- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2632: Added documentation and exception handling for...
by Greg Von Kuster 29 Aug '09

29 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/31150f0b216d changeset: 2632:31150f0b216d user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Aug 28 12:52:43 2009 -0400 description: Added documentation and exception handling for mysql index error. 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0015_tagging.py diffs (98 lines): diff -r 4b4bac1f66bd -r 31150f0b216d lib/galaxy/model/migrate/versions/0015_tagging.py --- a/lib/galaxy/model/migrate/versions/0015_tagging.py Thu Aug 27 16:27:10 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0015_tagging.py Fri Aug 28 12:52:43 2009 -0400 @@ -1,3 +1,15 @@ +""" +This migration script adds the tables necessary to support tagging of histories, +datasets, and history-dataset associations (user views of datasets). + +If using mysql, this script will display the following error, which is corrected in the next +migration script: + +history_dataset_association_tag_association table failed: (OperationalError) +(1059, "Identifier name 'ix_history_dataset_association_tag_association_history_dataset_association_id' +is too long) +""" + from sqlalchemy import * from migrate import * @@ -11,6 +23,19 @@ log = logging.getLogger( __name__ ) metadata = MetaData( migrate_engine ) + +def display_migration_details(): + print "" + print "This migration script adds the tables necessary to support tagging of histories," + print "datasets, and history-dataset associations (user views of datasets)." + print "" + print "If using mysql, this script will display the following error, which is " + print "corrected in the next migration script:" + print "history_dataset_association_tag_association table failed: " + print "(OperationalError) (1059, 'Identifier name " + print "'ix_history_dataset_association_tag_association_history_dataset_association_id'" + print "is too long)" + # New tables to support tagging of histories, datasets, and history-dataset associations. Tag_table = Table( "tag", metadata, @@ -42,15 +67,48 @@ Column( "user_value", TrimmedString(255), index=True) ) def upgrade(): + display_migration_details() metadata.reflect() - Tag_table.create() - HistoryTagAssociation_table.create() - DatasetTagAssociation_table.create() - HistoryDatasetAssociationTagAssociation_table.create() + try: + Tag_table.create() + except Exception, e: + print str(e) + log.debug( "Creating tag table failed: %s" % str( e ) ) + try: + HistoryTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating history_tag_association table failed: %s" % str( e ) ) + try: + DatasetTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating dataset_tag_association table failed: %s" % str( e ) ) + try: + HistoryDatasetAssociationTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating history_dataset_association_tag_association table failed: %s" % str( e ) ) def downgrade(): metadata.reflect() - Tag_table.drop() - HistoryTagAssociation_table.drop() - DatasetTagAssociation_table.drop() - HistoryDatasetAssociationTagAssociation_table.drop() \ No newline at end of file + try: + Tag_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping tag table failed: %s" % str( e ) ) + try: + HistoryTagAssociation_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping history_tag_association table failed: %s" % str( e ) ) + try: + DatasetTagAssociation_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping dataset_tag_association table failed: %s" % str( e ) ) + try: + HistoryDatasetAssociationTagAssociation_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping history_dataset_association_tag_association table failed: %s" % str( e ) ) \ No newline at end of file

1 0

[hg] galaxy 2631: Image files for tagging UI
by Greg Von Kuster 29 Aug '09

29 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4b4bac1f66bd changeset: 2631:4b4bac1f66bd user: jeremy goecks <jeremy.goecks at emory.edu> date: Thu Aug 27 16:27:10 2009 -0400 description: Image files for tagging UI 4 file(s) affected in this change: static/images/add_icon.png static/images/add_icon_dark.png static/images/delete_tag_icon_gray.png static/images/delete_tag_icon_white.png diffs (8 lines): diff -r 3c48856d80eb -r 4b4bac1f66bd static/images/add_icon.png Binary file static/images/add_icon.png has changed diff -r 3c48856d80eb -r 4b4bac1f66bd static/images/add_icon_dark.png Binary file static/images/add_icon_dark.png has changed diff -r 3c48856d80eb -r 4b4bac1f66bd static/images/delete_tag_icon_gray.png Binary file static/images/delete_tag_icon_gray.png has changed diff -r 3c48856d80eb -r 4b4bac1f66bd static/images/delete_tag_icon_white.png Binary file static/images/delete_tag_icon_white.png has changed

