- galaxy-dev - lists.galaxyproject.org

Links in help
by Pieter Neerincx 29 Jul '09

29 Jul '09

Hi, After Googling and browsing the tool config files for some time I found the syntax for adding a link to the help section... To make a future lookup a bit faster: could this please be added to http://g2.trac.bx.psu.edu/wiki/ToolConfigSyntax on the Wiki? Thanks, Pi ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

2 1

[hg] galaxy 2506: Allow the upload of PDF files to libraries via...
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ae750790079a changeset: 2506:ae750790079a user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jul 27 11:33:12 2009 -0400 description: Allow the upload of PDF files to libraries via the admin interface. A more generic method of determining binary files' type and whether they are allowed to be uploaded via the various upload methods should be created. 1 file(s) affected in this change: lib/galaxy/web/controllers/library_dataset.py diffs (29 lines): diff -r 5a92b5877cf7 -r ae750790079a lib/galaxy/web/controllers/library_dataset.py --- a/lib/galaxy/web/controllers/library_dataset.py Mon Jul 27 10:46:25 2009 -0400 +++ b/lib/galaxy/web/controllers/library_dataset.py Mon Jul 27 11:33:12 2009 -0400 @@ -73,12 +73,19 @@ ext = name.split( "." )[1].strip().lower() except: ext = '' - if not( ext == 'ab1' or ext == 'scf' ): - raise BadFileException( "you attempted to upload an inappropriate file." ) - if ext == 'ab1' and file_format != 'ab1': - raise BadFileException( "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files." ) - elif ext == 'scf' and file_format != 'scf': - raise BadFileException( "you must manually set the 'File Format' to 'Scf' when uploading scf files." ) + try: + is_pdf = open( temp_name ).read( len( '%PDF' ) ) == '%PDF' + except: + is_pdf = False #file failed to open or contents are smaller than pdf header + if is_pdf: + file_format = 'pdf' #allow the upload of PDFs to library via the admin interface. + else: + if not( ext == 'ab1' or ext == 'scf' ): + raise BadFileException( "you attempted to upload an inappropriate file." ) + if ext == 'ab1' and file_format != 'ab1': + raise BadFileException( "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files." ) + elif ext == 'scf' and file_format != 'scf': + raise BadFileException( "you must manually set the 'File Format' to 'Scf' when uploading scf files." ) data_type = 'binary' if not data_type: # We must have a text file

