February 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dannon: Cloudlaunch: During bucket scanning, catch S3ResponseError. Boto should handle this better in future versions, but for now this can happen if a non-us bucket is accessed.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cdd8b8a66a98/ changeset: cdd8b8a66a98 user: dannon date: 2013-02-06 03:55:12 summary: Cloudlaunch: During bucket scanning, catch S3ResponseError. Boto should handle this better in future versions, but for now this can happen if a non-us bucket is accessed. affected #: 1 file diff -r 022fd520c8ec2eee6221c44213c034be504735b8 -r cdd8b8a66a980d1761e47f9202114fbcfd218cf7 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -19,7 +19,7 @@ from galaxy.web.base.controller import BaseUIController from galaxy.util.json import to_json_string from boto.ec2.regioninfo import RegionInfo -from boto.exception import EC2ResponseError +from boto.exception import EC2ResponseError, S3ResponseError from boto.s3.connection import OrdinaryCallingFormat, S3Connection log = logging.getLogger(__name__) @@ -28,6 +28,7 @@ DEFAULT_KEYPAIR = 'cloudman_keypair' DEFAULT_AMI = 'ami-da58aab3' + class CloudController(BaseUIController): def __init__(self, app): @@ -55,7 +56,12 @@ buckets = s3_conn.get_all_buckets() clusters = [] for bucket in buckets: - pd = bucket.get_key('persistent_data.yaml') + try: + pd = bucket.get_key('persistent_data.yaml') + except S3ResponseError, e: + # This can fail for a number of reasons for non-us and/or CNAME'd buckets. + log.error("Problem fetching persistent_data.yaml from bucket: %s \n%s" % (e, e.body)) + continue if pd: # This is a cloudman bucket. # We need to get persistent data, and the cluster name. 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: dannon: Update controller url_for invocations, preparation for enforcing explicit controller specification in the mapper.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/022fd520c8ec/ changeset: 022fd520c8ec user: dannon date: 2013-02-06 03:48:24 summary: Update controller url_for invocations, preparation for enforcing explicit controller specification in the mapper. affected #: 7 files diff -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 -r 022fd520c8ec2eee6221c44213c034be504735b8 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -599,7 +599,7 @@ def get_name_and_link_async( self, trans, id=None ): """ Returns dataset's name and link. """ dataset = self.get_dataset( trans, id, False, True ) - return_dict = { "name" : dataset.name, "link" : url_for( action="display_by_username_and_slug", username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) ) } + return_dict = { "name" : dataset.name, "link" : url_for( controller='dataset', action="display_by_username_and_slug", username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) ) } return return_dict @web.expose diff -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 -r 022fd520c8ec2eee6221c44213c034be504735b8 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -624,7 +624,7 @@ # If no source to create archive from, show form to upload archive or specify URL. if not archive_source: return trans.show_form( - web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) \ + web.FormBuilder( web.url_for(controller='history', action='import_archive'), "Import a History from an Archive", submit_text="Submit" ) \ .add_input( "text", "Archived History URL", "archive_url", value="", error=None ) # TODO: add support for importing via a file. #.add_input( "file", "Archived History File", "archive_file", value=None, error=None ) @@ -684,7 +684,7 @@ return open( trans.app.object_store.get_filename( jeha.dataset ) ) elif jeha.job.state in [ model.Job.states.RUNNING, model.Job.states.QUEUED, model.Job.states.WAITING ]: return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>" \ - % ( { 'n' : history.name, 's' : url_for( action="export_archive", id=id, qualified=True ) } ) ) + % ( { 'n' : history.name, 's' : url_for( controller='history', action="export_archive", id=id, qualified=True ) } ) ) # Run job to do export. history_exp_tool = trans.app.toolbox.get_tool( '__EXPORT_HISTORY__' ) @@ -697,7 +697,7 @@ return trans.show_message( "Exporting History '%(n)s'. Use this link to download \ the archive or import it to another Galaxy server: \ <a href='%(u)s'>%(u)s</a>" \ - % ( { 'n' : history.name, 'u' : url_for( action="export_archive", id=id, qualified=True ) } ) ) + % ( { 'n' : history.name, 'u' : url_for(controller='history', action="export_archive", id=id, qualified=True ) } ) ) @web.expose @web.json @@ -709,7 +709,7 @@ trans.sa_session.flush() return_dict = { "name" : history.name, - "link" : url_for( action="display_by_username_and_slug", username=history.user.username, slug=history.slug ) } + "link" : url_for(controller='history', action="display_by_username_and_slug", username=history.user.username, slug=history.slug ) } return return_dict @web.expose @@ -823,7 +823,7 @@ return trans.show_warn_message( """ Warning! If you import this history, you will lose your current history. <br>You can <a href="%s">continue and import this history</a> or %s. - """ % ( web.url_for( id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) + """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) @web.expose def view( self, trans, id=None, show_deleted=False, use_panels=True ): diff -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 -r 022fd520c8ec2eee6221c44213c034be504735b8 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -18,7 +18,7 @@ # Custom column. class URLColumn( grids.PublicURLColumn ): def get_value( self, trans, grid, item ): - return url_for( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) + return url_for(controller='page', action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) # Grid definition use_panels = True @@ -365,9 +365,9 @@ session.flush() # Display the management page ## trans.set_message( "Page '%s' created" % page.title ) - return trans.response.send_redirect( web.url_for( action='list' ) ) + return trans.response.send_redirect( web.url_for(controller='page', action='list' ) ) return trans.show_form( - web.FormBuilder( web.url_for(), "Create new page", submit_text="Submit" ) + web.FormBuilder( web.url_for(controller='page', action='create'), "Create new page", submit_text="Submit" ) .add_text( "page_title", "Page title", value=page_title, error=page_title_err ) .add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err, help="""A unique identifier that will be used for @@ -410,7 +410,7 @@ self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation ) session.flush() # Redirect to page list. - return trans.response.send_redirect( web.url_for( action='list' ) ) + return trans.response.send_redirect( web.url_for(controller='page', action='list' ) ) else: page_title = page.title page_slug = page.slug @@ -418,7 +418,7 @@ if not page_annotation: page_annotation = "" return trans.show_form( - web.FormBuilder( web.url_for( id=encoded_id ), "Edit page attributes", submit_text="Submit" ) + web.FormBuilder( web.url_for(controller='page', action='edit', id=encoded_id ), "Edit page attributes", submit_text="Submit" ) .add_text( "page_title", "Page title", value=page_title, error=page_title_err ) .add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err, help="""A unique identifier that will be used for @@ -656,7 +656,7 @@ if self.create_item_slug( trans.sa_session, page ): trans.sa_session.flush() - return_dict = { "name" : page.title, "link" : url_for( action="display_by_username_and_slug", username=page.user.username, slug=page.slug ) } + return_dict = { "name" : page.title, "link" : url_for(controller='page', action="display_by_username_and_slug", username=page.user.username, slug=page.slug ) } return return_dict @web.expose diff -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 -r 022fd520c8ec2eee6221c44213c034be504735b8 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -418,7 +418,7 @@ return trans.show_warn_message( """ Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. - """ % web.url_for( id=id, confirm=True ) ) + """ % web.url_for( controller='root', action='history_import', id=id, confirm=True ) ) @web.expose def history_new( self, trans, name=None ): trans.new_history( name=name ) diff -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 -r 022fd520c8ec2eee6221c44213c034be504735b8 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -443,7 +443,7 @@ if not user and trans.app.config.require_login: if trans.app.config.allow_user_creation: create_account_str = " If you don't already have an account, <a href='%s'>you may create one</a>." % \ - web.url_for( action='create', cntrller='user' ) + web.url_for( controller='user', action='create', cntrller='user' ) if trans.webapp.name == 'galaxy': header = require_login_template % ( "Galaxy instance", create_account_str ) else: @@ -912,7 +912,7 @@ trans.sa_session.add( reset_user ) trans.sa_session.flush() trans.log_event( "User reset password: %s" % email ) - message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( action='login' ) ) + message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login' ) ) except