March 2010 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3551: Can customize main logo link url, rename viz l...
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/84386da2a3f3 changeset: 3551:84386da2a3f3 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Mar 22 16:59:20 2010 -0400 description: Can customize main logo link url, rename viz links diffstat: templates/base_panels.mako | 8 ++++---- universe_wsgi.ini.sample | 2 ++ 2 files changed, 6 insertions(+), 4 deletions(-) diffs (45 lines): diff -r 8938319bf173 -r 84386da2a3f3 templates/base_panels.mako --- a/templates/base_panels.mako Mon Mar 22 12:32:14 2010 -0400 +++ b/templates/base_panels.mako Mon Mar 22 16:59:20 2010 -0400 @@ -205,9 +205,9 @@ Visualization <div class="submenu"> <ul> - <li><a href="${h.url_for( controller='/tracks', action='index' )}">Build track browser</a></li> + <li><a href="${h.url_for( controller='/tracks', action='index' )}">New Track Browser</a></li> <li><hr style="color: inherit; background-color: gray"/></li> - <li><a href="${h.url_for( controller='/visualization', action='list' )}">Stored visualizations</a></li> + <li><a href="${h.url_for( controller='/visualization', action='list' )}">Saved Visualizations</a></li> </ul> </div> </td> @@ -287,11 +287,11 @@ ## Logo, layered over tabs to be clickable <div class="title" style="position: absolute; top: 0; left: 0;"> - <a href="/"> + <a href="${app.config.get( 'logo_url', '/' )}"> <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> Galaxy %if app.config.brand: - <span class='brand'>/${app.config.brand}</span> + <span class='brand'>/ ${app.config.brand}</span> %endif </a> </div> diff -r 8938319bf173 -r 84386da2a3f3 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Mon Mar 22 12:32:14 2010 -0400 +++ b/universe_wsgi.ini.sample Mon Mar 22 16:59:20 2010 -0400 @@ -126,10 +126,12 @@ ## for a local mirror where you are doing private software development ## ## Brand: appends "/[brand]" to the "Galaxy" text in the masthead +## logo_url: replaces the default "Galaxy + brand" link url ## wiki_url: replaces the default galaxy main wiki ## bugs_email: replaces the default galaxy bugs email list ##citation_url: point to a URL listing citations #brand = Private local mirror +#logo_url = / #wiki_url = /path/to/my/local/wiki #bugs_email = mailto:galaxy-bugs@example.org #citation_url = /path/to/my/citations

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[hg] galaxy 3550: Assume plink is on the executing node path for...
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8938319bf173 changeset: 3550:8938319bf173 user: fubar: ross Lazarus at gmail period com date: Mon Mar 22 12:32:14 2010 -0400 description: Assume plink is on the executing node path for converters Add a non-specific exception catcher to archive creation code in library_common diffstat: lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml | 2 +- lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml | 2 +- lib/galaxy/datatypes/genetics.py | 5 ++++- lib/galaxy/web/controllers/dataset.py | 2 +- lib/galaxy/web/controllers/library_common.py | 5 +++++ 5 files changed, 12 insertions(+), 4 deletions(-) diffs (66 lines): diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml --- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml Mon Mar 22 12:32:14 2010 -0400 @@ -3,7 +3,7 @@  <command interpreter="python"> lped_to_pbed_converter.py '$input1.extra_files_path/$input1.metadata.base_name' - '$output1' '$output1.files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' + '$output1' '$output1.files_path' 'plink' </command> <inputs> <param format="lped" name="input1" type="data" label="Choose linkage pedigree file"/> diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml --- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml Mon Mar 22 12:32:14 2010 -0400 @@ -3,7 +3,7 @@  <command interpreter="python"> pbed_to_lped_converter.py '$input1.extra_files_path/$input1.metadata.base_name' - '$output1' '$output1.files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' + '$output1' '$output1.files_path' 'plink' </command> <inputs> <param format="pbed" name="input1" type="data" label="Choose compressed Plink binary format genotype file"/> diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/datatypes/genetics.py Mon Mar 22 12:32:14 2010 -0400 @@ -114,7 +114,10 @@ npeek = 5 out = ['<table cellspacing="0" cellpadding="3">'] f = open(dataset.file_name,'r') - d = [f.next() for x in range(npeek)] + d = f.readlines()[:5] + if len(d) == 0: + out = "Cannot find anything to parse in %s" % dataset.name + return out hasheader = 0 try: test = ['%f' % x for x in d[0][1:]] # first is name - see if starts all numerics diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Mon Mar 22 12:32:14 2010 -0400 @@ -332,7 +332,7 @@ trans.response.set_content_type( mime ) return open( file_path ) else: - return "Could not find '%s' on the extra files path." % filename + return "Could not find '%s' on the extra files path %s." % (filename,file_path) mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) trans.response.set_content_type(mime) diff -r 7120c4848270 -r 8938319bf173 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Mar 22 11:06:40 2010 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Mon Mar 22 12:32:14 2010 -0400 @@ -1334,6 +1334,11 @@ log.exception( "Unable to create archive for download" ) msg = "Unable to create archive for download, please report this error" messagetype = 'error' + except: + error = True + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0]) + msg = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + messagetype = 'error' if not error: composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) seen = []