1 0

[hg] galaxy 2508: More secure 'display at' functionality - allow...
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e01bfc281e09 changeset: 2508:e01bfc281e09 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jul 28 14:16:19 2009 -0400 description: More secure 'display at' functionality - allows "private" datasets to be displayed at external sites without making them public. Here's how: 1. Replace the 'display at UCSC <site>' direct link with one back to Galaxy at /dataset/<id>/display_at/ucsc_<site> 2. When the client requests the above path, if the dataset is "private", add a record to the new history_dataset_association_display_at_authorization table. note: DATASET_MANAGE_PERMISSIONS is required for this step. If the user doesn't have appropriate permissions, an error is displayed. note 2: "public" datasets don't get a record since they are already readable by external sites. 3. Send the client a redirect to the appropriate external URL. 4. When the external resource requests the dataset (via /root/display_as), allow access if: a. an associated (by hda id) record exists in the above table AND b. the remote host matches one of the known valid servers for that <site> AND c. it's been no longer than 60 seconds since the record was updated (e.g. the lame host authorization expires after 60 seconds) During the 60 second window, anyone could potentially view the authorized dataset via UCSC, but they'd have to know the ID *and* know that it was just authorized. In the future, it'd be more secure to exchange keys with external sites or similar strategies, but this would require modifications to these external applications. This new method is implemented for UCSC, other display apps will need to be handled as well, but this should be as simple as adding those sites/servers to the list in lib/galaxy/security/__init__.py and modifying the link generation in the display app. 9 file(s) affected in this change: lib/galaxy/app.py lib/galaxy/datatypes/genetics.py lib/galaxy/datatypes/interval.py lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py lib/galaxy/security/__init__.py lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/root.py diffs (295 lines): diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/app.py --- a/lib/galaxy/app.py Mon Jul 27 15:55:32 2009 -0400 +++ b/lib/galaxy/app.py Tue Jul 28 14:16:19 2009 -0400 @@ -41,6 +41,7 @@ self.datatypes_registry.load_datatype_indexers( self.toolbox ) #Load security policy self.security_agent = self.model.security_agent + self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions ) # Heartbeat and memdump for thread / heap profiling self.heartbeat = None self.memdump = None diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon Jul 27 15:55:32 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Tue Jul 28 14:16:19 2009 -0400 @@ -86,9 +86,10 @@ sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) sl.append("&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess") sl.append("&hgGenome_columnLabels=first%20row&hgGenome_maxVal=&hgGenome_labelVals=") - sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=") - s = ''.join(sl) - link = "%s%s%s" % (s, display_url, ggtail ) + sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%%s") + sl.append(ggtail) + s = urllib.quote_plus( ''.join(sl) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, s, display_url ) ret_val.append( (site_name, link) ) return ret_val diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Mon Jul 27 15:55:32 2009 -0400 +++ b/lib/galaxy/datatypes/interval.py Tue Jul 28 14:16:19 2009 -0400 @@ -233,10 +233,12 @@ # if our URL scheme is https. Making this work # requires additional hackery in your upstream proxy. # If UCSC ever supports https, remove this hack. + internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) if base_url.startswith( 'https://' ): base_url = base_url.replace( 'https', 'http', 1 ) - display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type) ) - link = "%sdb=%s&position=%s:%s-%s&hgt.customText=%s" % (site_url, dataset.dbkey, chrom, start, stop, display_url ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) + redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) ret_val.append( (site_name, link) ) return ret_val @@ -892,8 +894,12 @@ stop = viewport_tuple[2] for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: - display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type) ) - link = "%sdb=%s&position=%s:%s-%s&hgt.customText=%s" % (site_url, dataset.dbkey, chrom, start, stop, display_url ) + internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) + redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) ret_val.append( (site_name, link) ) return ret_val def sniff( self, filename ): diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Jul 27 15:55:32 2009 -0400 +++ b/lib/galaxy/model/__init__.py Tue Jul 28 14:16:19 2009 -0400 @@ -689,6 +689,12 @@ if not metadata_safe or not assoc.metadata_safe: assoc.clear( purge = purge ) +class HistoryDatasetAssociationDisplayAtAuthorization( object ): + def __init__( self, hda=None, user=None, site=None ): + self.history_dataset_association = hda + self.user = user + self.site = site + class Library( object ): permitted_actions = get_permitted_actions( filter='LIBRARY' ) def __init__( self, name = None, description = None, root_folder = None ): diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Jul 27 15:55:32 2009 -0400 +++ b/lib/galaxy/model/mapping.py Tue Jul 28 14:16:19 2009 -0400 @@ -96,6 +96,14 @@ Column( "external_filename" , TEXT ), Column( "_extra_files_path", TEXT ), Column( 'file_size', Numeric( 15, 0 ) ) ) + +HistoryDatasetAssociationDisplayAtAuthorization.table = Table( "history_dataset_association_display_at_authorization", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "site", TrimmedString( 255 ) ) ) ImplicitlyConvertedDatasetAssociation.table = Table( "implicitly_converted_dataset_association", metadata, Column( "id", Integer, primary_key=True ), @@ -710,6 +718,10 @@ primaryjoin=( ( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) & ( LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) ) ) ) +assign_mapper( context, HistoryDatasetAssociationDisplayAtAuthorization, HistoryDatasetAssociationDisplayAtAuthorization.table, + properties=dict( history_dataset_association = relation( HistoryDatasetAssociation ), + user = relation( User ) ) ) + assign_mapper( context, ImplicitlyConvertedDatasetAssociation, ImplicitlyConvertedDatasetAssociation.table, properties=dict( parent=relation( HistoryDatasetAssociation, diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Tue Jul 28 14:16:19 2009 -0400 @@ -0,0 +1,47 @@ +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exceptions import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) + +HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "site", TrimmedString( 255 ) ) ) + +def upgrade(): + # Load existing tables + metadata.reflect() + try: + HistoryDatasetAssociationDisplayAtAuthorization_table.create() + except Exception, e: + log.debug( "Creating history_dataset_association_display_at_authorization table failed: %s" % str( e ) ) + +def downgrade(): + # Load existing tables + metadata.reflect() + try: + HistoryDatasetAssociationDisplayAtAuthorization_table.drop() + except Exception, e: + log.debug( "Dropping history_dataset_association_display_at_authorization table failed: %s" % str( e ) ) diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Mon Jul 27 15:55:32 2009 -0400 +++ b/lib/galaxy/security/__init__.py Tue Jul 28 14:16:19 2009 -0400 @@ -2,7 +2,8 @@ Galaxy Security """ -import logging +import logging, socket +from datetime import datetime, timedelta from galaxy.util.bunch import Bunch from galaxy.model.orm import * @@ -484,6 +485,65 @@ else: raise 'Passed an illegal object to check_folder_contents: %s' % type( entry ) +class HostAgent( RBACAgent ): + """ + A simple security agent which allows access to datasets based on host. + This exists so that externals sites such as UCSC can gain access to + datasets which have permissions which would normally prevent such access. + """ + # TODO: Make sites user configurable + sites = Bunch( + ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', + 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), + ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) + ) + def __init__( self, model, permitted_actions=None ): + self.model = model + if permitted_actions: + self.permitted_actions = permitted_actions + def allow_action( self, addr, action, **kwd ): + if 'dataset' in kwd and action == self.permitted_actions.DATASET_ACCESS: + hda = kwd['dataset'] + if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in hda.dataset.actions ]: + log.debug( 'Allowing access to public dataset with hda: %i.' % hda.id ) + return True # dataset has no roles associated with the access permission, thus is already public + hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization.filter_by( history_dataset_association_id = hda.id ).first() + if not hdadaa: + log.debug( 'Denying access to private dataset with hda: %i. No hdadaa record for this dataset.' % hda.id ) + return False # no auth + # We could just look up the reverse of addr, but then we'd also + # have to verify it with the forward address and special case any + # IPs (instead of hosts) in the server list. + # + # This would be improved by caching, but that's what the OS's name + # service cache daemon is for (you ARE running nscd, right?). + for server in HostAgent.sites.get( hdadaa.site, [] ): + # We're going to search in order, but if the remote site is load + # balancing their connections (as UCSC does), this is okay. + try: + if socket.gethostbyname( server ) == addr: + break # remote host is in the server list + except ( socket.error, socket.gaierror ): + pass # can't resolve, try next + else: + log.debug( 'Denying access to private dataset with hda: %i. Remote addr is not a valid server for site: %s.' % ( hda.id, hdadaa.site ) ) + return False # remote addr is not in the server list + if ( datetime.utcnow() - hdadaa.update_time ) > timedelta( seconds=60 ): + log.debug( 'Denying access to private dataset with hda: %i. Authorization was granted, but has expired.' % hda.id ) + return False # not authz'd in the last 60 seconds + log.debug( 'Allowing access to private dataset with hda: %i. Remote server is: %s.' % ( hda.id, server ) ) + return True + else: + raise 'The dataset access permission is the only valid permission in the host security agent.' + def set_dataset_permissions( self, hda, user, site ): + hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization.filter_by( history_dataset_association_id = hda.id ).first() + if hdadaa: + hdadaa.update_time = datetime.utcnow() + else: + hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization( hda=hda, user=user, site=site ) + hdadaa.flush() + def get_permitted_actions( filter=None ): '''Utility method to return a subset of RBACAgent's permitted actions''' if filter is None: diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Jul 27 15:55:32 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Tue Jul 28 14:16:19 2009 -0400 @@ -1,4 +1,4 @@ -import logging, os, sets, string, shutil, re, socket, mimetypes, smtplib +import logging, os, sets, string, shutil, re, socket, mimetypes, smtplib, urllib from galaxy.web.base.controller import * from galaxy import util, datatypes, jobs, web, model @@ -132,6 +132,24 @@ else: return trans.show_error_message( "You are not allowed to access this dataset" ) + @web.expose + def display_at( self, trans, dataset_id, filename=None, **kwd ): + """Sets up a dataset permissions so it is viewable at an external site""" + site = filename + data = trans.app.model.HistoryDatasetAssociation.get( dataset_id ) + if not data: + raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) + if 'display_url' not in kwd or 'redirect_url' not in kwd: + return trans.show_error_message( 'Invalid parameters specified for "display at" link, please contact a Galaxy administrator' ) + redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) + if trans.app.security_agent.allow_action( None, data.permitted_actions.DATASET_ACCESS, dataset = data ): + return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac + if trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset = data ): + trans.app.host_security_agent.set_dataset_permissions( data, trans.user, site ) + return trans.response.send_redirect( redirect_url ) + else: + return trans.show_error_message( "You are not allowed to view this dataset at external sites. Please contact your Galaxy administrator to acquire management permissions for this dataset." ) + def _undelete( self, trans, id ): try: id = int( id ) diff -r 0f18a77ca03e -r e01bfc281e09 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Jul 27 15:55:32 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Tue Jul 28 14:16:19 2009 -0400 @@ -197,13 +197,19 @@ def display_as( self, trans, id=None, display_app=None, **kwd ): """Returns a file in a format that can successfully be displayed in display_app""" data = self.app.model.HistoryDatasetAssociation.get( id ) + authz_method = 'rbac' + if 'authz_method' in kwd: + authz_method = kwd['authz_method'] if data: - if trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_ACCESS, dataset = data ): + if authz_method == 'rbac' and trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_ACCESS, dataset = data ): trans.response.set_content_type( data.get_mime() ) trans.log_event( "Formatted dataset id %s for display at %s" % ( str( id ), display_app ) ) return data.as_display_type( display_app, **kwd ) + elif authz_method == 'display_at' and trans.app.host_security_agent.allow_action( trans.request.remote_addr, data.permitted_actions.DATASET_ACCESS, dataset = data ): + trans.response.set_content_type( data.get_mime() ) + return data.as_display_type( display_app, **kwd ) else: - return "You are not privileged to access this dataset." + return "You are not allowed to access this dataset." else: return "No data with id=%d" % id

