root/galaxy-central/lib/galaxy/web/controllers/workflow.py

リビジョン 2, 83.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1from galaxy.web.base.controller import *
2
3import pkg_resources
4pkg_resources.require( "simplejson" )
5pkg_resources.require( "SVGFig" )
6import simplejson
7import base64, httplib, urllib2, sgmllib, svgfig
8
9from galaxy.web.framework.helpers import time_ago, grids
10from galaxy.tools.parameters import *
11from galaxy.tools import DefaultToolState
12from galaxy.tools.parameters.grouping import Repeat, Conditional
13from galaxy.datatypes.data import Data
14from galaxy.util.odict import odict
15from galaxy.util.sanitize_html import sanitize_html
16from galaxy.util.topsort import topsort, topsort_levels, CycleError
17from galaxy.workflow.modules import *
18from galaxy import model
19from galaxy.model.mapping import desc
20from galaxy.model.orm import *
21from galaxy.model.item_attrs import *
22from galaxy.web.framework.helpers import to_unicode
23from galaxy.jobs.actions.post import ActionBox
24
25class StoredWorkflowListGrid( grids.Grid ):   
26    class StepsColumn( grids.GridColumn ):
27        def get_value(self, trans, grid, workflow):
28            return len( workflow.latest_workflow.steps )
29   
30    # Grid definition
31    use_panels = True
32    title = "Saved Workflows"
33    model_class = model.StoredWorkflow
34    default_filter = { "name" : "All", "tags": "All" }
35    default_sort_key = "-update_time"
36    columns = [
37        grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ),
38        grids.IndividualTagsColumn( "Tags", "tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ),
39        StepsColumn( "Steps" ),
40        grids.GridColumn( "Created", key="create_time", format=time_ago ),
41        grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
42    ]
43    columns.append(
44        grids.MulticolFilterColumn( 
45        "Search",
46        cols_to_filter=[ columns[0], columns[1] ],
47        key="free-text-search", visible=False, filterable="standard" )
48                )
49    operations = [
50        grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
51        grids.GridOperation( "Run", condition=( lambda item: not item.deleted ), async_compatible=False ),
52        grids.GridOperation( "Clone", condition=( lambda item: not item.deleted ), async_compatible=False  ),
53        grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False  ),
54        grids.GridOperation( "Sharing", condition=( lambda item: not item.deleted ), async_compatible=False ),
55        grids.GridOperation( "Delete", condition=( lambda item: item.deleted ), async_compatible=True ),
56    ]
57    def apply_query_filter( self, trans, query, **kwargs ):
58        return query.filter_by( user=trans.user, deleted=False )
59
60class StoredWorkflowAllPublishedGrid( grids.Grid ):
61    title = "Published Workflows"
62    model_class = model.StoredWorkflow
63    default_sort_key = "update_time"
64    default_filter = dict( public_url="All", username="All", tags="All" )
65    use_async = True
66    columns = [
67        grids.PublicURLColumn( "Name", key="name", filterable="advanced" ),
68        grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ),
69        grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ),
70        grids.CommunityRatingColumn( "Community Rating", key="rating" ),
71        grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ),
72        grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago )
73    ]
74    columns.append(
75        grids.MulticolFilterColumn( 
76        "Search",
77        cols_to_filter=[ columns[0], columns[1], columns[2] ],
78        key="free-text-search", visible=False, filterable="standard" )
79                )
80    operations = []
81    def build_initial_query( self, trans, **kwargs ):
82        # Join so that searching stored_workflow.user makes sense.
83        return trans.sa_session.query( self.model_class ).join( model.User.table )
84    def apply_query_filter( self, trans, query, **kwargs ):
85        # A public workflow is published, has a slug, and is not deleted.
86        return query.filter( self.model_class.published==True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False )
87       
88# Simple SGML parser to get all content in a single tag.
89class SingleTagContentsParser( sgmllib.SGMLParser ):
90   
91    def __init__( self, target_tag ):
92        sgmllib.SGMLParser.__init__( self )
93        self.target_tag = target_tag
94        self.cur_tag = None
95        self.tag_content = ""
96       
97    def unknown_starttag( self, tag, attrs ):
98        """ Called for each start tag. """
99        self.cur_tag = tag
100       
101    def handle_data( self, text ):
102        """ Called for each block of plain text. """
103        if self.cur_tag == self.target_tag:
104            self.tag_content += text
105
106class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnnotations, UsesItemRatings ):
107    stored_list_grid = StoredWorkflowListGrid()
108    published_list_grid = StoredWorkflowAllPublishedGrid()
109   
110    __myexp_url = "sandbox.myexperiment.org:80"
111   
112    @web.expose
113    def index( self, trans ):
114        return self.list( trans )
115       
116    @web.expose
117    @web.require_login( "use Galaxy workflows" )
118    def list_grid( self, trans, **kwargs ):
119        """ List user's stored workflows. """
120        status = message = None
121        if 'operation' in kwargs:
122            operation = kwargs['operation'].lower()
123            if operation == "rename":
124                return self.rename( trans, **kwargs )
125            history_ids = util.listify( kwargs.get( 'id', [] ) )
126            if operation == "sharing":
127                return self.sharing( trans, id=history_ids )
128        return self.stored_list_grid( trans, **kwargs )
129                                   
130    @web.expose
131    @web.require_login( "use Galaxy workflows", use_panels=True )
132    def list( self, trans ):
133        """
134        Render workflow main page (management of existing workflows)
135        """
136        user = trans.get_user()
137        workflows = trans.sa_session.query( model.StoredWorkflow ) \
138            .filter_by( user=user, deleted=False ) \
139            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
140            .all()
141        shared_by_others = trans.sa_session \
142            .query( model.StoredWorkflowUserShareAssociation ) \
143            .filter_by( user=user ) \
144            .join( 'stored_workflow' ) \
145            .filter( model.StoredWorkflow.deleted == False ) \
146            .order_by( desc( model.StoredWorkflow.update_time ) ) \
147            .all()
148           
149        # Legacy issue: all shared workflows must have slugs.
150        slug_set = False
151        for workflow_assoc in shared_by_others:
152            slug_set = self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow )
153        if slug_set:
154            trans.sa_session.flush()
155
156        return trans.fill_template( "workflow/list.mako",
157                                    workflows = workflows,
158                                    shared_by_others = shared_by_others )
159   
160    @web.expose
161    @web.require_login( "use Galaxy workflows" )
162    def list_for_run( self, trans ):
163        """
164        Render workflow list for analysis view (just allows running workflow
165        or switching to management view)
166        """
167        user = trans.get_user()
168        workflows = trans.sa_session.query( model.StoredWorkflow ) \
169            .filter_by( user=user, deleted=False ) \
170            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
171            .all()
172        shared_by_others = trans.sa_session \
173            .query( model.StoredWorkflowUserShareAssociation ) \
174            .filter_by( user=user ) \
175            .filter( model.StoredWorkflow.deleted == False ) \
176            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
177            .all()
178        return trans.fill_template( "workflow/list_for_run.mako",
179                                    workflows = workflows,
180                                    shared_by_others = shared_by_others )
181                                   
182    @web.expose
183    def list_published( self, trans, **kwargs ):
184        grid = self.published_list_grid( trans, **kwargs )
185        if 'async' in kwargs:
186            return grid
187        else:
188            # Render grid wrapped in panels
189            return trans.fill_template( "workflow/list_published.mako", grid=grid )
190                                   
191    @web.expose
192    def display_by_username_and_slug( self, trans, username, slug ):
193        """ Display workflow based on a username and slug. """
194       
195        # Get workflow.
196        session = trans.sa_session
197        user = session.query( model.User ).filter_by( username=username ).first()
198        stored_workflow = trans.sa_session.query( model.StoredWorkflow ).filter_by( user=user, slug=slug, deleted=False ).first()
199        if stored_workflow is None:
200           raise web.httpexceptions.HTTPNotFound()
201        # Security check raises error if user cannot access workflow.
202        self.security_check( trans.get_user(), stored_workflow, False, True)
203       
204        # Get data for workflow's steps.
205        self.get_stored_workflow_steps( trans, stored_workflow )
206        # Get annotations.
207        stored_workflow.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow )
208        for step in stored_workflow.latest_workflow.steps:
209            step.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, step )
210
211        # Get rating data.
212        user_item_rating = 0
213        if trans.get_user():
214            user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), stored_workflow )
215            if user_item_rating:
216                user_item_rating = user_item_rating.rating
217            else:
218                user_item_rating = 0
219        ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, stored_workflow )           
220        return trans.fill_template_mako( "workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps,
221                                            user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings )
222
223    @web.expose
224    def get_item_content_async( self, trans, id ):
225        """ Returns item content in HTML format. """
226       
227        stored = self.get_stored_workflow( trans, id, False, True )
228        if stored is None:
229            raise web.httpexceptions.HTTPNotFound()
230           
231        # Get data for workflow's steps.
