1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0da18c7ba18d/
changeset: 0da18c7ba18d
user: jgoecks
date: 2012-07-14 01:44:21
summary: Trackster: make sliders more responsive by waiting before drawing.
affected #: 1 file
diff -r 02ce2ca3fa2dac4c4155b7f07f0699d519b4d853 -r 0da18c7ba18dcc0eaf9e14596b5ff0dc348457bc static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -2083,7 +2083,6 @@
// Set up slider for filter.
var slider_div = $("<div/>").addClass("slider").appendTo(filter.parent_div);
filter.control_element = $("<div/>").attr("id", filter.name + "-filter-control").appendTo(slider_div);
- var prev_values = [0,0];
filter.control_element.slider({
range: true,
min: this.min,
@@ -2193,17 +2192,23 @@
* Handle slide events.
*/
slide: function(event, ui) {
- var values = ui.values;
+ var values = ui.values;
+
+ // Set new values in UI.
+ this.values_span.text(values[0] + "-" + values[1]);
+
+ // Set new values in filter.
+ this.low = values[0];
+ this.high = values[1];
- // Set new values in UI.
- this.values_span.text(values[0] + "-" + values[1]);
+ // Set timeout to update if filter low, high are stable.
+ var self = this;
+ setTimeout(function() {
+ if (values[0] === self.low && values[1] === self.high) {
+ self.manager.track.request_draw(true, true);
+ }
+ }, 25);
- // Set new values in filter.
- this.low = values[0];
- this.high = values[1];
-
- // Redraw track.
- this.manager.track.request_draw(true, true);
},
/**
* Returns true if filter can be applied to element.
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/02ce2ca3fa2d/
changeset: 02ce2ca3fa2d
user: greg
date: 2012-07-14 01:09:51
summary: Make sure a shed related tool config is defined in universe_wsgi.ini before allowing automatic tool installs from a tool shed.
affected #: 1 file
diff -r 35ff11e3863804767d602d2fb8bff08f2c67e35f -r 02ce2ca3fa2dac4c4155b7f07f0699d519b4d853 lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -945,7 +945,7 @@
@web.expose
@web.require_admin
def prepare_for_install( self, trans, **kwd ):
- if not trans.app.toolbox.shed_tool_confs:
+ if not have_shed_tool_conf_for_install( trans ):
message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
@@ -1566,3 +1566,13 @@
def get_tool_dependency( trans, id ):
"""Get a tool_dependency from the database via id"""
return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) )
+def have_shed_tool_conf_for_install( trans ):
+ if not trans.app.toolbox.shed_tool_confs:
+ return False
+ migrated_tools_conf_path, migrated_tools_conf_name = os.path.split( trans.app.config.migrated_tools_config )
+ for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
+ shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ]
+ shed_tool_conf_path, shed_tool_conf_name = os.path.split( shed_tool_conf )
+ if shed_tool_conf_name != migrated_tools_conf_name:
+ return True
+ return 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/01c78c55b229/
changeset: 01c78c55b229
user: inithello
date: 2012-07-13 19:31:12
summary: Set tool dependency status to installed if the dependency is already installed.
affected #: 1 file
diff -r 2822e4550fc218bd1adc6d219bbcbbf11350afc9 -r 01c78c55b229e5e872ffb2320a51468a5c7ba7ee lib/galaxy/tool_shed/tool_dependencies/install_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py
@@ -83,6 +83,10 @@
# print 'Installing tool dependencies via fabric script ', proprietary_fabfile_path
else:
print '\nSkipping installation of tool dependency', package_name, 'version', package_version, 'since it is installed in', install_dir, '\n'
+ tool_dependency = get_tool_dependency_by_name_version_type_repository( app, tool_shed_repository, package_name, package_version, 'package' )
+ tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED
+ sa_session.add( tool_dependency )
+ sa_session.flush()
return tool_dependency
def install_via_fabric( app, tool_dependency, actions_elem, install_dir, package_name=None, proprietary_fabfile_path=None, **kwd ):
"""Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric."""