1 0

[hg] galaxy 2507: A new flag, force_history_refresh, has been ad...
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0f18a77ca03e changeset: 2507:0f18a77ca03e user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jul 27 15:55:32 2009 -0400 description: A new flag, force_history_refresh, has been added to Tool Configurations. When set to "True", this flag will cause the entire history to reload when one of its outputs has finished running. Default is False. This is useful, i.e., when a tool creates an indeterminate number of output datasets by dumping them into new_file_path. Example: <tool id="someTool" name="Some tool name" version="1.0.1" force_history_refresh="True"> ... </tool> 3 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/web/controllers/root.py templates/root/history.mako diffs (68 lines): diff -r ae750790079a -r 0f18a77ca03e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Jul 27 11:33:12 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Jul 27 15:55:32 2009 -0400 @@ -295,6 +295,8 @@ self.is_multi_byte = util.string_as_bool( root.get( "is_multi_byte", False ) ) # Type of tool self.tool_type = root.get( "tool_type", None ) + #Force history to fully refresh after job execution for this tool. Useful i.e. when an indeterminate number of outputs are created by a tool. + self.force_history_refresh = util.string_as_bool( root.get( 'force_history_refresh', 'False' ) ) # data_source tool if self.tool_type == "data_source": self.URL_method = root.get( "URL_method", "get" ) # get is the default diff -r ae750790079a -r 0f18a77ca03e lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Jul 27 11:33:12 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Mon Jul 27 15:55:32 2009 -0400 @@ -114,9 +114,16 @@ for id, state in zip( ids, states ): data = self.app.model.HistoryDatasetAssociation.get( id ) if data.state != state: + job_hda = data + while job_hda.copied_from_history_dataset_association: + job_hda = job_hda.copied_from_history_dataset_association + force_history_refresh = False + if job_hda.creating_job_associations: + force_history_refresh = trans.app.toolbox.tools_by_id[ job_hda.creating_job_associations[ 0 ].job.tool_id ].force_history_refresh rval[id] = { "state": data.state, - "html": unicode( trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ), 'utf-8' ) + "html": unicode( trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ), 'utf-8' ), + "force_history_refresh": force_history_refresh } return rval diff -r ae750790079a -r 0f18a77ca03e templates/root/history.mako --- a/templates/root/history.mako Mon Jul 27 11:33:12 2009 -0400 +++ b/templates/root/history.mako Mon Jul 27 15:55:32 2009 -0400 @@ -186,6 +186,7 @@ // Build request data var ids = [] var states = [] + var force_history_refresh = false $.each( tracked_datasets, function ( id, state ) { ids.push( id ); states.push( state ); @@ -205,13 +206,21 @@ initShowHide(); // If new state was terminal, stop tracking if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { + if ( val.force_history_refresh ){ + force_history_refresh = true; + } delete tracked_datasets[ parseInt(id) ]; } else { tracked_datasets[ parseInt(id) ] = val.state; } }); - // Keep going (if there are still any items to track) - updater( tracked_datasets ); + if ( force_history_refresh ) { + parent.frames.galaxy_history.location.reload(); + } + else { + // Keep going (if there are still any items to track) + updater( tracked_datasets ); + } }, error: function() { // Just retry, like the old method, should try to be smarter

1 0

[hg] galaxy 2505: Allow for multiple optional outputs to be spec...
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5a92b5877cf7 changeset: 2505:5a92b5877cf7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jul 27 10:46:25 2009 -0400 description: Allow for multiple optional outputs to be specified in a tool's xml file by specifying 'filter' tags. The text contents of the filter tag are evaled. If the result is False, the output will not be created. A NoneDataset object is provided in the param_dict for ease of constructing command lines. This allows a variable number of output files to be created before the tool is run in cases when the number of outputs is static and can be determined from tool parameters. Example of an output with filter: <data format="txt" name="optional_output"> <filter>some_parameter_name == 'some_parameter_value'</filter> </data> The output dataset, optional_output, will only be created when the tool parameter 'some_parameter_name' is 'some_parameter_value'. 2 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/__init__.py diffs (192 lines): diff -r 857d3a8ebd3d -r 5a92b5877cf7 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Sun Jul 26 12:08:44 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Jul 27 10:46:25 2009 -0400 @@ -235,12 +235,13 @@ (format, metadata_source, parent) """ def __init__( self, name, format=None, metadata_source=None, - parent=None, label=None ): + parent=None, label=None, filters = None ): self.name = name self.format = format self.metadata_source = metadata_source self.parent = parent self.label = label + self.filters = filters or [] # Tuple emulation @@ -413,6 +414,7 @@ output.metadata_source = data_elem.get("metadata_source", "") output.parent = data_elem.get("parent", None) output.label = util.xml_text( data_elem, "label" ) + output.filters = data_elem.findall( 'filter' ) self.outputs[ output.name ] = output # Any extra generated config files for the tool self.config_files = [] @@ -1294,6 +1296,10 @@ param_dict[name].files_path = os.path.abspath(os.path.join( job_working_directory, "dataset_%s_files" % (hda.dataset.id) )) for child in hda.children: param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) + for out_name, output in self.outputs.iteritems(): + if out_name not in param_dict and output.filters: + #assume the reason we lack this output is because a filter failed to pass; for tool writing convienence, provide a NoneDataset + param_dict[ out_name ] = NoneDataset( datatypes_registry = self.app.datatypes_registry, ext = output.format ) # We add access to app here, this allows access to app.config, etc param_dict['__app__'] = RawObjectWrapper( self.app ) # More convienent access to app.config.new_file_path; we don't need to wrap a string diff -r 857d3a8ebd3d -r 5a92b5877cf7 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Sun Jul 26 12:08:44 2009 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Mon Jul 27 10:46:25 2009 -0400 @@ -156,76 +156,83 @@ parent_to_child_pairs = [] child_dataset_names = set() for name, output in tool.outputs.items(): - if output.parent: - parent_to_child_pairs.append( ( output.parent, name ) ) - child_dataset_names.add( name ) - ## What is the following hack for? Need to document under what - ## conditions can the following occur? (james(a)bx.psu.edu) - # HACK: the output data has already been created - # this happens i.e. as a result of the async controller - if name in incoming: - dataid = incoming[name] - data = trans.app.model.HistoryDatasetAssociation.get( dataid ) - assert data != None - out_data[name] = data - else: - # the type should match the input - ext = output.format - if ext == "input": - ext = input_ext - #process change_format tags - if output.change_format: - for change_elem in output.change_format: - for when_elem in change_elem.findall( 'when' ): - check = incoming.get( when_elem.get( 'input' ), None ) - if check is not None: - if check == when_elem.get( 'value', None ): - ext = when_elem.get( 'format', ext ) - else: - check = when_elem.get( 'input_dataset', None ) + for filter in output.filters: + try: + if not eval( filter.text, globals(), incoming ): + break #do not create this dataset + except Exception, e: + log.debug( 'Dataset output filter failed: %s' % e ) + else: #all filters passed + if output.parent: + parent_to_child_pairs.append( ( output.parent, name ) ) + child_dataset_names.add( name ) + ## What is the following hack for? Need to document under what + ## conditions can the following occur? (james(a)bx.psu.edu) + # HACK: the output data has already been created + # this happens i.e. as a result of the async controller + if name in incoming: + dataid = incoming[name] + data = trans.app.model.HistoryDatasetAssociation.get( dataid ) + assert data != None + out_data[name] = data + else: + # the type should match the input + ext = output.format + if ext == "input": + ext = input_ext + #process change_format tags + if output.change_format: + for change_elem in output.change_format: + for when_elem in change_elem.findall( 'when' ): + check = incoming.get( when_elem.get( 'input' ), None ) if check is not None: - check = inp_data.get( check, None ) + if check == when_elem.get( 'value', None ): + ext = when_elem.get( 'format', ext ) + else: + check = when_elem.get( 'input_dataset', None ) if check is not None: - if str( getattr( check, when_elem.get( 'attribute' ) ) ) == when_elem.get( 'value', None ): - ext = when_elem.get( 'format', ext ) - data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True ) - # Commit the dataset immediately so it gets database assigned unique id - data.flush() - trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) - # Create an empty file immediately - open( data.file_name, "w" ).close() - # This may not be neccesary with the new parent/child associations - data.designation = name - # Copy metadata from one of the inputs if requested. - if output.metadata_source: - data.init_meta( copy_from=inp_data[output.metadata_source] ) - else: - data.init_meta() - # Take dbkey from LAST input - data.dbkey = str(input_dbkey) - # Set state - # FIXME: shouldn't this be NEW until the job runner changes it? - data.state = data.states.QUEUED - data.blurb = "queued" - # Set output label - if output.label: - params = make_dict_copy( incoming ) - # wrapping the params allows the tool config to contain things like - # <outputs> - # <data format="input" name="output" label="Blat on ${<input_param>.name}" /> - # </outputs> - wrap_values( tool.inputs, params ) - params['tool'] = tool - params['on_string'] = on_text - data.name = fill_template( output.label, context=params ) - else: - data.name = tool.name - if on_text: - data.name += ( " on " + on_text ) - # Store output - out_data[ name ] = data - # Store all changes to database - trans.app.model.flush() + check = inp_data.get( check, None ) + if check is not None: + if str( getattr( check, when_elem.get( 'attribute' ) ) ) == when_elem.get( 'value', None ): + ext = when_elem.get( 'format', ext ) + data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True ) + # Commit the dataset immediately so it gets database assigned unique id + data.flush() + trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) + # Create an empty file immediately + open( data.file_name, "w" ).close() + # This may not be neccesary with the new parent/child associations + data.designation = name + # Copy metadata from one of the inputs if requested. + if output.metadata_source: + data.init_meta( copy_from=inp_data[output.metadata_source] ) + else: + data.init_meta() + # Take dbkey from LAST input + data.dbkey = str(input_dbkey) + # Set state + # FIXME: shouldn't this be NEW until the job runner changes it? + data.state = data.states.QUEUED + data.blurb = "queued" + # Set output label + if output.label: + params = make_dict_copy( incoming ) + # wrapping the params allows the tool config to contain things like + # <outputs> + # <data format="input" name="output" label="Blat on ${<input_param>.name}" /> + # </outputs> + wrap_values( tool.inputs, params ) + params['tool'] = tool + params['on_string'] = on_text + data.name = fill_template( output.label, context=params ) + else: + data.name = tool.name + if on_text: + data.name += ( " on " + on_text ) + # Store output + out_data[ name ] = data + # Store all changes to database + trans.app.model.flush() # Add all the top-level (non-child) datasets to the history for name in out_data.keys(): if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created

