniff from galaxy.datatypes.registry import Registry @@ -92,7 +93,7 @@ stop_err( 'The size of the data (%d bytes) you have reques= ted exceeds the maximum allowed (%d bytes) on this server.' % ( file_size, = max_file_size ) ) #do sniff stream for multi_byte try: - cur_filename, is_multi_byte =3D sniff.stream_to_open_named_fil= e( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename ) + cur_filename, is_multi_byte =3D sniff.stream_to_open_named_fil= e( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename, s= ource_encoding=3Dget_charset_from_http_headers( page.headers ) ) except Exception, e: stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) ) =20 diff -r 6a644558eed7aba74a74060ccf0aa4ec211809c2 -r 07045f4895170a154c955f4= 8291f2b5e6feb94c2 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -90,7 +90,8 @@ =20 if dataset.type =3D=3D 'url': try: - temp_name, dataset.is_multi_byte =3D sniff.stream_to_file( url= lib.urlopen( dataset.path ), prefix=3D'url_paste' ) + page =3D urllib.urlopen( dataset.path ) #page will be .close()= ed by sniff methods + temp_name, dataset.is_multi_byte =3D sniff.stream_to_file( pag= e, prefix=3D'url_paste', source_encoding=3Dutil.get_charset_from_http_heade= rs( page.headers ) ) except Exception, e: file_err( 'Unable to fetch %s\n%s' % ( dataset.path, str( e ) = ), dataset, json_file ) return Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Made download status page more informative, fixed intermittent indexing error.
by Bitbucket 29 Aug '12

29 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8a8a37bbdc2f/ changeset: 8a8a37bbdc2f user: inithello date: 2012-08-29 16:16:11 summary: Made download status page more informative, fixed intermittent indexing error. affected #: 2 files diff -r 30c7f58f116d9e11a209ed8a5d193ec2d91de280 -r 8a8a37bbdc2fc233446966793b6545d553aa50d8 lib/galaxy/tools/genome_index/index_genome.py --- a/lib/galaxy/tools/genome_index/index_genome.py +++ b/lib/galaxy/tools/genome_index/index_genome.py @@ -54,6 +54,7 @@ self._log( self.locations ) self._log( 'Indexer %s completed successfully.' % indexer ) self._flush_files() + exit(0) def _check_link( self ): self._log( 'Checking symlink to %s' % self.fafile ) diff -r 30c7f58f116d9e11a209ed8a5d193ec2d91de280 -r 8a8a37bbdc2fc233446966793b6545d553aa50d8 lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -148,7 +148,8 @@ dbkey = build[0] longname = build[1] break - assert dbkey is not '?', 'That build was not found' + if dbkey == '?': + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid build was specified.' ) ftp = ftplib.FTP('hgdownload.cse.ucsc.edu') ftp.login('anonymous', trans.get_user().email) checker = [] @@ -189,7 +190,8 @@ dbkeys=trans.ucsc_builds ) elif source == 'Ensembl': dbkey = params.get( 'ensembl_dbkey', None ) - assert dbkey is not '?', 'That build was not found' + if dbkey == '?': + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid build was specified.' ) for build in trans.ensembl_builds: if build[ 'dbkey' ] == dbkey: dbkey = build[ 'dbkey' ] @@ -199,7 +201,7 @@ break url = 'ftp://ftp.ensembl.org/pub/release-%s/fasta/%s/dna/%s.%s.%s.dna.toplevel.fa.…' % ( release, pathname.lower(), pathname, dbkey, release ) else: - return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Somehow an invalid data source was specified.' ) + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='An invalid data source was specified.' ) if url is None: return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Unable to generate a valid URL with the specified parameters.' ) params = dict( protocol='http', name=dbkey, datatype='fasta', url=url, user=trans.user.id ) @@ -248,7 +250,8 @@ sa = trans.app.model.context.current if jobtype == 'liftover': job = sa.query( model.TransferJob ).filter_by( id=jobid ).first() - joblabel = 'Download liftOver' + liftover = trans.app.job_manager.deferred_job_queue.plugins['LiftOverTransferPlugin'].get_job_status( jobid ) + joblabel = 'Download liftOver (%s to %s)' % ( liftover.params[ 'from_genome' ], liftover.params[ 'to_genome' ] ) elif jobtype == 'transfer': job = sa.query( model.TransferJob ).filter_by( id=jobid ).first() joblabel = 'Download Genome' 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: Unicode fixes for annotations
by Bitbucket 29 Aug '12

29 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/30c7f58f116d/ changeset: 30c7f58f116d user: dan date: 2012-08-29 16:03:42 summary: Unicode fixes for annotations affected #: 2 files diff -r 80dd03582ea9041d0c897b3a2c58e12a5bb494bb -r 30c7f58f116d9e11a209ed8a5d193ec2d91de280 lib/galaxy/model/item_attrs.py --- a/lib/galaxy/model/item_attrs.py +++ b/lib/galaxy/model/item_attrs.py @@ -95,7 +95,7 @@ """ Returns a user's annotation string for an item. """ annotation_obj = self.get_item_annotation_obj( db_session, user, item ) if annotation_obj: - return annotation_obj.annotation + return galaxy.util.unicodify( annotation_obj.annotation ) return None def get_item_annotation_obj( self, db_session, user, item ): diff -r 80dd03582ea9041d0c897b3a2c58e12a5bb494bb -r 30c7f58f116d9e11a209ed8a5d193ec2d91de280 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -644,7 +644,10 @@ dataset = self.get_dataset( trans, id, False, True ) if not dataset: web.httpexceptions.HTTPNotFound() - return self.get_item_annotation_str( trans.sa_session, trans.user, dataset ) + annotation = self.get_item_annotation_str( trans.sa_session, trans.user, dataset ) + if annotation and isinstance( annotation, unicode ): + annotation = annotation.encode( 'ascii', 'replace' ) #paste needs ascii here + return annotation @web.expose def display_at( self, trans, dataset_id, filename=None, **kwd ): 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: 5 new changesets
by Bitbucket 29 Aug '12

29 Aug '12

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1aee30671c45/ changeset: 1aee30671c45 user: dan date: 2012-08-29 01:23:39 summary: Handle non-ascii unicode in data source tools. Add util.is_binary() method that returns true when provided string contains a null byte. affected #: 3 files diff -r 738b703f725c1ade02018489e1c8e197236e30cd -r 1aee30671c45ecf045e33fe472525b814b97838d lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -6,6 +6,7 @@ from galaxy import util from galaxy.datatypes.checkers import * from galaxy.datatypes.binary import unsniffable_binary_formats +from encodings import search_function as encodings_search_function log = logging.getLogger(__name__) @@ -15,7 +16,7 @@ full_path = os.path.join(path, 'test', fname) return full_path -def stream_to_open_named_file( stream, fd, filename ): +def stream_to_open_named_file( stream, fd, filename, source_encoding=None, source_error='strict', target_encoding=None, target_error='strict' ): """Writes a stream to the provided file descriptor, returns the file's name and bool( is_multi_byte ). Closes file descriptor""" #signature and behavor is somewhat odd, due to backwards compatibility, but this can/should be done better CHUNK_SIZE = 1048576 @@ -23,6 +24,10 @@ is_compressed = False is_binary = False is_multi_byte = False + if not target_encoding or not encodings_search_function( target_encoding ): + target_encoding = util.DEFAULT_ENCODING #utf-8 + if not source_encoding: + source_encoding = util.DEFAULT_ENCODING #sys.getdefaultencoding() would mimic old behavior (defaults to ascii) while 1: chunk = stream.read( CHUNK_SIZE ) if not chunk: @@ -42,13 +47,12 @@ chars = chunk[:100] is_multi_byte = util.is_multi_byte( chars ) if not is_multi_byte: - for char in chars: - if ord( char ) > 128: - is_binary = True - break + is_binary = util.is_binary( chunk ) data_checked = True if not is_compressed and not is_binary: - os.write( fd, chunk.encode( "utf-8" ) ) + if not isinstance( chunk, unicode ): + chunk = chunk.decode( source_encoding, source_error ) + os.write( fd, chunk.encode( target_encoding, target_error ) ) else: # Compressed files must be encoded after they are uncompressed in the upload utility, # while binary files should not be encoded at all. @@ -56,10 +60,10 @@ os.close( fd ) return filename, is_multi_byte -def stream_to_file( stream, suffix='', prefix='', dir=None, text=False ): +def stream_to_file( stream, suffix='', prefix='', dir=None, text=False, **kwd ): """Writes a stream to a temporary file, returns the temporary file's name""" fd, temp_name = tempfile.mkstemp( suffix=suffix, prefix=prefix, dir=dir, text=text ) - return stream_to_open_named_file( stream, fd, temp_name ) + return stream_to_open_named_file( stream, fd, temp_name, **kwd ) def check_newlines( fname, bytes_to_read=52428800 ): """ @@ -305,14 +309,9 @@ else: for hdr in headers: for char in hdr: - if len( char ) > 1: - for c in char: - if ord( c ) > 128: - is_binary = True - break - elif ord( char ) > 128: - is_binary = True - break + #old behavior had 'char' possibly having length > 1, + #need to determine when/if this occurs + is_binary = util.is_binary( char ) if is_binary: break if is_binary: diff -r 738b703f725c1ade02018489e1c8e197236e30cd -r 1aee30671c45ecf045e33fe472525b814b97838d lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -34,6 +34,9 @@ gzip_magic = '\037\213' bz2_magic = 'BZh' +DEFAULT_ENCODING = 'utf-8' +NULL_CHAR = '\000' +BINARY_CHARS = [ NULL_CHAR ] from inflection import Inflector, English inflector = Inflector(English) @@ -57,6 +60,32 @@ return True return False +def is_binary( value, binary_chars=None ): + """ + File is binary if it contains a null-byte by default (e.g. behavior of grep, etc.). + This may fail for utf-16 files, but so would ASCII encoding. + >>> is_binary( string.printable ) + False + >>> is_binary( '\\xce\\x94' ) + False + >>> is_binary( '\\000' ) + True + """ + if binary_chars is None: + binary_chars = BINARY_CHARS + for binary_char in binary_chars: + if binary_char in value: + return True + return False + +def get_charset_from_http_headers( headers, default=None ): + rval = headers.get('content-type', None ) + if rval and 'charset=' in rval: + rval = rval.split('charset=')[-1].split(';')[0].strip() + if rval: + return rval + return default + def synchronized(func): """This wrapper will serialize access to 'func' to a single thread. Use it as a decorator.""" def caller(*params, **kparams): @@ -333,6 +362,17 @@ else: return amount[0:sfs] + '0'*(len(amount) - sfs) +def unicodify( value, encoding=DEFAULT_ENCODING, error='replace', default=None ): + """ + Returns a unicode string or None + """ + if isinstance( value, unicode ): + return value + try: + return unicode( value, encoding, error ) + except: + return default + def object_to_string( obj ): return binascii.hexlify( pickle.dumps( obj, 2 ) ) @@ -502,7 +542,7 @@ def recursively_stringify_dictionary_keys( d ): if isinstance(d, dict): - return dict([(k.encode('utf-8'), recursively_stringify_dictionary_keys(v)) for k,v in d.iteritems()]) + return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k,v in d.iteritems()]) elif isinstance(d, list): return [recursively_stringify_dictionary_keys(x) for x in d] else: @@ -622,7 +662,7 @@ Sends an email. """ to = listify( to ) - msg = MIMEText( body ) + msg = MIMEText( body.encode( 'ascii', 'replace' ) ) msg[ 'To' ] = ', '.join( to ) msg[ 'From' ] = frm msg[ 'Subject' ] = subject diff -r 738b703f725c1ade02018489e1c8e197236e30cd -r 1aee30671c45ecf045e33fe472525b814b97838d tools/data_source/data_source.py --- a/tools/data_source/data_source.py +++ b/tools/data_source/data_source.py @@ -4,6 +4,7 @@ import socket, urllib, sys, os from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg... from galaxy.util.json import from_json_string, to_json_string +from galaxy.util import get_charset_from_http_headers import galaxy.model # need to import model before sniff to resolve a circular import dependency from galaxy.datatypes import sniff from galaxy.datatypes.registry import Registry @@ -92,7 +93,7 @@ stop_err( 'The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server.' % ( file_size, max_file_size ) ) #do sniff stream for multi_byte try: - cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename ) + cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename, source_encoding=get_charset_from_http_headers( page.headers ) ) except Exception, e: stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) ) https://bitbucket.org/galaxy/galaxy-central/changeset/577498958c37/ changeset: 577498958c37 user: dan date: 2012-08-29 01:23:39 summary: Handle non-ascii unicode in upload tool. Significant pre-existing refactoring still needed. affected #: 1 file diff -r 1aee30671c45ecf045e33fe472525b814b97838d -r 577498958c37cb3c0702b06a048bb51b2d82257a tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -90,7 +90,8 @@ if dataset.type == 'url': try: - temp_name, dataset.is_multi_byte = sniff.stream_to_file( urllib.urlopen( dataset.path ), prefix='url_paste' ) + page = urllib.urlopen( dataset.path ) #page will be .close()ed by sniff methods + temp_name, dataset.is_multi_byte = sniff.stream_to_file( page, prefix='url_paste', source_encoding=util.get_charset_from_http_headers( page.headers ) ) except Exception, e: file_err( 'Unable to fetch %s\n%s' % ( dataset.path, str( e ) ), dataset, json_file ) return https://bitbucket.org/galaxy/galaxy-central/changeset/fca4e12478d6/ changeset: fca4e12478d6 user: dan date: 2012-08-29 01:23:39 summary: Handle non-ascii unicode in dataset edit attributes. affected #: 1 file diff -r 577498958c37cb3c0702b06a048bb51b2d82257a -r fca4e12478d62162cb486422c79687587209c639 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -58,7 +58,7 @@ Info: </label><div style="float: left; width: 250px; margin-right: 10px;"> - <textarea name="info" cols="40" rows="2">${data.info | h}</textarea> + <textarea name="info" cols="40" rows="2">${ util.unicodify( data.info ) | h}</textarea></div><div style="clear: both"></div></div> https://bitbucket.org/galaxy/galaxy-central/changeset/efefe08d6dd0/ changeset: efefe08d6dd0 user: dan date: 2012-08-29 01:23:39 summary: Handle non-ascii unicode in dataset error page. affected #: 1 file diff -r fca4e12478d62162cb486422c79687587209c639 -r efefe08d6dd0c70055a80953007e312e1d85d271 templates/dataset/errors.mako --- a/templates/dataset/errors.mako +++ b/templates/dataset/errors.mako @@ -24,21 +24,21 @@ <% job = hda.creating_job_associations[0].job %> %if job.traceback: The Galaxy framework encountered the following error while attempting to run the tool: - <pre>${job.traceback | h}</pre> + <pre>${ util.unicodify( job.traceback ) | h}</pre> %endif %if job.stderr or job.info: Tool execution generated the following error message: %if job.stderr: - <pre>${job.stderr | h}</pre> + <pre>${ util.unicodify( job.stderr ) | h}</pre> %elif job.info: - <pre>${job.info | h}</pre> + <pre>${ util.unicodify( job.info ) | h}</pre> %endif %else: Tool execution did not generate any error messages. %endif %if job.stdout: The tool produced the following additional output: - <pre>${job.stdout | h}</pre> + <pre>${ util.unicodify( job.stdout ) | h}</pre> %endif %else: The tool did not create any additional job / error info. https://bitbucket.org/galaxy/galaxy-central/changeset/80dd03582ea9/ changeset: 80dd03582ea9 user: dan date: 2012-08-29 01:23:40 summary: Handle non-ascii unicode in dataset error report emails. affected #: 1 file diff -r efefe08d6dd0c70055a80953007e312e1d85d271 -r 80dd03582ea9041d0c897b3a2c58e12a5bb494bb lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -203,12 +203,12 @@ job_id=job.id, job_tool_id=job.tool_id, job_command_line=job.command_line, - job_stderr=job.stderr, - job_stdout=job.stdout, - job_info=job.info, - job_traceback=job.traceback, + job_stderr=util.unicodify( job.stderr ), + job_stdout=util.unicodify( job.stdout ), + job_info=util.unicodify( job.info ), + job_traceback=util.unicodify( job.traceback ), email=email, - message=message ) + message=util.unicodify( message ) ) frm = to_address # Check email a bit email = email.strip() 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 handling of ToolSectionLabel objects in the tool panel.
by Bitbucket 28 Aug '12

28 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/738b703f725c/ changeset: 738b703f725c user: greg date: 2012-08-28 20:32:04 summary: Fix handling of ToolSectionLabel objects in the tool panel. affected #: 1 file diff -r 483cbfc5341a0331cc86185f8821cdecec52a0b4 -r 738b703f725c1ade02018489e1c8e197236e30cd lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -187,7 +187,9 @@ section.elems[ section_key ] = workflow log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) ) elif section_key.startswith( 'label_' ): - section.elems[ section_key ] = section_val + if section_val: + section.elems[ section_key ] = section_val + log.debug( "Loaded label: %s" % ( section_val.text ) ) self.tool_panel[ key ] = section def load_integrated_tool_panel_keys( self ): """ @@ -215,12 +217,12 @@ section.elems[ key ] = None elif section_elem.tag == 'label': key = 'label_%s' % section_elem.get( 'id' ) - section.elems[ key ] = ToolSectionLabel( section_elem ) + section.elems[ key ] = None key = 'section_%s' % elem.get( 'id' ) self.integrated_tool_panel[ key ] = section elif elem.tag == 'label': key = 'label_%s' % elem.get( 'id' ) - self.integrated_tool_panel[ key ] = ToolSectionLabel( elem ) + self.integrated_tool_panel[ key ] = None def write_integrated_tool_panel_config_file( self ): """ Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators @@ -254,10 +256,11 @@ if section_item: os.write( fd, ' <workflow id="%s" />\n' % section_item.id ) elif section_key.startswith( 'label_' ): - label_id = section_item.id or '' - label_text = section_item.text or '' - label_version = section_item.version or '' - os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) ) + if section_item: + label_id = section_item.id or '' + label_text = section_item.text or '' + label_version = section_item.version or '' + os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) ) os.write( fd, ' </section>\n' ) os.write( fd, '</toolbox>\n' ) os.close( fd ) 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: natefoo: Don't attempt to run util.umask_fix_perms() on data that is being linked to. Fixes #801.
by Bitbucket 28 Aug '12

28 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/483cbfc5341a/ changeset: 483cbfc5341a user: natefoo date: 2012-08-28 19:50:54 summary: Don't attempt to run util.umask_fix_perms() on data that is being linked to. Fixes #801. affected #: 1 file diff -r d8bff94d8aac276ff77b65104c958ab5cc9ee243 -r 483cbfc5341a0331cc86185f8821cdecec52a0b4 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -471,7 +471,7 @@ job.user.total_disk_usage += bytes # fix permissions - for path in [ dp.real_path for dp in self.get_output_fnames() ]: + for path in [ dp.real_path for dp in self.get_mutable_output_fnames() ]: util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) @@ -679,6 +679,11 @@ self.compute_outputs() return self.output_paths + def get_mutable_output_fnames( self ): + if self.output_paths is None: + self.compute_outputs() + return filter( lambda dsp: dsp.mutable, self.output_paths ) + def get_output_hdas_and_fnames( self ): if self.output_hdas_and_paths is None: self.compute_outputs() @@ -686,10 +691,11 @@ def compute_outputs( self ) : class DatasetPath( object ): - def __init__( self, dataset_id, real_path, false_path = None ): + def __init__( self, dataset_id, real_path, false_path = None, mutable = True ): self.dataset_id = dataset_id self.real_path = real_path self.false_path = false_path + self.mutable = mutable def __str__( self ): if self.false_path is None: return self.real_path @@ -706,13 +712,13 @@ self.output_hdas_and_paths = {} for name, hda in [ ( da.name, da.dataset ) for da in job.output_datasets + job.output_library_datasets ]: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % hda.dataset.id ) ) - dsp = DatasetPath( hda.dataset.id, hda.dataset.file_name, false_path ) + dsp = DatasetPath( hda.dataset.id, hda.dataset.file_name, false_path, mutable = hda.dataset.external_filename is None ) self.output_paths.append( dsp ) self.output_hdas_and_paths[name] = hda, dsp if special: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % special.dataset.id ) ) else: - results = [ ( da.name, da.dataset, DatasetPath( da.dataset.dataset.id, da.dataset.file_name ) ) for da in job.output_datasets + job.output_library_datasets ] + results = [ ( da.name, da.dataset, DatasetPath( da.dataset.dataset.id, da.dataset.file_name, mutable = da.dataset.dataset.external_filename is None ) ) for da in job.output_datasets + job.output_library_datasets ] self.output_paths = [t[2] for t in results] self.output_hdas_and_paths = dict([(t[0], t[1:]) for t in results]) if special: 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: Apply the improvements for generation of tool shed URLs to the repository controller.
by Bitbucket 28 Aug '12

28 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d8bff94d8aac/ changeset: d8bff94d8aac user: greg date: 2012-08-28 17:49:43 summary: Apply the improvements for generation of tool shed URLs to the repository controller. affected #: 2 files diff -r 4b05f621540cb46fd8b120997258008b37050f63 -r d8bff94d8aac276ff77b65104c958ab5cc9ee243 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -392,8 +392,9 @@ # Send a request to the relevant tool shed to see if there are any updates. repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - url = url_join( tool_shed_url, 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) + url = url_join( tool_shed_url, + 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -634,8 +635,9 @@ tool_shed_repository, trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) - url = url_join( tool_shed_url, '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) + url = url_join( tool_shed_url, + '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() response.close() @@ -954,7 +956,9 @@ repository_ids = kwd.get( 'repository_ids', None ) changeset_revisions = kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. - url = url_join( tool_shed_url, 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % ( repository_ids, changeset_revisions ) ) + url = url_join( tool_shed_url, + 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % \ + ( repository_ids, changeset_revisions ) ) response = urllib2.urlopen( url ) raw_text = response.read() response.close() @@ -1097,8 +1101,9 @@ name = repo_info_dict.keys()[ 0 ] repo_info_tuple = repo_info_dict[ name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple - url = url_join( tool_shed_url, 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( name, repository_owner, changeset_revision ) ) + url = url_join( tool_shed_url, + 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() response.close() @@ -1273,8 +1278,9 @@ tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. - url = url_join( tool_shed_url, 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) ) + url = url_join( tool_shed_url, + 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() response.close() @@ -1350,8 +1356,9 @@ # Get the tool_versions from the tool shed for each tool in the installed change set. repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - url = url_join( tool_shed_url, 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( repository.name, repository.owner, repository.changeset_revision ) ) + url = url_join( tool_shed_url, + 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( repository.name, repository.owner, repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() response.close() diff -r 4b05f621540cb46fd8b120997258008b37050f63 -r d8bff94d8aac276ff77b65104c958ab5cc9ee243 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -11,7 +11,7 @@ from galaxy.model.orm import * from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, NOT_TOOL_CONFIGS from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path -from galaxy.util.shed_util import to_html_escaped, update_repository +from galaxy.util.shed_util import to_html_escaped, update_repository, url_join from galaxy.tool_shed.encoding_util import * from common import * @@ -749,9 +749,10 @@ update = 'true' no_update = 'false' else: - # Start building up the url to redirect back to the calling Galaxy instance. - url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) ) - url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % ( repository.name, repository.user.username, changeset_revision ) + # Start building up the url to redirect back to the calling Galaxy instance. + url = url_join( galaxy_url, + 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ + ( url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) if changeset_revision == repository.tip: # If changeset_revision is the repository tip, there are no additional updates. if from_update_manager: @@ -1395,10 +1396,9 @@ """Send the list of repository_ids and changeset_revisions to Galaxy so it can begin the installation process.""" galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) # Redirect back to local Galaxy to perform install. - url = '%sadmin_toolshed/prepare_for_install' % galaxy_url - url += '?tool_shed_url=%s' % url_for( '/', qualified=True ) - url += '&repository_ids=%s' % ','.join( util.listify( repository_ids ) ) - url += '&changeset_revisions=%s' % ','.join( util.listify( changeset_revisions ) ) + url = url_join( galaxy_url, + 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ + ( url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) return trans.response.send_redirect( url ) @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): 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: inithello: Improved generation of tool shed URLs
by Bitbucket 28 Aug '12

28 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4b05f621540c/ changeset: 4b05f621540c user: inithello date: 2012-08-28 17:32:17 summary: Improved generation of tool shed URLs affected #: 2 files diff -r c87370c5340d359d72301234a958c138adfecd7e -r 4b05f621540cb46fd8b120997258008b37050f63 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -454,7 +454,7 @@ def generate_clone_url( trans, repository ): """Generate the URL for cloning a repository.""" tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - return '%s/repos/%s/%s' % ( tool_shed_url, repository.owner, repository.name ) + return url_join( tool_shed_url, 'repos', repository.owner, repository.name ) def generate_datatypes_metadata( datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree = ElementTree.parse( datatypes_config ) @@ -993,7 +993,7 @@ break return converter_path, display_path def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): - url = '%s/repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( tool_shed_url, name, owner, changeset_revision ) + url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() response.close() @@ -1221,8 +1221,8 @@ def get_update_to_changeset_revision_and_ctx_rev( trans, repository ): """Return the changeset revision hash to which the repository can be updated.""" tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - url = '%s/repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \ - ( tool_shed_url, repository.name, repository.owner, repository.installed_changeset_revision ) + url = url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \ + ( repository.name, repository.owner, repository.installed_changeset_revision ) ) try: response = urllib2.urlopen( url ) encoded_update_dict = response.read() @@ -1645,3 +1645,8 @@ tool_shed_repository.status = status sa_session.add( tool_shed_repository ) sa_session.flush() +def url_join( *args ): + parts = [] + for arg in args: + parts.append( arg.strip( '/' ) ) + return '/'.join( parts ) diff -r c87370c5340d359d72301234a958c138adfecd7e -r 4b05f621540cb46fd8b120997258008b37050f63 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -374,7 +374,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = '%srepository/browse_valid_categories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s&webapp=galaxy' % ( galaxy_url ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -392,8 +392,8 @@ # Send a request to the relevant tool shed to see if there are any updates. repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_url, url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) + url = url_join( tool_shed_url, 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -467,14 +467,14 @@ def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = '%srepository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s&webapp=galaxy' % galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = '%srepository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s&webapp=galaxy' % galaxy_url ) return trans.response.send_redirect( url ) def generate_tool_path( self, repository_clone_url, changeset_revision ): """ @@ -489,7 +489,7 @@ tool_shed_url = items[ 0 ] repo_path = items[ 1 ] tool_shed_url = clean_tool_shed_url( tool_shed_url ) - return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_revision ) + return url_join( tool_shed_url, 'repos', repo_path, changeset_revision ) @web.json @web.require_admin def get_file_contents( self, trans, file_path ): @@ -634,8 +634,8 @@ tool_shed_repository, trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) - url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) + url = url_join( tool_shed_url, '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() response.close() @@ -954,7 +954,7 @@ repository_ids = kwd.get( 'repository_ids', None ) changeset_revisions = kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. - url = '%srepository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % ( tool_shed_url, repository_ids, changeset_revisions ) + url = url_join( tool_shed_url, 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % ( repository_ids, changeset_revisions ) ) response = urllib2.urlopen( url ) raw_text = response.read() response.close() @@ -1097,8 +1097,8 @@ name = repo_info_dict.keys()[ 0 ] repo_info_tuple = repo_info_dict[ name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple - url = '%srepository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_url, name, repository_owner, changeset_revision ) + url = url_join( tool_shed_url, 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() response.close() @@ -1273,8 +1273,8 @@ tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. - url = '%s/repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_url, url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) + url = url_join( tool_shed_url, 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() response.close() @@ -1350,8 +1350,8 @@ # Get the tool_versions from the tool shed for each tool in the installed change set. repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) + url = url_join( tool_shed_url, 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( repository.name, repository.owner, repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() response.close() @@ -1522,7 +1522,7 @@ def __generate_clone_url( self, trans, repository ): """Generate the URL for cloning a repository.""" tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) - return '%s/repos/%s/%s' % ( tool_shed_url, repository.owner, repository.name ) + return url_join( tool_shed_url, 'repos', repository.owner, repository.name ) ## ---- Utility methods ------------------------------------------------------- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add the ability to browse writable repositories in a tool shed.
by Bitbucket 28 Aug '12

28 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c87370c5340d/ changeset: c87370c5340d user: greg date: 2012-08-28 17:01:07 summary: Add the ability to browse writable repositories in a tool shed. affected #: 2 files diff -r 5adbc8515631847cb66378ea28e644344d890265 -r c87370c5340d359d72301234a958c138adfecd7e lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -246,6 +246,25 @@ grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository', webapp='community' ) ) ] +class WritableRepositoryListGrid( RepositoryListGrid ): + def build_initial_query( self, trans, **kwd ): + # TODO: improve performance by adding a db table associating users with repositories for which they have write access. + username = kwd[ 'username' ] + clause_list = [] + for repository in trans.sa_session.query( self.model_class ): + allow_push_usernames = repository.allow_push.split( ',' ) + if username in allow_push_usernames: + clause_list.append( self.model_class.table.c.id == repository.id ) + if clause_list: + return trans.sa_session.query( self.model_class ) \ + .filter( or_( *clause_list ) ) \ + .join( model.User.table ) \ + .outerjoin( model.RepositoryCategoryAssociation.table ) \ + .outerjoin( model.Category.table ) + # Return an empty query. + return trans.sa_session.query( self.model_class ) \ + .filter( self.model_class.table.c.id < 0 ) + class ValidRepositoryListGrid( RepositoryListGrid ): class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): @@ -393,6 +412,7 @@ email_alerts_repository_list_grid = EmailAlertsRepositoryListGrid() category_list_grid = CategoryListGrid() valid_category_list_grid = ValidCategoryListGrid() + writable_repository_list_grid = WritableRepositoryListGrid() def __add_hgweb_config_entry( self, trans, repository, repository_path ): # Add an entry in the hgweb.config file for a new repository. An entry looks something like: @@ -519,12 +539,15 @@ repository_id = kwd.get( 'id', None ) repository = get_repository( trans, repository_id ) kwd[ 'f-email' ] = repository.user.email - elif operation == "my_repositories": + elif operation == "repositories_i_own": # Eliminate the current filters if any exist. for k, v in kwd.items(): if k.startswith( 'f-' ): del kwd[ k ] kwd[ 'f-email' ] = trans.user.email + elif operation == "writable_repositories": + kwd[ 'username' ] = trans.user.username + return self.writable_repository_list_grid( trans, **kwd ) elif operation == "repositories_by_category": # Eliminate the current filters if any exist. for k, v in kwd.items(): diff -r 5adbc8515631847cb66378ea28e644344d890265 -r c87370c5340d359d72301234a958c138adfecd7e templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -60,34 +60,41 @@ %endif <div class="toolSectionPad"></div><div class="toolSectionTitle"> - Repositories + All Repositories </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> - </div> - %if trans.user: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository', webapp='community' )}">Browse my invalid tools</a> - </div> - %endif + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + </div> + %if trans.user: + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + My Repositories and Tools </div> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - %if trans.user: - <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository', webapp='community' )}">Create new repository</a> - %else: - <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to create a repository</a> - %endif - </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own', webapp='community' )}">Repositories I own</a></div> - </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='writable_repositories', webapp='community' )}">My writable repositories</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository', webapp='community' )}">My invalid tools</a> + </div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + Available Actions + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository', webapp='community' )}">Create new repository</a> + </div> + %else: + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + Available Actions + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to create a repository</a> + </div> + %endif </div></div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fixes for phyloviz parser and a4c7aeb61c7b.
by Bitbucket 28 Aug '12