Exception, e: message = 'Failed to reset password: %s' % str( e ) status = 'error' diff -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 -r 022fd520c8ec2eee6221c44213c034be504735b8 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -4,7 +4,7 @@ from galaxy import model, web from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin -from galaxy.web.framework.helpers import time_ago, grids, iff +from galaxy.web.framework.helpers import time_ago, grids from galaxy import util from galaxy.util.json import from_json_string from galaxy.util.sanitize_html import sanitize_html @@ -503,7 +503,7 @@ self.create_item_slug( session, visualization ) session.flush() trans.set_message( "Visualization '%s' shared with user '%s'" % ( visualization.title, other.email ) ) - return trans.response.send_redirect( url_for( action='sharing', id=id ) ) + return trans.response.send_redirect( url_for(controller='visualization', action='sharing', id=id ) ) return trans.fill_template( "/ind_share_base.mako", message = msg, messagetype = mtype, @@ -551,7 +551,7 @@ if self.create_item_slug( trans.sa_session, visualization ): trans.sa_session.flush() - return_dict = { "name" : visualization.title, "link" : url_for( action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) } + return_dict = { "name" : visualization.title, "link" : url_for(controller='visualization', action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) } return return_dict @web.expose @@ -588,11 +588,11 @@ visualization_slug_err = rval[ 'slug_err' ] else: # Successfully created viz. - return trans.response.send_redirect( web.url_for( action='list' ) ) + return trans.response.send_redirect( web.url_for(controller='visualization', action='list' ) ) viz_type_options = [ ( t, t ) for t in self.viz_types ] return trans.show_form( - web.FormBuilder( web.url_for(), "Create new visualization", submit_text="Submit" ) + web.FormBuilder( web.url_for(controller='visualization', action='create'), "Create new visualization", submit_text="Submit" ) .add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err ) .add_select( "visualization_type", "Type", options=viz_type_options, error=None ) .add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err, @@ -649,7 +649,7 @@ self.add_item_annotation( trans.sa_session, trans.get_user(), visualization, visualization_annotation ) session.flush() # Redirect to visualization list. - return trans.response.send_redirect( web.url_for( action='list' ) ) + return trans.response.send_redirect( web.url_for(controller='visualization', action='list' ) ) else: visualization_title = visualization.title # Create slug if it's not already set. @@ -660,7 +660,7 @@ if not visualization_annotation: visualization_annotation = "" return trans.show_form( - web.FormBuilder( web.url_for( id=id ), "Edit visualization attributes", submit_text="Submit" ) + web.FormBuilder( web.url_for(controller='visualization', action='edit', id=id ), "Edit visualization attributes", submit_text="Submit" ) .add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err ) .add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err, help="""A unique identifier that will be used for diff -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 -r 022fd520c8ec2eee6221c44213c034be504735b8 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -113,6 +113,7 @@ @web.expose def index( self, trans ): + print trans.request.host_url return self.list( trans ) @web.expose @@ -410,7 +411,7 @@ #message = "Workflow renamed to '%s'." % new_name #return self.list_grid( trans, message=message, status='done' ) else: - return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), + return form( url_for(controller='workflow', action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename", use_panels=True ) \ .add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) ) @@ -485,7 +486,7 @@ if self.create_item_slug( trans.sa_session, stored ): trans.sa_session.flush() - return_dict = { "name" : stored.name, "link" : url_for( action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } + return_dict = { "name" : stored.name, "link" : url_for(controller='workflow', action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } return return_dict @web.expose @@ -559,7 +560,7 @@ trans.set_message( "Workflow '%s' created" % stored_workflow.name ) return self.list( trans ) else: - return form( url_for(), "Create New Workflow", submit_text="Create", use_panels=True ) \ + return form( url_for(controller="workflow", action="create"), "Create New Workflow", submit_text="Create", use_panels=True ) \ .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) @@ -910,7 +911,7 @@ pass # Provide user feedback. - workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( action='list' ) + workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( controller='workflow', action='list' ) if response.status != 200: return trans.show_error_message( "There was a problem importing the workflow. Error: %s %s" % (response_data, workflow_list_str) ) if workflow.has_errors: @@ -968,7 +969,7 @@ parser = SingleTagContentsParser( 'id' ) parser.feed( response_data ) myexp_workflow_id = parser.tag_content - workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( action='list' ) + workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( controller='workflow', action='list' ) if myexp_workflow_id: return trans.show_message( \ """Workflow '%s' successfully exported to myExperiment. <br/> @@ -1299,7 +1300,7 @@ # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>" - ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) + ## % ( workflow_name, web.url_for(controller='workflow', action='editor', id=trans.security.encode_id(stored.id) ) ) ) @web.expose def run( self, trans, id, history_id=None, multiple_input_mode="product", hide_fixed_params=False, **kwargs ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Update all template url_for invocations to explicitly specify a controller. This is preparation for removing the deprecated Routes mapper.explicit option.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7db12eb10dbb/ changeset: 7db12eb10dbb user: dannon date: 2013-02-06 03:42:21 summary: Update all template url_for invocations to explicitly specify a controller. This is preparation for removing the deprecated Routes mapper.explicit option. affected #: 46 files diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/dataset_security/group/group.mako --- a/templates/admin/dataset_security/group/group.mako +++ b/templates/admin/dataset_security/group/group.mako @@ -50,7 +50,7 @@ <div class="toolForm"><div class="toolFormTitle">Group '${group.name}'</div><div class="toolFormBody"> - <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='manage_users_and_roles_for_group', id=trans.security.encode_id( group.id ) )}" method="post" > + <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for(controller='admin', action='manage_users_and_roles_for_group', id=trans.security.encode_id( group.id ) )}" method="post" ><div class="form-row"><div style="float: left; margin-right: 10px;"><label>Roles associated with '${group.name}'</label> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/dataset_security/group/group_create.mako --- a/templates/admin/dataset_security/group/group_create.mako +++ b/templates/admin/dataset_security/group/group_create.mako @@ -55,7 +55,7 @@ <div class="toolForm"><div class="toolFormTitle">Create Group</div><div class="toolFormBody"> - <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='create_group' )}" method="post" > + <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for(controller='admin', action='create_group' )}" method="post" ><div class="form-row"><label>Name:</label><input name="name" type="textfield" value="${name}" size=40"/> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/dataset_security/role/role.mako --- a/templates/admin/dataset_security/role/role.mako +++ b/templates/admin/dataset_security/role/role.mako @@ -50,7 +50,7 @@ <div class="toolForm"><div class="toolFormTitle">Role '${role.name}'</div><div class="toolFormBody"> - <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='manage_users_and_groups_for_role', id=trans.security.encode_id( role.id ) )}" method="post" > + <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for(controller='admin', action='manage_users_and_groups_for_role', id=trans.security.encode_id( role.id ) )}" method="post" ><div class="form-row"><div style="float: left; margin-right: 10px;"><label>Users associated with '${role.name}'</label> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/dataset_security/role/role_create.mako --- a/templates/admin/dataset_security/role/role_create.mako +++ b/templates/admin/dataset_security/role/role_create.mako @@ -55,7 +55,7 @@ <div class="toolForm"><div class="toolFormTitle">Create Role</div><div class="toolFormBody"> - <form name="associate_role_group_user" id="associate_role_group_user" action="${h.url_for( action='create_role' )}" method="post" > + <form name="associate_role_group_user" id="associate_role_group_user" action="${h.url_for(controller='admin', action='create_role' )}" method="post" ><div class="form-row"><label>Name:</label><input name="name" type="textfield" value="${name}" size=40"/> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/jobs.mako --- a/templates/admin/jobs.mako +++ b/templates/admin/jobs.mako @@ -37,7 +37,7 @@ <p/> %if jobs: -<form name="jobs" action="${h.url_for()}" method="POST"> +<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST"><table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"><tr class="header"><td><input type="checkbox" onClick="toggle_all(this)"/></td> @@ -101,7 +101,7 @@ <div class="infomessage">There are no unfinished jobs to show with current cutoff time.