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[hg] galaxy 2504: Fix problem with history icons repeating
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/857d3a8ebd3d changeset: 2504:857d3a8ebd3d user: James Taylor <james(a)jamestaylor.org> date: Sun Jul 26 12:08:44 2009 -0400 description: Fix problem with history icons repeating 3 file(s) affected in this change: static/june_2007_style/blue/history.css static/june_2007_style/history.css.tmpl templates/root/history_common.mako diffs (132 lines): diff -r cbdd394a265c -r 857d3a8ebd3d static/june_2007_style/blue/history.css --- a/static/june_2007_style/blue/history.css Fri Jul 24 17:06:12 2009 -0400 +++ b/static/june_2007_style/blue/history.css Sun Jul 26 12:08:44 2009 -0400 @@ -2,22 +2,23 @@ a{color:#303030;} div.historyLinks{padding:5px;margin:5px 0 5px 0;} div.historyItem{margin:5px -5px 5px 0px;padding:5px 11px 5px 5px;border:solid #888888 1px;border-left:solid #888888 5px;border-right:none;background:#EEEEEE;} -div.historyItem div.historyItemTitleBar{padding-left:20px;background-position:0 1px;background-repeat:no-repeat;} +div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} +div.historyItem .historyItemTitle{line-height:16px;} div.historyItem div.historyItem{margin-right:-11px;} div.historyItem-ok{border-color:#66AA66;background:#CCFFCC;} -div.historyItem-ok div.historyItemTitleBar{padding-left:0;} +div.historyItem-ok .state-icon{display:none;} div.historyItem-error{border-color:#AA6666;background:#FFCCCC;} -div.historyItem-error div.historyItemTitleBar{background:url(history-states.png) no-repeat 0px -0px;} +div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px -0px;} div.historyItem-empty{border-color:#AA6666;background:#FFCCCC;} -div.historyItem-empty div.historyItemTitleBar{background:url(history-states.png) no-repeat 0px -25px;} +div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} div.historyItem-running{border-color:#AAAA66;background:#FFFFCC;} -div.historyItem-running div.historyItemTitleBar{background-image:url(data_running.gif);} +div.historyItem-running .state-icon{background-image:url(data_running.gif);} div.historyItem-upload{border-color:#6666AA;background:#CCCCFF;} -div.historyItem-upload div.historyItemTitleBar{background-image:url(data_upload.gif);} +div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} div.historyItem-queued{background:#EEEEEE;} -div.historyItem-queued div.historyItemTitleBar{background:url(history-states.png) no-repeat 0px -50px;} +div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} -div.historyItemTitleBar.spinner{background:url(data_running.gif) 0 1px no-repeat !important;padding-left:20px !important;} +div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} div.historyItemButtons{float:right;} .icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;} diff -r cbdd394a265c -r 857d3a8ebd3d static/june_2007_style/history.css.tmpl --- a/static/june_2007_style/history.css.tmpl Fri Jul 24 17:06:12 2009 -0400 +++ b/static/june_2007_style/history.css.tmpl Sun Jul 26 12:08:44 2009 -0400 @@ -27,10 +27,16 @@ border-left: solid $history_queued_border 5px; border-right: none; background: $history_queued_bg; - div.historyItemTitleBar { - padding-left: 20px; + .state-icon { + display: inline-block; + vertical-align: middle; + width: 16px; + height: 16px; background-position: 0 1px; background-repeat: no-repeat; + } + .historyItemTitle { + line-height: 16px; } } @@ -43,14 +49,14 @@ div.historyItem-ok { border-color: $history_ok_border; background: $history_ok_bg; - div.historyItemTitleBar { - padding-left: 0; + .state-icon { + display: none; } } div.historyItem-error { border-color: $history_error_border; background: $history_error_bg; - div.historyItemTitleBar { + .state-icon { -sprite-group: history-states; -sprite-image: data_error.png; } @@ -59,7 +65,7 @@ div.historyItem-empty { border-color: $history_error_border; background: $history_error_bg; - div.historyItemTitleBar { + .state-icon { -sprite-group: history-states; -sprite-image: data_empty.png; } @@ -68,7 +74,7 @@ div.historyItem-running { border-color: $history_running_border; background: $history_running_bg; - div.historyItemTitleBar { + .state-icon { background-image: url(data_running.gif); } } @@ -76,14 +82,14 @@ div.historyItem-upload { border-color: $history_upload_border; background: $history_upload_bg; - div.historyItemTitleBar { + .state-icon { background-image: url(data_upload.gif); } } div.historyItem-queued { background: $history_queued_bg; - div.historyItemTitleBar { + .state-icon { -sprite-group: history-states; -sprite-image: data_queued.png; } @@ -96,9 +102,8 @@ } ## Special case for showing the spinner but not changing the background -div.historyItemTitleBar.spinner { +div.historyItemTitleBar.spinner .state-icon { background: url(data_running.gif) 0 1px no-repeat !important; - padding-left: 20px !important; } ## Buttons diff -r cbdd394a265c -r 857d3a8ebd3d templates/root/history_common.mako --- a/templates/root/history_common.mako Fri Jul 24 17:06:12 2009 -0400 +++ b/templates/root/history_common.mako Sun Jul 26 12:08:44 2009 -0400 @@ -34,6 +34,7 @@ %endif <a class="icon-button delete" title="delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a> </div> + <span class="state-icon"></span> <span class="historyItemTitle"><b>${hid}: ${data.display_name()}</b></span> </div>