28 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5adbc8515631/ changeset: 5adbc8515631 user: jgoecks date: 2012-08-28 15:05:31 summary: Fixes for phyloviz parser and a4c7aeb61c7b. affected #: 2 files diff -r a4c7aeb61c7b8e76fcf3fd96d0d351be88d1c1d1 -r 5adbc8515631847cb66378ea28e644344d890265 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- a/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py +++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py @@ -1,6 +1,6 @@ from newickparser import Newick_Parser from nexusparser import Nexus_Parser -#from phyloxmlparser import Phyloxml_Parser +from phyloxmlparser import Phyloxml_Parser class Phyloviz_DataProvider(object): @@ -16,9 +16,9 @@ if fileExt == "nhx": # parses newick files newickParser = Newick_Parser() jsonDicts, parseMsg = newickParser.parseFile(filepath) - #elif fileExt == "phyloxml": # parses phyloXML files - # phyloxmlParser = Phyloxml_Parser() - # jsonDicts, parseMsg = phyloxmlParser.parseFile(filepath) + elif fileExt == "phyloxml": # parses phyloXML files + phyloxmlParser = Phyloxml_Parser() + jsonDicts, parseMsg = phyloxmlParser.parseFile(filepath) elif fileExt == "nex": # parses nexus files nexusParser = Nexus_Parser() jsonDicts, parseMsg = nexusParser.parseFile(filepath) diff -r a4c7aeb61c7b8e76fcf3fd96d0d351be88d1c1d1 -r 5adbc8515631847cb66378ea28e644344d890265 lib/galaxy/visualization/phyloviz/phyloxmlparser.py --- a/lib/galaxy/visualization/phyloviz/phyloxmlparser.py +++ b/lib/galaxy/visualization/phyloviz/phyloxmlparser.py @@ -1,8 +1,5 @@ from baseparser import Base_Parser, PhyloTree, Node - -''' -TOD0: use native Python XML parser. -from lxml import etree +from xml.etree import ElementTree class Phyloxml_Parser(Base_Parser): """Parses a phyloxml file into a json file that will be passed to PhyloViz for display""" @@ -22,7 +19,7 @@ """passes a file and extracts its Phylogeny Tree content.""" phyloXmlFile = open(filePath, "r") - xmlTree = etree.parse(phyloXmlFile) + xmlTree = ElementTree.parse(phyloXmlFile) xmlRoot = xmlTree.getroot()[0] self.nameSpaceIndex = xmlRoot.tag.rfind("}") + 1 # used later by the clean tag method to remove the name space in every element.tag @@ -134,16 +131,4 @@ def cleanTag(self, tagString): return tagString[self.nameSpaceIndex:] - - -if __name__=="__main__": - - # Files tested against - parser = Phyloxml_Parser() - filepath = "../data/" +"apaf.xml" - # filepath = "../data/" +"12_multiple_supports.xml" - - # filepath = "../data/" +"bcl_2.xml" - # filepath = "../data/" +"reducedXml.xml" - parser.parseFile(filepath) -''' \ No newline at end of file + \ No newline at end of file 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: jgoecks: Comment out phyloviz XML parser until native Python XML parsing is used.
by Bitbucket 27 Aug '12

27 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a4c7aeb61c7b/ changeset: a4c7aeb61c7b user: jgoecks date: 2012-08-27 21:44:01 summary: Comment out phyloviz XML parser until native Python XML parsing is used. affected #: 2 files diff -r 75a03bacdc7a3dc5b1c03f8b02df0ab383366955 -r a4c7aeb61c7b8e76fcf3fd96d0d351be88d1c1d1 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- a/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py +++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py @@ -1,6 +1,6 @@ from newickparser import Newick_Parser from nexusparser import Nexus_Parser -from phyloxmlparser import Phyloxml_Parser +#from phyloxmlparser import Phyloxml_Parser class Phyloviz_DataProvider(object): @@ -16,9 +16,9 @@ if fileExt == "nhx": # parses newick files newickParser = Newick_Parser() jsonDicts, parseMsg = newickParser.parseFile(filepath) - elif fileExt == "phyloxml": # parses phyloXML files - phyloxmlParser = Phyloxml_Parser() - jsonDicts, parseMsg = phyloxmlParser.parseFile(filepath) + #elif fileExt == "phyloxml": # parses phyloXML files + # phyloxmlParser = Phyloxml_Parser() + # jsonDicts, parseMsg = phyloxmlParser.parseFile(filepath) elif fileExt == "nex": # parses nexus files nexusParser = Nexus_Parser() jsonDicts, parseMsg = nexusParser.parseFile(filepath) diff -r 75a03bacdc7a3dc5b1c03f8b02df0ab383366955 -r a4c7aeb61c7b8e76fcf3fd96d0d351be88d1c1d1 lib/galaxy/visualization/phyloviz/phyloxmlparser.py --- a/lib/galaxy/visualization/phyloviz/phyloxmlparser.py +++ b/lib/galaxy/visualization/phyloviz/phyloxmlparser.py @@ -1,4 +1,7 @@ from baseparser import Base_Parser, PhyloTree, Node + +''' +TOD0: use native Python XML parser. from lxml import etree class Phyloxml_Parser(Base_Parser): @@ -143,3 +146,4 @@ # filepath = "../data/" +"bcl_2.xml" # filepath = "../data/" +"reducedXml.xml" parser.parseFile(filepath) +''' \ No newline at end of file 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 Bitbucket 27 Aug '12

