- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Trackster: add support for including a global model when running tools in Trackster. This is done by using a new HiddenDataToolParameter and implementing 'set parameter' actions in a tool's trackster configuration. Cufflinks now uses a global model to produce correct output when run in Trackster.
by Bitbucket 21 Dec '11

21 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/356e8b9510a9/ changeset: 356e8b9510a9 user: jgoecks date: 2011-12-21 23:04:23 summary: Trackster: add support for including a global model when running tools in Trackster. This is done by using a new HiddenDataToolParameter and implementing 'set parameter' actions in a tool's trackster configuration. Cufflinks now uses a global model to produce correct output when run in Trackster. affected #: 6 files diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -29,6 +29,7 @@ from cgi import FieldStorage from galaxy.util.hash_util import * from galaxy.util import listify +from galaxy.visualization.tracks.visual_analytics import TracksterConfig log = logging.getLogger( __name__ ) @@ -567,7 +568,11 @@ # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible() # Trackster configuration. - self.trackster_conf = ( root.find( "trackster_conf" ) is not None ) + trackster_conf = root.find( "trackster_conf" ) + if trackster_conf: + self.trackster_conf = TracksterConfig.parse( trackster_conf ) + else: + self.trackster_conf = None def parse_inputs( self, root ): """ diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1549,6 +1549,22 @@ if call_attribute: ref = ref() return ref + +class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): + """ + Hidden parameter that behaves as a DataToolParameter. As with all hidden + parameters, this is a HACK. + """ + def __init__( self, tool, elem ): + DataToolParameter.__init__( self, tool, elem ) + self.value = "None" + + def get_initial_value( self, trans, context ): + return None + + def get_html_field( self, trans=None, value=None, other_values={} ): + return form_builder.HiddenField( self.name, self.value ) + class LibraryDatasetToolParameter( ToolParameter ): """ @@ -1644,6 +1660,7 @@ select = SelectToolParameter, data_column = ColumnListParameter, hidden = HiddenToolParameter, + hidden_data = HiddenDataToolParameter, baseurl = BaseURLToolParameter, file = FileToolParameter, ftpfile = FTPFileToolParameter, diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/visualization/tracks/visual_analytics.py --- a/lib/galaxy/visualization/tracks/visual_analytics.py +++ b/lib/galaxy/visualization/tracks/visual_analytics.py @@ -3,6 +3,31 @@ from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter from galaxy.tools.parameters.dynamic_options import DynamicOptions +class TracksterConfig: + """ Trackster configuration encapsulation. """ + + def __init__( self, actions ): + self.actions = actions + + @staticmethod + def parse( root ): + actions = [] + for action_elt in root.findall( "action" ): + actions.append( SetParamAction.parse( action_elt ) ) + return TracksterConfig( actions ) + +class SetParamAction: + """ Set parameter action. """ + + def __init__( self, name, output_name ): + self.name = name + self.output_name = output_name + + @staticmethod + def parse( elt ): + """ Parse action from element. """ + return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) ) + def get_dataset_job( hda ): # Get dataset's job. job = None diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -824,7 +824,7 @@ return to_json_string( msg ) # - # Set tool parameters--except dataset parameters--using combination of + # Set tool parameters--except non-hidden dataset parameters--using combination of # job's previous parameters and incoming parameters. Incoming parameters # have priority. # @@ -872,15 +872,10 @@ else: target_history = trans.get_history( create=True ) hda_permissions = trans.app.security_agent.history_get_default_permissions( target_history ) - - # - # Set input datasets for tool. If running on region, extract and use subset - # when possible. - # def set_param_value( param_dict, param_name, param_value ): """ - Set new parameter value in a parameter dictionary. + Set new parameter value in a tool's parameter dictionary. """ # Recursive function to set param value. @@ -913,8 +908,30 @@ group_index = int( group[ index + 1: ] ) return set_value( param_dict, group_name, group_index, param_name, param_value ) - + + # Set parameters based tool's trackster config. + params_set = {} + for action in tool.trackster_conf.actions: + success = False + for joda in original_job.output_datasets: + if joda.name == action.output_name: + set_param_value( tool_params, action.name, joda.dataset ) + params_set[ action.name ] = True + success = True + break + + if not success: + return messages.ERROR + + # + # Set input datasets for tool. If running on region, extract and use subset + # when possible. + # for jida in original_job.input_datasets: + # If param set previously by config actions, do nothing. + if jida.name in params_set: + continue + input_dataset = jida.dataset if input_dataset is None: #optional dataset and dataset wasn't selected tool_params[ jida.name ] = None diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -1,6 +1,8 @@ #!