</div><p/> %endif -<form name="jobs" action="${h.url_for()}" method="POST"> +<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST"><div class="toolForm"><div class="toolFormTitle"> Update Jobs @@ -125,7 +125,7 @@ </div></div></form> -<form name="jobs" action="${h.url_for()}" method="POST"> +<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST"><p/><div class="toolForm"><div class="toolFormTitle"> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/memdump.mako --- a/templates/admin/memdump.mako +++ b/templates/admin/memdump.mako @@ -37,7 +37,7 @@ id = None new_s += re.sub( id_re, r'\1<a href="' + h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_id=id ) + r'">\2</a>', line ) if id and heap[int(id)].count == 1: - new_s += " <a href='%s'>theone</a>\n" % h.url_for( ids=ids, sorts=sorts, new_id=id, theone=True ) + new_s += " <a href='%s'>theone</a>\n" % h.url_for( controller='admin', action='memdump', ids=ids, sorts=sorts, new_id=id, theone=True ) else: new_s += "\n" return new_s diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/quota/quota.mako --- a/templates/admin/quota/quota.mako +++ b/templates/admin/quota/quota.mako @@ -50,7 +50,7 @@ <div class="toolForm"><div class="toolFormTitle">Quota '${name}'</div><div class="toolFormBody"> - <form name="associate_quota_user_group" id="associate_quota_user_group" action="${h.url_for( action='manage_users_and_groups_for_quota', id=id )}" method="post" > + <form name="associate_quota_user_group" id="associate_quota_user_group" action="${h.url_for(controller='admin', action='manage_users_and_groups_for_quota', id=id )}" method="post" ><div class="form-row"><div style="float: left; margin-right: 10px;"><label>Users associated with '${name}'</label> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/quota/quota_create.mako --- a/templates/admin/quota/quota_create.mako +++ b/templates/admin/quota/quota_create.mako @@ -64,7 +64,7 @@ <div class="toolForm"><div class="toolFormTitle">Create quota</div><div class="toolFormBody"> - <form name="associate_quota_group_user" id="associate_quota_group_user" action="${h.url_for( action='create_quota' )}" method="post" > + <form name="associate_quota_group_user" id="associate_quota_group_user" action="${h.url_for(controller='admin', action='create_quota' )}" method="post" ><div class="form-row"><label>Name:</label><input name="name" type="textfield" value="${name}" size=40"/> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/quota/quota_set_default.mako --- a/templates/admin/quota/quota_set_default.mako +++ b/templates/admin/quota/quota_set_default.mako @@ -27,7 +27,7 @@ <div class="toolForm"><div class="toolFormTitle">Set quota default</div><div class="toolFormBody"> - <form name="set_quota_default" id="set_quota_default" action="${h.url_for( action='set_quota_default' )}" method="post" > + <form name="set_quota_default" id="set_quota_default" action="${h.url_for(controller='admin', action='set_quota_default' )}" method="post" ><input name="id" type="hidden" value="${id}"/><div class="form-row"><label>Is this quota a default for a class of users (if yes, what type)?</label> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/admin/user/user.mako --- a/templates/admin/user/user.mako +++ b/templates/admin/user/user.mako @@ -50,7 +50,7 @@ <div class="toolForm"><div class="toolFormTitle">User '${user.email}'</div><div class="toolFormBody"> - <form name="associate_user_role_group" id="associate_user_role_group" action="${h.url_for( action='manage_roles_and_groups_for_user', id=trans.security.encode_id( user.id ) )}" method="post" > + <form name="associate_user_role_group" id="associate_user_role_group" action="${h.url_for(controller='admin', action='manage_roles_and_groups_for_user', id=trans.security.encode_id( user.id ) )}" method="post" ><div class="form-row"><div style="float: left; margin-right: 10px;"><label>Roles associated with '${user.email}'</label> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/export_base.mako --- a/templates/export_base.mako +++ b/templates/export_base.mako @@ -37,6 +37,7 @@ self.item_class_name_lc = self.item_class_name.lower() self.item_class_plural_name = get_class_plural_display_name( item.__class__ ) self.item_class_plural_name_lc = self.item_class_plural_name.lower() + self.controller = get_controller_name(item) %></%def> @@ -77,18 +78,18 @@ %if item.importable: Use this URL to import the ${get_class_display_name( item.__class__ ).lower()} directly into another Galaxy server: <div class="display-url"> - ${h.url_for( action='for_direct_import', id=trans.security.encode_id( item.id ), qualified=True )} + ${h.url_for(controller=self.controller, action='for_direct_import', id=trans.security.encode_id( item.id ), qualified=True )} </div> (Copy this URL into the box titled 'Workflow URL' in the Import Workflow page.) %else: - <a href="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ) )}">This ${get_class_display_name( item.__class__ ).lower()} must be accessible before it can be imported into another Galaxy.</a> + <a href="${h.url_for(controller=self.controller, action='sharing', id=trans.security.encode_id( item.id ) )}">This ${get_class_display_name( item.__class__ ).lower()} must be accessible before it can be imported into another Galaxy.</a> %endif </%def><%def name="render_download_to_file(item)"><h3>Download to File</h3> - <a href="${h.url_for( action='export_to_file', id=trans.security.encode_id( item.id ) )}"> + <a href="${h.url_for(controller=self.controller, action='export_to_file', id=trans.security.encode_id( item.id ) )}"> Download ${get_class_display_name( item.__class__ ).lower()} to file so that it can be saved or imported into another Galaxy server.</a></%def> @@ -98,7 +99,7 @@ <%def name="render_footer()"><p><br><br> - <a href="${h.url_for( action="list" )}">Back to ${self.item_class_plural_name} List</a> + <a href="${h.url_for(controller=self.controller, action="list" )}">Back to ${self.item_class_plural_name} List</a></%def><%def name="body()"> @@ -114,4 +115,4 @@ ${self.render_more(item)} ${self.render_footer()} -</%def> \ No newline at end of file +</%def> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/ind_share_base.mako --- a/templates/ind_share_base.mako +++ b/templates/ind_share_base.mako @@ -76,6 +76,7 @@ item_class_name_lc = item_class_name.lower() item_class_plural_name = get_class_plural_display_name( item.__class__ ) item_class_plural_name_lc = item_class_plural_name.lower() + item_controller = get_controller_name(item) # Get item name. item_name = get_item_name(item) @@ -84,7 +85,7 @@ <div class="toolForm"><div class="toolFormTitle">Share ${item_class_name} '${item_name}' with Another User</div><div class="toolFormBody"> - <form action="${h.url_for( action='share', id=trans.security.encode_id( item.id ) )}" method="POST"> + <form action="${h.url_for(controller=item_controller, action='share', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"><label> Email address of user to share with @@ -98,11 +99,11 @@ <input type="submit" value="Share"></input></div><div class="form-row"> - <a href="${h.url_for( action="sharing", id=trans.security.encode_id( item.id ) )}">Back to ${item_class_name}'s Sharing Home</a> + <a href="${h.url_for(controller=item_controller, action="sharing", id=trans.security.encode_id( item.id ) )}">Back to ${item_class_name}'s Sharing Home</a></div></form></div></div></div> -</%def> \ No newline at end of file +</%def> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/sharing_base.mako --- a/templates/sharing_base.mako +++ b/templates/sharing_base.mako @@ -100,6 +100,7 @@ <%def name="body()"> ## Set use_panels var for use in page's URLs. <% use_panels = context.get('use_panels', False) %> + <% controller_name = get_controller_name( item ) %> ## Render message. %if message: @@ -127,7 +128,7 @@ %if trans.get_user().username is None or trans.get_user().username is "": <p>To make a ${item_class_name_lc} accessible via link or publish it, you must create a public username:</p> - <form action="${h.url_for( action='set_public_username', id=trans.security.encode_id( item.id ) )}" + <form action="${h.url_for( controller=controller_name, action='set_public_username', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"><label>Public Username:</label> @@ -157,7 +158,7 @@ <blockquote><% - url = h.url_for( action='display_by_username_and_slug', username=trans.get_user().username, slug=item.slug, qualified=True ) + url = h.url_for( controller=controller_name, action='display_by_username_and_slug', username=trans.get_user().username, slug=item.slug, qualified=True ) url_parts = url.split("/") %><a id="item-url" href="${url}" target="_top">${url}</a> @@ -169,29 +170,29 @@ </blockquote> %if item.published: - This ${item_class_name_lc} is publicly listed and searchable in Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section. + This ${item_class_name_lc} is publicly listed and searchable in Galaxy's <a href='${h.url_for( controller=controller_name, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section. %endif </div><p>You can: <div> - <form action="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ) )}" method="POST"> + <form action="${h.url_for( controller=controller_name, action='sharing', id=trans.security.encode_id( item.id ) )}" method="POST"> %if not item.published: ## Item is importable but not published. User can disable importable or publish. <input class="action-button" type="submit" name="disable_link_access" value="Disable Access to ${item_class_name} Link"><div class="toolParamHelp">Disables ${item_class_name_lc}'s link so that it is not accessible.