[2] | 1 | from galaxy.web.base.controller import * |
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| 2 | |
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| 3 | import pkg_resources |
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| 4 | pkg_resources.require( "simplejson" ) |
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| 5 | pkg_resources.require( "SVGFig" ) |
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| 6 | import simplejson |
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| 7 | import base64, httplib, urllib2, sgmllib, svgfig |
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| 8 | |
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| 9 | from galaxy.web.framework.helpers import time_ago, grids |
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| 10 | from galaxy.tools.parameters import * |
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| 11 | from galaxy.tools import DefaultToolState |
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| 12 | from galaxy.tools.parameters.grouping import Repeat, Conditional |
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| 13 | from galaxy.datatypes.data import Data |
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| 14 | from galaxy.util.odict import odict |
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| 15 | from galaxy.util.sanitize_html import sanitize_html |
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| 16 | from galaxy.util.topsort import topsort, topsort_levels, CycleError |
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| 17 | from galaxy.workflow.modules import * |
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| 18 | from galaxy import model |
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| 19 | from galaxy.model.mapping import desc |
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| 20 | from galaxy.model.orm import * |
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| 21 | from galaxy.model.item_attrs import * |
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| 22 | from galaxy.web.framework.helpers import to_unicode |
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| 23 | from galaxy.jobs.actions.post import ActionBox |
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| 24 | |
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| 25 | class StoredWorkflowListGrid( grids.Grid ): |
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| 26 | class StepsColumn( grids.GridColumn ): |
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| 27 | def get_value(self, trans, grid, workflow): |
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| 28 | return len( workflow.latest_workflow.steps ) |
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| 29 | |
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| 30 | # Grid definition |
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| 31 | use_panels = True |
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| 32 | title = "Saved Workflows" |
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| 33 | model_class = model.StoredWorkflow |
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| 34 | default_filter = { "name" : "All", "tags": "All" } |
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| 35 | default_sort_key = "-update_time" |
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| 36 | columns = [ |
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| 37 | grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), |
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| 38 | grids.IndividualTagsColumn( "Tags", "tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), |
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| 39 | StepsColumn( "Steps" ), |
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| 40 | grids.GridColumn( "Created", key="create_time", format=time_ago ), |
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| 41 | grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), |
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| 42 | ] |
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| 43 | columns.append( |
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| 44 | grids.MulticolFilterColumn( |
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| 45 | "Search", |
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| 46 | cols_to_filter=[ columns[0], columns[1] ], |
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| 47 | key="free-text-search", visible=False, filterable="standard" ) |
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| 48 | ) |
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| 49 | operations = [ |
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| 50 | grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), |
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| 51 | grids.GridOperation( "Run", condition=( lambda item: not item.deleted ), async_compatible=False ), |
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| 52 | grids.GridOperation( "Clone", condition=( lambda item: not item.deleted ), async_compatible=False ), |
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| 53 | grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False ), |
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| 54 | grids.GridOperation( "Sharing", condition=( lambda item: not item.deleted ), async_compatible=False ), |
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| 55 | grids.GridOperation( "Delete", condition=( lambda item: item.deleted ), async_compatible=True ), |
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| 56 | ] |
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| 57 | def apply_query_filter( self, trans, query, **kwargs ): |
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| 58 | return query.filter_by( user=trans.user, deleted=False ) |
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| 59 | |
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| 60 | class StoredWorkflowAllPublishedGrid( grids.Grid ): |
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| 61 | title = "Published Workflows" |
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| 62 | model_class = model.StoredWorkflow |
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| 63 | default_sort_key = "update_time" |
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| 64 | default_filter = dict( public_url="All", username="All", tags="All" ) |
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| 65 | use_async = True |
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| 66 | columns = [ |
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| 67 | grids.PublicURLColumn( "Name", key="name", filterable="advanced" ), |
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| 68 | grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), |
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| 69 | grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), |
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| 70 | grids.CommunityRatingColumn( "Community Rating", key="rating" ), |
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| 71 | grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), |
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| 72 | grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) |
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| 73 | ] |
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| 74 | columns.append( |
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| 75 | grids.MulticolFilterColumn( |
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| 76 | "Search", |
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| 77 | cols_to_filter=[ columns[0], columns[1], columns[2] ], |
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| 78 | key="free-text-search", visible=False, filterable="standard" ) |
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| 79 | ) |
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| 80 | operations = [] |
