1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3a2753976434/
Changeset: 3a2753976434
User: carlfeberhard
Date: 2013-07-22 21:48:50
Summary: library upload: sort dbkeys, default to unspecified, remove unneeded call to replace_big_select_inputs
Affected #: 2 files
diff -r b72d967e0cf4a506f0bfbcef0f068fe1709659e9 -r 3a27539764348d4099669bc7fe94c9432e62aff0 lib/galaxy/webapps/galaxy/controllers/library_common.py
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -949,7 +949,10 @@
# Send list of data formats to the upload form so the "extension" select list can be populated dynamically
file_formats = trans.app.datatypes_registry.upload_file_formats
+
dbkeys = trans.app.genomes.get_dbkeys( trans )
+ dbkeys.sort( key=lambda dbkey: dbkey[0].lower() )
+
# Send the current history to the form to enable importing datasets from history to library
history = trans.get_history()
if history is not None:
diff -r b72d967e0cf4a506f0bfbcef0f068fe1709659e9 -r 3a27539764348d4099669bc7fe94c9432e62aff0 templates/webapps/galaxy/library/common/common.mako
--- a/templates/webapps/galaxy/library/common/common.mako
+++ b/templates/webapps/galaxy/library/common/common.mako
@@ -271,8 +271,16 @@
<label>Genome:</label><div class="form-row-input"><select name="dbkey" last_selected_value="?">
+ <%
+ # move unspecified to the first option and set as default if not last_used_build
+ #TODO: remove when we decide on a common dbkey selector widget
+ unspecified = ('unspecified (?)', '?')
+ dbkeys.remove( unspecified )
+ dbkeys.insert( 0, unspecified )
+ default_selected = last_used_build or '?'
+ %>
%for dbkey in dbkeys:
- %if dbkey[1] == last_used_build:
+ %if dbkey[1] == default_selected:
<option value="${dbkey[1]}" selected>${dbkey[0]}</option>
%else:
<option value="${dbkey[1]}">${dbkey[0]}</option>
@@ -331,13 +339,6 @@
</form></div></div>
- ## Script to replace dbkey select with select+search.
- <script type="text/javascript">
- // Replace dbkey select with search+select.
- jQuery(document).ready( function() {
- replace_big_select_inputs();
- });
- </script>
%elif upload_option == 'import_from_history':
<div class="toolForm"><div class="toolFormTitle">Active datasets in your current history (${ util.unicodify( history.name )})</div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b72d967e0cf4/
Changeset: b72d967e0cf4
User: Dave Bouvier
Date: 2013-07-22 19:14:58
Summary: Wrap the repository type select in form tags so that Twill will correctly parse the HTML on the browse repository files page. This resolves failing functional tests in the test_0440_deleting_dependency_definitions script.
Affected #: 2 files
diff -r 559effee9eb7a5b0b78fea2df900e35dd5cf7d04 -r b72d967e0cf4a506f0bfbcef0f068fe1709659e9 templates/webapps/tool_shed/repository/browse_repository.mako
--- a/templates/webapps/tool_shed/repository/browse_repository.mako
+++ b/templates/webapps/tool_shed/repository/browse_repository.mako
@@ -46,7 +46,9 @@
${render_clone_str( repository )}
</div>
%endif
- ${render_repository_type_select_field( repository_type_select_field, render_help=False )}
+ <form name="repository_type">
+ ${render_repository_type_select_field( repository_type_select_field, render_help=False )}
+ </form>
%if can_push:
<form name="select_files_to_delete" id="select_files_to_delete" action="${h.url_for( controller='repository', action='select_files_to_delete', id=trans.security.encode_id( repository.id ))}" method="post" ><div class="form-row" >
diff -r 559effee9eb7a5b0b78fea2df900e35dd5cf7d04 -r b72d967e0cf4a506f0bfbcef0f068fe1709659e9 test/tool_shed/base/twilltestcase.py
--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -348,7 +348,7 @@
# Twill sets hidden form fields to read-only by default. We need to write to this field.
form = tc.browser.get_form( 'select_files_to_delete' )
form.find_control( "selected_files_to_delete" ).readonly = False
- tc.fv( "1", "selected_files_to_delete", ','.join( files_to_delete ) )
+ tc.fv( "2", "selected_files_to_delete", ','.join( files_to_delete ) )
tc.submit( 'select_files_to_delete_button' )
self.check_for_strings( strings_displayed, strings_not_displayed )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2ba6bd8a9d25/
Changeset: 2ba6bd8a9d25
User: greg
Date: 2013-07-19 21:19:04
Summary: Enhance the change_directory action for installing tool dependencies via fabric to allow for changing the current directory to a location above the current working directory as long as the location is still within the defined working_directory.