</div><br /><input class="action-button" type="submit" name="publish" value="Publish ${item_class_name}" method="POST"> - <div class="toolParamHelp">Publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div> + <div class="toolParamHelp">Publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( controller=controller_name, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div><br /> %else: ## item.published == True ## Item is importable and published. User can unpublish or disable import and unpublish. <input class="action-button" type="submit" name="unpublish" value="Unpublish ${item_class_name}"> - <div class="toolParamHelp">Removes this ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> + <div class="toolParamHelp">Removes this ${item_class_name_lc} from Galaxy's <a href='${h.url_for(controller=controller_name, action='list_published' )}' target="_top">Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div><br /><input class="action-button" type="submit" name="disable_link_access_and_unpublish" value="Disable Access to ${item_class_name} via Link and Unpublish"> - <div class="toolParamHelp">Disables this ${item_class_name_lc}'s link so that it is not accessible and removes ${item_class_name_lc} from Galaxy's <a href='${h.url_for( action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> + <div class="toolParamHelp">Disables this ${item_class_name_lc}'s link so that it is not accessible and removes ${item_class_name_lc} from Galaxy's <a href='${h.url_for(controller=controller_name, action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section so that it is not publicly listed or searchable.</div> %endif </form></div> @@ -200,13 +201,13 @@ <p>This ${item_class_name_lc} is currently restricted so that only you and the users listed below can access it. You can:</p> - <form action="${h.url_for( action='sharing', id=trans.security.encode_id(item.id) )}" method="POST"> + <form action="${h.url_for(controller=controller_name, action='sharing', id=trans.security.encode_id(item.id) )}" method="POST"><input class="action-button" type="submit" name="make_accessible_via_link" value="Make ${item_class_name} Accessible via Link"><div class="toolParamHelp">Generates a web link that you can share with other people so that they can view and import the ${item_class_name_lc}.</div><br /><input class="action-button" type="submit" name="make_accessible_and_publish" value="Make ${item_class_name} Accessible and Publish" method="POST"> - <div class="toolParamHelp">Makes the ${item_class_name_lc} accessible via link (see above) and publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for( action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div> + <div class="toolParamHelp">Makes the ${item_class_name_lc} accessible via link (see above) and publishes the ${item_class_name_lc} to Galaxy's <a href='${h.url_for(controller=controller_name, action='list_published' )}' target='_top'>Published ${item_class_plural_name}</a> section, where it is publicly listed and searchable.</div></form> %endif @@ -237,7 +238,7 @@ </td><td><div popupmenu="user-${i}-popup"> - <a class="action-button" href="${h.url_for( action='sharing', id=trans.security.encode_id( item.id ), unshare_user=trans.security.encode_id( user.id ), use_panels=use_panels )}">Unshare</a> + <a class="action-button" href="${h.url_for(controller=controller_name, action='sharing', id=trans.security.encode_id( item.id ), unshare_user=trans.security.encode_id( user.id ), use_panels=use_panels )}">Unshare</a></div></td></tr> @@ -246,7 +247,7 @@ <p><a class="action-button" - href="${h.url_for( action='share', id=trans.security.encode_id(item.id), use_panels=use_panels )}"> + href="${h.url_for(controller=controller_name, action='share', id=trans.security.encode_id(item.id), use_panels=use_panels )}"><span>Share with another user</span></a> @@ -255,7 +256,7 @@ <p>You have not shared this ${item_class_name_lc} with any users.</p><a class="action-button" - href="${h.url_for( action='share', id=trans.security.encode_id(item.id), use_panels=use_panels )}"> + href="${h.url_for(controller=controller_name, action='share', id=trans.security.encode_id(item.id), use_panels=use_panels )}"><span>Share with a user</span></a><br /> @@ -266,5 +267,5 @@ %endif <br /><br /> - <a href="${h.url_for( action="list" )}">Back to ${item_class_plural_name} List</a> -</%def> \ No newline at end of file + <a href="${h.url_for(controller=controller_name, action="list" )}">Back to ${item_class_plural_name} List</a> +</%def> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -43,7 +43,7 @@ <p>${n_('You are currently not logged in.')}</p> %endif <ul> - <li><a href="${h.url_for( action='login' )}">${_('Login')}</li> - <li><a href="${h.url_for( action='create', cntrller='user' )}">${_('Register')}</a></li> + <li><a href="${h.url_for( controller='user', action='login' )}">${_('Login')}</li> + <li><a href="${h.url_for( controller='user', action='create', cntrller='user' )}">${_('Register')}</a></li></ul> %endif diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/user/openid_associate.mako --- a/templates/user/openid_associate.mako +++ b/templates/user/openid_associate.mako @@ -59,7 +59,7 @@ %endif <br/> - <% form_action = h.url_for( cntrller=cntrller, use_panels=use_panels ) %> + <% form_action = h.url_for( controller='user', action='openid_associate', cntrller=cntrller, use_panels=use_panels ) %> ${render_login_form( form_action=form_action )} diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -133,7 +133,7 @@ <%def name="center_panel()"><% - center_url = h.url_for( action='center' ) + center_url = h.url_for(controller='admin', action='center' ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/community/category/create_category.mako --- a/templates/webapps/community/category/create_category.mako +++ b/templates/webapps/community/category/create_category.mako @@ -17,7 +17,7 @@ <div class="toolForm"><div class="toolFormTitle">Create Category</div><div class="toolFormBody"> - <form name="create_category_form" id="create_category_form" action="${h.url_for( action='create_category' )}" method="post" > + <form name="create_category_form" id="create_category_form" action="${h.url_for(controller='admin', action='create_category' )}" method="post" ><div class="form-row"><label>Name:</label><input name="name" type="textfield" value="${name | h}" size=40"/> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -60,7 +60,7 @@ <div class="toolForm"><div class="toolFormTitle">Error Report</div><div class="toolFormBody"> - <form name="report_error" action="${h.url_for( action='report_error')}" method="post" > + <form name="report_error" action="${h.url_for(controller='dataset', action='report_error')}" method="post" ><input type="hidden" name="id" value="${hda.id}" /><div class="form-row"><label>Your email</label> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/history/permissions.mako --- a/templates/webapps/galaxy/history/permissions.mako +++ b/templates/webapps/galaxy/history/permissions.mako @@ -4,5 +4,5 @@ %if trans.user: <% history = trans.get_history() %> - ${render_permission_form( history, history.name, h.url_for(), trans.user.all_roles() )} + ${render_permission_form( history, history.name, h.url_for(controller='root'), trans.user.all_roles() )} %endif diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/history/share.mako --- a/templates/webapps/galaxy/history/share.mako +++ b/templates/webapps/galaxy/history/share.mako @@ -7,7 +7,7 @@ <div class="toolFormBody"> %if not can_change and not cannot_change and not no_change_needed: ## We are sharing histories that contain only public datasets - <form name='share' id='share' action="${h.url_for( action='share' )}" method="post" > + <form name='share' id='share' action="${h.url_for( controller='history', action='share' )}" method="post" ><div class="form-title-row"><b>Histories to be shared:</b></div><div class="form-row" style="padding-left: 2em;"><table