- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e7f83c2921c8/ Changeset: e7f83c2921c8 User: jmchilton Date: 2015-02-06 02:27:53+00:00 Summary: PEP-8 fixes for reports controllers and app. Affected #: 5 files diff -r 17ed2655b3052c047aba60013e0f9bb173ebee90 -r e7f83c2921c86bedea95425c213e4a467e64f0f3 lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -1,7 +1,9 @@ -import sys, config +import sys +import config import galaxy.model from galaxy.web import security + class UniverseApplication( object ): """Encapsulates the state of a Universe application""" def __init__( self, **kwargs ): @@ -20,8 +22,9 @@ self.model = galaxy.model.mapping.init( self.config.file_path, db_url, self.config.database_engine_options, - create_tables = True ) + create_tables=True ) # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + def shutdown( self ): pass diff -r 17ed2655b3052c047aba60013e0f9bb173ebee90 -r e7f83c2921c86bedea95425c213e4a467e64f0f3 lib/galaxy/webapps/reports/controllers/jobs.py --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -1,9 +1,8 @@ -import calendar, operator, os, socket +import calendar from datetime import datetime, date, timedelta -from time import mktime, strftime, localtime from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util -from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.web.framework.helpers import grids from galaxy.model.orm import and_, not_, or_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) @@ -11,37 +10,53 @@ import logging log = logging.getLogger( __name__ ) + class SpecifiedDateListGrid( grids.Grid ): + class JobIdColumn( grids.IntegerColumn ): + def get_value( self, trans, grid, job ): return job.id + class StateColumn( grids.TextColumn ): + def get_value( self, trans, grid, job ): return '<div class="count-box state-color-%s">%s</div>' % ( job.state, job.state ) + def filter( self, trans, user, query, column_filter ): if column_filter == 'Unfinished': return query.filter( not_( or_( model.Job.table.c.state == model.Job.states.OK, model.Job.table.c.state == model.Job.states.ERROR, model.Job.table.c.state == model.Job.states.DELETED ) ) ) return query + class ToolColumn( grids.TextColumn ): + def get_value( self, trans, grid, job ): return job.tool_id + class CreateTimeColumn( grids.DateTimeColumn ): + def get_value( self, trans, grid, job ): return job.create_time.strftime("%b %d, %Y, %H:%M:%S") + class UserColumn( grids.GridColumn ): + def get_value( self, trans, grid, job ): if job.user: return job.user.email return 'anonymous' + class EmailColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query return query.filter( and_( model.Job.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter ) ) + class SpecifiedDateColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query @@ -57,7 +72,7 @@ end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) return query.filter( and_( self.model_class.table.c.create_time >= start_date, - self.model_class.table.c.create_time < end_date ) ) + self.model_class.table.c.create_time < end_date ) ) # Grid definition use_async = False @@ -72,8 +87,8 @@ attach_popup=False, filterable="advanced" ), StateColumn( "State", - key="state", - attach_popup=False ), + key="state", + attach_popup=False ), ToolColumn( "Tool Id", key="tool_id", link=( lambda item: dict( operation="tool_per_month", id=item.id, webapp="reports" ) ), @@ -105,7 +120,7 @@ visible=False, filterable="standard" ) ) standard_filters = [] - default_filter = { 'specified_date' : 'All' } + default_filter = { 'specified_date': 'All' } num_rows_per_page = 50 preserve_state = False use_paging = True @@ -119,7 +134,9 @@ .filter( model.Job.table.c.user_id != monitor_user_id )\ .enable_eagerloads( False ) + class Jobs( BaseUIController ): + """ Class contains functions for querying data requested by user via the webapp. It exposes the functions and responds to requests with the filled .mako templates. @@ -198,15 +215,14 @@ month_label = start_date.strftime( "%B" ) year_label = start_date.strftime( "%Y" ) - month_jobs = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ), - sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), - whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id, - model.Job.table.c.create_time >= start_date, - model.Job.table.c.create_time < end_date ), - from_obj=[ model.Job.table ], - group_by=[ 'date' ], - order_by=[ sa.desc( 'date' ) ] ) + sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), + whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id, + model.Job.table.c.create_time >= start_date, + model.Job.table.c.create_time < end_date ), + from_obj=[ model.Job.table ], + group_by=[ 'date' ], + order_by=[ sa.desc( 'date' ) ] ) jobs = [] for row in month_jobs.execute(): @@ -214,7 +230,7 @@ row.date.strftime( "%d" ), row.total_jobs, row.date - ) ) + ) ) return trans.fill_template( '/webapps/reports/jobs_specified_month_all.mako', month_label=month_label, year_label=year_label, @@ -222,6 +238,7 @@ jobs=jobs, is_user_jobs_only=monitor_user_id, message=message ) + @web.expose def specified_month_in_error( self, trans, **kwd ): """ @@ -244,14 +261,14 @@ year_label = start_date.strftime( "%Y" ) month_jobs_in_error = sa.select( ( sa.func.date( model.Job.table.c.create_time ).label( 'date' ), - sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), - whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id, - model.Job.table.c.state == 'error', - model.Job.table.c.create_time >= start_date, - model.Job.table.c.create_time < end_date ), - from_obj=[ model.Job.table ], - group_by=[ 'date' ], - order_by=[ sa.desc( 'date' ) ] ) + sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), + whereclause=sa.and_( model.Job.table.c.user_id != monitor_user_id, + model.Job.table.c.state == 'error', + model.Job.table.c.create_time >= start_date, + model.Job.table.c.create_time < end_date ), + from_obj=[ model.Job.table ], + group_by=[ 'date' ], + order_by=[ sa.desc( 'date' ) ] ) jobs = [] for row in month_jobs_in_error.execute(): @@ -266,6 +283,7 @@ jobs=jobs, message=message, is_user_jobs_only=monitor_user_id ) + @web.expose def per_month_all( self, trans, **kwd ): """ @@ -280,25 +298,26 @@ monitor_user_id = get_monitor_id( trans, monitor_email ) jobs_by_month = sa.select( ( sa.func.date_trunc( 'month', model.Job.table.c.create_time ).label( 'date' ), - sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), - whereclause=model.Job.table.c.user_id != monitor_user_id, - from_obj=[ model.Job.table ], - group_by=[ 'date' ], - order_by=[ sa.desc( 'date' ) ] ) + sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), + whereclause=model.Job.table.c.user_id != monitor_user_id, + from_obj=[ model.Job.table ], + group_by=[ 'date' ], + order_by=[ sa.desc( 'date' ) ] ) jobs = [] for row in jobs_by_month.execute(): - jobs.append( ( - row.date.strftime( "%Y-%m" ), - row.total_jobs, - row.date.strftime( "%B" ), - row.date.strftime( "%y" ) - ) ) + jobs.append( ( + row.date.strftime( "%Y-%m" ), + row.total_jobs, + row.date.strftime( "%B" ), + row.date.strftime( "%y" ) + ) ) return trans.fill_template( '/webapps/reports/jobs_per_month_all.mako', jobs=jobs, is_user_jobs_only=monitor_user_id, message=message ) + @web.expose def per_month_in_error( self, trans, **kwd ): """ @@ -314,11 +333,11 @@ jobs_in_error_by_month = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), - whereclause=sa.and_ ( model.Job.table.c.state == 'error', - model.Job.table.c.user_id != monitor_user_id ), - from_obj=[ model.Job.table ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], - order_by=[ sa.desc( 'date' ) ] ) + whereclause=sa.and_( model.Job.table.c.state == 'error', + model.Job.table.c.user_id != monitor_user_id ), + from_obj=[ model.Job.table ], + group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], + order_by=[ sa.desc( 'date' ) ] ) jobs = [] for row in jobs_in_error_by_month.execute(): @@ -339,19 +358,19 @@ jobs = [] jobs_per_user = sa.select( ( model.User.table.c.email.label( 'user_email' ), - sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), - from_obj=[ sa.outerjoin( model.Job.table, model.User.table ) ], - group_by=[ 'user_email' ], - order_by=[ sa.desc( 'total_jobs' ), 'user_email' ] ) + sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), + from_obj=[ sa.outerjoin( model.Job.table, model.User.table ) ], + group_by=[ 'user_email' ], + order_by=[ sa.desc( 'total_jobs' ), 'user_email' ] ) for row in jobs_per_user.execute(): - if ( row.user_email == None ): - jobs.append ( ( 'Anonymous', - row.total_jobs ) ) + if ( row.user_email is None ): + jobs.append( ( 'Anonymous', + row.total_jobs ) ) elif ( row.user_email == monitor_email ): continue else: jobs.append( ( row.user_email, - row.total_jobs ) ) + row.total_jobs ) ) return trans.fill_template( '/webapps/reports/jobs_per_user.mako', jobs=jobs, message=message ) @@ -364,8 +383,8 @@ q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id, - model.GalaxySession.table.c.user_id == model.User.table.c.id, - model.User.table.c.email == email + model.GalaxySession.table.c.user_id == model.User.table.c.id, + model.User.table.c.email == email ), from_obj=[ sa.join( model.Job.table, model.User.table ) ], group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], @@ -420,7 +439,7 @@ q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=sa.and_( model.Job.table.c.tool_id == tool_id, - model.Job.table.c.user_id != monitor_user_id ), + model.Job.table.c.user_id != monitor_user_id ), from_obj=[ model.Job.table ], group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], order_by=[ sa.desc( 'date' ) ] ) @@ -439,7 +458,6 @@ @web.expose def job_info( self, trans, **kwd ): - params = util.Params( kwd ) message = '' job = trans.sa_session.query( model.Job ) \ .get( trans.security.decode_id( kwd.get( 'id', '' ) ) ) @@ -447,19 +465,21 @@ job=job, message=message ) -## ---- Utility methods ------------------------------------------------------- +# ---- Utility methods ------------------------------------------------------- + def get_job( trans, id ): return trans.sa_session.query( trans.model.Job ).get( trans.security.decode_id( id ) ) + def get_monitor_id( trans, monitor_email ): """ A convenience method to obtain the monitor job id. """ monitor_user_id = None monitor_row = trans.sa_session.query( trans.model.User.table.c.id ) \ - .filter( trans.model.User.table.c.email == monitor_email ) \ - .first() + .filter( trans.model.User.table.c.email == monitor_email ) \ + .first() if monitor_row is not None: monitor_user_id = monitor_row[0] return monitor_user_id diff -r 17ed2655b3052c047aba60013e0f9bb173ebee90 -r e7f83c2921c86bedea95425c213e4a467e64f0f3 lib/galaxy/webapps/reports/controllers/sample_tracking.py --- a/lib/galaxy/webapps/reports/controllers/sample_tracking.py +++ b/lib/galaxy/webapps/reports/controllers/sample_tracking.py @@ -1,35 +1,45 @@ -import calendar, operator, os, socket -from datetime import datetime, date, timedelta -from time import mktime, strftime, localtime +import calendar +from datetime import date, timedelta from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util -from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.model.orm import and_, not_, or_ +from galaxy.web.framework.helpers import grids +from galaxy.model.orm import and_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa import logging log = logging.getLogger( __name__ ) + class SpecifiedDateListGrid( grids.Grid ): + class RequestNameColumn( grids.TextColumn ): + def get_value( self, trans, grid, request ): return request.name + class CreateTimeColumn( grids.DateTimeColumn ): + def get_value( self, trans, grid, request ): return request.create_time + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, request ): if request.user: return request.user.email return 'unknown' + class EmailColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query return query.filter( and_( model.Request.