232        self.get_stored_workflow_steps( trans, stored )
233        # Get annotations.
234        stored.annotation = self.get_item_annotation_str( trans.sa_session, stored.user, stored )
235        for step in stored.latest_workflow.steps:
236            step.annotation = self.get_item_annotation_str( trans.sa_session, stored.user, step )
237        return trans.stream_template_mako( "/workflow/item_content.mako", item = stored, item_data = stored.latest_workflow.steps )
238                             
239    @web.expose
240    @web.require_login( "use Galaxy workflows" )
241    def share( self, trans, id, email="", use_panels=False ):
242        msg = mtype = None
243        # Load workflow from database
244        stored = self.get_stored_workflow( trans, id )
245        if email:
246            other = trans.sa_session.query( model.User ) \
247                                    .filter( and_( model.User.table.c.email==email,
248                                                   model.User.table.c.deleted==False ) ) \
249                                    .first()
250            if not other:
251                mtype = "error"
252                msg = ( "User '%s' does not exist" % email )
253            elif other == trans.get_user():
254                mtype = "error"
255                msg = ( "You cannot share a workflow with yourself" )
256            elif trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \
257                    .filter_by( user=other, stored_workflow=stored ).count() > 0:
258                mtype = "error"
259                msg = ( "Workflow already shared with '%s'" % email )
260            else:
261                share = model.StoredWorkflowUserShareAssociation()
262                share.stored_workflow = stored
263                share.user = other
264                session = trans.sa_session
265                session.add( share )
266                self.create_item_slug( session, stored )
267                session.flush()
268                trans.set_message( "Workflow '%s' shared with user '%s'" % ( stored.name, other.email ) )
269                return trans.response.send_redirect( url_for( controller='workflow', action='sharing', id=id ) )
270        return trans.fill_template( "/ind_share_base.mako",
271                                    message = msg,
272                                    messagetype = mtype,
273                                    item=stored,
274                                    email=email,
275                                    use_panels=use_panels )
276   
277    @web.expose
278    @web.require_login( "use Galaxy workflows" )
279    def sharing( self, trans, id, **kwargs ):
280        """ Handle workflow sharing. """
281       
282        # Get session and workflow.
283        session = trans.sa_session
284        stored = self.get_stored_workflow( trans, id )
285        session.add( stored )
286       
287        # Do operation on workflow.
288        if 'make_accessible_via_link' in kwargs:
289            self._make_item_accessible( trans.sa_session, stored )
290        elif 'make_accessible_and_publish' in kwargs:
291            self._make_item_accessible( trans.sa_session, stored )
292            stored.published = True
293        elif 'publish' in kwargs:
294            stored.published = True
295        elif 'disable_link_access' in kwargs:
296            stored.importable = False
297        elif 'unpublish' in kwargs:
298            stored.published = False
299        elif 'disable_link_access_and_unpublish' in kwargs:
300            stored.importable = stored.published = False
301        elif 'unshare_user' in kwargs:
302            user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) )
303            if not user:
304                error( "User not found for provided id" )
305            association = session.query( model.StoredWorkflowUserShareAssociation ) \
306                                 .filter_by( user=user, stored_workflow=stored ).one()
307            session.delete( association )
308           
309        # Legacy issue: workflows made accessible before recent updates may not have a slug. Create slug for any workflows that need them.
310        if stored.importable and not stored.slug:
311            self._make_item_accessible( trans.sa_session, stored )
312           
313        session.flush()
314       
315        return trans.fill_template( "/workflow/sharing.mako", use_panels=True, item=stored )
316
317    @web.expose
318    @web.require_login( "to import a workflow", use_panels=True )
319    def imp( self, trans, id, **kwargs ):
320        # Set referer message.
321        referer = trans.request.referer
322        if referer is not "":
323            referer_message = "<a href='%s'>return to the previous page</a>" % referer
324        else:
325            referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' )
326                   
327        # Do import.
328        session = trans.sa_session
329        stored = self.get_stored_workflow( trans, id, check_ownership=False )
330        if stored.importable == False:
331            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 )
332        elif stored.user == trans.user:
333            return trans.show_error_message( "You can't import this workflow because you own it.<br>You can %s" % referer_message, use_panels=True )
334        elif stored.deleted:
335            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 )
336        else:
337            # Copy workflow.
338            imported_stored = model.StoredWorkflow()
339            imported_stored.name = "imported: " + stored.name
340            imported_stored.latest_workflow = stored.latest_workflow
341            imported_stored.user = trans.user
342            # Save new workflow.
343            session = trans.sa_session
344            session.add( imported_stored )
345            session.flush()
346           
347            # Copy annotations.
348            self.copy_item_annotation( session, stored.user, stored, imported_stored.user, imported_stored )
349            for order_index, step in enumerate( stored.latest_workflow.steps ):
350                self.copy_item_annotation( session, stored.user, step, \
351                                            imported_stored.user, imported_stored.latest_workflow.steps[order_index] )
352            session.flush()
353           
354            # Redirect to load galaxy frames.
355            return trans.show_ok_message(
356                message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s."""
357                % ( stored.name, web.url_for( controller='workflow' ), referer_message ), use_panels=True )
358           
359    @web.expose
360    @web.require_login( "use Galaxy workflows" )
361    def edit_attributes( self, trans, id, **kwargs ):
362        # Get workflow and do error checking.
363        stored = self.get_stored_workflow( trans, id )
364        if not stored:
365            error( "You do not own this workflow or workflow ID is invalid." )
366        # Update workflow attributes if new values submitted.
367        if 'name' in kwargs:
368            # Rename workflow.
369            stored.name = kwargs[ 'name' ]
370        if 'annotation' in kwargs:
371            # Set workflow annotation; sanitize annotation before adding it.
372            annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' )
373            self.add_item_annotation( trans.sa_session, trans.get_user(), stored,  annotation )
374        trans.sa_session.flush()
375        return trans.fill_template( 'workflow/edit_attributes.mako',
376                                    stored=stored,
377                                    annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored )
378                                    )
379   
380    @web.expose
381    @web.require_login( "use Galaxy workflows" )
382    def rename( self, trans, id, new_name=None, **kwargs ):
383        stored = self.get_stored_workflow( trans, id )
384        if new_name is not None:
385            stored.name = new_name
386            trans.sa_session.flush()
387            # For current workflows grid:
388            trans.set_message ( "Workflow renamed to '%s'." % new_name )
389            return self.list( trans )
390            # For new workflows grid:
391            #message = "Workflow renamed to '%s'." % new_name
392            #return self.list_grid( trans, message=message, status='done' )
393        else:
394            return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename" ) \
395                .add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) )
396               
397    @web.expose
398    @web.require_login( "use Galaxy workflows" )
399    def rename_async( self, trans, id, new_name=None, **kwargs ):
400        stored = self.get_stored_workflow( trans, id )
401        if new_name:
402            stored.name = new_name
403            trans.sa_session.flush()
404            return stored.name
405           
406    @web.expose
407    @web.require_login( "use Galaxy workflows" )
408    def annotate_async( self, trans, id, new_annotation=None, **kwargs ):
409        stored = self.get_stored_workflow( trans, id )
410        if new_annotation:
411            # Sanitize annotation before adding it.
412            new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' )
413            self.add_item_annotation( trans.sa_session, trans.get_user(), stored, new_annotation )
414            trans.sa_session.flush()
415            return new_annotation
416           
417    @web.expose
418    @web.require_login( "rate items" )
419    @web.json
420    def rate_async( self, trans, id, rating ):
421        """ Rate a workflow asynchronously and return updated community data. """
422
423        stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True )
424        if not stored:
425            return trans.show_error_message( "The specified workflow does not exist." )
426
427        # Rate workflow.
428        stored_rating = self.rate_item( trans.sa_session, trans.get_user(), stored, rating )
429
430        return self.get_ave_item_rating_data( trans.sa_session, stored )
431           
432    @web.expose
433    @web.require_login( "use Galaxy workflows" )
434    def set_accessible_async( self, trans, id=None, accessible=False ):
435        """ Set workflow's importable attribute and slug. """
436        stored = self.get_stored_workflow( trans, id )
437
438        # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed.
439        importable = accessible in ['True', 'true', 't', 'T'];
440        if stored and stored.importable != importable:
441            if importable:
442                self._make_item_accessible( trans.sa_session, stored )
443            else:
444                stored.importable = importable
445            trans.sa_session.flush()
446        return
447       
448    @web.expose
449    @web.require_login( "modify Galaxy items" )
450    def set_slug_async( self, trans, id, new_slug ):
451        stored = self.get_stored_workflow( trans, id )
452        if stored:
453            stored.slug = new_slug
454            trans.sa_session.flush()
455            return stored.slug
456           
457    @web.expose
458    def get_embed_html_async( self, trans, id ):
459        """ Returns HTML for embedding a workflow in a page. """
460
461        # TODO: user should be able to embed any item he has access to. see display_by_username_and_slug for security code.