1 0

[hg] galaxy 2502: Force browsers to recache the CSS
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/472bc69143be changeset: 2502:472bc69143be user: James Taylor <james(a)jamestaylor.org> date: Fri Jul 24 16:39:48 2009 -0400 description: Force browsers to recache the CSS 3 file(s) affected in this change: lib/galaxy/web/framework/helpers/__init__.py templates/base.mako templates/base_panels.mako diffs (66 lines): diff -r 0d7a8525da9e -r 472bc69143be lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py Fri Jul 24 16:26:32 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/__init__.py Fri Jul 24 16:39:48 2009 -0400 @@ -19,9 +19,12 @@ def css( *args ): """ Take a list of stylesheet names (no extension) and return appropriate string - of link tags. + of link tags. + + TODO: This has a hardcoded "?v=1" to defeat caching. This should be done + in a better way. """ - return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css" ) for name in args ] ) + return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=1" ) for name in args ] ) def js( *args ): """ diff -r 0d7a8525da9e -r 472bc69143be templates/base.mako --- a/templates/base.mako Fri Jul 24 16:26:32 2009 -0400 +++ b/templates/base.mako Fri Jul 24 16:39:48 2009 -0400 @@ -19,7 +19,7 @@ ## Default stylesheets <%def name="stylesheets()"> - <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + ${h.css('base')} </%def> ## Default javascripts diff -r 0d7a8525da9e -r 472bc69143be templates/base_panels.mako --- a/templates/base_panels.mako Fri Jul 24 16:26:32 2009 -0400 +++ b/templates/base_panels.mako Fri Jul 24 16:39:48 2009 -0400 @@ -20,8 +20,7 @@ ## Default stylesheets <%def name="stylesheets()"> - ## <link rel="stylesheet" type="text/css" href="${h.url_for('/static/style/reset.css')}" /> - <link rel="stylesheet" type="text/css" href="${h.url_for('/static/style/panel_layout.css')}" /> + ${h.css('panel_layout')} <style type="text/css"> #center { %if not self.has_left_panel: @@ -43,8 +42,7 @@ ## Default javascripts <%def name="javascripts()">  </%def> @@ -52,11 +50,7 @@ <%def name="late_javascripts()"> ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout - <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script> - <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.event.drag.js')}"></script> - <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.event.hover.js')}"></script> - <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.form.js')}"></script> - <script type="text/javascript" src="${h.url_for('/static/scripts/galaxy.panels.js')}"></script> + ${h.js( 'jquery', 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'galaxy.panels' )} <script type="text/javascript"> ensure_dd_helper();

1 0

[hg] galaxy 2503: Removed option to select indexing algorithm fr...
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cbdd394a265c changeset: 2503:cbdd394a265c user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Jul 24 17:06:12 2009 -0400 description: Removed option to select indexing algorithm from BWA wrapper and have it automatically determine the algorithm by file size. 2 file(s) affected in this change: tools/sr_mapping/bwa_wrapper.py tools/sr_mapping/bwa_wrapper.xml diffs (76 lines): diff -r 472bc69143be -r cbdd394a265c tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py Fri Jul 24 16:39:48 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Fri Jul 24 17:06:12 2009 -0400 @@ -17,7 +17,6 @@ #Parse Command Line parser = optparse.OptionParser() parser.add_option('', '--ref', dest='ref', help='The reference genome to use or index') - parser.add_option('', '--indexingAlg', dest='indexingAlg', help='The algorithm to use while indexing') parser.add_option('', '--fastq', dest='fastq', help='The (forward) fastq file to use for the mapping') parser.add_option('', '--rfastq', dest='rfastq', help='The reverse fastq file to use for mapping if paired-end data') parser.add_option('', '--output', dest='output', help='The file to save the output (SAM format)') @@ -53,10 +52,18 @@ os.system('cp %s %s' % (options.ref, tmp_dir)) except Exception, erf: stop_err('Error creating temp directory for indexing purposes\n' + str(erf)) + try: + size = os.stat(options.ref).st_size + if size <= 2**30: + indexingAlg = 'is' + else: + indexingAlg = 'bwtsw' + except: + indexingAlg = 'is' if options.fileType == 'solid': - indexing_cmds = '-c -a %s' % options.indexingAlg + indexing_cmds = '-c -a %s' % indexingAlg else: - indexing_cmds = '-a %s' % options.indexingAlg + indexing_cmds = '-a %s' % indexingAlg options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1]) cmd1 = 'bwa index %s %s 2> /dev/null' % (indexing_cmds, options.ref) try: diff -r 472bc69143be -r cbdd394a265c tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Fri Jul 24 16:39:48 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Fri Jul 24 17:06:12 2009 -0400 @@ -4,10 +4,8 @@ bwa_wrapper.py #if $solidOrSolexa.solidRefGenomeSource.refGenomeSource == "history": --ref=$solidOrSolexa.solidRefGenomeSource.ownFile - --indexingAlg=$solidOrSolexa.solidRefGenomeSource.algorithm #else: --ref=$solidOrSolexa.solidRefGenomeSource.indices.value - --indexingAlg="None" #end if --fastq=$paired.input1 #if $paired.sPaired == "paired": @@ -74,10 +72,6 @@ </param> <when value="history"> <param name="ownFile" type="data" label="Select a reference genome" /> - <param name="algorithm" type="select" label="Select an indexing algorithm" help="IS works on databses 2GB or less, and is linear-time. BWT-SW works on database 10MB and larger, and trades speed for memory."> - <option value="is">IS</option> - <option value="bwtsw">BWT-SW</option> - </param> </when> <when value="indexed"> <param name="indices" type="select" label="Select a reference genome"> @@ -98,10 +92,6 @@ </param> <when value="history"> <param name="ownFile" type="data" label="Select a reference genome" /> - <param name="algorithm" type="select" label="Select an indexing algorithm" help="IS works on databses 2GB or less, and is linear-time. BWT-SW works on database 10MB and larger, and trades speed for memory."> - <option value="is">IS</option> - <option value="bwtsw">BWT-SW</option> - </param> </when> <when value="indexed"> <param name="indices" type="select" label="Select a reference genome"> @@ -177,7 +167,6 @@ <param name="solidSolexa" value="solid" /> <param name="refGenomeSource" value="history" /> <param name="ownFile" value="phiX.fa" /> - <param name="algorithm" value="is" /> <param name="sPaired" value="single" /> <param name="input1" value="bwa_phiX_sanger.fastq" /> <param name="source_select" value="pre_set" />