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/2822e4550fc2/
changeset: 2822e4550fc2
user: greg
date: 2012-07-13 18:53:42
summary: Another change to installed changed revision for the freebayes tool migration process.
affected #: 1 file
diff -r 00af371b11a5ed5d0560865096d21baf99a28509 -r 2822e4550fc218bd1adc6d219bbcbbf11350afc9 scripts/migrate_tools/0003_tools.xml
--- a/scripts/migrate_tools/0003_tools.xml
+++ b/scripts/migrate_tools/0003_tools.xml
@@ -1,6 +1,6 @@
<?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu">
- <repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="838dd557c84c">
+ <repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="213a3d6b579a"><tool id="freebayes" version="0.0.2 " file="freebayes.xml" /></repository></toolshed>
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/1eba0880e52d/
changeset: 1eba0880e52d
user: greg
date: 2012-07-13 18:37:45
summary: Revert my last change set.
affected #: 1 file
diff -r 1da8fb882393c68f83d08f6c85023a0c3225513b -r 1eba0880e52d5b9955eea4df6fefdb1575fee09c lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -279,10 +279,6 @@
# Handle case where all metadata is the same.
if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal':
return 'equal'
- """
- # TODO: revisit after GCC - we temporarily prioritize contents as: 1) tools 2) datatypes 3) workflows
- # by only inspecting tools if they exist. If tools don't exist, next inspect only datatypes and, finally, workflows.
- # Here is the original code, with the code following the commented code replacing it.
if workflow_comparison == 'subset' and datatype_comparison == 'subset':
is_subset = True
for guid in ancestor_guids:
@@ -291,24 +287,6 @@
break
if is_subset:
return 'subset'
- """
- if ancestor_guids and current_guids:
- is_subset = True
- for guid in ancestor_guids:
- if guid not in current_guids:
- is_subset = False
- break
- if is_subset:
- return 'subset'
- else:
- return 'not equal and not subset'
- elif ancestor_guids and not current_guids:
- # There were tools in the ancestor changeset revision, but no tools in the current changeset revision, so no new metadata should be generated.
- return 'subset'
- elif datatype_comparison == 'subset':
- return 'subset'
- elif workflow_comparison == 'subset':
- return 'subset'
return 'not equal and not subset'
def compare_datatypes( ancestor_datatypes, current_datatypes ):
# Determine if ancestor_datatypes is the same as current_datatypes
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/1da8fb882393/
changeset: 1da8fb882393
user: greg
date: 2012-07-13 18:12:08
summary: Pritorize tools first, followed by proprietary datatypes and then workflows when setting metadata on tool shed repositories.
affected #: 1 file
diff -r 28b3364341b66ae9e3628d965db31c8dc3c57bfd -r 1da8fb882393c68f83d08f6c85023a0c3225513b lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -279,6 +279,10 @@
# Handle case where all metadata is the same.
if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal':
return 'equal'
+ """
+ # TODO: revisit after GCC - we temporarily prioritize contents as: 1) tools 2) datatypes 3) workflows
+ # by only inspecting tools if they exist. If tools don't exist, next inspect only datatypes and, finally, workflows.
+ # Here is the original code, with the code following the commented code replacing it.
if workflow_comparison == 'subset' and datatype_comparison == 'subset':
is_subset = True
for guid in ancestor_guids:
@@ -287,6 +291,24 @@
break
if is_subset:
return 'subset'
+ """
+ if ancestor_guids and current_guids:
+ is_subset = True
+ for guid in ancestor_guids:
+ if guid not in current_guids:
+ is_subset = False
+ break
+ if is_subset:
+ return 'subset'
+ else:
+ return 'not equal and not subset'
+ elif ancestor_guids and not current_guids:
+ # There were tools in the ancestor changeset revision, but no tools in the current changeset revision, so no new metadata should be generated.
+ return 'subset'
+ elif datatype_comparison == 'subset':
+ return 'subset'
+ elif workflow_comparison == 'subset':
+ return 'subset'
return 'not equal and not subset'
def compare_datatypes( ancestor_datatypes, current_datatypes ):
# Determine if ancestor_datatypes is the same as current_datatypes
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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