/usr/bin/env python import optparse, os, shutil, subprocess, sys, tempfile +from galaxy import eggs +from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attributes_to_str def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -51,6 +53,9 @@ parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) + # Global model. + parser.add_option( '', '--global_model', dest='global_model_file', help='Global model used for computing on local data' ) + (options, args) = parser.parse_args() # output version # of tool @@ -122,7 +127,9 @@ # Add input files. cmd += " " + options.input + # # Run command. + # try: tmp_name = tempfile.NamedTemporaryFile( dir="." ).name tmp_stderr = open( tmp_name, 'wb' ) @@ -130,7 +137,60 @@ returncode = proc.wait() tmp_stderr.close() - # Get stderr, allowing for case where it's very large. + # Read standard error to get total map mass. + total_map_mass = -1 + tmp_stderr = open( tmp_name, 'r' ) + for line in tmp_stderr: + if line.lower().find( "total map mass") >= 0: + total_map_mass = float( line.split(":")[1].strip() ) + break + tmp_stderr.close() + + # + # If there's a global model provided, use model's total map mass + # to adjust FPKM + confidence intervals. + # + if options.global_model_file: + # Global model is simply total map mass from original run. + global_model_file = open( options.global_model_file, 'r' ) + global_model_total_map_mass = float( global_model_file.readline() ) + global_model_file.close() + + # Ratio of global model's total map mass to original run's map mass is + # factor used to adjust FPKM. + fpkm_map_mass_ratio = total_map_mass / global_model_total_map_mass + + # Update FPKM values in transcripts.gtf file. + transcripts_file = open( "transcripts.gtf", 'r' ) + tmp_transcripts = tempfile.NamedTemporaryFile( dir="." ).name + new_transcripts_file = open( tmp_transcripts, 'w' ) + for line in transcripts_file: + fields = line.split( '\t' ) + attrs = parse_gff_attributes( fields[8] ) + attrs[ "FPKM" ] = str( float( attrs[ "FPKM" ] ) * fpkm_map_mass_ratio ) + attrs[ "conf_lo" ] = str( float( attrs[ "conf_lo" ] ) * fpkm_map_mass_ratio ) + attrs[ "conf_hi" ] = str( float( attrs[ "conf_hi" ] ) * fpkm_map_mass_ratio ) + fields[8] = gff_attributes_to_str( attrs, "GTF" ) + new_transcripts_file.write( "%s\n" % '\t'.join( fields ) ) + transcripts_file.close() + new_transcripts_file.close() + shutil.copyfile( tmp_transcripts, "transcripts.gtf" ) + + # TODO: update expression files as well. + + # Set outputs. Transcript and gene expression handled by wrapper directives. + shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file ) + if total_map_mass > -1: + f = open( "global_model.txt", 'w' ) + f.write( "%f\n" % total_map_mass ) + f.close() + + # Error checking. + if returncode != 0: + raise Exception, stderr + except Exception, e: + raise e + # Read stderr so that it can be reported: tmp_stderr = open( tmp_name, 'rb' ) stderr = '' buffsize = 1048576 @@ -142,14 +202,7 @@ except OverflowError: pass tmp_stderr.close() - - # Copy outputs. - shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file ) - # Error checking. - if returncode != 0: - raise Exception, stderr - except Exception, e: stop_err( 'Error running cufflinks. ' + str( e ) ) if __name__=="__main__": __main__() diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -43,6 +43,11 @@ --dbkey=${input.metadata.dbkey} --index_dir=${GALAXY_DATA_INDEX_DIR} #end if + + ## Include global model if available. + #if $global_model: + --global_model=$global_model + #end if </command><inputs><param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> @@ -97,15 +102,20 @@ <param name="inner_distance_std_dev" type="integer" value="20" label="Standard Deviation for Inner Distance between Mate Pairs"/></when></conditional> + <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/></inputs><outputs><data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/><data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/><data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/> + <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/></outputs> - <trackster_conf/> + <trackster_conf> + <action type="set_param" name="global_model" output_name="total_map_mass"/> + </trackster_conf> + <tests><!-- Simple test that uses test data included with cufflinks. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: clements: Updated "Example" images shown at the bottom of many
by Bitbucket 21 Dec '11