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter ) ) + class SpecifiedDateColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query @@ -54,14 +64,13 @@ use_async = False model_class = model.Request title = "Sequencing Requests" - template='/webapps/reports/grid.mako' + template = '/webapps/reports/grid.mako' default_sort_key = "name" columns = [ RequestNameColumn( "Name", - key="name", - #link=( lambda item: dict( operation="workflow_info", id=item.id, webapp="reports" ) ), - attach_popup=False, - filterable="advanced" ), + key="name", + attach_popup=False, + filterable="advanced" ), CreateTimeColumn( "Creation Time", key="create_time", attach_popup=False ), @@ -85,15 +94,17 @@ visible=False, filterable="standard" ) ) standard_filters = [] - default_filter = { 'specified_date' : 'All' } + default_filter = { 'specified_date': 'All' } num_rows_per_page = 50 preserve_state = False use_paging = True + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ) \ .join( model.User ) \ .enable_eagerloads( False ) + class SampleTracking( BaseUIController ): specified_date_list_grid = SpecifiedDateListGrid() @@ -124,19 +135,19 @@ if request.user: kwd[ 'email' ] = request.user.email else: - kwd[ 'email' ] = None # For anonymous users ( shouldn't happen with requests ) + kwd[ 'email' ] = None # For anonymous users ( shouldn't happen with requests ) return trans.response.send_redirect( web.url_for( controller='sample_tracking', action='user_per_month', **kwd ) ) return self.specified_date_list_grid( trans, **kwd ) + @web.expose def per_month_all( self, trans, **kwd ): - params = util.Params( kwd ) message = '' - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ).label( 'date' ),sa.func.count( model.Request.table.c.id ).label( 'total' ) ), - from_obj = [ sa.outerjoin( model.Request.table, model.User.table ) ], - group_by = [ sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ) ], - order_by = [ sa.desc( 'date' ) ] ) + q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Request.table.c.id ).label( 'total' ) ), + from_obj=[ sa.outerjoin( model.Request.table, model.User.table ) ], + group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ) ], + order_by=[ sa.desc( 'date' ) ] ) requests = [] for row in q.execute(): requests.append( ( row.date.strftime( "%Y-%m" ), @@ -146,20 +157,21 @@ return trans.fill_template( '/webapps/reports/requests_per_month_all.mako', requests=requests, message=message ) + @web.expose def per_user( self, trans, **kwd ): - params = util.Params( kwd ) message = '' requests = [] q = sa.select( ( model.User.table.c.email.label( 'user_email' ), sa.func.count( model.Request.table.c.id ).label( 'total' ) ), - from_obj = [ sa.outerjoin( model.Request.table, model.User.table ) ], - group_by = [ 'user_email' ], - order_by = [ sa.desc( 'total' ), 'user_email' ] ) + from_obj=[ sa.outerjoin( model.Request.table, model.User.table ) ], + group_by=[ 'user_email' ], + order_by=[ sa.desc( 'total' ), 'user_email' ] ) for row in q.execute(): requests.append( ( row.user_email, row.total ) ) return trans.fill_template( '/webapps/reports/requests_per_user.mako', requests=requests, message=message ) + @web.expose def user_per_month( self, trans, **kwd ): params = util.Params( kwd ) @@ -168,10 +180,10 @@ user_id = trans.security.decode_id( params.get( 'id', '' ) ) q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Request.table.c.id ).label( 'total' ) ), - whereclause = model.Request.table.c.user_id == user_id, - from_obj = [ model.Request.table ], - group_by = [ sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ) ], - order_by = [ sa.desc( 'date' ) ] ) + whereclause=model.Request.table.c.user_id == user_id, + from_obj=[ model.Request.table ], + group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ) ], + order_by=[ sa.desc( 'date' ) ] ) requests = [] for row in q.execute(): requests.append( ( row.date.strftime( "%Y-%m" ), @@ -183,7 +195,8 @@ requests=requests, message=message ) -## ---- Utility methods ------------------------------------------------------- +# ---- Utility methods ------------------------------------------------------- + def get_request( trans, id ): return trans.sa_session.query( trans.model.Workflow ).get( trans.security.decode_id( id ) ) diff -r 17ed2655b3052c047aba60013e0f9bb173ebee90 -r e7f83c2921c86bedea95425c213e4a467e64f0f3 lib/galaxy/webapps/reports/controllers/users.py --- a/lib/galaxy/webapps/reports/controllers/users.py +++ b/lib/galaxy/webapps/reports/controllers/users.py @@ -1,10 +1,9 @@ from datetime import datetime, date, timedelta -from time import strftime -import calendar, operator +import calendar +import operator from galaxy.web.base.controller import BaseUIController, web import galaxy.model from galaxy import util -from galaxy.model.orm import and_, not_, or_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa @@ -13,20 +12,23 @@ log = logging.getLogger( __name__ ) + class Users( BaseUIController ): + @web.expose def registered_users( self, trans, **kwd ): message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) num_users = trans.sa_session.query( galaxy.model.User ).count() return trans.fill_template( '/webapps/reports/registered_users.mako', num_users=num_users, message=message ) + @web.expose def registered_users_per_month( self, trans, **kwd ): message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ), - from_obj = [ galaxy.model.User.table ], - group_by = [ sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ) ], - order_by = [ sa.desc( 'date' ) ] ) + from_obj=[ galaxy.model.User.table ], + group_by=[ sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ) ], + order_by=[ sa.desc( 'date' ) ] ) users = [] for row in q.execute(): users.append( ( row.date.strftime( "%Y-%m" ), @@ -36,6 +38,7 @@ return trans.fill_template( '/webapps/reports/registered_users_per_month.mako', users=users, message=message ) + @web.expose def specified_month( self, trans, **kwd ): message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) @@ -49,11 +52,11 @@ year_label = start_date.strftime( "%Y" ) q = sa.select( ( sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ), - whereclause = sa.and_( galaxy.model.User.table.c.create_time >= start_date, - galaxy.model.User.table.c.create_time < end_date ), - from_obj = [ galaxy.model.User.table ], - group_by = [ sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ) ], - order_by = [ sa.desc( 'date' ) ] ) + whereclause=sa.and_( galaxy.model.User.table.c.create_time >= start_date, + galaxy.model.User.table.c.create_time < end_date ), + from_obj=[ galaxy.model.User.table ], + group_by=[ sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ) ], + order_by=[ sa.desc( 'date' ) ] ) users = [] for row in q.execute(): users.append( ( row.date.strftime( "%Y-%m-%d" ), @@ -66,6 +69,7 @@ month=month, users=users, message=message ) + @web.expose def specified_date( self, trans, **kwd ): message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) @@ -80,10 +84,10 @@ year_label = start_date.strftime( "%Y" ) q = sa.select( ( sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), galaxy.model.User.table.c.email ), - whereclause = sa.and_( galaxy.model.User.table.c.create_time >= start_date, - galaxy.model.User.table.c.create_time < end_date ), - from_obj = [ galaxy.model.User.table ], - order_by = [ galaxy.model.User.table.c.email ] ) + whereclause=sa.and_( galaxy.model.User.table.c.create_time >= start_date, + galaxy.model.User.table.c.create_time < end_date ), + from_obj=[ galaxy.model.User.table ], + order_by=[ galaxy.model.User.table.c.email ] ) users = [] for row in q.execute(): users.append( ( row.email ) ) @@ -95,6 +99,7 @@ day_of_month=day_of_month, users=users, message=message ) + @web.expose def last_access_date( self, trans, **kwd ): message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) @@ -102,10 +107,9 @@ if not not_logged_in_for_days: not_logged_in_for_days = 0 cutoff_time = datetime.utcnow() - timedelta( days=int( not_logged_in_for_days ) ) - now = strftime( "%Y-%m-%d %H:%M:%S" ) users = [] for user in trans.sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.deleted==False ) \ + .filter( galaxy.model.User.table.c.deleted == False ) \ .order_by( galaxy.model.User.table.c.email ): if user.galaxy_sessions: last_galaxy_session = user.galaxy_sessions[ 0 ] diff -r 17ed2655b3052c047aba60013e0f9bb173ebee90 -r e7f83c2921c86bedea95425c213e4a467e64f0f3 lib/galaxy/webapps/reports/controllers/workflows.py --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -15,20 +15,24 @@ class SpecifiedDateListGrid( grids.Grid ): class WorkflowNameColumn( grids.TextColumn ): + def get_value( self, trans, grid, stored_workflow ): return stored_workflow.name class CreateTimeColumn( grids.DateTimeColumn ): + def get_value( self, trans, grid, stored_workflow ): return stored_workflow.create_time class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, stored_workflow ): if stored_workflow.user: return stored_workflow.user.email return 'unknown' class EmailColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query @@ -36,6 +40,7 @@ model.User.table.c.email == column_filter ) ) class SpecifiedDateColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query @@ -60,12 +65,11 @@ use_async = False model_class = model.StoredWorkflow title = "Workflows" - template='/webapps/reports/grid.mako' + template = '/webapps/reports/grid.mako' default_sort_key = "name" columns = [ WorkflowNameColumn( "Name", key="name", - #link=( lambda item: dict( operation="workflow_info", id=item.id, webapp="reports" ) ), attach_popup=False, filterable="advanced" ), CreateTimeColumn( "Creation Time", @@ -91,10 +95,11 @@ visible=False, filterable="standard" ) ) standard_filters = [] - default_filter = { 'specified_date' : 'All' } + default_filter = { 'specified_date': 'All' } num_rows_per_page = 50 preserve_state = False use_paging = True + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ) \ .join( model.User ) \ @@ -131,7 +136,7 @@ if workflow.user: kwd[ 'email' ] = workflow.user.email else: - kwd[ 'email' ] = None # For anonymous users ( shouldn't happen with workflows ) + kwd[ 'email' ] = None # For anonymous users ( shouldn't happen with workflows ) return trans.response.send_redirect( web.url_for( controller='workflows', action='user_per_month', **kwd ) ) @@ -140,10 +145,10 @@ @web.expose def per_month_all( self, trans, **kwd ): message = '' - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ).label( 'date' ),sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), - from_obj = [ sa.outerjoin( model.StoredWorkflow.table, model.User.table ) ], - group_by = [ sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ) ], - order_by = [ sa.desc( 'date' ) ] ) + q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ).label( 'date' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), + from_obj=[ sa.outerjoin( model.StoredWorkflow.table, model.User.table ) ], + group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ) ], + order_by=[ sa.desc( 'date' ) ] ) workflows = [] for row in q.execute(): workflows.append( ( row.date.strftime( "%Y-%m" ), @@ -160,9 +165,9 @@ workflows = [] q = sa.select( ( model.User.table.c.email.label( 'user_email' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), - from_obj = [ sa.outerjoin( model.StoredWorkflow.table, model.User.table ) ], - group_by = [ 'user_email' ], - order_by = [ sa.desc( 'total_workflows' ), 'user_email' ] ) + from_obj=[ sa.outerjoin( model.StoredWorkflow.table, model.User.table ) ], + group_by=[ 'user_email' ], + order_by=[ sa.desc( 'total_workflows' ), 'user_email' ] ) for row in q.execute(): workflows.append( ( row.user_email, row.total_workflows ) ) @@ -176,10 +181,10 @@ user_id = trans.security.decode_id( params.get( 'id', '' ) ) q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ).label( 'date' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), - whereclause = model.StoredWorkflow.table.c.user_id == user_id, - from_obj = [ model.StoredWorkflow.table ], - group_by = [ sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ) ], - order_by = [ sa.desc( 'date' ) ] ) + whereclause=model.StoredWorkflow.table.c.user_id == user_id, + from_obj=[ model.StoredWorkflow.table ], + group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ) ], + order_by=[ sa.desc( 'date' ) ] ) workflows = [] for row in q.execute(): workflows.append( ( row.date.strftime( "%Y-%m" ), @@ -191,7 +196,8 @@ workflows=workflows, message=message ) -## ---- Utility methods ------------------------------------------------------- +# ---- Utility methods ------------------------------------------------------- + def get_workflow( trans, id ): return trans.sa_session.query( trans.model.Workflow ).get( trans.security.decode_id( id ) ) https://bitbucket.org/galaxy/galaxy-central/commits/ce2776f88e9d/ Changeset: ce2776f88e9d User: jmchilton Date: 2015-02-06 02:27:53+00:00 Summary: Fix reports webapp for MySQL. Big thanks for Eric Enns and Fernandez Edgar for contributing patches to the galaxy-dev list. Affected #: 6 files diff -r e7f83c2921c86bedea95425c213e4a467e64f0f3 -r ce2776f88e9db53886b8879a948b19ce2a513835 lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -23,6 +23,7 @@ db_url, self.config.database_engine_options, create_tables=True ) + self.targets_mysql = 'mysql' in self.config.database_connection # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) diff -r e7f83c2921c86bedea95425c213e4a467e64f0f3 -r ce2776f88e9db53886b8879a948b19ce2a513835 lib/galaxy/webapps/reports/controllers/jobs.py --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -7,6 +7,8 @@ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa +from galaxy.webapps.reports.controllers.query import ReportQueryBuilder + import logging log = logging.getLogger( __name__ ) @@ -135,7 +137,7 @@ .enable_eagerloads( False ) -class Jobs( BaseUIController ): +class Jobs( BaseUIController, ReportQueryBuilder ): """ Class contains functions for querying data requested by user via the webapp. It exposes the functions and @@ -297,11 +299,11 @@ # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) - jobs_by_month = sa.select( ( sa.func.date_trunc( 'month', model.Job.table.c.create_time ).label( 'date' ), + jobs_by_month = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=model.Job.table.c.user_id != monitor_user_id, from_obj=[ model.Job.table ], - group_by=[ 'date' ], + group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) jobs = [] @@ -331,12 +333,12 @@ # In case we don't know which is the monitor user we will query for all jobs monitor_user_id = get_monitor_id( trans, monitor_email ) - jobs_in_error_by_month = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), + jobs_in_error_by_month = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=sa.and_( model.Job.table.c.state == 'error', model.Job.table.c.user_id != monitor_user_id ), from_obj=[ model.Job.table ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], + group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) jobs = [] @@ -380,14 +382,14 @@ params = util.Params( kwd ) message = '' email = util.restore_text( params.get( 'email', '' ) ) - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), + q = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id, model.GalaxySession.table.c.user_id == model.User.table.c.id, model.User.table.c.email == email ), from_obj=[ sa.join( model.Job.table, model.User.table ) ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], + group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) jobs = [] for row in q.execute(): @@ -436,12 +438,12 @@ tool_id = params.get( 'tool_id', 'Add a column1' ) specified_date = params.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) ) - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ).label( 'date' ), + q = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ), sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ), whereclause=sa.and_( model.Job.table.c.tool_id == tool_id, model.Job.table.c.user_id != monitor_user_id ), from_obj=[ model.Job.table ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Job.table.c.create_time ) ) ], + group_by=self.group_by_month( model.Job.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) jobs = [] for row in q.execute(): diff -r e7f83c2921c86bedea95425c213e4a467e64f0f3 -r ce2776f88e9db53886b8879a948b19ce2a513835 lib/galaxy/webapps/reports/controllers/query.py --- /dev/null +++ b/lib/galaxy/webapps/reports/controllers/query.py @@ -0,0 +1,32 @@ +""" Mixin to help build advanced queries for reports interface. +""" +import pkg_resources +pkg_resources.require( "SQLAlchemy >= 0.4" ) +import sqlalchemy as sa + + +class ReportQueryBuilder: + + def group_by_month(self, column): + if self.app.targets_mysql: + return [ sa.func.year( column ), sa.func.month( sa.func.date( column ) ) ] + else: + return [ sa.func.date_trunc( 'month', sa.func.date( column ) ) ] + + def select_month(self, column): + if self.app.targets_mysql: + return sa.func.date( column ) + else: + return sa.func.date_trunc( 'month', sa.func.date( column ) ) + + def group_by_day(self, column): + if self.app.targets_mysql: + return [ sa.func.day( sa.func.date( column ) ) ] + else: + return [ sa.func.date_trunc( 'day', sa.func.date( column ) ) ] + + def select_day(self, column): + if self.app.targets_mysql: + return sa.func.date( column ) + else: + return sa.func.date_trunc( 'day', sa.func.date( column ) ) diff -r e7f83c2921c86bedea95425c213e4a467e64f0f3 -r ce2776f88e9db53886b8879a948b19ce2a513835 lib/galaxy/webapps/reports/controllers/sample_tracking.py --- a/lib/galaxy/webapps/reports/controllers/sample_tracking.py +++ b/lib/galaxy/webapps/reports/controllers/sample_tracking.py @@ -7,6 +7,8 @@ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa +from galaxy.webapps.reports.controllers.query import ReportQueryBuilder + import logging log = logging.getLogger( __name__ ) @@ -105,7 +107,7 @@ .enable_eagerloads( False ) -class SampleTracking( BaseUIController ): +class SampleTracking( BaseUIController, ReportQueryBuilder ): specified_date_list_grid = SpecifiedDateListGrid() @@ -144,9 +146,10 @@ @web.expose def per_month_all( self, trans, **kwd ): message = '' - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ).label( 'date' ), sa.func.count( model.Request.table.c.id ).label( 'total' ) ), + q = sa.select( ( self.select_month( model.Request.table.c.create_time ).label( 'date' ), + sa.func.count( model.Request.table.c.id ).label( 'total' ) ), from_obj=[ sa.outerjoin( model.Request.table, model.User.table ) ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ) ], + group_by=self.group_by_month( model.Request.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) requests = [] for row in q.execute(): @@ -178,11 +181,11 @@ message = '' email = util.restore_text( params.get( 'email', '' ) ) user_id = trans.security.decode_id( params.get( 'id', '' ) ) - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ).label( 'date' ), + q = sa.select( ( self.select_month( model.Request.table.c.create_time ).label( 'date' ), sa.func.count( model.Request.table.c.id ).label( 'total' ) ), whereclause=model.Request.table.c.user_id == user_id, from_obj=[ model.Request.table ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.Request.table.c.create_time ) ) ], + group_by=self.group_by_month( model.Request.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) requests = [] for row in q.execute(): diff -r e7f83c2921c86bedea95425c213e4a467e64f0f3 -r ce2776f88e9db53886b8879a948b19ce2a513835 lib/galaxy/webapps/reports/controllers/users.py --- a/lib/galaxy/webapps/reports/controllers/users.py +++ b/lib/galaxy/webapps/reports/controllers/users.py @@ -7,13 +7,14 @@ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa +from galaxy.webapps.reports.controllers.query import ReportQueryBuilder import logging from markupsafe import escape log = logging.getLogger( __name__ ) -class Users( BaseUIController ): +class Users( BaseUIController, ReportQueryBuilder ): @web.expose def registered_users( self, trans, **kwd ): @@ -24,10 +25,10 @@ @web.expose def registered_users_per_month( self, trans, **kwd ): message = escape( util.restore_text( kwd.get( 'message', '' ) ) ) - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), + q = sa.select( ( self.select_month( galaxy.model.User.table.c.create_time ).label( 'date' ), sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ), from_obj=[ galaxy.model.User.table ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ) ], + group_by=self.group_by_month( galaxy.model.User.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) users = [] for row in q.execute(): @@ -50,12 +51,12 @@ end_date = start_date + timedelta( days=calendar.monthrange( year, month )[1] ) month_label = start_date.strftime( "%B" ) year_label = start_date.strftime( "%Y" ) - q = sa.select( ( sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), + q = sa.select( ( self.select_day( galaxy.model.User.table.c.create_time ).label( 'date' ), sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ), whereclause=sa.and_( galaxy.model.User.table.c.create_time >= start_date, galaxy.model.User.table.c.create_time < end_date ), from_obj=[ galaxy.model.User.table ], - group_by=[ sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ) ], + group_by=self.group_by_day( galaxy.model.User.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) users = [] for row in q.execute(): @@ -82,7 +83,7 @@ day_label = start_date.strftime( "%A" ) month_label = start_date.strftime( "%B" ) year_label = start_date.strftime( "%Y" ) - q = sa.select( ( sa.func.date_trunc( 'day', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ), + q = sa.select( ( self.select_day( galaxy.model.User.table.c.create_time ).label( 'date' ), galaxy.model.User.table.c.email ), whereclause=sa.and_( galaxy.model.User.table.c.create_time >= start_date, galaxy.model.User.table.c.create_time < end_date ), diff -r e7f83c2921c86bedea95425c213e4a467e64f0f3 -r ce2776f88e9db53886b8879a948b19ce2a513835 lib/galaxy/webapps/reports/controllers/workflows.py --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -7,6 +7,7 @@ from galaxy.web.framework.helpers import grids eggs.