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| 81 | def build_initial_query( self, trans, **kwargs ): |
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| 82 | # Join so that searching stored_workflow.user makes sense. |
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| 83 | return trans.sa_session.query( self.model_class ).join( model.User.table ) |
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| 84 | def apply_query_filter( self, trans, query, **kwargs ): |
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| 85 | # A public workflow is published, has a slug, and is not deleted. |
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| 86 | return query.filter( self.model_class.published==True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) |
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| 87 | |
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| 88 | # Simple SGML parser to get all content in a single tag. |
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| 89 | class SingleTagContentsParser( sgmllib.SGMLParser ): |
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| 90 | |
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| 91 | def __init__( self, target_tag ): |
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| 92 | sgmllib.SGMLParser.__init__( self ) |
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| 93 | self.target_tag = target_tag |
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| 94 | self.cur_tag = None |
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| 95 | self.tag_content = "" |
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| 96 | |
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| 97 | def unknown_starttag( self, tag, attrs ): |
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| 98 | """ Called for each start tag. """ |
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| 99 | self.cur_tag = tag |
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| 100 | |
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| 101 | def handle_data( self, text ): |
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| 102 | """ Called for each block of plain text. """ |
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| 103 | if self.cur_tag == self.target_tag: |
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| 104 | self.tag_content += text |
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| 105 | |
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| 106 | class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnnotations, UsesItemRatings ): |
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| 107 | stored_list_grid = StoredWorkflowListGrid() |
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| 108 | published_list_grid = StoredWorkflowAllPublishedGrid() |
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| 109 | |
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| 110 | __myexp_url = "sandbox.myexperiment.org:80" |
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| 111 | |
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| 112 | @web.expose |
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| 113 | def index( self, trans ): |
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| 114 | return self.list( trans ) |
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| 115 | |
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| 116 | @web.expose |
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| 117 | @web.require_login( "use Galaxy workflows" ) |
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| 118 | def list_grid( self, trans, **kwargs ): |
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| 119 | """ List user's stored workflows. """ |
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| 120 | status = message = None |
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| 121 | if 'operation' in kwargs: |
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| 122 | operation = kwargs['operation'].lower() |
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| 123 | if operation == "rename": |
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| 124 | return self.rename( trans, **kwargs ) |
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| 125 | history_ids = util.listify( kwargs.get( 'id', [] ) ) |
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| 126 | if operation == "sharing": |
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| 127 | return self.sharing( trans, id=history_ids ) |
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| 128 | return self.stored_list_grid( trans, **kwargs ) |
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| 129 | |
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| 130 | @web.expose |
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| 131 | @web.require_login( "use Galaxy workflows", use_panels=True ) |
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| 132 | def list( self, trans ): |
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| 133 | """ |
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| 134 | Render workflow main page (management of existing workflows) |
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| 135 | """ |
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| 136 | user = trans.get_user() |
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| 137 | workflows = trans.sa_session.query( model.StoredWorkflow ) \ |
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| 138 | .filter_by( user=user, deleted=False ) \ |
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| 139 | .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ |
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| 140 | .all() |
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| 141 | shared_by_others = trans.sa_session \ |
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| 142 | .query( model.StoredWorkflowUserShareAssociation ) \ |
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| 143 | .filter_by( user=user ) \ |
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| 144 | .join( 'stored_workflow' ) \ |
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| 145 | .filter( model.StoredWorkflow.deleted == False ) \ |
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| 146 | .order_by( desc( model.StoredWorkflow.update_time ) ) \ |
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| 147 | .all() |
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| 148 | |
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| 149 | # Legacy issue: all shared workflows must have slugs. |
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| 150 | slug_set = False |
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| 151 | for workflow_assoc in shared_by_others: |
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| 152 | slug_set = self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow ) |
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| 153 | if slug_set: |
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| 154 | trans.sa_session.flush() |
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| 155 | |
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| 156 | return trans.fill_template( "workflow/list.mako", |
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| 157 | workflows = workflows, |
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| 158 | shared_by_others = shared_by_others ) |
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| 159 | |
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| 160 | @web.expose |
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| 161 | @web.require_login( "use Galaxy workflows" ) |
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| 162 | def list_for_run( self, trans ): |
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| 163 | """ |
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| 164 | Render workflow list for analysis view (just allows running workflow |
