1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/88873eed0092/
Changeset: 88873eed0092
User: greg
Date: 2013-06-09 14:50:20
Summary: Fix for rendering the number of tool dependencies and repository dependencies that failed to install in the tool shed automated test framework rss feed.
Affected #: 1 file
diff -r af5c9914169f7920b5c132f587ddfad1507d1aa3 -r 88873eed009229288e76637246a76746ea63ef57 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1482,7 +1482,7 @@
description_lines.append( '\nThis repository did not install correctly. ' )
if tool_dependency_errors or repository_dependency_errors:
description_lines.append( '\n%d tool dependencies and %d repository dependencies failed to install. ' % \
- len( tool_dependency_errors ), len( repository_dependency_errors ) )
+ ( len( tool_dependency_errors ), len( repository_dependency_errors ) ) )
title = 'Revision %s of %s' % ( metadata_row.changeset_revision, repository.name )
# The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated
# if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable
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/af5c9914169f/
Changeset: af5c9914169f
User: jgoecks
Date: 2013-06-08 00:01:36
Summary: Viz framework: (a) use features/pixel rather than features/base to determine what type of data to provide and (b) enable variant tracks to use coverage data.
Affected #: 2 files
diff -r 7add3a6019d30318ed8fa0f757f020a560e32c41 -r af5c9914169f7920b5c132f587ddfad1507d1aa3 lib/galaxy/webapps/galaxy/api/datasets.py
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -169,12 +169,16 @@
return { 'dataset_type': indexer.dataset_type, 'data': None }
else:
return stats
+
+ # Stats provides features/base and resolution is bases/pixel, so
+ # multiplying them yields features/pixel.
+ features_per_pixel = stats[ 'data' ][ 'max' ] * float( kwargs[ 'resolution' ] )
- # Use heuristic based on max depth and region size to determine whether to
- # return coverage data. When zoomed out and region is large, max depth
+ # Use heuristic based on features/pixel and region size to determine whether to
+ # return coverage data. When zoomed out and region is large, features/pixel
# is determining factor. However, when sufficiently zoomed in and region is
# small, coverage data is no longer provided.
- if int( high ) - int( low ) > 50000 and stats[ 'data' ][ 'max' ] > 1000:
+ if int( high ) - int( low ) > 50000 and features_per_pixel > 1000:
return indexer.get_data( chrom, low, high )
#
diff -r 7add3a6019d30318ed8fa0f757f020a560e32c41 -r af5c9914169f7920b5c132f587ddfad1507d1aa3 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -3379,11 +3379,24 @@
},
/**
- * Returns true if data is compatible with a given mode. Defaults to true because, for many tracks,
- * all data is compatible with all modes.
+ * Returns true if data is compatible with a given mode.
*/
data_and_mode_compatible: function(data, mode) {
- return true;
+ // Only handle modes that user can set.
+ if (mode === "Auto") {
+ return true;
+ }
+ // Histogram mode requires bigwig data.
+ else if (mode === "Coverage") {
+ return data.dataset_type === "bigwig";
+ }
+ // All other modes--Dense, Squish, Pack--require data + details.
+ else if (data.extra_info === "no_detail") {
+ return false;
+ }
+ else {
+ return true;
+ }
},
/**
@@ -4174,27 +4187,6 @@
}
return new FeatureTrackTile(track, region, resolution, canvas, result.data, w_scale, mode, result.message, all_slotted, feature_mapper);
- },
-
- /**
- * Returns true if data is compatible with a given mode.
- */
- data_and_mode_compatible: function(data, mode) {
- // Only handle modes that user can set.
- if (mode === "Auto") {
- return true;
- }
- // Histogram mode requires bigwig data.
- else if (mode === "Coverage") {
- return data.dataset_type === "bigwig";
- }
- // All other modes--Dense, Squish, Pack--require data + details.
- else if (data.extra_info === "no_detail") {
- return false;
- }
- else {
- return true;
- }
}
});
@@ -4209,6 +4201,7 @@
track: this,
params: [
{ key: 'name', label: 'Name', type: 'text', default_value: this.name },
+ { key: 'color', label: 'Histogram color', type: 'color', default_value: util.get_random_color() },
{ key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true },
{ key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true },
{ key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 },
@@ -4296,8 +4289,12 @@
postdraw_actions: function(tiles, width, w_scale, clear_after) {
TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after);
+ var line_track_tiles = _.filter(tiles, function(t) {
+ return (t instanceof LineTrackTile);
+ });
+
// Add summary/sample labels if needed and not already included.
- if ( !(tiles[0] instanceof LineTrackTile) && this.prefs.show_labels) {
+ if ( line_track_tiles.length === 0 && this.prefs.show_labels) {
var font_size;
// Add and/or style labels.