462        stored = self.get_stored_workflow( trans, id )
463        if stored:
464            return "Embedded Workflow '%s'" % stored.name
465       
466    @web.expose
467    @web.json
468    @web.require_login( "use Galaxy workflows" )
469    def get_name_and_link_async( self, trans, id=None ):
470        """ Returns workflow's name and link. """
471        stored = self.get_stored_workflow( trans, id )
472
473        if self.create_item_slug( trans.sa_session, stored ):
474            trans.sa_session.flush()
475        return_dict = { "name" : stored.name, "link" : url_for( action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) }
476        return return_dict
477   
478    @web.expose
479    @web.require_login( "use Galaxy workflows" )
480    def gen_image( self, trans, id ):
481        stored = self.get_stored_workflow( trans, id, check_ownership=True )
482        session = trans.sa_session
483               
484        workflow = stored.latest_workflow
485        data = []
486       
487        canvas = svgfig.canvas(style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left")
488        text = svgfig.SVG("g")
489        connectors = svgfig.SVG("g")
490        boxes = svgfig.SVG("g")
491        svgfig.Text.defaults["font-size"] = "10px"
492       
493        in_pos = {}
494        out_pos = {}
495        margin = 5
496        line_px = 16 # how much spacing between input/outputs
497        widths = {} # store px width for boxes of each step
498        max_width, max_x, max_y = 0, 0, 0
499       
500        for step in workflow.steps:
501            # Load from database representation
502            module = module_factory.from_workflow_step( trans, step )
503           
504            # Pack attributes into plain dictionary
505            step_dict = {
506                'id': step.order_index,
507                'data_inputs': module.get_data_inputs(),
508                'data_outputs': module.get_data_outputs(),
509                'position': step.position
510            }
511           
512            input_conn_dict = {}
513            for conn in step.input_connections:
514                input_conn_dict[ conn.input_name ] = \
515                    dict( id=conn.output_step.order_index, output_name=conn.output_name )
516            step_dict['input_connections'] = input_conn_dict
517                   
518            data.append(step_dict)
519           
520            x, y = step.position['left'], step.position['top']
521            count = 0
522           
523            max_len = len(module.get_name()) * 1.5
524            text.append( svgfig.Text(x, y + 20, module.get_name(), **{"font-size": "14px"} ).SVG() )
525           
526            y += 45
527            for di in module.get_data_inputs():
528                cur_y = y+count*line_px
529                if step.order_index not in in_pos:
530                    in_pos[step.order_index] = {}
531                in_pos[step.order_index][di['name']] = (x, cur_y)
532                text.append( svgfig.Text(x, cur_y, di['label']).SVG() )
533                count += 1
534                max_len = max(max_len, len(di['label']))
535               
536           
537            if len(module.get_data_inputs()) > 0:
538                y += 15
539               
540            for do in module.get_data_outputs():
541                cur_y = y+count*line_px
542                if step.order_index not in out_pos:
543                    out_pos[step.order_index] = {}
544                out_pos[step.order_index][do['name']] = (x, cur_y)
545                text.append( svgfig.Text(x, cur_y, do['name']).SVG() )
546                count += 1
547                max_len = max(max_len, len(do['name']))
548           
549            widths[step.order_index] = max_len*5.5
550            max_x = max(max_x, step.position['left'])
551            max_y = max(max_y, step.position['top'])
552            max_width = max(max_width, widths[step.order_index])
553           
554        for step_dict in data:
555            width = widths[step_dict['id']]
556            x, y = step_dict['position']['left'], step_dict['position']['top']
557            boxes.append( svgfig.Rect(x-margin, y, x+width-margin, y+30, fill="#EBD9B2").SVG() )
558            box_height = (len(step_dict['data_inputs']) + len(step_dict['data_outputs'])) * line_px + margin
559
560            # Draw separator line
561            if len(step_dict['data_inputs']) > 0:
562                box_height += 15
563                sep_y = y + len(step_dict['data_inputs']) * line_px + 40
564                text.append( svgfig.Line(x-margin, sep_y, x+width-margin, sep_y).SVG() ) #
565               
566            # input/output box
567            boxes.append( svgfig.Rect(x-margin, y+30, x+width-margin, y+30+box_height, fill="#ffffff").SVG() )
568                       
569            for conn, output_dict in step_dict['input_connections'].iteritems():
570                in_coords = in_pos[step_dict['id']][conn]
571                out_conn_pos = out_pos[output_dict['id']][output_dict['output_name']]
572                adjusted = (out_conn_pos[0] + widths[output_dict['id']], out_conn_pos[1])
573                text.append( svgfig.SVG("circle", cx=out_conn_pos[0]+widths[output_dict['id']]-margin, cy=out_conn_pos[1]-margin, r=5, fill="#ffffff" ) )
574                connectors.append( svgfig.Line(adjusted[0], adjusted[1]-margin, in_coords[0]-10, in_coords[1], arrow_end="true" ).SVG() )
575           
576        canvas.append(connectors)
577        canvas.append(boxes)
578        canvas.append(text)
579        width, height = (max_x + max_width + 50), max_y + 300
580        canvas['width'] = "%s px" % width
581        canvas['height'] = "%s px" % height
582        canvas['viewBox'] = "0 0 %s %s" % (width, height)
583        trans.response.set_content_type("image/svg+xml")
584        return canvas.standalone_xml()
585       
586       
587    @web.expose
588    @web.require_login( "use Galaxy workflows" )
589    def clone( self, trans, id ):
590        stored = self.get_stored_workflow( trans, id, check_ownership=False )
591        user = trans.get_user()
592        if stored.user == user:
593            owner = True
594        else:
595            if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \
596                    .filter_by( user=user, stored_workflow=stored ).count() == 0:
597                error( "Workflow is not owned by or shared with current user" )
598            owner = False
599        new_stored = model.StoredWorkflow()
600        new_stored.name = "Clone of '%s'" % stored.name
601        new_stored.latest_workflow = stored.latest_workflow
602        if not owner:
603            new_stored.name += " shared by '%s'" % stored.user.email
604        new_stored.user = user
605        # Persist
606        session = trans.sa_session
607        session.add( new_stored )
608        session.flush()
609        # Display the management page
610        trans.set_message( 'Clone created with name "%s"' % new_stored.name )
611        return self.list( trans )
612   
613    @web.expose
614    @web.require_login( "create workflows" )
615    def create( self, trans, workflow_name=None, workflow_annotation="" ):
616        """
617        Create a new stored workflow with name `workflow_name`.
618        """
619        user = trans.get_user()
620        if workflow_name is not None:
621            # Create the new stored workflow
622            stored_workflow = model.StoredWorkflow()
623            stored_workflow.name = workflow_name
624            stored_workflow.user = user
625            # And the first (empty) workflow revision
626            workflow = model.Workflow()
627            workflow.name = workflow_name
628            workflow.stored_workflow = stored_workflow
629            stored_workflow.latest_workflow = workflow
630            # Add annotation.
631            workflow_annotation = sanitize_html( workflow_annotation, 'utf-8', 'text/html' )
632            self.add_item_annotation( trans.sa_session, trans.get_user(), stored_workflow, workflow_annotation )
633            # Persist
634            session = trans.sa_session
635            session.add( stored_workflow )
636            session.flush()
637            # Display the management page
638            trans.set_message( "Workflow '%s' created" % stored_workflow.name )
639            return self.list( trans )
640        else:
641            return form( url_for(), "Create New Workflow", submit_text="Create" ) \
642                    .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \
643                    .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." )
644   
645    @web.expose
646    def delete( self, trans, id=None ):
647        """
648        Mark a workflow as deleted
649        """       
650        # Load workflow from database
651        stored = self.get_stored_workflow( trans, id )
652        # Marke as deleted and save
653        stored.deleted = True
654        trans.sa_session.add( stored )
655        trans.sa_session.flush()
656        # Display the management page
657        trans.set_message( "Workflow '%s' deleted" % stored.name )
658        return self.list( trans )
659       
660    @web.expose
661    @web.require_login( "edit workflows" )
662    def editor( self, trans, id=None ):
663        """
664        Render the main workflow editor interface. The canvas is embedded as
665        an iframe (necessary for scrolling to work properly), which is
666        rendered by `editor_canvas`.
667        """
668        if not id:
669            error( "Invalid workflow id" )
670        stored = self.get_stored_workflow( trans, id )
671        return trans.fill_template( "workflow/editor.mako", stored=stored, annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) )
672       
673    @web.json
674    def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, **incoming ):
675        """
676        Accepts a tool state and incoming values, and generates a new tool
677        form and some additional information, packed into a json dictionary.