1 0

<param> multiple formats
by Dominic Tolle 28 Aug '09

28 Aug '09

Hi, is it possible for a input parameter to accept multiple format types (e.g csfasta and fast), or do I need to write two separate tool configs? For example if I have a format conversion tool which accepts a number of input formats and converts them to a specific output format do I need to write a tool config for each conversion? One way around this would be to include a conditional in the tool config and let the user specify the input type, but is there another way (preferably not involving writing large conditionals)? Cheers Dominic

2 1

[hg] galaxy 2628: Fix for importing a shared history via a link ...
by Greg Von Kuster 26 Aug '09

26 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d99cee3a4efd changeset: 2628:d99cee3a4efd user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Aug 26 07:12:04 2009 -0400 description: Fix for importing a shared history via a link for an anonymous user with no existing Galaxy cookies. 1 file(s) affected in this change: lib/galaxy/web/controllers/history.py diffs (12 lines): diff -r 03accd13066e -r d99cee3a4efd lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Aug 25 16:59:28 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Wed Aug 26 07:12:04 2009 -0400 @@ -322,7 +322,7 @@ return trans.show_ok_message( """ History "%s" has been imported. Click <a href="%s">here</a> to begin.""" % ( new_history.name, web.url_for( '/' ) ) ) - elif not user_history.datasets or confirm: + elif not user_history or not user_history.datasets or confirm: new_history = import_history.copy() new_history.name = "imported: " + new_history.name new_history.user_id = None

1 0

[hg] galaxy 2627: Fix for importing a shared history via a link ...
by Greg Von Kuster 25 Aug '09

25 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/03accd13066e changeset: 2627:03accd13066e user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 25 16:59:28 2009 -0400 description: Fix for importing a shared history via a link if not logged in. 1 file(s) affected in this change: lib/galaxy/web/controllers/history.py diffs (21 lines): diff -r 4759e4bd03aa -r 03accd13066e lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Aug 25 16:35:11 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Tue Aug 25 16:59:28 2009 -0400 @@ -738,10 +738,11 @@ history = trans.sa_session.query( model.History ).get( id ) if not history: err+msg( "History not found" ) - # Verify ownership - user = trans.get_user() - if not user: - error( "Must be logged in to manage histories" ) - if check_ownership and not( history.user == user ): - error( "History is not owned by current user" ) + if check_ownership: + # Verify ownership + user = trans.get_user() + if not user: + error( "Must be logged in to manage histories" ) + if history.user != user: + error( "History is not owned by current user" ) return history

1 0

[hg] galaxy 2624: Some styles for text content areas. Pages will...
by Greg Von Kuster 25 Aug '09