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa +from galaxy.webapps.reports.controllers.query import ReportQueryBuilder import logging log = logging.getLogger( __name__ ) @@ -106,7 +107,7 @@ .enable_eagerloads( False ) -class Workflows( BaseUIController ): +class Workflows( BaseUIController, ReportQueryBuilder ): specified_date_list_grid = SpecifiedDateListGrid() @@ -145,9 +146,9 @@ @web.expose def per_month_all( self, trans, **kwd ): message = '' - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ).label( 'date' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), + q = sa.select( ( self.select_month( model.StoredWorkflow.table.c.create_time ).label( 'date' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), from_obj=[ sa.outerjoin( model.StoredWorkflow.table, model.User.table ) ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ) ], + group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) workflows = [] for row in q.execute(): @@ -179,11 +180,11 @@ message = '' email = util.restore_text( params.get( 'email', '' ) ) user_id = trans.security.decode_id( params.get( 'id', '' ) ) - q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ).label( 'date' ), + q = sa.select( ( self.select_month( model.StoredWorkflow.table.c.create_time ).label( 'date' ), sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ), whereclause=model.StoredWorkflow.table.c.user_id == user_id, from_obj=[ model.StoredWorkflow.table ], - group_by=[ sa.func.date_trunc( 'month', sa.func.date( model.StoredWorkflow.table.c.create_time ) ) ], + group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ), order_by=[ sa.desc( 'date' ) ] ) workflows = [] for row in q.execute(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5ff4dc352d74/ Changeset: 5ff4dc352d74 User: dannon Date: 2015-02-06 00:13:59+00:00 Summary: Relocate is_uwsgi to app.config (determined at configuration time via import). Affected #: 2 files diff -r 8f1d5b7b30c62231bfa4fa8f39fc6338726020ee -r 5ff4dc352d748b18fa1b8e75c68877b27108deb6 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -428,6 +428,18 @@ self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) ) self.citation_cache_lock_dir = self.resolve_path( kwargs.get( "citation_cache_lock_dir", "database/citations/locks" ) ) + # TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once. + self.is_uwsgi = False + try: + # The uwsgi module is automatically injected by the parent uwsgi + # process and only exists that way. If anything works, this is a + # uwsgi-managed process. + import uwsgi + if uwsgi.numproc: + self.is_uwsgi = True + except ImportError: + # This is not a uwsgi process, or something went horribly wrong. + pass @property def sentry_dsn_public( self ): diff -r 8f1d5b7b30c62231bfa4fa8f39fc6338726020ee -r 5ff4dc352d748b18fa1b8e75c68877b27108deb6 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -86,20 +86,8 @@ # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) - # TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once. - is_uwsgi = False - try: - # The uwsgi module is automatically injected by the parent uwsgi - # process and only exists that way. If anything works, this is a - # uwsgi-managed process. - import uwsgi - is_uwsgi = uwsgi.numproc - is_uwsgi = True - except ImportError: - # This is not a uwsgi process, or something went horribly wrong. - pass if asbool( kwargs.get( 'static_enabled', True) ): - if is_uwsgi: + if app.config.is_uwsgi: log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.") else: webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) https://bitbucket.org/galaxy/galaxy-central/commits/20bd598e1f53/ Changeset: 20bd598e1f53 User: dannon Date: 2015-02-06 00:15:10+00:00 Summary: Remove TODO about moving uwsgi test since I did it. Affected #: 1 file diff -r 5ff4dc352d748b18fa1b8e75c68877b27108deb6 -r 20bd598e1f5363518c8bfe44697a8e6f0dacff4e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -428,7 +428,7 @@ self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) ) self.citation_cache_lock_dir = self.resolve_path( kwargs.get( "citation_cache_lock_dir", "database/citations/locks" ) ) - # TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once. + # TEST FOR UWSGI self.is_uwsgi = False try: # The uwsgi module is automatically injected by the parent uwsgi https://bitbucket.org/galaxy/galaxy-central/commits/17ed2655b305/ Changeset: 17ed2655b305 User: dannon Date: 2015-02-06 00:16:19+00:00 Summary: Minor pep8'ing in lib/galaxy/config.py Affected #: 1 file diff -r 20bd598e1f5363518c8bfe44697a8e6f0dacff4e -r 17ed2655b3052c047aba60013e0f9bb173ebee90 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -124,7 +124,7 @@ self.hours_between_check = 12 self.update_integrated_tool_panel = kwargs.get( "update_integrated_tool_panel", True ) self.enable_data_manager_user_view = string_as_bool( kwargs.get( "enable_data_manager_user_view", "False" ) ) - self.galaxy_data_manager_data_path = kwargs.get( 'galaxy_data_manager_data_path', self.tool_data_path ) + self.galaxy_data_manager_data_path = kwargs.get( 'galaxy_data_manager_data_path', self.tool_data_path ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) ) @@ -381,7 +381,7 @@ self.amqp_internal_connection = kwargs.get('amqp_internal_connection') # TODO Get extra amqp args as necessary for ssl elif 'database_connection' in kwargs: - self.amqp_internal_connection = "sqlalchemy+"+self.database_connection + self.amqp_internal_connection = "sqlalchemy+" + self.database_connection else: self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path( "database/control.sqlite", self.root ) self.biostar_url = kwargs.get( 'biostar_url', None ) @@ -485,7 +485,10 @@ # [0], probably moved their shed_tool_conf.xml as well # [2]: user has done nothing, use the old files # [3]: fresh install - tool_config_file=[ 'config/tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml,config/shed_tool_conf.xml', 'tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] + tool_config_file=[ 'config/tool_conf.xml,shed_tool_conf.xml', + 'config/tool_conf.xml,config/shed_tool_conf.xml', + 'tool_conf.xml,shed_tool_conf.xml', + 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] ) for var, defaults in defaults.items(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0b15f8124467/ Changeset: 0b15f8124467 User: dannon Date: 2015-02-05 23:35:43+00:00 Summary: Add reference to the webapp to galaxy.app Affected #: 2 files diff -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 -r 0b15f8124467ff74da92f74f5f5977147ee6fc4c lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -23,7 +23,7 @@ import logging log = logging.getLogger( __name__ ) - +app = None class UniverseApplication( object, config.ConfiguresGalaxyMixin ): """Encapsulates the state of a Universe application""" diff -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 -r 0b15f8124467ff74da92f74f5f5977147ee6fc4c lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -10,6 +10,7 @@ from paste import httpexceptions import pkg_resources +import galaxy.app import galaxy.model import galaxy.model.mapping import galaxy.datatypes.registry @@ -39,8 +40,8 @@ app = kwargs.pop( 'app' ) else: try: - from galaxy.app import UniverseApplication - app = UniverseApplication( global_conf=global_conf, **kwargs ) + app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs ) + galaxy.app.app = app except: import traceback traceback.print_exc() https://bitbucket.org/galaxy/galaxy-central/commits/65870b9e3c18/ Changeset: 65870b9e3c18 User: dannon Date: 2015-02-05 23:55:15+00:00 Summary: Fix lunr availability for tool form. Turns out javascript define needs a target. Oops. Affected #: 3 files diff -r 0b15f8124467ff74da92f74f5f5977147ee6fc4c -r 65870b9e3c1801e6e6ae9667f46baaec4ddba4b1 client/galaxy/scripts/mvc/tools.js --- a/client/galaxy/scripts/mvc/tools.js +++ b/client/galaxy/scripts/mvc/tools.js @@ -3,7 +3,7 @@ */ define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr" ], - function(_, util, data) { + function(_, util, data, lunr) { /** * Mixin for tracking model visibility. diff -r 0b15f8124467ff74da92f74f5f5977147ee6fc4c -r 65870b9e3c1801e6e6ae9667f46baaec4ddba4b1 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -3,7 +3,7 @@ */ define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr" ], - function(_, util, data) { + function(_, util, data, lunr) { /** * Mixin for tracking model visibility. diff -r 0b15f8124467ff74da92f74f5f5977147ee6fc4c -r 65870b9e3c1801e6e6ae9667f46baaec4ddba4b1 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){var z=$("<div/>");z.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){z.find("a").on("click",function(A){A.preventDefault();Galaxy.upload.show()})}this.$el.append(z);return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(y,a,z,s){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(A){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(A){this.set("value",A||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(A){this.set("value",parseInt(A,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(A){this.set("value",parseFloat(A))}});var u=e.extend({get_samples:function(){return y.map(this.get("options"),function(A){return A[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:u};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(A){this.set("inputs",new i(y.map(A.inputs,function(B){var C=e.subModelTypes[B.type]||e;return new C(B)})))},toJSON:function(){var A=Backbone.Model.prototype.toJSON.call(this);A.inputs=this.get("inputs").map(function(B){return B.toJSON()});return A},remove_inputs:function(B){var A=this,C=A.get("inputs").filter(function(D){return(B.indexOf(D.get("type"))!==-1)});A.get("inputs").remove(C)},copy:function(B){var C=new j(this.toJSON());if(B){var A=new Backbone.Collection();C.get("inputs").each(function(D){if(D.get_samples()){A.push(D)}});C.set("inputs",A)}return C},apply_search_results:function(A){(y.indexOf(A,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(A,B){this.get("inputs").find(function(C){return C.get("name")===A}).set("value",B)},set_input_values:function(B){var A=this;y.each(y.keys(B),function(C){A.set_input_value(C,B[C])})},run:function(){return this._run()},rerun:function(B,A){return this._run({action:"rerun",target_dataset_id:B.id,regions:A})},get_inputs_dict:function(){var A={};this.get("inputs").each(function(B){A[B.get("name")]=B.get("value")});return A},_run:function(C){var D=y.extend({tool_id:this.id,inputs:this.get_inputs_dict()},C);var B=$.Deferred(),A=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(D),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(E){return E!=="pending"}});$.when(A.go()).then(function(E){B.resolve(new z.DatasetCollection().reset(E))});return B}});y.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var w=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){y.each(this.attributes.elems,function(A){A.show()});this.show();this.set("open",false)},apply_search_results:function(B){var C=true,A;y.each(this.attributes.elems,function(D){if(D instanceof w){A=D;A.hide()}else{if(D instanceof j){if(D.apply_search_results(B)){C=false;if(A){A.show()}}}}});if(C){this.hide()}else{this.show();this.set("open",true)}}});y.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var C=this.attributes.query;if(C.length<this.attributes.min_chars_for_search){this.set("results",null);return}var B=C+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var A=this;this.timer=setTimeout(function(){$.get(A.attributes.search_url,{query:B},function(D){A.set("results",D);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});y.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(A){this.attributes.tool_search=A.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=A.tools;this.attributes.layout=new Backbone.Collection(this.parse(A.layout))},parse:function(B){var A=this,C=function(F){var E=F.model_class;if(E.indexOf("Tool")===E.length-4){return A.attributes.tools.get(F.id)}else{if(E==="ToolSection"){var D=y.map(F.elems,C);F.elems=D;return new l(F)}else{if(E==="ToolSectionLabel"){return new w(F)}}}};return y.map(B,C)},clear_search_results:function(){this.get("layout").each(function(A){if(A instanceof l){A.clear_search_results()}else{A.show()}})},apply_search_results:function(){var B=this.get("tool_search").get("results");if(B===null){this.clear_search_results();return}var A=null;this.get("layout").each(function(C){if(C instanceof w){A=C;A.hide()}else{if(C instanceof j){if(C.apply_search_results(B)){if(A){A.show()}}}else{A=null;C.apply_search_results(B)}}})}});var t=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=t.extend({tagName:"div",render:function(){var A=$("<div/>");A.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){A.find("a").on("click",function(B){B.preventDefault();Galaxy.upload.show()})}this.$el.append(A);return this}});var b=t.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=t.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){t.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var A=this.