678        This is used for the form shown in the right pane when a node
679        is selected.
680        """
681       
682        trans.workflow_building_mode = True
683        module = module_factory.from_dict( trans, {
684            'type': type,
685            'tool_id': tool_id,
686            'tool_state': incoming.pop("tool_state")
687        } )
688        module.update_state( incoming )
689       
690        if type=='tool':
691            return {
692                'tool_state': module.get_state(),
693                'data_inputs': module.get_data_inputs(),
694                'data_outputs': module.get_data_outputs(),
695                'tool_errors': module.get_errors(),
696                'form_html': module.get_config_form(),
697                'annotation': annotation,
698                'post_job_actions': module.get_post_job_actions()
699            }
700        else:
701            return {
702                'tool_state': module.get_state(),
703                'data_inputs': module.get_data_inputs(),
704                'data_outputs': module.get_data_outputs(),
705                'tool_errors': module.get_errors(),
706                'form_html': module.get_config_form(),
707                'annotation': annotation
708            }
709       
710    @web.json
711    def get_new_module_info( self, trans, type, **kwargs ):
712        """
713        Get the info for a new instance of a module initialized with default
714        parameters (any keyword arguments will be passed along to the module).
715        Result includes data inputs and outputs, html representation
716        of the initial form, and the initial tool state (with default values).
717        This is called asynchronously whenever a new node is added.
718        """
719        trans.workflow_building_mode = True
720        module = module_factory.new( trans, type, **kwargs )
721        return {
722            'type': module.type,
723            'name':  module.get_name(),
724            'tool_id': module.get_tool_id(),
725            'tool_state': module.get_state(),
726            'tooltip': module.get_tooltip(),
727            'data_inputs': module.get_data_inputs(),
728            'data_outputs': module.get_data_outputs(),
729            'form_html': module.get_config_form(),
730            'annotation': ""
731        }
732
733    @web.json
734    def load_workflow( self, trans, id ):
735        """
736        Get the latest Workflow for the StoredWorkflow identified by `id` and
737        encode it as a json string that can be read by the workflow editor
738        web interface.
739        """
740        user = trans.get_user()
741        id = trans.security.decode_id( id )
742        trans.workflow_building_mode = True
743        # Load encoded workflow from database
744        stored = trans.sa_session.query( model.StoredWorkflow ).get( id )
745        assert stored.user == user
746        workflow = stored.latest_workflow
747        # Pack workflow data into a dictionary and return
748        data = {}
749        data['name'] = workflow.name
750        data['steps'] = {}
751        data['upgrade_messages'] = {}
752        # For each step, rebuild the form and encode the state
753        for step in workflow.steps:
754            # Load from database representation
755            module = module_factory.from_workflow_step( trans, step )
756            # Fix any missing parameters
757            upgrade_message = module.check_and_update_state()
758            if upgrade_message:
759                # FIXME: Frontend should be able to handle workflow messages
760                #        as a dictionary not just the values
761                data['upgrade_messages'][step.order_index] = upgrade_message.values()
762            # Get user annotation.
763            step_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, step )
764            annotation_str = ""
765            if step_annotation:
766                annotation_str = step_annotation.annotation
767            # Pack attributes into plain dictionary
768            step_dict = {
769                'id': step.order_index,
770                'type': module.type,
771                'tool_id': module.get_tool_id(),
772                'name': module.get_name(),
773                'tool_state': module.get_state(),
774                'tooltip': module.get_tooltip(),
775                'tool_errors': module.get_errors(),
776                'data_inputs': module.get_data_inputs(),
777                'data_outputs': module.get_data_outputs(),
778                'form_html': module.get_config_form(),
779                'annotation' : annotation_str,
780                'post_job_actions' : {},
781                'workflow_outputs' : []
782            }
783            # Connections
784            input_connections = step.input_connections
785            if step.type is None or step.type == 'tool':
786                # Determine full (prefixed) names of valid input datasets
787                data_input_names = {}
788                def callback( input, value, prefixed_name, prefixed_label ):
789                    if isinstance( input, DataToolParameter ):
790                        data_input_names[ prefixed_name ] = True
791                visit_input_values( module.tool.inputs, module.state.inputs, callback )
792                # Filter
793                # FIXME: this removes connection without displaying a message currently!
794                input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ]
795                # post_job_actions
796                pja_dict = {}
797                for pja in step.post_job_actions:
798                    pja_dict[pja.action_type+pja.output_name] = dict(action_type = pja.action_type,
799                                            output_name = pja.output_name,
800                                            action_arguments = pja.action_arguments)
801                step_dict['post_job_actions'] = pja_dict
802                #workflow outputs
803                outputs = []
804                for output in step.workflow_outputs:
805                    outputs.append(output.output_name)
806                step_dict['workflow_outputs'] = outputs
807            # Encode input connections as dictionary
808            input_conn_dict = {}
809            for conn in input_connections:
810                input_conn_dict[ conn.input_name ] = \
811                    dict( id=conn.output_step.order_index, output_name=conn.output_name )
812            step_dict['input_connections'] = input_conn_dict
813            # Position
814            step_dict['position'] = step.position
815            # Add to return value
816            data['steps'][step.order_index] = step_dict
817        return data
818
819    @web.json
820    def save_workflow( self, trans, id, workflow_data ):
821        """
822        Save the workflow described by `workflow_data` with id `id`.
823        """
824        # Get the stored workflow
825        stored = self.get_stored_workflow( trans, id )
826        # Put parameters in workflow mode
827        trans.workflow_building_mode = True
828        # Convert incoming workflow data from json
829        data = simplejson.loads( workflow_data )
830        # Create new workflow from incoming data
831        workflow = model.Workflow()
832        # Just keep the last name (user can rename later)
833        workflow.name = stored.name
834        # Assume no errors until we find a step that has some
835        workflow.has_errors = False
836        # Create each step
837        steps = []
838        # The editor will provide ids for each step that we don't need to save,
839        # but do need to use to make connections
840        steps_by_external_id = {}
841        # First pass to build step objects and populate basic values
842        for key, step_dict in data['steps'].iteritems():
843            # Create the model class for the step
844            step = model.WorkflowStep()
845            steps.append( step )
846            steps_by_external_id[ step_dict['id' ] ] = step
847            # FIXME: Position should be handled inside module
848            step.position = step_dict['position']
849            module = module_factory.from_dict( trans, step_dict )
850            module.save_to_step( step )
851            if step_dict.has_key('workflow_outputs'):
852                for output_name in step_dict['workflow_outputs']:
853                    m = model.WorkflowOutput(workflow_step = step, output_name = output_name)
854                    trans.sa_session.add(m)
855            if step.tool_errors:
856                workflow.has_errors = True
857            # Stick this in the step temporarily
858            step.temp_input_connections = step_dict['input_connections']
859            # Save step annotation.
860            annotation = step_dict[ 'annotation' ]
861            if annotation:
862                annotation = sanitize_html( annotation, 'utf-8', 'text/html' )
863                self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation )
864        # Second pass to deal with connections between steps
865        for step in steps:
866            # Input connections
867            for input_name, conn_dict in step.temp_input_connections.iteritems():
868                if conn_dict:
869                    conn = model.WorkflowStepConnection()
870                    conn.input_step = step
871                    conn.input_name = input_name
872                    conn.output_name = conn_dict['output_name']
873                    conn.output_step = steps_by_external_id[ conn_dict['id'] ]
874            del step.temp_input_connections
875        # Order the steps if possible
876        attach_ordered_steps( workflow, steps )
877        # Connect up
878        workflow.stored_workflow = stored
879        stored.latest_workflow = workflow
880        # Persist
881        trans.sa_session.flush()
882        # Return something informative
883        errors = []
884        if workflow.has_errors:
885            errors.append( "Some steps in this workflow have validation errors" )
886        if workflow.has_cycles:
887            errors.append( "This workflow contains cycles" )
888        if errors:
889            rval = dict( message="Workflow saved, but will not be runnable due to the following errors",
890                         errors=errors )
891        else:
892            rval = dict( message="Workflow saved" )
893        rval['name'] = workflow.name
894        return rval
895       
896    @web.expose
897    @web.require_login( "use workflows" )
898    def export( self, trans, id=None, **kwd ):
899        """
900        Handles download/export workflow command.
901        """
902        stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True )
903        return trans.fill_template( "/workflow/export.mako", item=stored, use_panels=True )
904       
905       
906    @web.expose
907    @web.require_login( "use workflows" )
908    def import_from_myexp( self, trans, myexp_id, myexp_username=None, myexp_password=None ):
909        """
910        Imports a workflow from the myExperiment website.
911        """
912       
913        #
914        # Get workflow XML.
915        #
916       
917        # Get workflow content.
918        conn = httplib.HTTPConnection( self.__myexp_url )
919        # NOTE: blocks web thread.