Affected #: 1 file
diff -r 5d0cfe53740b554f2643a3518ea23807dfdb26a5 -r 2ba6bd8a9d25e26ce6668c2a0219199b49e255d7 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
@@ -339,9 +339,13 @@
extract = action_dict.get( 'extract', False )
common_util.url_download( current_dir, filename, url, extract=extract )
elif action_type == 'change_directory':
- target_directory = os.path.realpath( os.path.join( current_dir, action_dict[ 'directory' ] ) )
+ target_directory = os.path.realpath( os.path.normpath( os.path.join( current_dir, action_dict[ 'directory' ] ) ) )
if target_directory.startswith( os.path.realpath( current_dir ) ) and os.path.exists( target_directory ):
+ # Change directory to a directory within the current working directory.
dir = target_directory
+ elif target_directory.startswith( os.path.realpath( work_dir ) ) and os.path.exists( target_directory ):
+ # Change directory to a directory above the current working directory, but within the defined work_dir.
+ dir = target_directory.replace( os.path.realpath( work_dir ), '' ).lstrip( '/' )
else:
log.error( 'Invalid or nonexistent directory %s specified, ignoring change_directory action.', target_directory )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5d0cfe53740b/
Changeset: 5d0cfe53740b
User: guerler
Date: 2013-07-19 20:56:39
Summary: bowtie2 wrapper update
Affected #: 1 file
diff -r 883d7c4b387c0e701539b49e593144b7c027a64c -r 5d0cfe53740b554f2643a3518ea23807dfdb26a5 tools/sr_mapping/bowtie2_wrapper.xml
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -99,7 +99,7 @@
## rename unaligned sequence files
#if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
- #set left = str(str($output_unaligned_reads_l).replace( '.dat', '.1.dat' ))
+ #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' )
#set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' )
mv $left $output_unaligned_reads_l;
@@ -317,6 +317,7 @@
Trim n-bases from 5' (left) end of each read before alignment.
*-3/--trim3 (default: 0)*
+
Trim n-bases from 3' (right) end of each read before alignment.
*--nofw/--norc (default: both strands enabled)*
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cd7fe5ef5328/
Changeset: cd7fe5ef5328
User: greg
Date: 2013-07-19 20:14:59
Summary: More fixes for managing tool dependencies for installed tool shed repositories.
Affected #: 1 file
diff -r 2c257f0cbeb8a09e9b04a67ae59bf68a46e650e9 -r cd7fe5ef532822f778dda054ec434aec6ce17eee lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -731,9 +731,15 @@
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
- # We need a tool_shed_repository, so get it from one of the tool_dependencies.
- tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
- tool_shed_repository = tool_dependency.tool_shed_repository
+ repository_id = kwd.get( 'repository_id', None )
+ if tool_dependency_ids:
+ # We need a tool_shed_repository, so get it from one of the tool_dependencies.
+ tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
+ tool_shed_repository = tool_dependency.tool_shed_repository
+ else:
+ # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
+ # tool dependency, but they didn't check any of the available tool dependencies on which to perform the action.
+ tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, repository_id )
self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % tool_shed_repository.name
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
@@ -773,6 +779,7 @@
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='manage_repository_tool_dependencies',
tool_dependency_ids=tool_dependency_ids,
+ repository_id=repository_id,
message=message,
status=status ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2c257f0cbeb8/
Changeset: 2c257f0cbeb8
User: greg
Date: 2013-07-19 19:57:31
Summary: Fixes for managing the tool dependencies of an installed tool shed repository.
Affected #: 3 files
diff -r 25a0393e91120b4e0fa79b868f5fafc8ea14843b -r 2c257f0cbeb8a09e9b04a67ae59bf68a46e650e9 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -653,9 +653,15 @@
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
- # We need a tool_shed_repository, so get it from one of the tool_dependencies.
- tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
- tool_shed_repository = tool_dependency.tool_shed_repository
+ if tool_dependency_ids:
+ # We need a tool_shed_repository, so get it from one of the tool_dependencies.
+ tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
+ tool_shed_repository = tool_dependency.tool_shed_repository
+ else:
+ # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
+ # tool dependency, but they didn't check any of the available tool dependencies on which to perform the action.