27 Aug '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f6d9557b6d77/ changeset: f6d9557b6d77 user: Tomithy date: 2012-08-26 12:22:23 summary: re-integrated phyloviz to a new fork of galaxy-central with a = tat of minor touch up; save and edit now works affected #: 19 files diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -719,7 +719,49 @@ pass =20 class Newick( Text ): - pass + """New Hampshire/Newick Format""" + file_ext =3D "nhx" + + MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu= mns", readonly=3DTrue ) + + def __init__(self, **kwd): + """Initialize foobar datatype""" + Text.__init__(self, **kwd) + + def init_meta( self, dataset, copy_from=3DNone ): + Text.init_meta( self, dataset, copy_from=3Dcopy_from ) + + + def sniff( self, filename ): + """ Returning false as the newick format is too general and cannot= be sniffed.""" + return False + + +class Nexus( Text ): + """Nexus format as used By Paup, Mr Bayes, etc""" + file_ext =3D "nex" + + MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu= mns", readonly=3DTrue ) + + def __init__(self, **kwd): + """Initialize foobar datatype""" + Text.__init__(self, **kwd) + + def init_meta( self, dataset, copy_from=3DNone ): + Text.init_meta( self, dataset, copy_from=3Dcopy_from ) + + + def sniff( self, filename ): + """All Nexus Files Simply puts a '#NEXUS' in its first line""" + f =3D open(filename, "r") + firstline =3D f.readline().upper() + f.close() + + if "#NEXUS" in firstline: + return True + else: + return False + =20 # ------------- Utility methods -------------- =20 diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -76,3 +76,24 @@ dataset.blurb =3D 'file purged from disk' def sniff( self, filename ): return False + +class Phyloxml( GenericXml ): + """Format for defining phyloxml data http://www.phyloxml.org/""" + file_ext =3D "phyloxml" + def set_peek( self, dataset, is_multi_byte=3DFalse ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek =3D data.get_file_peek( dataset.file_name, is_mul= ti_byte=3Dis_multi_byte ) + dataset.blurb =3D 'Phyloxml data' + else: + dataset.peek =3D 'file does not exist' + dataset.blurb =3D 'file purged from disk' + + def sniff( self, filename ): + """"Checking for keyword - 'phyloxml' always in lowercase in the f= irst few lines""" + f =3D open(filename, "r") + firstlines =3D "".join(f.readlines(5)) + f.close() + if "phyloxml" in firstlines: + return True + return False \ No newline at end of file diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/visualization/phyloviz/__init__.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/__init__.py @@ -0,0 +1,1 @@ +__author__ =3D 'Tomithy' diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/visualization/phyloviz/baseparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/baseparser.py @@ -0,0 +1,125 @@ +import json + +class Node(object): + """Node class of PhyloTree, which represents a CLAUDE in a phylogeneti= c tree""" + def __init__(self, nodeName, **kwargs): + """Creates a node and adds in the typical annotations""" + self.name, self.id =3D nodeName, kwargs.get("id", 0) + self.depth =3D kwargs.get("depth", 0) + self.children =3D [] + + self.isInternal =3D kwargs.get("isInternal", 0) + self.length, self.bootstrap =3D kwargs.get("length", 0), kwargs.ge= t("bootstrap", None) + self.events =3D kwargs.get("events", "") + + # clean up boot strap values + if self.bootstrap =3D=3D -1: + self.bootstrap =3D None + + def addChildNode(self, child): + """Adds a child node to the current node""" + if isinstance(child, Node): + self.children.append(child) + else: + self.children +=3D child + + + def __str__(self): + return self.name + " id:" + str(self.id) + ", depth: " + str(self.= depth) + + + def toJson(self): + """Converts the data in the node to a dict representation of json"= "" + thisJson =3D { + "name" : self.name, + "id" : self.id, + "depth" : self.depth, + "dist" : self.length + } + thisJson =3D self.addChildrenToJson(thisJson) + thisJson =3D self.addMiscToJson(thisJson) + return thisJson + + def addChildrenToJson(self, jsonDict): + """Needs a special method to addChildren, such that the key does n= ot appear in the Jsondict when the children is empty + this requirement is due to the layout algorithm used by d3 layout = for hiding subtree """ + if len(self.children) > 0: + children =3D [ node.toJson() for node in self.children] + jsonDict["children"] =3D children + return jsonDict + + + def addMiscToJson(self, jsonDict): + """Adds other misc attributes to json if they are present""" + if not self.events =3D=3D "": + jsonDict["events"] =3D self.events + if not self.bootstrap =3D=3D None: + jsonDict["bootstrap"] =3D self.bootstrap + return jsonDict + + + +class PhyloTree(object): + """Standardized python based class to represent the phylogenetic tree = parsed from different + phylogenetic file formats.""" + + def __init__(self): + self.root, self.rootAttr =3D None, {} + self.nodes =3D {} + self.title =3D None + self.id =3D 1 + + def addAttributesToRoot(self, attrDict): + """Adds attributes to root, but first we put it in a temp store an= d bind it with root when .toJson is called""" + for key, value in attrDict.items(): + self.rootAttr[key] =3D value + + def makeNode(self, nodeName, **kwargs): + """Called to make a node within PhyloTree, arbitrary kwargs can be= passed to annotate nodes + Tracks the number of nodes via internally incremented id""" + kwargs["id"] =3D self.id + self.id +=3D 1 + return Node(nodeName, **kwargs) + + def addRoot(self, root): + """Creates a root for phyloTree""" + assert isinstance(root, Node) + root.parent =3D None + self.root =3D root + + def generateJsonableDict(self): + """Changes itself into a dictonary by recurssively calling the toj= son on all its nodes. Think of it + as a dict in an array of dict in an array of dict and so on...""" + jsonTree =3D "" + if self.root: + assert isinstance(self.root, Node) + jsonTree =3D self.root.toJson() + for key, value in self.rootAttr.items(): + # transfer temporary stored attr to root + jsonTree[key] =3D value + else: + raise Exception("Root is not assigned!") + return jsonTree + + + +class Base_Parser(object): + """Base parsers contain all the methods to handle phylogeny tree creat= ion and + converting the data to json that all parsers should have""" + + def __init__(self): + self.phyloTrees =3D [] + + def parseFile(self, filePath): + """Base method that all phylogeny file parser should have""" + raise Exception("Base method for phylogeny file parsers is not imp= lemented") + + def toJson(self, jsonDict): + """Convenience method to get a json string from a python json dict= """ + return json.dumps(jsonDict) + + def _writeJsonToFile(self, filepath, json): + """Writes the file out to the system""" + f =3D open(filepath, "w") + f.writelines(json) + f.close() diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/visualization/phyloviz/newickparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/newickparser.py @@ -0,0 +1,185 @@ +from baseparser import Base_Parser, PhyloTree +import re + +class Newick_Parser(Base_Parser): + """For parsing trees stored in the newick format (.nhx) + It is necessarily more complex because this parser is later extended b= y Nexus for parsing newick as well..""" + + + def __init__(self): + super(Newick_Parser, self).__init__() + + + def parseFile(self, filePath): + """Parses a newick file to obtain the string inside. Returns: json= ableDict""" + with open(filePath, "r") as newickFile: + newickString =3D newickFile.read() + newickString =3D newickString.replace("\n", "").replace("\r", = "") + return [self.parseData(newickString)], "Success" + + + def parseData(self, newickString): + """To be called on a newickString directly to parse it. Returns: j= sonableDict""" + return self._parseNewickToJson(newickString) + + + def _parseNewickToJson(self, newickString, treeName=3DNone, nameMap=3D= None): + """parses a newick representation of a tree into a PhyloTree data = structure, + which can be easily converted to json""" + self.phyloTree =3D PhyloTree() + newickString =3D self.cleanNewickString(newickString) + if nameMap: + newickString =3D self._mapName(newickString, nameMap) + + self.phyloTree.root =3D self.parseNode(newickString, 0) + if nameMap: + self.phyloTree.addAttributesToRoot({"treeName": treeName}) + + return self.phyloTree.generateJsonableDict() + + + def cleanNewickString(self, rawNewick): + """removing semi colon, and illegal json characters (\,',") and wh= ite spaces""" + return re.sub(r'\s|;|\"|\'|\\', '', rawNewick) + + + def _makeNodesFromString(self, string, depth): + """elements separated by comma could be empty""" + + if string.find("(") !=3D -1: + raise Exception("Tree is not well form, location: " + string) + + childrenString =3D string.split(",") + childrenNodes =3D [] + + for childString in childrenString: + if len(childString) =3D=3D 0: + continue + nodeInfo =3D childString.split(":") + name, length, bootstrap =3D "", None, -1 + if len(nodeInfo) =3D=3D 2: # has length info + length =3D nodeInfo[1] + # checking for bootstap values + name =3D nodeInfo[0] + try: # Nexus may bootstrap in names position + name =3D float(name) + if 0<=3D name <=3D 1: + bootstrap =3D name + elif 1 <=3D name <=3D 100: + bootstrap =3D name / 100 + name =3D "" + except ValueError: + name =3D nodeInfo[0] + else: + name =3D nodeInfo[0] # string only contains name + node =3D self.phyloTree.makeNode(name, length=3Dlength, depth= =3Ddepth, bootstrap=3D bootstrap) + childrenNodes +=3D [node] + return childrenNodes + + + + def _mapName(self, newickString, nameMap): + """ + Necessary to replace names of terms inside nexus representation + Also, its here because Mailaud's doesnt deal with id_strings outsi= de of quotes(" ") + """ + newString =3D "" + start =3D 0 + end =3D 0 + + for i in xrange(len(newickString)): + if newickString[i] =3D=3D "(" or newickString[i] =3D=3D ",": + if re.match(r"[,(]", newickString[i+1:]): + continue + else: + end =3D i + 1 + # i now refers to the starting position of the term to= be replaced, + # we will next find j which is the ending pos of the t= erm + for j in xrange(i+1, len(newickString)): + enclosingSymbol =3D newickString[j] # the immedi= ate symbol after a common or left bracket which denotes the end of a term + if enclosingSymbol =3D=3D ")" or enclosingSymbol = =3D=3D ":" or enclosingSymbol =3D=3D ",": + termToReplace =3D newickString[end:j] + + newString +=3D newickString[start : end] + na= meMap[termToReplace] #+ "'" "'" + + start =3D j + break + + newString +=3D newickString[start:] + return newString + + + def parseNode(self, string, depth): + """ Recursive method for parsing newick string, works by stripping= down the string into substring + of newick contained with brackers, which is used to call itself. + Eg ... ( A, B, (D, E)C, F, G ) ... + We will make the preceeding nodes first A, B, then the internal no= de C, its children D, E, + and finally the succeeding nodes F, G""" + + # Base case where there is only an empty string + if string =3D=3D "": + return + # Base case there its only an internal claude + if string.find("(") =3D=3D -1: + return self._makeNodesFromString(string, depth) + + nodes, children =3D [], [] # nodes refer to the nodes on this= level, children refers to the child of the + start =3D 0 + lenOfPreceedingInternalNodeString =3D 0 + bracketStack =3D [] + + for j in xrange(len(string)): + if string[j] =3D=3D "(": #finding the positions of all the = open brackets + bracketStack.append(j) + continue + if string[j] =3D=3D ")": #finding the positions of all the = closed brackets to extract claude + i =3D bracketStack.pop() + + if len(bracketStack) =3D=3D 0: # is child of current node + + InternalNode =3D None + + #First flat call to make nodes of the same depth but f= rom the preceeding string. + startSubstring =3D string[start + lenOfPreceedingInter= nalNodeString: i] + preceedingNodes =3D self._makeNodesFromString(startSu= bstring, depth) + nodes +=3D preceedingNodes + + # Then We will try to see if the substring has any int= ernal nodes first, make it then make nodes preceeding it and succeeding it. + if j + 1 < len(string): + stringRightOfBracket =3D string[j+1:] # Eg. '= (b:0.4,a:0.3)c:0.3, stringRightOfBracket =3D c:0.3 + match =3D re.search(r"[\)\,\(]", stringRightOfBrac= ket) + if match: + indexOfNextSymbol =3D match.start() + stringRepOfInternalNode =3D stringRightOfBrack= et[:indexOfNextSymbol] + internalNodes =3D self._makeNodesFromString( s= tringRepOfInternalNode, depth) + if len(internalNodes) > 0: + InternalNode =3D internalNodes[0] + lenOfPreceedingInternalNodeString =3D len(stri= ngRepOfInternalNode) + else: # sometimes the node can be the last eleme= nt of a string + InternalNode =3D self._makeNodesFromString(str= ing[j+1:], depth)[0] + lenOfPreceedingInternalNodeString =3D len(stri= ng) - j + if InternalNode =3D=3D None: #creating a generic= node if it is unnamed + InternalNode =3D self.phyloTree.makeNode( "", dept= h=3Ddepth, isInternal=3DTrue ) #"internal-" + str(depth) + lenOfPreceedingInternalNodeString =3D 0 + + # recussive call to make the internal claude + childSubString =3D string[ i + 1 : j ] + InternalNode.addChildNode(self.parseNode(childSubStrin= g, depth + 1)) + + nodes.append(InternalNode) # we append the internal n= ode later to preserve order + + start =3D j + 1 + continue + + if depth =3D=3D 0: # if its the root node, we do nothing about = it and return + return nodes[0] + + # Adding last most set of children + endString =3D string[start:] + if string[start-1] =3D=3D ")": # if the symbol belongs to an inte= rnal node which is created previously, then we remove it from the string le= ft to parse + match =3D re.search(r"[\)\,\(]", endString) + if match: + endOfNodeName =3D start + match.start() + 1 + endString =3D string[endOfNodeName:] + nodes +=3D self._makeNodesFromString(endString, depth) + + return nodes diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/visualization/phyloviz/nexusparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/nexusparser.py @@ -0,0 +1,107 @@ +from newickparser import Newick_Parser +import re + +MAX_READLINES =3D 200000 + + +class Nexus_Parser(Newick_Parser): + + def __init__(self): + super(Nexus_Parser, self).__init__() + + def parseFile(self, filePath): + """passes a file and extracts its Nexus content.""" + return self.parseNexus(filePath) + + + def parseNexus(self, filename): + """ Nexus data is stored in blocks between a line starting with be= gin and another line starting with end; + Commends inside square brackets are to be ignored, + For more information: http://wiki.christophchamp.com/index.php/NEX= US_file_format + Nexus can store multiple trees + """ + + with open( filename, "rt") as nex_file: + nexlines =3D nex_file.readlines() + + rowCount =3D 0 + inTreeBlock =3D False # sentinel to check if we are in a t= ree block + intranslateBlock =3D False # sentinel to check if we are in the= translate region of the tree. Stores synonyms of the labellings + self.inCommentBlock =3D False + self.nameMapping =3D None # stores mapping representation us= ed in nexus format + treeNames =3D [] + + for line in nexlines: + line =3D line.replace(";\n", "") + lline =3D line.lower() + + if rowCount > MAX_READLINES or (not nex_file) : + break + rowCount +=3D1 + # We are only interested in the tree block. + if "begin" in lline and "tree" in lline and not inTreeBlock: + inTreeBlock =3D True + continue + if inTreeBlock and "end" in lline[:3]: + inTreeBlock, currPhyloTree =3D False, None + continue + + if inTreeBlock: + + if "title" in lline: # Adding title to the tree + titleLoc =3D lline.find("title") + title =3D line[titleLoc + 5:].replace(" ", "") + + continue + + if "translate" in lline: + intranslateBlock =3D True + self.nameMapping =3D {} + continue + + if intranslateBlock: + mappingLine =3D self.splitLinebyWhitespaces(line) + key, value =3D mappingLine[1], mappingLine[2].replace(= ",", "").replace("'","") #replacing illegal json characters + self.nameMapping[key] =3D value + + # Extracting newick Trees + if "tree" in lline: + intranslateBlock =3D False + + treeLineCols =3D self.splitLinebyWhitespaces(line) + treeName, newick =3D treeLineCols[2], treeLineCols[-1] + + if newick =3D=3D "": # Empty lines can be found in = tree blocks + continue + + currPhyloTree =3D self._parseNewickToJson(newick, tree= Name, nameMap=3Dself.nameMapping) + + self.phyloTrees.append(currPhyloTree) + treeIndex =3D len(self.phyloTrees) - 1 + treeNames.append( (treeName, treeIndex) ) # appendi= ng name of tree, and its index + continue + + return self.phyloTrees, treeNames + + + def splitLinebyWhitespaces(self, line): + """replace tabs and write spaces to a single write space, so we ca= n properly split it.""" + return re.split(r"\s+", line) + + + def checkComments(self, line): + """Check to see if the line/lines is a comment.""" + if not self.inCommentBlock: + if "[" in line: + if "]" not in line: + self.inCommentBlock =3D True + else: + return "Nextline" # need to move on to the nextline = after getting out of comment + else : + if "]" in line: + if line.rfind("[") > line.rfind("]"): + pass # a comment block is closed but an= other is open. + else: + self.inCommentBlock =3D False + return "Nextline" # need to move on to the nextline = after getting out of comment + return "" \ No newline at end of file diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py @@ -0,0 +1,35 @@ +from newickparser import Newick_Parser +from nexusparser import Nexus_Parser +from phyloxmlparser import Phyloxml_Parser + +class Phyloviz_DataProvider(object): + + def __init__(self): + pass + + def parseFile(self, filepath, fileExt): + """returns [trees], meta + Trees are actually an array of JsonDicts. It's usually one tre= e, except in the case of Nexus + """ + jsonDicts, meta =3D [], {} + try: + if fileExt =3D=3D "nhx": # parses newick files + newickParser =3D Newick_Parser() + jsonDicts, parseMsg =3D newickParser.parseFile(filepath) + elif fileExt =3D=3D "phyloxml": # parses phyloXML files + phyloxmlParser =3D Phyloxml_Parser() + jsonDicts, parseMsg =3D phyloxmlParser.parseFile(filepath) + elif fileExt =3D=3D "nex": # parses nexus files + nexusParser =3D Nexus_Parser() + jsonDicts, parseMsg =3D nexusParser.parseFile(filepath) + meta["trees"] =3D parseMsg + else: + raise Exception("File type is not supported") + + meta["msg"] =3D parseMsg + + except Exception: + jsonDicts, meta["msg"] =3D [], "Parse failed" + + return jsonDicts, meta + diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/visualization/phyloviz/phyloxmlparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/phyloxmlparser.py @@ -0,0 +1,145 @@ +from baseparser import Base_Parser, PhyloTree, Node +from lxml import etree + +class Phyloxml_Parser(Base_Parser): + """Parses a phyloxml file into a json file that will be passed to Phyl= oViz for display""" + + def __init__(self): + super(Phyloxml_Parser, self).__init__() + self.phyloTree =3D PhyloTree() + self.tagsOfInterest =3D { + "clade": "", + "name" : "name", + "branch_length" : "length", + "confidence" : "bootstrap", + "events" : "events" + } + + def parseFile(self, filePath): + """passes a file and extracts its Phylogeny Tree content.""" + phyloXmlFile =3D open(filePath, "r") + + xmlTree =3D etree.parse(phyloXmlFile) + xmlRoot =3D xmlTree.getroot()[0] + self.nameSpaceIndex =3D xmlRoot.tag.rfind("}") + 1 # used later by= the clean tag method to remove the name space in every element.tag + + phyloRoot =3D None + for child in xmlRoot: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + phyloRoot =3D child + elif childTag =3D=3D "name": + self.phyloTree.title =3D child.text + + self.phyloTree.root =3D self.parseNode(phyloRoot, 0) + jsonDict =3D self.phyloTree.generateJsonableDict() + return [jsonDict], "Success" + + + def parseNode(self, node, depth): + """Parses any node within a phyloxml tree and looks out for claude= , which signals the creation of + nodes - internal OR leaf""" + assert isinstance(node, etree._Element) + + tag =3D self.cleanTag(node.tag) + if not tag =3D=3D "clade": + return None + hasInnerClade =3D False + + # peeking once for parent and once for child to check if the node = is internal + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + hasInnerClade =3D True + break + + if hasInnerClade: # this node is an internal node + currentNode =3D self._makeInternalNode(node, depth=3D depth) + for child in node: + child =3D self.parseNode(child, depth + 1) + if isinstance(child, Node): + currentNode.addChildNode(child) + + else: # this node is a leaf node + currentNode =3D self._makeLeafNode(node, depth=3Ddepth+1) + + return currentNode + + + def _makeLeafNode(self, leafNode, depth =3D 0 ): + """Makes leaf nodes by calling Phylotree methods""" + node =3D {} + for child in leafNode: + childTag =3D self.cleanTag(child.tag) + if childTag in self.tagsOfInterest: + key =3D self.tagsOfInterest[childTag] # need to map phy= loxml terms to ours + node[key] =3D child.text + + node["depth"] =3D depth + return self.phyloTree.makeNode(self._getNodeName(leafNode), **node) + + def _getNodeName(self, node, depth=3D-1): + """Gets the name of a claude. It handles the case where a taxonomy= node is involved""" + + def getTagFromTaxonomyNode(node): + """Returns the name of a taxonomy node. A taxonomy node have t= o be treated differently as the name + is embedded one level deeper""" + phyloxmlTaxoNames =3D { + "common_name" : "", + "scientific_name" : "", + "code" : "" + } + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag in phyloxmlTaxoNames: + return child.text + return "" + + nodeName =3D "" + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "name" : + nodeName =3D child.text + break + elif childTag =3D=3D "taxonomy": + nodeName =3D getTagFromTaxonomyNode(child) + break + + return nodeName + + + def _makeInternalNode(self, internalNode, depth=3D0): + """ Makes an internal node from an element object that is gurantee= d to be a parent node. + Gets the value of interests like events and appends it to a custom= node object that will be passed to PhyloTree to make nodes + """ + node =3D {} + for child in internalNode: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + continue + elif childTag in self.tagsOfInterest: + if childTag =3D=3D "events": # events is nested 1 more = level deeper than others + key, text =3D "events", self.cleanTag(child[0].tag) + else: + key =3D self.tagsOfInterest[childTag] + text =3D child.text + node[key] =3D text + + + return self.phyloTree.makeNode(self._getNodeName(internalNode, dep= th), **node) + + + def cleanTag(self, tagString): + return tagString[self.nameSpaceIndex:] + + +if __name__=3D=3D"__main__": + + # Files tested against + parser =3D Phyloxml_Parser() + filepath =3D "../data/" +"apaf.xml" + # filepath =3D "../data/" +"12_multiple_supports.xml" + + # filepath =3D "../data/" +"bcl_2.xml" + # filepath =3D "../data/" +"reducedXml.xml" + parser.parseFile(filepath) diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/web/controllers/phyloviz.py --- /dev/null +++ b/lib/galaxy/web/controllers/phyloviz.py @@ -0,0 +1,97 @@ +import pkg_resources +pkg_resources.require( "bx-python" ) + +from galaxy.util.json import to_json_string, from_json_string +from galaxy.web.base.controller import * +from galaxy.visualization.phyloviz.phyloviz_dataprovider import Phyloviz_D= ataProvider + + +class PhyloVizController( BaseUIController, UsesVisualizationMixin, UsesHi= storyDatasetAssociationMixin, SharableMixin ): + """ + Controller for phyloViz browser interface. + """ + def __init__(self, app ): + BaseUIController.__init__( self, app ) + + @web.expose + @web.require_login() + def index( self, trans, dataset_id =3D None, **kwargs ): + """ + The index method is called using phyloviz/ with a dataset id passe= d in. + The relevant data set is then retrieved via get_json_from_datasetI= d which interfaces with the parser + The json representation of the phylogenetic tree along with the co= nfig is then written in the .mako template and passed back to the user + """ + json, config =3D self.get_json_from_datasetId(trans, dataset_id) + config["saved_visualization"] =3D False + return trans.fill_template( "visualization/phyloviz.mako", data = =3D json, config=3Dconfig) + + + @web.expose + def visualization(self, trans, id): + """ + Called using a viz_id (id) to retrieved stored visualization data = (in json format) and all the viz_config + """ + viz =3D self.get_visualization(trans, id) + config =3D self.get_visualization_config(trans, viz) + config["saved_visualization"] =3D True + data =3D config["root"] + + return trans.fill_template( "visualization/phyloviz.mako", data = =3D data, config=3Dconfig) + + + @web.expose + @web.json + def load_visualization_json(self, trans, viz_id): + """ + Though not used in current implementation, this provides user with= a convenient method to retrieve the viz_data & viz_config via json. + """ + viz =3D self.get_visualization(trans, viz_id) + viz_config =3D self.get_visualization_config(trans, viz) + viz_config["saved_visualization"] =3D True + return { + "data" : viz_config["root"], + "config" : viz_config + } + + + @web.expose + @web.json + def getJsonData(self, trans, dataset_id, treeIndex=3D0): + """ + Method to retrieve data asynchronously via json format. Retriving = from here rather than + making a direct datasets/ call allows for some processing and even= t capturing + """ + treeIndex =3D int(treeIndex) + json, config =3D self.get_json_from_datasetId(trans, dataset_id, t= reeIndex) + packedJson =3D { + "data" : json, + "config" : config + } + + return packedJson + + + def get_json_from_datasetId(self, trans, dataset_id, treeIndex=3D0): + """ + For interfacing phyloviz controllers with phyloviz visualization d= ata provider (parsers) + """ + dataset =3D self.get_dataset(trans, dataset_id) + fileExt, filepath =3D dataset.ext, dataset.file_name # .name= stores the name of the dataset from the orginal upload + json, config =3D "", {} # config contains propertie= s of the tree and file + + if fileExt =3D=3D "json": + something, json =3D self.get_data(dataset) + else: + try: + pd =3D Phyloviz_DataProvider() + json, config =3D pd.parseFile(filepath, fileExt) + json =3D json[treeIndex] + except Exception: + pass + + config["title"] =3D dataset.display_name() + config["ext"] =3D fileExt + config["dataset_id"] =3D dataset_id + config["treeIndex"] =3D treeIndex + + return json, config diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -16,6 +16,10 @@ action =3D "paramamonster" elif item.type =3D=3D "circster": action =3D "circster" + elif item.type =3D=3D "phyloviz": + # Support phyloviz + controller =3D "phyloviz" + action =3D "visualization" return dict( controller=3Dcontroller, action=3Daction, id=3Ditem.i= d ) =20 # Grid definition diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 static/scripts/viz/phyloviz.js --- /dev/null +++ b/static/scripts/viz/phyloviz.js @@ -0,0 +1,955 @@ +var UserMenuBase =3D Backbone.View.extend({ + /** + * Base class of any menus that takes in user interaction. Contains ch= ecking methods. + */ + + className: 'UserMenuBase', + + isAcceptableValue : function ($inputKey, min, max) { + /** + * Check if an input value is a number and falls within max min. + */ + var self =3D this, + value =3D $inputKey.val(), + fieldName =3D $inputKey.attr("displayLabel") || $inputKey.attr= ("id").replace("phyloViz", ""); + + function isNumeric(n) { + return !isNaN(parseFloat(n)) && isFinite(n); + } + + if (!isNumeric(value)){ + alert(fieldName + " is not a number!"); + return false; + } + + if ( value > max){ + alert(fieldName + " is too large."); + return false; + } else if ( value < min) { + alert(fieldName + " is too small."); + return false; + } + return true; + }, + + hasIllegalJsonCharacters : function($inputKey) { + /** + * Check if any user string inputs has illegal characters that jso= n cannot accept + */ + if ($inputKey.val().search(/"|'|\\/) !=3D=3D -1){ + alert("Named fields cannot contain these illegal characters: d= ouble quote(\"), single guote(\'), or back slash(\\). "); + return true; + } + return false; + } +}); + + +function PhyloTreeLayout() { + /** + * -- Custom Layout call for phyloViz to suit the needs of a phylogene= tic tree. + * -- Specifically: 1) Nodes have a display display of (=3D evo dist X= depth separation) from their parent + * 2) Nodes must appear in other after they have expa= nd and contracted + */ + + var self =3D this, + hierarchy =3D d3.layout.hierarchy().sort(null).value(null), + height =3D 360, // ! represents both the layout angle and the heig= ht of the layout, in px + layoutMode =3D "Linear", + leafHeight =3D 18, // height of each individual leaf node + depthSeparation =3D 200, // separation between nodes of different = depth, in px + leafIndex =3D 0, // change to recurssive call + defaultDist =3D 0.5, // tree defaults to 0.5 dist if no dist is sp= ecified + maxTextWidth =3D 50; // maximum length of the text labels + + + self.leafHeight =3D function(inputLeafHeight){ + if (typeof inputLeafHeight =3D=3D=3D "undefined"){ return leafHeig= ht; } + else { leafHeight =3D inputLeafHeight; return self;} + }; + + self.layoutMode =3D function(mode){ + if (typeof mode =3D=3D=3D "undefined"){ return layoutMode; } + else { layoutMode =3D mode; return self;} + }; + + self.layoutAngle =3D function(angle) { // changes the layout angle = of the display, which is really changing the height + if (typeof angle =3D=3D=3D "undefined"){ return height; } + if (isNaN(angle) || angle < 0 || angle > 360) { return self; } // = to use default if the user puts in strange values + else { height =3D angle; return self;} + }; + + self.separation =3D function(dist){ // changes the dist between the = nodes of different depth + if (typeof dist =3D=3D=3D "undefined"){ return depthSeparation; } + else { depthSeparation =3D dist; return self;} + }; + + self.links =3D function (nodes) { // uses d3 native method to gene= rate links. Done. + return d3.layout.tree().links(nodes); + }; + + // -- Custom method for laying out phylogeny tree in a linear fashion + self.nodes =3D function (d, i) { + var _nodes =3D hierarchy.call(self, d, i), // self is to f= ind the depth of all the nodes, assumes root is passed in + nodes =3D [], + maxDepth =3D 0, + numLeaves =3D 0; + + // changing from hierarchy's custom format for data to usable form= at + _nodes.forEach(function (_node){ + var node =3D _node.data; + node.depth =3D _node.depth; + maxDepth =3D node.depth > maxDepth ? node.depth : maxDepth; /= /finding max depth of tree + nodes.push(node); + }); + // counting the number of leaf nodes and assigning max depth to no= des that do not have children to flush all the leave nodes + nodes.forEach(function(node){ + if ( !node.children ) { //&& !node._children + numLeaves +=3D 1; + node.depth =3D maxDepth; // if a leaf has no child it woul= d be assigned max depth + } + }); + + leafHeight =3D layoutMode =3D=3D=3D "Circular" ? height / numLeave= s : leafHeight; + leafIndex =3D 0; + layout(nodes[0], maxDepth, leafHeight, null); + + return nodes; + }; + + + function layout (node, maxDepth, vertSeparation, parent) { + /** + * -- Function with side effect of adding x0, y0 to all child; tak= e in the root as starting point + * assuming that the leave nodes would be sorted in presented ord= er + * horizontal(y0) is calculated according to (=3D evo dis= t X depth separation) from their parent + * vertical (x0) - if leave node: find its order in all o= f the leave node =3D=3D=3D node.id, then multiply by verticalSeparation + * - if parent node: is place in the mid point al= l of its children nodes + * -- The layout will first calculate the y0 field going towards t= he leaves, and x0 when returning + */ + var children =3D node.children, + sumChildVertSeparation =3D 0; + + // calculation of node's dist from parents, going down. + var dist =3D node.dist || defaultDist; + dist =3D dist > 1 ? 1 : dist; // We constrain all dist to be l= ess than one + node.dist =3D dist; + if (parent !=3D=3D null){ + node.y0 =3D parent.y0 + dist * depthSeparation; + } else { //root node + node.y0 =3D maxTextWidth; + } + + + // if a node have no children, we will treat it as a leaf and star= t laying it out first + if (!children) { + node.x0 =3D leafIndex++ * vertSeparation; + } else { + // if it has children, we will visit all its children and calc= ulate its position from its children + children.forEach( function (child) { + child.parent =3D node; + sumChildVertSeparation +=3D layout(child, maxDepth, vertSe= paration, node); + }); + node.x0 =3D sumChildVertSeparation / children.length; + } + + // adding properties to the newly created node + node.x =3D node.x0; + node.y =3D node.y0; + return node.x0; + } + return self; +} + + +/** + * -- PhyloTree Model -- + */ +var PhyloTree =3D Visualization.extend({ + defaults : { + layout: "Linear", + separation : 250, // px dist between nodes of different depth t= o represent 1 evolutionary until + leafHeight: 18, + type : "phyloviz", // visualization type + title : "Title", + scaleFactor: 1, + translate: [0,0], + fontSize: 12, //fontSize of node label + selectedNode : null, + nodeAttrChangedTime : 0 + }, + + root : {}, // Root has to be its own independent object because it is = not part of the viz_config + + toggle : function (d) { + /** + * Mechanism to expand or contract a single node. Expanded nodes h= ave a children list, while for + * contracted nodes the list is stored in _children. Nodes with th= eir children data stored in _children will not have their + * children rendered. + */ + if(typeof d =3D=3D=3D "undefined") {return ;} + if (d.children ) { + d._children =3D d.children; + d.children =3D null; + } else { + d.children =3D d._children; + d._children =3D null; + } + }, + + toggleAll : function(d) { + /** + * Contracts the phylotree to a single node by repeatedly calling= itself to place all the list + * of children under _children. + */ + if (d.children && d.children.length !=3D=3D 0) { + d.children.forEach(this.toggleAll); + toggle(d); + } + }, + + getData : function (){ + /** + * Return the data of the tree. Used for preserving state. + */ + return this.root; + }, + + save: function() { + /** + * Overriding the default save mechanism to do some clean of circu= lar reference of the + * phyloTree and to include phyloTree in the saved json + */ + var root =3D this.root; + cleanTree(root); + this.set("root", root); + + function cleanTree(node){ + // we need to remove parent to delete circular reference + delete node.parent; + + // removing unnecessary attributes + if (node._selected){ delete node._selected;} + + node.children ? node.children.forEach(cleanTree) : 0; + node._children ? node._children.forEach(cleanTree) : 0; + } + + var config =3D jQuery.extend(true, {}, this.attributes); + config["selectedNode"] =3D null; + + show_message("Saving to Galaxy", "progress"); + + return $.ajax({ + url: this.url(), + type: "POST", + dataType: "json", + data: { + vis_json: JSON.stringify(config) + }, + success: function(res){ + var viz_id =3D res.url.split("id=3D")[1].split("&")[0], + viz_url =3D "/phyloviz/visualization?id=3D" + viz_id; + window.history.pushState({}, "", viz_url + window.location= .hash); + hide_modal(); + } + }); + } +}); + + + +/** + * -- Views -- + */ +var PhylovizLayoutBase =3D Backbone.View.extend({ + /** + * Stores the default variable for setting up the visualization + */ + defaults : { + nodeRadius : 4.5 // radius of each node in the diagram + }, + + + stdInit : function (options) { + /** + * Common initialization in layouts + */ + + var self =3D this; + self.model.on("change:separation change:leafHeight change:fontSize= change:nodeAttrChangedTime", self.updateAndRender, self); + + self.vis =3D options.vis; + self.i =3D 0; + self.maxDepth =3D -1; // stores the max depth of the tree + + self.width =3D options.width; + self.height =3D options.height; + }, + + + updateAndRender : function(source) { + /** + * Updates the visualization whenever there are changes in the ex= pansion and contraction of nodes + * AND possibly when the tree is edited. + */ + var vis =3D d3.select(".vis"), + self =3D this; + source =3D source || self.model.root; + + self.renderNodes(source); + self.renderLinks(source); + self.addTooltips(); + }, + + + renderLinks : function(source) { + /** + * Renders the links for the visualization. + */ + var self =3D this; + var diagonal =3D self.diagonal; + var duration =3D self.duration; + var layoutMode =3D self.layoutMode; + var link =3D self.vis.selectAll("g.completeLink") + .data(self.tree.links(self.nodes), function(d) { return d.targ= et.id; }); + + var calcalateLinePos =3D function(d) { + d.pos0 =3D d.source.y0 + " " + d.source.x0; // position of t= he source node <=3D> starting location of the line drawn + d.pos1 =3D d.source.y0 + " " + d.target.x0; // position where= the line makes a right angle bend + d.pos2 =3D d.target.y0 + " " + d.target.x0; // point where= the horizontal line becomes a dotted line + }; + + var linkEnter =3D link.enter().insert("svg:g","g.node") + .attr("class", "completeLink"); + + + linkEnter.append("svg:path") + .attr("class", "link") + .attr("d", function(d) { + calcalateLinePos(d); + return "M " + d.pos0 + " L " + d.pos1; + }); + + var linkUpdate =3D link.transition().duration(500); + + linkUpdate.select("path.link") + .attr("d", function(d) { + calcalateLinePos(d); + return "M " + d.pos0 + " L " + d.pos1 + " L " + d.pos2; + }); + + var linkExit =3D link.exit().remove(); + + }, + + // User Interaction methods below + + selectNode : function(node){ + /** + * Displays the information for editting + */ + var self =3D this; + d3.selectAll("g.node") + .classed("selectedHighlight", function(d){ + if (node.id =3D=3D=3D d.id){ + if(node._selected) { // for de=3Dselecting node. + delete node._selected; + return false; + } else { + node._selected =3D true; + return true; + } + } + return false; + }); + + self.model.set("selectedNode", node); + $("#phyloVizSelectedNodeName").val(node.name); + $("#phyloVizSelectedNodeDist").val(node.dist); + $("#phyloVizSelectedNodeAnnotation").val(node.annotation || ""); + }, + + addTooltips : function (){ + /** + * Creates bootstrap tooltip for the visualization. Has to be cal= led repeatedly due to newly generated + * enterNodes + */ + $(".bs-tooltip").remove(); //clean up tooltip, just in case i= ts listeners are removed by d3 + $(".node") + .attr("data-original-title", function(){ + var d =3D this.__data__, + annotation =3D d.annotation || "None" ; + return d ? (d.name ? d.name + "<br/>" : "") + "Dist: " + d= .dist + " <br/>Annotation: " + annotation: ""; + }) + .tooltip({'placement':'top', 'trigger' : 'hover'}); + + } +}); + + + + +var PhylovizLinearView =3D PhylovizLayoutBase.extend({ + /** + * Linea layout class of Phyloviz, is responsible for rendering the no= des + * calls PhyloTreeLayout to determine the positions of the nodes + */ + initialize : function(options){ + // Default values of linear layout + var self =3D this; + self.margins =3D options.margins; + self.layoutMode =3D "Linear"; + + self.stdInit(options); + + self.layout(); + self.updateAndRender(self.model.root); + }, + + layout : function() { + /** + * Creates the basic layout of a linear tree by precalculating fix= ed values. + * One of calculations are also made here + */ + + var self =3D this; + + self.tree =3D new PhyloTreeLayout().layoutMode("Linear"); + self.diagonal =3D d3.svg.diagonal() + .projection(function(d) { return [d.y, d.x ]; }); + }, + + renderNodes : function (source) { + /** + * Renders the nodes base on Linear layout. + */ + var self =3D this, + fontSize =3D self.model.get("fontSize") + "px"; + + // assigning properties from models + self.tree.separation(self.model.get("separation")).leafHeight(self= .model.get("leafHeight")); + + var duration =3D 500, + nodes =3D self.tree.separation(self.model.get("separation")).n= odes(self.model.root); + + var node =3D self.vis.selectAll("g.node") + .data(nodes, function(d) { return d.name + d.id || (d.id =3D += +self.i); }); + + // These variables has to be passed into update links which are in= the base methods + self.nodes =3D nodes; + self.duration =3D duration; + + // ------- D3 ENTRY -------- + // Enter any new nodes at the parent's previous position. + var nodeEnter =3D node.enter().append("svg:g") + .attr("class", "node") + .on("dblclick", function(){ d3.event.stopPropagation(); }) + .on("click", function(d) { + if (d3.event.altKey) { + self.selectNode(d); // display info if alt is p= ressed + } else { + if(d.children && d.children.length =3D=3D=3D 0){ retur= n;} // there is no need to toggle leaves + self.model.toggle(d); // contract/expand nodes at da= ta level + self.updateAndRender(d); // re-render the tree + } + }); + + nodeEnter.attr("transform", function(d) { return "translate(" + so= urce.y0 + "," + source.x0 + ")"; }); + + nodeEnter.append("svg:circle") + .attr("r", 1e-6) + .style("fill", function(d) { return d._children ? "lightsteelb= lue" : "#fff"; }); + + nodeEnter.append("svg:text") + .attr("class", "nodeLabel") + .attr("x", function(d) { return d.children || d._children ? -1= 0 : 10; }) + .attr("dy", ".35em") + .attr("text-anchor", function(d) { return d.children || d._chi= ldren ? "end" : "start"; }) + .style("fill-opacity", 1e-6); + + // ------- D3 TRANSITION -------- + // Transition nodes to their new position. + var nodeUpdate =3D node.transition() + .duration(duration); + + nodeUpdate.attr("transform", function(d) { + return "translate(" + d.y + "," + d.x + ")"; }); + + nodeUpdate.select("circle") + .attr("r", self.defaults.nodeRadius) + .style("fill", function(d) { return d._children ? "lightsteelb= lue" : "#fff"; }); + + nodeUpdate.select("text") + .style("fill-opacity", 1) + .style("font-size", fontSize) + .text(function(d) { return d.name; }); + + // ------- D3 EXIT -------- + // Transition exiting nodes to the parent's new position. + var nodeExit =3Dnode.exit().transition() + .duration(duration) + .remove(); + + nodeExit.select("circle") + .attr("r", 1e-6); + + nodeExit.select("text") + .style("fill-opacity", 1e-6); + + // Stash the old positions for transition. + nodes.forEach(function(d) { + d.x0 =3D d.x; // we need the x0, y0 for parents with children + d.y0 =3D d.y; + }); + } + +}); + +var PhylovizView =3D Backbone.View.extend({ + + className: 'phyloviz', + + initialize: function(options) { + var self =3D this; + // -- Default values of the vis + self.MIN_SCALE =3D 0.05; //for zooming + self.MAX_SCALE =3D 5; + self.MAX_DISPLACEMENT =3D 500; + self.margins =3D [10, 60, 10, 80]; + + self.width =3D $("#PhyloViz").width(); + self.height =3D $("#PhyloViz").height(); + self.radius =3D self.width; + self.data =3D options.data; + + // -- Events Phyloviz view responses to + $(window).resize(function(){ + self.width =3D $("#PhyloViz").width(); + self.height =3D $("#PhyloViz").height(); + self.render(); + }); + + // -- Create phyloTree model + self.phyloTree =3D new PhyloTree(options.config); + self.phyloTree.root =3D self.data; + + // -- Set up UI functions of main view + self.zoomFunc =3D d3.behavior.zoom().scaleExtent([self.MIN_SCALE, = self.MAX_SCALE]); + self.zoomFunc.translate(self.phyloTree.get("translate")); + self.zoomFunc.scale(self.phyloTree.get("scaleFactor")); + + // -- set up header buttons, search and settings menu + self.navMenu =3D new HeaderButtons(self); + self.settingsMenu =3D new SettingsMenu({phyloTree : self.phyloTree= }); + self.nodeSelectionView =3D new NodeSelectionView({phyloTree : self= .phyloTree}); + self.search =3D new PhyloVizSearch(); + + + setTimeout(function(){ // using settimeout to call the zoomAn= dPan function according to the stored attributes in viz_config + self.zoomAndPan(); + }, 1000); + }, + + render: function(){ + // -- Creating helper function for vis. -- + var self =3D this; + $("#PhyloViz").empty(); + + // -- Layout viz. -- + self.mainSVG =3D d3.select("#PhyloViz").append("svg:svg") + .attr("width", self.width) + .attr("height", self.height) + .attr("pointer-events", "all") + .call(self.zoomFunc.on("zoom", function(){ + self.zoomAndPan(); + })); + + self.boundingRect =3D self.mainSVG.append("svg:rect") + .attr("class", "boundingRect") + .attr("width", self.width) + .attr("height", self.height) + .attr("stroke", "black") + .attr("fill", "white"); + + self.vis =3D self.mainSVG + .append("svg:g") + .attr("class", "vis"); + + self.layoutOptions =3D { + model : self.phyloTree, + width : self.width, + height : self.height, + vis: self.vis, + margins: self.margins + }; + + // -- Creating Title + $("#title").text("Phylogenetic Tree from " + self.phyloTree.get("t= itle") + ":"); + + // -- Create Linear view instance -- + var linearView =3D new PhylovizLinearView(self.layoutOptions) + }, + + zoomAndPan : function(event){ + /** + * Function to zoom and pan the svg element which the entire tree = is contained within + * Uses d3.zoom events, and extend them to allow manual updates an= d keeping states in model + */ + if (typeof event !=3D=3D "undefined") { + var zoomParams =3D event.zoom, + translateParams =3D event.translate; + } + + var self =3D this, + scaleFactor =3D self.zoomFunc.scale(), + translationCoor =3D self.zoomFunc.translate(), + zoomStatement =3D "", + translateStatement =3D ""; + + // Do manual scaling. + switch (zoomParams) { + case "reset": + scaleFactor =3D 1.0; + translationCoor =3D [0,0]; break; + case "+": + scaleFactor *=3D 1.1; break; + case "-": + scaleFactor *=3D 0.9; break; + default: + if (typeof zoomParams =3D=3D=3D "number") { + scaleFactor =3D zoomParams; + } else if (d3.event !=3D=3D null) { + scaleFactor =3D d3.event.scale; + } + } + if (scaleFactor < self.MIN_SCALE || scaleFactor > self.MAX_SCALE) = { return;} + self.zoomFunc.scale(scaleFactor); //update scale Factor + zoomStatement =3D "translate(" + self.margins[3] + "," + self.mar= gins[0] + ")" + + " scale(" + scaleFactor + ")"; + + // Do manual translation. + if( d3.event !=3D=3D null) { + translateStatement =3D "translate(" + d3.event.translate + ")"; + } else { + if(typeof translateParams !=3D=3D "undefined") { + var x =3D translateParams.split(",")[0]; + var y =3D translateParams.split(",")[1]; + if (!isNaN(x) && !isNaN(y)){ + translationCoor =3D [translationCoor[0] + parseFloat(x= ), translationCoor[1] + parseFloat(y)]; + } + } + self.zoomFunc.translate(translationCoor); // update zoomFunc + translateStatement =3D "translate(" + translationCoor + ")"; + } + + self.phyloTree.set("scaleFactor", scaleFactor); + self.phyloTree.set("translate", translationCoor); + self.vis.attr("transform", translateStatement + zoomStatement); //= refers to the view that we are actually zooming + }, + + + reloadViz : function() { + /** + * Primes the Ajax URL to load another Nexus tree + */ + var self =3D this, + treeIndex =3D $("#phylovizNexSelector :selected").val(), + dataset_id =3D self.phyloTree.get("dataset_id"), + url =3D "phyloviz/getJsonData?dataset_id=3D" + dataset_id + "&= treeIndex=3D" + String(treeIndex); + $.getJSON(url, function(packedJson){ + window.initPhyloViz(packedJson.data, packedJson.config); + }); + } +}); + + +var HeaderButtons =3D Backbone.View.extend({ + + initialize : function(phylovizView){ + var self =3D this; + self.phylovizView =3D phylovizView; + + // Clean up code - if the class initialized more than once + $("#panelHeaderRightBtns").empty(); + $("#phyloVizNavBtns").empty(); + $("#phylovizNexSelector").off(); + + self.initNavBtns(); + self.initRightHeaderBtns(); + + // Initial a tree selector in the case of nexus + $("#phylovizNexSelector").off().on("change", function() {self.phy= lovizView.reloadViz();} ); + + }, + + initRightHeaderBtns : function(){ + var self =3D this; + + rightMenu =3D create_icon_buttons_menu([ + { icon_class: 'gear', title: 'PhyloViz Settings', on_click: fu= nction(){ + $("#SettingsMenu").show(); + self.settingsMenu.updateUI(); + } }, + { icon_class: 'disk', title: 'Save visualization', on_click: f= unction() { + var nexSelected =3D $("#phylovizNexSelector option:selecte= d").text(); + if(nexSelected) { + self.phylovizView.phyloTree.set("title", nexSelected); + } + self.phylovizView.phyloTree.save(); + } }, + { icon_class: 'chevron-expand', title: 'Search / Edit Nodes', = on_click: function() { + $("#nodeSelectionView").show(); + } }, + { icon_class: 'information', title: 'Phyloviz Help', on_click:= function() { + window.open('http://wiki.g2.bx.psu.edu/Learn/Visualization= /PhylogeneticTree'); + // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs= 3EyMe1B1X_KFPouzIgrCz3zk/edit + } } + ], + { + tooltip_config: { placement: 'bottom' } + }); + $("#panelHeaderRightBtns").append(rightMenu.$el); + }, + + initNavBtns: function() { + var self =3D this, + navMenu =3D create_icon_buttons_menu([ + { icon_class: 'zoom-in', title: 'Zoom in', on_click: funct= ion() { + self.phylovizView.zoomAndPan({ zoom : "+"}); + } }, + { icon_class: 'zoom-out', title: 'Zoom out', on_click: fun= ction() { + self.phylovizView.zoomAndPan({ zoom : "-"}); + } }, + { icon_class: 'arrow-circle', title: 'Reset Zoom/Pan', on_= click: function() { + self.phylovizView.zoomAndPan({ zoom : "reset"}); + } } + ], + { + tooltip_config: { placement: 'bottom' } + }); + $("#phyloVizNavBtns").append(navMenu.$el); + } +}); + + +var SettingsMenu =3D UserMenuBase.extend({ + + className: 'Settings', + + initialize: function(options){ + // settings needs to directly interact with the phyloviz model so = it will get access to it. + var self =3D this; + self.phyloTree =3D options.phyloTree; + self.el =3D $("#SettingsMenu"); + self.inputs =3D { + separation : $("#phyloVizTreeSeparation"), + leafHeight : $("#phyloVizTreeLeafHeight"), + fontSize : $("#phyloVizTreeFontSize") + }; + + //init all buttons of settings + $("#settingsCloseBtn").off().on("click", function() { self.el.hide= (); }); + $("#phylovizResetSettingsBtn").off().on("click", function() { self= .resetToDefaults(); }); + $("#phylovizApplySettingsBtn").off().on("click", function() { self= .apply(); }); + }, + + apply : function(){ + /** + * Applying user values to phylotree model. + */ + var self =3D this; + if (!self.isAcceptableValue(self.inputs["separation"], 50, 2500) || + !self.isAcceptableValue(self.inputs["leafHeight"], 5, 30) || + !self.isAcceptableValue(self.inputs["fontSize"], 5, 20)){ + return; + } + $.each(self.inputs, function(key, $input){ + self.phyloTree.set(key, $input.val()); + }); + }, + updateUI : function(){ + /** + * Called to update the values input to that stored in the model + */ + var self =3D this; + $.each(self.inputs, function(key, $input){ + $input.val(self.phyloTree.get(key)); + }); + }, + resetToDefaults : function(){ + /** + * Resets the value of the phyloTree model to its default + */ + $(".bs-tooltip").remove(); // just in case the tool tip was n= ot removed + var self =3D this; + $.each(self.phyloTree.defaults, function(key, value) { + self.phyloTree.set(key, value); + }); + self.updateUI(); + }, + + render: function(){ + + } + +}); + + +var NodeSelectionView =3D UserMenuBase.extend({ + /** + * View for inspecting node properties and editing them + */ + className: 'Settings', + + initialize : function (options){ + var self =3D this; + self.el =3D $("#nodeSelectionView"); + self.phyloTree =3D options.phyloTree; + + self.UI =3D { + enableEdit : $('#phylovizEditNodesCheck'), + saveChanges : $('#phylovizNodeSaveChanges'), + cancelChanges : $("#phylovizNodeCancelChanges"), + name : $("#phyloVizSelectedNodeName"), + dist : $("#phyloVizSelectedNodeDist"), + annotation : $("#phyloVizSelectedNodeAnnotation") + }; + + self.valuesOfConcern =3D { + name : null, + dist : null, + annotation : null + }; // temporarily stores the values in case user change their mind + + //init UI buttons + $("#nodeSelCloseBtn").off().on("click", function() { self.el.hide(= ); }); + self.UI.saveChanges.off().on("click", function(){ self.updateNodes= (); }); + self.UI.cancelChanges.off().on("click", function(){ self.cancelCha= nges(); }); + + (function ($) { + // extending jquery fxn for enabling and disabling nodes. + $.fn.enable =3D function (isEnabled) { + return $(this).each(function () { + if(isEnabled){ + $(this).removeAttr('disabled'); + } else { + $(this).attr('disabled', 'disabled'); + } + }); + }; + })(jQuery); + + self.UI.enableEdit.off().on("click", function () { + self.toggleUI(); + }); + }, + + toggleUI : function(){ + /** + * For turning on and off the child elements + */ + var self =3D this, + checked =3D self.UI.enableEdit.is(':checked'); + + !checked ? self.cancelChanges() : ""; + + $.each(self.valuesOfConcern, function(key, value) { + self.UI[key].enable(checked); + }); + if(checked){ + self.UI.saveChanges.show(); + self.UI.cancelChanges.show(); + } else { + self.UI.saveChanges.hide(); + self.UI.cancelChanges.hide(); + } + + }, + + cancelChanges : function() { + /** + * Reverting to previous values in case user change their minds + */ + var self =3D this, + node =3D self.phyloTree.get("selectedNode"); + if (node){ + $.each(self.valuesOfConcern, function(key, value) { + self.UI[key].val(node[key]); + }); + } + }, + + updateNodes : function (){ + /** + * Changing the data in the underlying tree with user-specified va= lues + */ + var self =3D this, + node =3D self.phyloTree.get("selectedNode"); + if (node){ + if (!self.isAcceptableValue(self.UI.dist, 0, 1) || + self.hasIllegalJsonCharacters(self.UI.name) || + self.hasIllegalJsonCharacters(self.UI.annotation) ) { + return; + } + $.each(self.valuesOfConcern, function(key, value) { + (node[key]) =3D self.UI[key].val(); + }); + self.phyloTree.set("nodeAttrChangedTime", new Date()); + } else { + alert("No node selected"); + } + } + + +}); + + + +var PhyloVizSearch =3D UserMenuBase.extend({ + /** + * Initializes the search panel on phyloviz and handles its user inter= action + * It allows user to search the entire free based on some qualifer, li= ke dist <=3D val. + */ + initialize : function () { + var self =3D this; + + $("#phyloVizSearchBtn").on("click", function(){ + var searchTerm =3D $("#phyloVizSearchTerm"), + searchConditionVal =3D $("#phyloVizSearchCondition").val()= .split("-"), + attr =3D searchConditionVal[0], + condition =3D searchConditionVal[1]; + self.hasIllegalJsonCharacters(searchTerm); + + if (attr =3D=3D=3D "dist"){ + self.isAcceptableValue(searchTerm, 0, 1); + } + self.searchTree(attr, condition, searchTerm.val()); + }); + }, + + searchTree : function (attr, condition, val){ + /** + * Searches the entire tree and will highlight the nodes that matc= h the condition in green + */ + d3.selectAll("g.node") + .classed("searchHighlight", function(d){ + var attrVal =3D d[attr]; + if (typeof attrVal !=3D=3D "undefined" && attrVal !=3D=3D = null){ + if (attr =3D=3D=3D "dist"){ + switch (condition) { + case "greaterEqual": + return attrVal >=3D +val; + case "lesserEqual": + return attrVal <=3D +val; + default: + return; + } + + } else if (attr =3D=3D=3D "name" || attr =3D=3D=3D "an= notation") { + return attrVal.toLowerCase().indexOf(val.toLowerCa= se()) !=3D=3D -1; + } + } + }); + } +}); \ No newline at end of file diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -272,6 +272,17 @@ } =20 init_trackster_links(); + + function init_phyloviz_links() { + // PhyloViz links + // Add to trackster browser functionality + $(".phyloviz-add").live("click", function() { + var dataset =3D this, + dataset_jquery =3D $(this); + window.parent.location =3D dataset_jquery.attr("new-url"); + }); + } + init_phyloviz_links(); =20 // History rename functionality. async_save_text("history-name-container", "history-name", "${h.url_for= ( controller=3D"/history", action=3D"rename_async", id=3Dtrans.security.enc= ode_id(history.id) )}", "new_name", 18); diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -29,6 +29,9 @@ ## Render the dataset `data` as history item, using `hid` as the displayed= id <%def name=3D"render_dataset( data, hid, show_deleted_on_refresh =3D False= , for_editing =3D True, display_structured =3D False )"><% + + from galaxy.datatypes.xml import Phyloxml + from galaxy.datatypes.data import Newick, Nexus dataset_id =3D trans.security.encode_id( data.id ) =20 if data.state in ['no state','',None]: @@ -230,6 +233,14 @@ action-url=3D"${h.url_for( controller=3D't= racks', action=3D'browser', dataset_id=3Ddataset_id)}" new-url=3D"${h.url_for( controller=3D'trac= ks', action=3D'index', dataset_id=3Ddataset_id, default_dbkey=3Ddata.dbkey)= }" title=3D"View in Trackster"></a> %endif + <% + isPhylogenyData =3D isinstance(data.datatype, = (Phyloxml, Nexus, Newick)) + %> + %if isPhylogenyData: + <a href=3D"javascript:void(0)" class=3D"i= con-button chart_curve phyloviz-add" + action-url=3D"${h.url_for( controller= =3D'phyloviz', action=3D'-', dataset_id=3Ddataset_id)}" + new-url=3D"${h.url_for( controller=3D'p= hyloviz', action=3D'index', dataset_id=3Ddataset_id)}" title=3D"View in Phy= loviz"></a> + %endif %if trans.user: %if not display_structured: <div style=3D"float: right"> diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 templates/visualization/phyloviz.mako --- /dev/null +++ b/templates/visualization/phyloviz.mako @@ -0,0 +1,320 @@ +<%inherit file=3D"/webapps/galaxy/base_panels.mako"/> +## +<%def name=3D"init()"> + <% + self.has_left_panel=3DFalse + self.has_right_panel=3DFalse + self.active_view=3D"visualization" + self.message_box_visible=3DFalse + %> +</%def> + +<%def name=3D"stylesheets()"> + ${parent.stylesheets()} + <style> + + .node circle { + cursor: pointer; + fill: #fff; + stroke: steelblue; + stroke-width: 1.5px; + } + + .node.searchHighlight circle { + stroke-width: 3px; + stroke: #7adc26; + } + + .node.selectedHighlight circle { + stroke-width: 3px; + stroke: #dc143c; + } + + path.link { + fill: none; + stroke: #B5BBFF; + stroke-width: 4.0px; + } + + + div #phyloVizNavContainer{ + text-align: center; + width: 100%; + height: 0px; + } + + div #phyloVizNav{ + font-weight: bold; + display: inline-block; + background: transparent; + top: -2em; + position: relative; + } + + div .navControl{ + float: left; + } + + div#FloatingMenu { + left: 0; + top: 15%; + width:20%; + z-index:100; + padding: 5px; + + } + + div#SettingsMenu { + width: 25%; + top: 350px; + + } + + div#nodeSelectionView { + width: 25%; + top:70px; + } + + .Panel { + right: 0%; + z-index: 101; + position: fixed; + + ## Borrowed from galaxy modal_dialogues + background-color: white; + border: 1px solid #999; + border: 1px solid rgba(0, 0, 0, 0.3); + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; + } + + span.PhylovizCloseBtn{ + cursor: pointer; + float : right; + } + + #PhyloViz{ + width: 100%; + height: 95%; + } + + h2.PhyloVizMenuTitle{ + color: white; + } + + ## Settings Menu + .SettingMenuRows{ + margin: 2px 0 2px 0; + } + + + ## Helper Styles + .PhyloVizFloatLeft{ + float : left; + } + .icon-button.zoom-in,.icon-button.zoom-out{display:inline-block;he= ight:16px;width:16px;margin-bottom:-3px;cursor:pointer;} + .icon-button.zoom-out{background:transparent url(../images/fugue/m= agnifier-zoom-out.png) center center no-repeat;} + .icon-button.zoom-in{margin-left:10px;background:transparent url(.= ./images/fugue/magnifier-zoom.png) center center no-repeat;} + + </style> +</%def> + + +<%def name=3D"javascripts()"> + ${parent.javascripts()} + ${h.js( "galaxy.panels", "libs/d3", "mvc/data", "viz/visualization", "= viz/phyloviz")} +</%def> + + + +<%def name=3D"center_panel()"> + + <div class=3D"unified-panel-header" unselectable=3D"on"> + <div class=3D"unified-panel-header-inner"> + <div style=3D"float:left;" id=3D"title"></div> + <div style=3D"float:right;" id=3D"panelHeaderRightBtns"></div> + </div> + <div style=3D"clear: both"></div> + </div> + + + <div id=3D"phyloVizNavContainer"> + <div id=3D"phyloVizNav"> + %if config["ext"] =3D=3D "nex" and not config["saved_visualiza= tion"]: + <div id =3D "phylovizNexInfo" class=3D"navControl"> + <p>Select a tree to view:    + <select id=3D"phylovizNexSelector"> + % for tree, index in config["trees"]: + <option value=3D"${index}">${tree}</option> + % endfor + </select> + </p> + </div> + %endif + <div id=3D"phyloVizNavBtns" class=3D"navControl"> + </div> + <div class=3D"navControl"> + <p> | Alt+click to select nodes</p> + </div> + + + </div> + + </div> + + ## Node Selection Menu + <div id=3D"nodeSelectionView" class=3D"Panel"> + <div class=3D"modal-header"> + <h3 class=3D"PhyloVizMenuTitle">Search / Edit Nodes : + <span class=3D"PhylovizCloseBtn" id=3D"nodeSelCloseBtn"> X= </span> + </h3> + </div> + + <div class=3D"modal-body"> + + <div class=3D"SettingMenuRows"> + Search for nodes with: + <select id=3D"phyloVizSearchCondition" style=3D"width: 55%= "> + <option value=3D"name-containing">Name (containing)</o= ption> + <option value=3D"annotation-containing">Annotation (co= ntaining)</option> + <option value=3D"dist-greaterEqual">Distance (>=3D)</o= ption> + <option value=3D"dist-lesserEqual">Distance (<=3D)</op= tion> + </select> + <input type=3D"text" id=3D"phyloVizSearchTerm" value=3D"N= one" size=3D"15" displayLabel=3D"Distance"> + + <div class=3D"SettingMenuRows" style=3D"text-align: center= ;"> + <button id=3D"phyloVizSearchBtn" > Search! </button> + </div> + </div> + + <br/> + + <div class=3D"SettingMenuRows"> + Name: <input type=3D"text" id=3D"phyloVizSelectedNodeName"= value=3D"None" size=3D"15" disabled=3D"disabled" > + </div> + <div class=3D"SettingMenuRows"> + Dist: <input type=3D"text" id=3D"phyloVizSelectedNodeDist"= value=3D"None" size=3D"15" disabled=3D"disabled" displayLabel=3D"Distance"> + </div> + <div class=3D"SettingMenuRows"> + Annotation: + <textarea id=3D"phyloVizSelectedNodeAnnotation" disabled= =3D"disabled" ></textarea> + </div> + <div class=3D"SettingMenuRows"> + Edit: <input type=3D"checkbox" id=3D"phylovizEditNodesChec= k" value=3D"You can put custom annotations here and it will be saved"> + <button id=3D"phylovizNodeSaveChanges" style=3D"display: n= one;"> Save edits</button> + <button id=3D"phylovizNodeCancelChanges" style=3D"display:= none;"> Cancel</button> + </div> + </div> + </div> + + ## Settings Menus + <div id=3D"SettingsMenu" class=3D"Panel"> + <div class=3D"modal-header"> + <h3 class=3D"PhyloVizMenuTitle">Phyloviz Settings: + <span class=3D"PhylovizCloseBtn" id=3D"settingsCloseBtn"> = X </span> + </h3> + </div> + <div class=3D"modal-body"> + <div class=3D"SettingMenuRows"> + Phylogenetic Spacing (px per unit): <input id=3D"phyloVizT= reeSeparation" type=3D"text" value=3D"250" size=3D"10" displayLabel=3D"Phyl= ogenetic Separation"> (50-2500) + </div> + <div class=3D"SettingMenuRows"> + Vertical Spacing (px): <input type=3D"text" id=3D"phyloViz= TreeLeafHeight" value=3D"18" size=3D"10" displayLabel=3D"Vertical Spacing">= (5-30) + </div> + <div class=3D"SettingMenuRows"> + Font Size (px): <input type=3D"text" id=3D"phyloVizTreeFon= tSize" value=3D"12" size=3D"4" displayLabel=3D"Font Size"> (5-20) + </div> + + </div> + <div class=3D"modal-footer"> + <button id=3D"phylovizResetSettingsBtn" class=3D"PhyloVizFloat= Left" > Reset </button> + <button id=3D"phylovizApplySettingsBtn" class=3D"PhyloVizFloat= Right" > Apply </button> + </div> + </div> + + + + + + + <div class=3D"Panel" id=3D"FloatingMenu" style=3D"display: None;"> + + <h2>PhyloViz (<a onclick=3D"displayHelp()" href=3D"javascript:void= (0);">?</a>)</h2> + <div style=3D"display: none;"> + <h2>Summary of Interactions and Functions:</h2> + <div class=3D"hint">1. Expansion of Nodes: click or option-cli= ck to expand or collapse</div> + <div class=3D"hint">2. Zooming and translation: mousewheel, bu= ttons, click and drag, double click. Reset</div> + <div class=3D"hint">3. Tooltip: Displays "Name and Size" on mo= useOver on nodes</div> + <div class=3D"hint">4. Minimap: Currently displays an exact bu= t scaled down replicate of the tree, orange bounding box is correct for lin= ear only<br/> + Can be switched on or off</div> + <div class=3D"hint">5. Changing Layouts: Able to change betwee= n circular and linear layouts.</div> + + </div> + + <h5>Scaling & Rotation:</h5> + <button id=3D"phylovizZoomInBtn" class=3D"" > + </button> + <button id=3D"phylovizZoomOutBtn" class=3D"" > - </button> + + + <h5>Translation:</h5> + <button id=3D"phylovizTranslateUpBtn" > Up </button> + <button id=3D"phylovizTranslateDownBtn" > Down </button> + <br/> + <button id=3D"phylovizTranslateLeftBtn" > Left </button> + <button id=3D"phylovizTranslateRightBtn" > Right </button> + + + + <h5>Others:</h5> + <button id=3D"phylovizResetBtn" > Reset Zoom/Translate </button> + <button id=3D"phylovizSaveBtn" > Save vizualization </button> + <button id=3D"phylovizOpenSettingsBtn" > Settings </button> + </div> + + <div id=3D"PhyloViz" > + </div> + + <script type=3D"text/javascript"> + + function initPhyloViz(data, config) { + var phyloviz; + + // -- Initialization code |--> + phyloviz =3D new PhylovizView({ + data: data, + layout : "Linear", + config : config + }); + + // -- Render viz. -- + phyloviz.render(); + + } + + $(function firstVizLoad(){ // calls when viz is loaded for t= he first time + var config =3D JSON.parse( '${ h.to_json_string( config )}'); + var data =3D JSON.parse('${h.to_json_string(data)}'); + initPhyloViz(data, config); + }); + + </script> + +</%def> + + diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 test-data/visualization/phyloviz/1_nexus.nex --- /dev/null +++ b/test-data/visualization/phyloviz/1_nexus.nex @@ -0,0 +1,87 @@ +#NEXUS + +[!This data set was downloaded from TreeBASE, a relational database of phy= logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer= sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl= edgment from the Nexus file. + + +Generated on June 12, 2012; 23:00 GMT + +TreeBASE (cc) 1994-2008 + +Study reference: +Olariaga I., Grebenc T., Salcedo I., & Mart=C3=ADn M.P. 2012. Two new spec= ies of Hydnum +with ovoid basidiospores: H. ovoideisporum and H. vesterholtii. Mycologia,= . + +TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S128= 31] + +BEGIN TREES; + TITLE Hydnum_ITS_result; + LINK TAXA =3D Taxa1; + TRANSLATE + 1 Hydnum_aff_ellipsosporum_RUFHYD1_AJ535304, + 2 Hydnum_albidum_ALB_AY817135, + 3 Hydnum_albidum_ALBHYD1_AJ534974, + 4 Hydnum_albomagnum_ALM_DQ218305, + 5 Hydnum_ellipsosporum_ELL_AY817138, + 6 Hydnum_ellipsosporum_RUFHYD8_AJ547882, + 7 Hydnum_ovoidisporum_12317BIOFungi, + 8 Hydnum_ovoidisporum_12683BIOFungi, + 9 Hydnum_ovoidisporum_12902BIOFungi, + 10 Hydnum_ovoidisporum_14130BIOFungi, + 11 Hydnum_repandum_RE1_REP1_AJ889978, + 12 Hydnum_repandum_RE1_REP2_AJ889949, + 13 Hydnum_repandum_RE1_REP3_AY817136, + 14 Hydnum_repandum_RE1_REP6_UDB000025, + 15 Hydnum_repandum_RE1_REP7_UDB000096, + 16 Hydnum_repandum_RE1_REP8_UDB001479, + 17 Hydnum_repandum_RE1_REPHYD10_AJ547888, + 18 Hydnum_repandum_RE1_REPHYD11_AJ547886, + 19 Hydnum_repandum_RE1_REPHYD1_AJ547871, + 20 Hydnum_repandum_RE1_REPHYD3_AJ547874, + 21 Hydnum_repandum_RE1_REPHYD4_AJ547876, + 22 Hydnum_repandum_RE1_REPHYD5_AJ547875, + 23 Hydnum_repandum_RE1_REPHYD6_AJ547877, + 24 Hydnum_repandum_RE1_REPHYD7_AJ547878, + 25 Hydnum_repandum_RE1_REPHYD8_AJ547881, + 26 Hydnum_repandum_RE1_REPHYD9_AJ547883, + 27 Hydnum_repandum_RE1_RUFHYD10_AJ547866, + 28 Hydnum_repandum_RE1_RUFHYD11_AJ547889, + 29 Hydnum_repandum_RE1_RUFHYD9_AJ535305, + 30 Hydnum_rufescens_RU1_RUFHYD5_AJ547869, + 31 Hydnum_rufescens_RU1_RUFHYD6_AJ547884, + 32 Hydnum_rufescens_RU1_RUFHYD7_AJ547870, + 33 Hydnum_rufescens_RU2_REP5_DQ367902, + 34 Hydnum_rufescens_RU2_RUFHYD2_AJ535301, + 35 Hydnum_rufescens_RU3_12901BIOFungi, + 36 Hydnum_rufescens_RU3_REP4_DQ218306, + 37 Hydnum_rufescens_RU3_RUFHYD3_AJ535303, + 38 Hydnum_rufescens_RU3_RUFHYD4_AJ535302, + 39 Hydnum_rufescens_RU4_RUFHYD12_AJ839969, + 40 Hydnum_rufescens_RU4_RUFHYD16_AJ547868, + 41 Hydnum_rufescens_RU4_RUFHYD17_AJ547885, + 42 Hydnum_rufescens_RU4_UMB1_DQ367903, + 43 Hydnum_rufescens_RU5_12760BIOFungi, + 44 Hydnum_rufescens_RU5_ALBHYD2_AJ534975, + 45 Hydnum_rufescens_RU5_RUF2_DQ658890, + 46 Hydnum_rufescens_RU5_RUF4_UDB001465, + 47 Hydnum_rufescens_RU5_RUF5_UDB002423, + 48 Hydnum_rufescens_RU5_RUFHYD14_AJ547872, + 49 Hydnum_rufescens_RU6_RUF1_AY817137, + 50 Hydnum_rufescens_RU6_RUFHYD15_AJ547867, + 51 Hydnum_rufescens_wrong_taxonomy_RUF3_AM087246, + 52 Hydnum_umbilicatum_UMBHYD1_AJ534972, + 53 Hydnum_umbilicatum_UMBHYD2_AJ534973, + 54 Hydnum_vesterholtii_10429BIOFungi, + 55 Hydnum_vesterholtii_10452BIOFungi, + 56 Hydnum_vesterholtii_12330BIOFungi, + 57 Hydnum_vesterholtii_12904BIOFungi, + 58 Hydnum_vesterholtii_REPHYD12A_AJ547879, + 59 Hydnum_vesterholtii_REPHYD12C_AJ783968, + 60 Hydnum_vesterholtii_REPHYD13_AJ547887, + 61 Sistotrema_muscicola_AJ606040, + 62 Sistotrema_alboluteum_AJ606042; + TREE Fig._2 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66= ,((4:100.0,(2:100.0,3:100.0):100.0):60.639999,(((56:100.0,58:100.0,59:100.0= ):84.639999,(54:100.0,55:100.0,57:100.0,60:100.0):98.330002):92.5,(((30:100= .0,31:100.0,32:100.0):100.0,(11:100.0,12:100.0,13:100.0,14:100.0,15:100.0,1= 6:100.0,17:100.0,18:100.0,19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,24:1= 00.0,25:100.0,26:100.0):99.93):68.690002,(((33:100.0,34:100.0):49.8050005,(= 35:100.0,36:100.0,37:100.0,38:100.0):99.989998):49.8050005,((7:100.0,8:100.= 0,9:100.0,10:100.0):100.0,(42:100.0,(39:100.0,40:100.0,41:100.0):98.449997)= :86.790001,((52:100.0,53:100.0):99.93,(1:100.0,(5:97.47999949999999,6:100.0= ):97.47999949999999):100.0):53.310001,(27:100.0,(28:100.0,29:100.0,49:100.0= ,50:100.0):47.404999):47.404999,(43:100.0,44:100.0,45:100.0,46:100.0,47:100= .0,48:100.0):99.459999):29.245001):29.245001):51.580002):61.540001):49.66); + TREE PAUP_1 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66= ,((4:100.0,(3:100.0,2:100.0):100.0):60.639999,(((58:100.0,59:100.0,56:100.0= ):84.639999,(60:100.0,54:100.0,55:100.0,57:100.0):98.330002):92.5,(((30:100= .0,31:100.0,32:100.0):100.0,(19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,2= 4:100.0,25:100.0,26:100.0,17:100.0,18:100.0,11:100.0,12:100.0,13:100.0,14:1= 00.0,15:100.0,16:100.0):99.93):68.690002,((34:100.0,33:100.0):99.610001,(37= :100.0,38:100.0,35:100.0,36:100.0):99.989998,(42:100.0,(39:100.0,41:100.0,4= 0:100.0):98.449997):86.790001,(8:100.0,7:100.0,9:100.0,10:100.0):100.0,((52= :100.0,53:100.0):99.93,(1:100.0,(5:100.0,6:100.0):94.959999):100.0):53.3100= 01,(29:100.0,27:100.0,28:100.0,50:100.0,49:100.0):94.809998,(44:100.0,43:10= 0.0,48:100.0,45:100.0,46:100.0,47:100.0):99.459999):58.490002):51.580002):6= 1.540001):49.66); + + + +END; diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 test-data/visualization/phyloviz/2_nexus.nex --- /dev/null +++ b/test-data/visualization/phyloviz/2_nexus.nex @@ -0,0 +1,96 @@ +#NEXUS + +[!This data set was downloaded from TreeBASE, a relational database of phy= logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer= sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl= edgment from the Nexus file. + + +Generated on August 18, 2012; 12:14 GMT + +TreeBASE (cc) 1994-2008 + +Study reference: +Naish D., Dyke G., Cau A., & Escuilli=C3=A9 F. 2012. A gigantic bird from = the Upper Cretaceous +of Central Asia. Biology Letters, 8(1): 97-100. + +TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S130= 08] + +BEGIN TREES; + TITLE Imported_trees; + LINK TAXA =3D Taxa1; + TRANSLATE + 1 Herrerasaurus, + 2 Tawa, + 3 Allosaurus, + 4 Alvarezsaurus, + 5 Anchiornis, + 6 Archaeopteryx, + 7 Archaeorhynchus, + 8 Avimimus, + 9 Baryonyx, + 10 Beipiaosaurus, + 11 Caenagnathus, + 12 Caudipteryx, + 13 Ceratosaurus, + 14 Chirostenotes, + 15 Citipati, + 16 Compsognathus, + 17 Confuciusornis, + 18 Dilong, + 19 Dilophosaurus, + 20 Epidendrosaurus, + 21 Epidexipteryx, + 22 Erlicosaurus, + 23 Eustreptospondylus, + 24 Gallimimus, + 25 Garudimimus, + 26 Gobipteryx, + 27 Guanlong, + 28 Haplocheirus, + 29 Harpymimus, + 30 Hebeiornis, + 31 Hongshanornis, + 32 Huoshanornis, + 33 Iberomesornis, + 34 Ichthyornis, + 35 Incisivosaurus, + 36 Jeholornis, + 37 Limusaurus, + 38 Longicrusavis, + 39 Longipteryx, + 40 Longirostravis, + 41 Majungasaurus, + 42 Masiakasaurus, + 43 Monolophosaurus, + 44 Mononykus, + 45 Neornithes, + 46 Ornitholestes, + 47 Ornithomimus, + 48 Patagonykus, + 49 Patagopteryx, + 50 Pelecanimimus, + 51 Pengornis, + 52 Protarchaeopteryx, + 53 Protopteryx, + 54 Rinchenia, + 55 Sapeornis, + 56 Segnosaurus, + 57 Shenzhousaurus, + 58 Shuvuuia, + 59 Sinornithosaurus, + 60 Sinosauropteryx, + 61 Sinovenator, + 62 Sinraptor, + 63 Syntarsus_kayentakatae, + 64 Troodon, + 65 Tyrannosaurus, + 66 Velociraptor, + 67 Yanornis, + 68 Yixianornis, + 69 Zhongjianornis, + 70 Zhongornis, + 71 Zuolong, + 72 Samrukia; + TREE Figure_1A =3D [&R] (1,(2,(((((43,(3,62)),(71,((46,((((28,(4,(48= ,(44,58)))),((((5,(61,(64,(59,66)))),(6,((36,(55,(69,(((7,34,45,49,72,(31,3= 8),(67,68)),(33,((32,((26,30),(39,40))),(51,53)))),(17,70))))),(20,21)))),(= (11,(12,(8,(14,(15,54))))),(35,52))),(10,(22,56)))),(50,(57,(29,(25,(24,47)= ))))),(16,60))),(27,(18,65))))),(9,23)),(13,(41,(37,42)))),(19,63)))); + + + +END; diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 test-data/visualization/phyloviz/3_phyloxml.xml --- /dev/null +++ b/test-data/visualization/phyloviz/3_phyloxml.xml @@ -0,0 +1,257 @@ +<?xml version=3D"1.0" encoding=3D"UTF-8"?> +<phyloxml xmlns:xsi=3D"http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation=3D"http://www.phyloxml.org http://www.phyloxml.org/1= .10/phyloxml.xsd" + xmlns=3D"http://www.phyloxml.org"> + <phylogeny rooted=3D"true"> + <clade> + <clade> + <branch_length>0.18105</branch_length> + <confidence type=3D"unknown">89.0</confidence> + <clade> + <branch_length>0.07466</branch_length> + <confidence type=3D"unknown">32.0</confidence> + <clade> + <branch_length>0.26168</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.22058</branch_length> + <confidence type=3D"unknown">89.0</confidence> + <clade> + <branch_length>0.28901</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.06584</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.02309</branch_length> + <confidence type=3D"unknown">43.0</confidenc= e> + <clade> + <branch_length>0.0746</branch_length> + <confidence type=3D"unknown">100.0</confi= dence> + <clade> + <branch_length>0.02365</branch_length> + <confidence type=3D"unknown">88.0</con= fidence> + <clade> + <name>22_MOUSE</name> + <branch_length>0.05998</branch_leng= th> + <taxonomy> + <code>MOUSE</code> + </taxonomy> + </clade> + <clade> + <name>Apaf-1_HUMAN</name> + <branch_length>0.01825</branch_leng= th> + <taxonomy> + <code>HUMAN</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>12_CANFA</name> + <branch_length>0.04683</branch_length> + <taxonomy> + <code>CANFA</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>11_CHICK</name> + <branch_length>0.15226</branch_length> + <taxonomy> + <code>CHICK</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>16_XENLA</name> + <branch_length>0.4409</branch_length> + <taxonomy> + <code>XENLA</code> + </taxonomy> + </clade> + </clade> + <clade> + <branch_length>0.17031</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.10929</branch_length> + <confidence type=3D"unknown">100.0</confiden= ce> + <clade> + <name>14_FUGRU</name> + <branch_length>0.02255</branch_length> + <taxonomy> + <code>FUGRU</code> + </taxonomy> + </clade> + <clade> + <name>15_TETNG</name> + <branch_length>0.09478</branch_length> + <taxonomy> + <code>TETNG</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>17_BRARE</name> + <branch_length>0.1811</branch_length> + <taxonomy> + <code>BRARE</code> + </taxonomy> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.01594</branch_length> + <confidence type=3D"unknown">53.0</confidence> + <clade> + <branch_length>0.10709</branch_length> + <confidence type=3D"unknown">68.0</confidence> + <clade> + <name>1_BRAFL</name> + <branch_length>0.26131</branch_length> + <taxonomy> + <code>BRAFL</code> + </taxonomy> + </clade> + <clade> + <name>18_NEMVE</name> + <branch_length>0.38014</branch_length> + <taxonomy> + <code>NEMVE</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>23_STRPU</name> + <branch_length>0.48179</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.34475</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>26_STRPU</name> + <branch_length>0.36374</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1319"> + <domain from=3D"18" to=3D"98" confidence=3D"= 3.4E-5">Death</domain> + <domain from=3D"189" to=3D"481" confidence= =3D"1.8E-10">NB-ARC</domain> + <domain from=3D"630" to=3D"668" confidence= =3D"8.2E-5">WD40</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>25_STRPU</name> + <branch_length>0.33137</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1947"> + <domain from=3D"143" to=3D"227" confidence= =3D"7.4E-5">Death</domain> + <domain from=3D"227" to=3D"550" confidence= =3D"2.0E-13">NB-ARC</domain> + <domain from=3D"697" to=3D"736" confidence= =3D"7.9E-4">WD40</domain> + <domain from=3D"745" to=3D"785" confidence= =3D"1.5">WD40</domain> + <domain from=3D"1741" to=3D"1836" confidence= =3D"2.0">Adeno_VII</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + </clade> + <clade> + <branch_length>1.31498</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>CED4_CAEEL</name> + <branch_length>0.13241</branch_length> + <taxonomy> + <code>CAEEL</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"714"> + <domain from=3D"7" to=3D"90" confidence=3D"9.2E= -14">CARD</domain> + <domain from=3D"116" to=3D"442" confidence=3D"5= .8E-151">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>31_CAEBR</name> + <branch_length>0.04777</branch_length> + <taxonomy> + <code>CAEBR</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"554"> + <domain from=3D"1" to=3D"75" confidence=3D"0.00= 46">CARD</domain> + <domain from=3D"101" to=3D"427" confidence=3D"2= .1E-123">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.13172</branch_length> + <confidence type=3D"unknown">45.0</confidence> + <clade> + <branch_length>0.24915</branch_length> + <confidence type=3D"unknown">95.0</confidence> + <clade> + <branch_length>0.76898</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>28_DROPS</name> + <branch_length>0.1732</branch_length> + <taxonomy> + <code>DROPS</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"535"> + <domain from=3D"112" to=3D"399" confidence= =3D"1.4E-5">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>Dark_DROME</name> + <branch_length>0.18863</branch_length> + <taxonomy> + <code>DROME</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1421"> + <domain from=3D"108" to=3D"397" confidence= =3D"2.1E-5">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + <clade> + <name>29_AEDAE</name> + <branch_length>0.86398</branch_length> + <taxonomy> + <code>AEDAE</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"423"> + <domain from=3D"109" to=3D"421" confidence=3D"9= .3E-6">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + <clade> + <name>30_TRICA</name> + <branch_length>0.97698</branch_length> + <taxonomy> + <code>TRICA</code> + </taxonomy> + </clade> + </clade> + </clade> + </clade> + </phylogeny> +</phyloxml> diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 test-data/visualization/phyloviz/4_newick.nhx --- /dev/null +++ b/test-data/visualization/phyloviz/4_newick.nhx @@ -0,0 +1,33 @@ +(((BGIOSIBCA028421_ORYSA:0.423485[&&NHX:S=3DORYSA:O=3DBGIOSIBCA028421.1:G= =3DBGIOSIBCA028421], +At5g41150_ARATH:0.273135[&&NHX:S=3DARATH:O=3DAt5g41150.1:G=3DAt5g41150] +):0.690991[&&NHX:S=3DMagnoliophyta:D=3DN:B=3D100], +(rad16_SCHPO:0.718598[&&NHX:S=3DSCHPO:O=3DSPCC970.01:G=3DSPCC970.01], +RAD1_YEAST:1.05456[&&NHX:S=3DYEAST:O=3DYPL022W.1:G=3DYPL022W] +):0.344838[&&NHX:S=3DAscomycota:D=3DN:B=3D100] +):0.103849[&&NHX:S=3DEukaryota:D=3DN:B=3D61], +((((((((ERCC4_HUMAN:0.067531[&&NHX:S=3DHUMAN:O=3DENST00000311895.3:G=3DENS= G00000175595], +Ercc4_MOUSE:0.17422[&&NHX:S=3DMOUSE:O=3DENSMUST00000023206.5:G=3DENSMUSG00= 000022545] +):0.065513[&&NHX:S=3DEuarchontoglires:D=3DN:B=3D100], +ENSMODT00000006086_MONDO:0.104633[&&NHX:S=3DMONDO:O=3DENSMODT00000006086.2= :G=3DENSMODG00000004840] +):0.083764[&&NHX:S=3DTheria:D=3DN:B=3D100], +Q5ZJP8_CHICK:0.153132[&&NHX:S=3DCHICK:O=3DENSGALT00000004716.2:G=3DENSGALG= 00000002981] +):0.057998[&&NHX:S=3DAmniota:D=3DN:B=3D100], +ENSXETT00000024054_XENTR:0.288632[&&NHX:S=3DXENTR:O=3DENSXETT00000024054.2= :G=3DENSXETG00000010991] +):0.075713[&&NHX:S=3DTetrapoda:D=3DN:B=3D100], +(zgc-63468_BRARE:0.2218[&&NHX:S=3DBRARE:O=3DENSDART00000015780.4:G=3DENSDA= RG00000014161], +NEWSINFRUT00000137921_FUGRU:0.220441[&&NHX:S=3DFUGRU:O=3DNEWSINFRUT0000013= 7921.3:G=3DNEWSINFRUG00000130312] +):0.170605[&&NHX:S=3DClupeocephala:D=3DN:B=3D100] +):0.238713[&&NHX:S=3DEuteleostomi:D=3DN:B=3D100], +ENSCINT00000011737_CIOIN:0.623567[&&NHX:S=3DCIOIN:O=3DENSCINT00000011737.2= :G=3DENSCING00000005673] +):0.07499[&&NHX:S=3DChordata:D=3DN:B=3D100], +(Sm00.scaff00195.0600_SCHMA:0.784609[&&NHX:S=3DSCHMA:O=3DSm00.scaff00195.0= 600:G=3DSm00.scaff00195.0600], +(CBG03141_CAEBR:0.093703[&&NHX:S=3DCAEBR:O=3DCBG03141:G=3DCBG03141], +NP_496498_CAEEL:0.212236[&&NHX:S=3DCAEEL:O=3DC47D12.8.1:G=3DC47D12.8] +):1.47416[&&NHX:S=3DCaenorhabditis:D=3DN:B=3D94] +):0.26906[&&NHX:S=3DBilateria:D=3DN:B=3D97] +):0.071406[&&NHX:S=3DBilateria:D=3DN:B=3D1], +(mei-9-RA_DROME:0.170289[&&NHX:S=3DDROME:O=3DCG3697-RA.3:G=3DCG3697], +GA17620-PA_DROPS:0.154817[&&NHX:S=3DDROPS:O=3DGA17620-PA:G=3DGA17620] +):0.818474[&&NHX:S=3DSophophora:D=3DN:B=3D100] +):0 +)[&&NHX:S=3DEukaryota:D=3DN]; \ No newline at end of file diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r f6d9557b6d77bde1c8049ba= ffb65374729d51b89 test-data/visualization/phyloviz/5_newick.nhx --- /dev/null +++ b/test-data/visualization/phyloviz/5_newick.nhx @@ -0,0 +1,1 @@ +(CAE_ELE_PORCN:0.303421 ,((((DRO_PER_PORCN:0.001000 ,DRO_PSE_PORCN:0.00100= 0 )67:0.141994 ,(DRO_ANA_PORCN:0.111899 ,(DRO_ERE_PORCN:0.030516 ,(DRO_MEL_= PORCN:0.021127 ,DRO_SEC_PORCN:0.021127 )38:0.030516 )35:0.111899 )18:0.1419= 94 )16:0.162611 ,(DRO_WIL_PORCN:0.152225 ,(DRO_VIR_PORCN:0.085057 ,DRO_MOJ_= PORCN:0.085057 )24:0.152225 )15:0.162611 )13:0.295081 ,(ANO_GAM_PORCN:0.287= 545 ,((CIO_INT_PORCN:0.100686 ,CIO_SAV_PORCN:0.100686 )19:0.275542 ,((LOA_L= OA_PORCN:0.036278 ,BRU_MAL_PORCN:0.036278 )29:0.272631 ,(((((DAN_RER_PORCN:= 0.086499 ,((TAK_RUB_PORCN:0.032609 ,TET_NIG_PORCN:0.032609 )32:0.048864 ,(G= AD_MOR_PORCN:0.039387 ,(ORY_LAT_PORCN:0.031729 ,(GAS_ACU_PORCN:0.021882 ,OR= E_NIL_PORCN:0.021882 )37:0.031729 )34:0.039387 )28:0.048864 )27:0.086499 )2= 3:0.119618 ,(LAT_CHA_PORCN:0.099348 ,((XEN_LAE_PORCN:0.033333 ,XEN_TRO_PORC= N:0.033333 )31:0.091250 ,(ANO_CAR_PORCN:0.086538 ,((MON_DOM_PORCN:0.014100 = ,(MAC_EUG_PORCN:0.005423 ,SAR_HAR_PORCN:0.005423 )57:0.014100 )42:0.062862 = ,(ORN_ANA_PORCN:0.057974 ,(GOR_GOR_PORCN:0.033876 ,(FEL_CAT_PORCN:0.022851 = ,(PRO_CAP_PORCN:0.019716 ,(CAV_POR_PORCN:0.018599 ,(ERI_EUR_PORCN:0.015518 = ,((DIP_ORD_PORCN:0.007231 ,(MUS_MUS_PORCN:0.001085 ,(RAT_NOR_PORCN:0.001000= ,CRI_GRI_PORCN:0.001000 )69:0.001085 )64:0.007231 )53:0.012954 ,(DAS_NOV_P= ORCN:0.011362 ,(LOX_AFR_PORCN:0.010575 ,(CAL_JAC_PORCN:0.010332 ,(OCH_PRI_P= ORCN:0.010063 ,(MIC_MUR_PORCN:0.009123 ,(SUS_SCR_PORCN:0.008880 ,(MYO_LUC_P= ORCN:0.008460 ,((CAN_FAM_PORCN:0.005423 ,AIL_MEL_PORCN:0.005423 )58:0.00809= 3 ,((PTE_VAM_PORCN:0.006508 ,BOS_TAU_PORCN:0.006508 )55:0.007494 ,((SPE_TRI= _PORCN:0.003254 ,TUP_BEL_PORCN:0.003254 )61:0.006929 ,((OTO_GAR_PORCN:0.001= 085 ,(ORY_CUN_PORCN:0.001000 ,TUR_TRU_PORCN:0.001000 )68:0.001085 )65:0.005= 965 ,(EQU_CAB_PORCN:0.003688 ,(MAC_MUL_PORCN:0.002711 ,(PAN_TRO_PORCN:0.001= 446 ,(HOM_SAP_PORCN:0.001085 ,(PON_ABE_PORCN:0.001000 ,NOM_LEU_PORCN:0.0010= 00 )70:0.001085 )66:0.001446 )63:0.002711 )62:0.003688 )60:0.005965 )56:0.0= 06929 )54:0.007494 )52:0.008093 )51:0.008460 )50:0.008880 )49:0.009123 )48:= 0.010063 )47:0.010332 )46:0.010575 )45:0.011362 )44:0.012954 )43:0.015518 )= 41:0.018599 )40:0.019716 )39:0.022851 )36:0.033876 )30:0.057974 )26:0.06286= 2 )25:0.086538 )22:0.091250 )21:0.099348 )20:0.119618 )17:0.214465 ,(BRA_FL= O_PORCN:0.189220 ,SAC_KOW_PORCN:0.189220 )12:0.214465 )11:0.257058 ,(NEM_VE= C_PORCN:0.246631 ,AMP_QUE_PORCN:0.246631 )9:0.257058 )8:0.266904 ,(TRI_CAS_= PORCN:0.259494 ,(PED_HUM_PORCN:0.227009 ,(NAS_VIT_PORCN:0.160241 ,(API_MEL_= PORCN:0.031851 ,(BOM_TER_PORCN:0.004808 ,BOM_IMP_PORCN:0.004808 )59:0.03185= 1 )33:0.160241 )14:0.227009 )10:0.259494 )7:0.266904 )6:0.272631 )5:0.27554= 2 )4:0.287545 )3:0.295081 )2:0.303421 )1:0.0001; https://bitbucket.org/galaxy/galaxy-central/changeset/75a03bacdc7a/ changeset: 75a03bacdc7a user: jgoecks date: 2012-08-27 20:08:55 summary: Merged in Tomithy/galaxy-central-phyloviz-2 (pull request #65) affected #: 19 files diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -719,7 +719,49 @@ pass =20 class Newick( Text ): - pass + """New Hampshire/Newick Format""" + file_ext =3D "nhx" + + MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu= mns", readonly=3DTrue ) + + def __init__(self, **kwd): + """Initialize foobar datatype""" + Text.