920        headers = {}
921        if myexp_username and myexp_password:
922            auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password ))[:-1]
923            headers = { "Authorization" : "Basic %s" % auth_header }
924        conn.request( "GET", "/workflow.xml?id=%s&elements=content" % myexp_id, headers=headers )
925        response = conn.getresponse()
926        workflow_xml = response.read()
927        conn.close()
928        parser = SingleTagContentsParser( "content" )
929        parser.feed( workflow_xml )
930        workflow_content = base64.b64decode( parser.tag_content )
931       
932        #
933        # Process workflow XML and create workflow.
934        #
935        parser = SingleTagContentsParser( "galaxy_json" )
936        parser.feed( workflow_content )
937        workflow_dict = from_json_string( parser.tag_content )
938       
939        # Create workflow.
940        workflow = self._workflow_from_dict( trans, workflow_dict, source="myExperiment" ).latest_workflow
941       
942        # Provide user feedback.
943        if workflow.has_errors:
944            return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors" )
945        if workflow.has_cycles:
946            return trans.show_warn_message( "Imported, but this workflow contains cycles" )
947        else:
948            return trans.show_message( "Workflow '%s' imported" % workflow.name )
949         
950    @web.expose
951    @web.require_login( "use workflows" )
952    def export_to_myexp( self, trans, id, myexp_username, myexp_password ):
953        """
954        Exports a workflow to myExperiment website.
955        """
956       
957        # Load encoded workflow from database       
958        user = trans.get_user()
959        id = trans.security.decode_id( id )
960        trans.workflow_building_mode = True
961        stored = trans.sa_session.query( model.StoredWorkflow ).get( id )
962        self.security_check( trans.get_user(), stored, False, True )
963       
964        # Convert workflow to dict.
965        workflow_dict = self._workflow_to_dict( trans, stored )
966       
967        #
968        # Create and submit workflow myExperiment request.
969        #
970       
971        # Create workflow content XML.
972        workflow_dict_packed = simplejson.dumps( workflow_dict, indent=4, sort_keys=True )
973        workflow_content = trans.fill_template( "workflow/myexp_export_content.mako", \
974                                                 workflow_dict_packed=workflow_dict_packed, \
975                                                 workflow_steps=workflow_dict['steps'] )
976                                               
977        # Create myExperiment request.
978        request_raw = trans.fill_template( "workflow/myexp_export.mako", \
979                                            workflow_name=workflow_dict['name'], \
980                                            workflow_description=workflow_dict['annotation'], \
981                                            workflow_content=workflow_content
982                                            )
983        # strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters.
984        request = unicode( request_raw.strip(), 'utf-8' )
985       
986        # Do request and get result.
987        auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password ))[:-1]
988        headers = { "Content-type": "text/xml", "Accept": "text/plain", "Authorization" : "Basic %s" % auth_header }
989        conn = httplib.HTTPConnection( self.__myexp_url )
990        # NOTE: blocks web thread.
991        conn.request("POST", "/workflow.xml", request, headers)
992        response = conn.getresponse()
993        response_data = response.read()
994        conn.close()
995       
996        # Do simple parse of response to see if export successful and provide user feedback.
997        parser = SingleTagContentsParser( 'id' )
998        parser.feed( response_data )
999        myexp_workflow_id = parser.tag_content
1000        workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( action='list' )
1001        if myexp_workflow_id:
1002            return trans.show_message( \
1003                "Workflow '%s' successfully exported to myExperiment. %s" % \
1004                ( stored.name, workflow_list_str ),
1005                use_panels=True )
1006        else:
1007            return trans.show_error_message( \
1008                "Workflow '%s' could not be exported to myExperiment. Error: %s. %s" % \
1009                ( stored.name, response_data, workflow_list_str ), use_panels=True )
1010           
1011    @web.json_pretty
1012    def export_workflow( self, trans, id ):
1013        """
1014        Get the latest Workflow for the StoredWorkflow identified by `id` and
1015        encode it as a json string that can be imported back into Galaxy
1016
1017        This has slightly different information than the above. In particular,
1018        it does not attempt to decode forms and build UIs, it just stores
1019        the raw state.
1020       
1021        TODO: this is a legacy method; it should be removed once we have UI
1022        support for exporting/importing a workflow.
1023        """
1024        user = trans.get_user()
1025        id = trans.security.decode_id( id )
1026        trans.workflow_building_mode = True
1027        # Load encoded workflow from database
1028        stored = trans.sa_session.query( model.StoredWorkflow ).get( id )
1029        self.security_check( trans.get_user(), stored, False, True )
1030        return self._workflow_to_dict( trans, stored )
1031
1032    @web.json_pretty
1033    @web.require_login( "use workflows" )
1034    def export_to_file( self, trans, id ):
1035        """
1036        Get the latest Workflow for the StoredWorkflow identified by `id` and
1037        encode it as a json string that can be imported back into Galaxy
1038       
1039        This has slightly different information than the above. In particular,
1040        it does not attempt to decode forms and build UIs, it just stores
1041        the raw state.
1042        """
1043       
1044        # Get workflow.
1045        stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True )
1046       
1047        # Stream workflow to file.
1048        stored_dict = self._workflow_to_dict( trans, stored )
1049        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
1050        sname = stored.name
1051        sname = ''.join(c in valid_chars and c or '_' for c in sname)[0:150]
1052        trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-Workflow-%s.ga" % ( sname )
1053        trans.response.set_content_type( 'application/galaxy-archive' )
1054        return stored_dict
1055
1056    @web.expose
1057    def import_workflow( self, trans, workflow_text=None, url=None ):
1058        if workflow_text is None and url is None:
1059            return form( url_for(), "Import Workflow", submit_text="Import" ) \
1060                    .add_text( "url", "URL to load workflow from", "" ) \
1061                    .add_input( "textarea", "Encoded workflow (as generated by export workflow)", "workflow_text", "" )
1062        if url:
1063            # Load workflow from external URL
1064            # NOTE: blocks the web thread.
1065            try:
1066                workflow_data = urllib2.urlopen( url ).read()
1067            except Exception, e:
1068                return trans.show_error_message( "Failed to open URL %s<br><br>Message: %s" % ( url, str( e ) ) )
1069        else:
1070            workflow_data = workflow_text
1071        # Convert incoming workflow data from json
1072        try:
1073            data = simplejson.loads( workflow_data )
1074        except Exception, e:
1075            return trans.show_error_message( "Data at '%s' does not appear to be a Galaxy workflow<br><br>Message: %s" % ( url, str( e ) ) )
1076           
1077        # Create workflow.
1078        workflow = self._workflow_from_dict( trans, data, source="uploaded file" ).latest_workflow
1079       
1080        # Provide user feedback and show workflow list.
1081        if workflow.has_errors:
1082            trans.set_message( "Imported, but some steps in this workflow have validation errors",
1083                                type="warning" )
1084        if workflow.has_cycles:
1085            trans.set_message( "Imported, but this workflow contains cycles",
1086                                type="warning" )
1087        else:
1088            trans.set_message( "Workflow '%s' imported" % workflow.name )
1089        return self.list( trans )
1090       
1091    @web.json
1092    def get_datatypes( self, trans ):
1093        ext_to_class_name = dict()
1094        classes = []
1095        for k, v in trans.app.datatypes_registry.datatypes_by_extension.iteritems():
1096            c = v.__class__
1097            ext_to_class_name[k] = c.__module__ + "." + c.__name__
1098            classes.append( c )
1099        class_to_classes = dict()
1100        def visit_bases( types, cls ):
1101            for base in cls.__bases__:
1102                if issubclass( base, Data ):
1103                    types.add( base.__module__ + "." + base.__name__ )
1104                visit_bases( types, base )
1105        for c in classes:     
1106            n =  c.__module__ + "." + c.__name__
1107            types = set( [ n ] )
1108            visit_bases( types, c )
1109            class_to_classes[ n ] = dict( ( t, True ) for t in types )
1110        return dict( ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes )
1111   
1112    @web.expose
1113    def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, workflow_name=None ):
1114        user = trans.get_user()
1115        history = trans.get_history()
1116        if not user:
1117            return trans.show_error_message( "Must be logged in to create workflows" )
1118        if ( job_ids is None and dataset_ids is None ) or workflow_name is None:
1119            jobs, warnings = get_job_dict( trans )
1120            # Render
1121            return trans.fill_template(
1122                        "workflow/build_from_current_history.mako",
1123                        jobs=jobs,
1124                        warnings=warnings,
1125                        history=history )
1126        else:
1127            # Ensure job_ids and dataset_ids are lists (possibly empty)
1128            if job_ids is None:
1129                job_ids = []
1130            elif type( job_ids ) is not list:
1131                job_ids = [ job_ids ]
1132            if dataset_ids is None:
1133                dataset_ids = []
1134            elif type( dataset_ids ) is not list:
1135                dataset_ids = [ dataset_ids ]
1136            # Convert both sets of ids to integers
1137            job_ids = [ int( id ) for id in job_ids ]
1138            dataset_ids = [ int( id ) for id in dataset_ids ]
1139            # Find each job, for security we (implicately) check that they are
1140            # associated witha job in the current history.