21 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/38fcdb8f0e63/ changeset: 38fcdb8f0e63 user: clements date: 2011-12-19 11:44:31 summary: Updated "Example" images shown at the bottom of many "Operate on Genomic Invervals" tool pages. Old onew were looking dated. New ones look, well, newer, and cover more cases. affected #: 20 files diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_baseCoverage.gif Binary file static/operation_icons/gops_baseCoverage.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_clusterFind.gif Binary file static/operation_icons/gops_clusterFind.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_clusterMerge.gif Binary file static/operation_icons/gops_clusterMerge.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_complement.gif Binary file static/operation_icons/gops_complement.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_concatenate.gif Binary file static/operation_icons/gops_concatenate.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_intersectOverlappingIntervals.gif Binary file static/operation_icons/gops_intersectOverlappingIntervals.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_intersectOverlappingPieces.gif Binary file static/operation_icons/gops_intersectOverlappingPieces.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinFullOuter.gif Binary file static/operation_icons/gops_joinFullOuter.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinInner.gif Binary file static/operation_icons/gops_joinInner.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinLeftOuter.gif Binary file static/operation_icons/gops_joinLeftOuter.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinRecordsList.gif Binary file static/operation_icons/gops_joinRecordsList.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinRightOuter.gif Binary file static/operation_icons/gops_joinRightOuter.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_merge.gif Binary file static/operation_icons/gops_merge.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_subtractOverlappingIntervals.gif Binary file static/operation_icons/gops_subtractOverlappingIntervals.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_subtractOverlappingPieces.gif Binary file static/operation_icons/gops_subtractOverlappingPieces.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/basecoverage.xml --- a/tools/new_operations/basecoverage.xml +++ b/tools/new_operations/basecoverage.xml @@ -36,6 +36,10 @@ .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations +**Example** + +.. image:: ./static/operation_icons/gops_baseCoverage.gif + </help> -</tool> \ No newline at end of file +</tool> diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/cluster.xml --- a/tools/new_operations/cluster.xml +++ b/tools/new_operations/cluster.xml @@ -82,9 +82,15 @@ ----- -**Example** +**Examples** -.. image:: ./static/operation_icons/gops_cluster.gif +Find Clusters: + +.. image:: ./static/operation_icons/gops_clusterFind.gif + +Merge Clusters: + +.. image:: ./static/operation_icons/gops_clusterMerge.gif </help> -</tool> \ No newline at end of file +</tool> diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml +++ b/tools/new_operations/intersect.xml @@ -129,9 +129,15 @@ ----- -**Example** +**Examples** -.. image:: ./static/operation_icons/gops_intersect.gif +Overlapping Intervals: + +.. image:: ./static/operation_icons/gops_intersectOverlappingIntervals.gif + +Overlapping Pieces of Intervals: + +.. image:: ./static/operation_icons/gops_intersectOverlappingPieces.gif </help> -</tool> \ No newline at end of file +</tool> diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/join.xml --- a/tools/new_operations/join.xml +++ b/tools/new_operations/join.xml @@ -92,48 +92,26 @@ ----- -**Example** +**Examples** -If **First dataset** is:: +.. image:: ./static/operation_icons/gops_joinRecordsList.gif - chr1 10 100 Query1.1 - chr1 500 1000 Query1.2 - chr1 1100 1250 Query1.3 +Only records that are joined (inner join): -and **Second dataset** is:: +.. image:: ./static/operation_icons/gops_joinInner.gif - chr1 20 80 Query2.1 - chr1 2000 2204 Query2.2 - chr1 2500 3000 Query2.3 +All records of first dataset: +.. image:: ./static/operation_icons/gops_joinLeftOuter.gif -The four return options will generate: +All records of second dataset: +.. image:: ./static/operation_icons/gops_joinRightOuter.gif -- **Return only records that are joined**:: +All records of both datasets: - chr1 10 100 Query1.1 chr1 20 80 Query2.1 +.. image:: ./static/operation_icons/gops_joinFullOuter.gif -- **Return all records of first dataset**:: - - chr1 10 100 Query1.1 chr1 20 80 Query2.1 - chr1 500 1000 Query1.2 . . . . - chr1 1100 1250 Query1.3 . . . . - -- **Return all records of second dataset**:: - - chr1 10 100 Query1.1 chr1 20 80 Query2.1 - . . . . chr1 2000 2204 Query2.2 - . . . . chr1 2500 3000 Query2.3 - -- **Return all records of both datasets**:: - - chr1 10 100 Query1.1 chr1 20 80 Query2.1 - chr1 500 1000 Query1.2 . . . . - chr1 1100 1250 Query1.3 . . . . - . . . . chr1 2000 2204 Query2.2 - . . . . chr1 2500 3000 Query2.3 - </help> -</tool> \ No newline at end of file +</tool> diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml +++ b/tools/new_operations/subtract.xml @@ -112,7 +112,13 @@ **Example** -.. image:: ./static/operation_icons/gops_subtract.gif +Intervals with no overlap: + +.. image:: ./static/operation_icons/gops_subtractOverlappingIntervals.gif + +Non-overlapping pieces of intervals: + +.. image:: ./static/operation_icons/gops_subtractOverlappingPieces.gif </help> -</tool> \ No newline at end of file +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Add UCSC VCF external display application.