__init__(self, **kwd) + + def init_meta( self, dataset, copy_from=3DNone ): + Text.init_meta( self, dataset, copy_from=3Dcopy_from ) + + + def sniff( self, filename ): + """ Returning false as the newick format is too general and cannot= be sniffed.""" + return False + + +class Nexus( Text ): + """Nexus format as used By Paup, Mr Bayes, etc""" + file_ext =3D "nex" + + MetadataElement( name=3D"columns", default=3D3, desc=3D"Number of colu= mns", readonly=3DTrue ) + + def __init__(self, **kwd): + """Initialize foobar datatype""" + Text.__init__(self, **kwd) + + def init_meta( self, dataset, copy_from=3DNone ): + Text.init_meta( self, dataset, copy_from=3Dcopy_from ) + + + def sniff( self, filename ): + """All Nexus Files Simply puts a '#NEXUS' in its first line""" + f =3D open(filename, "r") + firstline =3D f.readline().upper() + f.close() + + if "#NEXUS" in firstline: + return True + else: + return False + =20 # ------------- Utility methods -------------- =20 diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -76,3 +76,24 @@ dataset.blurb =3D 'file purged from disk' def sniff( self, filename ): return False + +class Phyloxml( GenericXml ): + """Format for defining phyloxml data http://www.phyloxml.org/""" + file_ext =3D "phyloxml" + def set_peek( self, dataset, is_multi_byte=3DFalse ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek =3D data.get_file_peek( dataset.file_name, is_mul= ti_byte=3Dis_multi_byte ) + dataset.blurb =3D 'Phyloxml data' + else: + dataset.peek =3D 'file does not exist' + dataset.blurb =3D 'file purged from disk' + + def sniff( self, filename ): + """"Checking for keyword - 'phyloxml' always in lowercase in the f= irst few lines""" + f =3D open(filename, "r") + firstlines =3D "".join(f.readlines(5)) + f.close() + if "phyloxml" in firstlines: + return True + return False \ No newline at end of file diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/visualization/phyloviz/__init__.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/__init__.py @@ -0,0 +1,1 @@ +__author__ =3D 'Tomithy' diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/visualization/phyloviz/baseparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/baseparser.py @@ -0,0 +1,125 @@ +import json + +class Node(object): + """Node class of PhyloTree, which represents a CLAUDE in a phylogeneti= c tree""" + def __init__(self, nodeName, **kwargs): + """Creates a node and adds in the typical annotations""" + self.name, self.id =3D nodeName, kwargs.get("id", 0) + self.depth =3D kwargs.get("depth", 0) + self.children =3D [] + + self.isInternal =3D kwargs.get("isInternal", 0) + self.length, self.bootstrap =3D kwargs.get("length", 0), kwargs.ge= t("bootstrap", None) + self.events =3D kwargs.get("events", "") + + # clean up boot strap values + if self.bootstrap =3D=3D -1: + self.bootstrap =3D None + + def addChildNode(self, child): + """Adds a child node to the current node""" + if isinstance(child, Node): + self.children.append(child) + else: + self.children +=3D child + + + def __str__(self): + return self.name + " id:" + str(self.id) + ", depth: " + str(self.= depth) + + + def toJson(self): + """Converts the data in the node to a dict representation of json"= "" + thisJson =3D { + "name" : self.name, + "id" : self.id, + "depth" : self.depth, + "dist" : self.length + } + thisJson =3D self.addChildrenToJson(thisJson) + thisJson =3D self.addMiscToJson(thisJson) + return thisJson + + def addChildrenToJson(self, jsonDict): + """Needs a special method to addChildren, such that the key does n= ot appear in the Jsondict when the children is empty + this requirement is due to the layout algorithm used by d3 layout = for hiding subtree """ + if len(self.children) > 0: + children =3D [ node.toJson() for node in self.children] + jsonDict["children"] =3D children + return jsonDict + + + def addMiscToJson(self, jsonDict): + """Adds other misc attributes to json if they are present""" + if not self.events =3D=3D "": + jsonDict["events"] =3D self.events + if not self.bootstrap =3D=3D None: + jsonDict["bootstrap"] =3D self.bootstrap + return jsonDict + + + +class PhyloTree(object): + """Standardized python based class to represent the phylogenetic tree = parsed from different + phylogenetic file formats.""" + + def __init__(self): + self.root, self.rootAttr =3D None, {} + self.nodes =3D {} + self.title =3D None + self.id =3D 1 + + def addAttributesToRoot(self, attrDict): + """Adds attributes to root, but first we put it in a temp store an= d bind it with root when .toJson is called""" + for key, value in attrDict.items(): + self.rootAttr[key] =3D value + + def makeNode(self, nodeName, **kwargs): + """Called to make a node within PhyloTree, arbitrary kwargs can be= passed to annotate nodes + Tracks the number of nodes via internally incremented id""" + kwargs["id"] =3D self.id + self.id +=3D 1 + return Node(nodeName, **kwargs) + + def addRoot(self, root): + """Creates a root for phyloTree""" + assert isinstance(root, Node) + root.parent =3D None + self.root =3D root + + def generateJsonableDict(self): + """Changes itself into a dictonary by recurssively calling the toj= son on all its nodes. Think of it + as a dict in an array of dict in an array of dict and so on...""" + jsonTree =3D "" + if self.root: + assert isinstance(self.root, Node) + jsonTree =3D self.root.toJson() + for key, value in self.rootAttr.items(): + # transfer temporary stored attr to root + jsonTree[key] =3D value + else: + raise Exception("Root is not assigned!") + return jsonTree + + + +class Base_Parser(object): + """Base parsers contain all the methods to handle phylogeny tree creat= ion and + converting the data to json that all parsers should have""" + + def __init__(self): + self.phyloTrees =3D [] + + def parseFile(self, filePath): + """Base method that all phylogeny file parser should have""" + raise Exception("Base method for phylogeny file parsers is not imp= lemented") + + def toJson(self, jsonDict): + """Convenience method to get a json string from a python json dict= """ + return json.dumps(jsonDict) + + def _writeJsonToFile(self, filepath, json): + """Writes the file out to the system""" + f =3D open(filepath, "w") + f.writelines(json) + f.close() diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/visualization/phyloviz/newickparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/newickparser.py @@ -0,0 +1,185 @@ +from baseparser import Base_Parser, PhyloTree +import re + +class Newick_Parser(Base_Parser): + """For parsing trees stored in the newick format (.nhx) + It is necessarily more complex because this parser is later extended b= y Nexus for parsing newick as well..""" + + + def __init__(self): + super(Newick_Parser, self).__init__() + + + def parseFile(self, filePath): + """Parses a newick file to obtain the string inside. Returns: json= ableDict""" + with open(filePath, "r") as newickFile: + newickString =3D newickFile.read() + newickString =3D newickString.replace("\n", "").replace("\r", = "") + return [self.parseData(newickString)], "Success" + + + def parseData(self, newickString): + """To be called on a newickString directly to parse it. Returns: j= sonableDict""" + return self._parseNewickToJson(newickString) + + + def _parseNewickToJson(self, newickString, treeName=3DNone, nameMap=3D= None): + """parses a newick representation of a tree into a PhyloTree data = structure, + which can be easily converted to json""" + self.phyloTree =3D PhyloTree() + newickString =3D self.cleanNewickString(newickString) + if nameMap: + newickString =3D self._mapName(newickString, nameMap) + + self.phyloTree.root =3D self.parseNode(newickString, 0) + if nameMap: + self.phyloTree.addAttributesToRoot({"treeName": treeName}) + + return self.phyloTree.generateJsonableDict() + + + def cleanNewickString(self, rawNewick): + """removing semi colon, and illegal json characters (\,',") and wh= ite spaces""" + return re.sub(r'\s|;|\"|\'|\\', '', rawNewick) + + + def _makeNodesFromString(self, string, depth): + """elements separated by comma could be empty""" + + if string.find("(") !=3D -1: + raise Exception("Tree is not well form, location: " + string) + + childrenString =3D string.split(",") + childrenNodes =3D [] + + for childString in childrenString: + if len(childString) =3D=3D 0: + continue + nodeInfo =3D childString.split(":") + name, length, bootstrap =3D "", None, -1 + if len(nodeInfo) =3D=3D 2: # has length info + length =3D nodeInfo[1] + # checking for bootstap values + name =3D nodeInfo[0] + try: # Nexus may bootstrap in names position + name =3D float(name) + if 0<=3D name <=3D 1: + bootstrap =3D name + elif 1 <=3D name <=3D 100: + bootstrap =3D name / 100 + name =3D "" + except ValueError: + name =3D nodeInfo[0] + else: + name =3D nodeInfo[0] # string only contains name + node =3D self.phyloTree.makeNode(name, length=3Dlength, depth= =3Ddepth, bootstrap=3D bootstrap) + childrenNodes +=3D [node] + return childrenNodes + + + + def _mapName(self, newickString, nameMap): + """ + Necessary to replace names of terms inside nexus representation + Also, its here because Mailaud's doesnt deal with id_strings outsi= de of quotes(" ") + """ + newString =3D "" + start =3D 0 + end =3D 0 + + for i in xrange(len(newickString)): + if newickString[i] =3D=3D "(" or newickString[i] =3D=3D ",": + if re.match(r"[,(]", newickString[i+1:]): + continue + else: + end =3D i + 1 + # i now refers to the starting position of the term to= be replaced, + # we will next find j which is the ending pos of the t= erm + for j in xrange(i+1, len(newickString)): + enclosingSymbol =3D newickString[j] # the immedi= ate symbol after a common or left bracket which denotes the end of a term + if enclosingSymbol =3D=3D ")" or enclosingSymbol = =3D=3D ":" or enclosingSymbol =3D=3D ",": + termToReplace =3D newickString[end:j] + + newString +=3D newickString[start : end] + na= meMap[termToReplace] #+ "'" "'" + + start =3D j + break + + newString +=3D newickString[start:] + return newString + + + def parseNode(self, string, depth): + """ Recursive method for parsing newick string, works by stripping= down the string into substring + of newick contained with brackers, which is used to call itself. + Eg ... ( A, B, (D, E)C, F, G ) ... + We will make the preceeding nodes first A, B, then the internal no= de C, its children D, E, + and finally the succeeding nodes F, G""" + + # Base case where there is only an empty string + if string =3D=3D "": + return + # Base case there its only an internal claude + if string.find("(") =3D=3D -1: + return self._makeNodesFromString(string, depth) + + nodes, children =3D [], [] # nodes refer to the nodes on this= level, children refers to the child of the + start =3D 0 + lenOfPreceedingInternalNodeString =3D 0 + bracketStack =3D [] + + for j in xrange(len(string)): + if string[j] =3D=3D "(": #finding the positions of all the = open brackets + bracketStack.append(j) + continue + if string[j] =3D=3D ")": #finding the positions of all the = closed brackets to extract claude + i =3D bracketStack.pop() + + if len(bracketStack) =3D=3D 0: # is child of current node + + InternalNode =3D None + + #First flat call to make nodes of the same depth but f= rom the preceeding string. + startSubstring =3D string[start + lenOfPreceedingInter= nalNodeString: i] + preceedingNodes =3D self._makeNodesFromString(startSu= bstring, depth) + nodes +=3D preceedingNodes + + # Then We will try to see if the substring has any int= ernal nodes first, make it then make nodes preceeding it and succeeding it. + if j + 1 < len(string): + stringRightOfBracket =3D string[j+1:] # Eg. '= (b:0.4,a:0.3)c:0.3, stringRightOfBracket =3D c:0.3 + match =3D re.search(r"[\)\,\(]", stringRightOfBrac= ket) + if match: + indexOfNextSymbol =3D match.start() + stringRepOfInternalNode =3D stringRightOfBrack= et[:indexOfNextSymbol] + internalNodes =3D self._makeNodesFromString( s= tringRepOfInternalNode, depth) + if len(internalNodes) > 0: + InternalNode =3D internalNodes[0] + lenOfPreceedingInternalNodeString =3D len(stri= ngRepOfInternalNode) + else: # sometimes the node can be the last eleme= nt of a string + InternalNode =3D self._makeNodesFromString(str= ing[j+1:], depth)[0] + lenOfPreceedingInternalNodeString =3D len(stri= ng) - j + if InternalNode =3D=3D None: #creating a generic= node if it is unnamed + InternalNode =3D self.phyloTree.makeNode( "", dept= h=3Ddepth, isInternal=3DTrue ) #"internal-" + str(depth) + lenOfPreceedingInternalNodeString =3D 0 + + # recussive call to make the internal claude + childSubString =3D string[ i + 1 : j ] + InternalNode.addChildNode(self.parseNode(childSubStrin= g, depth + 1)) + + nodes.append(InternalNode) # we append the internal n= ode later to preserve order + + start =3D j + 1 + continue + + if depth =3D=3D 0: # if its the root node, we do nothing about = it and return + return nodes[0] + + # Adding last most set of children + endString =3D string[start:] + if string[start-1] =3D=3D ")": # if the symbol belongs to an inte= rnal node which is created previously, then we remove it from the string le= ft to parse + match =3D re.search(r"[\)\,\(]", endString) + if match: + endOfNodeName =3D start + match.start() + 1 + endString =3D string[endOfNodeName:] + nodes +=3D self._makeNodesFromString(endString, depth) + + return nodes diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/visualization/phyloviz/nexusparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/nexusparser.py @@ -0,0 +1,107 @@ +from newickparser import Newick_Parser +import re + +MAX_READLINES =3D 200000 + + +class Nexus_Parser(Newick_Parser): + + def __init__(self): + super(Nexus_Parser, self).__init__() + + def parseFile(self, filePath): + """passes a file and extracts its Nexus content.""" + return self.parseNexus(filePath) + + + def parseNexus(self, filename): + """ Nexus data is stored in blocks between a line starting with be= gin and another line starting with end; + Commends inside square brackets are to be ignored, + For more information: http://wiki.christophchamp.com/index.php/NEX= US_file_format + Nexus can store multiple trees + """ + + with open( filename, "rt") as nex_file: + nexlines =3D nex_file.readlines() + + rowCount =3D 0 + inTreeBlock =3D False # sentinel to check if we are in a t= ree block + intranslateBlock =3D False # sentinel to check if we are in the= translate region of the tree. Stores synonyms of the labellings + self.inCommentBlock =3D False + self.nameMapping =3D None # stores mapping representation us= ed in nexus format + treeNames =3D [] + + for line in nexlines: + line =3D line.replace(";\n", "") + lline =3D line.lower() + + if rowCount > MAX_READLINES or (not nex_file) : + break + rowCount +=3D1 + # We are only interested in the tree block. + if "begin" in lline and "tree" in lline and not inTreeBlock: + inTreeBlock =3D True + continue + if inTreeBlock and "end" in lline[:3]: + inTreeBlock, currPhyloTree =3D False, None + continue + + if inTreeBlock: + + if "title" in lline: # Adding title to the tree + titleLoc =3D lline.find("title") + title =3D line[titleLoc + 5:].replace(" ", "") + + continue + + if "translate" in lline: + intranslateBlock =3D True + self.nameMapping =3D {} + continue + + if intranslateBlock: + mappingLine =3D self.splitLinebyWhitespaces(line) + key, value =3D mappingLine[1], mappingLine[2].replace(= ",", "").replace("'","") #replacing illegal json characters + self.nameMapping[key] =3D value + + # Extracting newick Trees + if "tree" in lline: + intranslateBlock =3D False + + treeLineCols =3D self.splitLinebyWhitespaces(line) + treeName, newick =3D treeLineCols[2], treeLineCols[-1] + + if newick =3D=3D "": # Empty lines can be found in = tree blocks + continue + + currPhyloTree =3D self._parseNewickToJson(newick, tree= Name, nameMap=3Dself.nameMapping) + + self.phyloTrees.append(currPhyloTree) + treeIndex =3D len(self.phyloTrees) - 1 + treeNames.append( (treeName, treeIndex) ) # appendi= ng name of tree, and its index + continue + + return self.phyloTrees, treeNames + + + def splitLinebyWhitespaces(self, line): + """replace tabs and write spaces to a single write space, so we ca= n properly split it.""" + return re.split(r"\s+", line) + + + def checkComments(self, line): + """Check to see if the line/lines is a comment.""" + if not self.inCommentBlock: + if "[" in line: + if "]" not in line: + self.inCommentBlock =3D True + else: + return "Nextline" # need to move on to the nextline = after getting out of comment + else : + if "]" in line: + if line.rfind("[") > line.rfind("]"): + pass # a comment block is closed but an= other is open. + else: + self.inCommentBlock =3D False + return "Nextline" # need to move on to the nextline = after getting out of comment + return "" \ No newline at end of file diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py @@ -0,0 +1,35 @@ +from newickparser import Newick_Parser +from nexusparser import Nexus_Parser +from phyloxmlparser import Phyloxml_Parser + +class Phyloviz_DataProvider(object): + + def __init__(self): + pass + + def parseFile(self, filepath, fileExt): + """returns [trees], meta + Trees are actually an array of JsonDicts. It's usually one tre= e, except in the case of Nexus + """ + jsonDicts, meta =3D [], {} + try: + if fileExt =3D=3D "nhx": # parses newick files + newickParser =3D Newick_Parser() + jsonDicts, parseMsg =3D newickParser.parseFile(filepath) + elif fileExt =3D=3D "phyloxml": # parses phyloXML files + phyloxmlParser =3D Phyloxml_Parser() + jsonDicts, parseMsg =3D phyloxmlParser.parseFile(filepath) + elif fileExt =3D=3D "nex": # parses nexus files + nexusParser =3D Nexus_Parser() + jsonDicts, parseMsg =3D nexusParser.parseFile(filepath) + meta["trees"] =3D parseMsg + else: + raise Exception("File type is not supported") + + meta["msg"] =3D parseMsg + + except Exception: + jsonDicts, meta["msg"] =3D [], "Parse failed" + + return jsonDicts, meta + diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/visualization/phyloviz/phyloxmlparser.py --- /dev/null +++ b/lib/galaxy/visualization/phyloviz/phyloxmlparser.py @@ -0,0 +1,145 @@ +from baseparser import Base_Parser, PhyloTree, Node +from lxml import etree + +class Phyloxml_Parser(Base_Parser): + """Parses a phyloxml file into a json file that will be passed to Phyl= oViz for display""" + + def __init__(self): + super(Phyloxml_Parser, self).__init__() + self.phyloTree =3D PhyloTree() + self.tagsOfInterest =3D { + "clade": "", + "name" : "name", + "branch_length" : "length", + "confidence" : "bootstrap", + "events" : "events" + } + + def parseFile(self, filePath): + """passes a file and extracts its Phylogeny Tree content.""" + phyloXmlFile =3D open(filePath, "r") + + xmlTree =3D etree.parse(phyloXmlFile) + xmlRoot =3D xmlTree.getroot()[0] + self.nameSpaceIndex =3D xmlRoot.tag.rfind("}") + 1 # used later by= the clean tag method to remove the name space in every element.tag + + phyloRoot =3D None + for child in xmlRoot: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + phyloRoot =3D child + elif childTag =3D=3D "name": + self.phyloTree.title =3D child.text + + self.phyloTree.root =3D self.parseNode(phyloRoot, 0) + jsonDict =3D self.phyloTree.generateJsonableDict() + return [jsonDict], "Success" + + + def parseNode(self, node, depth): + """Parses any node within a phyloxml tree and looks out for claude= , which signals the creation of + nodes - internal OR leaf""" + assert isinstance(node, etree._Element) + + tag =3D self.cleanTag(node.tag) + if not tag =3D=3D "clade": + return None + hasInnerClade =3D False + + # peeking once for parent and once for child to check if the node = is internal + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + hasInnerClade =3D True + break + + if hasInnerClade: # this node is an internal node + currentNode =3D self._makeInternalNode(node, depth=3D depth) + for child in node: + child =3D self.parseNode(child, depth + 1) + if isinstance(child, Node): + currentNode.addChildNode(child) + + else: # this node is a leaf node + currentNode =3D self._makeLeafNode(node, depth=3Ddepth+1) + + return currentNode + + + def _makeLeafNode(self, leafNode, depth =3D 0 ): + """Makes leaf nodes by calling Phylotree methods""" + node =3D {} + for child in leafNode: + childTag =3D self.cleanTag(child.tag) + if childTag in self.tagsOfInterest: + key =3D self.tagsOfInterest[childTag] # need to map phy= loxml terms to ours + node[key] =3D child.text + + node["depth"] =3D depth + return self.phyloTree.makeNode(self._getNodeName(leafNode), **node) + + def _getNodeName(self, node, depth=3D-1): + """Gets the name of a claude. It handles the case where a taxonomy= node is involved""" + + def getTagFromTaxonomyNode(node): + """Returns the name of a taxonomy node. A taxonomy node have t= o be treated differently as the name + is embedded one level deeper""" + phyloxmlTaxoNames =3D { + "common_name" : "", + "scientific_name" : "", + "code" : "" + } + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag in phyloxmlTaxoNames: + return child.text + return "" + + nodeName =3D "" + for child in node: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "name" : + nodeName =3D child.text + break + elif childTag =3D=3D "taxonomy": + nodeName =3D getTagFromTaxonomyNode(child) + break + + return nodeName + + + def _makeInternalNode(self, internalNode, depth=3D0): + """ Makes an internal node from an element object that is gurantee= d to be a parent node. + Gets the value of interests like events and appends it to a custom= node object that will be passed to PhyloTree to make nodes + """ + node =3D {} + for child in internalNode: + childTag =3D self.cleanTag(child.tag) + if childTag =3D=3D "clade": + continue + elif childTag in self.tagsOfInterest: + if childTag =3D=3D "events": # events is nested 1 more = level deeper than others + key, text =3D "events", self.cleanTag(child[0].tag) + else: + key =3D self.tagsOfInterest[childTag] + text =3D child.text + node[key] =3D text + + + return self.phyloTree.makeNode(self._getNodeName(internalNode, dep= th), **node) + + + def cleanTag(self, tagString): + return tagString[self.nameSpaceIndex:] + + +if __name__=3D=3D"__main__": + + # Files tested against + parser =3D Phyloxml_Parser() + filepath =3D "../data/" +"apaf.xml" + # filepath =3D "../data/" +"12_multiple_supports.xml" + + # filepath =3D "../data/" +"bcl_2.xml" + # filepath =3D "../data/" +"reducedXml.xml" + parser.parseFile(filepath) diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/web/controllers/phyloviz.py --- /dev/null +++ b/lib/galaxy/web/controllers/phyloviz.py @@ -0,0 +1,97 @@ +import pkg_resources +pkg_resources.require( "bx-python" ) + +from galaxy.util.json import to_json_string, from_json_string +from galaxy.web.base.controller import * +from galaxy.visualization.phyloviz.phyloviz_dataprovider import Phyloviz_D= ataProvider + + +class PhyloVizController( BaseUIController, UsesVisualizationMixin, UsesHi= storyDatasetAssociationMixin, SharableMixin ): + """ + Controller for phyloViz browser interface. + """ + def __init__(self, app ): + BaseUIController.__init__( self, app ) + + @web.expose + @web.require_login() + def index( self, trans, dataset_id =3D None, **kwargs ): + """ + The index method is called using phyloviz/ with a dataset id passe= d in. + The relevant data set is then retrieved via get_json_from_datasetI= d which interfaces with the parser + The json representation of the phylogenetic tree along with the co= nfig is then written in the .mako template and passed back to the user + """ + json, config =3D self.get_json_from_datasetId(trans, dataset_id) + config["saved_visualization"] =3D False + return trans.fill_template( "visualization/phyloviz.mako", data = =3D json, config=3Dconfig) + + + @web.expose + def visualization(self, trans, id): + """ + Called using a viz_id (id) to retrieved stored visualization data = (in json format) and all the viz_config + """ + viz =3D self.get_visualization(trans, id) + config =3D self.get_visualization_config(trans, viz) + config["saved_visualization"] =3D True + data =3D config["root"] + + return trans.fill_template( "visualization/phyloviz.mako", data = =3D data, config=3Dconfig) + + + @web.expose + @web.json + def load_visualization_json(self, trans, viz_id): + """ + Though not used in current implementation, this provides user with= a convenient method to retrieve the viz_data & viz_config via json. + """ + viz =3D self.get_visualization(trans, viz_id) + viz_config =3D self.get_visualization_config(trans, viz) + viz_config["saved_visualization"] =3D True + return { + "data" : viz_config["root"], + "config" : viz_config + } + + + @web.expose + @web.json + def getJsonData(self, trans, dataset_id, treeIndex=3D0): + """ + Method to retrieve data asynchronously via json format. Retriving = from here rather than + making a direct datasets/ call allows for some processing and even= t capturing + """ + treeIndex =3D int(treeIndex) + json, config =3D self.get_json_from_datasetId(trans, dataset_id, t= reeIndex) + packedJson =3D { + "data" : json, + "config" : config + } + + return packedJson + + + def get_json_from_datasetId(self, trans, dataset_id, treeIndex=3D0): + """ + For interfacing phyloviz controllers with phyloviz visualization d= ata provider (parsers) + """ + dataset =3D self.get_dataset(trans, dataset_id) + fileExt, filepath =3D dataset.ext, dataset.file_name # .name= stores the name of the dataset from the orginal upload + json, config =3D "", {} # config contains propertie= s of the tree and file + + if fileExt =3D=3D "json": + something, json =3D self.get_data(dataset) + else: + try: + pd =3D Phyloviz_DataProvider() + json, config =3D pd.parseFile(filepath, fileExt) + json =3D json[treeIndex] + except Exception: + pass + + config["title"] =3D dataset.display_name() + config["ext"] =3D fileExt + config["dataset_id"] =3D dataset_id + config["treeIndex"] =3D treeIndex + + return json, config diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -16,6 +16,10 @@ action =3D "paramamonster" elif item.type =3D=3D "circster": action =3D "circster" + elif item.type =3D=3D "phyloviz": + # Support phyloviz + controller =3D "phyloviz" + action =3D "visualization" return dict( controller=3Dcontroller, action=3Daction, id=3Ditem.i= d ) =20 # Grid definition diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 static/scripts/viz/phyloviz.js --- /dev/null +++ b/static/scripts/viz/phyloviz.js @@ -0,0 +1,955 @@ +var UserMenuBase =3D Backbone.View.extend({ + /** + * Base class of any menus that takes in user interaction. Contains ch= ecking methods. + */ + + className: 'UserMenuBase', + + isAcceptableValue : function ($inputKey, min, max) { + /** + * Check if an input value is a number and falls within max min. + */ + var self =3D this, + value =3D $inputKey.val(), + fieldName =3D $inputKey.attr("displayLabel") || $inputKey.attr= ("id").replace("phyloViz", ""); + + function isNumeric(n) { + return !isNaN(parseFloat(n)) && isFinite(n); + } + + if (!isNumeric(value)){ + alert(fieldName + " is not a number!"); + return false; + } + + if ( value > max){ + alert(fieldName + " is too large."); + return false; + } else if ( value < min) { + alert(fieldName + " is too small."); + return false; + } + return true; + }, + + hasIllegalJsonCharacters : function($inputKey) { + /** + * Check if any user string inputs has illegal characters that jso= n cannot accept + */ + if ($inputKey.val().search(/"|'|\\/) !=3D=3D -1){ + alert("Named fields cannot contain these illegal characters: d= ouble quote(\"), single guote(\'), or back slash(\\). "); + return true; + } + return false; + } +}); + + +function PhyloTreeLayout() { + /** + * -- Custom Layout call for phyloViz to suit the needs of a phylogene= tic tree. + * -- Specifically: 1) Nodes have a display display of (=3D evo dist X= depth separation) from their parent + * 2) Nodes must appear in other after they have expa= nd and contracted + */ + + var self =3D this, + hierarchy =3D d3.layout.hierarchy().sort(null).value(null), + height =3D 360, // ! represents both the layout angle and the heig= ht of the layout, in px + layoutMode =3D "Linear", + leafHeight =3D 18, // height of each individual leaf node + depthSeparation =3D 200, // separation between nodes of different = depth, in px + leafIndex =3D 0, // change to recurssive call + defaultDist =3D 0.5, // tree defaults to 0.5 dist if no dist is sp= ecified + maxTextWidth =3D 50; // maximum length of the text labels + + + self.leafHeight =3D function(inputLeafHeight){ + if (typeof inputLeafHeight =3D=3D=3D "undefined"){ return leafHeig= ht; } + else { leafHeight =3D inputLeafHeight; return self;} + }; + + self.layoutMode =3D function(mode){ + if (typeof mode =3D=3D=3D "undefined"){ return layoutMode; } + else { layoutMode =3D mode; return self;} + }; + + self.layoutAngle =3D function(angle) { // changes the layout angle = of the display, which is really changing the height + if (typeof angle =3D=3D=3D "undefined"){ return height; } + if (isNaN(angle) || angle < 0 || angle > 360) { return self; } // = to use default if the user puts in strange values + else { height =3D angle; return self;} + }; + + self.separation =3D function(dist){ // changes the dist between the = nodes of different depth + if (typeof dist =3D=3D=3D "undefined"){ return depthSeparation; } + else { depthSeparation =3D dist; return self;} + }; + + self.links =3D function (nodes) { // uses d3 native method to gene= rate links. Done. + return d3.layout.tree().links(nodes); + }; + + // -- Custom method for laying out phylogeny tree in a linear fashion + self.nodes =3D function (d, i) { + var _nodes =3D hierarchy.call(self, d, i), // self is to f= ind the depth of all the nodes, assumes root is passed in + nodes =3D [], + maxDepth =3D 0, + numLeaves =3D 0; + + // changing from hierarchy's custom format for data to usable form= at + _nodes.forEach(function (_node){ + var node =3D _node.data; + node.depth =3D _node.depth; + maxDepth =3D node.depth > maxDepth ? node.depth : maxDepth; /= /finding max depth of tree + nodes.push(node); + }); + // counting the number of leaf nodes and assigning max depth to no= des that do not have children to flush all the leave nodes + nodes.forEach(function(node){ + if ( !node.children ) { //&& !node._children + numLeaves +=3D 1; + node.depth =3D maxDepth; // if a leaf has no child it woul= d be assigned max depth + } + }); + + leafHeight =3D layoutMode =3D=3D=3D "Circular" ? height / numLeave= s : leafHeight; + leafIndex =3D 0; + layout(nodes[0], maxDepth, leafHeight, null); + + return nodes; + }; + + + function layout (node, maxDepth, vertSeparation, parent) { + /** + * -- Function with side effect of adding x0, y0 to all child; tak= e in the root as starting point + * assuming that the leave nodes would be sorted in presented ord= er + * horizontal(y0) is calculated according to (=3D evo dis= t X depth separation) from their parent + * vertical (x0) - if leave node: find its order in all o= f the leave node =3D=3D=3D node.id, then multiply by verticalSeparation + * - if parent node: is place in the mid point al= l of its children nodes + * -- The layout will first calculate the y0 field going towards t= he leaves, and x0 when returning + */ + var children =3D node.children, + sumChildVertSeparation =3D 0; + + // calculation of node's dist from parents, going down. + var dist =3D node.dist || defaultDist; + dist =3D dist > 1 ? 1 : dist; // We constrain all dist to be l= ess than one + node.dist =3D dist; + if (parent !=3D=3D null){ + node.y0 =3D parent.y0 + dist * depthSeparation; + } else { //root node + node.y0 =3D maxTextWidth; + } + + + // if a node have no children, we will treat it as a leaf and star= t laying it out first + if (!children) { + node.x0 =3D leafIndex++ * vertSeparation; + } else { + // if it has children, we will visit all its children and calc= ulate its position from its children + children.forEach( function (child) { + child.parent =3D node; + sumChildVertSeparation +=3D layout(child, maxDepth, vertSe= paration, node); + }); + node.x0 =3D sumChildVertSeparation / children.length; + } + + // adding properties to the newly created node + node.x =3D node.x0; + node.y =3D node.y0; + return node.x0; + } + return self; +} + + +/** + * -- PhyloTree Model -- + */ +var PhyloTree =3D Visualization.extend({ + defaults : { + layout: "Linear", + separation : 250, // px dist between nodes of different depth t= o represent 1 evolutionary until + leafHeight: 18, + type : "phyloviz", // visualization type + title : "Title", + scaleFactor: 1, + translate: [0,0], + fontSize: 12, //fontSize of node label + selectedNode : null, + nodeAttrChangedTime : 0 + }, + + root : {}, // Root has to be its own independent object because it is = not part of the viz_config + + toggle : function (d) { + /** + * Mechanism to expand or contract a single node. Expanded nodes h= ave a children list, while for + * contracted nodes the list is stored in _children. Nodes with th= eir children data stored in _children will not have their + * children rendered. + */ + if(typeof d =3D=3D=3D "undefined") {return ;} + if (d.children ) { + d._children =3D d.children; + d.children =3D null; + } else { + d.children =3D d._children; + d._children =3D null; + } + }, + + toggleAll : function(d) { + /** + * Contracts the phylotree to a single node by repeatedly calling= itself to place all the list + * of children under _children. + */ + if (d.children && d.children.length !=3D=3D 0) { + d.children.forEach(this.toggleAll); + toggle(d); + } + }, + + getData : function (){ + /** + * Return the data of the tree. Used for preserving state. + */ + return this.root; + }, + + save: function() { + /** + * Overriding the default save mechanism to do some clean of circu= lar reference of the + * phyloTree and to include phyloTree in the saved json + */ + var root =3D this.root; + cleanTree(root); + this.set("root", root); + + function cleanTree(node){ + // we need to remove parent to delete circular reference + delete node.parent; + + // removing unnecessary attributes + if (node._selected){ delete node._selected;} + + node.children ? node.children.forEach(cleanTree) : 0; + node._children ? node._children.forEach(cleanTree) : 0; + } + + var config =3D jQuery.extend(true, {}, this.attributes); + config["selectedNode"] =3D null; + + show_message("Saving to Galaxy", "progress"); + + return $.ajax({ + url: this.url(), + type: "POST", + dataType: "json", + data: { + vis_json: JSON.stringify(config) + }, + success: function(res){ + var viz_id =3D res.url.split("id=3D")[1].split("&")[0], + viz_url =3D "/phyloviz/visualization?id=3D" + viz_id; + window.history.pushState({}, "", viz_url + window.location= .hash); + hide_modal(); + } + }); + } +}); + + + +/** + * -- Views -- + */ +var PhylovizLayoutBase =3D Backbone.View.extend({ + /** + * Stores the default variable for setting up the visualization + */ + defaults : { + nodeRadius : 4.5 // radius of each node in the diagram + }, + + + stdInit : function (options) { + /** + * Common initialization in layouts + */ + + var self =3D this; + self.model.on("change:separation change:leafHeight change:fontSize= change:nodeAttrChangedTime", self.updateAndRender, self); + + self.vis =3D options.vis; + self.i =3D 0; + self.maxDepth =3D -1; // stores the max depth of the tree + + self.width =3D options.width; + self.height =3D options.height; + }, + + + updateAndRender : function(source) { + /** + * Updates the visualization whenever there are changes in the ex= pansion and contraction of nodes + * AND possibly when the tree is edited. + */ + var vis =3D d3.select(".vis"), + self =3D this; + source =3D source || self.model.root; + + self.renderNodes(source); + self.renderLinks(source); + self.addTooltips(); + }, + + + renderLinks : function(source) { + /** + * Renders the links for the visualization. + */ + var self =3D this; + var diagonal =3D self.diagonal; + var duration =3D self.duration; + var layoutMode =3D self.layoutMode; + var link =3D self.vis.selectAll("g.completeLink") + .data(self.tree.links(self.nodes), function(d) { return d.targ= et.id; }); + + var calcalateLinePos =3D function(d) { + d.pos0 =3D d.source.y0 + " " + d.source.x0; // position of t= he source node <=3D> starting location of the line drawn + d.pos1 =3D d.source.y0 + " " + d.target.x0; // position where= the line makes a right angle bend + d.pos2 =3D d.target.y0 + " " + d.target.x0; // point where= the horizontal line becomes a dotted line + }; + + var linkEnter =3D link.enter().insert("svg:g","g.node") + .attr("class", "completeLink"); + + + linkEnter.append("svg:path") + .attr("class", "link") + .attr("d", function(d) { + calcalateLinePos(d); + return "M " + d.pos0 + " L " + d.pos1; + }); + + var linkUpdate =3D link.transition().duration(500); + + linkUpdate.select("path.link") + .attr("d", function(d) { + calcalateLinePos(d); + return "M " + d.pos0 + " L " + d.pos1 + " L " + d.pos2; + }); + + var linkExit =3D link.exit().remove(); + + }, + + // User Interaction methods below + + selectNode : function(node){ + /** + * Displays the information for editting + */ + var self =3D this; + d3.selectAll("g.node") + .classed("selectedHighlight", function(d){ + if (node.id =3D=3D=3D d.id){ + if(node._selected) { // for de=3Dselecting node. + delete node._selected; + return false; + } else { + node._selected =3D true; + return true; + } + } + return false; + }); + + self.model.set("selectedNode", node); + $("#phyloVizSelectedNodeName").val(node.name); + $("#phyloVizSelectedNodeDist").val(node.dist); + $("#phyloVizSelectedNodeAnnotation").val(node.annotation || ""); + }, + + addTooltips : function (){ + /** + * Creates bootstrap tooltip for the visualization. Has to be cal= led repeatedly due to newly generated + * enterNodes + */ + $(".bs-tooltip").remove(); //clean up tooltip, just in case i= ts listeners are removed by d3 + $(".node") + .attr("data-original-title", function(){ + var d =3D this.__data__, + annotation =3D d.annotation || "None" ; + return d ? (d.name ? d.name + "<br/>" : "") + "Dist: " + d= .dist + " <br/>Annotation: " + annotation: ""; + }) + .tooltip({'placement':'top', 'trigger' : 'hover'}); + + } +}); + + + + +var PhylovizLinearView =3D PhylovizLayoutBase.extend({ + /** + * Linea layout class of Phyloviz, is responsible for rendering the no= des + * calls PhyloTreeLayout to determine the positions of the nodes + */ + initialize : function(options){ + // Default values of linear layout + var self =3D this; + self.margins =3D options.margins; + self.layoutMode =3D "Linear"; + + self.stdInit(options); + + self.layout(); + self.updateAndRender(self.model.root); + }, + + layout : function() { + /** + * Creates the basic layout of a linear tree by precalculating fix= ed values. + * One of calculations are also made here + */ + + var self =3D this; + + self.tree =3D new PhyloTreeLayout().layoutMode("Linear"); + self.diagonal =3D d3.svg.diagonal() + .projection(function(d) { return [d.y, d.x ]; }); + }, + + renderNodes : function (source) { + /** + * Renders the nodes base on Linear layout. + */ + var self =3D this, + fontSize =3D self.model.get("fontSize") + "px"; + + // assigning properties from models + self.tree.separation(self.model.get("separation")).leafHeight(self= .model.get("leafHeight")); + + var duration =3D 500, + nodes =3D self.tree.separation(self.model.get("separation")).n= odes(self.model.root); + + var node =3D self.vis.selectAll("g.node") + .data(nodes, function(d) { return d.name + d.id || (d.id =3D += +self.i); }); + + // These variables has to be passed into update links which are in= the base methods + self.nodes =3D nodes; + self.duration =3D duration; + + // ------- D3 ENTRY -------- + // Enter any new nodes at the parent's previous position. + var nodeEnter =3D node.enter().append("svg:g") + .attr("class", "node") + .on("dblclick", function(){ d3.event.stopPropagation(); }) + .on("click", function(d) { + if (d3.event.altKey) { + self.selectNode(d); // display info if alt is p= ressed + } else { + if(d.children && d.children.length =3D=3D=3D 0){ retur= n;} // there is no need to toggle leaves + self.model.toggle(d); // contract/expand nodes at da= ta level + self.updateAndRender(d); // re-render the tree + } + }); + + nodeEnter.attr("transform", function(d) { return "translate(" + so= urce.y0 + "," + source.x0 + ")"; }); + + nodeEnter.append("svg:circle") + .attr("r", 1e-6) + .style("fill", function(d) { return d._children ? "lightsteelb= lue" : "#fff"; }); + + nodeEnter.append("svg:text") + .attr("class", "nodeLabel") + .attr("x", function(d) { return d.children || d._children ? -1= 0 : 10; }) + .attr("dy", ".35em") + .attr("text-anchor", function(d) { return d.children || d._chi= ldren ? "end" : "start"; }) + .style("fill-opacity", 1e-6); + + // ------- D3 TRANSITION -------- + // Transition nodes to their new position. + var nodeUpdate =3D node.transition() + .duration(duration); + + nodeUpdate.attr("transform", function(d) { + return "translate(" + d.y + "," + d.x + ")"; }); + + nodeUpdate.select("circle") + .attr("r", self.defaults.nodeRadius) + .style("fill", function(d) { return d._children ? "lightsteelb= lue" : "#fff"; }); + + nodeUpdate.select("text") + .style("fill-opacity", 1) + .style("font-size", fontSize) + .text(function(d) { return d.name; }); + + // ------- D3 EXIT -------- + // Transition exiting nodes to the parent's new position. + var nodeExit =3Dnode.exit().transition() + .duration(duration) + .remove(); + + nodeExit.select("circle") + .attr("r", 1e-6); + + nodeExit.select("text") + .style("fill-opacity", 1e-6); + + // Stash the old positions for transition. + nodes.forEach(function(d) { + d.x0 =3D d.x; // we need the x0, y0 for parents with children + d.y0 =3D d.y; + }); + } + +}); + +var PhylovizView =3D Backbone.View.extend({ + + className: 'phyloviz', + + initialize: function(options) { + var self =3D this; + // -- Default values of the vis + self.MIN_SCALE =3D 0.05; //for zooming + self.MAX_SCALE =3D 5; + self.MAX_DISPLACEMENT =3D 500; + self.margins =3D [10, 60, 10, 80]; + + self.width =3D $("#PhyloViz").width(); + self.height =3D $("#PhyloViz").height(); + self.radius =3D self.width; + self.data =3D options.data; + + // -- Events Phyloviz view responses to + $(window).resize(function(){ + self.width =3D $("#PhyloViz").width(); + self.height =3D $("#PhyloViz").height(); + self.render(); + }); + + // -- Create phyloTree model + self.phyloTree =3D new PhyloTree(options.config); + self.phyloTree.root =3D self.data; + + // -- Set up UI functions of main view + self.zoomFunc =3D d3.behavior.zoom().scaleExtent([self.MIN_SCALE, = self.MAX_SCALE]); + self.zoomFunc.translate(self.phyloTree.get("translate")); + self.zoomFunc.scale(self.phyloTree.get("scaleFactor")); + + // -- set up header buttons, search and settings menu + self.navMenu =3D new HeaderButtons(self); + self.settingsMenu =3D new SettingsMenu({phyloTree : self.phyloTree= }); + self.nodeSelectionView =3D new NodeSelectionView({phyloTree : self= .phyloTree}); + self.search =3D new PhyloVizSearch(); + + + setTimeout(function(){ // using settimeout to call the zoomAn= dPan function according to the stored attributes in viz_config + self.zoomAndPan(); + }, 1000); + }, + + render: function(){ + // -- Creating helper function for vis. -- + var self =3D this; + $("#PhyloViz").empty(); + + // -- Layout viz. -- + self.mainSVG =3D d3.select("#PhyloViz").append("svg:svg") + .attr("width", self.width) + .attr("height", self.height) + .attr("pointer-events", "all") + .call(self.zoomFunc.on("zoom", function(){ + self.zoomAndPan(); + })); + + self.boundingRect =3D self.mainSVG.append("svg:rect") + .attr("class", "boundingRect") + .attr("width", self.width) + .attr("height", self.height) + .attr("stroke", "black") + .attr("fill", "white"); + + self.vis =3D self.mainSVG + .append("svg:g") + .attr("class", "vis"); + + self.layoutOptions =3D { + model : self.phyloTree, + width : self.width, + height : self.height, + vis: self.vis, + margins: self.margins + }; + + // -- Creating Title + $("#title").text("Phylogenetic Tree from " + self.phyloTree.get("t= itle") + ":"); + + // -- Create Linear view instance -- + var linearView =3D new PhylovizLinearView(self.layoutOptions) + }, + + zoomAndPan : function(event){ + /** + * Function to zoom and pan the svg element which the entire tree = is contained within + * Uses d3.zoom events, and extend them to allow manual updates an= d keeping states in model + */ + if (typeof event !=3D=3D "undefined") { + var zoomParams =3D event.zoom, + translateParams =3D event.translate; + } + + var self =3D this, + scaleFactor =3D self.zoomFunc.scale(), + translationCoor =3D self.zoomFunc.translate(), + zoomStatement =3D "", + translateStatement =3D ""; + + // Do manual scaling. + switch (zoomParams) { + case "reset": + scaleFactor =3D 1.0; + translationCoor =3D [0,0]; break; + case "+": + scaleFactor *=3D 1.1; break; + case "-": + scaleFactor *=3D 0.9; break; + default: + if (typeof zoomParams =3D=3D=3D "number") { + scaleFactor =3D zoomParams; + } else if (d3.event !=3D=3D null) { + scaleFactor =3D d3.event.scale; + } + } + if (scaleFactor < self.MIN_SCALE || scaleFactor > self.MAX_SCALE) = { return;} + self.zoomFunc.scale(scaleFactor); //update scale Factor + zoomStatement =3D "translate(" + self.margins[3] + "," + self.mar= gins[0] + ")" + + " scale(" + scaleFactor + ")"; + + // Do manual translation. + if( d3.event !=3D=3D null) { + translateStatement =3D "translate(" + d3.event.translate + ")"; + } else { + if(typeof translateParams !=3D=3D "undefined") { + var x =3D translateParams.split(",")[0]; + var y =3D translateParams.split(",")[1]; + if (!isNaN(x) && !isNaN(y)){ + translationCoor =3D [translationCoor[0] + parseFloat(x= ), translationCoor[1] + parseFloat(y)]; + } + } + self.zoomFunc.translate(translationCoor); // update zoomFunc + translateStatement =3D "translate(" + translationCoor + ")"; + } + + self.phyloTree.set("scaleFactor", scaleFactor); + self.phyloTree.set("translate", translationCoor); + self.vis.attr("transform", translateStatement + zoomStatement); //= refers to the view that we are actually zooming + }, + + + reloadViz : function() { + /** + * Primes the Ajax URL to load another Nexus tree + */ + var self =3D this, + treeIndex =3D $("#phylovizNexSelector :selected").val(), + dataset_id =3D self.phyloTree.get("dataset_id"), + url =3D "phyloviz/getJsonData?dataset_id=3D" + dataset_id + "&= treeIndex=3D" + String(treeIndex); + $.getJSON(url, function(packedJson){ + window.initPhyloViz(packedJson.data, packedJson.config); + }); + } +}); + + +var HeaderButtons =3D Backbone.View.extend({ + + initialize : function(phylovizView){ + var self =3D this; + self.phylovizView =3D phylovizView; + + // Clean up code - if the class initialized more than once + $("#panelHeaderRightBtns").empty(); + $("#phyloVizNavBtns").empty(); + $("#phylovizNexSelector").off(); + + self.initNavBtns(); + self.initRightHeaderBtns(); + + // Initial a tree selector in the case of nexus + $("#phylovizNexSelector").off().on("change", function() {self.phy= lovizView.reloadViz();} ); + + }, + + initRightHeaderBtns : function(){ + var self =3D this; + + rightMenu =3D create_icon_buttons_menu([ + { icon_class: 'gear', title: 'PhyloViz Settings', on_click: fu= nction(){ + $("#SettingsMenu").show(); + self.settingsMenu.updateUI(); + } }, + { icon_class: 'disk', title: 'Save visualization', on_click: f= unction() { + var nexSelected =3D $("#phylovizNexSelector option:selecte= d").text(); + if(nexSelected) { + self.phylovizView.phyloTree.set("title", nexSelected); + } + self.phylovizView.phyloTree.save(); + } }, + { icon_class: 'chevron-expand', title: 'Search / Edit Nodes', = on_click: function() { + $("#nodeSelectionView").show(); + } }, + { icon_class: 'information', title: 'Phyloviz Help', on_click:= function() { + window.open('http://wiki.g2.bx.psu.edu/Learn/Visualization= /PhylogeneticTree'); + // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs= 3EyMe1B1X_KFPouzIgrCz3zk/edit + } } + ], + { + tooltip_config: { placement: 'bottom' } + }); + $("#panelHeaderRightBtns").append(rightMenu.$el); + }, + + initNavBtns: function() { + var self =3D this, + navMenu =3D create_icon_buttons_menu([ + { icon_class: 'zoom-in', title: 'Zoom in', on_click: funct= ion() { + self.phylovizView.zoomAndPan({ zoom : "+"}); + } }, + { icon_class: 'zoom-out', title: 'Zoom out', on_click: fun= ction() { + self.phylovizView.zoomAndPan({ zoom : "-"}); + } }, + { icon_class: 'arrow-circle', title: 'Reset Zoom/Pan', on_= click: function() { + self.phylovizView.zoomAndPan({ zoom : "reset"}); + } } + ], + { + tooltip_config: { placement: 'bottom' } + }); + $("#phyloVizNavBtns").append(navMenu.$el); + } +}); + + +var SettingsMenu =3D UserMenuBase.extend({ + + className: 'Settings', + + initialize: function(options){ + // settings needs to directly interact with the phyloviz model so = it will get access to it. + var self =3D this; + self.phyloTree =3D options.phyloTree; + self.el =3D $("#SettingsMenu"); + self.inputs =3D { + separation : $("#phyloVizTreeSeparation"), + leafHeight : $("#phyloVizTreeLeafHeight"), + fontSize : $("#phyloVizTreeFontSize") + }; + + //init all buttons of settings + $("#settingsCloseBtn").off().on("click", function() { self.el.hide= (); }); + $("#phylovizResetSettingsBtn").off().on("click", function() { self= .resetToDefaults(); }); + $("#phylovizApplySettingsBtn").off().on("click", function() { self= .apply(); }); + }, + + apply : function(){ + /** + * Applying user values to phylotree model. + */ + var self =3D this; + if (!self.isAcceptableValue(self.inputs["separation"], 50, 2500) || + !self.isAcceptableValue(self.inputs["leafHeight"], 5, 30) || + !self.isAcceptableValue(self.inputs["fontSize"], 5, 20)){ + return; + } + $.each(self.inputs, function(key, $input){ + self.phyloTree.set(key, $input.val()); + }); + }, + updateUI : function(){ + /** + * Called to update the values input to that stored in the model + */ + var self =3D this; + $.each(self.inputs, function(key, $input){ + $input.val(self.phyloTree.get(key)); + }); + }, + resetToDefaults : function(){ + /** + * Resets the value of the phyloTree model to its default + */ + $(".bs-tooltip").remove(); // just in case the tool tip was n= ot removed + var self =3D this; + $.each(self.phyloTree.defaults, function(key, value) { + self.phyloTree.set(key, value); + }); + self.updateUI(); + }, + + render: function(){ + + } + +}); + + +var NodeSelectionView =3D UserMenuBase.extend({ + /** + * View for inspecting node properties and editing them + */ + className: 'Settings', + + initialize : function (options){ + var self =3D this; + self.el =3D $("#nodeSelectionView"); + self.phyloTree =3D options.phyloTree; + + self.UI =3D { + enableEdit : $('#phylovizEditNodesCheck'), + saveChanges : $('#phylovizNodeSaveChanges'), + cancelChanges : $("#phylovizNodeCancelChanges"), + name : $("#phyloVizSelectedNodeName"), + dist : $("#phyloVizSelectedNodeDist"), + annotation : $("#phyloVizSelectedNodeAnnotation") + }; + + self.valuesOfConcern =3D { + name : null, + dist : null, + annotation : null + }; // temporarily stores the values in case user change their mind + + //init UI buttons + $("#nodeSelCloseBtn").off().on("click", function() { self.el.hide(= ); }); + self.UI.saveChanges.off().on("click", function(){ self.updateNodes= (); }); + self.UI.cancelChanges.off().on("click", function(){ self.cancelCha= nges(); }); + + (function ($) { + // extending jquery fxn for enabling and disabling nodes. + $.fn.enable =3D function (isEnabled) { + return $(this).each(function () { + if(isEnabled){ + $(this).removeAttr('disabled'); + } else { + $(this).attr('disabled', 'disabled'); + } + }); + }; + })(jQuery); + + self.UI.enableEdit.off().on("click", function () { + self.toggleUI(); + }); + }, + + toggleUI : function(){ + /** + * For turning on and off the child elements + */ + var self =3D this, + checked =3D self.UI.enableEdit.is(':checked'); + + !checked ? self.cancelChanges() : ""; + + $.each(self.valuesOfConcern, function(key, value) { + self.UI[key].enable(checked); + }); + if(checked){ + self.UI.saveChanges.show(); + self.UI.cancelChanges.show(); + } else { + self.UI.saveChanges.hide(); + self.UI.cancelChanges.hide(); + } + + }, + + cancelChanges : function() { + /** + * Reverting to previous values in case user change their minds + */ + var self =3D this, + node =3D self.phyloTree.get("selectedNode"); + if (node){ + $.each(self.valuesOfConcern, function(key, value) { + self.UI[key].val(node[key]); + }); + } + }, + + updateNodes : function (){ + /** + * Changing the data in the underlying tree with user-specified va= lues + */ + var self =3D this, + node =3D self.phyloTree.get("selectedNode"); + if (node){ + if (!self.isAcceptableValue(self.UI.dist, 0, 1) || + self.hasIllegalJsonCharacters(self.UI.name) || + self.hasIllegalJsonCharacters(self.UI.annotation) ) { + return; + } + $.each(self.valuesOfConcern, function(key, value) { + (node[key]) =3D self.UI[key].val(); + }); + self.phyloTree.set("nodeAttrChangedTime", new Date()); + } else { + alert("No node selected"); + } + } + + +}); + + + +var PhyloVizSearch =3D UserMenuBase.extend({ + /** + * Initializes the search panel on phyloviz and handles its user inter= action + * It allows user to search the entire free based on some qualifer, li= ke dist <=3D val. + */ + initialize : function () { + var self =3D this; + + $("#phyloVizSearchBtn").on("click", function(){ + var searchTerm =3D $("#phyloVizSearchTerm"), + searchConditionVal =3D $("#phyloVizSearchCondition").val()= .split("-"), + attr =3D searchConditionVal[0], + condition =3D searchConditionVal[1]; + self.hasIllegalJsonCharacters(searchTerm); + + if (attr =3D=3D=3D "dist"){ + self.isAcceptableValue(searchTerm, 0, 1); + } + self.searchTree(attr, condition, searchTerm.val()); + }); + }, + + searchTree : function (attr, condition, val){ + /** + * Searches the entire tree and will highlight the nodes that matc= h the condition in green + */ + d3.selectAll("g.node") + .classed("searchHighlight", function(d){ + var attrVal =3D d[attr]; + if (typeof attrVal !=3D=3D "undefined" && attrVal !=3D=3D = null){ + if (attr =3D=3D=3D "dist"){ + switch (condition) { + case "greaterEqual": + return attrVal >=3D +val; + case "lesserEqual": + return attrVal <=3D +val; + default: + return; + } + + } else if (attr =3D=3D=3D "name" || attr =3D=3D=3D "an= notation") { + return attrVal.toLowerCase().indexOf(val.toLowerCa= se()) !=3D=3D -1; + } + } + }); + } +}); \ No newline at end of file diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -272,6 +272,17 @@ } =20 init_trackster_links(); + + function init_phyloviz_links() { + // PhyloViz links + // Add to trackster browser functionality + $(".phyloviz-add").live("click", function() { + var dataset =3D this, + dataset_jquery =3D $(this); + window.parent.location =3D dataset_jquery.attr("new-url"); + }); + } + init_phyloviz_links(); =20 // History rename functionality. async_save_text("history-name-container", "history-name", "${h.url_for= ( controller=3D"/history", action=3D"rename_async", id=3Dtrans.security.enc= ode_id(history.id) )}", "new_name", 18); diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -29,6 +29,9 @@ ## Render the dataset `data` as history item, using `hid` as the displayed= id <%def name=3D"render_dataset( data, hid, show_deleted_on_refresh =3D False= , for_editing =3D True, display_structured =3D False )"><% + + from galaxy.datatypes.xml import Phyloxml + from galaxy.datatypes.data import Newick, Nexus dataset_id =3D trans.security.encode_id( data.id ) =20 if data.state in ['no state','',None]: @@ -230,6 +233,14 @@ action-url=3D"${h.url_for( controller=3D't= racks', action=3D'browser', dataset_id=3Ddataset_id)}" new-url=3D"${h.url_for( controller=3D'trac= ks', action=3D'index', dataset_id=3Ddataset_id, default_dbkey=3Ddata.dbkey)= }" title=3D"View in Trackster"></a> %endif + <% + isPhylogenyData =3D isinstance(data.datatype, = (Phyloxml, Nexus, Newick)) + %> + %if isPhylogenyData: + <a href=3D"javascript:void(0)" class=3D"i= con-button chart_curve phyloviz-add" + action-url=3D"${h.url_for( controller= =3D'phyloviz', action=3D'-', dataset_id=3Ddataset_id)}" + new-url=3D"${h.url_for( controller=3D'p= hyloviz', action=3D'index', dataset_id=3Ddataset_id)}" title=3D"View in Phy= loviz"></a> + %endif %if trans.user: %if not display_structured: <div style=3D"float: right"> diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 templates/visualization/phyloviz.mako --- /dev/null +++ b/templates/visualization/phyloviz.mako @@ -0,0 +1,320 @@ +<%inherit file=3D"/webapps/galaxy/base_panels.mako"/> +## +<%def name=3D"init()"> + <% + self.has_left_panel=3DFalse + self.has_right_panel=3DFalse + self.active_view=3D"visualization" + self.message_box_visible=3DFalse + %> +</%def> + +<%def name=3D"stylesheets()"> + ${parent.stylesheets()} + <style> + + .node circle { + cursor: pointer; + fill: #fff; + stroke: steelblue; + stroke-width: 1.5px; + } + + .node.searchHighlight circle { + stroke-width: 3px; + stroke: #7adc26; + } + + .node.selectedHighlight circle { + stroke-width: 3px; + stroke: #dc143c; + } + + path.link { + fill: none; + stroke: #B5BBFF; + stroke-width: 4.0px; + } + + + div #phyloVizNavContainer{ + text-align: center; + width: 100%; + height: 0px; + } + + div #phyloVizNav{ + font-weight: bold; + display: inline-block; + background: transparent; + top: -2em; + position: relative; + } + + div .navControl{ + float: left; + } + + div#FloatingMenu { + left: 0; + top: 15%; + width:20%; + z-index:100; + padding: 5px; + + } + + div#SettingsMenu { + width: 25%; + top: 350px; + + } + + div#nodeSelectionView { + width: 25%; + top:70px; + } + + .Panel { + right: 0%; + z-index: 101; + position: fixed; + + ## Borrowed from galaxy modal_dialogues + background-color: white; + border: 1px solid #999; + border: 1px solid rgba(0, 0, 0, 0.3); + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -webkit-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -moz-box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + box-shadow: 0 3px 7px rgba(0, 0, 0, 0.3); + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; + -webkit-background-clip: padding-box; + -moz-background-clip: padding-box; + background-clip: padding-box; + } + + span.PhylovizCloseBtn{ + cursor: pointer; + float : right; + } + + #PhyloViz{ + width: 100%; + height: 95%; + } + + h2.PhyloVizMenuTitle{ + color: white; + } + + ## Settings Menu + .SettingMenuRows{ + margin: 2px 0 2px 0; + } + + + ## Helper Styles + .PhyloVizFloatLeft{ + float : left; + } + .icon-button.zoom-in,.icon-button.zoom-out{display:inline-block;he= ight:16px;width:16px;margin-bottom:-3px;cursor:pointer;} + .icon-button.zoom-out{background:transparent url(../images/fugue/m= agnifier-zoom-out.png) center center no-repeat;} + .icon-button.zoom-in{margin-left:10px;background:transparent url(.= ./images/fugue/magnifier-zoom.png) center center no-repeat;} + + </style> +</%def> + + +<%def name=3D"javascripts()"> + ${parent.javascripts()} + ${h.js( "galaxy.panels", "libs/d3", "mvc/data", "viz/visualization", "= viz/phyloviz")} +</%def> + + + +<%def name=3D"center_panel()"> + + <div class=3D"unified-panel-header" unselectable=3D"on"> + <div class=3D"unified-panel-header-inner"> + <div style=3D"float:left;" id=3D"title"></div> + <div style=3D"float:right;" id=3D"panelHeaderRightBtns"></div> + </div> + <div style=3D"clear: both"></div> + </div> + + + <div id=3D"phyloVizNavContainer"> + <div id=3D"phyloVizNav"> + %if config["ext"] =3D=3D "nex" and not config["saved_visualiza= tion"]: + <div id =3D "phylovizNexInfo" class=3D"navControl"> + <p>Select a tree to view:    + <select id=3D"phylovizNexSelector"> + % for tree, index in config["trees"]: + <option value=3D"${index}">${tree}</option> + % endfor + </select> + </p> + </div> + %endif + <div id=3D"phyloVizNavBtns" class=3D"navControl"> + </div> + <div class=3D"navControl"> + <p> | Alt+click to select nodes</p> + </div> + + + </div> + + </div> + + ## Node Selection Menu + <div id=3D"nodeSelectionView" class=3D"Panel"> + <div class=3D"modal-header"> + <h3 class=3D"PhyloVizMenuTitle">Search / Edit Nodes : + <span class=3D"PhylovizCloseBtn" id=3D"nodeSelCloseBtn"> X= </span> + </h3> + </div> + + <div class=3D"modal-body"> + + <div class=3D"SettingMenuRows"> + Search for nodes with: + <select id=3D"phyloVizSearchCondition" style=3D"width: 55%= "> + <option value=3D"name-containing">Name (containing)</o= ption> + <option value=3D"annotation-containing">Annotation (co= ntaining)</option> + <option value=3D"dist-greaterEqual">Distance (>=3D)</o= ption> + <option value=3D"dist-lesserEqual">Distance (<=3D)</op= tion> + </select> + <input type=3D"text" id=3D"phyloVizSearchTerm" value=3D"N= one" size=3D"15" displayLabel=3D"Distance"> + + <div class=3D"SettingMenuRows" style=3D"text-align: center= ;"> + <button id=3D"phyloVizSearchBtn" > Search! </button> + </div> + </div> + + <br/> + + <div class=3D"SettingMenuRows"> + Name: <input type=3D"text" id=3D"phyloVizSelectedNodeName"= value=3D"None" size=3D"15" disabled=3D"disabled" > + </div> + <div class=3D"SettingMenuRows"> + Dist: <input type=3D"text" id=3D"phyloVizSelectedNodeDist"= value=3D"None" size=3D"15" disabled=3D"disabled" displayLabel=3D"Distance"> + </div> + <div class=3D"SettingMenuRows"> + Annotation: + <textarea id=3D"phyloVizSelectedNodeAnnotation" disabled= =3D"disabled" ></textarea> + </div> + <div class=3D"SettingMenuRows"> + Edit: <input type=3D"checkbox" id=3D"phylovizEditNodesChec= k" value=3D"You can put custom annotations here and it will be saved"> + <button id=3D"phylovizNodeSaveChanges" style=3D"display: n= one;"> Save edits</button> + <button id=3D"phylovizNodeCancelChanges" style=3D"display:= none;"> Cancel</button> + </div> + </div> + </div> + + ## Settings Menus + <div id=3D"SettingsMenu" class=3D"Panel"> + <div class=3D"modal-header"> + <h3 class=3D"PhyloVizMenuTitle">Phyloviz Settings: + <span class=3D"PhylovizCloseBtn" id=3D"settingsCloseBtn"> = X </span> + </h3> + </div> + <div class=3D"modal-body"> + <div class=3D"SettingMenuRows"> + Phylogenetic Spacing (px per unit): <input id=3D"phyloVizT= reeSeparation" type=3D"text" value=3D"250" size=3D"10" displayLabel=3D"Phyl= ogenetic Separation"> (50-2500) + </div> + <div class=3D"SettingMenuRows"> + Vertical Spacing (px): <input type=3D"text" id=3D"phyloViz= TreeLeafHeight" value=3D"18" size=3D"10" displayLabel=3D"Vertical Spacing">= (5-30) + </div> + <div class=3D"SettingMenuRows"> + Font Size (px): <input type=3D"text" id=3D"phyloVizTreeFon= tSize" value=3D"12" size=3D"4" displayLabel=3D"Font Size"> (5-20) + </div> + + </div> + <div class=3D"modal-footer"> + <button id=3D"phylovizResetSettingsBtn" class=3D"PhyloVizFloat= Left" > Reset </button> + <button id=3D"phylovizApplySettingsBtn" class=3D"PhyloVizFloat= Right" > Apply </button> + </div> + </div> + + + + + + + <div class=3D"Panel" id=3D"FloatingMenu" style=3D"display: None;"> + + <h2>PhyloViz (<a onclick=3D"displayHelp()" href=3D"javascript:void= (0);">?</a>)</h2> + <div style=3D"display: none;"> + <h2>Summary of Interactions and Functions:</h2> + <div class=3D"hint">1. Expansion of Nodes: click or option-cli= ck to expand or collapse</div> + <div class=3D"hint">2. Zooming and translation: mousewheel, bu= ttons, click and drag, double click. Reset</div> + <div class=3D"hint">3. Tooltip: Displays "Name and Size" on mo= useOver on nodes</div> + <div class=3D"hint">4. Minimap: Currently displays an exact bu= t scaled down replicate of the tree, orange bounding box is correct for lin= ear only<br/> + Can be switched on or off</div> + <div class=3D"hint">5. Changing Layouts: Able to change betwee= n circular and linear layouts.</div> + + </div> + + <h5>Scaling & Rotation:</h5> + <button id=3D"phylovizZoomInBtn" class=3D"" > + </button> + <button id=3D"phylovizZoomOutBtn" class=3D"" > - </button> + + + <h5>Translation:</h5> + <button id=3D"phylovizTranslateUpBtn" > Up </button> + <button id=3D"phylovizTranslateDownBtn" > Down </button> + <br/> + <button id=3D"phylovizTranslateLeftBtn" > Left </button> + <button id=3D"phylovizTranslateRightBtn" > Right </button> + + + + <h5>Others:</h5> + <button id=3D"phylovizResetBtn" > Reset Zoom/Translate </button> + <button id=3D"phylovizSaveBtn" > Save vizualization </button> + <button id=3D"phylovizOpenSettingsBtn" > Settings </button> + </div> + + <div id=3D"PhyloViz" > + </div> + + <script type=3D"text/javascript"> + + function initPhyloViz(data, config) { + var phyloviz; + + // -- Initialization code |--> + phyloviz =3D new PhylovizView({ + data: data, + layout : "Linear", + config : config + }); + + // -- Render viz. -- + phyloviz.render(); + + } + + $(function firstVizLoad(){ // calls when viz is loaded for t= he first time + var config =3D JSON.parse( '${ h.to_json_string( config )}'); + var data =3D JSON.parse('${h.to_json_string(data)}'); + initPhyloViz(data, config); + }); + + </script> + +</%def> + + diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 test-data/visualization/phyloviz/1_nexus.nex --- /dev/null +++ b/test-data/visualization/phyloviz/1_nexus.nex @@ -0,0 +1,87 @@ +#NEXUS + +[!This data set was downloaded from TreeBASE, a relational database of phy= logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer= sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl= edgment from the Nexus file. + + +Generated on June 12, 2012; 23:00 GMT + +TreeBASE (cc) 1994-2008 + +Study reference: +Olariaga I., Grebenc T., Salcedo I., & Mart=C3=ADn M.P. 2012. Two new spec= ies of Hydnum +with ovoid basidiospores: H. ovoideisporum and H. vesterholtii. Mycologia,= . + +TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S128= 31] + +BEGIN TREES; + TITLE Hydnum_ITS_result; + LINK TAXA =3D Taxa1; + TRANSLATE + 1 Hydnum_aff_ellipsosporum_RUFHYD1_AJ535304, + 2 Hydnum_albidum_ALB_AY817135, + 3 Hydnum_albidum_ALBHYD1_AJ534974, + 4 Hydnum_albomagnum_ALM_DQ218305, + 5 Hydnum_ellipsosporum_ELL_AY817138, + 6 Hydnum_ellipsosporum_RUFHYD8_AJ547882, + 7 Hydnum_ovoidisporum_12317BIOFungi, + 8 Hydnum_ovoidisporum_12683BIOFungi, + 9 Hydnum_ovoidisporum_12902BIOFungi, + 10 Hydnum_ovoidisporum_14130BIOFungi, + 11 Hydnum_repandum_RE1_REP1_AJ889978, + 12 Hydnum_repandum_RE1_REP2_AJ889949, + 13 Hydnum_repandum_RE1_REP3_AY817136, + 14 Hydnum_repandum_RE1_REP6_UDB000025, + 15 Hydnum_repandum_RE1_REP7_UDB000096, + 16 Hydnum_repandum_RE1_REP8_UDB001479, + 17 Hydnum_repandum_RE1_REPHYD10_AJ547888, + 18 Hydnum_repandum_RE1_REPHYD11_AJ547886, + 19 Hydnum_repandum_RE1_REPHYD1_AJ547871, + 20 Hydnum_repandum_RE1_REPHYD3_AJ547874, + 21 Hydnum_repandum_RE1_REPHYD4_AJ547876, + 22 Hydnum_repandum_RE1_REPHYD5_AJ547875, + 23 Hydnum_repandum_RE1_REPHYD6_AJ547877, + 24 Hydnum_repandum_RE1_REPHYD7_AJ547878, + 25 Hydnum_repandum_RE1_REPHYD8_AJ547881, + 26 Hydnum_repandum_RE1_REPHYD9_AJ547883, + 27 Hydnum_repandum_RE1_RUFHYD10_AJ547866, + 28 Hydnum_repandum_RE1_RUFHYD11_AJ547889, + 29 Hydnum_repandum_RE1_RUFHYD9_AJ535305, + 30 Hydnum_rufescens_RU1_RUFHYD5_AJ547869, + 31 Hydnum_rufescens_RU1_RUFHYD6_AJ547884, + 32 Hydnum_rufescens_RU1_RUFHYD7_AJ547870, + 33 Hydnum_rufescens_RU2_REP5_DQ367902, + 34 Hydnum_rufescens_RU2_RUFHYD2_AJ535301, + 35 Hydnum_rufescens_RU3_12901BIOFungi, + 36 Hydnum_rufescens_RU3_REP4_DQ218306, + 37 Hydnum_rufescens_RU3_RUFHYD3_AJ535303, + 38 Hydnum_rufescens_RU3_RUFHYD4_AJ535302, + 39 Hydnum_rufescens_RU4_RUFHYD12_AJ839969, + 40 Hydnum_rufescens_RU4_RUFHYD16_AJ547868, + 41 Hydnum_rufescens_RU4_RUFHYD17_AJ547885, + 42 Hydnum_rufescens_RU4_UMB1_DQ367903, + 43 Hydnum_rufescens_RU5_12760BIOFungi, + 44 Hydnum_rufescens_RU5_ALBHYD2_AJ534975, + 45 Hydnum_rufescens_RU5_RUF2_DQ658890, + 46 Hydnum_rufescens_RU5_RUF4_UDB001465, + 47 Hydnum_rufescens_RU5_RUF5_UDB002423, + 48 Hydnum_rufescens_RU5_RUFHYD14_AJ547872, + 49 Hydnum_rufescens_RU6_RUF1_AY817137, + 50 Hydnum_rufescens_RU6_RUFHYD15_AJ547867, + 51 Hydnum_rufescens_wrong_taxonomy_RUF3_AM087246, + 52 Hydnum_umbilicatum_UMBHYD1_AJ534972, + 53 Hydnum_umbilicatum_UMBHYD2_AJ534973, + 54 Hydnum_vesterholtii_10429BIOFungi, + 55 Hydnum_vesterholtii_10452BIOFungi, + 56 Hydnum_vesterholtii_12330BIOFungi, + 57 Hydnum_vesterholtii_12904BIOFungi, + 58 Hydnum_vesterholtii_REPHYD12A_AJ547879, + 59 Hydnum_vesterholtii_REPHYD12C_AJ783968, + 60 Hydnum_vesterholtii_REPHYD13_AJ547887, + 61 Sistotrema_muscicola_AJ606040, + 62 Sistotrema_alboluteum_AJ606042; + TREE Fig._2 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66= ,((4:100.0,(2:100.0,3:100.0):100.0):60.639999,(((56:100.0,58:100.0,59:100.0= ):84.639999,(54:100.0,55:100.0,57:100.0,60:100.0):98.330002):92.5,(((30:100= .0,31:100.0,32:100.0):100.0,(11:100.0,12:100.0,13:100.0,14:100.0,15:100.0,1= 6:100.0,17:100.0,18:100.0,19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,24:1= 00.0,25:100.0,26:100.0):99.93):68.690002,(((33:100.0,34:100.0):49.8050005,(= 35:100.0,36:100.0,37:100.0,38:100.0):99.989998):49.8050005,((7:100.0,8:100.= 0,9:100.0,10:100.0):100.0,(42:100.0,(39:100.0,40:100.0,41:100.0):98.449997)= :86.790001,((52:100.0,53:100.0):99.93,(1:100.0,(5:97.47999949999999,6:100.0= ):97.47999949999999):100.0):53.310001,(27:100.0,(28:100.0,29:100.0,49:100.0= ,50:100.0):47.404999):47.404999,(43:100.0,44:100.0,45:100.0,46:100.0,47:100= .0,48:100.0):99.459999):29.245001):29.245001):51.580002):61.540001):49.66); + TREE PAUP_1 =3D [&R] ((62:100.0,(51:100.0,61:100.0):93.269997):49.66= ,((4:100.0,(3:100.0,2:100.0):100.0):60.639999,(((58:100.0,59:100.0,56:100.0= ):84.639999,(60:100.0,54:100.0,55:100.0,57:100.0):98.330002):92.5,(((30:100= .0,31:100.0,32:100.0):100.0,(19:100.0,20:100.0,21:100.0,22:100.0,23:100.0,2= 4:100.0,25:100.0,26:100.0,17:100.0,18:100.0,11:100.0,12:100.0,13:100.0,14:1= 00.0,15:100.0,16:100.0):99.93):68.690002,((34:100.0,33:100.0):99.610001,(37= :100.0,38:100.0,35:100.0,36:100.0):99.989998,(42:100.0,(39:100.0,41:100.0,4= 0:100.0):98.449997):86.790001,(8:100.0,7:100.0,9:100.0,10:100.0):100.0,((52= :100.0,53:100.0):99.93,(1:100.0,(5:100.0,6:100.0):94.959999):100.0):53.3100= 01,(29:100.0,27:100.0,28:100.0,50:100.0,49:100.0):94.809998,(44:100.0,43:10= 0.0,48:100.0,45:100.0,46:100.0,47:100.0):99.459999):58.490002):51.580002):6= 1.540001):49.66); + + + +END; diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 test-data/visualization/phyloviz/2_nexus.nex --- /dev/null +++ b/test-data/visualization/phyloviz/2_nexus.nex @@ -0,0 +1,96 @@ +#NEXUS + +[!This data set was downloaded from TreeBASE, a relational database of phy= logenetic knowledge. TreeBASE has been supported by the NSF, Harvard Univer= sity, Yale University, SDSC and UC Davis. Please do not remove this acknowl= edgment from the Nexus file. + + +Generated on August 18, 2012; 12:14 GMT + +TreeBASE (cc) 1994-2008 + +Study reference: +Naish D., Dyke G., Cau A., & Escuilli=C3=A9 F. 2012. A gigantic bird from = the Upper Cretaceous +of Central Asia. Biology Letters, 8(1): 97-100. + +TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S130= 08] + +BEGIN TREES; + TITLE Imported_trees; + LINK TAXA =3D Taxa1; + TRANSLATE + 1 Herrerasaurus, + 2 Tawa, + 3 Allosaurus, + 4 Alvarezsaurus, + 5 Anchiornis, + 6 Archaeopteryx, + 7 Archaeorhynchus, + 8 Avimimus, + 9 Baryonyx, + 10 Beipiaosaurus, + 11 Caenagnathus, + 12 Caudipteryx, + 13 Ceratosaurus, + 14 Chirostenotes, + 15 Citipati, + 16 Compsognathus, + 17 Confuciusornis, + 18 Dilong, + 19 Dilophosaurus, + 20 Epidendrosaurus, + 21 Epidexipteryx, + 22 Erlicosaurus, + 23 Eustreptospondylus, + 24 Gallimimus, + 25 Garudimimus, + 26 Gobipteryx, + 27 Guanlong, + 28 Haplocheirus, + 29 Harpymimus, + 30 Hebeiornis, + 31 Hongshanornis, + 32 Huoshanornis, + 33 Iberomesornis, + 34 Ichthyornis, + 35 Incisivosaurus, + 36 Jeholornis, + 37 Limusaurus, + 38 Longicrusavis, + 39 Longipteryx, + 40 Longirostravis, + 41 Majungasaurus, + 42 Masiakasaurus, + 43 Monolophosaurus, + 44 Mononykus, + 45 Neornithes, + 46 Ornitholestes, + 47 Ornithomimus, + 48 Patagonykus, + 49 Patagopteryx, + 50 Pelecanimimus, + 51 Pengornis, + 52 Protarchaeopteryx, + 53 Protopteryx, + 54 Rinchenia, + 55 Sapeornis, + 56 Segnosaurus, + 57 Shenzhousaurus, + 58 Shuvuuia, + 59 Sinornithosaurus, + 60 Sinosauropteryx, + 61 Sinovenator, + 62 Sinraptor, + 63 Syntarsus_kayentakatae, + 64 Troodon, + 65 Tyrannosaurus, + 66 Velociraptor, + 67 Yanornis, + 68 Yixianornis, + 69 Zhongjianornis, + 70 Zhongornis, + 71 Zuolong, + 72 Samrukia; + TREE Figure_1A =3D [&R] (1,(2,(((((43,(3,62)),(71,((46,((((28,(4,(48= ,(44,58)))),((((5,(61,(64,(59,66)))),(6,((36,(55,(69,(((7,34,45,49,72,(31,3= 8),(67,68)),(33,((32,((26,30),(39,40))),(51,53)))),(17,70))))),(20,21)))),(= (11,(12,(8,(14,(15,54))))),(35,52))),(10,(22,56)))),(50,(57,(29,(25,(24,47)= ))))),(16,60))),(27,(18,65))))),(9,23)),(13,(41,(37,42)))),(19,63)))); + + + +END; diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 test-data/visualization/phyloviz/3_phyloxml.xml --- /dev/null +++ b/test-data/visualization/phyloviz/3_phyloxml.xml @@ -0,0 +1,257 @@ +<?xml version=3D"1.0" encoding=3D"UTF-8"?> +<phyloxml xmlns:xsi=3D"http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation=3D"http://www.phyloxml.org http://www.phyloxml.org/1= .10/phyloxml.xsd" + xmlns=3D"http://www.phyloxml.org"> + <phylogeny rooted=3D"true"> + <clade> + <clade> + <branch_length>0.18105</branch_length> + <confidence type=3D"unknown">89.0</confidence> + <clade> + <branch_length>0.07466</branch_length> + <confidence type=3D"unknown">32.0</confidence> + <clade> + <branch_length>0.26168</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.22058</branch_length> + <confidence type=3D"unknown">89.0</confidence> + <clade> + <branch_length>0.28901</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.06584</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.02309</branch_length> + <confidence type=3D"unknown">43.0</confidenc= e> + <clade> + <branch_length>0.0746</branch_length> + <confidence type=3D"unknown">100.0</confi= dence> + <clade> + <branch_length>0.02365</branch_length> + <confidence type=3D"unknown">88.0</con= fidence> + <clade> + <name>22_MOUSE</name> + <branch_length>0.05998</branch_leng= th> + <taxonomy> + <code>MOUSE</code> + </taxonomy> + </clade> + <clade> + <name>Apaf-1_HUMAN</name> + <branch_length>0.01825</branch_leng= th> + <taxonomy> + <code>HUMAN</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>12_CANFA</name> + <branch_length>0.04683</branch_length> + <taxonomy> + <code>CANFA</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>11_CHICK</name> + <branch_length>0.15226</branch_length> + <taxonomy> + <code>CHICK</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>16_XENLA</name> + <branch_length>0.4409</branch_length> + <taxonomy> + <code>XENLA</code> + </taxonomy> + </clade> + </clade> + <clade> + <branch_length>0.17031</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <branch_length>0.10929</branch_length> + <confidence type=3D"unknown">100.0</confiden= ce> + <clade> + <name>14_FUGRU</name> + <branch_length>0.02255</branch_length> + <taxonomy> + <code>FUGRU</code> + </taxonomy> + </clade> + <clade> + <name>15_TETNG</name> + <branch_length>0.09478</branch_length> + <taxonomy> + <code>TETNG</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>17_BRARE</name> + <branch_length>0.1811</branch_length> + <taxonomy> + <code>BRARE</code> + </taxonomy> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.01594</branch_length> + <confidence type=3D"unknown">53.0</confidence> + <clade> + <branch_length>0.10709</branch_length> + <confidence type=3D"unknown">68.0</confidence> + <clade> + <name>1_BRAFL</name> + <branch_length>0.26131</branch_length> + <taxonomy> + <code>BRAFL</code> + </taxonomy> + </clade> + <clade> + <name>18_NEMVE</name> + <branch_length>0.38014</branch_length> + <taxonomy> + <code>NEMVE</code> + </taxonomy> + </clade> + </clade> + <clade> + <name>23_STRPU</name> + <branch_length>0.48179</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.34475</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>26_STRPU</name> + <branch_length>0.36374</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1319"> + <domain from=3D"18" to=3D"98" confidence=3D"= 3.4E-5">Death</domain> + <domain from=3D"189" to=3D"481" confidence= =3D"1.8E-10">NB-ARC</domain> + <domain from=3D"630" to=3D"668" confidence= =3D"8.2E-5">WD40</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>25_STRPU</name> + <branch_length>0.33137</branch_length> + <taxonomy> + <code>STRPU</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1947"> + <domain from=3D"143" to=3D"227" confidence= =3D"7.4E-5">Death</domain> + <domain from=3D"227" to=3D"550" confidence= =3D"2.0E-13">NB-ARC</domain> + <domain from=3D"697" to=3D"736" confidence= =3D"7.9E-4">WD40</domain> + <domain from=3D"745" to=3D"785" confidence= =3D"1.5">WD40</domain> + <domain from=3D"1741" to=3D"1836" confidence= =3D"2.0">Adeno_VII</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + </clade> + <clade> + <branch_length>1.31498</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>CED4_CAEEL</name> + <branch_length>0.13241</branch_length> + <taxonomy> + <code>CAEEL</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"714"> + <domain from=3D"7" to=3D"90" confidence=3D"9.2E= -14">CARD</domain> + <domain from=3D"116" to=3D"442" confidence=3D"5= .8E-151">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>31_CAEBR</name> + <branch_length>0.04777</branch_length> + <taxonomy> + <code>CAEBR</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"554"> + <domain from=3D"1" to=3D"75" confidence=3D"0.00= 46">CARD</domain> + <domain from=3D"101" to=3D"427" confidence=3D"2= .1E-123">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + </clade> + <clade> + <branch_length>0.13172</branch_length> + <confidence type=3D"unknown">45.0</confidence> + <clade> + <branch_length>0.24915</branch_length> + <confidence type=3D"unknown">95.0</confidence> + <clade> + <branch_length>0.76898</branch_length> + <confidence type=3D"unknown">100.0</confidence> + <clade> + <name>28_DROPS</name> + <branch_length>0.1732</branch_length> + <taxonomy> + <code>DROPS</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"535"> + <domain from=3D"112" to=3D"399" confidence= =3D"1.4E-5">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + <clade> + <name>Dark_DROME</name> + <branch_length>0.18863</branch_length> + <taxonomy> + <code>DROME</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"1421"> + <domain from=3D"108" to=3D"397" confidence= =3D"2.1E-5">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + <clade> + <name>29_AEDAE</name> + <branch_length>0.86398</branch_length> + <taxonomy> + <code>AEDAE</code> + </taxonomy> + <sequence> + <domain_architecture length=3D"423"> + <domain from=3D"109" to=3D"421" confidence=3D"9= .3E-6">NB-ARC</domain> + </domain_architecture> + </sequence> + </clade> + </clade> + <clade> + <name>30_TRICA</name> + <branch_length>0.97698</branch_length> + <taxonomy> + <code>TRICA</code> + </taxonomy> + </clade> + </clade> + </clade> + </clade> + </phylogeny> +</phyloxml> diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 test-data/visualization/phyloviz/4_newick.nhx --- /dev/null +++ b/test-data/visualization/phyloviz/4_newick.nhx @@ -0,0 +1,33 @@ +(((BGIOSIBCA028421_ORYSA:0.423485[&&NHX:S=3DORYSA:O=3DBGIOSIBCA028421.1:G= =3DBGIOSIBCA028421], +At5g41150_ARATH:0.273135[&&NHX:S=3DARATH:O=3DAt5g41150.1:G=3DAt5g41150] +):0.690991[&&NHX:S=3DMagnoliophyta:D=3DN:B=3D100], +(rad16_SCHPO:0.718598[&&NHX:S=3DSCHPO:O=3DSPCC970.01:G=3DSPCC970.01], +RAD1_YEAST:1.05456[&&NHX:S=3DYEAST:O=3DYPL022W.1:G=3DYPL022W] +):0.344838[&&NHX:S=3DAscomycota:D=3DN:B=3D100] +):0.103849[&&NHX:S=3DEukaryota:D=3DN:B=3D61], +((((((((ERCC4_HUMAN:0.067531[&&NHX:S=3DHUMAN:O=3DENST00000311895.3:G=3DENS= G00000175595], +Ercc4_MOUSE:0.17422[&&NHX:S=3DMOUSE:O=3DENSMUST00000023206.5:G=3DENSMUSG00= 000022545] +):0.065513[&&NHX:S=3DEuarchontoglires:D=3DN:B=3D100], +ENSMODT00000006086_MONDO:0.104633[&&NHX:S=3DMONDO:O=3DENSMODT00000006086.2= :G=3DENSMODG00000004840] +):0.083764[&&NHX:S=3DTheria:D=3DN:B=3D100], +Q5ZJP8_CHICK:0.153132[&&NHX:S=3DCHICK:O=3DENSGALT00000004716.2:G=3DENSGALG= 00000002981] +):0.057998[&&NHX:S=3DAmniota:D=3DN:B=3D100], +ENSXETT00000024054_XENTR:0.288632[&&NHX:S=3DXENTR:O=3DENSXETT00000024054.2= :G=3DENSXETG00000010991] +):0.075713[&&NHX:S=3DTetrapoda:D=3DN:B=3D100], +(zgc-63468_BRARE:0.2218[&&NHX:S=3DBRARE:O=3DENSDART00000015780.4:G=3DENSDA= RG00000014161], +NEWSINFRUT00000137921_FUGRU:0.220441[&&NHX:S=3DFUGRU:O=3DNEWSINFRUT0000013= 7921.3:G=3DNEWSINFRUG00000130312] +):0.170605[&&NHX:S=3DClupeocephala:D=3DN:B=3D100] +):0.238713[&&NHX:S=3DEuteleostomi:D=3DN:B=3D100], +ENSCINT00000011737_CIOIN:0.623567[&&NHX:S=3DCIOIN:O=3DENSCINT00000011737.2= :G=3DENSCING00000005673] +):0.07499[&&NHX:S=3DChordata:D=3DN:B=3D100], +(Sm00.scaff00195.0600_SCHMA:0.784609[&&NHX:S=3DSCHMA:O=3DSm00.scaff00195.0= 600:G=3DSm00.scaff00195.0600], +(CBG03141_CAEBR:0.093703[&&NHX:S=3DCAEBR:O=3DCBG03141:G=3DCBG03141], +NP_496498_CAEEL:0.212236[&&NHX:S=3DCAEEL:O=3DC47D12.8.1:G=3DC47D12.8] +):1.47416[&&NHX:S=3DCaenorhabditis:D=3DN:B=3D94] +):0.26906[&&NHX:S=3DBilateria:D=3DN:B=3D97] +):0.071406[&&NHX:S=3DBilateria:D=3DN:B=3D1], +(mei-9-RA_DROME:0.170289[&&NHX:S=3DDROME:O=3DCG3697-RA.3:G=3DCG3697], +GA17620-PA_DROPS:0.154817[&&NHX:S=3DDROPS:O=3DGA17620-PA:G=3DGA17620] +):0.818474[&&NHX:S=3DSophophora:D=3DN:B=3D100] +):0 +)[&&NHX:S=3DEukaryota:D=3DN]; \ No newline at end of file diff -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 -r 75a03bacdc7a3dc5b1c03f8= b02df0ab383366955 test-data/visualization/phyloviz/5_newick.nhx --- /dev/null +++ b/test-data/visualization/phyloviz/5_newick.nhx @@ -0,0 +1,1 @@ +(CAE_ELE_PORCN:0.303421 ,((((DRO_PER_PORCN:0.001000 ,DRO_PSE_PORCN:0.00100= 0 )67:0.141994 ,(DRO_ANA_PORCN:0.111899 ,(DRO_ERE_PORCN:0.030516 ,(DRO_MEL_= PORCN:0.021127 ,DRO_SEC_PORCN:0.021127 )38:0.030516 )35:0.111899 )18:0.1419= 94 )16:0.162611 ,(DRO_WIL_PORCN:0.152225 ,(DRO_VIR_PORCN:0.085057 ,DRO_MOJ_= PORCN:0.085057 )24:0.152225 )15:0.162611 )13:0.295081 ,(ANO_GAM_PORCN:0.287= 545 ,((CIO_INT_PORCN:0.100686 ,CIO_SAV_PORCN:0.100686 )19:0.275542 ,((LOA_L= OA_PORCN:0.036278 ,BRU_MAL_PORCN:0.036278 )29:0.272631 ,(((((DAN_RER_PORCN:= 0.086499 ,((TAK_RUB_PORCN:0.032609 ,TET_NIG_PORCN:0.032609 )32:0.048864 ,(G= AD_MOR_PORCN:0.039387 ,(ORY_LAT_PORCN:0.031729 ,(GAS_ACU_PORCN:0.021882 ,OR= E_NIL_PORCN:0.021882 )37:0.031729 )34:0.039387 )28:0.048864 )27:0.086499 )2= 3:0.119618 ,(LAT_CHA_PORCN:0.099348 ,((XEN_LAE_PORCN:0.033333 ,XEN_TRO_PORC= N:0.033333 )31:0.091250 ,(ANO_CAR_PORCN:0.086538 ,((MON_DOM_PORCN:0.014100 = ,(MAC_EUG_PORCN:0.005423 ,SAR_HAR_PORCN:0.005423 )57:0.014100 )42:0.062862 = ,(ORN_ANA_PORCN:0.057974 ,(GOR_GOR_PORCN:0.033876 ,(FEL_CAT_PORCN:0.022851 = ,(PRO_CAP_PORCN:0.019716 ,(CAV_POR_PORCN:0.018599 ,(ERI_EUR_PORCN:0.015518 = ,((DIP_ORD_PORCN:0.007231 ,(MUS_MUS_PORCN:0.001085 ,(RAT_NOR_PORCN:0.001000= ,CRI_GRI_PORCN:0.001000 )69:0.001085 )64:0.007231 )53:0.012954 ,(DAS_NOV_P= ORCN:0.011362 ,(LOX_AFR_PORCN:0.010575 ,(CAL_JAC_PORCN:0.010332 ,(OCH_PRI_P= ORCN:0.010063 ,(MIC_MUR_PORCN:0.009123 ,(SUS_SCR_PORCN:0.008880 ,(MYO_LUC_P= ORCN:0.008460 ,((CAN_FAM_PORCN:0.005423 ,AIL_MEL_PORCN:0.005423 )58:0.00809= 3 ,((PTE_VAM_PORCN:0.006508 ,BOS_TAU_PORCN:0.006508 )55:0.007494 ,((SPE_TRI= _PORCN:0.003254 ,TUP_BEL_PORCN:0.003254 )61:0.006929 ,((OTO_GAR_PORCN:0.001= 085 ,(ORY_CUN_PORCN:0.001000 ,TUR_TRU_PORCN:0.001000 )68:0.001085 )65:0.005= 965 ,(EQU_CAB_PORCN:0.003688 ,(MAC_MUL_PORCN:0.002711 ,(PAN_TRO_PORCN:0.001= 446 ,(HOM_SAP_PORCN:0.001085 ,(PON_ABE_PORCN:0.001000 ,NOM_LEU_PORCN:0.0010= 00 )70:0.001085 )66:0.001446 )63:0.002711 )62:0.003688 )60:0.005965 )56:0.0= 06929 )54:0.007494 )52:0.008093 )51:0.008460 )50:0.008880 )49:0.009123 )48:= 0.010063 )47:0.010332 )46:0.010575 )45:0.011362 )44:0.012954 )43:0.015518 )= 41:0.018599 )40:0.019716 )39:0.022851 )36:0.033876 )30:0.057974 )26:0.06286= 2 )25:0.086538 )22:0.091250 )21:0.099348 )20:0.119618 )17:0.214465 ,(BRA_FL= O_PORCN:0.189220 ,SAC_KOW_PORCN:0.189220 )12:0.214465 )11:0.257058 ,(NEM_VE= C_PORCN:0.246631 ,AMP_QUE_PORCN:0.246631 )9:0.257058 )8:0.266904 ,(TRI_CAS_= PORCN:0.259494 ,(PED_HUM_PORCN:0.227009 ,(NAS_VIT_PORCN:0.160241 ,(API_MEL_= PORCN:0.031851 ,(BOM_TER_PORCN:0.004808 ,BOM_IMP_PORCN:0.004808 )59:0.03185= 1 )33:0.160241 )14:0.227009 )10:0.259494 )7:0.266904 )6:0.272631 )5:0.27554= 2 )4:0.287545 )3:0.295081 )2:0.303421 )1:0.0001; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Fixed truncation of downloaded fasta files.
by Bitbucket 27 Aug '12