1141            jobs, warnings = get_job_dict( trans )
1142            jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
1143            steps = []
1144            steps_by_job_id = {}
1145            hid_to_output_pair = {}
1146            # Input dataset steps
1147            for hid in dataset_ids:
1148                step = model.WorkflowStep()
1149                step.type = 'data_input'
1150                hid_to_output_pair[ hid ] = ( step, 'output' )
1151                steps.append( step )
1152            # Tool steps
1153            for job_id in job_ids:
1154                assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
1155                job = jobs_by_id[ job_id ]
1156                tool = trans.app.toolbox.tools_by_id[ job.tool_id ]
1157                param_values = job.get_param_values( trans.app )
1158                associations = cleanup_param_values( tool.inputs, param_values )
1159                step = model.WorkflowStep()
1160                step.type = 'tool'
1161                step.tool_id = job.tool_id
1162                step.tool_inputs = tool.params_to_strings( param_values, trans.app )
1163                # NOTE: We shouldn't need to do two passes here since only
1164                #       an earlier job can be used as an input to a later
1165                #       job.
1166                for other_hid, input_name in associations:
1167                    if other_hid in hid_to_output_pair:
1168                        other_step, other_name = hid_to_output_pair[ other_hid ]
1169                        conn = model.WorkflowStepConnection()
1170                        conn.input_step = step
1171                        conn.input_name = input_name
1172                        # Should always be connected to an earlier step
1173                        conn.output_step = other_step
1174                        conn.output_name = other_name
1175                steps.append( step )
1176                steps_by_job_id[ job_id ] = step               
1177                # Store created dataset hids
1178                for assoc in job.output_datasets:
1179                    hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name )
1180            # Workflow to populate
1181            workflow = model.Workflow()
1182            workflow.name = workflow_name
1183            # Order the steps if possible
1184            attach_ordered_steps( workflow, steps )
1185            # And let's try to set up some reasonable locations on the canvas
1186            # (these are pretty arbitrary values)
1187            levorder = order_workflow_steps_with_levels( steps )
1188            base_pos = 10
1189            for i, steps_at_level in enumerate( levorder ):
1190                for j, index in enumerate( steps_at_level ):
1191                    step = steps[ index ]
1192                    step.position = dict( top = ( base_pos + 120 * j ),
1193                                          left = ( base_pos + 220 * i ) )
1194            # Store it
1195            stored = model.StoredWorkflow()
1196            stored.user = user
1197            stored.name = workflow_name
1198            workflow.stored_workflow = stored
1199            stored.latest_workflow = workflow
1200            trans.sa_session.add( stored )
1201            trans.sa_session.flush()
1202            # Index page with message
1203            return trans.show_message( "Workflow '%s' created from current history." % workflow_name )
1204            ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>"
1205            ##     % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) )       
1206       
1207    @web.expose
1208    def run( self, trans, id, check_user=True, **kwargs ):
1209        stored = self.get_stored_workflow( trans, id, check_ownership=False )
1210        if check_user:
1211            user = trans.get_user()
1212            if stored.user != user:
1213                if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \
1214                        .filter_by( user=user, stored_workflow=stored ).count() == 0:
1215                    error( "Workflow is not owned by or shared with current user" )
1216        # Get the latest revision
1217        workflow = stored.latest_workflow
1218        # It is possible for a workflow to have 0 steps
1219        if len( workflow.steps ) == 0:
1220            error( "Workflow cannot be run because it does not have any steps" )
1221        #workflow = Workflow.from_simple( simplejson.loads( stored.encoded_value ), trans.app )
1222        if workflow.has_cycles:
1223            error( "Workflow cannot be run because it contains cycles" )
1224        if workflow.has_errors:
1225            error( "Workflow cannot be run because of validation errors in some steps" )
1226        # Build the state for each step
1227        errors = {}
1228        has_upgrade_messages = False
1229        has_errors = False
1230        if kwargs:
1231            # If kwargs were provided, the states for each step should have
1232            # been POSTed
1233            for step in workflow.steps:
1234                step.upgrade_messages = {}
1235                # Connections by input name
1236                step.input_connections_by_name = \
1237                    dict( ( conn.input_name, conn ) for conn in step.input_connections )
1238                # Extract just the arguments for this step by prefix
1239                p = "%s|" % step.id
1240                l = len(p)
1241                step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) )
1242                step_errors = None
1243                if step.type == 'tool' or step.type is None:
1244                    module = module_factory.from_workflow_step( trans, step )
1245                    # Fix any missing parameters
1246                    step.upgrade_messages = module.check_and_update_state()
1247                    if step.upgrade_messages:
1248                        has_upgrade_messages = True
1249                    # Any connected input needs to have value DummyDataset (these
1250                    # are not persisted so we need to do it every time)
1251                    module.add_dummy_datasets( connections=step.input_connections )   
1252                    # Get the tool
1253                    tool = module.tool
1254                    # Get the state
1255                    step.state = state = module.state
1256                    # Get old errors
1257                    old_errors = state.inputs.pop( "__errors__", {} )
1258                    # Update the state
1259                    step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args,
1260                                                     update_only=True, old_errors=old_errors )
1261                else:
1262                    module = step.module = module_factory.from_workflow_step( trans, step )
1263                    state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) )
1264                    step_errors = module.update_runtime_state( trans, state, step_args )
1265                if step_errors:
1266                    errors[step.id] = state.inputs["__errors__"] = step_errors   
1267            if 'run_workflow' in kwargs and not errors:
1268                # Run each step, connecting outputs to inputs
1269                workflow_invocation = model.WorkflowInvocation()
1270                workflow_invocation.workflow = workflow
1271                outputs = odict()
1272                # Find out if there are any workflow outputs defined, as that influences our actions.
1273                use_workflow_outputs = False
1274                for step in workflow.steps:
1275                    if step.type == 'tool' or step.type is None:
1276                        if step.workflow_outputs:
1277                            use_workflow_outputs = True
1278                            break
1279                for i, step in enumerate( workflow.steps ):
1280                    # Execute module
1281                    job = None
1282                    if step.type == 'tool' or step.type is None:
1283                        tool = trans.app.toolbox.tools_by_id[ step.tool_id ]
1284                        input_values = step.state.inputs
1285                        # Connect up
1286                        def callback( input, value, prefixed_name, prefixed_label ):
1287                            if isinstance( input, DataToolParameter ):
1288                                if prefixed_name in step.input_connections_by_name:
1289                                    conn = step.input_connections_by_name[ prefixed_name ]
1290                                    return outputs[ conn.output_step.id ][ conn.output_name ]
1291                        visit_input_values( tool.inputs, step.state.inputs, callback )
1292                        # Execute it
1293                        job, out_data = tool.execute( trans, step.state.inputs )
1294                        outputs[ step.id ] = out_data
1295                        # Create new PJA associations with the created job, to be run on completion.
1296                        if use_workflow_outputs:
1297                            # We're using outputs.  Check the step for outputs to be displayed.  Create PJAs to hide the rest upon completion.
1298                            step_outputs = [s.output_name for s in step.workflow_outputs]
1299                            for output in tool.outputs.keys():
1300                                if output not in step_outputs:
1301                                    # Create a PJA for hiding this output.
1302                                    n_pja = PostJobAction('HideDatasetAction', step, output, {})
1303                                else:
1304                                    # Remove any HideDatasetActions, step is flagged for output.
1305                                    for pja in step.post_job_actions:
1306                                        if pja.action_type == "HideDatasetAction" and pja.output_name == output:
1307                                            step.post_job_actions.remove(pja)
1308                                            trans.sa_session.delete(pja)
1309                        for pja in step.post_job_actions:
1310                            if pja.action_type in ActionBox.immediate_actions:
1311                                ActionBox.execute(trans.app, trans.sa_session, pja, job)
1312                            else:
1313                                job.add_post_job_action(pja)
1314                    else:
1315                        job, out_data = step.module.execute( trans, step.state )
1316                        outputs[ step.id ] = out_data
1317                    # Record invocation
1318                    workflow_invocation_step = model.WorkflowInvocationStep()
1319                    workflow_invocation_step.workflow_invocation = workflow_invocation
1320                    workflow_invocation_step.workflow_step = step
1321                    workflow_invocation_step.job = job
1322                # All jobs ran sucessfully, so we can save now
1323                trans.sa_session.add( workflow_invocation )
1324                trans.sa_session.flush()
1325                return trans.fill_template( "workflow/run_complete.mako",
1326                                            workflow=stored,
1327                                            outputs=outputs )
1328        else:
1329            # Prepare each step
1330            for step in workflow.steps:
1331                step.upgrade_messages = {}
1332                # Contruct modules
1333                if step.type == 'tool' or step.type is None:
1334                    # Restore the tool state for the step
1335                    step.module = module_factory.from_workflow_step( trans, step )
1336                    # Fix any missing parameters
1337                    step.upgrade_messages = step.module.check_and_update_state()
1338                    if step.upgrade_messages:
1339                        has_upgrade_messages = True
1340                    # Any connected input needs to have value DummyDataset (these
1341                    # are not persisted so we need to do it every time)
1342                    step.module.add_dummy_datasets( connections=step.input_connections )                 
1343                    # Store state with the step
1344                    step.state = step.module.state
1345                    # Error dict
1346                    if step.tool_errors:
1347                        has_errors = True
1348                        errors[step.id] = step.tool_errors
1349                else:
1350                    ## Non-tool specific stuff?