1 0

[hg] galaxy 2499: Added BWA wrapper tool to Short Read Mapping T...
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0564441c5043 changeset: 2499:0564441c5043 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Jul 24 15:13:11 2009 -0400 description: Added BWA wrapper tool to Short Read Mapping Tools 5 file(s) affected in this change: tool-data/sequence_index_base.loc.sample tool-data/sequence_index_color.loc.sample tool_conf.xml.sample tools/sr_mapping/bwa_wrapper.py tools/sr_mapping/bwa_wrapper.xml diffs (614 lines): diff -r 643e3cd86e0b -r 0564441c5043 tool-data/sequence_index_base.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sequence_index_base.loc.sample Fri Jul 24 15:13:11 2009 -0400 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a sequence_index_base.loc file +#similar to this one (store it in this directory ) that points to +#the directories in which those files are stored. The sequence_index_base.loc +#file has this format (white space characters are TAB characters): +# +#<build> <file_base> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/base/, +#then the sequence_index_base.loc entry would look like this: +# +#phiX /depot/data2/galaxy/phiX/base/phiX.fa +# +#and your /depot/data2/galaxy/phiX/base/ directory +#would contain phiX.fa.* files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your sequence_index_base.loc file should include an entry per line for +#each index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX /depot/data2/galaxy/phiX/base/phiX.fa diff -r 643e3cd86e0b -r 0564441c5043 tool-data/sequence_index_color.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sequence_index_color.loc.sample Fri Jul 24 15:13:11 2009 -0400 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a sequence_index_color.loc file +#similar to this one (store it in this directory ) that points to +#the directories in which those files are stored. The sequence_index_color.loc +#file has this format (white space characters are TAB characters): +# +#<build> <file_base> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/color/, +#then the sequence_index_color.loc entry would look like this: +# +#phiX /depot/data2/galaxy/phiX/color/phiX.fa +# +#and your /depot/data2/galaxy/phiX/color/ directory +#would contain phiX.fa.* files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your sequence_index_color.loc file should include an entry per line for +#each index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX /depot/data2/galaxy/phiX/color/phiX.fa diff -r 643e3cd86e0b -r 0564441c5043 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Jul 24 12:16:32 2009 -0400 +++ b/tool_conf.xml.sample Fri Jul 24 15:13:11 2009 -0400 @@ -329,8 +329,9 @@ <tool file="metag_tools/megablast_xml_parser.xml" /> <tool file="metag_tools/blat_wrapper.xml" /> <tool file="metag_tools/mapping_to_ucsc.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> </section> <section name="Tracks" id="tracks"> <tool file="visualization/genetrack.xml" /> - </section> + </section> </toolbox> diff -r 643e3cd86e0b -r 0564441c5043 tools/sr_mapping/bwa_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/sr_mapping/bwa_wrapper.py Fri Jul 24 15:13:11 2009 -0400 @@ -0,0 +1,119 @@ +#! /usr/bin/python + +""" +Runs BWA on single-end or paired-end data. +Produces a SAM file containing the mappings. + +usage: python bwa_wrapper.py reference_sequence indexing_algorithm(is_or_bwtsw) forward_fastq_file reverse_fastq_file(or_None) output alignment_type(single_or_paired) parameters(pre_set_or_full) file_type(solexa_or_solid) file_source(indexed_or_history) maxEditDist fracMissingAligns maxGapOpens maxGapExtens disallowLongDel disallowIndel seed maxEditDistSeed numThreads mismatchPenalty gapOpenPenalty gapExtensPenalty colorSpaceRev suboptAlign noIterSearch outputTopN maxInsertSize maxOccurPairing\nThe last eighteen need to all be specified, or all be None +""" + +import optparse, os, sys, tempfile + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option('', '--ref', dest='ref', help='The reference genome to use or index') + parser.add_option('', '--indexingAlg', dest='indexingAlg', help='The algorithm to use while indexing') + parser.add_option('', '--fastq', dest='fastq', help='The (forward) fastq file to use for the mapping') + parser.add_option('', '--rfastq', dest='rfastq', help='The reverse fastq file to use for mapping if paired-end data') + parser.add_option('', '--output', dest='output', help='The file to save the output (SAM format)') + parser.add_option('', '--genAlignType', dest='genAlignType', help='The type of pairing (single or paired)') + parser.add_option('', '--params', dest='params', help='Parameter setting to use (pre_set or full)') + parser.add_option('', '--fileType', dest='fileType', help='Type of reference sequence file (solid or solexa)') + parser.add_option('', '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)') + parser.add_option('-n', '--maxEditDist', dest='maxEditDist', help='Maximum edit distance if integer') + parser.add_option('', '--fracMissingAligns', dest='fracMissingAligns', help='Fraction of missing alignments given 2% uniform base error rate if fraction') + parser.add_option('-o', '--maxGapOpens', dest='maxGapOpens', help='Maximum number of gap opens') + parser.add_option('-e', '--maxGapExtens', dest='maxGapExtens', help='Maximum number of gap extensions') + parser.add_option('-d', '--disallowLongDel', dest='disallowLongDel', help='Disallow a long deletion within specified bps') + parser.add_option('-i', '--disallowIndel', dest='disallowIndel', help='Disallow indel within specified bps') + parser.add_option('-l', '--seed', dest='seed', help='Take the first specified subsequences') + parser.add_option('-k', '--maxEditDistSeed', dest='maxEditDistSeed', help='Maximum edit distance to the seed') + parser.add_option('-t', '--numThreads', dest='numThreads', help='Number of threads') + parser.add_option('-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty') + parser.add_option('-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty') + parser.add_option('-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty') + parser.add_option('-c', '--colorSpaceRev', dest='colorSpaceRev', help="Reverse query but don't complement it") + parser.add_option('-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat') + parser.add_option('-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search') + parser.add_option('', '--outputTopN', dest='outputTopN', help='Output top specified hits') + parser.add_option('', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good') + parser.add_option('', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings') + (options, args) = parser.parse_args() + + # index if necessary + if options.fileSource == 'history': + # make temp directory for placement of indices and copy reference file there + tmp_dir = tempfile.gettempdir() + try: + os.system('cp %s %s' % (options.ref, tmp_dir)) + except Exception, erf: + stop_err('Error creating temp directory for indexing purposes\n' + str(erf)) + if options.fileType == 'solid': + indexing_cmds = '-c -a %s' % options.indexingAlg + else: + indexing_cmds = '-a %s' % options.indexingAlg + options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1]) + cmd1 = 'bwa index %s %s 2> /dev/null' % (indexing_cmds, options.ref) + try: + os.system(cmd1) + except Exception, erf: + stop_err('Error indexing reference sequence\n' + str(erf)) + + # set up aligning and generate aligning command options + if options.params == 'pre_set': + if options.fileType == 'solid': + aligning_cmds = '-c' + else: + aligning_cmds = '' + gen_alignment_cmds = '' + else: + aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s' % \ + ((options.fracMissingAligns, options.maxEditDist)[options.maxEditDist != '0'], + options.maxGapOpens, options.maxGapExtens, options.disallowLongDel, + options.disallowIndel, ('',' -l %s'%options.seed)[options.seed!=-1], + options.maxEditDistSeed, options.numThreads, options.mismatchPenalty, + options.gapOpenPenalty, options.gapExtensPenalty, ('',' -c')[options.colorSpaceRev=='true'], + ('',' -R')[options.suboptAlign=='true'], ('',' -N')[options.noIterSearch=='true']) + if options.genAlignType == 'single': + gen_alignment_cmds = '-n %s' % options.outputTopN + elif options.genAlignType == 'paired': + gen_alignment_cmds = '-a %s -o %s' % (options.maxInsertSize, options.maxOccurPairing) + + # set up output file + file(options.output,'w').write('QNAME\tFLAG\tRNAME\tPOS\tMAPQ\tCIGAR\tMRNM\tMPOS\tISIZE\tSEQ\tQUAL\tOPT\n') + tmp_align_out = tempfile.NamedTemporaryFile() + + # prepare actual aligning and generate aligning commands + cmd2 = 'bwa aln %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.fastq, tmp_align_out.name) + cmd2b = '' + if options.genAlignType == 'paired': + tmp_align_out2 = tempfile.NamedTemporaryFile() + cmd2b = 'bwa aln %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.rfastq, tmp_align_out2.name) + cmd3 = 'bwa sampe %s %s %s %s %s %s >> %s 2> /dev/null' % (gen_alignment_cmds, options.ref, tmp_align_out.name, tmp_align_out2.name, options.fastq, options.rfastq, options.output) + else: + cmd3 = 'bwa samse %s %s %s %s >> %s 2> /dev/null' % (gen_alignment_cmds, options.ref, tmp_align_out.name, options.fastq, options.output) + + # align + try: + os.system(cmd2) + except Exception, erf: + stop_err("Error aligning sequence\n" + str(erf)) + # and again if paired data + try: + if cmd2b: + os.system(cmd2b) + except Exception, erf: + stop_err("Error aligning second sequence\n" + str(erf)) + + # generate align + try: + os.system(cmd3) + except Exception, erf: + stop_err("Error sequence aligning sequence\n" + str(erf)) + +if __name__=="__main__": __main__() diff -r 643e3cd86e0b -r 0564441c5043 tools/sr_mapping/bwa_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/sr_mapping/bwa_wrapper.xml Fri Jul 24 15:13:11 2009 -0400 @@ -0,0 +1,409 @@ +<tool id="bwa_wrapper" name="BWA" version="1.0.0"> + <description> fast mapping of reads against reference sequence</description> + <command interpreter="python"> + bwa_wrapper.py + #if $solidOrSolexa.solidRefGenomeSource.refGenomeSource == "history": + --ref=$solidOrSolexa.solidRefGenomeSource.ownFile + --indexingAlg=$solidOrSolexa.solidRefGenomeSource.algorithm + #else: + --ref=$solidOrSolexa.solidRefGenomeSource.indices.value + --indexingAlg="None" + #end