27 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/89dbce43ba88/ changeset: 89dbce43ba88 user: inithello date: 2012-08-27 18:52:43 summary: Fixed truncation of downloaded fasta files. affected #: 1 file diff -r 90aa7ae565d60d38c90f444322a68b55fc895701 -r 89dbce43ba88afdc3e6265feea7e7e042bb030a7 lib/galaxy/jobs/deferred/genome_transfer.py --- a/lib/galaxy/jobs/deferred/genome_transfer.py +++ b/lib/galaxy/jobs/deferred/genome_transfer.py @@ -115,15 +115,16 @@ files = tar.getmembers() for filename in files: z = tar.extractfile(filename) - try: - chunk = z.read( CHUNK_SIZE ) - except IOError: - os.close( fd ) - log.error( 'Problem decompressing compressed data' ) - exit() - if not chunk: - break - os.write( fd, chunk ) + while 1: + try: + chunk = z.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + log.error( 'Problem decompressing compressed data' ) + exit() + if not chunk: + break + os.write( fd, chunk ) os.write( fd, '\n' ) os.close( fd ) tar.close() 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: afgane: style: explicitly define a color for the masthead highlight (i.e., gradient top)
by Bitbucket 27 Aug '12

27 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/90aa7ae565d6/ changeset: 90aa7ae565d6 user: afgane date: 2012-08-27 02:57:31 summary: style: explicitly define a color for the masthead highlight (i.e., gradient top) affected #: 2 files diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r 90aa7ae565d60d38c90f444322a68b55fc895701 static/june_2007_style/blue_colors.ini --- a/static/june_2007_style/blue_colors.ini +++ b/static/june_2007_style/blue_colors.ini @@ -55,6 +55,7 @@ peek_table_header=#023858 # Masthead masthead_bg=#2C3143 +masthead_bg_highlight=#333 masthead_text=#eeeeee masthead_bg_hatch=- masthead_link=#eeeeee diff -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec -r 90aa7ae565d60d38c90f444322a68b55fc895701 static/june_2007_style/galaxy_bootstrap_variables.less --- a/static/june_2007_style/galaxy_bootstrap_variables.less +++ b/static/june_2007_style/galaxy_bootstrap_variables.less @@ -144,7 +144,7 @@ // ------------------------- @navbarHeight: 32px; @navbarBackground: @masthead_bg; -@navbarBackgroundHighlight: @grayDark; +@navbarBackgroundHighlight: @masthead_bg_highlight; @navbarText: @grayLight; @navbarLinkColor: @grayLight; 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: jgoecks: Do not use enable_tracks or enable_pages options anymore; visualizations and pages are enabled for all instances.
by Bitbucket 25 Aug '12