1351                    step.module = module_factory.from_workflow_step( trans, step )
1352                    step.state = step.module.get_runtime_state()
1353                # Connections by input name
1354                step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
1355        # Render the form
1356        return trans.fill_template(
1357                    "workflow/run.mako",
1358                    steps=workflow.steps,
1359                    workflow=stored,
1360                    has_upgrade_messages=has_upgrade_messages,
1361                    errors=errors,
1362                    incoming=kwargs )
1363   
1364    @web.expose
1365    def tag_outputs( self, trans, id, check_user=True, **kwargs ):
1366        stored = self.get_stored_workflow( trans, id, check_ownership=False )
1367        if check_user:
1368            user = trans.get_user()
1369            if stored.user != user:
1370                if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \
1371                        .filter_by( user=user, stored_workflow=stored ).count() == 0:
1372                    error( "Workflow is not owned by or shared with current user" )
1373        # Get the latest revision
1374        workflow = stored.latest_workflow
1375        # It is possible for a workflow to have 0 steps
1376        if len( workflow.steps ) == 0:
1377            error( "Workflow cannot be tagged for outputs because it does not have any steps" )
1378        if workflow.has_cycles:
1379            error( "Workflow cannot be tagged for outputs because it contains cycles" )
1380        if workflow.has_errors:
1381            error( "Workflow cannot be tagged for outputs because of validation errors in some steps" )
1382        # Build the state for each step
1383        errors = {}
1384        has_upgrade_messages = False
1385        has_errors = False
1386        if kwargs:
1387            # If kwargs were provided, the states for each step should have
1388            # been POSTed
1389            for step in workflow.steps:
1390                if step.type == 'tool':
1391                    # Extract just the output flags for this step.
1392                    p = "%s|otag|" % step.id
1393                    l = len(p)
1394                    outputs = [k[l:] for ( k, v ) in kwargs.iteritems() if k.startswith( p )]
1395                    if step.workflow_outputs:
1396                        for existing_output in step.workflow_outputs:
1397                            if existing_output.output_name not in outputs:
1398                                trans.sa_session.delete(existing_output)
1399                            else:
1400                                outputs.remove(existing_output.output_name)
1401                    for outputname in outputs:
1402                        m = model.WorkflowOutput(workflow_step_id = int(step.id), output_name = outputname)
1403                        trans.sa_session.add(m)
1404        # Prepare each step
1405        trans.sa_session.flush()
1406        for step in workflow.steps:
1407            step.upgrade_messages = {}
1408            # Contruct modules
1409            if step.type == 'tool' or step.type is None:
1410                # Restore the tool state for the step
1411                step.module = module_factory.from_workflow_step( trans, step )
1412                # Fix any missing parameters
1413                step.upgrade_messages = step.module.check_and_update_state()
1414                if step.upgrade_messages:
1415                    has_upgrade_messages = True
1416                # Any connected input needs to have value DummyDataset (these
1417                # are not persisted so we need to do it every time)
1418                step.module.add_dummy_datasets( connections=step.input_connections )                 
1419                # Store state with the step
1420                step.state = step.module.state
1421                # Error dict
1422                if step.tool_errors:
1423                    has_errors = True
1424                    errors[step.id] = step.tool_errors
1425            else:
1426                ## Non-tool specific stuff?
1427                step.module = module_factory.from_workflow_step( trans, step )
1428                step.state = step.module.get_runtime_state()
1429            # Connections by input name
1430            step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections )
1431        # Render the form
1432        return trans.fill_template(
1433                    "workflow/tag_outputs.mako",
1434                    steps=workflow.steps,
1435                    workflow=stored,
1436                    has_upgrade_messages=has_upgrade_messages,
1437                    errors=errors,
1438                    incoming=kwargs )
1439   
1440    @web.expose
1441    def configure_menu( self, trans, workflow_ids=None ):
1442        user = trans.get_user()
1443        if trans.request.method == "POST":
1444            if workflow_ids is None:
1445                workflow_ids = []
1446            elif type( workflow_ids ) != list:
1447                workflow_ids = [ workflow_ids ]
1448            sess = trans.sa_session
1449            # This explicit remove seems like a hack, need to figure out
1450            # how to make the association do it automatically.
1451            for m in user.stored_workflow_menu_entries:
1452                sess.delete( m )
1453            user.stored_workflow_menu_entries = []
1454            q = sess.query( model.StoredWorkflow )
1455            # To ensure id list is unique
1456            seen_workflow_ids = set()
1457            for id in workflow_ids:
1458                if id in seen_workflow_ids:
1459                    continue
1460                else:
1461                    seen_workflow_ids.add( id )
1462                m = model.StoredWorkflowMenuEntry()
1463                m.stored_workflow = q.get( id )
1464                user.stored_workflow_menu_entries.append( m )
1465            sess.flush()
1466            return trans.show_message( "Menu updated", refresh_frames=['tools'] )
1467        else:               
1468            user = trans.get_user()
1469            ids_in_menu = set( [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ] )
1470            workflows = trans.sa_session.query( model.StoredWorkflow ) \
1471                .filter_by( user=user, deleted=False ) \
1472                .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
1473                .all()
1474            shared_by_others = trans.sa_session \
1475                .query( model.StoredWorkflowUserShareAssociation ) \
1476                .filter_by( user=user ) \
1477                .filter( model.StoredWorkflow.deleted == False ) \
1478                .all()
1479            return trans.fill_template( "workflow/configure_menu.mako",
1480                                        workflows=workflows,
1481                                        shared_by_others=shared_by_others,
1482                                        ids_in_menu=ids_in_menu )
1483       
1484    def _workflow_to_dict( self, trans, stored ):
1485        """
1486        Converts a workflow to a dict of attributes suitable for exporting.
1487        """
1488        workflow = stored.latest_workflow
1489        workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored )
1490        annotation_str = ""
1491        if workflow_annotation:
1492            annotation_str = workflow_annotation.annotation
1493        # Pack workflow data into a dictionary and return
1494        data = {}
1495        data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow
1496        data['format-version'] = "0.1"
1497        data['name'] = workflow.name
1498        data['annotation'] = annotation_str
1499        data['steps'] = {}
1500        # For each step, rebuild the form and encode the state
1501        for step in workflow.steps:
1502            # Load from database representation
1503            module = module_factory.from_workflow_step( trans, step )
1504            # Get user annotation.
1505            step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step )
1506            annotation_str = ""
1507            if step_annotation:
1508                annotation_str = step_annotation.annotation
1509                       
1510            # Step info
1511            step_dict = {
1512                'id': step.order_index,
1513                'type': module.type,
1514                'tool_id': module.get_tool_id(),
1515                'tool_version' : step.tool_version,
1516                'name': module.get_name(),
1517                'tool_state': module.get_state( secure=False ),
1518                'tool_errors': module.get_errors(),
1519                ## 'data_inputs': module.get_data_inputs(),
1520                ## 'data_outputs': module.get_data_outputs(),
1521                'annotation' : annotation_str
1522            }
1523           
1524            # Data inputs
1525            step_dict['inputs'] = []
1526            if module.type == "data_input":
1527                # Get input dataset name; default to 'Input Dataset'
1528                name = module.state.get( 'name', 'Input Dataset')
1529                step_dict['inputs'].append( { "name" : name, "description" : annotation_str } )
1530            else:
1531                # Step is a tool and may have runtime inputs.
1532                for name, val in module.state.inputs.items():
1533                    input_type = type( val )
1534                    if input_type == RuntimeValue:
1535                        step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } )
1536                    elif input_type == dict:
1537                        # Input type is described by a dict, e.g. indexed parameters.
