[galaxy-commits] commit/galaxy-central: 5 new changesets

16 Jan 2014

5 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/315465b38434/
Changeset:   315465b38434
User:        nsoranzo
Date:        2014-01-15 17:51:36
Summary:     PEP-8 and unused variables fixes.
Affected #:  1 file

diff -r 8deba81aad81fd565a7e33bad10bb8e741a6172b -r 315465b38434aff44e8863c6f2ea7e9ab549beb2 lib/galaxy/webapps/galaxy/api/workflows.py

--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -241,7 +241,7 @@
         outputs = util.odict.odict()
         rval['history'] = trans.security.encode_id(history.id)
         rval['outputs'] = []
-        for i, step in enumerate( workflow.steps ):
+        for step in workflow.steps:
             job = None
             if step.type == 'tool' or step.type is None:
                 tool = self.app.toolbox.get_tool( step.tool_id )
@@ -285,7 +285,7 @@
         """
         try:
             stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id))
-        except Exception,e:
+        except Exception, e:
             return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e ))
         # check to see if user has permissions to selected workflow
         if stored_workflow.user != trans.user and not trans.user_is_admin():
@@ -293,7 +293,7 @@
                 trans.response.status = 400
                 return("Workflow is not owned by or shared with current user")
 
-        ret_dict = self._workflow_to_dict( trans, stored_workflow );
+        ret_dict = self._workflow_to_dict( trans, stored_workflow )
         if not ret_dict:
             #This workflow has a tool that's missing from the distribution
             trans.response.status = 400
@@ -309,7 +309,7 @@
 
         copied from galaxy.web.controllers.workflows.py (delete)
         """
-        workflow_id = id;
+        workflow_id = id
 
         try:
             stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id))
@@ -341,23 +341,23 @@
         # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database
         """
 
-        data = payload['workflow'];
+        data = payload['workflow']
         workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" )
 
         # galaxy workflow newly created id
-        workflow_id = workflow.id;
+        workflow_id = workflow.id
         # api encoded, id
-        encoded_id = trans.security.encode_id(workflow_id);
+        encoded_id = trans.security.encode_id(workflow_id)
 
         # return list
-        rval= [];
+        rval = []
 
         item = workflow.to_dict(value_mapper={'id':trans.security.encode_id})
         item['url'] = url_for('workflow', id=encoded_id)
 
-        rval.append(item);
+        rval.append(item)
 
-        return item;
+        return item
 
     def _workflow_from_dict( self, trans, data, source=None ):
         """
@@ -386,7 +386,7 @@
         # will be ( tool_id, tool_name, tool_version ).
         missing_tool_tups = []
         # First pass to build step objects and populate basic values
-        for key, step_dict in data[ 'steps' ].iteritems():
+        for step_dict in data[ 'steps' ].itervalues():
             # Create the model class for the step
             step = model.WorkflowStep()
             steps.append( step )
@@ -530,7 +530,7 @@
                         step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } )
                     elif input_type == dict:
                         # Input type is described by a dict, e.g. indexed parameters.
-                        for partname, partval in val.items():
+                        for partval in val.values():
                             if type( partval ) == RuntimeValue:
                                 step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } )
             # User outputs


https://bitbucket.org/galaxy/galaxy-central/commits/4fb2ce004601/
Changeset:   4fb2ce004601
User:        nsoranzo
Date:        2014-01-15 18:04:33
Summary:     Let /api/workflows show() method display also importable workflows.
Affected #:  1 file

diff -r 315465b38434aff44e8863c6f2ea7e9ab549beb2 -r 4fb2ce004601f50d63c4884006d453eee580a85a lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -60,10 +60,10 @@
             return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id)
         try:
             stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id)
-            if stored_workflow.user != trans.user and not trans.user_is_admin():
+            if stored_workflow.importable == False and stored_workflow.user != trans.user and not trans.user_is_admin():
                 if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
                     trans.response.status = 400
-                    return("Workflow is not owned by or shared with current user")
+                    return("Workflow is neither importable, nor owned by or shared with current user")
         except:
             trans.response.status = 400
             return "That workflow does not exist."


https://bitbucket.org/galaxy/galaxy-central/commits/33af32773cba/
Changeset:   33af32773cba
User:        nsoranzo
Date:        2014-01-15 18:22:51
Summary:     Add show_published param to /api/workflows index() method to display also published workflows.
Affected #:  1 file

diff -r 4fb2ce004601f50d63c4884006d453eee580a85a -r 33af32773cba309fde44ced5fba78ce8fc64078b lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -5,7 +5,7 @@
 """
 
 import logging
-from sqlalchemy import desc
+from sqlalchemy import desc, or_
 from galaxy import util
 from galaxy import web
 from galaxy import model
@@ -26,10 +26,17 @@
         GET /api/workflows
 
