January 2010 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3229: Small style updates to tags.
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b78de785df21 changeset: 3229:b78de785df21 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Jan 12 15:48:21 2010 -0500 description: Small style updates to tags. diffstat: static/june_2007_style/autocomplete_tagging.css.tmpl | 5 +++-- static/june_2007_style/blue/autocomplete_tagging.css | 6 +++--- templates/tagging_common.mako | 2 +- 3 files changed, 7 insertions(+), 6 deletions(-) diffs (59 lines): diff -r 6741f6000e03 -r b78de785df21 static/june_2007_style/autocomplete_tagging.css.tmpl --- a/static/june_2007_style/autocomplete_tagging.css.tmpl Tue Jan 12 14:08:17 2010 -0500 +++ b/static/june_2007_style/autocomplete_tagging.css.tmpl Tue Jan 12 15:48:21 2010 -0500 @@ -66,12 +66,12 @@ /****************************************************************************/ .tag-area { width: 100%; - cursor: pointer; } -.individual-tags +.individual-tag-area { border:solid 1px #eee; + cursor: pointer; } .active-tag-area { @@ -128,6 +128,7 @@ vertical-align: bottom; border: none; outline: none; + resize: none; } .delete-tag-img diff -r 6741f6000e03 -r b78de785df21 static/june_2007_style/blue/autocomplete_tagging.css --- a/static/june_2007_style/blue/autocomplete_tagging.css Tue Jan 12 14:08:17 2010 -0500 +++ b/static/june_2007_style/blue/autocomplete_tagging.css Tue Jan 12 15:48:21 2010 -0500 @@ -6,8 +6,8 @@ .ac_even{margin-left:0.3em;} .ac_over{background-color:#0A246A;color:white;} .ac_header{font-style:normal;color:gray;border-bottom:0.1em solid gray;} -.tag-area{width:100%;cursor:pointer;} -.individual-tags{border:solid 1px #eee;} +.tag-area{width:100%;} +.individual-tag-area{border:solid 1px #eee;cursor:pointer;} .active-tag-area{background-color:white;} .toggle-link{font-weight:normal;padding:0.3em;margin-bottom:1em;width:100%;padding:0.2em 0em 0.2em 0em;} .tag-button{width:auto;color:#444;text-decoration:none;display:inline-block;cursor:pointer;margin:0.2em;border:0;padding:0.1em 0.5em 0.1em 0.5em;-moz-border-radius:.5em;-webkit-border-radius:.5em;border-radius:.5em;background:#bbb;} @@ -15,5 +15,5 @@ .tag-button .tag-name:hover{color:white;} .add-tag-button{margin-bottom:0.3em;vertical-align:middle;padding:0.3em;} .add-tag-button:hover{cursor:pointer;} -.tag-input{vertical-align:bottom;border:none;outline:none;} +.tag-input{vertical-align:bottom;border:none;outline:none;resize:none;} .delete-tag-img{margin-left:0.3em;} diff -r 6741f6000e03 -r b78de785df21 templates/tagging_common.mako --- a/templates/tagging_common.mako Tue Jan 12 14:08:17 2010 -0500 +++ b/templates/tagging_common.mako Tue Jan 12 15:48:21 2010 -0500 @@ -39,7 +39,7 @@ %endif <div class="tag-area %if tag_type == 'individual': - individual-tags + individual-tag-area %endif ">

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[hg] galaxy 3228: Preserve teh order of a tool's output datasets...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6741f6000e03 changeset: 3228:6741f6000e03 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 12 14:08:17 2010 -0500 description: Preserve teh order of a tool's output datasets by storing them in an odict rather than a dict - loosely based on the "patch" contributed by Alexander Rose. diffstat: lib/galaxy/tools/__init__.py | 6 +++--- lib/galaxy/tools/actions/__init__.py | 3 ++- lib/galaxy/tools/actions/metadata.py | 3 ++- lib/galaxy/tools/actions/upload_common.py | 6 +++++- test/base/twilltestcase.py | 3 +-- 5 files changed, 13 insertions(+), 8 deletions(-) diffs (95 lines): diff -r 892199a8078e -r 6741f6000e03 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue Jan 12 11:42:22 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Tue Jan 12 14:08:17 2010 -0500 @@ -372,7 +372,7 @@ # Parse tool help self.parse_help( root ) # Description of outputs produced by an invocation of the tool - self.outputs = {} + self.outputs = odict() out_elem = root.find("outputs") if out_elem: for data_elem in out_elem.findall("data"): @@ -790,10 +790,10 @@ elif state.page == self.last_page: out_data = self.execute( trans, incoming=params ) try: - assert type( out_data ) is types.DictType + assert isinstance( out_data, odict ) return 'tool_executed.mako', dict( out_data=out_data ) except: - return 'message.mako', dict( message_type='error', message=out_data, refresh_frames=[] ) + return 'message.mako', dict( message_type='error', message='odict not returned from tool execution', refresh_frames=[] ) # Otherwise move on to the next page else: state.page += 1 diff -r 892199a8078e -r 6741f6000e03 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Tue Jan 12 11:42:22 2010 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Tue Jan 12 14:08:17 2010 -0500 @@ -1,4 +1,5 @@ from galaxy.util.bunch import Bunch +from galaxy.util.odict import odict from galaxy.tools.parameters import * from galaxy.tools.parameters.grouping import * from galaxy.util.template import fill_template @@ -107,7 +108,7 @@ input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming ) else: input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming ) - out_data = {} + out_data = odict() # Collect any input datasets from the incoming parameters inp_data = self.collect_input_datasets( tool, incoming, trans ) diff -r 892199a8078e -r 6741f6000e03 lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py Tue Jan 12 11:42:22 2010 -0500 +++ b/lib/galaxy/tools/actions/metadata.py Tue Jan 12 14:08:17 2010 -0500 @@ -1,5 +1,6 @@ from __init__ import ToolAction from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper +from galaxy.util.odict import odict import logging log = logging.getLogger( __name__ ) @@ -59,4 +60,4 @@ # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added set external metadata job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - return [] + return odict() diff -r 892199a8078e -r 6741f6000e03 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue Jan 12 11:42:22 2010 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Jan 12 14:08:17 2010 -0500 @@ -1,6 +1,7 @@ import os, tempfile, StringIO from cgi import FieldStorage from galaxy import datatypes, util +from galaxy.util.odict import odict from galaxy.datatypes import sniff from galaxy.util.json import to_json_string from galaxy.model.orm import eagerload_all @@ -321,7 +322,10 @@ # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - return dict( [ ( 'output%i' % i, v ) for i, v in enumerate( data_list ) ] ) + output = odict() + for i, v in enumerate( data_list ): + output[ 'output%i' % i ] = v + return output def active_folders( trans, folder ): # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues). # Much faster way of retrieving all active sub-folders within a given folder than the diff -r 892199a8078e -r 6741f6000e03 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Jan 12 11:42:22 2010 -0500 +++ b/test/base/twilltestcase.py Tue Jan 12 14:08:17 2010 -0500 @@ -81,8 +81,7 @@ def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)' ): """Uploads a file""" filename = self.get_filename(filename) - self.home() - self.visit_page( "tool_runner/index?tool_id=upload1" ) + self.visit_url( "%s/tool_runner?tool_id=upload1" % self.url ) try: tc.fv("1","file_type", ftype) tc.fv("1","dbkey", dbkey)