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[hg] galaxy 3549: Make boxplot tool respect exit codes when dete...
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7120c4848270 changeset: 3549:7120c4848270 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Mar 22 11:06:40 2010 -0400 description: Make boxplot tool respect exit codes when determining job errors: makes e.g. 'Could not find/open font when opening font "arial", using internal non-scalable font' a non-fatal warning. Add version attribute to gnuplot requirement tag. diffstat: tools/plotting/boxplot.xml | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (22 lines): diff -r ff39f033ce68 -r 7120c4848270 tools/plotting/boxplot.xml --- a/tools/plotting/boxplot.xml Fri Mar 19 15:09:13 2010 -0400 +++ b/tools/plotting/boxplot.xml Mon Mar 22 11:06:40 2010 -0400 @@ -1,8 +1,8 @@ <tool id="qual_stats_boxplot" name="Boxplot" version="1.0.0"> <description>of quality statistics</description> - <command>gnuplot < '$gnuplot_commands' > '$output_file'</command> + <command>gnuplot < '$gnuplot_commands' 2>&1 || echo "Error running gnuplot." >&2</command> <requirements> - <requirement type="binary">gnuplot</requirement> + <requirement type="binary" version="gnuplot 4.2 patchlevel 2">gnuplot</requirement> </requirements> <inputs> <param name="input_file" type="data" format="tabular" label="Quality Statistics File"/> @@ -30,6 +30,7 @@ </inputs> <configfiles> <configfile name="gnuplot_commands"> +set output '$output_file' set term png size ${graph_size} set boxwidth 0.8 set key right tmargin

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[hg] galaxy 3548: lims: fixed the search bug on the requests grid
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ff39f033ce68 changeset: 3548:ff39f033ce68 user: rc date: Fri Mar 19 15:09:13 2010 -0400 description: lims: fixed the search bug on the requests grid diffstat: lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diffs (24 lines): diff -r 49a7de2c4707 -r ff39f033ce68 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Thu Mar 18 22:41:15 2010 -0400 +++ b/lib/galaxy/web/controllers/requests.py Fri Mar 19 15:09:13 2010 -0400 @@ -107,7 +107,7 @@ link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) ) ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[6] ], + cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) diff -r 49a7de2c4707 -r ff39f033ce68 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu Mar 18 22:41:15 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Fri Mar 19 15:09:13 2010 -0400 @@ -124,7 +124,7 @@ ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[6] ], + cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) )