25 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/16fedfa03433 changeset: 2624:16fedfa03433 user: James Taylor <james(a)jamestaylor.org> date: Tue Aug 25 15:15:07 2009 -0400 description: Some styles for text content areas. Pages will use these. (Tables look slightly different in the editor because borders cannot be collapsed and still show the structure) 7 file(s) affected in this change: lib/galaxy/web/controllers/page.py static/june_2007_style/base.css.tmpl static/june_2007_style/blue/base.css static/june_2007_style/process_css.py static/wymeditor/iframe/galaxy/wymiframe.css static/wymeditor/iframe/galaxy/wymiframe.html templates/page/display.mako diffs (161 lines): diff -r 16b1ca0b2746 -r 16fedfa03433 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Tue Aug 25 14:58:37 2009 -0400 +++ b/lib/galaxy/web/controllers/page.py Tue Aug 25 15:15:07 2009 -0400 @@ -13,7 +13,7 @@ return username + "/" + item.slug def get_link( self, trans, grid, item ): if trans.user.username: - return dict( action='display_by_username_and_slug', username=trans.user.username, slug=item.slug ) + return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) else: return None # Grid definition @@ -44,7 +44,9 @@ @web.expose @web.require_admin def index( self, trans, *args, **kwargs ): + # Build grid grid = self.list( trans, *args, **kwargs ) + # Render grid wrapped in panels return trans.fill_template( "page/index.mako", grid=grid ) @web.expose diff -r 16b1ca0b2746 -r 16fedfa03433 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Tue Aug 25 14:58:37 2009 -0400 +++ b/static/june_2007_style/base.css.tmpl Tue Aug 25 15:15:07 2009 -0400 @@ -629,3 +629,45 @@ .grid .current { background-color: #EEEEFF; } + +## Styles for areas of text content + +.text-content { + + hr { + display:block; + background:black; + color:black; + width:100%; + height:1px; + border:none; + background:#aaa; + color:#aaa; + } + + table + { + border-collapse:collapse; + border-top:1px solid #ccc; + border-left:1px solid #ccc; + } + + blockquote { + color:#666; + } + + fieldset { + border-color:#ccc; + border:1px solid #ccc; + } + + th,td { + border-bottom:1px solid #ddd; + border-right:1px solid #ccc; + } + + th,td { + padding:.8em; + } + +} diff -r 16b1ca0b2746 -r 16fedfa03433 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Tue Aug 25 14:58:37 2009 -0400 +++ b/static/june_2007_style/blue/base.css Tue Aug 25 15:15:07 2009 -0400 @@ -106,3 +106,10 @@ .grid thead th{background:#ebd9b2;background-repeat:repeat-x;background-position:top;border-top:solid #d8b365 1px;border-bottom:solid #d8b365 1px;padding:0.5em 1em;text-align:left;} .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:0.5em 1em;} .grid .current{background-color:#EEEEFF;} +.text-content{} +.text-content hr{display:block;background:black;color:black;width:100%;height:1px;border:none;background:#aaa;color:#aaa;} +.text-content table{border-collapse:collapse;border-top:1px solid #ccc;border-left:1px solid #ccc;} +.text-content blockquote{color:#666;} +.text-content fieldset{border-color:#ccc;border:1px solid #ccc;} +.text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} +.text-content th,.text-content td{padding:.8em;} diff -r 16b1ca0b2746 -r 16fedfa03433 static/june_2007_style/process_css.py --- a/static/june_2007_style/process_css.py Tue Aug 25 14:58:37 2009 -0400 +++ b/static/june_2007_style/process_css.py Tue Aug 25 15:15:07 2009 -0400 @@ -12,7 +12,11 @@ import sys, string, os.path from pyparsing import * from odict import odict -import Image + +try: + import Image +except ImportError: + from PIL import Image def cross_lists(*sets): """ diff -r 16b1ca0b2746 -r 16fedfa03433 static/wymeditor/iframe/galaxy/wymiframe.css --- a/static/wymeditor/iframe/galaxy/wymiframe.css Tue Aug 25 14:58:37 2009 -0400 +++ b/static/wymeditor/iframe/galaxy/wymiframe.css Tue Aug 25 15:15:07 2009 -0400 @@ -19,11 +19,6 @@ /* VISUAL FEEDBACK */ -/* Galaxy font styles */ - -body{font:13px/1.231 verdana,arial,helvetica,clean,sans-serif;*font-size:small;*font:x-small;}select,input,button,textarea,button{font:99% verdana,arial,helvetica,clean,sans-serif;}table{font-size:inherit;font:100%;}pre,code,kbd,samp,tt{font-family:monospace;*font-size:108%;line-height:100%;} -body{font-size:75%;} - /* basic */ /* make HTML blocs visible */ @@ -38,15 +33,15 @@ ol, table, blockquote, - pre { background: #FFFFFF no-repeat 2px 2px; - padding:8px 5px 5px; - margin:10px; } + pre { background: #FFFFFF no-repeat 2px 2px !important; + padding:8px 5px 5px !important; + margin:10px !important; } td { background: #F0F4F8; } th { background: #ffffcc; } ul, ol { border-left:20px solid #B9C4D0; padding:0px 5px; } caption { background: #E4E4B0; padding: 5px; font-weight: bold; } - table { font-size: 12px; width: 500px; } + table { font-size: 12px; min-width: 500px; border: none !important; border-collapse: separate !important } td { width: 25%; } blockquote { margin-left: 30px; } pre { background-color:transparent; border: 1px solid white; } diff -r 16b1ca0b2746 -r 16fedfa03433 static/wymeditor/iframe/galaxy/wymiframe.html --- a/static/wymeditor/iframe/galaxy/wymiframe.html Tue Aug 25 14:58:37 2009 -0400 +++ b/static/wymeditor/iframe/galaxy/wymiframe.html Tue Aug 25 15:15:07 2009 -0400 @@ -20,7 +20,8 @@ <head> <title>WYMeditor iframe</title> <meta http-equiv="X-UA-Compatible" content="IE=EmulateIE7" /> +<link rel="stylesheet" type="text/css" media="screen" href="../../../style/base.css" /> <link rel="stylesheet" type="text/css" media="screen" href="wymiframe.css" /> </head> -<body class="wym_iframe"></body> +<body class="wym_iframe text-content"></body> </html> diff -r 16b1ca0b2746 -r 16fedfa03433 templates/page/display.mako --- a/templates/page/display.mako Tue Aug 25 14:58:37 2009 -0400 +++ b/templates/page/display.mako Tue Aug 25 15:15:07 2009 -0400 @@ -20,7 +20,7 @@ <div class="unified-panel-body"> <div style="overflow: auto; height: 100%;"> - <div class="page-container" style="padding: 10px;"> + <div class="page text-content" style="padding: 10px;"> ${page.latest_revision.content.decode( "utf-8" )} </div> </div>

