1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/dc67550cf28a/
Changeset: dc67550cf28a
User: jmchilton
Date: 2014-03-26 16:00:22
Summary: Update LWR client through LWR commit 2fec198.
Makes parsing LWR host more robust - auto-adding http to beginning and trailing / if needed. Also makes LWR runn compatible with forthcoming job metrics pull request and pulls in Python 3 fix for job_script module.
Affected #: 3 files
diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/lwr_client/interface.py
--- a/lib/galaxy/jobs/runners/lwr_client/interface.py
+++ b/lib/galaxy/jobs/runners/lwr_client/interface.py
@@ -36,8 +36,13 @@
def __init__(self, destination_params, transport):
self.transport = transport
- self.remote_host = destination_params.get("url")
- assert self.remote_host is not None, "Failed to determine url for LWR client."
+ remote_host = destination_params.get("url")
+ assert remote_host is not None, "Failed to determine url for LWR client."
+ if not remote_host.endswith("/"):
+ remote_host = "%s/" % remote_host
+ if not remote_host.startswith("http"):
+ remote_host = "http://%s" % remote_host
+ self.remote_host = remote_host
self.private_key = destination_params.get("private_token", None)
def execute(self, command, args={}, data=None, input_path=None, output_path=None):
diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/lwr_client/staging/down.py
--- a/lib/galaxy/jobs/runners/lwr_client/staging/down.py
+++ b/lib/galaxy/jobs/runners/lwr_client/staging/down.py
@@ -14,7 +14,7 @@
# this pattern picks up attiditional files to copy back - such as those
# associated with multiple outputs and metadata configuration. Set to .* to just
# copy everything
-COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|dataset_\d+_files.+")
+COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|__instrument_.*|dataset_\d+_files.+")
def finish_job(client, cleanup_job, job_completed_normally, client_outputs, lwr_outputs):
diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/util/job_script/__init__.py
--- a/lib/galaxy/jobs/runners/util/job_script/__init__.py
+++ b/lib/galaxy/jobs/runners/util/job_script/__init__.py
@@ -2,11 +2,11 @@
from pkg_resources import resource_string
DEFAULT_JOB_FILE_TEMPLATE = Template(
- resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh')
+ resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh').decode('UTF-8')
)
SLOTS_STATEMENT_CLUSTER_DEFAULT = \
- resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh')
+ resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh').decode('UTF-8')
SLOTS_STATEMENT_SINGLE = """
GALAXY_SLOTS="1"
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/47211cedc8d0/
Changeset: 47211cedc8d0
User: Jeremy Goecks
Date: 2014-03-25 20:41:40
Summary: Trackster: (a) fix bug when trying to subset from supersets with messages; (b) display vertical placeholder until bugs are resolved.
Affected #: 3 files
diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1106,6 +1106,10 @@
});
// For vertical alignment, track mouse with simple line.
+ // Fixes needed for this to work:
+ // (a) make work with embedded visualizations;
+ // (b) seems to get stuck on tile overlaps.
+ /*
var mouse_tracker_div = $('<div/>').addClass('mouse-pos').appendTo(parent_element);
// Show tracker only when hovering over view.
@@ -1125,6 +1129,7 @@
mouse_tracker_div.hide();
}
);
+ */
this.add_label_track( new LabelTrack( this, { content_div: this.top_labeltrack } ) );
this.add_label_track( new LabelTrack( this, { content_div: this.nav_labeltrack } ) );
@@ -3053,14 +3058,21 @@
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;
+
+ // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk
+ // that cannot be subsetted. This may occur if the superset has a message. If there is a
+ // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the
+ // GenomeDataManager in visualization module.
+ if (_.find(tile_data, function(d) { return util.is_deferred(d); })) {
+ track.tile_cache.set_elt(key, undefined);
+ $.when(track.draw_helper(region, w_scale, options)).then(function(tile) {
+ tile_drawn.resolve(tile);
+ });
+ return;
+ }
// If sequence data is available, subset to get only data in region.
if (view.reference_track) {
diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/trackster/util.js
--- a/static/scripts/viz/trackster/util.js
+++ b/static/scripts/viz/trackster/util.js
@@ -1,6 +1,13 @@
define(function(){
/**
+ * Helper to determine if object is jQuery deferred.
+ */
+var is_deferred = function ( d ) {
+ return ('promise' in d);
+};
+
+/**
* Implementation of a server-state based deferred. Server is repeatedly polled, and when
* condition is met, deferred is resolved.
*/
@@ -109,6 +116,7 @@
};
return {
+ is_deferred: is_deferred,
ServerStateDeferred : ServerStateDeferred,
get_random_color : get_random_color
};
diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -86,14 +86,6 @@
});
};
-
-/**
- * Helper to determine if object is jQuery deferred.
- */
-var is_deferred = function ( d ) {
- return ('promise' in d);
-};
-
// --------- Models ---------
/**
@@ -380,11 +372,10 @@
* Get data from dataset.
*/
get_data: function(region, mode, resolution, extra_params) {
-
// Look for entry and return if it's a deferred or if data available is compatible with mode.
var entry = this.get_elt(region);
if ( entry &&
- ( is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) {
+ ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) {
return entry;
}
@@ -405,12 +396,12 @@
// This entry has data in the requested range. Return if data
// is compatible and can be subsetted.
entry = obj_cache[entry_region.toString()];
- if ( is_deferred(entry) ||
+ if ( util_mod.is_deferred(entry) ||
( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) {
this.move_key_to_end(entry_region, i);
// If there's data, subset it.
- if ( !is_deferred(entry) ) {
+ if ( !util_mod.is_deferred(entry) ) {
var subset_entry = this.subset_entry(entry, region);
this.set(region, subset_entry);
entry = subset_entry;
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/208533b58c7e/
Changeset: 208533b58c7e
User: davebgx
Date: 2014-03-25 18:25:19
Summary: Fix server error when attempting to create a repository before any categories have been created.
Affected #: 1 file
diff -r cab5878ce755b1736d09a9a74e419eddb12c0f2d -r 208533b58c7e135e99a74e7cf5183a63020b3341 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
@@ -950,7 +950,7 @@
categories = suc.get_categories( trans )
if not categories:
message = 'No categories have been configured in this instance of the Galaxy Tool Shed. '
- message += 'An administrator needs to create some via the Administrator control panel before creating repositories.',
+ message += 'An administrator needs to create some via the Administrator control panel before creating repositories.'
status = 'error'
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories',
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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