1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/23b173247757/
changeset: 23b173247757
user: greg
date: 2012-02-07 22:20:48
summary: Fix for loading tools from an installed tool shed repository into the tool panel outside of any sections.
affected #: 4 files
diff -r 60231c4aab751817fc3937c1974e3fc11632df2e -r 23b173247757c383e9f1c4fb736008a6623e7327 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -317,10 +317,10 @@
id_elem.text = tool.id
version_elem = SubElement( tool_elem, 'version' )
version_elem.text = tool.version
+ if not tool_section:
+ elem_list.append( tool_elem )
if tool_section:
elem_list.append( root_elem )
- elif tool_elem:
- elem_list.append( tool_elem )
return elem_list
def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ):
"""
diff -r 60231c4aab751817fc3937c1974e3fc11632df2e -r 23b173247757c383e9f1c4fb736008a6623e7327 lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -435,9 +435,14 @@
original_section_name = tool_panel_section[ 'name' ]
tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
no_changes_check_box = CheckboxField( 'no_changes', checked=True )
- message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " % ( repository.name, original_section_name )
- message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a "
- message += "different section in the tool panel."
+ if original_section_name:
+ message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \
+ % ( repository.name, original_section_name )
+ message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a "
+ message += "different section in the tool panel."
+ else:
+ message = "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % repository.name
+ message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section."
status = 'done'
return trans.fill_template( '/admin/tool_shed_repository/reselect_tool_panel_section.mako',
repository=repository,
diff -r 60231c4aab751817fc3937c1974e3fc11632df2e -r 23b173247757c383e9f1c4fb736008a6623e7327 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
@@ -20,7 +20,7 @@
<label>Add new tool panel section:</label><input name="new_tool_panel_section" type="textfield" value="" size="40"/><div class="toolParamHelp" style="clear: both;">
- Add a new tool panel section contain the installed tools (optional).
+ Add a new tool panel section to contain the installed tools (optional).
</div></div><div class="form-row">
diff -r 60231c4aab751817fc3937c1974e3fc11632df2e -r 23b173247757c383e9f1c4fb736008a6623e7327 templates/admin/tool_shed_repository/select_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -43,7 +43,7 @@
<label>Add new tool panel section:</label><input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/><div class="toolParamHelp" style="clear: both;">
- Add a new tool panel section contain the installed tools (optional).
+ Add a new tool panel section to contain the installed tools (optional).
</div></div><div class="form-row">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/5c57dfac1e31/
changeset: 5c57dfac1e31
user: jgoecks
date: 2012-02-07 17:30:45
summary: Trackster: small variable reference fix.
affected #: 1 file
diff -r b4ba8b20d78d5ae92ebab85afeb6662ca602d427 -r 5c57dfac1e3143e3931bb5d5cc774248f8060113 static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -833,10 +833,11 @@
this.changed();
this.container.remove_drawable(this);
+ var view = this.view;
this.container_div.hide(0, function() {
$(this).remove();
// HACK: is there a better way to update the view?
- drawable.view.update_intro_div();
+ view.update_intro_div();
});
},
/**
https://bitbucket.org/galaxy/galaxy-central/changeset/9ba4435bfd4e/
changeset: 9ba4435bfd4e
user: jgoecks
date: 2012-02-07 17:35:48
summary: Fix bug in GFFDataProvider iterator.
affected #: 1 file
diff -r 5c57dfac1e3143e3931bb5d5cc774248f8060113 -r 9ba4435bfd4ee6111c511c003f1ba6a54b6cb91d lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -936,7 +936,7 @@
for feature in GFFReaderWrapper( source, fix_strand=True ):
# Only provide features that are in region.
feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] )
- if feature.chrom != chrom or feature_start < start or feature_end > end:
+ if feature.chrom != chrom or feature_end < start or feature_start > end:
continue
yield feature
return features_in_region_iter()
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/b4ba8b20d78d/
changeset: b4ba8b20d78d
user: greg
date: 2012-02-07 17:15:20
summary: Fix for loading proprietary datatype sniffers that are included in installed tool shed repositories.
affected #: 1 file
diff -r 271ccd09bc2367c7e20d59afb0a7307d4016a1f5 -r b4ba8b20d78d5ae92ebab85afeb6662ca602d427 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -187,11 +187,21 @@
try:
fields = dtype.split( ":" )
datatype_module = fields[0]
- datatype_class = fields[1]
- module = __import__( datatype_module )
- for comp in datatype_module.split( '.' )[ 1: ]:
- module = getattr( module, comp )
- aclass = getattr( module, datatype_class )()
+ datatype_class_name = fields[1]
+ module = None
+ if imported_modules:
+ # See if one of the imported modules contains the datatype class name.
+ for imported_module in imported_modules:
+ if hasattr( imported_module, datatype_class_name ):
+ module = imported_module
+ break
+ if module is None:
+ # The datatype class name must be contained in one of the datatype
+ # modules in the Galaxy distribution.