width="100%"> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -94,13 +94,13 @@ ## Render view of history. <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> %if not history.purged: - <a href="${h.url_for( action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | + <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | <a href="${get_history_link( history )}">${_('refresh')}</a> | %endif %if show_deleted: - <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | + <a href="${h.url_for(controller='history', id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | %else: - <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | + <a href="${h.url_for(controller='history', id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | %endif <a href="#" class="toggle">collapse all</a></div> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/mobile/dataset/detail.mako --- a/templates/webapps/galaxy/mobile/dataset/detail.mako +++ b/templates/webapps/galaxy/mobile/dataset/detail.mako @@ -20,7 +20,7 @@ </div> %if dataset.state == "ok": <div class="row"> - <a href="${h.url_for( action='dataset_peek', id=dataset.id )}">Peek</a> + <a href="${h.url_for(controller='mobile', action='dataset_peek', id=dataset.id )}">Peek</a></div> %endif </fieldset> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/mobile/history/detail.mako --- a/templates/webapps/galaxy/mobile/history/detail.mako +++ b/templates/webapps/galaxy/mobile/history/detail.mako @@ -30,7 +30,7 @@ %endif </div> - <a href="${h.url_for( action="dataset_detail", id=data.id )}"> + <a href="${h.url_for(controller='mobile', action="dataset_detail", id=data.id )}"><div>${data.hid}: ${data.display_name()}</div> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/mobile/history/list.mako --- a/templates/webapps/galaxy/mobile/history/list.mako +++ b/templates/webapps/galaxy/mobile/history/list.mako @@ -19,7 +19,7 @@ <li> - <a href="${h.url_for( action="history_detail", id=history.id )}"> + <a href="${h.url_for(controller='mobile', action="history_detail", id=history.id )}"> ${history.name} <div class="secondary">${h.date.distance_of_time_in_words( history.update_time, h.date.datetime.utcnow() )} ago</div> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/mobile/index.mako --- a/templates/webapps/galaxy/mobile/index.mako +++ b/templates/webapps/galaxy/mobile/index.mako @@ -30,7 +30,7 @@ <script type="text/javascript" src="${h.url_for('/static/scripts/libs/jquery/jqtouch.js')}"></script><script type="text/javascript" charset="utf-8"> $(document).jQTouch( { - icon: "${h.url_for('static/images/galaxyIcon_noText.png')}", + icon: "${h.url_for('/static/images/galaxyIcon_noText.png')}", slideInSelector: 'ul li a, .row a, a.async' }); </script> @@ -41,12 +41,12 @@ <div id="home" selected="true"><div class="toolbar"><h1><span class="logo">Galaxy</span></h1> - <a class="button async" href="${h.url_for( action='settings' )}">Settings</a> + <a class="button async" href="${h.url_for(controller='mobile', action='settings' )}">Settings</a></div><ul class="edgetoedge"> - <li><a href="${h.url_for( action='history_list' )}">Histories</a></li> + <li><a href="${h.url_for(controller='mobile', action='history_list' )}">Histories</a></li></ul></div></body> -</html> \ No newline at end of file +</html> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/mobile/settings.mako --- a/templates/webapps/galaxy/mobile/settings.mako +++ b/templates/webapps/galaxy/mobile/settings.mako @@ -1,4 +1,4 @@ -<form id="settings" class="panel" action="${h.url_for( action='settings' )}" method="post"> +<form id="settings" class="panel" action="${h.url_for(controller='mobile', action='settings' )}" method="post"><div class="toolbar"><h1>Settings</h1> @@ -31,4 +31,4 @@ <div>${message}</div> %endif </div> -</form> \ No newline at end of file +</form> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/page/editor.mako --- a/templates/webapps/galaxy/page/editor.mako +++ b/templates/webapps/galaxy/page/editor.mako @@ -114,7 +114,7 @@ // Build ajax URL that lists items for selection. var item_list_action = "list_" + item_plural.toLowerCase() + "_for_selection"; - var url_template = "${h.url_for( action='LIST_ACTION' )}"; + var url_template = "${h.url_for(controller='page', action='LIST_ACTION' )}"; var ajax_url = url_template.replace( "LIST_ACTION", item_list_action ); // Set up and return dict. @@ -522,7 +522,7 @@ if ( dialogType == Galaxy.DIALOG_ANNOTATE_HISTORY ) { $.ajax( { - url: "${h.url_for( action='list_histories_for_selection' )}", + url: "${h.url_for(controller='page', action='list_histories_for_selection' )}", data: {}, error: function() { alert( "Grid refresh failed" ) }, success: function(table_html) @@ -541,7 +541,7 @@ // Get annotation table for history. $.ajax( { - url: "${h.url_for( action='get_history_annotation_table' )}", + url: "${h.url_for(controller='page', action='get_history_annotation_table' )}", data: { id : item_id }, error: function() { alert( "Grid refresh failed" ) }, success: function(result) @@ -638,7 +638,7 @@ // Do save. $.ajax( { - url: "${h.url_for( action='save' )}", + url: "${h.url_for(controller='page', action='save' )}", type: "POST", data: { id: "${trans.security.encode_id(page.id)}", diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/page/index.mako --- a/templates/webapps/galaxy/page/index.mako +++ b/templates/webapps/galaxy/page/index.mako @@ -29,12 +29,12 @@ <% page = association.page %><tr><td> - <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title}</a> + <a class="menubutton" id="shared-${i}-popup" href="${h.url_for(controller='page', action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}">${page.title}</a></td><td>${page.user.username}</td><td><div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}" target="_top">View</a> + <a class="action-button" href="${h.url_for(controller='page', action='display_by_username_and_slug', username=page.user.username, slug=page.slug)}" target="_top">View</a></div></td></tr> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/root/alternate_history.mako --- a/templates/webapps/galaxy/root/alternate_history.mako +++ b/templates/webapps/galaxy/root/alternate_history.mako @@ -95,11 +95,11 @@ url_dict = { ##TODO: into their own MVs - 'rename' : h.url_for( controller="/history", action="rename_async", + 'rename' : h.url_for( controller="history", action="rename_async", id=encoded_id_template ), 'tag' : h.url_for( controller='tag', action='get_tagging_elt_async', item_class=history_class_name, item_id=encoded_id_template ), - 'annotate' : h.url_for( controller="/history", action="annotate_async", + 'annotate' : h.url_for( controller="history", action="annotate_async", id=encoded_id_template ) } %> @@ -148,9 +148,9 @@ 'delete' : h.url_for( controller='dataset', action='delete_async', dataset_id=encoded_id_template ), # ................................................................ download links (and associated meta files), - 'download' : h.url_for( controller='/dataset', action='display', + 'download' : h.url_for( controller='dataset', action='display', dataset_id=encoded_id_template, to_ext=hda_ext_template ), - 'meta_download' : h.url_for( controller='/dataset', action='get_metadata_file', + 'meta_download' : h.url_for( controller='dataset', action='get_metadata_file', hda_id=encoded_id_template, metadata_name=meta_type_template ), # ................................................................ primary actions (errors, params, rerun), @@ -160,7 +160,7 @@ dataset_id=encoded_id_template ), 'rerun' : h.url_for( controller='tool_runner', action='rerun', id=encoded_id_template ), - 'visualization' : h.url_for( controller='visualization' ), + 'visualization' : h.url_for( controller='visualization', action='index' ), # ................................................................ secondary actions (tagging, annotation), 'tags' : { diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -98,7 +98,7 @@ annotation_area.find(".tooltip").tooltip({ placement : 'bottom' }); async_save_text( annotation_elt.attr("id"), annotation_elt.attr("id"), - "${h.url_for( controller='/dataset', action='annotate_async')}?" + href_parms, + "${h.url_for( controller='dataset', action='annotate_async')}?" + href_parms, "new_annotation", 18, true, 4); annotation_area.slideDown("fast"); } @@ -594,7 +594,7 @@ <div id="top-links" class="historyLinks"> - <a title="${_('refresh')}" class="icon-button arrow-circle tooltip" href="${h.url_for('history', show_deleted=show_deleted)}"></a> + <a title="${_('refresh')}" class="icon-button arrow-circle tooltip" href="${h.url_for(controller='history', show_deleted=show_deleted)}"></a><a title='${_('collapse all')}' class='icon-button toggle tooltip' href='#' style="display: none"></a> %if trans.get_user(): @@ -609,13 +609,13 @@ %if show_deleted: <div class="historyLinks"> - <a href="${h.url_for('history', show_deleted=False)}">${_('hide deleted')}</a> + <a href="${h.url_for(controller='history', show_deleted=False)}">${_('hide deleted')}</a></div> %endif %if show_hidden: <div class="historyLinks"> - <a href="${h.url_for('history', show_hidden=False)}">${_('hide hidden')}</a> + <a href="${h.url_for(controller='history', show_hidden=False)}">${_('hide hidden')}</a></div> %endif diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/tracks/browser.mako --- a/templates/webapps/galaxy/tracks/browser.mako +++ b/templates/webapps/galaxy/tracks/browser.mako @@ -96,7 +96,7 @@ hide_modal(); }; $.ajax({ - url: "${h.url_for( action='new_browser', default_dbkey=default_dbkey )}", + url: "${h.url_for( controller='visualization', action='new_browser', default_dbkey=default_dbkey )}", data: {}, error: function() { alert( "Couldn't create new browser" ) }, success: function(form_html) { diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/tracks/history_select_grid.mako --- a/templates/webapps/galaxy/tracks/history_select_grid.mako +++ b/templates/webapps/galaxy/tracks/history_select_grid.mako @@ -76,8 +76,8 @@ if cur_filter_dict: dbkey = cur_filter_dict.get( 'dbkey', '?' ) %> - <a class="addtracktab${histories_active}" href="${h.url_for( action='list_histories')}?f-dbkey=${dbkey}">Histories</a> - <a class="addtracktab${data_libraries_active}" href="${h.url_for( action='list_libraries' )}">Data Libraries</a> + <a class="addtracktab${histories_active}" href="${h.url_for(controller='visualization', action='list_histories')}?f-dbkey=${dbkey}">Histories</a> + <a class="addtracktab${data_libraries_active}" href="${h.url_for(controller='visualization', action='list_libraries' )}">Data Libraries</a><div class="divider"></div></%def> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/visualization/circster.mako --- a/templates/webapps/galaxy/visualization/circster.mako +++ b/templates/webapps/galaxy/visualization/circster.mako @@ -70,7 +70,7 @@ show_modal("Saving...", "progress"); $.ajax({ - url: "${h.url_for( action='save' )}", + url: "${h.url_for( controller='visualization', action='save' )}", type: "POST", data: { 'id': view.vis_id, diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/visualization/list.mako --- a/templates/webapps/galaxy/visualization/list.mako +++ b/templates/webapps/galaxy/visualization/list.mako @@ -42,13 +42,13 @@ <% visualization = association.visualization %><tr><td> - <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}">${visualization.title}</a> + <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( controller='visualization', action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}">${visualization.title}</a></td><td>${visualization.user.username}</td><td><div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> - <a class="action-button" href="${h.url_for( action='copy', id=trans.security.encode_id(visualization.id) )}">Copy</a> + <a class="action-button" href="${h.url_for( controller='visualization', action='display_by_username_and_slug', username=visualization.user.username, slug=visualization.slug)}" target="_top">View</a> + <a class="action-button" href="${h.url_for( controller='visualization', action='copy', id=trans.security.encode_id(visualization.id) )}">Copy</a></div></td></tr> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/visualization/scatterplot.mako --- a/templates/webapps/galaxy/visualization/scatterplot.mako +++ b/templates/webapps/galaxy/visualization/scatterplot.mako @@ -238,7 +238,7 @@ var settingsForm = new ScatterplotControlForm({ dataset : hda, - apiDatasetsURL : "${h.url_for( controller='/api/datasets' )}", + apiDatasetsURL : "${h.url_for( controller='/api/datasets', action='index' )}", el : $( '#scatterplot' ), chartConfig : chartConfig }).render(); diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/build_from_current_history.mako --- a/templates/webapps/galaxy/workflow/build_from_current_history.mako +++ b/templates/webapps/galaxy/workflow/build_from_current_history.mako @@ -76,7 +76,7 @@ <div class="warningmark">${warning}</div> %endfor -<form method="post" action="${h.url_for()}"> +<form method="post" action="${h.url_for(controller='workflow', action='build_from_current_history')}"><div class='form-row'><label>${_('Workflow name')}</label><input name="workflow_name" type="text" value="Workflow constructed from history '${ util.unicodify( history.name )}'" size="60"/> @@ -149,4 +149,4 @@ </table> -</form> \ No newline at end of file +</form> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/configure_menu.mako --- a/templates/webapps/galaxy/workflow/configure_menu.mako +++ b/templates/webapps/galaxy/workflow/configure_menu.mako @@ -15,7 +15,7 @@ </div> %endif -<form action="${h.url_for()}" method="POST"> +<form action="${h.url_for(controller='workflow', action='configure_menu')}" method="POST"><table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"><tr class="header"> @@ -74,4 +74,4 @@ <p /><input type="Submit" /> -</form> \ No newline at end of file +</form> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/edit_attributes.mako --- a/templates/webapps/galaxy/workflow/edit_attributes.mako +++ b/templates/webapps/galaxy/workflow/edit_attributes.mako @@ -20,7 +20,7 @@ <div class="toolForm"><div class="toolFormTitle">${_('Edit Workflow Attributes')}</div><div class="toolFormBody"> - <form name="edit_attributes" action="${h.url_for( action='edit_attributes' )}" method="post"> + <form name="edit_attributes" action="${h.url_for(controller='workflow', action='edit_attributes' )}" method="post"><input type="hidden" name="id" value="${trans.security.encode_id( stored.id )}"/><div class="form-row"><label> @@ -63,4 +63,4 @@ </form></div></div> -</%def> \ No newline at end of file +</%def> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -135,14 +135,14 @@ reset(); // Load the datatype info $.ajax( { - url: "${h.url_for( action='get_datatypes' )}", + url: "${h.url_for( controller='workflow', action='get_datatypes' )}", dataType: "json", cache: false, success: function( data ) { populate_datatype_info( data ); // Load workflow definition $.ajax( { - url: "${h.url_for( action='load_workflow' )}", + url: "${h.url_for( controller='workflow', action='load_workflow' )}", data: { id: "${trans.security.encode_id( stored.id )}", "_": "true" }, dataType: 'json', cache: false, @@ -333,7 +333,7 @@ }); // Rename async. - async_save_text("workflow-name", "workflow-name", "${h.url_for( action='rename_async', id=trans.security.encode_id(stored.id) )}", "new_name"); + async_save_text("workflow-name", "workflow-name", "${h.url_for( controller='workflow', action='rename_async', id=trans.security.encode_id(stored.id) )}", "new_name"); // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging. $('#workflow-tag').click( function() { @@ -341,7 +341,7 @@ return false; }); // Annotate async. - async_save_text("workflow-annotation", "workflow-annotation", "${h.url_for( action='annotate_async', id=trans.security.encode_id(stored.id) )}", "new_annotation", 25, true, 4); + async_save_text("workflow-annotation", "workflow-annotation", "${h.url_for( controller='workflow', action='annotate_async', id=trans.security.encode_id(stored.id) )}", "new_annotation", 25, true, 4); }); // Global state for the whole workflow @@ -377,7 +377,7 @@ canvas_manager.draw_overview(); workflow.activate_node( node ); $.ajax( { - url: "${h.url_for( action='get_new_module_info' )}", + url: "${h.url_for(controller='workflow', action='get_new_module_info' )}", data: { type: "tool", tool_id: id, "_": "true" }, global: false, dataType: "json", @@ -401,7 +401,7 @@ canvas_manager.draw_overview(); workflow.activate_node( node ); $.ajax( { - url: "${h.url_for( action='get_new_module_info' )}", + url: "${h.url_for(controller='workflow', action='get_new_module_info' )}", data: { type: type, "_": "true" }, dataType: "json", success: function( data ) { @@ -624,7 +624,7 @@ workflow.rectify_workflow_outputs(); var savefn = function(callback) { $.ajax( { - url: "${h.url_for( action='save_workflow' )}", + url: "${h.url_for(controller='workflow', action='save_workflow' )}", type: "POST", data: { id: "${trans.security.encode_id( stored.id )}", diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/editor_generic_form.mako --- a/templates/webapps/galaxy/workflow/editor_generic_form.mako +++ b/templates/webapps/galaxy/workflow/editor_generic_form.mako @@ -1,4 +1,4 @@ -<form name="${form.name}" action="${h.url_for( action='editor_form_post' )}" method="post"> +<form name="${form.name}" action="${h.url_for( controller='workflow', action='editor_form_post' )}" method="post"><div class="toolForm"><div class="toolFormTitle">${form.title}</div><div class="toolFormBody"> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/editor_tool_form.mako --- a/templates/webapps/galaxy/workflow/editor_tool_form.mako +++ b/templates/webapps/galaxy/workflow/editor_tool_form.mako @@ -94,7 +94,7 @@ </div></%def> -<form method="post" action="${h.url_for( action='editor_form_post' )}"> +<form method="post" action="${h.url_for(controller='workflow', action='editor_form_post' )}"><div class="toolForm"><div class="toolFormTitle">Tool: ${tool.name}</div> @@ -113,4 +113,4 @@ </div> -</form> \ No newline at end of file +</form> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/export.mako --- a/templates/webapps/galaxy/workflow/export.mako +++ b/templates/webapps/galaxy/workflow/export.mako @@ -25,7 +25,7 @@ <h3>Export to myExperiment</h3><div class="toolForm"> - <form action="${h.url_for( action='export_to_myexp', id=trans.security.encode_id( item.id ) )}" + <form action="${h.url_for(controller='workflow', action='export_to_myexp', id=trans.security.encode_id( item.id ) )}" method="POST"><div class="form-row"><label>myExperiment username:</label> @@ -49,7 +49,7 @@ ## Add link to render as SVG image. <h3>Create Image</h3> - <a href="${h.url_for( action='gen_image', id=trans.security.encode_id( item.id ) )}"> + <a href="${h.url_for(controller='workflow', action='gen_image', id=trans.security.encode_id( item.id ) )}"> Create image of ${get_class_display_name( item.