25 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b1f2c51d6bd8/ changeset: b1f2c51d6bd8 user: jgoecks date: 2012-08-25 00:43:33 summary: Do not use enable_tracks or enable_pages options anymore; visualizations and pages are enabled for all instances. affected #: 3 files diff -r 3d32fa091951e9aa72f3c69272960b3f6b648722 -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -218,7 +218,7 @@ %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> - %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks(): + %if data.ext in app.datatypes_registry.get_available_tracks(): <% if data.dbkey != '?': data_url = h.url_for( controller='tracks', action='list_tracks', dbkey=data.dbkey ) diff -r 3d32fa091951e9aa72f3c69272960b3f6b648722 -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -78,12 +78,10 @@ [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], None, [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], - [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ] - ] - if app.config.get_bool( 'enable_tracks', False ): - menu_options.append( [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ] ) - if app.config.get_bool( 'enable_pages', False ): - menu_options.append( [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] ) + [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ], + [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ], + [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] + ] tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options ) %> @@ -98,15 +96,13 @@ %> ## Visualization menu. - %if app.config.get_bool( 'enable_tracks', False ): - <% - menu_options = [ - [_('New Visualization'), h.url_for( controller='/tracks', action='index' ) ], - [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] - ] - tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) - %> - %endif + <% + menu_options = [ + [_('New Visualization'), h.url_for( controller='/tracks', action='index' ) ], + [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] + ] + tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) + %> ## Cloud menu. %if app.config.get_bool( 'enable_cloud_launch', False ): @@ -155,8 +151,7 @@ menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) else: menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - if app.config.get_bool( 'enable_tracks', False ): - menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) + menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) if app.config.require_login: logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' ) else: @@ -165,8 +160,7 @@ menu_options.append( None ) menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) - if app.config.get_bool( 'enable_pages', False ): - menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) + menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) if app.config.use_remote_user: menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) diff -r 3d32fa091951e9aa72f3c69272960b3f6b648722 -r b1f2c51d6bd8d8b1aecce8f62304cc2df278ccec universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -506,15 +506,6 @@ # Enable Galaxy to communicate directly with a sequencer #enable_sequencer_communication = False -# Enable Galaxy's built-in visualization module, Trackster. -#enable_tracks = True - -# Enable Galaxy Pages. Pages are custom webpages that include embedded Galaxy items, -# such as datasets, histories, workflows, and visualizations; pages are useful for -# documenting and sharing multiple analyses or workflows. Pages are created using a -# WYSIWYG editor that is very similar to a word processor. -#enable_pages = True - # Enable authentication via OpenID. Allows users to log in to their Galaxy # account by authenticating with an OpenID provider. #enable_openid = False 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: jgoecks: Enable function to be used for generating a grid operation link; use this functionality to generate link for viewing/editing visualization.
by Bitbucket 25 Aug '12