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[hg] galaxy 3547: Fix tag filtering bug for published item grids.
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/49a7de2c4707 changeset: 3547:49a7de2c4707 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Mar 18 22:41:15 2010 -0400 description: Fix tag filtering bug for published item grids. diffstat: templates/display_base.mako | 2 +- templates/grid_base.mako | 2 +- templates/history/view.mako | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diffs (36 lines): diff -r be396d94ca5a -r 49a7de2c4707 templates/display_base.mako --- a/templates/display_base.mako Thu Mar 18 16:02:09 2010 -0400 +++ b/templates/display_base.mako Thu Mar 18 22:41:15 2010 -0400 @@ -43,7 +43,7 @@ <% controller_name = get_controller_name( item ) %> var href = '${h.url_for ( controller='/' + controller_name , action='list_published')}'; href = href + "?f-tags=" + tag_name; - if (tag_value != null && tag_value != "") + if (tag_value != undefined && tag_value != "") href = href + ":" + tag_value; self.location = href; } diff -r be396d94ca5a -r 49a7de2c4707 templates/grid_base.mako --- a/templates/grid_base.mako Thu Mar 18 16:02:09 2010 -0400 +++ b/templates/grid_base.mako Thu Mar 18 22:41:15 2010 -0400 @@ -345,7 +345,7 @@ // Add tag to grid filter. function add_tag_to_grid_filter(tag_name, tag_value) { // Put tag name and value together. - var tag = tag_name + (tag_value !== null && tag_value != "" ? ":" + tag_value : ""); + var tag = tag_name + (tag_value !== undefined && tag_value != "" ? ":" + tag_value : ""); $('#more-search-options').show('fast'); add_filter_condition("tags", tag, true); } diff -r be396d94ca5a -r 49a7de2c4707 templates/history/view.mako --- a/templates/history/view.mako Thu Mar 18 16:02:09 2010 -0400 +++ b/templates/history/view.mako Thu Mar 18 22:41:15 2010 -0400 @@ -258,7 +258,7 @@ { var href = '${h.url_for( controller='/history', action='list_published')}'; href = href + "?f-tags=" + tag_name; - if (tag_value != null && tag_value != "") + if (tag_value != undefined && tag_value != "") href = href + ":" + tag_value; self.location = href; }