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/7add3a6019d3/
Changeset: 7add3a6019d3
User: carlfeberhard
Date: 2013-06-07 22:09:34
Summary: model.HDA.to_library_dataset...: remove list from method defaults
Affected #: 1 file
diff -r ef514ac8de1df7e49e4dfbb0ca7a399449693873 -r 7add3a6019d30318ed8fa0f757f020a560e32c41 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1542,7 +1542,7 @@
return hda
def to_library_dataset_dataset_association( self, trans, target_folder,
- replace_dataset=None, parent_id=None, user=None, roles=[], ldda_message='' ):
+ replace_dataset=None, parent_id=None, user=None, roles=None, ldda_message='' ):
"""
Copy this HDA to a library optionally replacing an existing LDDA.
"""
@@ -1577,6 +1577,7 @@
object_session( self ).add( ldda )
object_session( self ).flush()
# If roles were selected on the upload form, restrict access to the Dataset to those roles
+ roles = roles or []
for role in roles:
dp = trans.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action,
ldda.dataset, role )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7794e02d5ee5/
Changeset: 7794e02d5ee5
User: dannon
Date: 2013-06-07 18:11:58
Summary: Remove select2 from all standard edit permissions forms -- this fixes library permission page (and others).
Affected #: 1 file
diff -r 3b3f95704d2c093192fe82e687b0be5057600dfb -r 7794e02d5ee53d6302100606e6a18674f29bebf0 templates/webapps/galaxy/dataset/security_common.mako
--- a/templates/webapps/galaxy/dataset/security_common.mako
+++ b/templates/webapps/galaxy/dataset/security_common.mako
@@ -99,6 +99,8 @@
$( this ).attr( "selected", "selected" );
});
});
+ // Temporary removal of select2 for all permissions forms
+ $('#edit_role_associations select').select2("destroy");
});
</script><div class="toolForm">
https://bitbucket.org/galaxy/galaxy-central/commits/094dbdc2b169/
Changeset: 094dbdc2b169
Branch: stable
User: dannon
Date: 2013-06-07 18:11:58
Summary: Remove select2 from all standard edit permissions forms -- this fixes library permission page (and others).
Affected #: 1 file
diff -r 68db2c6900376fb8b56dae6b501c68cb598fd153 -r 094dbdc2b16994279fe3609a1f9b3edf395361e6 templates/webapps/galaxy/dataset/security_common.mako
--- a/templates/webapps/galaxy/dataset/security_common.mako
+++ b/templates/webapps/galaxy/dataset/security_common.mako
@@ -99,6 +99,8 @@
$( this ).attr( "selected", "selected" );
});
});
+ // Temporary removal of select2 for all permissions forms
+ $('#edit_role_associations select').select2("destroy");
});
</script><div class="toolForm">
https://bitbucket.org/galaxy/galaxy-central/commits/eddaf1b06063/
Changeset: eddaf1b06063
User: dannon
Date: 2013-06-07 18:12:36
Summary: Merge with stable.
Affected #: 1 file
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/f9e3822c6407/
Changeset: f9e3822c6407
User: lance_parsons
Date: 2012-12-10 22:23:11
Summary: Fix for Postgres versions < 9 (see https://trello.com/c/Z0EynAV2)
Affected #: 1 file
diff -r c3acc86490780d1949c4a3abf1263ace7c5ece6c -r f9e3822c64072c8466a39b5cbeaa4387e0c28ac8 scripts/set_user_disk_usage.py
--- a/scripts/set_user_disk_usage.py
+++ b/scripts/set_user_disk_usage.py
@@ -52,7 +52,7 @@
sql = """
UPDATE galaxy_user
SET disk_usage = (SELECT COALESCE(SUM(total_size), 0)
- FROM ( SELECT d.total_size
+ FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id
FROM history_dataset_association hda
JOIN history h ON h.id = hda.history_id
JOIN dataset d ON hda.dataset_id = d.id
@@ -62,7 +62,7 @@
AND d.purged = false
AND d.id NOT IN (SELECT dataset_id
FROM library_dataset_dataset_association)
- GROUP BY d.id) sizes)
+ ) sizes)
WHERE id = :id
RETURNING disk_usage;
"""
https://bitbucket.org/galaxy/galaxy-central/commits/5de636ce68fa/
Changeset: 5de636ce68fa
User: dannon
Date: 2013-06-06 16:21:57
Summary: Merged in lance_parsons/galaxy-central_postgres-user-disk-usage-fix (pull request #97)
Fix for Postgres versions < 9
Affected #: 1 file
diff -r af91c734dbb76b8c0e3166c7471370f9ba8260b5 -r 5de636ce68faededc52d7b0c16167fbef98be786 scripts/set_user_disk_usage.py
--- a/scripts/set_user_disk_usage.py
+++ b/scripts/set_user_disk_usage.py
@@ -52,7 +52,7 @@
sql = """
UPDATE galaxy_user
SET disk_usage = (SELECT COALESCE(SUM(total_size), 0)
- FROM ( SELECT d.total_size
+ FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id
FROM history_dataset_association hda
JOIN history h ON h.id = hda.history_id
JOIN dataset d ON hda.dataset_id = d.id
@@ -62,7 +62,7 @@
AND d.purged = false
AND d.id NOT IN (SELECT dataset_id
FROM library_dataset_dataset_association)
- GROUP BY d.id) sizes)
+ ) sizes)
WHERE id = :id
RETURNING disk_usage;
"""
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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