25 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3d32fa091951/ changeset: 3d32fa091951 user: jgoecks date: 2012-08-25 00:15:29 summary: Enable function to be used for generating a grid operation link; use this functionality to generate link for viewing/editing visualization. affected #: 2 files diff -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d -r 3d32fa091951e9aa72f3c69272960b3f6b648722 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -5,7 +5,7 @@ from galaxy.util.sanitize_html import sanitize_html class VisualizationListGrid( grids.Grid ): - def get_link( item ): + def get_url_args( item ): """ Returns dictionary used to create item link. """ @@ -24,7 +24,7 @@ default_sort_key = "-update_time" default_filter = dict( title="All", deleted="False", tags="All", sharing="All" ) columns = [ - grids.TextColumn( "Title", key="title", attach_popup=True, link=get_link ), + grids.TextColumn( "Title", key="title", attach_popup=True, link=get_url_args ), grids.TextColumn( "Type", key="type" ), grids.TextColumn( "Dbkey", key="dbkey" ), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), @@ -42,7 +42,7 @@ grids.GridAction( "Create new visualization", dict( action='create' ) ) ] operations = [ - grids.GridOperation( "View/Edit", allow_multiple=False, url_args=dict( controller='tracks', action='browser' ) ), + grids.GridOperation( "View/Edit", allow_multiple=False, url_args=get_url_args ), grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ), grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='clone') ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), diff -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d -r 3d32fa091951e9aa72f3c69272960b3f6b648722 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -728,9 +728,12 @@ self.global_operation = global_operation def get_url_args( self, item ): if self.url_args: - temp = dict( self.url_args ) - temp['id'] = item.id - return temp + if hasattr( self.url_args, '__call__' ): + url_args = self.url_args( item ) + else: + url_args = dict( self.url_args ) + url_args['id'] = item.id + return url_args else: return dict( operation=self.label, id=item.id ) def allowed( self, item ): 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: inithello: Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/df99df26d92f/ changeset: df99df26d92f user: inithello date: 2012-08-23 22:36:58 summary: Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text. affected #: 4 files diff -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d cron/get_ncbi.py --- /dev/null +++ b/cron/get_ncbi.py @@ -0,0 +1,93 @@ +import urllib, pkg_resources, os +pkg_resources.require( 'elementtree' ) +from elementtree import ElementTree, ElementInclude +from xml.parsers.expat import ExpatError as XMLParseErrorThing +import sys + +import pkg_resources + +class GetListing: + def __init__( self, data ): + self.tree = ElementTree.parse( data ) + self.root = self.tree.getroot() + ElementInclude.include(self.root) + + def xml_text(self, name=None): + """Returns the text inside an element""" + root = self.root + if name is not None: + # Try attribute first + val = root.get(name) + if val: + return val + # Then try as element + elem = root.find(name) + else: + elem = root + if elem is not None and elem.text: + text = ''.join(elem.text.splitlines()) + return text.strip() + # No luck, return empty string + return '' + +def dlcachefile( webenv, querykey, i, results ): + url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehis…' + fp = urllib.urlopen( url ) + search = GetListing( fp ) + fp.close() + webenv = search.xml_text( 'WebEnv' ) + querykey = search.xml_text( 'QueryKey' ) + url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&WebEn…' % ( webenv, querykey, i, results ) + fp = urllib.urlopen( url ) + cachefile = os.tmpfile() + for line in fp: + cachefile.write( line ) + fp.close() + cachefile.flush() + cachefile.seek(0) + return cachefile + + +url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehis…' +fp = urllib.urlopen( url ) +results = GetListing( fp ) +fp.close() + +webenv = results.xml_text( 'WebEnv' ) +querykey = results.xml_text( 'QueryKey' ) +counts = int( results.xml_text( 'Count' ) ) +results = 10000 +found = 0 + +for i in range(0, counts + results, results): + rets = dict() + cache = dlcachefile( webenv, querykey, i, results ) + try: + xmldoc = GetListing( cache ) + except (IOError, XMLParseErrorThing): + cache = dlcachefile( webenv, querykey, i, results ) + try: + xmldoc = GetListing( cache ) + except (IOError, XMLParseErrorThing): + cache.close() + exit() + pass + finally: + cache.close() + entries = xmldoc.root.findall( 'DocSum' ) + for entry in entries: + dbkey = None + children = entry.findall('Item') + for item in children: + rets[ item.get('Name') ] = item.text + if not rets['Caption'].startswith('NC_'): + continue + + for ret in rets['Extra'].split('|'): + if not ret.startswith('NC_'): + continue + else: + dbkey = ret + break + if dbkey is not None: + print '\t'.join( [ dbkey, rets['Title'] ] ) diff -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d cron/updatencbi.sh.sample --- /dev/null +++ b/cron/updatencbi.sh.sample @@ -0,0 +1,42 @@ +#!/bin/sh +# +# Script to update NCBI shared data tables. The idea is to update, but if +# the update fails, not replace current data/tables with error +# messages. + +# Edit this line to refer to galaxy's path: +GALAXY=/path/to/galaxy +PYTHONPATH=${GALAXY}/lib +export PYTHONPATH + +# setup directories +echo "Creating required directories." +DIRS=" +${GALAXY}/tool-data/shared/ncbi +${GALAXY}/tool-data/shared/ncbi/new +" +for dir in $DIRS; do + if [ ! -d $dir ]; then + echo "Creating $dir" + mkdir $dir + else + echo "$dir already exists, continuing." + fi +done + +date +echo "Updating NCBI shared data tables." + +# Try to build "builds.txt" +echo "Updating builds.txt" +python ${GALAXY}/cron/get_ncbi.py > ${GALAXY}/tool-data/shared/ncbi/new/builds.txt +if [ $? -eq 0 ] +then + diff ${GALAXY}/tool-data/shared/ncbi/new/builds.txt ${GALAXY}/tool-data/shared/ncbi/builds.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ncbi/new/builds.txt ${GALAXY}/tool-data/shared/ncbi/builds.txt + fi +else + echo "Failed to update builds.txt" >&2 +fi diff -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -75,7 +75,7 @@ @web.require_admin def add_genome( self, trans, **kwd ): if trans.app.config.get_bool( 'enable_beta_job_managers', False ) == False: - return trans.fill_template( '/admin/data_admin/betajob.mako' ) + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.' ) dbkeys = trans.ucsc_builds ensemblkeys = trans.ensembl_builds ncbikeys = trans.ncbi_builds @@ -137,9 +137,10 @@ dbkey = build.split( ': ' )[0] longname = build.split( ': ' )[-1] url = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' % dbkey - elif source == 'Broad': - dbkey = params.get('broad_dbkey', '')[0] - url = 'ftp://ftp.broadinstitute.org/pub/seq/references/%s.fasta' % dbkey + elif source == 'URL': + dbkey = params.get( 'url_dbkey', '' ) + url = params.get( 'url', None ) + longname = params.get( 'longname', None ) elif source == 'UCSC': longname = None for build in trans.ucsc_builds: @@ -198,7 +199,9 @@ break url = 'ftp://ftp.ensembl.org/pub/release-%s/fasta/%s/dna/%s.%s.%s.dna.toplevel.fa.…' % ( release, pathname.lower(), pathname, dbkey, release ) else: - raise ValueError, 'Somehow an invalid data source was specified.' + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Somehow an invalid data source was specified.' ) + if url is None: + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='Unable to generate a valid URL with the specified parameters.' ) params = dict( protocol='http', name=dbkey, datatype='fasta', url=url, user=trans.user.id ) jobid = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job( trans, url, dbkey, longname, indexers ) chainjob = [] diff -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c -r df99df26d92fa8a5e3eaef4fd1eef4b6ee18f86d templates/admin/data_admin/data_form.mako --- a/templates/admin/data_admin/data_form.mako +++ b/templates/admin/data_admin/data_form.mako @@ -53,7 +53,7 @@ <label for="source">Data Source</label><select id="datasource" name="source" label="Data Source"><option value="UCSC">UCSC</option> - <option value="Broad">Broad Institute</option> + <option value="URL">Direct Link</option><option value="NCBI">NCBI</option><option value="Ensembl">EnsemblGenome</option></select> @@ -75,22 +75,31 @@ </div></div><h2>Parameters</h2> - <div id="params_Broad" class="params-block"> + <div id="params_URL" class="params-block"><div class="form-row"> - <label for="longname">Internal Name</label> - <input name="longname" type="text" label="Internal Name" /> + <label for="longname">Long Name</label> + <input name="longname" type="text" label="Long Name" /><div style="clear: both;"> </div> + <div class="toolParamHelp" style="clear: both;"> + A descriptive name for this build. + </div></div><div class="form-row"> - <label for="uniqid">Internal Unique Identifier</label> - <input name="uniqid" type="text" label="Internal Identifier" /> + <label for="url_dbkey">DB Key</label> + <input name="url_dbkey" type="text" label="DB Key" /><div style="clear: both;"> </div> + <div class="toolParamHelp" style="clear: both;"> + The internal DB key for this build. WARNING: Using a value that already exists in one or more .loc files may have unpredictable results. + </div></div><div id="dlparams"><div class="form-row"> - <label for="broad_dbkey">External Name</label> - <input name="broad_dbkey" type="text" label="Genome Unique Name" /> + <label for="url">URL</label> + <input name="url" type="text" label="URL" /><div style="clear: both;"> </div> + <div class="toolParamHelp" style="clear: both;"> + The URL to download this build from. + </div></div></div></div> @@ -101,7 +110,9 @@ <input type="text" class="text-and-autocomplete-select ac_input" size="40" name="ncbi_name" id="ncbi_name" value="" /></div><div class="toolParamHelp" style="clear: both;"> - If you can't find the build you want in this list, <insert link to instructions here> + If you can't find the build you want in this list, open a terminal and execute + <pre>sh cron/updatencbi.sh</pre> + in your galaxy root directory. </div></div></div> @@ -116,7 +127,9 @@ </select></div><div class="toolParamHelp" style="clear: both;"> - If you can't find the build you want in this list, <insert link to instructions here> + If you can't find the build you want in this list, open a terminal and execute + <pre>sh cron/updateensembl.sh</pre> + in your galaxy root directory. </div></div></div> @@ -135,7 +148,9 @@ </select></div><div class="toolParamHelp" style="clear: both;"> - If you can't find the build you want in this list, <insert link to instructions here> + If you can't find the build you want in this list, open a terminal and execute + <pre>sh cron/updateucsc.sh</pre> + in your galaxy root directory. </div></div></div> @@ -145,7 +160,6 @@ <script type="text/javascript"> $(document).ready(function() { checkDataSource(); - // Replace dbkey select with search+select. }); $('#datasource').change(function() { checkDataSource(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Require pileup format as input to pileup parser tool.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/429c1054c13e/ changeset: 429c1054c13e user: jgoecks date: 2012-08-23 21:58:11 summary: Require pileup format as input to pileup parser tool. affected #: 1 file diff -r 3bd47802bff7946958b0a616e3d42aef50c63277 -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml +++ b/tools/samtools/pileup_parser.xml @@ -7,7 +7,7 @@ #end if# </command><inputs> - <param name="input" type="data" format="tabular" label="Select dataset"/> + <param name="input" type="data" format="pileup" label="Select dataset"/><conditional name="pileup_type"><param name="type_select" type="select" label="which contains" help="See "Types of pileup datasets" below for examples"><option value="six" selected="true">Pileup with six columns (simple)</option> 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: jgoecks: Trackster: for feature tracks, only draw name if available.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3bd47802bff7/ changeset: 3bd47802bff7 user: jgoecks date: 2012-08-23 19:56:34 summary: Trackster: for feature tracks, only draw name if available. affected #: 1 file diff -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 -r 3bd47802bff7946958b0a616e3d42aef50c63277 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -5690,7 +5690,7 @@ ctx.globalAlpha = 1; // Draw label for Pack mode. - if (mode === "Pack" && feature_start > tile_low) { + if (feature_name && mode === "Pack" && feature_start > tile_low) { ctx.fillStyle = label_color; // FIXME: assumption here that the entire view starts at 0 if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { 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: 5 new changesets
by Bitbucket 23 Aug '12