if + --fastq=$paired.input1 + #if $paired.sPaired == "paired": + --rfastq=$paired.input2 + #else: + --rfastq="None" + #end if + --output=$output + --genAlignType=$paired.sPaired + --params=$params.source_select + --fileType=$solidOrSolexa.solidSolexa + --fileSource=$solidOrSolexa.solidRefGenomeSource.refGenomeSource + #if $params.source_select == "pre_set": + --maxEditDist="None" + --fracMissingAligns="None" + --maxGapOpens="None" + --maxGapExtens="None" + --disallowLongDel="None" + --disallowIndel="None" + --seed="None" + --maxEditDistSeed="None" + --numThreads="None" + --mismatchPenalty="None" + --gapOpenPenalty="None" + --gapExtensPenalty="None" + --colorSpaceRev="None" + --suboptAlign="None" + --noIterSearch="None" + --outputTopN="None" + --maxInsertSize="None" + --maxOccurPairing="None" + #else: + --maxEditDist=$params.maxEditDist + --fracMissingAligns=$params.fracMissingAligns + --maxGapOpens=$params.maxGapOpens + --maxGapExtens=$params.maxGapExtens + --disallowLongDel=$params.disallowLongDel + --disallowIndel=$params.disallowIndel + --seed=$params.seed + --maxEditDistSeed=$params.maxEditDistSeed + --numThreads=$params.numThreads + --mismatchPenalty=$params.mismatchPenalty + --gapOpenPenalty=$params.gapOpenPenalty + --gapExtensPenalty=$params.gapExtensPenalty + --colorSpaceRev=$params.colorSpaceRev + --suboptAlign=$params.suboptAlign + --noIterSearch=$params.noIterSearch + --outputTopN=$params.outputTopN + --maxInsertSize=$params.maxInsertSize + --maxOccurPairing=$params.maxOccurPairing + #end if + </command> + <inputs> + <conditional name="solidOrSolexa"> + <param name="solidSolexa" type="select" label="Select SOLiD or Solexa format for the original dataset"> + <option value="solexa">Solexa</option> + <option value="solid">SOLiD</option> + </param> + <when value="solid"> + <conditional name="solidRefGenomeSource"> + <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="history"> + <param name="ownFile" type="data" label="Select a reference genome" /> + <param name="algorithm" type="select" label="Select an indexing algorithm" help="IS works on databses 2GB or less, and is linear-time. BWT-SW works on database 10MB and larger, and trades speed for memory."> + <option value="is">IS</option> + <option value="bwtsw">BWT-SW</option> + </param> + </when> + <when value="indexed"> + <param name="indices" type="select" label="Select a reference genome"> + <options from_file="sequence_index_color.loc"> + <column name="value" index="1" /> + <column name="name" index="0" /> + <filter type="sort_by" column="0" /> + </options> + </param> + </when> + </conditional> + </when> + <when value="solexa"> + <conditional name="solidRefGenomeSource"> + <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="history"> + <param name="ownFile" type="data" label="Select a reference genome" /> + <param name="algorithm" type="select" label="Select an indexing algorithm" help="IS works on databses 2GB or less, and is linear-time. BWT-SW works on database 10MB and larger, and trades speed for memory."> + <option value="is">IS</option> + <option value="bwtsw">BWT-SW</option> + </param> + </when> + <when value="indexed"> + <param name="indices" type="select" label="Select a reference genome"> + <options from_file="sequence_index_base.loc"> + <column name="value" index="1" /> + <column name="name" index="0" /> + <filter type="sort_by" column="0" /> + </options> + </param> + </when> + </conditional> + </when> + </conditional> + <conditional name="paired"> + <param name="sPaired" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="input1" type="data" label="FASTQ file" /> + </when> + <when value="paired"> + <param name="input1" type="data" label="Forward FASTQ file" /> + <param name="input2" type="data" label="Reverse FASTQ file" /> + </when> + </conditional> + <conditional name="params"> + <param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List"> + <option value="pre_set">Commonly used</option> + <option value="full">Full Parameter List</option> + </param> + <when value="pre_set" /> + <when value="full"> + <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance" help="Enter this value OR a fraction of missing alignments, not both" /> + <param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate" help="Enter this value OR maximum edit distance, not both" /> + <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens" /> + <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions" help="-1 for k-difference mode (disallowing long gaps)" /> + <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] towards the 3'-end" /> + <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end" /> + <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed" help="Enter -1 for infinity" /> + <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed" /> + <param name="numThreads" type="integer" value="1" label="Number of threads, in multi-threading mode" /> + <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty" help="BWA will not search for suboptimal hits with a score lower than [value]" /> + <param name="gapOpenPenalty" type="integer" value="1" label="Gap open penalty" /> + <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty" /> + <param name="colorSpaceRev" type="select" label="Reverse query but don't compement it" help="Reverse query for all alignment in color space"> + <option value="false">Don't reverse query</option> + <option value="true">Reverse query</option> + </param> + <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat" help="By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> + <param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default." /> + <param name="outputTopN" type="integer" value="-1" label="Output top [value] hits" help="For single-end reads only. Enter -1 to disable outputting multiple hits" /> + <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly" help="For paired-end reads only. Only used when there are not enough good alignment to infer the distribution of insert sizes" /> + <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +**What it does** + +**BWA** is a high performance sequence aligner that succeeds MAQ. It is based on BWT-SW but uses a completely different algorithm, and it is aimed toward short read alignments. It is fast--it can map the human genome in only 15-25 minutes. Heng Li of the Sanger Institute wrote the majority of the code, with contributions by Chi-Kwong Wong at the University of Hong Kong, Nong Ge at Sun Yat-Sen University, and Yuta Mori. + +------ + +**Input formats** + +BWA accepts files in FASTQ format. + +------ + +**Outputs** + +The output is in SAM format, and has the following columns:: + + 1 QNAME - Query (pair) NAME + 2 FLAG - bitwise FLAG + 3 RNAME - Reference sequence NAME + 4 POS - 1-based leftmost POSition/coordinate of clipped sequence + 5 MAPQ - MAPping Quality (Phred-scaled) + 6 CIGAR - extended CIGAR string + 7 MRNM - Mate Reference sequence NaMe ('=' if same as RNAME) + 8 MPOS - 1-based Mate POSition + 9 ISIZE - Inferred insert SIZE + 10 SEQ - query SEQuence on the same strand as the reference + 11 QUAL - query QUALity (ASCII-33 gives the Phred base quality) + 12 OPT - variable OPTional fields in the format TAG:VTYPE:VALU + +The flags are as follows:: + + Flag - Description + 0x0001 - the read is paired in sequencing + 0x0002 - the read is mapped in a proper pair + 0x0004 - the query sequence itself is unmapped + 0x0008 - the mate is unmapped + 0x0010 - strand of the query (1 for reverse) + 0x0020 - strand of the mate + 0x0040 - the read is the first read in a pair + 0x0080 - the read is the second read in a pair + 0x0100 - the alignment is not primary + +It looks like this (scroll sideways to see the entire example):: + + QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT + HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh + HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh + +------- + +**BWA Settings** + +All of the options have a default value. You can change any of them. All of the options in BWA have been implemented here. + +------ + +**BWA parameter list** + +This is an exhaustive list of BWA options: + +For **aln**:: + + -n NUM Maximum edit distance if the value is INT, or the fraction of missing + alignments given 2% uniform base error rate if FLOAT. In the latter + case, the maximum edit distance is automatically chosen for different + read lengths. [0.04] + -o INT Maximum number of gap opens [1] + -e INT Maximum number of gap extensions, -1 for k-difference mode + (disallowing long gaps) [-1] + -d INT Disallow a long deletion within INT bp towards the 3'-end [16] + -i INT Disallow an indel within INT bp towards the ends [5] + -l INT Take the first INT subsequence as seed. If INT is larger than the + query sequence, seeding will be disabled. For long reads, this option + is typically ranged from 25 to 35 for '-k 2'. [inf] + -k INT Maximum edit distance in the seed [2] + -t INT Number of threads (multi-threading mode) [1] + -M INT Mismatch penalty. BWA will not search for suboptimal hits with a score + lower than (bestScore-misMsc). [3] + -O INT Gap open penalty [11] + -E INT Gap extension penalty [4] + -c Reverse query but not complement it, which is required for alignment + in the color space. + -R Proceed with suboptimal alignments even if the top hit is a repeat. By + default, BWA only searches for suboptimal alignments if the top hit is + unique. Using this option has no effect on accuracy for single-end + reads. It is mainly designed for improving the alignment accuracy of + paired-end reads. However, the pairing procedure will be slowed down, + especially for very short reads (~32bp). + -N Disable iterative search. All hits with no more than maxDiff + differences will be found. This mode is much slower than the default. + +For **samse**:: + + -n INT Output up to INT top hits. Value -1 to disable outputting multiple + hits. [-1] + +For **sampe**:: + + -a INT Maximum insert size for a read pair to be considered as being mapped + properly. Since 0.4.5, this option is only used when there are not + enough good alignment to infer the distribution of insert sizes. [500] + -o INT Maximum occurrences of a read for pairing. A read with more + occurrences will be treated as a single-end read. Reducing this + parameter helps faster pairing. [100000] + + + </help> +</tool> + +

