July 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2511: Fix a problem introduced in db version 10 (MyS...
by Nate Coraor 30 Jul '09

30 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ec59d6bcf827 changeset: 2511:ec59d6bcf827 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Jul 30 12:12:26 2009 -0400 description: Fix a problem introduced in db version 10 (MySQL's length limits prevent the creation of an index) 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py diffs (55 lines): diff -r fab59b1e756d -r ec59d6bcf827 lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Thu Jul 30 12:12:26 2009 -0400 @@ -0,0 +1,51 @@ +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(): + if migrate_engine.name == 'mysql': + # Load existing tables + metadata.reflect() + i = Index( "ix_hdadaa_history_dataset_association_id", HistoryDatasetAssociationDisplayAtAuthorization_table.c.history_dataset_association_id ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_hdadaa_history_dataset_association_id' to table 'history_dataset_association_display_at_authorization' table failed: %s" % str( e ) ) + +def downgrade(): + if migrate_engine.name == 'mysql': + # Load existing tables + metadata.reflect() + i = Index( "ix_hdadaa_history_dataset_association_id", HistoryDatasetAssociationDisplayAtAuthorization_table.c.history_dataset_association_id ) + try: + i.drop() + except Exception, e: + log.debug( "Removing index 'ix_hdadaa_history_dataset_association_id' from table 'history_dataset_association_display_at_authorization' table failed: %s" % str( e ) )

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[hg] galaxy 2509: Add a new config setting to universe_wsgi.ini:...
by Nate Coraor 30 Jul '09

30 Jul '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f06777cbd5bb changeset: 2509:f06777cbd5bb user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Jul 30 11:05:03 2009 -0400 description: Add a new config setting to universe_wsgi.ini: new_user_dataset_access_role_default_private. When set to True, new users will have default dataset access permissions for histories set to their Private role. Default is False (original behavior); datasets are left as public. Resolves ticket #111. 4 file(s) affected in this change: lib/galaxy/config.py lib/galaxy/security/__init__.py lib/galaxy/web/controllers/user.py universe_wsgi.ini.sample diffs (58 lines): diff -r e01bfc281e09 -r f06777cbd5bb lib/galaxy/config.py --- a/lib/galaxy/config.py Tue Jul 28 14:16:19 2009 -0400 +++ b/lib/galaxy/config.py Thu Jul 30 11:05:03 2009 -0400 @@ -46,6 +46,7 @@ self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) + self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) ) diff -r e01bfc281e09 -r f06777cbd5bb lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Tue Jul 28 14:16:19 2009 -0400 +++ b/lib/galaxy/security/__init__.py Thu Jul 30 11:05:03 2009 -0400 @@ -206,12 +206,16 @@ else: return None return role - def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False, bypass_manage_permission=False ): + def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False, bypass_manage_permission=False, default_access_private = False ): # bypass_manage_permission is used to change permissions of datasets in a userless history when logging in if user is None: return None if not permissions: - permissions = { self.permitted_actions.DATASET_MANAGE_PERMISSIONS : [ self.get_private_user_role( user, auto_create=True ) ] } + #default permissions + permissions = { self.permitted_actions.DATASET_MANAGE_PERMISSIONS : [ self.get_private_user_role( user, auto_create=True ) ] } + #new_user_dataset_access_role_default_private is set as True in config file + if default_access_private: + permissions[ self.permitted_actions.DATASET_ACCESS ] = permissions.values()[ 0 ] # Delete all of the current default permissions for the user for dup in user.default_permissions: dup.delete() diff -r e01bfc281e09 -r f06777cbd5bb lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Tue Jul 28 14:16:19 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu Jul 30 11:05:03 2009 -0400 @@ -157,7 +157,7 @@ user.flush() trans.app.security_agent.create_private_user_role( user ) # We set default user permissions, before we log in and set the default history permissions - trans.app.security_agent.user_set_default_permissions( user ) + trans.app.security_agent.user_set_default_permissions( user, default_access_private = trans.app.config.new_user_dataset_access_role_default_private ) # The handle_user_login() method has a call to the history_set_default_permissions() method # (needed when logging in with a history), user needs to have default permissions set before logging in trans.handle_user_login( user ) diff -r e01bfc281e09 -r f06777cbd5bb universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Tue Jul 28 14:16:19 2009 -0400 +++ b/universe_wsgi.ini.sample Thu Jul 30 11:05:03 2009 -0400 @@ -156,6 +156,9 @@ # Can an admin user delete user accounts? #allow_user_deletion = False +# Should default dataset access permissions be private for new users; default is False (datasets are public) +new_user_dataset_access_role_default_private = False + # ---- Job Execution -------------------------------------------------------- # Number of concurrent jobs to run (local job runner)

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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 ------------------------------------------------------------

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[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

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[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

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[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 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

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 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>

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