+ repository_id = kwd.get( 'repository_id', None )
+ tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, repository_id )
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if not tool_dependency_ids:
@@ -664,7 +670,7 @@
kwd[ 'status' ] = 'error'
del kwd[ 'operation' ]
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='manage_installed_tool_dependencies',
+ action='manage_repository_tool_dependencies',
**kwd ) )
if operation == 'browse':
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
@@ -720,7 +726,7 @@
@web.expose
@web.require_admin
def manage_tool_dependencies( self, trans, **kwd ):
- # This method is called when tool dependencies are being installed. See the related manage_repository_tool-dependencies
+ # This method is called when tool dependencies are being installed. See the related manage_repository_tool_dependencies
# method for managing the tool dependencies for a specified installed tool shed repository.
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
diff -r 25a0393e91120b4e0fa79b868f5fafc8ea14843b -r 2c257f0cbeb8a09e9b04a67ae59bf68a46e650e9 templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
--- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
+++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
@@ -44,7 +44,7 @@
<tr><td>
%if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]:
- <a target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='browse', tool_dependency_ids=trans.security.encode_id( tool_dependency.id ) )}">
+ <a target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='browse', tool_dependency_ids=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}">
${tool_dependency.name}
</a>
%else:
@@ -60,7 +60,7 @@
</table>
%if can_install:
<br/>
- <form name="install_tool_dependencies" id="install_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='install' )}" method="post" >
+ <form name="install_tool_dependencies" id="install_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='install', repository_id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row">
Check each tool dependency that you want to install and click <b>Install</b>.
</div>
@@ -81,7 +81,7 @@
%endif
%if can_uninstall:
<br/>
- <form name="uninstall_tool_dependencies" id="uninstall_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='uninstall' )}" method="post" >
+ <form name="uninstall_tool_dependencies" id="uninstall_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='uninstall', repository_id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row">
Check each tool dependency that you want to uninstall and click <b>Uninstall</b>.
</div>
diff -r 25a0393e91120b4e0fa79b868f5fafc8ea14843b -r 2c257f0cbeb8a09e9b04a67ae59bf68a46e650e9 templates/admin/tool_shed_repository/repository_actions_menu.mako
--- a/templates/admin/tool_shed_repository/repository_actions_menu.mako
+++ b/templates/admin/tool_shed_repository/repository_actions_menu.mako
@@ -32,7 +32,7 @@
<a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a>
%endif
%if tool_dependency_ids:
- <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a>
+ <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', tool_dependency_ids=tool_dependency_ids, repository_id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a>
%endif
<a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a>
%endif
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/25a0393e9112/
Changeset: 25a0393e9112
User: dan
Date: 2013-07-19 19:40:39
Summary: Fix server error when an invalid locale is provided by a clients browser. Better handling of locales provided with surrounding whitespace.
Affected #: 1 file
diff -r a498340fed83e012e23f83f00d63b6ddaa5687cb -r 25a0393e91120b4e0fa79b868f5fafc8ea14843b lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -367,9 +367,9 @@
client_locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split( ',' )
for locale in client_locales:
try:
- locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language )
- except UnknownLocaleError:
- pass
+ locales.append( Locale.parse( locale.split( ';' )[0].strip(), sep='-' ).language )
+ except Exception, e:
+ log.debug( "Error parsing locale '%s'. %s: %s", locale, type( e ), e )
if not locales:
# Default to English
locales = 'en'
https://bitbucket.org/galaxy/galaxy-central/commits/cd6fec2f5cba/
Changeset: cd6fec2f5cba
Branch: stable
User: dan
Date: 2013-07-19 19:40:39
Summary: Fix server error when an invalid locale is provided by a clients browser. Better handling of locales provided with surrounding whitespace.
Affected #: 1 file
diff -r 9ebd7732e616492f4570587496f1b9074cb2eac7 -r cd6fec2f5cba878de9943dd00abe816a65dc96db lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -367,9 +367,9 @@
client_locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split( ',' )
for locale in client_locales:
try:
- locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language )
- except UnknownLocaleError:
- pass
+ locales.append( Locale.parse( locale.split( ';' )[0].strip(), sep='-' ).language )
+ except Exception, e:
+ log.debug( "Error parsing locale '%s'. %s: %s", locale, type( e ), e )
if not locales:
# Default to English
locales = 'en'
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a498340fed83/
Changeset: a498340fed83
User: greg
Date: 2013-07-19 15:47:41
Summary: Filter out repository dependencies that have been deleted from the repository grids in the tool shed.
Affected #: 1 file
diff -r d9fe5bea5a43c4c4645408a9035ad818d89d012c -r a498340fed83e012e23f83f00d63b6ddaa5687cb lib/tool_shed/grids/repository_grids.py
--- a/lib/tool_shed/grids/repository_grids.py
+++ b/lib/tool_shed/grids/repository_grids.py
@@ -1270,7 +1270,7 @@
owner = rd_tup[ 2 ]
changeset_revision = rd_tup[ 3 ]
required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
- if required_repository:
+ if required_repository and not required_repository.deleted:
required_repository_id = trans.security.encode_id( required_repository.id )
required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans,
required_repository_id,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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