$el.find(".toolSectionBody");y.each(this.model.attributes.elems,function(B){if(B instanceof j){var C=new m({model:B,className:"toolTitle"});C.render();A.append(C.$el)}else{if(B instanceof w){var D=new b({model:B});D.render();A.append(D.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(A){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===A.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var x=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var A=this;var B=new p({model:this.model.get("tool_search")});B.render();A.$el.append(B.$el);this.model.get("layout").each(function(D){if(D instanceof l){var C=new r({model:D});C.render();A.$el.append(C.$el)}else{if(D instanceof j){var E=new m({model:D,className:"toolTitleNoSection"});E.render();A.$el.append(E.$el)}else{if(D instanceof w){var F=new b({model:D});F.render();A.$el.append(F.$el)}}}});A.$el.find("a.tool-link").click(function(E){var D=$(this).attr("class").split(/\s+/)[0],C=A.model.get("tools").get(D);A.trigger("tool_link_click",E,C)});return this},handle_search_results:function(){var A=this.model.get("tool_search").get("results");if(A&&A.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var v=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new x({collection:this.collection});this.tool_form_view=new v()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var A=this;this.tool_panel_view.on("tool_link_click",function(C,B){C.preventDefault();A.show_tool(B)})},show_tool:function(B){var A=this;B.fetch().done(function(){A.tool_form_view.model=B;A.tool_form_view.render();A.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:u,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:x,ToolFormView:v}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/8f1d5b7b30c6/ Changeset: 8f1d5b7b30c6 User: dannon Date: 2015-02-05 23:55:20+00:00 Summary: Merge. Affected #: 4 files diff -r 65870b9e3c1801e6e6ae9667f46baaec4ddba4b1 -r 8f1d5b7b30c62231bfa4fa8f39fc6338726020ee lib/galaxy/managers/datasets.py --- a/lib/galaxy/managers/datasets.py +++ b/lib/galaxy/managers/datasets.py @@ -274,3 +274,15 @@ def add_deserializers( self ): super( DatasetAssociationDeserializer, self ).add_deserializers() deletable.PurgableDeserializerMixin.add_deserializers( self ) + +class DatasetAssociationFilters( base.ModelFilterParser, deletable.PurgableFiltersMixin ): + + def _add_parsers( self ): + super( DatasetAssociationFilters, self )._add_parsers() + deletable.PurgableFiltersMixin._add_parsers( self ) + + self.orm_filter_parsers.update({ + 'name' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'state' : { 'op': ( 'eq', 'in' ) }, + }) + #self.fn_filter_parsers.update({}) diff -r 65870b9e3c1801e6e6ae9667f46baaec4ddba4b1 -r 8f1d5b7b30c62231bfa4fa8f39fc6338726020ee lib/galaxy/managers/hdas.py --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -592,3 +592,25 @@ }) self.deserializable_keyset.update( self.deserializers.keys() ) + + +class HDAFilters( datasets.DatasetAssociationFilters ): + model_class = model.HistoryDatasetAssociation + + def _add_parsers( self ): + super( HDAFilters, self )._add_parsers() + + self.fn_filter_parsers.update({ + #TODO: filter_string_attr_contains, filter_string_attr_eq + #'dbkey' : { 'op': { 'has' : self.filter_annotation_contains, } }, + + #TODO: add this in annotatable mixin + 'annotation' : { 'op': { 'has' : self.filter_annotation_contains, } }, + #TODO: add this in taggable mixin + 'tag' : { + 'op': { + 'eq' : self.filter_has_tag, + 'has': self.filter_has_partial_tag, + } + } + }) diff -r 65870b9e3c1801e6e6ae9667f46baaec4ddba4b1 -r 8f1d5b7b30c62231bfa4fa8f39fc6338726020ee lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -310,7 +310,7 @@ 'contents' : self.serialize_contents }) - def serialize_contents( self, trans, history, key ): + def serialize_contents( self, trans, history, *args ): contents_dictionaries = [] for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ): contents_dict = {} diff -r 65870b9e3c1801e6e6ae9667f46baaec4ddba4b1 -r 8f1d5b7b30c62231bfa4fa8f39fc6338726020ee lib/galaxy/managers/users.py --- a/lib/galaxy/managers/users.py +++ b/lib/galaxy/managers/users.py @@ -8,15 +8,17 @@ from galaxy import model from galaxy import exceptions +from galaxy import util from galaxy.managers import base +from galaxy.managers import deletable from galaxy.managers import api_keys import logging log = logging.getLogger( __name__ ) -class UserManager( base.ModelManager ): +class UserManager( base.ModelManager, deletable.PurgableManagerMixin ): model_class = model.User foreign_key_name = 'user' @@ -107,7 +109,7 @@ """ Return a list of admin email addresses from the config file. """ - return [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ] + return [ email.strip() for email in self.app.config.get( "admin_users", "" ).split( "," ) ] def admins( self, trans, filters=None, **kwargs ): """ @@ -193,14 +195,19 @@ #TODO: not sure we need to go through sec agent... it's just the first role of type private return self.app.security_agent.get_private_user_role( user ) + def quota( self, trans, user ): + #TODO: use quota manager + return self.app.quota_agent.get_percent( user=user ) -class UserSerializer( base.ModelSerializer ): - def __init__( self ): +class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ): + + def __init__( self, app ): """ Convert a User and associated data to a dictionary representation. """ - super( UserSerializer, self ).__init__() + super( UserSerializer, self ).__init__( app ) + self.user_manager = UserManager( app ) self.default_view = 'summary' self.add_view( 'summary', [ @@ -209,23 +216,80 @@ self.add_view( 'detailed', [ 'update_time', 'create_time', + + 'deleted', + 'purged', + 'active', + 'total_disk_usage', 'nice_total_disk_usage', - 'deleted', - 'purged', - 'active' - ], include_keys_from='summary' ) - #self.add_view( 'summary', [ + 'quota_percent' # 'preferences', # # all tags # 'tags', # # all annotations # 'annotations' - #], include_keys_from='detailed' ) + ], include_keys_from='summary' ) def add_serializers( self ): + super( UserSerializer, self ).add_serializers() + deletable.PurgableSerializerMixin.add_serializers( self ) + self.serializers.update({ 'id' : self.serialize_id, 'create_time' : self.serialize_date, 'update_time' : self.serialize_date, + 'is_admin' : lambda t, i, k: self.user_manager.is_admin( t, i ), + 'quota_percent' : lambda t, i, k: self.user_manager.quota( t, i ) }) + + def serialize_current_anonymous_user( self, trans, user, keys ): + # use the current history if any to get usage stats for trans' anonymous user + #TODO: might be better as sep. Serializer class + history = trans.history + if not history: + raise exceptions.AuthenticationRequired( 'No history for anonymous user usage stats' ); + + usage = trans.app.quota_agent.get_usage( trans, history=trans.history ) + percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) + + # a very small subset of keys available + values = { + 'id' : None, + 'total_disk_usage' : int( usage ), + 'nice_total_disk_usage' : util.nice_size( usage ), + 'quota_percent' : percent, + } + serialized = {} + for key in keys: + if key in values: + serialized[ key ] = values[ key ] + return serialized + + def serialize( self, trans, user, keys ): + """ + Override to return at least some usage info if user is anonymous. + """ + if self.user_manager.is_anonymous( user ): + return self.serialize_current_anonymous_user( trans, user, keys ) + return super( UserSerializer, self ).serialize( trans, user, keys ) + + +class AdminUserFilters( base.ModelFilterParser, deletable.PurgableFiltersMixin ): + model_class = model.User + + def _add_parsers( self ): + super( AdminUserFilters, self )._add_parsers() + deletable.PurgableFiltersMixin._add_parsers( self ) + + #PRECONDITION: user making the query has been verified as an admin + self.orm_filter_parsers.update({ + 'name' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'email' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'username' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'active' : { 'op': ( 'eq' ) }, + 'disk_usage' : { 'op': ( 'le', 'ge' ) } + }) + + self.fn_filter_parsers.update({ + }) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix to 3abf1c3: pass app to super
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e7e6758d12d7/ Changeset: e7e6758d12d7 User: carlfeberhard Date: 2015-02-05 22:36:26+00:00 Summary: Fix to 3abf1c3: pass app to super Affected #: 1 file diff -r 3abf1c30e4730fb84c8a3ab764661e19071a8e45 -r e7e6758d12d7835c843bf978061cf410e1cc778f lib/galaxy/managers/users.py --- a/lib/galaxy/managers/users.py +++ b/lib/galaxy/managers/users.py @@ -206,7 +206,7 @@ """ Convert a User and associated data to a dictionary representation. """ - super( UserSerializer, self ).__init__() + super( UserSerializer, self ).__init__( app ) self.user_manager = UserManager( app ) self.default_view = 'summary' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Managers, users: add filters for later admin use, quota serializers, and a fallback anonymous user serialization; DatasetAssociations & HDAs: add filters
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3abf1c30e473/ Changeset: 3abf1c30e473 User: carlfeberhard Date: 2015-02-05 21:55:23+00:00 Summary: Managers, users: add filters for later admin use, quota serializers, and a fallback anonymous user serialization; DatasetAssociations & HDAs: add filters Affected #: 4 files diff -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 -r 3abf1c30e4730fb84c8a3ab764661e19071a8e45 lib/galaxy/managers/datasets.py --- a/lib/galaxy/managers/datasets.py +++ b/lib/galaxy/managers/datasets.py @@ -274,3 +274,15 @@ def add_deserializers( self ): super( DatasetAssociationDeserializer, self ).add_deserializers() deletable.PurgableDeserializerMixin.add_deserializers( self ) + +class DatasetAssociationFilters( base.ModelFilterParser, deletable.PurgableFiltersMixin ): + + def _add_parsers( self ): + super( DatasetAssociationFilters, self )._add_parsers() + deletable.PurgableFiltersMixin._add_parsers( self ) + + self.orm_filter_parsers.update({ + 'name' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'state' : { 'op': ( 'eq', 'in' ) }, + }) + #self.fn_filter_parsers.update({}) diff -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 -r 3abf1c30e4730fb84c8a3ab764661e19071a8e45 lib/galaxy/managers/hdas.py --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -592,3 +592,25 @@ }) self.deserializable_keyset.update( self.deserializers.keys() ) + + +class HDAFilters( datasets.DatasetAssociationFilters ): + model_class = model.HistoryDatasetAssociation + + def _add_parsers( self ): + super( HDAFilters, self )._add_parsers() + + self.fn_filter_parsers.update({ + #TODO: filter_string_attr_contains, filter_string_attr_eq + #'dbkey' : { 'op': { 'has' : self.filter_annotation_contains, } }, + + #TODO: add this in annotatable mixin + 'annotation' : { 'op': { 'has' : self.filter_annotation_contains, } }, + #TODO: add this in taggable mixin + 'tag' : { + 'op': { + 'eq' : self.filter_has_tag, + 'has': self.filter_has_partial_tag, + } + } + }) diff -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 -r 3abf1c30e4730fb84c8a3ab764661e19071a8e45 lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -310,7 +310,7 @@ 'contents' : self.serialize_contents }) - def serialize_contents( self, trans, history, key ): + def serialize_contents( self, trans, history, *args ): contents_dictionaries = [] for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ): contents_dict = {} diff -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 -r 3abf1c30e4730fb84c8a3ab764661e19071a8e45 lib/galaxy/managers/users.py --- a/lib/galaxy/managers/users.py +++ b/lib/galaxy/managers/users.py @@ -8,15 +8,17 @@ from galaxy import model from galaxy import exceptions +from galaxy import util from galaxy.managers import base +from galaxy.managers import deletable from galaxy.managers import api_keys import logging log = logging.getLogger( __name__ ) -class UserManager( base.ModelManager ): +class UserManager( base.ModelManager, deletable.PurgableManagerMixin ): model_class = model.User foreign_key_name = 'user' @@ -107,7 +109,7 @@ """ Return a list of admin email addresses from the config file. """ - return [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ] + return [ email.strip() for email in self.app.config.get( "admin_users", "" ).split( "," ) ] def admins( self, trans, filters=None, **kwargs ): """ @@ -193,14 +195,19 @@ #TODO: not sure we need to go through sec agent... it's just the first role of type private return self.app.security_agent.get_private_user_role( user ) + def quota( self, trans, user ): + #TODO: use quota manager + return self.app.quota_agent.get_percent( user=user ) -class UserSerializer( base.ModelSerializer ): - def __init__( self ): +class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ): + + def __init__( self, app ): """ Convert a User and associated data to a dictionary representation. """ super( UserSerializer, self ).