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| 165 | or switching to management view) |
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| 166 | """ |
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| 167 | user = trans.get_user() |
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| 168 | workflows = trans.sa_session.query( model.StoredWorkflow ) \ |
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| 169 | .filter_by( user=user, deleted=False ) \ |
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| 170 | .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ |
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| 171 | .all() |
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| 172 | shared_by_others = trans.sa_session \ |
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| 173 | .query( model.StoredWorkflowUserShareAssociation ) \ |
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| 174 | .filter_by( user=user ) \ |
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| 175 | .filter( model.StoredWorkflow.deleted == False ) \ |
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| 176 | .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ |
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| 177 | .all() |
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| 178 | return trans.fill_template( "workflow/list_for_run.mako", |
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| 179 | workflows = workflows, |
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| 180 | shared_by_others = shared_by_others ) |
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| 181 | |
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| 182 | @web.expose |
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| 183 | def list_published( self, trans, **kwargs ): |
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| 184 | grid = self.published_list_grid( trans, **kwargs ) |
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| 185 | if 'async' in kwargs: |
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| 186 | return grid |
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| 187 | else: |
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| 188 | # Render grid wrapped in panels |
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| 189 | return trans.fill_template( "workflow/list_published.mako", grid=grid ) |
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| 190 | |
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| 191 | @web.expose |
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| 192 | def display_by_username_and_slug( self, trans, username, slug ): |
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| 193 | """ Display workflow based on a username and slug. """ |
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| 194 | |
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| 195 | # Get workflow. |
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| 196 | session = trans.sa_session |
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| 197 | user = session.query( model.User ).filter_by( username=username ).first() |
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| 198 | stored_workflow = trans.sa_session.query( model.StoredWorkflow ).filter_by( user=user, slug=slug, deleted=False ).first() |
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| 199 | if stored_workflow is None: |
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| 200 | raise web.httpexceptions.HTTPNotFound() |
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| 201 | # Security check raises error if user cannot access workflow. |
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| 202 | self.security_check( trans.get_user(), stored_workflow, False, True) |
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| 203 | |
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| 204 | # Get data for workflow's steps. |
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| 205 | self.get_stored_workflow_steps( trans, stored_workflow ) |
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| 206 | # Get annotations. |
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| 207 | stored_workflow.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow ) |
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| 208 | for step in stored_workflow.latest_workflow.steps: |
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| 209 | step.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, step ) |
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| 210 | |
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| 211 | # Get rating data. |
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| 212 | user_item_rating = 0 |
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| 213 | if trans.get_user(): |
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| 214 | user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), stored_workflow ) |
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| 215 | if user_item_rating: |
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| 216 | user_item_rating = user_item_rating.rating |
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| 217 | else: |
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| 218 | user_item_rating = 0 |
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| 219 | ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, stored_workflow ) |
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| 220 | return trans.fill_template_mako( "workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps, |
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| 221 | user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) |
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| 222 | |
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| 223 | @web.expose |
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| 224 | def get_item_content_async( self, trans, id ): |
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| 225 | """ Returns item content in HTML format. """ |
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| 226 | |
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| 227 | stored = self.get_stored_workflow( trans, id, False, True ) |
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| 228 | if stored is None: |
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| 229 | raise web.httpexceptions.HTTPNotFound() |
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| 230 | |
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| 231 | # Get data for workflow's steps. |
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| 232 | self.get_stored_workflow_steps( trans, stored ) |
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| 233 | # Get annotations. |
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| 234 | stored.annotation = self.get_item_annotation_str( trans.sa_session, stored.user, stored ) |
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| 235 | for step in stored.latest_workflow.steps: |
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| 236 | step.annotation = self.get_item_annotation_str( trans.sa_session, stored.user, step ) |
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| 237 | return trans.stream_template_mako( "/workflow/item_content.mako", item = stored, item_data = stored.latest_workflow.steps ) |
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| 238 | |
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| 239 | @web.expose |
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| 240 | @web.require_login( "use Galaxy workflows" ) |
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| 241 | def share( self, trans, id, email="", use_panels=False ): |
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| 242 | msg = mtype = None |
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| 243 | # Load workflow from database |