by Bitbucket 20 Dec '11

20 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb5e05256c29/ changeset: bb5e05256c29 user: dan date: 2011-12-20 21:40:07 summary: Add UCSC VCF external display application. affected #: 2 files diff -r f22a8a7bd077a118bcfa71430f345ff46873757f -r bb5e05256c2997892f5cac6b1998bbe90896372d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -162,6 +162,7 @@ <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/><converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <display file="ucsc/vcf.xml" /><display file="igv/vcf.xml" /></datatype><datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True"/> diff -r f22a8a7bd077a118bcfa71430f345ff46873757f -r bb5e05256c2997892f5cac6b1998bbe90896372d display_applications/ucsc/vcf.xml --- /dev/null +++ b/display_applications/ucsc/vcf.xml @@ -0,0 +1,17 @@ +<display id="ucsc_vcf" version="1.0.0" name="display at UCSC"> +  + <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> +  + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="ucsc_link" value="1"/> + <dynamic_param name="builds" value="2" split="True" separator="," /> +  + <filter>${site_id in $APP.config.ucsc_display_sites}</filter> + <filter>${dataset.dbkey in $builds}</filter> +  + <url>${ucsc_link}db=${qp($bgzip_file.dbkey)}&hgt.customText=${qp($track.url)}</url> + <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /> + <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /> + <param type="template" name="track" viewable="True">track type="vcfTabix" name="${bgzip_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bgzip_file.url}" db="${bgzip_file.dbkey}"</param> + </dynamic_links> +</display> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Don't allow repository names to be changed if the repository has been cloned at least 1 time.
by Bitbucket 20 Dec '11

20 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f22a8a7bd077/ changeset: f22a8a7bd077 user: greg date: 2011-12-20 20:31:13 summary: Don't allow repository names to be changed if the repository has been cloned at least 1 time. affected #: 1 file diff -r 8458fa9dd5590e0890effaf04c50ba19013a280c -r f22a8a7bd077a118bcfa71430f345ff46873757f templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -139,7 +139,14 @@ %endif <div class="form-row"><label>Name:</label> - <input name="repo_name" type="textfield" value="${repo_name}" size="40"/> + %if repository.times_downloaded > 0: + ${repo_name} + %else: + <input name="repo_name" type="textfield" value="${repo_name}" size="40"/> + %endif + <div class="toolParamHelp" style="clear: both;"> + Repository names cannot be changed if the repository has been cloned. + </div><div style="clear: both"></div></div><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Make the tool_shed_install.xml.sample file ready for installing the correct versions of the emboss_5 and emboss_datatypes repositories from the main Galaxy tool shed.