__init__() + self.user_manager = UserManager( app ) self.default_view = 'summary' self.add_view( 'summary', [ @@ -209,23 +216,80 @@ self.add_view( 'detailed', [ 'update_time', 'create_time', + + 'deleted', + 'purged', + 'active', + 'total_disk_usage', 'nice_total_disk_usage', - 'deleted', - 'purged', - 'active' - ], include_keys_from='summary' ) - #self.add_view( 'summary', [ + 'quota_percent' # 'preferences', # # all tags # 'tags', # # all annotations # 'annotations' - #], include_keys_from='detailed' ) + ], include_keys_from='summary' ) def add_serializers( self ): + super( UserSerializer, self ).add_serializers() + deletable.PurgableSerializerMixin.add_serializers( self ) + self.serializers.update({ 'id' : self.serialize_id, 'create_time' : self.serialize_date, 'update_time' : self.serialize_date, + 'is_admin' : lambda t, i, k: self.user_manager.is_admin( t, i ), + 'quota_percent' : lambda t, i, k: self.user_manager.quota( t, i ) }) + + def serialize_current_anonymous_user( self, trans, user, keys ): + # use the current history if any to get usage stats for trans' anonymous user + #TODO: might be better as sep. Serializer class + history = trans.history + if not history: + raise exceptions.AuthenticationRequired( 'No history for anonymous user usage stats' ); + + usage = trans.app.quota_agent.get_usage( trans, history=trans.history ) + percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) + + # a very small subset of keys available + values = { + 'id' : None, + 'total_disk_usage' : int( usage ), + 'nice_total_disk_usage' : util.nice_size( usage ), + 'quota_percent' : percent, + } + serialized = {} + for key in keys: + if key in values: + serialized[ key ] = values[ key ] + return serialized + + def serialize( self, trans, user, keys ): + """ + Override to return at least some usage info if user is anonymous. + """ + if self.user_manager.is_anonymous( user ): + return self.serialize_current_anonymous_user( trans, user, keys ) + return super( UserSerializer, self ).serialize( trans, user, keys ) + + +class AdminUserFilters( base.ModelFilterParser, deletable.PurgableFiltersMixin ): + model_class = model.User + + def _add_parsers( self ): + super( AdminUserFilters, self )._add_parsers() + deletable.PurgableFiltersMixin._add_parsers( self ) + + #PRECONDITION: user making the query has been verified as an admin + self.orm_filter_parsers.update({ + 'name' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'email' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'username' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'active' : { 'op': ( 'eq' ) }, + 'disk_usage' : { 'op': ( 'le', 'ge' ) } + }) + + self.fn_filter_parsers.update({ + }) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2248c4d82151/ Changeset: 2248c4d82151 Branch: stable User: jmchilton Date: 2015-02-05 17:14:01+00:00 Summary: Workflow scheduling delay fix. There were problems if all three of these conditions were met - 1) workflow from GUI, 2) workflow evaluation delayed, and 3) a delayed step was connected to a input dataset. This fixes these workflows. Affected #: 3 files diff -r 097bbb3b7d3246faaa5188a1fc2a79b01630025c -r 2248c4d82151c928a7615f9335b55aa0c55c9446 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3202,6 +3202,27 @@ def update( self ): self.update_time = galaxy.model.orm.now.now() + def add_input( self, content, step_id ): + if content.history_content_type == "dataset": + request_to_content = WorkflowRequestToInputDatasetAssociation() + request_to_content.dataset = content + request_to_content.workflow_step_id = step_id + self.input_datasets.append( request_to_content ) + else: + request_to_content = WorkflowRequestToInputDatasetCollectionAssociation() + request_to_content.dataset_collection = content + request_to_content.workflow_step_id = step_id + self.input_dataset_collections.append( request_to_content ) + + def has_input_for_step( self, step_id ): + for content in self.input_datasets: + if content.workflow_step_id == step_id: + return True + for content in self.input_dataset_collections: + if content.workflow_step_id == step_id: + return True + return False + class WorkflowInvocationStep( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' ) diff -r 097bbb3b7d3246faaa5188a1fc2a79b01630025c -r 2248c4d82151c928a7615f9335b55aa0c55c9446 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -320,6 +320,11 @@ step_outputs[ 'input_ds_copy' ] = new_hdca else: raise Exception("Unknown history content encountered") + # If coming from UI - we haven't registered invocation inputs yet, + # so do that now so dependent steps can be recalculated. In the future + # everything should come in from the API and this can be eliminated. + if not invocation.has_input_for_step( step.id ): + invocation.add_input( step_outputs.values()[ 0 ], step.id ) progress.set_outputs_for_input( step, step_outputs ) return job diff -r 097bbb3b7d3246faaa5188a1fc2a79b01630025c -r 2248c4d82151c928a7615f9335b55aa0c55c9446 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -284,18 +284,8 @@ value=value, type=param_types.REPLACEMENT_PARAMETERS, ) - for step_id, content in run_config.inputs.iteritems(): - if content.history_content_type == "dataset": - request_to_content = model.WorkflowRequestToInputDatasetAssociation() - request_to_content.dataset = content - request_to_content.workflow_step_id = step_id - workflow_invocation.input_datasets.append( request_to_content ) - else: - request_to_content = model.WorkflowRequestToInputDatasetCollectionAssociation() - request_to_content.dataset_collection = content - request_to_content.workflow_step_id = step_id - workflow_invocation.input_dataset_collections.append( request_to_content ) + workflow_invocation.add_input( content, step_id ) for step in workflow.steps: state = step.state https://bitbucket.org/galaxy/galaxy-central/commits/e07163fe8bdb/ Changeset: e07163fe8bdb Branch: stable User: jmchilton Date: 2015-02-05 17:14:01+00:00 Summary: Fix scheduling_manager.py for unknown attribute reference. Not sure if this was a poor rebasing or a copy and paste error. Affected #: 1 file diff -r 2248c4d82151c928a7615f9335b55aa0c55c9446 -r e07163fe8bdbc3e85f48b308ed293c46578b3294 lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -116,7 +116,6 @@ for plugin_element in plugins_element.getchildren(): plugin_type = plugin_element.tag plugin_kwds = dict( plugin_element.items() ) - plugin_kwds.update( self.extra_kwargs ) workflow_scheduler_id = plugin_kwds.get( 'id', None ) self.__init_plugin( plugin_type, workflow_scheduler_id, **plugin_kwds ) https://bitbucket.org/galaxy/galaxy-central/commits/644deef1a578/ Changeset: 644deef1a578 Branch: stable User: jmchilton Date: 2015-02-05 18:33:59+00:00 Summary: Bugfix for bugfix d3b1f6b. d3b1f6b fix the GUI (in an obsecure use) but broke fairly typical uses of the API. Affected #: 1 file diff -r e07163fe8bdbc3e85f48b308ed293c46578b3294 -r 644deef1a5789b788552a6db7f3d6fe07d81c79d lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -324,7 +324,9 @@ # so do that now so dependent steps can be recalculated. In the future # everything should come in from the API and this can be eliminated. if not invocation.has_input_for_step( step.id ): - invocation.add_input( step_outputs.values()[ 0 ], step.id ) + content = step_outputs.values()[ 0 ] + if content: + invocation.add_input( content, step.id ) progress.set_outputs_for_input( step, step_outputs ) return job Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] f0c67a: make toolform fancy again; update mutable configs
by GitHub 06 Feb '15

06 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f0c67a17684293e648e79eb1dae8c8116aed4e22 https://github.com/galaxyproject/usegalaxy-playbook/commit/f0c67a17684293e6… Author: martenson <cech.marten(a)gmail.com> Date: 2015-02-05 (Thu, 05 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M stage/group_vars/galaxyservers.yml Log Message: ----------- make toolform fancy again; update mutable configs

1 0

commit/galaxy-central: guerler: ToolForm: Update version selection, use underscores for internal parameters
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/494418e72cf0/ Changeset: 494418e72cf0 User: guerler Date: 2015-02-05 18:34:51+00:00 Summary: ToolForm: Update version selection, use underscores for internal parameters Affected #: 12 files diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -15,12 +15,10 @@ this.optionsDefault = { // uses dynamic fields instead of text fields is_dynamic : true, - // shows form in compact view mode - compact : false, + // shows form in narrow view mode + narrow : false, // shows errors on start - initial_errors : false, - // use default value for disabled fields - use_defaults : false + initial_errors : false }; // configure options @@ -58,9 +56,66 @@ $(this.container).append(this.$el); // build this form - this._buildForm(); + this.build(this.options); }, + /** Main tool form build function. This function is called once a new model is available. + */ + build: function(options) { + // link this + var self = this; + + // reset events + this.off('refresh'); + this.off('reset'); + + // reset field list, which contains the input field elements + this.field_list = {}; + + // reset sequential input definition list, which contains the input definitions as provided from the api + this.input_list = {}; + + // reset input element list, which contains the dom elements of each input element (includes also the input field) + this.element_list = {}; + + // creates a tree/json data structure from the input form + this.tree = new ToolTree(this); + + // request history content and build form + this.content = new ToolContent(this); + + // update model data + self.options.inputs = options && options.inputs; + + // create ui elements + this._renderForm(options); + + // rebuild the underlying data structure + this.tree.finalize(); + + // show errors on startup + if (options.initial_errors) { + this._errors(options); + } + + // add refresh listener + this.on('refresh', function() { + // by using/resetting the deferred ajax queue the number of redundant calls is reduced + self.deferred.reset(); + self.deferred.execute(function(){self._updateModel()}); + }); + + // add reset listener + this.on('reset', function() { + for (var i in this.element_list) { + this.element_list[i].reset(); + } + }); + + // refresh + this.trigger('refresh'); + }, + /** Shows the final message (usually upon successful job submission) */ reciept: function($el) { @@ -105,63 +160,6 @@ } } }, - - /** Main tool form build function. This function is called once a new model is available. - */ - _buildForm: function() { - // link this - var self = this; - - // reset events - this.off('refresh'); - this.off('reset'); - - // reset field list, which contains the input field elements - this.field_list = {}; - - // reset sequential input definition list, which contains the input definitions as provided from the api - this.input_list = {}; - - // reset input element list, which contains the dom elements of each input element (includes also the input field) - this.element_list = {}; - - // creates a tree/json data structure from the input form - this.tree = new ToolTree(this); - - // request history content and build form - this.content = new ToolContent(this); - - // link model options - var options = this.options; - - // create ui elements - this._renderForm(options); - - // rebuild the underlying data structure - this.tree.finalize(); - - // show errors on startup - if (options.initial_errors) { - this._errors(options); - } - - // add refresh listener - this.on('refresh', function() { - // by using/resetting the deferred ajax queue the number of redundant calls is reduced - self.deferred.reset(); - self.deferred.execute(function(){self._updateModel()}); - }); - - // add reset listener - this.on('reset', function() { - for (var i in this.element_list) { - this.element_list[i].reset(); - } - }); - - // refresh - this.trigger('refresh'); - }, /** Renders the UI elements required for the form */ @@ -175,7 +173,7 @@ // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', - title : (!options.compact && 'Requirements') || null, + title : (!options.narrow && 'Requirements') || null, tooltip : 'Display tool requirements', onclick : function() { if (!this.visible) { @@ -200,7 +198,7 @@ // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', - title : (!options.compact && 'Versions') || null, + title : (!options.narrow && 'Versions') || null, tooltip : 'Select another tool version' }); if (options.versions && options.versions.length > 1) { @@ -213,8 +211,8 @@ icon : 'fa-cube', onclick : function() { // here we update the tool version (some tools encode the version also in the id) - options.id = options.id.replace(options.version, this.version); - options.version = this.version; + self.options.id = self.options.id.replace(self.options.version, this.version); + self.options.version = this.version; // rebuild the model and form self.deferred.reset(); @@ -230,7 +228,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', - title : (!options.compact && 'Options') || null, + title : (!options.narrow && 'Options') || null, tooltip : 'View available options' }); @@ -306,7 +304,7 @@ }); // remove padding - if (options.compact) { + if (options.narrow) { this.portlet.$content.css('padding', '0px'); } diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -21,9 +21,13 @@ this.options = options; // set labels - this.options.text_enable = 'In Advance'; - this.options.text_disable = 'At Runtime'; - this.options.use_defaults = true; + this.options.text_enable = 'In Advance'; + this.options.text_disable = 'At Runtime'; + + // configure workflow style + this.options.is_dynamic = false; + this.options.narrow = true; + this.options.initial_errors = true; // declare fields as optional Utils.deepeach(options.inputs, function(item) { diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -24,7 +24,7 @@ } ToolFormBase.prototype.initialize.call(this, options); }, - + /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { @@ -47,31 +47,28 @@ } } } - + // register process var process_id = this.deferred.register(); - + // get initial model Utils.request({ type : 'GET', url : model_url, success : function(response) { - // link model data update options - self.options = response; - - // build form - self._buildForm(); - + // build new tool form + self.build(response); + // notification self.message.update({ status : 'success', message : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.', persistent : false }); - + // process completed self.deferred.done(process_id); - + // log success console.debug('tools-form::initialize() - Initial tool model ready.'); console.debug(response); @@ -79,11 +76,11 @@ error : function(response) { // process completed self.deferred.done(process_id); - + // log error console.debug('tools-form::initialize() - Initial tool model request failed.'); console.debug(response); - + // show error var error_message = response.error || 'Uncaught error.'; self.modal.show({ @@ -98,7 +95,7 @@ } }); }, - + /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { @@ -112,11 +109,11 @@ return null; } }); - + // log tool state console.debug('tools-form::_refreshForm() - Refreshing states.'); console.debug(current_state); - + // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { @@ -131,10 +128,10 @@ } } } - + // set wait mode wait(true); - + // register process var process_id = this.deferred.register(); @@ -179,13 +176,13 @@ } } }); - + // unset wait mode wait(false); - + // process completed self.deferred.done(process_id); - + // log success console.debug('tools-form::_refreshForm() - States refreshed.'); console.debug(new_model); @@ -193,7 +190,7 @@ error : function(response) { // process completed self.deferred.done(process_id); - + // log error console.debug('tools-form::_refreshForm() - Refresh request failed.'); console.debug(response); diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2254,8 +2254,8 @@ """ Recursively creates a tool dictionary containing repeats, dynamic options and updated states. """ - job_id = kwd.get('job_id', None) - dataset_id = kwd.get('dataset_id', None) + job_id = kwd.get('__job_id__', None) + dataset_id = kwd.get('__dataset_id__', None) is_dynamic = string_as_bool(kwd.get('__is_dynamic__', True)) # load job details if provided diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -15,12 +15,10 @@ this.optionsDefault = { // uses dynamic fields instead of text fields is_dynamic : true, - // shows form in compact view mode - compact : false, + // shows form in narrow view mode + narrow : false, // shows errors on start - initial_errors : false, - // use default value for disabled fields - use_defaults : false + initial_errors : false }; // configure options @@ -58,9 +56,66 @@ $(this.container).append(this.$el); // build this form - this._buildForm(); + this.build(this.options); }, + /** Main tool form build function. This function is called once a new model is available. + */ + build: function(options) { + // link this + var self = this; + + // reset events + this.off('refresh'); + this.off('reset'); + + // reset field list, which contains the input field elements + this.field_list = {}; + + // reset sequential input definition list, which contains the input definitions as provided from the api + this.input_list = {}; + + // reset input element list, which contains the dom elements of each input element (includes also the input field) + this.element_list = {}; + + // creates a tree/json data structure from the input form + this.tree = new ToolTree(this); + + // request history content and build form + this.content = new ToolContent(this); + + // update model data + self.options.inputs = options && options.inputs; + + // create ui elements + this._renderForm(options); + + // rebuild the underlying data structure + this.tree.finalize(); + + // show errors on startup + if (options.initial_errors) { + this._errors(options); + } + + // add refresh listener + this.on('refresh', function() { + // by using/resetting the deferred ajax queue the number of redundant calls is reduced + self.deferred.reset(); + self.deferred.execute(function(){self._updateModel()}); + }); + + // add reset listener + this.on('reset', function() { + for (var i in this.element_list) { + this.element_list[i].reset(); + } + }); + + // refresh + this.trigger('refresh'); + }, + /** Shows the final message (usually upon successful job submission) */ reciept: function($el) { @@ -105,63 +160,6 @@ } } }, - - /** Main tool form build function. This function is called once a new model is available. - */ - _buildForm: function() { - // link this - var self = this; - - // reset events - this.off('refresh'); - this.off('reset'); - - // reset field list, which contains the input field elements - this.field_list = {}; - - // reset sequential input definition list, which contains the input definitions as provided from the api - this.input_list = {}; - - // reset input element list, which contains the dom elements of each input element (includes also the input field) - this.element_list = {}; - - // creates a tree/json data structure from the input form - this.tree = new ToolTree(this); - - // request history content and build form - this.content = new ToolContent(this); - - // link model options - var options = this.options; - - // create ui elements - this._renderForm(options); - - // rebuild the underlying data structure - this.tree.finalize(); - - // show errors on startup - if (options.initial_errors) { - this._errors(options); - } - - // add refresh listener - this.on('refresh', function() { - // by using/resetting the deferred ajax queue the number of redundant calls is reduced - self.deferred.reset(); - self.deferred.execute(function(){self._updateModel()}); - }); - - // add reset listener - this.on('reset', function() { - for (var i in this.element_list) { - this.element_list[i].reset(); - } - }); - - // refresh - this.trigger('refresh'); - }, /** Renders the UI elements required for the form */ @@ -175,7 +173,7 @@ // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', - title : (!options.compact && 'Requirements') || null, + title : (!options.narrow && 'Requirements') || null, tooltip : 'Display tool requirements', onclick : function() { if (!this.visible) { @@ -200,7 +198,7 @@ // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', - title : (!options.compact && 'Versions') || null, + title : (!options.narrow && 'Versions') || null, tooltip : 'Select another tool version' }); if (options.versions && options.versions.length > 1) { @@ -213,8 +211,8 @@ icon : 'fa-cube', onclick : function() { // here we update the tool version (some tools encode the version also in the id) - options.id = options.id.replace(options.version, this.version); - options.version = this.version; + self.options.id = self.options.id.replace(self.options.version, this.version); + self.options.version = this.version; // rebuild the model and form self.deferred.reset(); @@ -230,7 +228,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', - title : (!options.compact && 'Options') || null, + title : (!options.narrow && 'Options') || null, tooltip : 'View available options' }); @@ -306,7 +304,7 @@ }); // remove padding - if (options.compact) { + if (options.narrow) { this.portlet.