2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/014548c6843c/
Changeset: 014548c6843c
User: dan
Date: 2013-05-23 17:11:37
Summary: Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name.
Affected #: 1 file
diff -r 23dcf647ab620a032be9cbc3805707dff75f63b5 -r 014548c6843c8aa507719e4831f982ac967c5d4c lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -297,9 +297,12 @@
found_column = False
for name, index in self.columns.iteritems():
if index == i:
- rval.append( name )
+ if not found_column:
+ rval.append( name )
+ elif name == 'value':
+ #the column named 'value' always has priority over other named columns
+ rval[ -1 ] = name
found_column = True
- break
if not found_column:
rval.append( None )
return rval
https://bitbucket.org/galaxy/galaxy-central/commits/03ebba1d1de6/
Changeset: 03ebba1d1de6
Branch: stable
User: dan
Date: 2013-05-23 17:11:37
Summary: Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name.
Affected #: 1 file
diff -r 0f51ae4f1c84c5bab6cd1c93ae837696be9565e1 -r 03ebba1d1de6f14ccb00e08795ef2f1896135bae lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -273,9 +273,12 @@
found_column = False
for name, index in self.columns.iteritems():
if index == i:
- rval.append( name )
+ if not found_column:
+ rval.append( name )
+ elif name == 'value':
+ #the column named 'value' always has priority over other named columns
+ rval[ -1 ] = name
found_column = True
- break
if not found_column:
rval.append( None )
return rval
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/064ea784eae7/
Changeset: 064ea784eae7
Branch: next-stable
User: Dave Bouvier
Date: 2013-05-23 15:45:24
Summary: Fix for missing tool test results display on manage repository page.
Affected #: 1 file
diff -r 252027d00b441db33005080860970c3441399a77 -r 064ea784eae74cdb7b4ac0319ec0aa13ee55fcbd lib/galaxy/webapps/tool_shed/util/container_util.py
--- a/lib/galaxy/webapps/tool_shed/util/container_util.py
+++ b/lib/galaxy/webapps/tool_shed/util/container_util.py
@@ -801,7 +801,7 @@
if tool_test_results:
# Only create and populate this folder if there are actual tool test results to display, since the
# display of the 'Test environment' folder by itself can be misleading.
- if 'passed_tests' in tool_test_results or 'failed_tests' in tool_test_results or 'installation_errors' in tool_test_results:
+ if len( tool_test_results ) > 1:
folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested )
containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder
# Workflows container.
https://bitbucket.org/galaxy/galaxy-central/commits/23dcf647ab62/
Changeset: 23dcf647ab62
User: Dave Bouvier
Date: 2013-05-23 15:45:50
Summary: Merge in fix from next-stable.
Affected #: 1 file
diff -r ee040d59779808ec5d748f3df04377b333b74a54 -r 23dcf647ab620a032be9cbc3805707dff75f63b5 lib/galaxy/webapps/tool_shed/util/container_util.py
--- a/lib/galaxy/webapps/tool_shed/util/container_util.py
+++ b/lib/galaxy/webapps/tool_shed/util/container_util.py
@@ -801,7 +801,7 @@
if tool_test_results:
# Only create and populate this folder if there are actual tool test results to display, since the
# display of the 'Test environment' folder by itself can be misleading.
- if 'passed_tests' in tool_test_results or 'failed_tests' in tool_test_results or 'installation_errors' in tool_test_results:
+ if len( tool_test_results ) > 1:
folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested )
containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder
# Workflows container.
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/1021adf47016/
Changeset: 1021adf47016
User: greg
Date: 2013-05-22 21:28:40
Summary: Fix recent changes to the tool shed menu to allow a logged in user to create a new repository.
Affected #: 1 file
diff -r 901cf978cef1199ed230790b2837854c66ab7f79 -r 1021adf470168815b1066c4c9022cb4136edf84c templates/webapps/tool_shed/index.mako
--- a/templates/webapps/tool_shed/index.mako
+++ b/templates/webapps/tool_shed/index.mako
@@ -131,15 +131,14 @@
<div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_my_writable_repositories_with_invalid_tools' )}">Latest revision: invalid tools</a></div>
- %else:
- <div class="toolSectionPad"></div>
- <div class="toolSectionTitle">
- Available Actions
- </div>
- <div class="toolTitle">
- <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a>
- </div>
%endif
+ <div class="toolSectionPad"></div>
+ <div class="toolSectionTitle">
+ Available Actions
+ </div>
+ <div class="toolTitle">
+ <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a>
+ </div>
%if can_review_repositories:
<div class="toolSectionPad"></div><div class="toolSectionTitle">
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/a3909b1eebdc/
Changeset: a3909b1eebdc
Branch: next-stable
User: jgoecks
Date: 2013-05-22 20:47:37
Summary: Trackster: fix for subsetting variant tracks.