         Displays a collection of workflows.
+
+        :param  show_published:      if True, show also published workflows
+        :type   show_published:      boolean
         """
+        show_published = util.string_as_bool( kwd.get( 'show_published', 'False' ) )
         rval = []
-        for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).filter_by(
-                user=trans.user, deleted=False).order_by(
+        filter1 = ( trans.app.model.StoredWorkflow.user == trans.user )
+        if show_published:
+            filter1 = or_( filter1, ( trans.app.model.StoredWorkflow.published == True ) )
+        for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).filter(
+                filter1, trans.app.model.StoredWorkflow.table.c.deleted == False ).order_by(
                 desc(trans.app.model.StoredWorkflow.table.c.update_time)).all():
             item = wf.to_dict(value_mapper={'id':trans.security.encode_id})
             encoded_id = trans.security.encode_id(wf.id)


https://bitbucket.org/galaxy/galaxy-central/commits/f4be6a4360b6/
Changeset:   f4be6a4360b6
User:        nsoranzo
Date:        2014-01-15 18:17:24
Summary:     Move core code for importing a shared workflow to UsesStoredWorkflowMixin.
Affected #:  4 files

diff -r 33af32773cba309fde44ced5fba78ce8fc64078b -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -33,7 +33,7 @@
 from galaxy.model.orm import eagerload, eagerload_all, desc
 from galaxy.security.validate_user_input import validate_publicname
 from galaxy.util.sanitize_html import sanitize_html
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.model.item_attrs import Dictifiable, UsesAnnotations
 
 from galaxy.datatypes.interval import ChromatinInteractions
 from galaxy.datatypes.data import Text
@@ -1497,7 +1497,7 @@
         return return_message
 
 
-class UsesStoredWorkflowMixin( SharableItemSecurityMixin ):
+class UsesStoredWorkflowMixin( SharableItemSecurityMixin, UsesAnnotations ):
     """ Mixin for controllers that use StoredWorkflow objects. """
 
     def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ):
@@ -1539,6 +1539,26 @@
             # Connections by input name
             step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
 
+    def _import_shared_workflow( self, trans, stored):
+        """ """
+        # Copy workflow.
+        imported_stored = model.StoredWorkflow()
+        imported_stored.name = "imported: " + stored.name
+        imported_stored.latest_workflow = stored.latest_workflow
+        imported_stored.user = trans.user
+        # Save new workflow.
+        session = trans.sa_session
+        session.add( imported_stored )
+        session.flush()
+
+        # Copy annotations.
+        self.copy_item_annotation( session, stored.user, stored, imported_stored.user, imported_stored )
+        for order_index, step in enumerate( stored.latest_workflow.steps ):
+            self.copy_item_annotation( session, stored.user, step, \
+                                        imported_stored.user, imported_stored.latest_workflow.steps[order_index] )
+        session.flush()
+        return imported_stored
+
 
 class UsesFormDefinitionsMixin:
     """Mixin for controllers that use Galaxy form objects."""

diff -r 33af32773cba309fde44ced5fba78ce8fc64078b -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 lib/galaxy/webapps/galaxy/api/annotations.py
--- a/lib/galaxy/webapps/galaxy/api/annotations.py
+++ b/lib/galaxy/webapps/galaxy/api/annotations.py
@@ -3,14 +3,13 @@
 """
 import logging
 from galaxy import web
-from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web.base.controller import BaseAPIController, HTTPNotImplemented, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesStoredWorkflowMixin
 
 log = logging.getLogger( __name__ )
 
 
-class BaseAnnotationsController( BaseAPIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ):
+class BaseAnnotationsController( BaseAPIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ):
 
     @web.expose_api
     def index( self, trans, **kwd ):

diff -r 33af32773cba309fde44ced5fba78ce8fc64078b -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 lib/galaxy/webapps/galaxy/controllers/page.py
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -1,7 +1,7 @@
 from sqlalchemy import desc, and_
 from galaxy import model, web
 from galaxy.web import error, url_for
-from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
+from galaxy.model.item_attrs import UsesItemRatings
 from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesHistoryMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin
 from galaxy.web.framework.helpers import time_ago, grids
 from galaxy import util
@@ -274,7 +274,7 @@
         # Default behavior:
         _BaseHTMLProcessor.unknown_endtag( self, tag )
 
-class PageController( BaseUIController, SharableMixin, UsesAnnotations, UsesHistoryMixin,
+class PageController( BaseUIController, SharableMixin, UsesHistoryMixin,
                       UsesStoredWorkflowMixin, UsesVisualizationMixin, UsesItemRatings ):
 
     _page_list = PageListGrid()

diff -r 33af32773cba309fde44ced5fba78ce8fc64078b -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -19,7 +19,7 @@
 from galaxy import web
 from galaxy.datatypes.data import Data
 from galaxy.jobs.actions.post import ActionBox
-from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
+from galaxy.model.item_attrs import UsesItemRatings
 from galaxy.model.mapping import desc
 from galaxy.tools.parameters import RuntimeValue, visit_input_values
 from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue
@@ -132,7 +132,7 @@
             self.tag_content += text
 
 
-class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesAnnotations, UsesItemRatings ):
+class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesItemRatings ):
     stored_list_grid = StoredWorkflowListGrid()
     published_list_grid = StoredWorkflowAllPublishedGrid()
 