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[hg] galaxy 3546: Eliminate the pop-up menus for folders and dat...
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/be396d94ca5a changeset: 3546:be396d94ca5a user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Mar 18 16:02:09 2010 -0400 description: Eliminate the pop-up menus for folders and datasets if the library is deleted. diffstat: templates/library/common/browse_library.mako | 130 +++++++++++++------------- 1 files changed, 67 insertions(+), 63 deletions(-) diffs (187 lines): diff -r 2590120aed68 -r be396d94ca5a templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Thu Mar 18 12:57:29 2010 -0400 +++ b/templates/library/common/browse_library.mako Thu Mar 18 16:02:09 2010 -0400 @@ -208,38 +208,40 @@ %if ldda.library_dataset.deleted: </span> %endif - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="dataset-${ldda.id}-popup"> - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> - %else: - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_manage ): - <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> - %endif - %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> - %endif - %if cntrller in [ 'library_admin', 'requests_admin' ]: - %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: - <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> - %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + %if not library.deleted: + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="dataset-${ldda.id}-popup"> + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_edit_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + %else: + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_info', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">View information</a> %endif - %endif - </div> + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='ldda', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), ldda_id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_manage ): + <a class="action-button" href="${h.url_for( controller='library_common', action='ldda_permissions', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), id=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ( cntrller == 'library_admin' or can_modify ): + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> + %endif + %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> + %endif + %if cntrller in [ 'library_admin', 'requests_admin' ]: + %if not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.deleted: + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Delete this dataset</a> + %elif not library.deleted and not branch_deleted( folder ) and not ldda.library_dataset.purged and ldda.library_dataset.deleted: + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library_dataset.id ), item_type='library_dataset', show_deleted=show_deleted )}">Undelete this dataset</a> + %endif + %endif + </div> + %endif </td> <td id="libraryItemInfo">${render_library_item_info( ldda )}</td> <td>${uploaded_by}</td> @@ -252,7 +254,7 @@ %endif </%def> -<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library_id, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False )"> +<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False )"> <% from galaxy.web.controllers.library_common import active_folders, active_folders_and_lddas, activatable_folders_and_lddas, branch_deleted @@ -300,40 +302,42 @@ %if folder.deleted: <span class="libraryItem-error"> %endif - <a href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted )}">${folder.name}</a> + <a href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), show_deleted=show_deleted )}">${folder.name}</a> %if folder.description: <i>- ${folder.description}</i> %endif %if folder.deleted: </span> %endif - <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="folder_img-${folder.id}-popup"> - %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_add ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> - %endif - %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_modify ): - <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> - %endif - %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> - %endif - %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): - <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> - <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> - %endif - %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_manage ): - <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=library_id, use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> - %endif - %if cntrller in [ 'library_admin', 'requests_admin' ]: - %if not library.deleted and not folder.deleted: - <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library_id, item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> - %elif not library.deleted and folder.deleted and not folder.purged: - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=library_id, item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> + %if not library.deleted: + <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="folder_img-${folder.id}-popup"> + %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_add ): + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> %endif - %endif - </div> + %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_modify ): + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a> + %endif + %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and not info_association ): + <a class="action-button" href="${h.url_for( controller='library_common', action='add_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add template</a> + %endif + %if not branch_deleted( folder ) and ( ( cntrller == 'library_admin' or can_modify ) and info_association ): + <a class="action-button" href="${h.url_for( controller='library_common', action='edit_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit template</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='delete_template', cntrller=cntrller, item_type='folder', library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Delete template</a> + %endif + %if not branch_deleted( folder ) and ( cntrller == 'library_admin' or can_manage ): + <a class="action-button" href="${h.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> + %endif + %if cntrller in [ 'library_admin', 'requests_admin' ]: + %if not library.deleted and not folder.deleted: + <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Delete this folder</a> + %elif not library.deleted and folder.deleted and not folder.purged: + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( folder.id ), item_type='folder', show_deleted=show_deleted )}">Undelete this folder</a> + %endif + %endif + </div> + %endif </div> <td colspan="3"></td> </tr> @@ -345,7 +349,7 @@ %if cntrller == 'library': <% sub_folders = active_folders( trans, folder ) %> %for sub_folder in sub_folders: - ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library_id, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} + ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} %endfor %for library_dataset in folder.active_library_datasets: <% @@ -365,7 +369,7 @@ sub_folders, lddas = active_folders_and_lddas( trans, folder ) %> %for sub_folder in sub_folders: - ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library_id, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} + ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )} %endfor %for ldda in lddas: <% @@ -470,12 +474,12 @@ </tr> <% row_counter = RowCounter() %> %if cntrller in [ 'library', 'requests' ]: - ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, trans.security.encode_id( library.id ), hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} + ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} %if not library.deleted: ${render_actions_on_multiple_items()} %endif %elif cntrller in [ 'library_admin', 'requests_admin' ]: - ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, trans.security.encode_id( library.id ), [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} + ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} %if not library.deleted and not show_deleted: ${render_actions_on_multiple_items()} %endif