by Bitbucket 20 Dec '11

20 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8458fa9dd559/ changeset: 8458fa9dd559 user: greg date: 2011-12-20 20:15:39 summary: Make the tool_shed_install.xml.sample file ready for installing the correct versions of the emboss_5 and emboss_datatypes repositories from the main Galaxy tool shed. affected #: 1 file diff -r 0497ba5576facae84f7b9a44092d0f67a61788ef -r 8458fa9dd5590e0890effaf04c50ba19013a280c tool_shed_install.xml.sample --- a/tool_shed_install.xml.sample +++ b/tool_shed_install.xml.sample @@ -1,114 +1,116 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"> +  + <repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /><section name="EMBOSS" id="EMBOSSLite"> - <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5 tools" changeset_revision="PlaceHereWhenKnown"> - <tool file="emboss_5/emboss_antigenic.xml" id="EMBOSS: antigenic1" version="5.0.0" /> - <tool file="emboss_5/emboss_backtranseq.xml" id="EMBOSS: backtranseq2" version="5.0.0" /> - <tool file="emboss_5/emboss_banana.xml" id="EMBOSS: banana3" version="5.0.0" /> - <tool file="emboss_5/emboss_biosed.xml" id="EMBOSS: biosed4" version="5.0.0" /> - <tool file="emboss_5/emboss_btwisted.xml" id="EMBOSS: btwisted5" version="5.0.0" /> - <tool file="emboss_5/emboss_cai_custom.xml" id="EMBOSS: cai_custom6" version="5.0.0" /> - <tool file="emboss_5/emboss_cai.xml" id="EMBOSS: cai6" version="5.0.0" /> - <tool file="emboss_5/emboss_chaos.xml" id="EMBOSS: chaos7" version="5.0.0" /> - <tool file="emboss_5/emboss_charge.xml" id="EMBOSS: charge8" version="5.0.0" /> - <tool file="emboss_5/emboss_checktrans.xml" id="EMBOSS: checktrans9" version="5.0.0" /> - <tool file="emboss_5/emboss_chips.xml" id="EMBOSS: chips10" version="5.0.0" /> - <tool file="emboss_5/emboss_cirdna.xml" id="EMBOSS: cirdna11" version="5.0.0" /> - <tool file="emboss_5/emboss_codcmp.xml" id="EMBOSS: codcmp12" version="5.0.0" /> - <tool file="emboss_5/emboss_coderet.xml" id="EMBOSS: coderet13" version="5.0.0" /> - <tool file="emboss_5/emboss_compseq.xml" id="EMBOSS: compseq14" version="5.0.0" /> - <tool file="emboss_5/emboss_cpgplot.xml" id="EMBOSS: cpgplot15" version="5.0.0" /> - <tool file="emboss_5/emboss_cpgreport.xml" id="EMBOSS: cpgreport16" version="5.0.0" /> - <tool file="emboss_5/emboss_cusp.xml" id="EMBOSS: cusp17" version="5.0.0" /> - <tool file="emboss_5/emboss_cutseq.xml" id="EMBOSS: cutseq18" version="5.0.0" /> - <tool file="emboss_5/emboss_dan.xml" id="EMBOSS: dan19" version="5.0.0" /> - <tool file="emboss_5/emboss_degapseq.xml" id="EMBOSS: degapseq20" version="5.0.0" /> - <tool file="emboss_5/emboss_descseq.xml" id="EMBOSS: descseq21" version="5.0.0" /> - <tool file="emboss_5/emboss_diffseq.xml" id="EMBOSS: diffseq22" version="5.0.0" /> - <tool file="emboss_5/emboss_digest.xml" id="EMBOSS: digest23" version="5.0.0" /> - <tool file="emboss_5/emboss_dotmatcher.xml" id="EMBOSS: dotmatcher24" version="5.0.0" /> - <tool file="emboss_5/emboss_dotpath.xml" id="EMBOSS: dotpath25" version="5.0.0" /> - <tool file="emboss_5/emboss_dottup.xml" id="EMBOSS: dottup26" version="5.0.0" /> - <tool file="emboss_5/emboss_dreg.xml" id="EMBOSS: dreg27" version="5.0.0" /> - <tool