Affected #: 2 files
diff -r 1b279375e33d1139b60f8e13c4b1de8a0c27b438 -r a3909b1eebdc7b34fb16b5276464892431528177 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -3139,6 +3139,11 @@
var tile_drawn = $.Deferred();
track.tile_cache.set_elt(key, tile_drawn);
$.when.apply($, get_tile_data()).then( function() {
+ // If deferred objects ever show up in tile data, that is likely because a
+ // Deferred-subsetting interaction failed. Specifically, a Deferred for a superset
+ // was returned but then couldn't be used). It's not clear whether this will happen
+ // in practice, and currently the code doesn't handle it. It could probably handle it
+ // by recursively calling draw_helper.
var tile_data = get_tile_data(),
tracks_data = tile_data,
seq_data;
@@ -3313,10 +3318,15 @@
},
/**
- * Returns true if data can be subsetted. Defaults to false to ensure data is fetched when needed.
+ * Returns true if data can be subsetted.
*/
can_subset: function(data) {
- return false;
+ // Do not subset entries with a message or data with no detail.
+ if (data.dataset_type === 'bigwig' || data.message || data.extra_info === "no_detail") {
+ return false;
+ }
+
+ return true;
},
/**
@@ -4116,18 +4126,6 @@
else {
return true;
}
- },
-
- /**
- * Returns true if data can be subsetted.
- */
- can_subset: function(data) {
- // Do not subset entries with a message or data with no detail.
- if (data.dataset_type === 'bigwig' || data.message || data.extra_info === "no_detail") {
- return false;
- }
-
- return true;
}
});
diff -r 1b279375e33d1139b60f8e13c4b1de8a0c27b438 -r a3909b1eebdc7b34fb16b5276464892431528177 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -68,7 +68,7 @@
* Helper to determine if object is jQuery deferred.
*/
var is_deferred = function ( d ) {
- return ( 'isResolved' in d );
+ return ('promise' in d);
};
// --------- Models ---------
@@ -331,14 +331,6 @@
* Get data from dataset.
*/
get_data: function(region, mode, resolution, extra_params) {
- // Debugging:
- //console.log("get_data", low, high, mode);
- /*
- console.log("cache contents:")
- for (var i = 0; i < this.key_ary.length; i++) {
- console.log("\t", this.key_ary[i], this.obj_cache[this.key_ary[i]]);
- }
- */
// Look for entry and return if it's a deferred or if data available is compatible with mode.
var entry = this.get_elt(region);
@@ -348,8 +340,7 @@
}
//
- // Look in cache for data that can be used. Data can be reused if it
- // has the requested data and is not summary tree and has details.
+ // Look in cache for data that can be used.
// TODO: this logic could be improved if the visualization knew whether
// the data was "index" or "data."
//
https://bitbucket.org/galaxy/galaxy-central/commits/ff27d341f6e9/
Changeset: ff27d341f6e9
User: jgoecks
Date: 2013-05-22 20:48:02
Summary: Merge in next-stable
Affected #: 2 files
diff -r 921ad3745ba304aed12b0d3425cf9c6f9b727f7c -r ff27d341f6e9f7efe80f5af66fd7a811f77b2501 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -3139,6 +3139,11 @@
var tile_drawn = $.Deferred();
track.tile_cache.set_elt(key, tile_drawn);
$.when.apply($, get_tile_data()).then( function() {
+ // If deferred objects ever show up in tile data, that is likely because a
+ // Deferred-subsetting interaction failed. Specifically, a Deferred for a superset
+ // was returned but then couldn't be used). It's not clear whether this will happen
+ // in practice, and currently the code doesn't handle it. It could probably handle it
+ // by recursively calling draw_helper.
var tile_data = get_tile_data(),
tracks_data = tile_data,
seq_data;
@@ -3313,10 +3318,15 @@
},
/**
- * Returns true if data can be subsetted. Defaults to false to ensure data is fetched when needed.
+ * Returns true if data can be subsetted.
*/
can_subset: function(data) {
- return false;
+ // Do not subset entries with a message or data with no detail.
+ if (data.dataset_type === 'bigwig' || data.message || data.extra_info === "no_detail") {
+ return false;
+ }
+
+ return true;
},
/**
@@ -4116,18 +4126,6 @@
else {
return true;
}
- },
-
- /**
- * Returns true if data can be subsetted.
- */
- can_subset: function(data) {
- // Do not subset entries with a message or data with no detail.