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| 244 | stored = self.get_stored_workflow( trans, id ) |
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| 245 | if email: |
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| 246 | other = trans.sa_session.query( model.User ) \ |
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| 247 | .filter( and_( model.User.table.c.email==email, |
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| 248 | model.User.table.c.deleted==False ) ) \ |
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| 249 | .first() |
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| 250 | if not other: |
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| 251 | mtype = "error" |
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| 252 | msg = ( "User '%s' does not exist" % email ) |
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| 253 | elif other == trans.get_user(): |
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| 254 | mtype = "error" |
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| 255 | msg = ( "You cannot share a workflow with yourself" ) |
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| 256 | elif trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ |
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| 257 | .filter_by( user=other, stored_workflow=stored ).count() > 0: |
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| 258 | mtype = "error" |
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| 259 | msg = ( "Workflow already shared with '%s'" % email ) |
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| 260 | else: |
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| 261 | share = model.StoredWorkflowUserShareAssociation() |
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| 262 | share.stored_workflow = stored |
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| 263 | share.user = other |
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| 264 | session = trans.sa_session |
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| 265 | session.add( share ) |
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| 266 | self.create_item_slug( session, stored ) |
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| 267 | session.flush() |
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| 268 | trans.set_message( "Workflow '%s' shared with user '%s'" % ( stored.name, other.email ) ) |
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| 269 | return trans.response.send_redirect( url_for( controller='workflow', action='sharing', id=id ) ) |
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| 270 | return trans.fill_template( "/ind_share_base.mako", |
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| 271 | message = msg, |
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| 272 | messagetype = mtype, |
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| 273 | item=stored, |
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| 274 | email=email, |
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| 275 | use_panels=use_panels ) |
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| 276 | |
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| 277 | @web.expose |
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| 278 | @web.require_login( "use Galaxy workflows" ) |
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| 279 | def sharing( self, trans, id, **kwargs ): |
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| 280 | """ Handle workflow sharing. """ |
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| 281 | |
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| 282 | # Get session and workflow. |
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| 283 | session = trans.sa_session |
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| 284 | stored = self.get_stored_workflow( trans, id ) |
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| 285 | session.add( stored ) |
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| 286 | |
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| 287 | # Do operation on workflow. |
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| 288 | if 'make_accessible_via_link' in kwargs: |
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| 289 | self._make_item_accessible( trans.sa_session, stored ) |
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| 290 | elif 'make_accessible_and_publish' in kwargs: |
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| 291 | self._make_item_accessible( trans.sa_session, stored ) |
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| 292 | stored.published = True |
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| 293 | elif 'publish' in kwargs: |
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| 294 | stored.published = True |
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| 295 | elif 'disable_link_access' in kwargs: |
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| 296 | stored.importable = False |
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| 297 | elif 'unpublish' in kwargs: |
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| 298 | stored.published = False |
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| 299 | elif 'disable_link_access_and_unpublish' in kwargs: |
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| 300 | stored.importable = stored.published = False |
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| 301 | elif 'unshare_user' in kwargs: |
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| 302 | user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) ) |
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| 303 | if not user: |
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| 304 | error( "User not found for provided id" ) |
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| 305 | association = session.query( model.StoredWorkflowUserShareAssociation ) \ |
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| 306 | .filter_by( user=user, stored_workflow=stored ).one() |
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| 307 | session.delete( association ) |
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| 308 | |
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| 309 | # Legacy issue: workflows made accessible before recent updates may not have a slug. Create slug for any workflows that need them. |
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| 310 | if stored.importable and not stored.slug: |
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| 311 | self._make_item_accessible( trans.sa_session, stored ) |
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| 312 | |
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| 313 | session.flush() |
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| 314 | |
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| 315 | return trans.fill_template( "/workflow/sharing.mako", use_panels=True, item=stored ) |
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| 316 | |
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| 317 | @web.expose |
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| 318 | @web.require_login( "to import a workflow", use_panels=True ) |
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| 319 | def imp( self, trans, id, **kwargs ): |
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| 320 | # Set referer message. |
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| 321 | referer = trans.request.referer |
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| 322 | if referer is not "": |
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| 323 | referer_message = "<a href='%s'>return to the previous page</a>" % referer |
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| 324 | else: |
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| 325 | referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) |
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| 326 | |