$content.css('padding', '0px'); } diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -21,9 +21,13 @@ this.options = options; // set labels - this.options.text_enable = 'In Advance'; - this.options.text_disable = 'At Runtime'; - this.options.use_defaults = true; + this.options.text_enable = 'In Advance'; + this.options.text_disable = 'At Runtime'; + + // configure workflow style + this.options.is_dynamic = false; + this.options.narrow = true; + this.options.initial_errors = true; // declare fields as optional Utils.deepeach(options.inputs, function(item) { diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -24,7 +24,7 @@ } ToolFormBase.prototype.initialize.call(this, options); }, - + /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { @@ -47,31 +47,28 @@ } } } - + // register process var process_id = this.deferred.register(); - + // get initial model Utils.request({ type : 'GET', url : model_url, success : function(response) { - // link model data update options - self.options = response; - - // build form - self._buildForm(); - + // build new tool form + self.build(response); + // notification self.message.update({ status : 'success', message : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.', persistent : false }); - + // process completed self.deferred.done(process_id); - + // log success console.debug('tools-form::initialize() - Initial tool model ready.'); console.debug(response); @@ -79,11 +76,11 @@ error : function(response) { // process completed self.deferred.done(process_id); - + // log error console.debug('tools-form::initialize() - Initial tool model request failed.'); console.debug(response); - + // show error var error_message = response.error || 'Uncaught error.'; self.modal.show({ @@ -98,7 +95,7 @@ } }); }, - + /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { @@ -112,11 +109,11 @@ return null; } }); - + // log tool state console.debug('tools-form::_refreshForm() - Refreshing states.'); console.debug(current_state); - + // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { @@ -131,10 +128,10 @@ } } } - + // set wait mode wait(true); - + // register process var process_id = this.deferred.register(); @@ -179,13 +176,13 @@ } } }); - + // unset wait mode wait(false); - + // process completed self.deferred.done(process_id); - + // log success console.debug('tools-form::_refreshForm() - States refreshed.'); console.debug(new_model); @@ -193,7 +190,7 @@ error : function(response) { // process completed self.deferred.done(process_id); - + // log error console.debug('tools-form::_refreshForm() - Refresh request failed.'); console.debug(response); diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,compact:false,initial_errors:false,use_defaults:false};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var m=this.options;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.compact&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.compact&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.compact&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(u.compact){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.narrow&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){t.options.id=t.options.id.replace(t.options.version,this.version);t.options.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.narrow&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(u.narrow){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.use_defaults=true;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.options=k;f._buildForm();f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(){var f=this;var g=this.tree.finalize({data:function(k){if(k.values.length>0&&k.values[0]&&k.values[0].src==="hda"){return f.content.get({id:k.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(g);function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();var h=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;c.request({type:"GET",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});j(false);f.deferred.done(i);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(k)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(){var f=this;var g=this.tree.finalize({data:function(k){if(k.values.length>0&&k.values[0]&&k.values[0].src==="hda"){return f.content.get({id:k.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(g);function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();var h=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;c.request({type:"GET",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});j(false);f.deferred.done(i);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(k)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -9,8 +9,7 @@ ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. ## This avoids making two separate requests since the classic form requires the mako anyway. params = dict(trans.request.params) - if 'id' in params: - params['dataset_id'] = params['id'] + params['__dataset_id__'] = params.get('id', None) self.form_config = tool.to_json(trans, **params) self.form_config.update({ 'id' : tool.id, diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 templates/webapps/galaxy/workflow/editor_tool_form.mako --- a/templates/webapps/galaxy/workflow/editor_tool_form.mako +++ b/templates/webapps/galaxy/workflow/editor_tool_form.mako @@ -15,9 +15,6 @@ 'id' : tool.id, 'job_id' : trans.security.encode_id( job.id ) if job else None, 'history_id' : trans.security.encode_id( trans.history.id ), - 'is_dynamic' : False, - 'compact' : True, - 'initial_errors' : True, 'container' : '#right-content' }) %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Bugfix for bugfix d3b1f6b.
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff2b00fcbd70/ Changeset: ff2b00fcbd70 User: jmchilton Date: 2015-02-05 18:32:56+00:00 Summary: Bugfix for bugfix d3b1f6b. d3b1f6b fix the GUI (in an obsecure use) but broke fairly typical uses of the API. Affected #: 1 file diff -r b6349ba5cda26cdea678c4842136e50363c0629f -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -330,7 +330,9 @@ # so do that now so dependent steps can be recalculated. In the future # everything should come in from the API and this can be eliminated. if not invocation.has_input_for_step( step.id ): - invocation.add_input( step_outputs.values()[ 0 ], step.id ) + content = step_outputs.values()[ 0 ] + if content: + invocation.add_input( content, step.id ) progress.set_outputs_for_input( step, step_outputs ) return job Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 06 Feb '15

06 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/73e9ca698df3/ Changeset: 73e9ca698df3 User: jmchilton Date: 2015-02-05 17:27:46+00:00 Summary: Fix workflow schedulers to fallback onto sample like other config files. Affected #: 1 file diff -r 2f436edb5288bf750382ae1ccddd95ed611db6a1 -r 73e9ca698df3f0da3fe145878938cdf60978d17c lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -143,7 +143,6 @@ self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ] self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) - self.workflow_schedulers_config_file = resolve_path( kwargs.get( 'workflow_schedulers_config_file', 'config/workflow_schedulers_conf.xml' ), self.root ) self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) ) self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) ) self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") ) @@ -459,6 +458,7 @@ shed_data_manager_config_file=[ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], shed_tool_data_table_config=[ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], tool_sheds_config_file=[ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], + workflow_schedulers_config_file=['config/workflow_schedulers_conf.xml', 'config/workflow_schedulers_conf.xml.sample'], ) listify_defaults = dict( https://bitbucket.org/galaxy/galaxy-central/commits/d3b1f6b04d4b/ Changeset: d3b1f6b04d4b User: jmchilton Date: 2015-02-05 17:27:46+00:00 Summary: Workflow scheduling delay fix. There were problems if all three of these conditions were met - 1) workflow from GUI, 2) workflow evaluation delayed, and 3) a delayed step was connected to a input dataset. This fixes these workflows. Affected #: 3 files diff -r 73e9ca698df3f0da3fe145878938cdf60978d17c -r d3b1f6b04d4b4fb9db667afdfb2beb78db5226a0 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3253,6 +3253,27 @@ def update( self ): self.update_time = galaxy.model.orm.now.now() + def add_input( self, content, step_id ): + if content.history_content_type == "dataset": + request_to_content = WorkflowRequestToInputDatasetAssociation() + request_to_content.dataset = content + request_to_content.workflow_step_id = step_id + self.input_datasets.append( request_to_content ) + else: + request_to_content = WorkflowRequestToInputDatasetCollectionAssociation() + request_to_content.dataset_collection = content + request_to_content.workflow_step_id = step_id + self.input_dataset_collections.append( request_to_content ) + + def has_input_for_step( self, step_id ): + for content in self.input_datasets: + if content.workflow_step_id == step_id: + return True + for content in self.input_dataset_collections: + if content.workflow_step_id == step_id: + return True + return False + class WorkflowInvocationStep( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' ) diff -r 73e9ca698df3f0da3fe145878938cdf60978d17c -r d3b1f6b04d4b4fb9db667afdfb2beb78db5226a0 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -326,6 +326,11 @@ step_outputs[ 'input_ds_copy' ] = new_hdca else: raise Exception("Unknown history content encountered") + # If coming from UI - we haven't registered invocation inputs yet, + # so do that now so dependent steps can be recalculated. In the future + # everything should come in from the API and this can be eliminated. + if not invocation.has_input_for_step( step.id ): + invocation.add_input( step_outputs.values()[ 0 ], step.id ) progress.set_outputs_for_input( step, step_outputs ) return job diff -r 73e9ca698df3f0da3fe145878938cdf60978d17c -r d3b1f6b04d4b4fb9db667afdfb2beb78db5226a0 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -297,18 +297,8 @@ value=value, type=param_types.REPLACEMENT_PARAMETERS, ) - for step_id, content in run_config.inputs.iteritems(): - if content.history_content_type == "dataset": - request_to_content = model.WorkflowRequestToInputDatasetAssociation() - request_to_content.dataset = content - request_to_content.workflow_step_id = step_id - workflow_invocation.input_datasets.append( request_to_content ) - else: - request_to_content = model.WorkflowRequestToInputDatasetCollectionAssociation() - request_to_content.dataset_collection = content - request_to_content.workflow_step_id = step_id - workflow_invocation.input_dataset_collections.append( request_to_content ) + workflow_invocation.add_input( content, step_id ) for step in workflow.steps: state = step.state https://bitbucket.org/galaxy/galaxy-central/commits/ff56bdbf7b3e/ Changeset: ff56bdbf7b3e User: jmchilton Date: 2015-02-05 17:27:46+00:00 Summary: Fix scheduling_manager.py for unknown attribute reference. Not sure if this was a poor rebasing or a copy and paste error. Affected #: 1 file diff -r d3b1f6b04d4b4fb9db667afdfb2beb78db5226a0 -r ff56bdbf7b3e1a7a19eaab24be8d2ac6b8aa970c lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -116,7 +116,6 @@ for plugin_element in plugins_element.getchildren(): plugin_type = plugin_element.tag plugin_kwds = dict( plugin_element.items() ) - plugin_kwds.update( self.extra_kwargs ) workflow_scheduler_id = plugin_kwds.get( 'id', None ) self.__init_plugin( plugin_type, workflow_scheduler_id, **plugin_kwds ) https://bitbucket.org/galaxy/galaxy-central/commits/b6349ba5cda2/ Changeset: b6349ba5cda2 User: jmchilton Date: 2015-02-05 17:27:46+00:00 Summary: Improved error message if things don't match up when recovering workflows. Ideally this shouldn't really happen - but this should help if it does. Affected #: 1 file diff -r ff56bdbf7b3e1a7a19eaab24be8d2ac6b8aa970c -r b6349ba5cda26cdea678c4842136e50363c0629f lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -251,7 +251,13 @@ step_outputs = self.outputs[ connection.output_step.id ] if step_outputs is STEP_OUTPUT_DELAYED: raise modules.DelayedWorkflowEvaluation() - replacement = step_outputs[ connection.output_name ] + output_name = connection.output_name + try: + replacement = step_outputs[ output_name ] + except KeyError: + template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s" + message = template % ( output_name, step_outputs ) + raise Exception( message ) if isinstance( replacement, model.HistoryDatasetCollectionAssociation ): if not replacement.collection.populated: if not replacement.collection.waiting_for_elements: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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