file="emboss_5/emboss_einverted.xml" id="EMBOSS: einverted28" version="5.0.0" /> - <tool file="emboss_5/emboss_epestfind.xml" id="EMBOSS: epestfind29" version="5.0.0" /> - <tool file="emboss_5/emboss_equicktandem.xml" id="EMBOSS: equicktandem31" version="5.0.0" /> - <tool file="emboss_5/emboss_est2genome.xml" id="EMBOSS: est2genome32" version="5.0.0" /> - <tool file="emboss_5/emboss_etandem.xml" id="EMBOSS: etandem33" version="5.0.0" /> - <tool file="emboss_5/emboss_extractfeat.xml" id="EMBOSS: extractfeat34" version="5.0.0" /> - <tool file="emboss_5/emboss_extractseq.xml" id="EMBOSS: extractseq35" version="5.0.0" /> - <tool file="emboss_5/emboss_freak.xml" id="EMBOSS: freak36" version="5.0.0" /> - <tool file="emboss_5/emboss_fuzznuc.xml" id="EMBOSS: fuzznuc37" version="5.0.0" /> - <tool file="emboss_5/emboss_fuzzpro.xml" id="EMBOSS: fuzzpro38" version="5.0.0" /> - <tool file="emboss_5/emboss_fuzztran.xml" id="EMBOSS: fuzztran39" version="5.0.0" /> - <tool file="emboss_5/emboss_garnier.xml" id="EMBOSS: garnier40" version="5.0.0" /> - <tool file="emboss_5/emboss_geecee.xml" id="EMBOSS: geecee41" version="5.0.0" /> - <tool file="emboss_5/emboss_getorf.xml" id="EMBOSS: getorf42" version="5.0.0" /> - <tool file="emboss_5/emboss_helixturnhelix.xml" id="EMBOSS: helixturnhelix43" version="5.0.0" /> - <tool file="emboss_5/emboss_hmoment.xml" id="EMBOSS: hmoment44" version="5.0.0" /> - <tool file="emboss_5/emboss_iep.xml" id="EMBOSS: iep45" version="5.0.0" /> - <tool file="emboss_5/emboss_infoseq.xml" id="EMBOSS: infoseq46" version="5.0.0" /> - <tool file="emboss_5/emboss_isochore.xml" id="EMBOSS: isochore47" version="5.0.0" /> - <tool file="emboss_5/emboss_lindna.xml" id="EMBOSS: lindna48" version="5.0.0" /> - <tool file="emboss_5/emboss_marscan.xml" id="EMBOSS: marscan49" version="5.0.0" /> - <tool file="emboss_5/emboss_maskfeat.xml" id="EMBOSS: maskfeat50" version="5.0.0" /> - <tool file="emboss_5/emboss_maskseq.xml" id="EMBOSS: maskseq51" version="5.0.0" /> - <tool file="emboss_5/emboss_matcher.xml" id="EMBOSS: matcher52" version="5.0.0" /> - <tool file="emboss_5/emboss_megamerger.xml" id="EMBOSS: megamerger53" version="5.0.0" /> - <tool file="emboss_5/emboss_merger.xml" id="EMBOSS: merger54" version="5.0.0" /> - <tool file="emboss_5/emboss_msbar.xml" id="EMBOSS: msbar55" version="5.0.0" /> - <tool file="emboss_5/emboss_needle.xml" id="EMBOSS: needle56" version="5.0.0" /> - <tool file="emboss_5/emboss_newcpgreport.xml" id="EMBOSS: newcpgreport57" version="5.0.0" /> - <tool file="emboss_5/emboss_newcpgseek.xml" id="EMBOSS: newcpgseek58" version="5.0.0" /> - <tool file="emboss_5/emboss_newseq.xml" id="EMBOSS: newseq59" version="5.0.0" /> - <tool file="emboss_5/emboss_noreturn.xml" id="EMBOSS: noreturn60" version="5.0.0" /> - <tool file="emboss_5/emboss_notseq.xml" id="EMBOSS: notseq61" version="5.0.0" /> - <tool file="emboss_5/emboss_nthseq.xml" id="EMBOSS: nthseq62" version="5.0.0" /> - <tool file="emboss_5/emboss_octanol.xml" id="EMBOSS: octanol63" version="5.0.0" /> - <tool file="emboss_5/emboss_oddcomp.xml" id="EMBOSS: oddcomp64" version="5.0.0" /> - <tool file="emboss_5/emboss_palindrome.xml" id="EMBOSS: palindrome65" version="5.0.0" /> - <tool