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[hg] galaxy 3227: Tweaking style of panel header buttons
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/892199a8078e changeset: 3227:892199a8078e user: James Taylor <james(a)jamestaylor.org> date: Tue Jan 12 11:42:22 2010 -0500 description: Tweaking style of panel header buttons diffstat: static/june_2007_style/blue/panel_layout.css | 4 ++-- static/june_2007_style/panel_layout.css.tmpl | 5 +++-- 2 files changed, 5 insertions(+), 4 deletions(-) diffs (42 lines): diff -r a7deb5c197ad -r 892199a8078e static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Tue Jan 12 11:37:45 2010 -0500 +++ b/static/june_2007_style/blue/panel_layout.css Tue Jan 12 11:42:22 2010 -0500 @@ -24,9 +24,9 @@ .unified-panel-header-inner{padding-top:0.45em;} .menu-bg{background:#C1C9E5 url(menu_bg.png) top repeat-x;} div.unified-panel-body{position:absolute;top:2em;bottom:0;width:100%;margin-top:1px;} -.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;background:#bbb;} +.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;border:solid #999 1px;padding-right:0.5em;padding-left:0.5em;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} -.panel-header-button:hover{color:black;background-color:#aaaaaa;} +.panel-header-button:hover{color:black;background-color:#ccc;} .panel-header-button:active{color:white;background-color:#aaaaaa;} #overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} .dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;} diff -r a7deb5c197ad -r 892199a8078e static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Tue Jan 12 11:37:45 2010 -0500 +++ b/static/june_2007_style/panel_layout.css.tmpl Tue Jan 12 11:42:22 2010 -0500 @@ -144,12 +144,13 @@ display: inline-block; cursor: pointer; margin: -1px; padding: 1px; + margin-top: -0.2em; + border: solid #999 1px; padding-right: 0.5em; padding-left: 0.5em; -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; - background: #bbb; } .panel-header-button.popup { @@ -159,7 +160,7 @@ .panel-header-button:hover { color: black; - background-color: #aaaaaa; + background-color: #ccc; } .panel-header-button:active {

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[hg] galaxy 3226: Enhancements to personal and public grids for ...
by Greg Von Kuster 22 Jan '10