+ module = __import__( datatype_module )
+ for comp in datatype_module.split( '.' )[ 1: ]:
+ module = getattr( module, comp )
+ aclass = getattr( module, datatype_class_name )()
if deactivate:
self.sniff_order.remove( aclass )
self.log.debug( 'Deactivated sniffer for datatype: %s' % dtype )
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/271ccd09bc23/
changeset: 271ccd09bc23
user: greg
date: 2012-02-07 17:06:17
summary: Fix for 39e03997f78f - change buffer to string so older postgres versions work.
affected #: 1 file
diff -r 39e03997f78f7dcea23915cffe5f924e7b6bd957 -r 271ccd09bc2367c7e20d59afb0a7307d4016a1f5 lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
--- a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
+++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
@@ -76,7 +76,7 @@
for row in result:
if row[1]:
tool_shed_repository_id = row[0]
- repository_metadata = from_json_string( _sniffnfix_pg9_hex( row[1] ) )
+ repository_metadata = from_json_string( _sniffnfix_pg9_hex( str( row[1] ) ) )
# Create a new row in the tool table for each tool included in repository. We will NOT
# handle tool_version_associaions because we do not have the information we need to do so.
tools = repository_metadata.get( 'tools', [] )
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/39e03997f78f/
changeset: 39e03997f78f
user: natefoo
date: 2012-02-07 16:41:22
summary: Use PG9 hex bytea fix to decode tool shed repository metadata in migration script 91.
affected #: 1 file
diff -r f2ed09e52dfd51fb1e95dec0ec1379edefe6d56a -r 39e03997f78f7dcea23915cffe5f924e7b6bd957 lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
--- a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
+++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
@@ -11,6 +11,7 @@
now = datetime.datetime.utcnow
# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import *
+from galaxy.model.custom_types import _sniffnfix_pg9_hex
from galaxy.util.json import from_json_string, to_json_string
import sys, logging
@@ -75,7 +76,7 @@
for row in result:
if row[1]:
tool_shed_repository_id = row[0]
- repository_metadata = from_json_string( str( row[1] ) )
+ repository_metadata = from_json_string( _sniffnfix_pg9_hex( row[1] ) )
# Create a new row in the tool table for each tool included in repository. We will NOT
# handle tool_version_associaions because we do not have the information we need to do so.
tools = repository_metadata.get( 'tools', [] )
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/f2ed09e52dfd/
changeset: f2ed09e52dfd
user: jgoecks
date: 2012-02-07 16:17:44
summary: Trackster: renable data subsetting for all non-LineTracks.
affected #: 1 file
diff -r 5e1534bae3f22cb00382d4b5fe8143a2a3a70be7 -r f2ed09e52dfd51fb1e95dec0ec1379edefe6d56a static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -524,8 +524,7 @@
// only data points in request are returned.
//
- /* Disabling for now, more detailed data is never loaded for line tracks
- TODO: can using resolution in the key solve this problem?
+ // TODO: can using resolution in the key enable LineTrack data to be subsetted appropriately?
if (this.subset) {
var key, split_key, entry_low, entry_high, mode, entry;
for (var i = 0; i < this.key_ary.length; i++) {
@@ -535,20 +534,20 @@
entry_high = split_key[1];
if (low >= entry_low && high <= entry_high) {
- // This track has the range of data needed; check other attributes.
+ // This entry has requested data; return if compatible.
entry = this.obj_cache[key];
- if (entry.dataset_type !== "summary_tree" && entry.extra_info !== "no_detail") {
- // Data is usable.
+ if ( is_deferred(entry) || this.track.data_and_mode_compatible(entry, mode) ) {
+ // TODO: for fast lookup and processing, create new entry with only data subset?
+ // Entry is usable.
this.move_key_to_end(key, i);
return entry;
}
}
}
}
- */
// Load data from server. The deferred is immediately saved until the
- // data is ready, it then replaces itself with the actual data
+ // data is ready, it then replaces itself with the actual data.
entry = this.load_data(low, high, mode, resolution, extra_params);
this.set_data(low, high, entry);
return entry;
@@ -4042,6 +4041,10 @@
this.display_modes = ["Histogram", "Line", "Filled", "Intensity"];
this.mode = "Histogram";
TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager);
+
+ // Cannot subset LineTrack data right now; see note in DataManager about using resolution in key
+ // to address this issue.
+ this.data_manager.subset = false;
this.min_height_px = 16;
this.max_height_px = 400;
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/5e1534bae3f2/
changeset: 5e1534bae3f2
user: dannon
date: 2012-02-07 15:45:19
summary: Multiple-run workflows: When run into separate new histories, naming is now based on the varied input dataset instead of the execution number, so "<workflowname> on <varied_input>".
affected #: 1 file
diff -r b45af710a58bbe64a2d98faee53e8baf6d6314a8 -r 5e1534bae3f22cb00382d4b5fe8143a2a3a70be7 lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1489,7 +1489,8 @@
else:
nh_name = "History from %s workflow" % workflow.name
if multiple_input_key:
- nh_name = '%s %d' % (nh_name, input_number + 1)
+ mx_ds_name = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get( single_input ).name
+ nh_name = '%s on %s' % (nh_name, mx_ds_name)
new_history = trans.app.model.History( user=trans.user, name=nh_name )
trans.sa_session.add( new_history )
# Run each step, connecting outputs to inputs
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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