1538                        for partname, partval in val.items():
1539                            if type( partval ) == RuntimeValue:
1540                                step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } )
1541
1542            # User outputs
1543            step_dict['user_outputs'] = []
1544            """
1545            module_outputs = module.get_data_outputs()
1546            step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step )
1547            for output in step_outputs:
1548                name = output.output_name
1549                annotation = ""
1550                for module_output in module_outputs:
1551                    if module_output.get( 'name', None ) == name:
1552                        output_type = module_output.get( 'extension', '' )
1553                        break
1554                data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type }
1555            """
1556
1557            # All step outputs
1558            step_dict['outputs'] = []
1559            if type( module ) is ToolModule:
1560                for output in module.get_data_outputs():
1561                    step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } )
1562       
1563            # Connections
1564            input_connections = step.input_connections
1565            if step.type is None or step.type == 'tool':
1566                # Determine full (prefixed) names of valid input datasets
1567                data_input_names = {}
1568                def callback( input, value, prefixed_name, prefixed_label ):
1569                    if isinstance( input, DataToolParameter ):
1570                        data_input_names[ prefixed_name ] = True
1571                visit_input_values( module.tool.inputs, module.state.inputs, callback )
1572                # Filter
1573                # FIXME: this removes connection without displaying a message currently!
1574                input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ]
1575            # Encode input connections as dictionary
1576            input_conn_dict = {}
1577            for conn in input_connections:
1578                input_conn_dict[ conn.input_name ] = \
1579                    dict( id=conn.output_step.order_index, output_name=conn.output_name )
1580            step_dict['input_connections'] = input_conn_dict
1581            # Position
1582            step_dict['position'] = step.position
1583            # Add to return value
1584            data['steps'][step.order_index] = step_dict
1585        return data
1586       
1587    def _workflow_from_dict( self, trans, data, source=None ):
1588        """
1589        Creates a workflow from a dict. Created workflow is stored in the database and returned.
1590        """
1591        # Put parameters in workflow mode
1592        trans.workflow_building_mode = True
1593        # Create new workflow from incoming dict
1594        workflow = model.Workflow()
1595        # If there's a source, put it in the workflow name.
1596        if source:
1597            name = "%s (imported from %s)" % ( data['name'], source )
1598        else:
1599            name = data['name']
1600        workflow.name = name
1601        # Assume no errors until we find a step that has some
1602        workflow.has_errors = False
1603        # Create each step
1604        steps = []
1605        # The editor will provide ids for each step that we don't need to save,
1606        # but do need to use to make connections
1607        steps_by_external_id = {}
1608        # First pass to build step objects and populate basic values
1609        for key, step_dict in data['steps'].iteritems():
1610            # Create the model class for the step
1611            step = model.WorkflowStep()
1612            steps.append( step )
1613            steps_by_external_id[ step_dict['id' ] ] = step
1614            # FIXME: Position should be handled inside module
1615            step.position = step_dict['position']
1616            module = module_factory.from_dict( trans, step_dict, secure=False )
1617            module.save_to_step( step )
1618            if step.tool_errors:
1619                workflow.has_errors = True
1620            # Stick this in the step temporarily
1621            step.temp_input_connections = step_dict['input_connections']
1622            # Save step annotation.
1623            annotation = step_dict[ 'annotation' ]
1624            if annotation:
1625                annotation = sanitize_html( annotation, 'utf-8', 'text/html' )
1626                self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation )
1627        # Second pass to deal with connections between steps
1628        for step in steps:
1629            # Input connections
1630            for input_name, conn_dict in step.temp_input_connections.iteritems():
1631                if conn_dict:
1632                    conn = model.WorkflowStepConnection()
1633                    conn.input_step = step
1634                    conn.input_name = input_name
1635                    conn.output_name = conn_dict['output_name']
1636                    conn.output_step = steps_by_external_id[ conn_dict['id'] ]
1637            del step.temp_input_connections
1638        # Order the steps if possible
1639        attach_ordered_steps( workflow, steps )
1640        # Connect up
1641        stored = model.StoredWorkflow()
1642        stored.name = workflow.name
1643        workflow.stored_workflow = stored
1644        stored.latest_workflow = workflow
1645        stored.user = trans.user
1646        # Persist
1647        trans.sa_session.add( stored )
1648        trans.sa_session.flush()
1649        return stored
1650   
1651## ---- Utility methods -------------------------------------------------------
1652
1653def attach_ordered_steps( workflow, steps ):
1654    ordered_steps = order_workflow_steps( steps )
1655    if ordered_steps:
1656        workflow.has_cycles = False
1657        for i, step in enumerate( ordered_steps ):
1658            step.order_index = i
1659            workflow.steps.append( step )
1660    else:
1661        workflow.has_cycles = True
1662        workflow.steps = steps
1663
1664def edgelist_for_workflow_steps( steps ):
1665    """
1666    Create a list of tuples representing edges between `WorkflowSteps` based
1667    on associated `WorkflowStepConnection`s
1668    """
1669    edges = []
1670    steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) )
1671    for step in steps:
1672        edges.append( ( steps_to_index[step], steps_to_index[step] ) )
1673        for conn in step.input_connections:
1674            edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) )
1675    return edges
1676
1677def order_workflow_steps( steps ):
1678    """
1679    Perform topological sort of the steps, return ordered or None
1680    """
1681    try:
1682        edges = edgelist_for_workflow_steps( steps )
1683        node_order = topsort( edges )
1684        return [ steps[i] for i in node_order ]
1685    except CycleError:
1686        return None
1687   
1688def order_workflow_steps_with_levels( steps ):
1689    try:
1690        return topsort_levels( edgelist_for_workflow_steps( steps ) )
1691    except CycleError:
1692        return None
1693   
1694class FakeJob( object ):
1695    """
1696    Fake job object for datasets that have no creating_job_associations,
1697    they will be treated as "input" datasets.
1698    """
1699    def __init__( self, dataset ):
1700        self.is_fake = True
1701        self.id = "fake_%s" % dataset.id
1702   
1703def get_job_dict( trans ):
1704    """
1705    Return a dictionary of Job -> [ Dataset ] mappings, for all finished
1706    active Datasets in the current history and the jobs that created them.
1707    """
1708    history = trans.get_history()
1709    # Get the jobs that created the datasets
1710    warnings = set()
1711    jobs = odict()
1712    for dataset in history.active_datasets:
1713        # FIXME: Create "Dataset.is_finished"
1714        if dataset.state in ( 'new', 'running', 'queued' ):
1715            warnings.add( "Some datasets still queued or running were ignored" )
1716            continue
1717       
1718        #if this hda was copied from another, we need to find the job that created the origial hda
1719        job_hda = dataset
1720        while job_hda.copied_from_history_dataset_association:
1721            job_hda = job_hda.copied_from_history_dataset_association
1722       
1723        if not job_hda.creating_job_associations:
1724            jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
1725       
1726        for assoc in job_hda.creating_job_associations:
1727            job = assoc.job
1728            if job in jobs:
1729                jobs[ job ].append( ( assoc.name, dataset ) )
1730            else:
1731                jobs[ job ] = [ ( assoc.name, dataset ) ]
1732    return jobs, warnings   
1733
1734def cleanup_param_values( inputs, values ):
1735    """
1736    Remove 'Data' values from `param_values`, along with metadata cruft,
1737    but track the associations.
1738    """
1739    associations = []
1740    names_to_clean = []
1741    # dbkey is pushed in by the framework
1742    if 'dbkey' in values:
1743        del values['dbkey']
1744    root_values = values
1745    # Recursively clean data inputs and dynamic selects
1746    def cleanup( prefix, inputs, values ):
1747        for key, input in inputs.items():
1748            if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
1749                if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
1750                    values[key] = UnvalidatedValue( values[key] )
1751            if isinstance( input, DataToolParameter ):
1752                tmp = values[key]
1753                values[key] = None
1754                # HACK: Nested associations are not yet working, but we
1755                #       still need to clean them up so we can serialize
1756                # if not( prefix ):
1757                if tmp: #this is false for a non-set optional dataset
1758                    associations.append( ( tmp.hid, prefix + key ) )
1759                # Cleanup the other deprecated crap associated with datasets
1760                # as well. Worse, for nested datasets all the metadata is
1761                # being pushed into the root. FIXME: MUST REMOVE SOON
1762                key = prefix + key + "_"
1763                for k in root_values.keys():
1764                    if k.startswith( key ):
1765                        del root_values[k]           
1766            elif isinstance( input, Repeat ):
1767                group_values = values[key]
1768                for i, rep_values in enumerate( group_values ):
1769                    rep_index = rep_values['__index__']
1770                    prefix = "%s_%d|" % ( key, rep_index )
1771                    cleanup( prefix, input.inputs, group_values[i] )
1772            elif isinstance( input, Conditional ):
1773                group_values = values[input.name]
1774                current_case = group_values['__current_case__']
1775                prefix = "%s|" % ( key )
1776                cleanup( prefix, input.cases[current_case].inputs, group_values )
1777    cleanup( "", inputs, values )
1778    return associations
1779   
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