22 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a7deb5c197ad changeset: 3226:a7deb5c197ad user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Jan 12 11:37:45 2010 -0500 description: Enhancements to personal and public grids for pages, published histories, and workflows. Specific improvements: (a) added community tags to grids for published pages and published histories; (b) bug fixes for grids for published pages and published histories; © added individual tags for pages and workflows; (d) added user grid for stored/saved workflows (not yet included in default workflow view); (e) added grid for publicly available workflows; (f) added pretty URLs for public workflows and ability to view a public workflow. Fixes #232 diffstat: lib/galaxy/model/__init__.py | 1 + lib/galaxy/model/mapping.py | 1 + lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py | 38 + lib/galaxy/tags/tag_handler.py | 23 +- lib/galaxy/web/base/controller.py | 18 +- lib/galaxy/web/buildapp.py | 1 + lib/galaxy/web/controllers/history.py | 46 +- lib/galaxy/web/controllers/page.py | 24 +- lib/galaxy/web/controllers/tag.py | 18 +- lib/galaxy/web/controllers/workflow.py | 138 ++++++- lib/galaxy/web/framework/__init__.py | 6 + static/june_2007_style/autocomplete_tagging.css.tmpl | 6 +- static/june_2007_style/blue/autocomplete_tagging.css | 3 +- templates/history/list_public.mako | 2 +- templates/history/view.mako | 136 +++--- templates/page/display.mako | 2 - templates/page/editor.mako | 7 +- templates/root/history.mako | 21 +- templates/tagging_common.mako | 12 +- templates/workflow/display.mako | 195 ++++++++++ templates/workflow/list_public.mako | 23 + templates/workflow/sharing.mako | 7 + 22 files changed, 566 insertions(+), 162 deletions(-) diffs (1192 lines): diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/model/__init__.py Tue Jan 12 11:37:45 2010 -0500 @@ -1114,6 +1114,7 @@ self.id = None self.user = None self.name = None + self.slug = None self.latest_workflow_id = None self.workflows = [] diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/model/mapping.py Tue Jan 12 11:37:45 2010 -0500 @@ -513,6 +513,7 @@ Column( "name", TEXT ), Column( "deleted", Boolean, default=False ), Column( "importable", Boolean, default=False ), + Column( "slug", TEXT, index=True ) ) Workflow.table = Table( "workflow", metadata, diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py Tue Jan 12 11:37:45 2010 -0500 @@ -0,0 +1,38 @@ +""" +Migration script to add slug column for stored workflow. +""" + +from sqlalchemy import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def upgrade(): + + print __doc__ + metadata.reflect() + + StoredWorkflow_table = Table( "stored_workflow", metadata, autoload=True ) + + # Create slug column. + c = Column( "slug", TEXT, index=True ) + c.create( StoredWorkflow_table ) + assert c is StoredWorkflow_table.c.slug + + # Create slug index. + try: + i = Index( "ix_stored_workflow_slug", StoredWorkflow_table.c.slug ) + i.create() + except: + # Mysql doesn't have a named index, but alter should work + StoredWorkflow_table.c.slug.alter( unique=False ) + +def downgrade(): + metadata.reflect() + + StoredWorkflow_table = Table( "stored_workflow", metadata, autoload=True ) + StoredWorkflow_table.c.slug.drop() diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/tags/tag_handler.py Tue Jan 12 11:37:45 2010 -0500 @@ -1,9 +1,7 @@ -from galaxy.model import Tag +from galaxy import model import re from sqlalchemy.sql.expression import func, and_ from sqlalchemy.sql import select -from galaxy.model import History, HistoryTagAssociation, Dataset, DatasetTagAssociation, \ - HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation, Page, PageTagAssociation class TagHandler( object ): @@ -31,10 +29,11 @@ # Initialize with known classes. item_tag_assoc_info = {} - item_tag_assoc_info["History"] = ItemTagAssocInfo( History, HistoryTagAssociation, HistoryTagAssociation.table.c.history_id ) + item_tag_assoc_info["History"] = ItemTagAssocInfo( model.History, model.HistoryTagAssociation, model.HistoryTagAssociation.table.c.history_id ) item_tag_assoc_info["HistoryDatasetAssociation"] = \ - ItemTagAssocInfo( HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation, HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id ) - item_tag_assoc_info["Page"] = ItemTagAssocInfo( Page, PageTagAssociation, PageTagAssociation.table.c.page_id ) + ItemTagAssocInfo( model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, model.HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id ) + item_tag_assoc_info["Page"] = ItemTagAssocInfo( model.Page, model.PageTagAssociation, model.PageTagAssociation.table.c.page_id ) + item_tag_assoc_info["StoredWorkflow"] = ItemTagAssocInfo( model.StoredWorkflow, model.StoredWorkflowTagAssociation, model.StoredWorkflowTagAssociation.table.c.stored_workflow_id ) def get_tag_assoc_class(self, item_class): """ Returns tag association class for item class. """ @@ -55,7 +54,7 @@ # Build select statement. cols_to_select = [ item_tag_assoc_class.table.c.tag_id, func.count('*') ] - from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag.table) + from_obj = item_tag_assoc_class.table.join( item_class.table ).join( model.Tag.table ) where_clause = ( self.get_id_col_in_item_tag_assoc_table(item_class) == item.id ) order_by = [ func.count("*").desc() ] group_by = item_tag_assoc_class.table.c.tag_id @@ -101,7 +100,7 @@ # Get tag name. if isinstance(tag, basestring): tag_name = tag - elif isinstance(tag, Tag): + elif isinstance(tag, model.Tag): tag_name = tag.name # Check for an item-tag association to see if item has a given tag. @@ -168,12 +167,12 @@ def get_tag_by_id(self, db_session, tag_id): """Get a Tag object from a tag id.""" - return db_session.query(Tag).filter(Tag.id==tag_id).first() + return db_session.query( model.Tag ).filter_by( id=tag_id) .first() def get_tag_by_name(self, db_session, tag_name): """Get a Tag object from a tag name (string).""" if tag_name: - return db_session.query( Tag ).filter( Tag.name==tag_name.lower() ).first() + return db_session.query( model.Tag ).filter_by( name=tag_name.lower() ).first() return None def _create_tag(self, db_session, tag_str): @@ -184,9 +183,9 @@ for sub_tag in tag_hierarchy: # Get or create subtag. tag_name = tag_prefix + self._scrub_tag_name(sub_tag) - tag = db_session.query(Tag).filter(Tag.name==tag_name).first() + tag = db_session.query( model.Tag ).filter_by( name=tag_name).first() if not tag: - tag = Tag(type=0, name=tag_name) + tag = model.Tag(type=0, name=tag_name) # Set tag parent. tag.parent = parent_tag diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/web/base/controller.py Tue Jan 12 11:37:45 2010 -0500 @@ -2,7 +2,7 @@ Contains functionality needed in every web interface """ -import os, time, logging +import os, time, logging, re # Pieces of Galaxy to make global in every controller from galaxy import config, tools, web, model, util @@ -28,7 +28,7 @@ return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) else: return None - + class BaseController( object ): """ Base class for Galaxy web application controllers. @@ -57,6 +57,20 @@ if history.user != user: error( "History is not owned by current user" ) return history + + def make_item_importable( self, sa_session, item ): + """ Makes item importable and sets item's slug. Does not flush/commit changes, however. Item must have name, user, importable, and slug attributes. """ + item.importable = True + + # Set history slug. Slug must be unique among user's importable pages. + slug_base = re.sub( "\s+", "-", item.name.lower() ) + slug = slug_base + count = 1 + while sa_session.query( item.