1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/34b5ed4d756e/
changeset: 34b5ed4d756e
user: dan
date: 2012-04-05 23:13:15
summary: In tool_form, have call to unicode on non unicode field_html use 'replace' instead of raising a server error. Fixes issues seen with non unicode characters in history item names.
affected #: 1 file
diff -r 5946d6694829ba6377c33ec2cfab91bbaff5671a -r 34b5ed4d756ec979eecc77c8dae2a09a1112ad2d templates/tool_form.mako
--- a/templates/tool_form.mako
+++ b/templates/tool_form.mako
@@ -218,7 +218,7 @@
# Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully.
field_html = field.get_html( prefix )
if type( field_html ) is not unicode:
- field_html = unicode( field_html, 'utf-8' )
+ field_html = unicode( field_html, 'utf-8', 'replace' )
if param.type == "hidden":
return field_html
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/fc4e6592a6d7/
changeset: fc4e6592a6d7
user: dan
date: 2012-04-05 23:00:33
summary: Add some missing cgi.escape calls around values in form_builder.py.
affected #: 45 files
Diff too large to display.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e95c01831a8a/
changeset: e95c01831a8a
user: jgoecks
date: 2012-04-05 19:50:22
summary: All models have id attribute, so do not declare explicitly.
affected #: 1 file
diff -r 0f53915212d0a9e7b8f135c4bb557e8281ab879c -r e95c01831a8ad31b1bf0205004dd93ccb7dc0976 static/scripts/backbone/tools.js
--- a/static/scripts/backbone/tools.js
+++ b/static/scripts/backbone/tools.js
@@ -10,7 +10,6 @@
*/
var BaseModel = Backbone.Model.extend({
defaults: {
- id: null,
name: null,
hidden: false
},
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/cbaeb519256d/
changeset: cbaeb519256d
user: dan
date: 2012-04-05 03:12:31
summary: DrillDown parameter now uses slideUp/Down.
affected #: 1 file
diff -r 9c80a2995cc9ca4248d4673d553461d739142371 -r cbaeb519256d71124294ecc4351c031670a72d40 templates/tool_form.mako
--- a/templates/tool_form.mako
+++ b/templates/tool_form.mako
@@ -43,14 +43,14 @@
}
show_hide_click_elt.click( function() {
if ( show_hide_click_elt.hasClass("toggle") ){
+ show_hide_click_elt.addClass("toggle-expand");
show_hide_click_elt.removeClass("toggle");
- show_hide_click_elt.addClass("toggle-expand");
- show_hide_elt.hide()
+ show_hide_elt.slideUp( 'fast' );
}
else {
show_hide_click_elt.addClass("toggle");
show_hide_click_elt.removeClass("toggle-expand");
- show_hide_elt.show();
+ show_hide_elt.slideDown( 'fast' );
}
});
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9c80a2995cc9/
changeset: 9c80a2995cc9
user: greg
date: 2012-04-04 21:01:09
summary: Only include invalid tools in the metadata for the repository tip - supporting this in older revisions is a bit more complex and will be supported at a later time.
affected #: 3 files
diff -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 -r 9c80a2995cc9ca4248d4673d553461d739142371 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -427,8 +427,13 @@
metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict )
except Exception, e:
invalid_files.append( ( name, str( e ) ) )
+ """
+ FIXME: Handling invalid tools in change sets that are not the repository tip are a bit complex, so this is currently not
+ supported. One example is the Emboss tools that have a <code file> tag set, which requires the file to exist in a location
+ that can be found.
if invalid_tool_configs:
metadata_dict[ 'invalid_tools' ] = invalid_tool_configs
+ """
return metadata_dict, invalid_files
def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ):
"""Set repository metadata"""
diff -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 -r 9c80a2995cc9ca4248d4673d553461d739142371 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -428,6 +428,7 @@
for invalid_tool_config in invalid_tools:
invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision )
return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako',
+ cntrller=cntrller,
invalid_tools_dict=invalid_tools_dict,
webapp=webapp,
message=message,
@@ -1867,6 +1868,7 @@
break
if found:
break
+ metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, repository_id, ctx, changeset_revision, repo_dir )
else:
for filename in ctx:
if filename == tool_config:
@@ -1879,7 +1881,7 @@
fh.write( fctx.data() )
fh.close()
break
- metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, repository_id, ctx, changeset_revision, repo_dir )
+ metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, repository_id, ctx, changeset_revision, repo_dir )
for invalid_file_tup in invalid_files:
invalid_tool_config, invalid_msg = invalid_file_tup
if tool_config == invalid_tool_config:
diff -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 -r 9c80a2995cc9ca4248d4673d553461d739142371 templates/webapps/community/repository/browse_invalid_tools.mako
--- a/templates/webapps/community/repository/browse_invalid_tools.mako
+++ b/templates/webapps/community/repository/browse_invalid_tools.mako
@@ -32,7 +32,11 @@
</div>
%else:
<div class="form-row">
- You do not own any repositories that contain invalid tools.
+ %if cntrller == 'admin' and trans.user_is_admin():
+ No repositories in this tool shed contain invalid tools.
+ %else:
+ None of your repositories contain invalid tools.
+ %endif
</div>
%endif
</div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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