23 Aug '12

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5e12fae63066/ changeset: 5e12fae63066 user: jmchilton date: 2012-08-22 04:05:53 summary: Roles API bug fixes. affected #: 1 file diff -r e27c236c05e5d65f3ce92f271a712419e7fd73a5 -r 5e12fae63066b12cf3f7f4342ad0ebecb5407a72 lib/galaxy/web/api/roles.py --- a/lib/galaxy/web/api/roles.py +++ b/lib/galaxy/web/api/roles.py @@ -17,7 +17,7 @@ """ rval = [] for role in trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.deleted == False ): - if trans.app.security_agent.ok_to_display( trans.user, role ): + if trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role ): item = role.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id( role.id ) item['url'] = url_for( 'role', id=encoded_id ) @@ -32,7 +32,7 @@ """ role_id = id try: - role_id = trans.security.decode_id( role_id ) + decoded_role_id = trans.security.decode_id( role_id ) except TypeError: trans.response.status = 400 return "Malformed role id ( %s ) specified, unable to decode." % str( role_id ) @@ -40,7 +40,7 @@ role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) except: role = None - if not role or not trans.app.security_agent.ok_to_display( trans.user, role ): + if not role or not (trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role )): trans.response.status = 400 return "Invalid role id ( %s ) specified." % str( role_id ) item = role.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } ) https://bitbucket.org/galaxy/galaxy-central/changeset/558547d5329f/ changeset: 558547d5329f user: jmchilton date: 2012-08-22 06:05:05 summary: Fix library permissions API which has been broken since security API changes in 8731db1b2bfb (June 2011). affected #: 1 file diff -r 5e12fae63066b12cf3f7f4342ad0ebecb5407a72 -r 558547d5329f49cad685056cd4284e8e7661cffc lib/galaxy/web/api/permissions.py --- a/lib/galaxy/web/api/permissions.py +++ b/lib/galaxy/web/api/permissions.py @@ -40,10 +40,10 @@ role_params = params.get( k + '_in', [] ) in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( trans.security.decode_id( x ) ) for x in util.listify( role_params ) ] permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( library, permissions ) + trans.app.security_agent.set_all_library_permissions( trans, library, permissions ) trans.sa_session.refresh( library ) # Copy the permissions to the root folder - trans.app.security_agent.copy_library_permissions( library, library.root_folder ) + trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder ) message = "Permissions updated for library '%s'." % library.name item = library.get_api_value( view='element' ) https://bitbucket.org/galaxy/galaxy-central/changeset/a186a4bd7bae/ changeset: a186a4bd7bae user: jmchilton date: 2012-08-22 23:57:04 summary: Create method in libraries API should return the created library not an array containing only the created library. This was confirmed by dannon in the comments on issue 802. affected #: 1 file diff -r 558547d5329f49cad685056cd4284e8e7661cffc -r a186a4bd7bae84459de066b22d49e226e2112ce1 lib/galaxy/web/api/libraries.py --- a/lib/galaxy/web/api/libraries.py +++ b/lib/galaxy/web/api/libraries.py @@ -98,7 +98,7 @@ rval['url'] = url_for( 'library', id=encoded_id ) rval['name'] = name rval['id'] = encoded_id - return [ rval ] + return rval @web.expose_api def delete( self, trans, id, **kwd ): https://bitbucket.org/galaxy/galaxy-central/changeset/bec712216582/ changeset: bec712216582 user: jmchilton date: 2012-08-23 00:05:53 summary: Include created history url in json rendered by histories API on successful history creation. Dannon verified this is the desired behvaior in the comments on issue 802 in bitbucket. affected #: 1 file diff -r a186a4bd7bae84459de066b22d49e226e2112ce1 -r bec712216582134338a733ccd85bc4dac25353c4 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -109,6 +109,7 @@ trans.sa_session.add( new_history ) trans.sa_session.flush() item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) + item['url'] = url_for( 'history', id=item['id'] ) return item @web.expose_api https://bitbucket.org/galaxy/galaxy-central/changeset/c06d0ea23c90/ changeset: c06d0ea23c90 user: dannon date: 2012-08-23 15:34:43 summary: Merged in jmchilton/galaxy-central-roles-api-fixes (pull request #62) affected #: 4 files diff -r 146d0f4c29decefb441a7133b4aa16442afdacb1 -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -109,6 +109,7 @@ trans.sa_session.add( new_history ) trans.sa_session.flush() item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) + item['url'] = url_for( 'history', id=item['id'] ) return item @web.expose_api diff -r 146d0f4c29decefb441a7133b4aa16442afdacb1 -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 lib/galaxy/web/api/libraries.py --- a/lib/galaxy/web/api/libraries.py +++ b/lib/galaxy/web/api/libraries.py @@ -98,7 +98,7 @@ rval['url'] = url_for( 'library', id=encoded_id ) rval['name'] = name rval['id'] = encoded_id - return [ rval ] + return rval @web.expose_api def delete( self, trans, id, **kwd ): diff -r 146d0f4c29decefb441a7133b4aa16442afdacb1 -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 lib/galaxy/web/api/permissions.py --- a/lib/galaxy/web/api/permissions.py +++ b/lib/galaxy/web/api/permissions.py @@ -40,10 +40,10 @@ role_params = params.get( k + '_in', [] ) in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( trans.security.decode_id( x ) ) for x in util.listify( role_params ) ] permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( library, permissions ) + trans.app.security_agent.set_all_library_permissions( trans, library, permissions ) trans.sa_session.refresh( library ) # Copy the permissions to the root folder - trans.app.security_agent.copy_library_permissions( library, library.root_folder ) + trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder ) message = "Permissions updated for library '%s'." % library.name item = library.get_api_value( view='element' ) diff -r 146d0f4c29decefb441a7133b4aa16442afdacb1 -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 lib/galaxy/web/api/roles.py --- a/lib/galaxy/web/api/roles.py +++ b/lib/galaxy/web/api/roles.py @@ -17,7 +17,7 @@ """ rval = [] for role in trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.deleted == False ): - if trans.app.security_agent.ok_to_display( trans.user, role ): + if trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role ): item = role.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id( role.id ) item['url'] = url_for( 'role', id=encoded_id ) @@ -32,7 +32,7 @@ """ role_id = id try: - role_id = trans.security.decode_id( role_id ) + decoded_role_id = trans.security.decode_id( role_id ) except TypeError: trans.response.status = 400 return "Malformed role id ( %s ) specified, unable to decode." % str( role_id ) @@ -40,7 +40,7 @@ role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) except: role = None - if not role or not trans.app.security_agent.ok_to_display( trans.user, role ): + if not role or not (trans.user_is_admin() or trans.app.security_agent.ok_to_display( trans.user, role )): trans.response.status = 400 return "Invalid role id ( %s ) specified." % str( role_id ) item = role.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fix for handling missing quality values in VCF data provider + some whitespace. Thanks to Jim Johnson for fix.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/146d0f4c29de/ changeset: 146d0f4c29de user: jgoecks date: 2012-08-23 15:04:08 summary: Fix for handling missing quality values in VCF data provider + some whitespace. Thanks to Jim Johnson for fix. affected #: 1 file diff -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 -r 146d0f4c29decefb441a7133b4aa16442afdacb1 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -625,7 +625,8 @@ end = start + len( new_seq ) # Pack line. - payload = [ hash( line ), + payload = [ + hash( line ), start, end, # ID: @@ -634,7 +635,8 @@ # TODO? VCF does not have strand, so default to positive. "+", new_seq, - float( feature[5] ) ] + None if feature[5] == '.' else float( feature[5] ) + ] rval.append(payload) return { 'data': rval, 'message': message } 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: jgoecks: Update datatypes conf sample to include bedgraph to bigwig converter.
by Bitbucket 23 Aug '12

23 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dd8a939cf0a2/ changeset: dd8a939cf0a2 user: jgoecks date: 2012-08-23 04:54:54 summary: Update datatypes conf sample to include bedgraph to bigwig converter. affected #: 1 file diff -r f0e26a4f7dd91d9a632913ae450e285e37a9a302 -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -23,7 +23,9 @@ <display file="genetrack.xml" /><display file="igb/bed.xml" /></datatype> - <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" /> + <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"> + <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + </datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"><converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/> 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: jgoecks: Output sorted BAM from Bowtie2.
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f0e26a4f7dd9/ changeset: f0e26a4f7dd9 user: jgoecks date: 2012-08-22 22:49:12 summary: Output sorted BAM from Bowtie2. affected #: 1 file diff -r 695159af542b44ac5038d1b3cc401b3f4b98d2e3 -r f0e26a4f7dd91d9a632913ae450e285e37a9a302 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -64,8 +64,8 @@ else: index_path = options.index_path - # Build bowtie command. - cmd = 'bowtie2 %s -x %s %s | samtools view -Sb - > %s' + # Build bowtie command; use view and sort to create sorted bam. + cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - sorted > %s' # Set up reads. if options.single_paired == 'paired': 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: dannon: Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this.
by Bitbucket 22 Aug '12

22 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/695159af542b/ changeset: 695159af542b user: dannon date: 2012-08-22 22:12:59 summary: Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this. affected #: 36 files Diff too large to display. 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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