__class__ ).filter_by( user=item.user, slug=slug, importable=True ).count() != 0: + # Slug taken; choose a new slug based on count. This approach can handle numerous histories with the same name gracefully. + slug = '%s-%i' % ( slug_base, count ) + count += 1 + item.slug = slug Root = BaseController """ diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/web/buildapp.py Tue Jan 12 11:37:45 2010 -0500 @@ -81,6 +81,7 @@ webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) + webapp.add_route( '/u/:username/w/:slug', controller='workflow', action='display_by_username_and_slug' ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Jan 12 11:37:45 2010 -0500 @@ -10,19 +10,18 @@ import webhelpers, logging, operator from datetime import datetime from cgi import escape -import re log = logging.getLogger( __name__ ) # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" +class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, history ): + return history.get_display_name() + class HistoryListGrid( grids.Grid ): # Custom column types - class NameColumn( grids.TextColumn ): - def get_value(self, trans, grid, history): - return history.get_display_name() - class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): rval = [] @@ -174,21 +173,24 @@ return query.filter( model.HistoryUserShareAssociation.user == trans.user ) class PublicHistoryListGrid( grids.Grid ): + class NameURLColumn( PublicURLColumn, NameColumn ): + pass + title = "Public Histories" model_class = model.History default_sort_key = "-update_time" default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - PublicURLColumn( "Name", key="name", model_class=model.History, filterable="advanced"), + NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[0], columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [] @@ -213,7 +215,6 @@ public_list_grid = PublicHistoryListGrid() @web.expose - @web.require_login() def list_public( self, trans, **kwargs ): grid = self.public_list_grid( trans, **kwargs ) if 'async' in kwargs: @@ -272,7 +273,7 @@ elif operation == "enable import via link": for history in histories: if not history.importable: - self.make_history_importable( trans.sa_session, history ) + self.make_item_importable( trans.sa_session, history ) elif operation == "disable import via link": if history_ids: histories = [ self.get_history( trans, history_id ) for history_id in history_ids ] @@ -432,7 +433,7 @@ importable = importable in ['True', 'true', 't', 'T']; if history and history.importable != importable: if importable: - self.make_history_importable( trans.sa_session, history ) + self.make_item_importable( trans.sa_session, history ) else: history.importable = importable trans.sa_session.flush() @@ -536,8 +537,9 @@ user_owns_history = user_owns_history, show_deleted = False ) - @web.expose + @web.expose def display_by_username_and_slug( self, trans, username, slug ): + """ Display history based on a username and slug. """ session = trans.sa_session user = session.query( model.User ).filter_by( username=username ).first() if user is None: @@ -545,7 +547,7 @@ history = trans.sa_session.query( model.History ).filter_by( user=user, slug=slug, deleted=False, importable=True ).first() if history is None: raise web.httpexceptions.HTTPNotFound() - + query = trans.sa_session.query( model.HistoryDatasetAssociation ) \ .filter( model.HistoryDatasetAssociation.history == history ) \ .options( eagerload( "children" ) ) \ @@ -848,7 +850,7 @@ for history in histories: trans.sa_session.add( history ) if params.get( 'enable_import_via_link', False ): - self.make_history_importable( trans.sa_session, history ) + self.make_item_importable( trans.sa_session, history ) trans.sa_session.flush() elif params.get( 'disable_import_via_link', False ): history.importable = False @@ -964,18 +966,4 @@ msg = 'Clone with name "%s" is now included in your previously stored histories.' % new_history.name else: msg = '%d cloned histories are now included in your previously stored histories.' % len( histories ) - return trans.show_ok_message( msg ) - - def make_history_importable( self, sa_session, history ): - """ Makes history importable and sets history's slug. Does not flush/commit changes, however. """ - history.importable = True - - # Set history slug. Slug must be unique among user's importable pages. - slug_base = re.sub( "\s+", "-", history.name.lower() ) - slug = slug_base - count = 1 - while sa_session.query( model.History ).filter_by( user=history.user, slug=slug, importable=True ).count() != 0: - # Slug taken; choose a new slug based on count. This approach can handle numerous histories with the same name gracefully. - slug = '%s-%i' % ( slug_base, count ) - count += 1 - history.slug = slug \ No newline at end of file + return trans.show_ok_message( msg ) \ No newline at end of file diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Tue Jan 12 11:37:45 2010 -0500 @@ -14,19 +14,31 @@ return "" class PageListGrid( grids.Grid ): + # Custom column. + class URLColumn( PublicURLColumn ): + def get_value( self, trans, grid, item ): + return url_for( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) + # Grid definition use_panels = True title = "Pages" model_class = model.Page - default_filter = { "published" : "All"} + default_filter = { "published" : "All", "tags" : "All", "title" : "All"} default_sort_key = "-create_time" columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="standard" ), - PublicURLColumn( "Public URL" ), - grids.GridColumn( "Published", key="published", format=format_bool, filterable="standard" ), + grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), + URLColumn( "Public URL" ), + grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), + grids.GridColumn( "Published", key="published", format=format_bool, filterable="advanced" ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[2] ], + key="free-text-search", visible=False, filterable="standard" ) + ) global_actions = [ grids.GridAction( "Add new page", dict( action='create' ) ) ] @@ -52,13 +64,13 @@ columns = [ PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"), OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[0], columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) def build_initial_query( self, session ): diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/web/controllers/tag.py --- a/lib/galaxy/web/controllers/tag.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/web/controllers/tag.py Tue Jan 12 11:37:45 2010 -0500 @@ -2,8 +2,6 @@ Tags Controller: handles tagging/untagging of entities and provides autocomplete support. """ -from galaxy.model import History, HistoryTagAssociation, Dataset, DatasetTagAssociation, \ - HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation, Page, PageTagAssociation from galaxy.web.base.controller import * from galaxy.tags.tag_handler import * from sqlalchemy.sql.expression import func, and_ @@ -75,11 +73,13 @@ # Get item class. TODO: we should have a mapper that goes from class_name to class object. if item_class == 'History': - item_class = History + item_class = model.History elif item_class == 'HistoryDatasetAssociation': - item_class = HistoryDatasetAssociation + item_class = model.HistoryDatasetAssociation elif item_class == 'Page': - item_class = Page + item_class = model.Page + elif item_class == 'StoredWorkflow': + item_class = model.StoredWorkflow q = q.encode('utf-8') if q.find(":") == -1: @@ -104,9 +104,9 @@ # Build select statement. cols_to_select = [ item_tag_assoc_class.table.c.tag_id, func.count('*') ] - from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag.table) + from_obj = item_tag_assoc_class.table.join( item_class.table ).join( model.Tag.table ) where_clause = and_( - Tag.table.c.name.like(q + "%"), + model.Tag.table.c.name.like(q + "%"), item_tag_assoc_class.table.c.user_id == user.id ) order_by = [ func.count("*").desc() ] @@ -155,9 +155,9 @@ # Build select statement. cols_to_select = [ item_tag_assoc_class.table.c.value, func.count('*') ] - from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag.table) + from_obj = item_tag_assoc_class.table.join( item_class.table ).join( model.Tag.table ) where_clause = and_( item_tag_assoc_class.table.c.user_id == user.id, - Tag.table.c.id==tag.id, + model.Tag.table.c.id==tag.id, item_tag_assoc_class.table.c.value.like(tag_value + "%") ) order_by = [ func.count("*").desc(), item_tag_assoc_class.table.c.value ] group_by = item_tag_assoc_class.table.c.value diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Tue Jan 12 11:37:45 2010 -0500 @@ -4,6 +4,7 @@ pkg_resources.require( "simplejson" ) import simplejson +from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.tools.parameters import * from galaxy.tools import DefaultToolState from galaxy.tools.parameters.grouping import Repeat, Conditional @@ -15,11 +16,89 @@ from galaxy.model.mapping import desc from galaxy.model.orm import * +class StoredWorkflowListGrid( grids.Grid ): + class StepsColumn( grids.GridColumn ): + def get_value(self, trans, grid, workflow): + return len( workflow.latest_workflow.steps ) + + # Grid definition + use_panels = True + title = "Saved Workflows" + model_class = model.StoredWorkflow + default_filter = { "name" : "All", "tags": "All" } + default_sort_key = "-update_time" + columns = [ + grids.TextColumn( "Name", key="name", model_class=model.StoredWorkflow, attach_popup=True, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), + StepsColumn( "Steps" ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + ] + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", visible=False, filterable="standard" ) + ) + operations = [ + grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Run", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Clone", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Sharing", condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Delete", condition=( lambda item: item.deleted ), async_compatible=True ), + ] + def apply_default_filter( self, trans, query, **kwargs ): + return query.filter_by( user=trans.user, deleted=False ) + +class PublicStoredWorkflowListGrid( grids.Grid ): + title = "Public Workflows" + model_class = model.StoredWorkflow + default_sort_key = "-update_time" + default_filter = dict( public_url="All", username="All", tags="All" ) + use_async = True + columns = [ + PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), + OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) + ] + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", visible=False, filterable="standard" ) + ) + operations = [] + def build_initial_query( self, session ): + # Join so that searching stored_workflow.user makes sense. + return session.query( self.model_class ).join( model.User.table ) + def apply_default_filter( self, trans, query, **kwargs ): + # A public workflow is importable, has a slug, and is not deleted. + return query.filter( self.model_class.importable==True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) + class WorkflowController( BaseController ): + stored_list_grid = StoredWorkflowListGrid() + public_list_grid = PublicStoredWorkflowListGrid() @web.expose def index( self, trans ): return trans.fill_template( "workflow/index.mako" ) + + @web.expose + @web.require_login( "use Galaxy workflows" ) + def list_grid( self, trans, **kwargs ): + """ List user's stored workflows. """ + status = message = None + if 'operation' in kwargs: + operation = kwargs['operation'].lower() + print operation + if operation == "rename": + return self.rename( trans, **kwargs ) + history_ids = util.listify( kwargs.get( 'id', [] ) ) + if operation == "sharing": + return self.sharing( trans, id=history_ids ) + return self.stored_list_grid( trans, **kwargs ) @web.expose @web.require_login( "use Galaxy workflows" ) @@ -64,7 +143,52 @@ return trans.fill_template( "workflow/list_for_run.mako", workflows = workflows, shared_by_others = shared_by_others ) - + + @web.expose + def list_public( self, trans, **kwargs ): + grid = self.public_list_grid( trans, **kwargs ) + if 'async' in kwargs: + return grid + else: + # Render grid wrapped in panels + return trans.fill_template( "workflow/list_public.mako", grid=grid ) + + @web.expose + def display_by_username_and_slug( self, trans, username, slug ): + """ View workflow based on a username and slug. """ + session = trans.sa_session + + # Get and verify user and stored workflow. + user = session.query( model.User ).filter_by( username=username ).first() + if user is None: + raise web.httpexceptions.HTTPNotFound() + stored_workflow = trans.sa_session.query( model.StoredWorkflow ).filter_by( user=user, slug=slug, deleted=False, importable=True ).first() + if stored_workflow is None: + raise web.httpexceptions.HTTPNotFound() + + # Get data for workflow's steps. + for step in stored_workflow.latest_workflow.steps: + if step.type == 'tool' or step.type is None: + # Restore the tool state for the step + module = module_factory.from_workflow_step( trans, step ) + # Any connected input needs to have value DummyDataset (these + # are not persisted so we need to do it every time) + module.add_dummy_datasets( connections=step.input_connections ) + # Store state with the step + step.module = module + step.state = module.state + # Error dict + if step.tool_errors: + errors[step.id] = step.tool_errors + else: + ## Non-tool specific stuff? + step.module = module_factory.from_workflow_step( trans, step ) + step.state = step.module.get_runtime_state() + # Connections by input name + step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) + + return trans.fill_template_mako( "workflow/display.mako", workflow = stored_workflow, steps = stored_workflow.latest_workflow.steps ) + @web.expose @web.require_login( "use Galaxy workflows" ) def share( self, trans, id, email="" ): @@ -108,7 +232,7 @@ stored = get_stored_workflow( trans, id ) session.add( stored ) if 'enable_import_via_link' in kwargs: - stored.importable = True + self.make_item_importable( trans.sa_session, stored ) session.flush() elif 'disable_import_via_link' in kwargs: stored.importable = False @@ -150,15 +274,19 @@ @web.expose @web.require_login( "use Galaxy workflows" ) - def rename( self, trans, id, new_name=None ): + def rename( self, trans, id, new_name=None, **kwargs ): stored = get_stored_workflow( trans, id ) if new_name is not None: stored.name = new_name trans.sa_session.flush() - trans.set_message( "Workflow renamed to '%s'." % new_name ) + # For current workflows grid: + trans.set_message ( "Workflow renamed to '%s'." % new_name ) return self.list( trans ) + # For new workflows grid: + #message = "Workflow renamed to '%s'." % new_name + #return self.list_grid( trans, message=message, status='done' ) else: - return form( url_for( id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename" ) \ + return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename" ) \ .add_text( "new_name", "Workflow Name", value=stored.name ) @web.expose diff -r 56efe838b9af -r a7deb5c197ad lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Jan 11 17:04:45 2010 -0500 +++ b/lib/galaxy/web/framework/__init__.py Tue Jan 12 11:37:45 2010 -0500 @@ -553,6 +553,12 @@ context. """ self.template_context['message'] = message + def get_message( self ): + """ + Convenience method for getting the 'message' element of the template + context. + """ + return self.template_context['message'] def show_message( self, message, type='info', refresh_frames=[], cont=None ): """ Convenience method for displaying a simple page with a single message. diff -r 56efe838b9af -r a7deb5c197ad static/june_2007_style/autocomplete_tagging.css.tmpl --- a/static/june_2007_style/autocomplete_tagging.css.tmpl Mon Jan 11 17:04:45 2010 -0500 +++ b/static/june_2007_style/autocomplete_tagging.css.tmpl Tue Jan 12 11:37:45 2010 -0500 @@ -67,7 +67,11 @@ .tag-area { width: 100%; cursor: pointer; - border: solid 1px #eee; +} + +.individual-tags +{ + border:solid 1px #eee; } .active-tag-area { diff -r 56efe838b9af -r a7deb5c197ad static/june_2007_style/blue/autocomplete_tagging.css --- a/static/june_2007_style/blue/autocomplete_tagging.css Mon Jan 11 17:04:45 2010 -0500 +++ b/static/june_2007_style/blue/autocomplete_tagging.css Tue Jan 12 11:37:45 2010 -0500 @@ -6,7 +6,8 @@ .ac_even{margin-left:0.3em;} .ac_over{background-color:#0A246A;color:white;} .ac_header{font-style:normal;color:gray;border-bottom:0.1em solid gray;} -.tag-area{width:100%;cursor:pointer;border:solid 1px #eee;} +.tag-area{width:100%;cursor:pointer;} +.individual-tags{border:solid 1px #eee;} .active-tag-area{background-color:white;} .toggle-link{font-weight:normal;padding:0.3em;margin-bottom:1em;width:100%;padding:0.2em 0em 0.2em 0em;} .tag-button{width:auto;color:#444;text-decoration:none;display:inline-block;cursor:pointer;margin:0.2em;border:0;padding:0.1em 0.5em 0.1em 0.5em;-moz-border-radius:.5em;-webkit-border-radius:.5em;border-radius:.5em;background:#bbb;} diff -r 56efe838b9af -r a7deb5c197ad templates/history/list_public.mako --- a/templates/history/list_public.mako Mon Jan 11 17:04:45 2010 -0500 +++ b/templates/history/list_public.mako Tue Jan 12 11:37:45 2010 -0500 @@ -15,7 +15,7 @@ <div style="overflow: auto; height: 100%;"> <div class="page-container" style="padding: 10px;"> - ${grid} + ${unicode( grid, 'utf-8' )} </div> </div> diff -r 56efe838b9af -r a7deb5c197ad templates/history/view.mako --- a/templates/history/view.mako Mon Jan 11 17:04:45 2010 -0500 +++ b/templates/history/view.mako Tue Jan 12 11:37:45 2010 -0500 @@ -256,14 +256,11 @@ // function community_tag_click(tag_name, tag_value) { - // Do nothing until community tags are implemented in public histories grid. - /* var href = '${h.url_for( controller='/history', action='list_public')}'; href = href + "?f-tags=" + tag_name; if (tag_value != null && tag_value != "") href = href + ":" + tag_value; self.location = href; - */ } </script> </%def> @@ -339,78 +336,79 @@ </div> <div class="unified-panel-body"> - <div class="page-body"> - ## Render view of history. - <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not user_owns_history: - <a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | + <div style="overflow: auto; height: 100%;"> + <div class="page-body"> + ## Render view of history. + <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> + %if not user_owns_history: + <a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | + %endif + <a href="${get_history_link( history )}">${_('refresh')}</a> + %if show_deleted: + | <a href="${h.url_for('history', show_deleted=False)}">${_('hide deleted')}</a> + %endif + </div> + + <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> + %if user_owns_history: + <div style="float: right"><a id="history-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='rename' )}"></a></div> + %endif + <div id="history-name">${history.get_display_name()}</div> + </div> + + %if history.deleted: + <div class="warningmessagesmall"> + ${_('You are currently viewing a deleted history!')} + </div> + <p></p> %endif - <a href="${get_history_link( history )}">${_('refresh')}</a> - %if show_deleted: - | <a href="${h.url_for('history', show_deleted=False)}">${_('hide deleted')}</a> + + %if not datasets: + + <div class="infomessagesmall" id="emptyHistoryMessage"> + + %else: + + ## Render requested datasets, ordered from newest to oldest + %for data in datasets: + %if data.visible: + <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset=user_owns_history )} + </div> + %endif + %endfor + + <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> %endif + ${_("Your history is empty. Click 'Get Data' on the left pane to start")} + </div> </div> - - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - %if user_owns_history: - <div style="float: right"><a id="history-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='rename' )}"></a></div> - %endif - <div id="history-name">${history.get_display_name()}</div> - </div> - - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} + + <div class="page-meta"> + ## Histories. + <div><strong>Related Histories</strong></div> + <p> + <a href="${h.url_for ( controller='/history', action='list_public' )}">All public histories</a><br> + <a href="${href_to_user_histories}">Histories owned by ${history.user.username}</a> + + ## Tags. + <div><strong>Tags</strong></div> + <p> + ## Community tags. + <div> + Community: + ${render_community_tagging_element( tagged_item=history, tag_click_fn='community_tag_click', use_toggle_link=False )} + %if len ( history.tags ) == 0: + none + %endif </div> - <p></p> - %endif - - %if not datasets: - - <div class="infomessagesmall" id="emptyHistoryMessage"> - - %else: - - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset=user_owns_history )} - </div> - %endif - %endfor - - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} + ## Individual tags. + <p> + <div> + Yours: + ${render_individual_tagging_element( user=trans.get_user(), tagged_item=history, elt_context='view.mako', use_toggle_link=False )} </div> - </div> - - <div class="page-meta"> - ## Histories. - <div><strong>Related Histories</strong></div> - <p> - <a href="${h.url_for ( controller='/history', action='list_public' )}">All public histories</a><br> - <a href="${href_to_user_histories}">Histories owned by ${history.user.username}</a> - - ## Tags. - <div><strong>Tags</strong></div> - <p> - ## Community tags. - <div> - Community: - ${render_community_tagging_element( tagged_item=history, tag_click_fn='community_tag_click', use_toggle_link=False )} - %if len ( history.tags ) == 0: - none - %endif - </div> - ## Individual tags. - <p> - <div> - Yours: - ${render_individual_tagging_element( user=trans.get_user(), tagged_item=history, elt_context='view.mako', use_toggle_link=False )} </div> </div> - </div> </%def> diff -r 56efe838b9af -r a7deb5c197ad templates/page/display.mako --- a/templates/page/display.mako Mon Jan 11 17:04:45 2010 -0500 +++ b/templates/page/display.mako Tue Jan 12 11:37:45 2010 -0500 @@ -151,13 +151,11 @@ function community_tag_click(tag_name, tag_value) { // Do nothing until community tags implemented in published pages grid. - /* var href = '${h.url_for( controller='/page', action='list_published')}'; href = href + "?f-tags=" + tag_name; if (tag_value != null && tag_value != "") href = href + ":" + tag_value; self.location = href; - */ } </script> </%def> diff -r 56efe838b9af -r a7deb5c197ad templates/page/editor.mako --- a/templates/page/editor.mako Mon Jan 11 17:04:45 2010 -0500 +++ b/templates/page/editor.mako Tue Jan 12 11:37:45 2010 -0500 @@ -260,7 +260,12 @@ // Build href from history info. var href; if (history_slug != "" && history_user_username != "") - var href = "/u/" + history_user_username + "/h/" + history_slug; + { + var href = + '${h.url_for( controller='/history', action='display_by_username_and_slug', username='USERNAME', slug='SLUG' )}'; + href = href.replace('USERNAME', history_user_username); + href = href.replace('SLUG', history_slug); + } else var href = '${h.url_for( controller='/history', action='view' )}?id=' + item_id; wym.insert("<a href='" + href + "'>History '" + history_name + "'</a>"); diff -r 56efe838b9af -r a7deb5c197ad templates/root/history.mako --- a/templates/root/history.mako Mon Jan 11 17:04:45 2010 -0500 +++ b/templates/root/history.mako Tue Jan 12 11:37:45 2010 -0500 @@ -260,25 +260,6 @@ count++; return count; }; - - // - // Function provides text for tagging toggle link. - // - var get_toggle_link_text = function(tags) - { - var text = ""; - var num_tags = array_length(tags); - if (num_tags != 0) - { - text = num_tags + (num_tags != 1 ? " Tags" : " Tag"); - } - else - { - // No tags. - text = "Add tags to history"; - } - return text; - }; </script> <style> @@ -327,7 +308,7 @@ margin-bottom: 0.5em; } </style> - ${render_individual_tagging_element( user=trans.get_user(), tagged_item=history, elt_context='history.mako', get_toggle_link_text_fn='get_toggle_link_text' )} + ${render_individual_tagging_element( user=trans.get_user(), tagged_item=history, elt_context='history.mako' )} %endif %if not datasets: diff -r 56efe838b9af -r a7deb5c197ad templates/tagging_common.mako --- a/templates/tagging_common.mako Mon Jan 11 17:04:45 2010 -0500 +++ b/templates/tagging_common.mako Tue Jan 12 11:37:45 2010 -0500 @@ -20,7 +20,7 @@ %endif ## Render HTML for a list of tags. -<%def name="render_tagging_element_html(elt_id=None, tags=None, editable=True, use_toggle_link=True, input_size='15', in_form=False)"> +<%def name="render_tagging_element_html(elt_id=None, tags=None, editable=True, use_toggle_link=True, input_size='15', in_form=False, tag_type='individual')"> ## Useful attributes. <% num_tags = len( tags ) @@ -35,9 +35,13 @@ %endif > %if use_toggle_link: - <a class="toggle-link" href="#">${num_tags} Tags</a> + <a class="toggle-link" href="#">${num_tags} Tag${iff( num_tags == 1, "", "s")}</a> %endif - <div class="tag-area"> + <div class="tag-area + %if tag_type == 'individual': + individual-tags + %endif + "> ## Build buttons for current tags. %for tag in tags: @@ -88,7 +92,7 @@ elt_id = int ( floor ( random()*maxint ) ) community_tags = tag_handler.get_community_tags(trans.sa_session, tagged_item, 10) %> - ${self.render_tagging_element_html(elt_id=elt_id, tags=community_tags, use_toggle_link=use_toggle_link, editable=False)} + ${self.render_tagging_element_html(elt_id=elt_id, tags=community_tags, use_toggle_link=use_toggle_link, editable=False, tag_type="community")} ## Set up tag click function. <script type="text/javascript"> diff -r 56efe838b9af -r a7deb5c197ad templates/workflow/display.