- if (data.dataset_type === 'bigwig' || data.message || data.extra_info === "no_detail") {
- return false;
- }
-
- return true;
}
});
diff -r 921ad3745ba304aed12b0d3425cf9c6f9b727f7c -r ff27d341f6e9f7efe80f5af66fd7a811f77b2501 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -68,7 +68,7 @@
* Helper to determine if object is jQuery deferred.
*/
var is_deferred = function ( d ) {
- return ( 'isResolved' in d );
+ return ('promise' in d);
};
// --------- Models ---------
@@ -331,14 +331,6 @@
* Get data from dataset.
*/
get_data: function(region, mode, resolution, extra_params) {
- // Debugging:
- //console.log("get_data", low, high, mode);
- /*
- console.log("cache contents:")
- for (var i = 0; i < this.key_ary.length; i++) {
- console.log("\t", this.key_ary[i], this.obj_cache[this.key_ary[i]]);
- }
- */
// Look for entry and return if it's a deferred or if data available is compatible with mode.
var entry = this.get_elt(region);
@@ -348,8 +340,7 @@
}
//
- // Look in cache for data that can be used. Data can be reused if it
- // has the requested data and is not summary tree and has details.
+ // Look in cache for data that can be used.
// TODO: this logic could be improved if the visualization knew whether
// the data was "index" or "data."
//
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/921ad3745ba3/
Changeset: 921ad3745ba3
User: greg
Date: 2013-05-22 20:36:08
Summary: Delete the original copy of the install_repository_tools.py Galaxy API script since it has been renamed to install_tool_shed_repositories.py
Affected #: 1 file
diff -r 2a630237801ffefdd63e47c5acdcc1abadba23ef -r 921ad3745ba304aed12b0d3425cf9c6f9b727f7c scripts/api/install_repository_tools.py
--- a/scripts/api/install_repository_tools.py
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env python
-"""
-Install a specified repository revision from a specified tool shed into Galaxy. This example demonstrates installation of a repository that contains
-valid tools, loading them into a section of the Galaxy tool panel or creating a new tool panel section.
-You can choose if tool dependencies or repository dependencies should be installed, use --repository-deps or --tool-deps.
-
-This example requires a tool panel config file (e.g., tool_conf.xml, shed_tool_conf.xml, etc) to contain a tool panel section like the following:
-
-<section id="from_test_tool_shed" name="From Test Tool Shed" version="">
-</section>
-
-Here is a working example of how to use this script to install a repository from the test tool shed.
-./install_repository_tools.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --revision f28d5018f9cb --tool-deps
-"""
-
-import os
-import sys
-import argparse
-sys.path.insert( 0, os.path.dirname( __file__ ) )
-from common import submit
-
-def main( options ):
- """Collect all user data and install the tools via the Galaxy API."""
- data = {}
- data[ 'tool_shed_url' ] = options.tool_shed_url
- data[ 'name' ] = options.name
- data[ 'owner' ] = options.owner
- data[ 'changeset_revision' ] = options.changeset_revision
- if options.tool_panel_section_id:
- data[ 'tool_panel_section_id' ] = options.tool_panel_section_id
- elif options.new_tool_panel_section_label:
- data[ 'new_tool_panel_section_label' ] = options.new_tool_panel_section_label
- if options.install_repository_dependencies:
- data[ 'install_repository_dependencies' ] = options.install_repository_dependencies
- if options.install_tool_dependencies:
- data[ 'install_tool_dependencies' ] = options.install_tool_dependencies
- submit( options.api, '%s%s' % ( options.local_url.strip('/'), '/api/tool_shed_repositories/new/install_repository_revision' ), data )
-
-if __name__ == '__main__':
- parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' )
- parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" )
- parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key" )
- parser.add_argument( "-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance." )
- parser.add_argument( "-n", "--name", required=True, help="Repository name." )
- parser.add_argument( "-o", "--owner", required=True, help="Repository owner." )
- parser.add_argument( "-r", "--revision", dest="changeset_revision", required=True, help="Repository owner." )
- parser.add_argument( "--panel-section-id", dest="tool_panel_section_id", help="Tool panel section id if you want to add your repository to an existing tool section." )
- parser.add_argument( "--panel-section-name", dest="new_tool_panel_section_label", help="New tool panel section label. If specified a new tool section will be created." )
- parser.add_argument( "--repository-deps", dest="install_repository_dependencies", action="store_true", default=False, help="Install repository dependencies. [False]")
- parser.add_argument( "--tool-deps", dest="install_tool_dependencies", action="store_true", default=False, help="Install tool dependencies. [False]" )
- options = parser.parse_args()
- main( options )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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