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| 327 | # Do import. |
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| 328 | session = trans.sa_session |
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| 329 | stored = self.get_stored_workflow( trans, id, check_ownership=False ) |
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| 330 | if stored.importable == False: |
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| 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 ) |
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| 332 | elif stored.user == trans.user: |
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| 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 ) |
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| 334 | elif stored.deleted: |
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| 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 ) |
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| 336 | else: |
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| 337 | # Copy workflow. |
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| 338 | imported_stored = model.StoredWorkflow() |
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| 339 | imported_stored.name = "imported: " + stored.name |
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| 340 | imported_stored.latest_workflow = stored.latest_workflow |
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| 341 | imported_stored.user = trans.user |
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| 342 | # Save new workflow. |
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| 343 | session = trans.sa_session |
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| 344 | session.add( imported_stored ) |
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| 345 | session.flush() |
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| 346 | |
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| 347 | # Copy annotations. |
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| 348 | self.copy_item_annotation( session, stored.user, stored, imported_stored.user, imported_stored ) |
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| 349 | for order_index, step in enumerate( stored.latest_workflow.steps ): |
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| 350 | self.copy_item_annotation( session, stored.user, step, \ |
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| 351 | imported_stored.user, imported_stored.latest_workflow.steps[order_index] ) |
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| 352 | session.flush() |
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| 353 | |
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| 354 | # Redirect to load galaxy frames. |
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| 355 | return trans.show_ok_message( |
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| 356 | message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s.""" |
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| 357 | % ( stored.name, web.url_for( controller='workflow' ), referer_message ), use_panels=True ) |
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| 358 | |
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| 359 | @web.expose |
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| 360 | @web.require_login( "use Galaxy workflows" ) |
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| 361 | def edit_attributes( self, trans, id, **kwargs ): |
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| 362 | # Get workflow and do error checking. |
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| 363 | stored = self.get_stored_workflow( trans, id ) |
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| 364 | if not stored: |
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| 365 | error( "You do not own this workflow or workflow ID is invalid." ) |
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| 366 | # Update workflow attributes if new values submitted. |
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| 367 | if 'name' in kwargs: |
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| 368 | # Rename workflow. |
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| 369 | stored.name = kwargs[ 'name' ] |
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| 370 | if 'annotation' in kwargs: |
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| 371 | # Set workflow annotation; sanitize annotation before adding it. |
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| 372 | annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) |
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| 373 | self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) |
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| 374 | trans.sa_session.flush() |
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| 375 | return trans.fill_template( 'workflow/edit_attributes.mako', |
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| 376 | stored=stored, |
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| 377 | annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) |
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| 378 | ) |
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| 379 | |
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| 380 | @web.expose |
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| 381 | @web.require_login( "use Galaxy workflows" ) |
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| 382 | def rename( self, trans, id, new_name=None, **kwargs ): |
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| 383 | stored = self.get_stored_workflow( trans, id ) |
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| 384 | if new_name is not None: |
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| 385 | stored.name = new_name |
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| 386 | trans.sa_session.flush() |
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| 387 | # For current workflows grid: |
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| 388 | trans.set_message ( "Workflow renamed to '%s'." % new_name ) |
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| 389 | return self.list( trans ) |
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| 390 | # For new workflows grid: |
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| 391 | #message = "Workflow renamed to '%s'." % new_name |
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| 392 | #return self.list_grid( trans, message=message, status='done' ) |
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| 393 | else: |
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| 394 | return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename" ) \ |
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| 395 | .add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) ) |
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| 396 | |
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| 397 | @web.expose |
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| 398 | @web.require_login( "use Galaxy workflows" ) |
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| 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 | |
---|
| 1653 | def 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 | |
---|
| 1664 | def 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 | |
---|
| 1677 | def 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 | |
---|
| 1688 | def order_workflow_steps_with_levels( steps ): |
---|
| 1689 | try: |
---|
| 1690 | return topsort_levels( edgelist_for_workflow_steps( steps ) ) |
---|
| 1691 | except CycleError: |
---|
| 1692 | return None |
---|
| 1693 | |
---|
| 1694 | class 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 | |
---|
| 1703 | def 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 | |
---|
| 1734 | def 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 | |
---|