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/workflow/display.mako Tue Jan 12 11:37:45 2010 -0500 @@ -0,0 +1,195 @@ +<%inherit file="/base_panels.mako"/> +<%namespace file="/display_common.mako" import="get_history_link" /> +<%namespace file="../tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> + +<%! from galaxy.tools.parameters import DataToolParameter %> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "galaxy.base", "jquery", "json2", "jquery.autocomplete", "autocomplete_tagging" )} + + <script type="text/javascript"> + // + // Handle click on community tag. + // + function community_tag_click(tag_name, tag_value) + { + var href = '${h.url_for( controller='/workflow', action='list_public')}'; + href = href + "?f-tags=" + tag_name; + if (tag_value != null && tag_value != "") + href = href + ":" + tag_value; + self.location = href; + } + </script> +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "workflow", "autocomplete_tagging" )} + <style type="text/css"> + .page-body + { + padding: 10px; + float: left; + width: 65%; + } + .page-meta + { + float: right; + width: 27%; + padding: 0.5em; + margin: 0.25em; + vertical-align: text-top; + border: 2px solid #DDDDDD; + border-top: 4px solid #DDDDDD; + } + div.toolForm{ + margin-top: 10px; + margin-bottom: 10px; + } + </style> + <noscript> + <style> + .historyItemBody { + display: block; + } + </style> + </noscript> +</%def> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False +%> +</%def> + +<%def name="do_inputs( inputs, values, prefix, step, other_values=None )"> + %for input_index, input in enumerate( inputs.itervalues() ): + %if input.type == "repeat": + <div class="repeat-group"> + <div class="form-title-row"><b>${input.title_plural}</b></div> + <% repeat_values = values[input.name] %> + %for i in range( len( repeat_values ) ): + <div class="repeat-group-item"> + <% index = repeat_values[i]['__index__'] %> + <div class="form-title-row"><b>${input.title} ${i + 1}</b></div> + ${do_inputs( input.inputs, repeat_values[ i ], prefix + input.name + "_" + str(index) + "|", step, other_values )} + + </div> + %endfor + </div> + %elif input.type == "conditional": + <% group_values = values[input.name] %> + <% current_case = group_values['__current_case__'] %> + <% new_prefix = prefix + input.name + "|" %> + ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, prefix, step )} + ${do_inputs( input.cases[ current_case ].inputs, group_values, new_prefix, step, other_values )} + %else: + ${row_for_param( input, values[ input.name ], other_values, prefix, step )} + %endif + %endfor +</%def> + +<%def name="row_for_param( param, value, other_values, prefix, step )"> + <% cls = "form-row" %> + <div class="${cls}"> + <label>${param.get_label()}</label> + <div> + %if isinstance( param, DataToolParameter ): + %if ( prefix + param.name ) in step.input_connections_by_name: + <% + conn = step.input_connections_by_name[ prefix + param.name ] + %> + Output dataset '${conn.output_name}' from step ${int(conn.output_step.order_index)+1} + %else: + ## FIXME: Initialize in the controller + <% + if value is None: + value = other_values[ param.name ] = param.get_initial_value( t, other_values ) + %> + ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + %endif + %else: + ${param.value_to_display_text( value, app )} + %endif + </div> + </div> +</%def> + +<%def name="center_panel()"> + ## Get URL to other workflows owned by user that owns this workflow. + <% + ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. + href_to_user_workflows = h.url_for( action='list_public', xxx=workflow.user.username ) + href_to_user_workflows = href_to_user_workflows.replace( 'xxx', 'f-username' ) + %> + + <div class="unified-panel-header" unselectable="on"> + <div class="unified-panel-header-inner"> + <a href="${h.url_for ( action='list_public' )}">Public Workflows</a> | + <a href="${href_to_user_workflows}">${workflow.user.username}</a> | ${workflow.name} + </div> + </div> + + <div class="unified-panel-body"> + <div style="overflow: auto; height: 100%;"> + <div class="page-body"> + ## Render top links. + <div id="top-links" style="padding: 0px 0px 5px 0px"> + %if workflow.user != trans.get_user(): + <a href="${h.url_for( action='imp', id=trans.security.encode_id(workflow.id) )}">import and start using workflow</a> + %endif + </div> + + ## Render Workflow. + <h2>${workflow.name}</h2> + %for i, step in enumerate( steps ): + %if step.type == 'tool' or step.type is None: + <% tool = app.toolbox.tools_by_id[step.tool_id] %> + <div class="toolForm"> + <div class="toolFormTitle">Step ${int(step.order_index)+1}: ${tool.name}</div> + <div class="toolFormBody"> + ${do_inputs( tool.inputs, step.state.inputs, "", step )} + </div> + </div> + %else: + <% module = step.module %> + <div class="toolForm"> + <div class="toolFormTitle">Step ${int(step.order_index)+1}: ${module.name}</div> + <div class="toolFormBody"> + </div> + </div> + %endif + %endfor + </div> + + <div class="page-meta"> + ## Workflows. + <div><strong>Related Workflows</strong></div> + <p> + <a href="${h.url_for ( action='list_public' )}">All public workflows</a><br> + <a href="${href_to_user_workflows}">Workflows owned by ${workflow.user.username}</a> + + ## Tags. + <div><strong>Tags</strong></div> + <p> + ## Community tags. + <div> + Community: + ${render_community_tagging_element( tagged_item=workflow, tag_click_fn='community_tag_click', use_toggle_link=False )} + %if len ( workflow.tags ) == 0: + none + %endif + </div> + ## Individual tags. + <p> + <div> + Yours: + ${render_individual_tagging_element( user=trans.get_user(), tagged_item=workflow, elt_context='view.mako', use_toggle_link=False )} + </div> + </div> + </div> + </div> +</%def> diff -r 56efe838b9af -r a7deb5c197ad templates/workflow/list_public.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/workflow/list_public.mako Tue Jan 12 11:37:45 2010 -0500 @@ -0,0 +1,23 @@ +<%inherit file="/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view="page" + self.message_box_visible=False +%> +</%def> + +<%def name="center_panel()"> + + ## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"> </iframe> + + <div style="overflow: auto; height: 100%;"> + <div class="page-container" style="padding: 10px;"> + ${unicode( grid, 'utf-8' )} + </div> + </div> + + +</%def> diff -r 56efe838b9af -r a7deb5c197ad templates/workflow/sharing.mako --- a/templates/workflow/sharing.mako Mon Jan 11 17:04:45 2010 -0500 +++ b/templates/workflow/sharing.mako Tue Jan 12 11:37:45 2010 -0500 @@ -4,7 +4,14 @@ <p> %if stored.importable: + <p> + Anyone can view this workflow by visiting the following URL: + <% url = h.url_for( action='display_by_username_and_slug', username=trans.get_user().username, slug=stored.slug, qualified=True ) %> + <blockquote> + <a href="${url}">${url}</a> + </blockquote> + <p> Anyone can import this workflow into their history via the following URL: <% url = h.url_for( action='imp', id=trans.security.encode_id(stored.id), qualified=True ) %> <blockquote>