@@ -372,34 +372,17 @@
             referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' )
 
         # Do import.
-        session = trans.sa_session
         stored = self.get_stored_workflow( trans, id, check_ownership=False )
         if stored.importable == False:
             return trans.show_error_message( "The owner of this workflow has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True )
         elif stored.deleted:
             return trans.show_error_message( "You can't import this workflow because it has been deleted.<br>You can %s" % referer_message, use_panels=True )
-        else:
-            # Copy workflow.
-            imported_stored = model.StoredWorkflow()
-            imported_stored.name = "imported: " + stored.name
-            imported_stored.latest_workflow = stored.latest_workflow
-            imported_stored.user = trans.user
-            # Save new workflow.
-            session = trans.sa_session
-            session.add( imported_stored )
-            session.flush()
+        self._import_shared_workflow( trans, stored )
 
-            # Copy annotations.
-            self.copy_item_annotation( session, stored.user, stored, imported_stored.user, imported_stored )
-            for order_index, step in enumerate( stored.latest_workflow.steps ):
-                self.copy_item_annotation( session, stored.user, step, \
-                                            imported_stored.user, imported_stored.latest_workflow.steps[order_index] )
-            session.flush()
-
-            # Redirect to load galaxy frames.
-            return trans.show_ok_message(
-                message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s."""
-                % ( stored.name, web.url_for( controller='workflow' ), referer_message ), use_panels=True )
+        # Redirect to load galaxy frames.
+        return trans.show_ok_message(
+            message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s."""
+            % ( stored.name, web.url_for( controller='workflow' ), referer_message ), use_panels=True )
 
     @web.expose
     @web.require_login( "use Galaxy workflows" )


https://bitbucket.org/galaxy/galaxy-central/commits/2f7781fc4ce9/
Changeset:   2f7781fc4ce9
User:        nsoranzo
Date:        2014-01-15 18:28:21
Summary:     Add /api/workflows/import method to import a workflow shared by other users.
Affected #:  2 files

diff -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 -r 2f7781fc4ce9dbb1768fd345621ec2a62000f2ae lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -6,20 +6,21 @@
 
 import logging
 from sqlalchemy import desc, or_
+from galaxy import exceptions
 from galaxy import util
 from galaxy import web
 from galaxy import model
 from galaxy.tools.parameters import visit_input_values, DataToolParameter, RuntimeValue
-from galaxy.web.base.controller import BaseAPIController, url_for
+from galaxy.web import _future_expose_api as expose_api
+from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
 from galaxy.workflow.modules import module_factory, ToolModule
 from galaxy.jobs.actions.post import ActionBox
-from galaxy.model.item_attrs import UsesAnnotations
 
 from ..controllers.workflow import attach_ordered_steps
 
 log = logging.getLogger(__name__)
 
-class WorkflowsAPIController(BaseAPIController, UsesAnnotations):
+class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin):
     @web.expose_api
     def index(self, trans, **kwd):
         """
@@ -584,3 +585,31 @@
             data['steps'][step.order_index] = step_dict
         return data
 
+    @expose_api
+    def import_shared_worflow(self, trans, payload, **kwd):
+        """
+        POST /api/workflows/import
+        Import a workflow shared by other users.
+
+        :param  workflow_id:      the workflow id (required)
+        :type   workflow_id:      str
+
+        :raises: exceptions.MessageException, exceptions.ObjectNotFound
+        """
+        # Pull parameters out of payload.
+        workflow_id = payload.get('workflow_id', None)
+        if workflow_id == None:
+            raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." )
+        try:
+            stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False )
+        except:
+            raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id )
+        if stored_workflow.importable == False:
+            raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' )
+        elif stored_workflow.deleted:
+            raise exceptions.MessageException( "You can't import this workflow because it has been deleted." )
+        imported_workflow = self._import_shared_workflow( trans, stored_workflow )
+        item = imported_workflow.to_dict(value_mapper={'id':trans.security.encode_id})
+        encoded_id = trans.security.encode_id(imported_workflow.id)
+        item['url'] = url_for('workflow', id=encoded_id)
+        return item

diff -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 -r 2f7781fc4ce9dbb1768fd345621ec2a62000f2ae lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -163,10 +163,11 @@
 
     # "POST /api/workflows/import"  =>  ``workflows.import_workflow()``.
     # Defines a named route "import_workflow".
-    webapp.mapper.connect("import_workflow", "/api/workflows/upload", controller="workflows", action="import_new_workflow", conditions=dict(method=["POST"]))
-    webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET']))
+    webapp.mapper.connect( 'import_workflow', '/api/workflows/upload', controller='workflows', action='import_new_workflow', conditions=dict( method=['POST'] ) )
+    webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) )
     # Preserve the following download route for now for dependent applications  -- deprecate at some point
-    webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET']))
+    webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) )
+    webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_worflow', conditions=dict( method=['POST'] ) )
 
     # =======================
     # ===== LIBRARY API =====

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 5 new changesets

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