__class__ ).lower()} in SVG format </a></%def> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/list.mako --- a/templates/webapps/galaxy/workflow/list.mako +++ b/templates/webapps/galaxy/workflow/list.mako @@ -31,7 +31,7 @@ <ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( action='create' )}"> + <a class="action-button" href="${h.url_for( controller='workflow', action='create' )}"><img src="${h.url_for('/static/images/silk/add.png')}" /><span>Create new workflow</span></a> @@ -94,7 +94,7 @@ <% workflow = association.stored_workflow %><tr><td> - <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name )}</a> + <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name )}</a></td><td>${workflow.user.email}</td><td>${len(workflow.latest_workflow.steps)}</td> @@ -115,7 +115,7 @@ <h2>Other options</h2> - <a class="action-button" href="${h.url_for( action='configure_menu' )}"> + <a class="action-button" href="${h.url_for( controller='workflow', action='configure_menu' )}"><span>Configure your workflow menu</span></a></div> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/list_for_run.mako --- a/templates/webapps/galaxy/workflow/list_for_run.mako +++ b/templates/webapps/galaxy/workflow/list_for_run.mako @@ -19,7 +19,7 @@ <ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller="workflow", action='index' )}" target="_parent"> + <a class="action-button" href="${h.url_for( controller='workflow', action='index' )}" target="_parent"><span>Switch to workflow management view</span></a></li> @@ -36,7 +36,7 @@ %for i, workflow in enumerate( workflows ): <tr><td> - <a href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name )}</a> + <a href="${h.url_for(controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name )}</a><a id="wf-${i}-popup" class="popup-arrow" style="display: none;">▼</a></td><td>${len(workflow.latest_workflow.steps)}</td> @@ -64,7 +64,7 @@ <% workflow = association.stored_workflow %><tr><td> - <a href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a><a id="shared-${i}-popup" class="popup-arrow" style="display: none;">▼</a></td><td>${workflow.user.email}</td> @@ -76,4 +76,4 @@ No workflows have been shared with you. -%endif \ No newline at end of file +%endif diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/rename.mako --- a/templates/webapps/galaxy/workflow/rename.mako +++ b/templates/webapps/galaxy/workflow/rename.mako @@ -17,7 +17,7 @@ <div class="toolForm"><div class="toolFormTitle">Rename workflow '${stored.name}'</div><div class="toolFormBody"> - <form action="${h.url_for( action='rename', id=trans.security.encode_id(stored.id) )}" method="POST"> + <form action="${h.url_for(controller='workflow', action='rename', id=trans.security.encode_id(stored.id) )}" method="POST"><div class="form-row"><label> New name @@ -33,4 +33,4 @@ </form></div></div> -</div> \ No newline at end of file +</div> diff -r ddc3b1579121233cec5b4c6717d43c97ddc040bc -r 7db12eb10dbb5f1857f27cab4cdefd7e86b892e1 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -463,7 +463,7 @@ %endfor %if missing_tools: <div class='errormessage'> - <strong>This workflow utilizes tools which are unavailable, and cannot be run. Enable the tools listed below, or <a href="${h.url_for( action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">edit the workflow</a> to correct these errors.</strong><br/> + <strong>This workflow utilizes tools which are unavailable, and cannot be run. Enable the tools listed below, or <a href="${h.url_for(controller='workflow', action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">edit the workflow</a> to correct these errors.</strong><br/><ul> %for i, tool in enumerate( missing_tools ): <li>${tool}</li> 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: dannon: Allow dynamic_options to use $__user_email__ as a filter_value. This would enable tools to use dynamic options defined in a file listing user_specific options for a tool (file paths, etc).
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ddc3b1579121/ changeset: ddc3b1579121 user: dannon date: 2013-02-06 03:11:32 summary: Allow dynamic_options to use $__user_email__ as a filter_value. This would enable tools to use dynamic options defined in a file listing user_specific options for a tool (file paths, etc). affected #: 1 file diff -r 6ff0b52b5850733ed05c06790b351a2bdf66de48 -r ddc3b1579121233cec5b4c6717d43c97ddc040bc lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -53,8 +53,14 @@ self.keep = string_as_bool( elem.get( "keep", 'True' ) ) def filter_options( self, options, trans, other_values ): rval = [] + filter_value = self.value + try: + if trans.user.email: + filter_value = filter_value.replace('$__user_email__',trans.user.email) + except: + pass for fields in options: - if ( self.keep and fields[self.column] == self.value ) or ( not self.keep and fields[self.column] != self.value ): + if ( self.keep and fields[self.column] == filter_value ) or ( not self.keep and fields[self.column] != filter_value ): rval.append( fields ) return rval 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: inithello: Bugfixes for tool shed functional test scripts.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6ff0b52b5850/ changeset: 6ff0b52b5850 user: inithello date: 2013-02-05 22:05:33 summary: Bugfixes for tool shed functional test scripts. affected #: 3 files diff -r 2b6800bbce751d434c9b22783a47de0ce522e355 -r 6ff0b52b5850733ed05c06790b351a2bdf66de48 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -127,6 +127,7 @@ def test_0065_verify_filtering_repository( self ): '''Verify the new tool versions and repository metadata.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) tip = self.get_repository_tip( repository ) self.check_for_valid_tools( repository ) strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' ) diff -r 2b6800bbce751d434c9b22783a47de0ce522e355 -r 6ff0b52b5850733ed05c06790b351a2bdf66de48 test/tool_shed/functional/test_0100_complex_repository_dependencies.py --- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py +++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py @@ -39,7 +39,7 @@ strings_displayed=[] ) self.upload_file( repository, 'bwa/complex/tool_dependencies.xml', - strings_displayed=[], + strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ], commit_message='Uploaded tool_dependencies.xml.' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) def test_0010_create_bwa_base_repository( self ): @@ -148,17 +148,23 @@ commit_message='Uploaded valid complex dependency on bwa_tool_0100.' ) self.check_repository_dependency( base_repository, tool_repository ) self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] ) - def test_0040_update_base_repository( self ): - '''Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset.''' + def test_0040_generate_tool_dependency( self ): + '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.''' base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) + old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) + new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) + xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) + # Generate a tool_dependencies.xml file that points to an arbitrary file in the local filesystem. + file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) + .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, - 'bwa/complex/readme/tool_dependencies.xml', + xml_filename, + filepath=new_tool_dependency_path, strings_displayed=[], commit_message='Uploaded new tool_dependencies.xml.' ) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. self.display_manage_repository_page( base_repository, strings_displayed=[ self.get_repository_tip( tool_repository ), 'bwa', '0.5.9', 'package' ], strings_not_displayed=[ previous_changeset ] ) - diff -r 2b6800bbce751d434c9b22783a47de0ce522e355 -r 6ff0b52b5850733ed05c06790b351a2bdf66de48 test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -1,7 +1,6 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util -import logging -log = logging.getLogger(__name__) + bwa_base_repository_name = 'bwa_base_repository_0100' bwa_base_repository_description = "BWA Base" bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at bwa_tool_repository_0100" @@ -45,7 +44,6 @@ old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'tool_dependencies.xml' ) ) new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) - log.debug( xml_filename ) file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( repository, @@ -182,7 +180,6 @@ old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] ) xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) ) - log.debug( xml_filename ) file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' ) .