1 0

Queuing/Scheduling question (long)
by Assaf Gordon 22 Jan '10

22 Jan '10

Hello, I have a question regarding the job queuing/scheduling in Galaxy, because although I assured my users that the scheduling is fair (using the "round robin" scheduler), what I'm seeing is not exactly fair (and so users wait a long time for their jobs to run). I'll try to explain the situation as best as I can, and I'll appreciate any feedback. The attached diagram shows a situation similar to what I have. At time "t0", user-A submits a workflow with many steps (the lines represent input-output connections, the numbers are job numbers). After a while, jobs 1,2,3 are done (green). and jobs 4,5 are running (yellow) - assuming I can run only two jobs at a time. If I understand correctly, jobs 6-12 are queued (i.e. their input dataset is "ready", so they are ready to run, and put on my local runner queue). Job 13 is still "new" because its input datasets (11,12,13) are not ready. At time "t1", (while jobs 4,5 are still running), user-B submits a single job (#14). If I understand correctly, it will go from "new" to "queued" immediately, because it isn't dependent on any input dataset and is ready to run. My question is: Once jobs 4 or 5 are completed, which job will run next ? If everything is "fair", I'd expect job #14 (from the second user) to run. But what I think I'm seeing, is that the "queued jobs" queue is actually FIFO, and jobs 6-12 will be run before job 14. (Job 14 however will run before job 13), Is the "round-robin" queue refers only to the transition from "new" to "queued" ? I could be completely wrong about this whole thing, but what I'm experiencing is that user-A submitted 5 workflows in parallel (all look very similar to the attached diagram), I have 7 runnings jobs (of user-A), 35 queued job from user-A and 2 queued job from user-B, and galaxy consistently chooses to run queued job from user-A instead of user-B (presumably because they were queued before user-B submitted the jobs). Is there a way to work around this issue ? a different configuration maybe ? Or, an old request: is it possible to limit the number of jobs-per-user at any single time (i.e. a single user can run 3 jobs at any given time, even if no other users are running jobs and there are 7 workers ready) ? Thanks for reading so far, -gordon

3 3

Grid Fadeout bug in histories list
by Assaf Gordon 21 Jan '10

21 Jan '10

Hello, A minor UI bug when switching histories (in a long history list): When clicking on one of the pages links (e.g. "7"), the history list grid is faded out - but only the upper part of it, not the entire list. It looks like the height of the fadeout region is the region that would have been visible if I hadn't scrolled the screen all the way down (but I have to scroll down to reach the pages links). See attached image for half faded / half not-faded history. This happens if I have a long history list (longer than what fits on screen), then scroll all the way down, click on the page link (to switch to another history page) and quickly scroll up (before the page is updated). Fade out by itself isn't critical, but the non-faded history items are still clickable. -gordon

1 0

Strange/Missing HTML code in history pane
by Assaf Gordon 21 Jan '10

21 Jan '10

Hello, Some of my galaxy users are seeing histories without being able to "expand" a dataset (see attached image). It seems some of the javascript/html code is somehow missing or not executed. The attached image is from Google Chrom on Windows XP. The user tried Firefox (on windows) and everything worked fine. I tried Google Chrom on Linux and it work fine, So reproducing it is a bit hard - but it does happen more than once. Any ideas on how to pin-point the problem ? Is it network related (the connection dropped before completion) ? thanks, -gordon

2 1

hardware requirements for galaxy server
by Maarten Kooyman 21 Jan '10

21 Jan '10

Dear list, I'm a employee for the The duch bioinformatics center (NBIC). We decided to set up national Galaxy server with a focus on Next Generation Sequences data. For this we need to acquire some hardware and services. I would like have a idea what kind of hardware is necessary to operate smoothly . We expect a the first month +- 30 (serious) users and will grow to 100 user in 3 months. I would like to get a rough estimate of: -number of cpu -memory -hard drive space needed -network usage etc. I known it it hard to predict what kind of hardware I need, because it depends on the user input. However I would like to get a indication. Kind Regards, Maarten Kooyman

2 1

Galaxy + NetCDF datatype support?
by Abma, T.W. 21 Jan '10

21 Jan '10

Goodday, I am experimenting with the Galaxy tool and adding a module itself is no problem. Furthermore there are a lot of datatypes supported (FASTA etc.), but it seems NetCDF is not yet 'supported'. So I found out that you can add your own datatype ( http://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes ), but before doing that, I was wondering how to support reading the NetCDF datatype - especially for mass spectrometry data? Or is there another datatype which I can use to read mass spectrometry NetCDF's in Galaxy? Thanks in advance and with kind regards, Tjeerd Abma Scientific programmer/Bioinformatician UMCU Metabolomics Centre Dept. Metabolic and Endocrine Diseases Wilhelmina Childrens Hospital, UMC Utrecht T: 088-7554330 E: t.w.abma(a)umcutrecht.nl http://www.metabolomics-utrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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can't run setup.sh
by Kaizaad Bilimorya 21 Jan '10

21 Jan '10

Hello, Standard CentOS 5.4 install [root@mako1 scripts]# python -V Python 2.4.3 Following the instructions http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy but fails at "sh setup.sh" because "check_python.py" throws and exeption and returns "python -ES". Note sure what this means. thanks kaizaad

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