1 0

[hg] galaxy 2625: Allow column parameters to be late validated i...
by Greg Von Kuster 25 Aug '09

25 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/50e4baed24f5 changeset: 2625:50e4baed24f5 user: James Taylor <james(a)jamestaylor.org> date: Tue Aug 25 16:25:50 2009 -0400 description: Allow column parameters to be late validated if the job is still running and metadata is not yet available 2 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/tools/parameters/basic.py diffs (52 lines): diff -r 16fedfa03433 -r 50e4baed24f5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Aug 25 15:15:07 2009 -0400 +++ b/lib/galaxy/model/__init__.py Tue Aug 25 16:25:50 2009 -0400 @@ -403,6 +403,7 @@ return self.get_size() > 0 def mark_deleted( self, include_children=True ): self.deleted = True + # FIXME: sqlalchemy will replace this def _delete(self): """Remove the file that corresponds to this data""" @@ -560,6 +561,14 @@ if self.purged: return False return True + @property + def is_pending( self ): + """ + Return true if the dataset is neither ready nor in error + """ + return self.state in ( self.states.NEW, self.states.UPLOAD, + self.states.QUEUED, self.states.RUNNING, + self.states.SETTING_METADATA ) @property def source_library_dataset( self ): def get_source( dataset ): diff -r 16fedfa03433 -r 50e4baed24f5 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Tue Aug 25 15:15:07 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Tue Aug 25 16:25:50 2009 -0400 @@ -793,7 +793,21 @@ return set( self.get_column_list( trans, other_values ) ) def get_dependencies( self ): return [ self.data_ref ] - + def need_late_validation( self, trans, context ): + if super( ColumnListParameter, self ).need_late_validation( trans, context ): + return True + # Get the selected dataset if selected + dataset = context[ self.data_ref ] + if dataset: + # Check if the dataset does not have the expected metadata for columns + if not dataset.metadata.columns: + # Only allow late validation if the dataset is not yet ready + # (since we have reason to expect the metadata to be ready eventually) + if dataset.is_pending: + return True + # No late validation + return False + class DrillDownSelectToolParameter( SelectToolParameter ): """