1 0

help with dynamic select parameters
by Lee, Joshua 24 Mar '10

24 Mar '10

Hi, I'm trying to create a tool where there are several select parameters whose choices are determine by the previous parameter(s). I have a toy example with three parameters: Category, Food, and Prep method. Depending on the chosen Category, only certain Foods are shown, which in turn determines which Prep methods are available. I'm trying to use the <options> tag with the "from_file" attribute. I have one column per parameter and one row per valid combination. My problem is that the front end can get into a state where a certain valid combinations will be unselectable. In the example below, I can never select "Fruit", "Kiwi", and "Raw". When I change the 1st select, the values for the 2nd select are loaded, but the values for the 3rd select cannot be updated. This is particularly problematic if there is only one choice for the 2nd select, because I cannot get it's "onchange" handler to fire (so the 3rd select is always empty). In my case, it would be nice if the first value of the 2nd select is chosen as a default, and the 3rd select is populated accordingly. Any help would be appreciated. Perhaps I'm not using these features as intended, but it seemed like a natural application. Thanks, Josh My data file looks like: Meat Chicken Fried Meat Chicken Grilled Meat Beef Grilled Meat Beef Stir-fried Veg Carrot Boiled Veg Fennel Raw Fruit Kiwi Raw And my tool's <inputs> section is: <inputs> <param name="paramA" type="select" label="Category"> <options from_file="test_select_options.txt"> <column name="value" index="0"/> <column name="name" index="0"/> <filter type="unique_value" name="unique" column="0"/> </options> </param> <param name="paramB" type="select" label="Food" > <options from_file="test_select_options.txt"> <column name="value" index="1"/> <column name="name" index="1"/> <filter type="unique_value" name="unique" column="1"/> <filter type="param_value" ref="paramA" name="A" column="0"/> </options> </param> <param name="paramC" type="select" label="How prepared"> <options from_file="test_select_options.txt"> <column name="value" index="2"/> <column name="name" index="2"/> <filter type="param_value" ref="paramA" name="A" column="0"/> <filter type="param_value" ref="paramB" name="B" column="1"/> </options> </param> </inputs>

2 1

Binary datatypes
by Pieter Neerincx 24 Mar '10

24 Mar '10

Hi Galaxy team, Some time ago I added a binary data type to my Galaxy development machine. I simply defined the input for a tool as the standard binary data type. Recently I upgraded my Galaxy instance and afterwards I could no longer upload binary data successfully :(. So, I looked at the docs to properly define a new binary data specific for that tool. I created a Python class, wrote a sniffer and listed the new stuff in the datatypes_conf.xml. To my surprise that did not work... After some digging I found that for a binary datatype I also had to hack the data upload tool in two places (see below). The word hack is maybe a bit too much for simply copying the lines for the already supported bam and Sff data types, but having to change code to support a new datatype sounds like a bad plan to me. Would it be possible to make sure support for a new binary data type is completely handled by config files and maybe a new python class, but without hacking code just like for non-binary data types? Cheers, Pi ------------------- def check_bam( temp_name ): return Bam().sniff( temp_name ) def check_sff( temp_name ): return Sff().sniff( temp_name ) # # Added mod for Thermo Finnigan RAW files START # def check_raw( temp_name ): return RAW().sniff( temp_name ) # # Added mod for Thermo Finnigan RAW files END # ..... # Is dataset content supported sniffable binary? elif check_bam( dataset.path ): ext = 'bam' data_type = 'bam' elif check_sff( dataset.path ): ext = 'sff' data_type = 'sff' # # Added mod for Thermo Finnigan RAW files START # elif check_raw( dataset.path ): ext = 'raw' data_type = 'raw' # # Added mod for Thermo Finnigan RAW files END #

2 2

Feature Request: customize name of history item in a collected primary dataset
by Lee, Joshua 23 Mar '10

23 Mar '10

Hi, I have a tool that produces a variable number of outputs, which are written to the tmp database path with the specially formatted name "%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type ). In lib/galaxy/tools/__init__.py, the history item's "designation" is set to "name" and the item's "name" is set to output1.name. This potentially creates many items with the same name, which must be differentiated either through meta data or by examining the contents of the file. I would like to request a means to customize the name of the collected dataset. A simple but hack-y method would be to append another token to the name of the file. If this token exists, it would be used as the history item's name e.g. "primary_123_NAME123_visible_txt_dbkey_NEWNAME". This would also require that the optional DBKEY token would have to be validated for non-blank values. Josh

1 0

format for csv file to import a sequencing request sample
by nsfox＠uwaterloo.ca 23 Mar '10

23 Mar '10

Hi, What is the order of the parameters/format for a csv file that I can use to import a sequencing request sample? Thanks, Natalie

2 3