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[hg] galaxy 2501: Fixes and missed files for CSS
by Nate Coraor 28 Jul '09

28 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0d7a8525da9e changeset: 2501:0d7a8525da9e user: James Taylor <james(a)jamestaylor.org> date: Fri Jul 24 16:26:32 2009 -0400 description: Fixes and missed files for CSS 5 file(s) affected in this change: static/june_2007_style/blue/base.css static/june_2007_style/blue/history-buttons.png static/june_2007_style/blue/history-states.png static/june_2007_style/blue/history.css static/june_2007_style/process_css.py diffs (43 lines): diff -r 3d4d44d7a275 -r 0d7a8525da9e static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Jul 24 16:14:46 2009 -0400 +++ b/static/june_2007_style/blue/base.css Fri Jul 24 16:26:32 2009 -0400 @@ -84,11 +84,8 @@ div.popupmenu{display:none;background:#eeeeee;color:#333;font-size:110%;font-weight:bold;font-style:normal;white-space:nowrap;position:absolute;z-index:20000;border:solid #aaaaaa 1px;padding:3px 0;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} div.popupmenu-item{padding:3px 1em;cursor:pointer;} div.popupmenu-item:hover{background:#aaaaaa;} -.popup-arrow{font-size:80%;cursor:pointer;text-decoration:none;color:#555 -} - -.popup-arrow:hover { - color: black;} +.popup-arrow{font-size:80%;cursor:pointer;text-decoration:none;color:#555;} +.popup-arrow:hover{color:black;} div.permissionContainer{padding-left:20px;} .grid-header{padding-bottom:1em;} .grid-header h2{margin:0;margin-bottom:0.5em;} diff -r 3d4d44d7a275 -r 0d7a8525da9e static/june_2007_style/blue/history-buttons.png Binary file static/june_2007_style/blue/history-buttons.png has changed diff -r 3d4d44d7a275 -r 0d7a8525da9e static/june_2007_style/blue/history-states.png Binary file static/june_2007_style/blue/history-states.png has changed diff -r 3d4d44d7a275 -r 0d7a8525da9e static/june_2007_style/blue/history.css --- a/static/june_2007_style/blue/history.css Fri Jul 24 16:14:46 2009 -0400 +++ b/static/june_2007_style/blue/history.css Fri Jul 24 16:26:32 2009 -0400 @@ -1,5 +1,5 @@ body{background:#C1C9E5;color:#303030;background-image:url(menu_bg.png);background-repeat:repeat-x;background-position:top;margin:5px;border:0;padding:0;} -a{color:#base_text;} +a{color:#303030;} div.historyLinks{padding:5px;margin:5px 0 5px 0;} div.historyItem{margin:5px -5px 5px 0px;padding:5px 11px 5px 5px;border:solid #888888 1px;border-left:solid #888888 5px;border-right:none;background:#EEEEEE;} div.historyItem div.historyItemTitleBar{padding-left:20px;background-position:0 1px;background-repeat:no-repeat;} diff -r 3d4d44d7a275 -r 0d7a8525da9e static/june_2007_style/process_css.py --- a/static/june_2007_style/process_css.py Fri Jul 24 16:14:46 2009 -0400 +++ b/static/june_2007_style/process_css.py Fri Jul 24 16:26:32 2009 -0400 @@ -11,7 +11,7 @@ import sys, string, os.path from pyparsing import * -from galaxy.util.odict import odict +from odict import odict import Image def cross_lists(*sets):

1 0