1 0

[hg] galaxy 2626: Fix for sharing a history via a link.
by Greg Von Kuster 25 Aug '09

25 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4759e4bd03aa changeset: 2626:4759e4bd03aa user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 25 16:35:11 2009 -0400 description: Fix for sharing a history via a link. 1 file(s) affected in this change: lib/galaxy/web/controllers/history.py diffs (12 lines): diff -r 50e4baed24f5 -r 4759e4bd03aa lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Aug 25 16:25:50 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Tue Aug 25 16:35:11 2009 -0400 @@ -298,7 +298,7 @@ user_history = trans.get_history() if not id: return trans.show_error_message( "You must specify a history you want to import." ) - import_history = get_history( trans, id ) + import_history = get_history( trans, id, check_ownership=False ) if not import_history: return trans.show_error_message( "The specified history does not exist.") if not import_history.importable:

1 0

[hg] galaxy 2623: Fix for multi-byte file uploads
by Greg Von Kuster 25 Aug '09

25 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/16b1ca0b2746 changeset: 2623:16b1ca0b2746 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Aug 25 14:58:37 2009 -0400 description: Fix for multi-byte file uploads 3 file(s) affected in this change: lib/galaxy/tools/actions/upload.py lib/galaxy/tools/parameters/grouping.py tools/data_source/upload.py diffs (46 lines): diff -r 3a22898d47f5 -r 16b1ca0b2746 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Tue Aug 25 12:58:38 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Tue Aug 25 14:58:37 2009 -0400 @@ -104,6 +104,7 @@ except: is_binary = None json = dict( file_type = uploaded_dataset.file_type, + ext = uploaded_dataset.ext, name = uploaded_dataset.name, dataset_id = data.dataset.id, dbkey = uploaded_dataset.dbkey, diff -r 3a22898d47f5 -r 16b1ca0b2746 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Tue Aug 25 12:58:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Tue Aug 25 14:58:37 2009 -0400 @@ -327,6 +327,8 @@ rval = [] for dataset in datasets: dataset.file_type = file_type + dataset.datatype = d_type + dataset.ext = self.get_datatype_ext( trans, context ) dataset.dbkey = dbkey rval.append( dataset ) return rval diff -r 3a22898d47f5 -r 16b1ca0b2746 tools/data_source/upload.py --- a/tools/data_source/upload.py Tue Aug 25 12:58:38 2009 -0400 +++ b/tools/data_source/upload.py Tue Aug 25 14:58:37 2009 -0400 @@ -136,7 +136,7 @@ file_err( 'The uploaded file is empty', dataset, json_file ) return if 'is_multi_byte' not in dir( dataset ): - dataset.is_multi_byte = util.is_multi_byte( open( dataset.path, 'r' ).read( 1024 )[:100] ) + dataset.is_multi_byte = util.is_multi_byte( open( dataset.path, 'r' ).read( 1024 ) ) if dataset.is_multi_byte: ext = sniff.guess_ext( dataset.path, is_multi_byte=True ) data_type = ext @@ -225,6 +225,10 @@ ext = dataset.file_type data_type = ext # Save job info for the framework + if ext == 'auto' and dataset.ext: + ext = dataset.ext + if ext == 'auto': + ext = 'data' info = dict( type = 'dataset', dataset_id = dataset.dataset_id, path = dataset.path,

1 0

IE bug
by SHAUN WEBB 25 Aug '09

25 Aug '09

Hello, I have a library of public datasets set up on our local install. When viewing the library in Internet Explorer I am unable to expand folders using the blue arrow, this isn't a problem in either Firefox or Safari. Thanks for your help Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

3 4