3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/71fdd146b95c/ Changeset: 71fdd146b95c User: jgoecks Date: 2013-04-20 17:05:42 Summary: Visual analysis enhancements: (a) do not manually convert to json because it is not necessary and (b) gracefully handle missing sample names. Affected #: 2 files diff -r 034b2d6118caa1dc6808f1570e92d927973a87ed -r 71fdd146b95ce53735003afa282f51fa188398ad lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -193,7 +193,7 @@ original_dataset = self.get_dataset( trans, payload[ 'target_dataset_id' ], check_ownership=False, check_accessible=True ) msg = self.check_dataset_state( trans, original_dataset ) if msg: - return to_json_string( msg ) + return msg # # Set tool parameters--except non-hidden dataset parameters--using combination of @@ -223,7 +223,8 @@ for jida in original_job.input_datasets: input_dataset = jida.dataset data_provider = data_provider_registry.get_data_provider( trans, original_dataset=input_dataset, source='data' ) - if data_provider and not data_provider.converted_dataset: + if data_provider and ( not data_provider.converted_dataset + or data_provider.converted_dataset.state != trans.app.model.Dataset.states.OK ): # Can convert but no converted dataset yet, so return message about why. data_sources = input_dataset.datatype.data_sources msg = input_dataset.convert_dataset( trans, data_sources[ 'data' ] ) @@ -233,7 +234,7 @@ # Return any messages generated during conversions. return_message = self._get_highest_priority_msg( messages_list ) if return_message: - return to_json_string( return_message ) + return return_message # # Set target history (the history that tool will use for inputs/outputs). @@ -371,7 +372,7 @@ # Add dataset to tool's parameters. if not set_param_value( tool_params, jida.name, subset_dataset ): - return to_json_string( { "error" : True, "message" : "error setting parameter %s" % jida.name } ) + return { "error" : True, "message" : "error setting parameter %s" % jida.name } # # Execute tool and handle outputs. @@ -382,7 +383,7 @@ job_params={ "source" : "trackster" } ) except Exception, e: # Lots of things can go wrong when trying to execute tool. - return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } ) + return { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } if run_on_regions: for output in subset_job_outputs.values(): output.visible = False diff -r 034b2d6118caa1dc6808f1570e92d927973a87ed -r 71fdd146b95ce53735003afa282f51fa188398ad static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1821,7 +1821,7 @@ // Start with this status message. //new_track.container_div.addClass("pending"); - //new_track.content_div.text("Converting input data so that it can be used quickly with tool."); + //new_track.content_div.html(DATA_PENDING); $.when(ss_deferred.go()).then(function(response) { if (response === "no converter") { @@ -4234,7 +4234,23 @@ } else { var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode); - return dummy_painter.get_required_height(this.dataset.get_metadata('sample_names').length); + // HACK: sample_names is not be defined when dataset definition is fetched before + // dataset is complete (as is done when running tools). In that case, fall back on + // # of samples in data. This can be fixed by re-requesting dataset definition + // in init. + var num_samples = ( this.dataset.get_metadata('sample_names') ? this.dataset.get_metadata('sample_names').length : 0); + if (num_samples === 0 && result.data.length !== 0) { + // Sample data is separated by commas, so this computes # of samples: + num_samples = result.data[0][7].match(/,/g); + if ( num_samples === null ) { + num_samples = 1; + } + else { + num_samples = num_samples.length + 1; + } + } + + return dummy_painter.get_required_height(num_samples); } }, https://bitbucket.org/galaxy/galaxy-central/commits/034b2d6118ca/ Changeset: 034b2d6118ca User: jgoecks Date: 2013-04-20 16:08:29 Summary: Remove debugging statement Affected #: 1 file diff -r 1fa1583641474f160ca1569ec91faf8f3d7093c8 -r 034b2d6118caa1dc6808f1570e92d927973a87ed lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -796,7 +796,6 @@ # Search for and yield other data lines. for data_line in source: if line_in_region( data_line, chrom, start, end ): - print chrom, start, end, ">>>", data_line, yield data_line return line_filter_iter() https://bitbucket.org/galaxy/galaxy-central/commits/1fa158364147/ Changeset: 1fa158364147 User: jgoecks Date: 2013-04-20 16:06:26 Summary: Use tabix rather than interval index for pileup data indexing. Affected #: 2 files diff -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 -r 1fa1583641474f160ca1569ec91faf8f3d7093c8 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -160,7 +160,8 @@ </datatype><datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/><datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true"> - <converter file="pileup_to_interval_index_converter.xml" target_datatype="interval_index"/> + <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/></datatype><datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> diff -r 8d72c9adccf92f8a1971ec7d9b622de43cbd6f48 -r 1fa1583641474f160ca1569ec91faf8f3d7093c8 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -474,11 +474,12 @@ """Tab delimited data in pileup (6- or 10-column) format""" file_ext = "pileup" line_class = "genomic coordinate" - data_sources = { "data": "interval_index" } + data_sources = { "data": "tabix" } """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter ) + MetadataElement( name="endCol", default=2, desc="End column", param=metadata.ColumnParameter ) MetadataElement( name="baseCol", default=3, desc="Reference base column", param=metadata.ColumnParameter ) def init_meta( self, dataset, copy_from=None ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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