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) ) self.upload_file( tool_repository, 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: jgoecks: Add 'log' level for stdio inspection.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b6800bbce75/ changeset: 2b6800bbce75 user: jgoecks date: 2013-02-05 20:28:28 summary: Add 'log' level for stdio inspection. affected #: 1 file diff -r 2b7503087b4c2520bd6d7639d07933f960281792 -r 2b6800bbce751d434c9b22783a47de0ce522e355 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -49,10 +49,16 @@ # that warning < fatal. This is really meant to just be an enum. class StdioErrorLevel( object ): NO_ERROR = 0 - WARNING = 1 - FATAL = 2 - MAX = 2 - descs = {NO_ERROR : 'No error', WARNING : 'Warning', FATAL : 'Fatal error'} + LOG = 1 + WARNING = 2 + FATAL = 3 + MAX = 3 + descs = { + NO_ERROR : 'No error', + LOG: 'Log', + WARNING : 'Warning', + FATAL : 'Fatal error' + } @staticmethod def desc( error_level ): err_msg = "Unknown error" @@ -1377,19 +1383,15 @@ # TODO: This method doesn't have to be part of the Tool class. def parse_error_level( self, err_level ): """ - Return fatal or warning depending on what's in the error level. - This will assume that the error level fatal is returned if it's - unparsable. + Parses error level and returns error level enumeration. If + unparsable, returns 'fatal' """ - # What should the default be? I'm claiming it should be fatal: - # if you went to the trouble to write the rule, then it's - # probably a problem. I think there are easily three substantial - # camps: make it fatal, make it a warning, or, if it's missing, - # just throw an exception and ignore the exit_code element. return_level = StdioErrorLevel.FATAL try: - if ( None != err_level ): - if ( re.search( "warning", err_level, re.IGNORECASE ) ): + if err_level: + if ( re.search( "log", err_level, re.IGNORECASE ) ): + return_level = StdioErrorLevel.LOG + elif ( re.search( "warning", err_level, re.IGNORECASE ) ): return_level = StdioErrorLevel.WARNING elif ( re.search( "fatal", err_level, re.IGNORECASE ) ): return_level = StdioErrorLevel.FATAL 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: jgoecks: Tool stdout/err checking: (a) add tool id to error message and (b) add support for specifying 'both' as an alias for searching both stdout and stderr, which matches the documentation.
by Bitbucket 05 Feb '13

05 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b7503087b4c/ changeset: 2b7503087b4c user: jgoecks date: 2013-02-05 18:36:59 summary: Tool stdout/err checking: (a) add tool id to error message and (b) add support for specifying 'both' as an alias for searching both stdout and stderr, which matches the documentation. affected #: 1 file diff -r 7b96c5b684d1dbf142a7f9caf7dce76c217d9e09 -r 2b7503087b4c2520bd6d7639d07933f960281792 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1086,7 +1086,7 @@ else: self.trackster_conf = None def parse_inputs( self, root ): - r""" + """ Parse the "<inputs>" element and create appropriate `ToolParameter`s. This implementation supports multiple pages and grouping constructs. """ @@ -1352,14 +1352,17 @@ # and anything to do with "err". If neither stdout nor # stderr were specified, then raise a warning and scan both. for src in src_list: + if re.search( "both", src, re.IGNORECASE ): + regex.stdout_match = True + regex.stderr_match = True if re.search( "out", src, re.IGNORECASE ): regex.stdout_match = True if re.search( "err", src, re.IGNORECASE ): regex.stderr_match = True if (not regex.stdout_match and not regex.stderr_match): - log.warning( "Unable to determine if tool stream " - + "source scanning is output, error, " - + "or both. Defaulting to use both." ) + log.warning( "Tool id %s: unable to determine if tool " + "stream source scanning is output, error, " + "or both. Defaulting to use both." % self.id ) regex.stdout_match = True regex.stderr_match = True self.stdio_regexes.append( regex ) 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: james_taylor: eggs: Update Paste and PasteDeploy
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b96c5b684d1/ changeset: 7b96c5b684d1 user: james_taylor date: 2013-02-05 05:30:32 summary: eggs: Update Paste and PasteDeploy affected #: 1 file diff -r 3720c0455a436c9812d8ccb8577fd042c59b2048 -r 7b96c5b684d1dbf142a7f9caf7dce76c217d9e09 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -46,8 +46,8 @@ nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 -Paste = 1.6 -PasteDeploy = 1.3.3 +Paste = 1.7.5.1 +PasteDeploy = 1.5.0 pexpect = 2.4 python_openid = 2.2.5 python_daemon = 1.5.5 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: james_taylor: logging: If sentry is configured attach to the root logger no matter how logging was originally configured
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3720c0455a43/ changeset: 3720c0455a43 user: james_taylor date: 2013-02-05 00:07:04 summary: logging: If sentry is configured attach to the root logger no matter how logging was originally configured affected #: 1 file diff -r 0856c4a75c92c56f54028f72502ce0ceb55b2e11 -r 3720c0455a436c9812d8ccb8577fd042c59b2048 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -401,36 +401,34 @@ """ Allow some basic logging configuration to be read from ini file. """ - # PasteScript will have already configured the logger if the appropriate - # sections were found in the config file, so we do nothing if the - # config has a loggers section, otherwise we do some simple setup - # using the 'log_*' values from the config. - if config.global_conf_parser.has_section( "loggers" ): - return - format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) - level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] - destination = config.get( "log_destination", "stdout" ) - log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) # Get root logger root = logging.getLogger() - # Set level - root.setLevel( level ) - # Turn down paste httpserver logging - if level <= logging.DEBUG: - logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) - # Remove old handlers - for h in root.handlers[:]: - root.removeHandler(h) - # Create handler - if destination == "stdout": - handler = logging.StreamHandler( sys.stdout ) - else: - handler = logging.FileHandler( destination ) - # Create formatter - formatter = logging.Formatter( format ) - # Hook everything up - handler.setFormatter( formatter ) - root.addHandler( handler ) + # PasteScript will have already configured the logger if the + # 'loggers' section was found in the config file, otherwise we do + # some simple setup using the 'log_*' values from the config. + if not config.global_conf_parser.has_section( "loggers" ): + format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) + level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] + destination = config.get( "log_destination", "stdout" ) + log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) + # Set level + root.setLevel( level ) + # Turn down paste httpserver logging + if level <= logging.DEBUG: + logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) + # Remove old handlers + for h in root.handlers[:]: + root.removeHandler(h) + # Create handler + if destination == "stdout": + handler = logging.StreamHandler( sys.stdout ) + else: + handler = logging.FileHandler( destination ) + # Create formatter + formatter = logging.Formatter( format ) + # Hook everything up + handler.setFormatter( formatter ) + root.addHandler( handler ) # If sentry is configured, also log to it if config.sentry_dsn: pkg_resources.require( "raven" ) 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: greg: Uncomment temporary file cleanup block in tool shed functiona tests.
by Bitbucket 04 Feb '13

04 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0856c4a75c92/ changeset: 0856c4a75c92 user: greg date: 2013-02-04 21:22:53 summary: Uncomment temporary file cleanup block in tool shed functiona tests. affected #: 1 file diff -r b6be9c3a2d2df94f4d5236184a4392ec00961743 -r 0856c4a75c92c56f54028f72502ce0ceb55b2e11 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -392,18 +392,18 @@ galaxyapp.shutdown() galaxyapp = None log.info( "Embedded galaxy application stopped" ) -# if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: -# try: -# for dir in [ tool_shed_test_tmp_dir ]: -# if os.path.exists( dir ): -# log.info( "Cleaning up temporary files in %s" % dir ) -# shutil.rmtree( dir ) -# except: -# pass -# if success: -# return 0 -# else: -# return 1 + if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ: + try: + for dir in [ tool_shed_test_tmp_dir ]: + if os.path.exists( dir ): + log.info( "Cleaning up temporary files in %s" % dir ) + shutil.rmtree( dir ) + except: + pass + if success: + return 0 + else: + return 1 if __name__ == "__main__": sys.exit( main() ) 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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