file="emboss_5/emboss_pasteseq.xml" id="EMBOSS: pasteseq66" version="5.0.0" /> - <tool file="emboss_5/emboss_patmatdb.xml" id="EMBOSS: patmatdb67" version="5.0.0" /> - <tool file="emboss_5/emboss_pepcoil.xml" id="EMBOSS: pepcoil68" version="5.0.0" /> - <tool file="emboss_5/emboss_pepinfo.xml" id="EMBOSS: pepinfo69" version="5.0.0" /> - <tool file="emboss_5/emboss_pepnet.xml" id="EMBOSS: pepnet70" version="5.0.0" /> - <tool file="emboss_5/emboss_pepstats.xml" id="EMBOSS: pepstats71" version="5.0.0" /> - <tool file="emboss_5/emboss_pepwheel.xml" id="EMBOSS: pepwheel72" version="5.0.0" /> - <tool file="emboss_5/emboss_pepwindow.xml" id="EMBOSS: pepwindow73" version="5.0.0" /> - <tool file="emboss_5/emboss_pepwindowall.xml" id="EMBOSS: pepwindowall74" version="5.0.0" /> - <tool file="emboss_5/emboss_plotcon.xml" id="EMBOSS: plotcon75" version="5.0.0" /> - <tool file="emboss_5/emboss_plotorf.xml" id="EMBOSS: plotorf76" version="5.0.0" /> - <tool file="emboss_5/emboss_polydot.xml" id="EMBOSS: polydot77" version="5.0.0" /> - <tool file="emboss_5/emboss_preg.xml" id="EMBOSS: preg78" version="5.0.0" /> - <tool file="emboss_5/emboss_prettyplot.xml" id="EMBOSS: prettyplot79" version="5.0.0" /> - <tool file="emboss_5/emboss_prettyseq.xml" id="EMBOSS: prettyseq80" version="5.0.0" /> - <tool file="emboss_5/emboss_primersearch.xml" id="EMBOSS: primersearch81" version="5.0.0" /> - <tool file="emboss_5/emboss_revseq.xml" id="EMBOSS: revseq82" version="5.0.0" /> - <tool file="emboss_5/emboss_seqmatchall.xml" id="EMBOSS: seqmatchall83" version="5.0.0" /> - <tool file="emboss_5/emboss_seqret.xml" id="EMBOSS: seqret84" version="5.0.0" /> - <tool file="emboss_5/emboss_showfeat.xml" id="EMBOSS: showfeat85" version="5.0.0" /> - <tool file="emboss_5/emboss_shuffleseq.xml" id="EMBOSS: shuffleseq87" version="5.0.0" /> - <tool file="emboss_5/emboss_sigcleave.xml" id="EMBOSS: sigcleave88" version="5.0.0" /> - <tool file="emboss_5/emboss_sirna.xml" id="EMBOSS: sirna89" version="5.0.0" /> - <tool file="emboss_5/emboss_sixpack.xml" id="EMBOSS: sixpack90" version="5.0.0" /> - <tool file="emboss_5/emboss_skipseq.xml" id="EMBOSS: skipseq91" version="5.0.0" /> - <tool file="emboss_5/emboss_splitter.xml" id="EMBOSS: splitter92" version="5.0.0" /> - <tool file="emboss_5/emboss_supermatcher.xml" id="EMBOSS: supermatcher95" version="5.0.0" /> - <tool file="emboss_5/emboss_syco.xml" id="EMBOSS: syco96" version="5.0.0" /> - <tool file="emboss_5/emboss_tcode.xml" id="EMBOSS: tcode97" version="5.0.0" /> - <tool file="emboss_5/emboss_textsearch.xml" id="EMBOSS: textsearch98" version="5.0.0" /> - <tool file="emboss_5/emboss_tmap.xml" id="EMBOSS: tmap99" version="5.0.0" /> - <tool file="emboss_5/emboss_tranalign.xml" id="EMBOSS: tranalign100" version="5.0.0" /> - <tool file="emboss_5/emboss_transeq.xml" id="EMBOSS: transeq101" version="5.0.0" /> - <tool file="emboss_5/emboss_trimest.xml" id="EMBOSS: trimest102" version="5.0.0" /> - <tool file="emboss_5/emboss_trimseq.xml" id="EMBOSS: trimseq103" version="5.0.0" /> - <tool file="emboss_5/emboss_twofeat.xml" id="EMBOSS: twofeat104" version="5.0.0" /> - <tool file="emboss_5/emboss_union.xml" id="EMBOSS: union105" version="5.0.0" /> - <tool file="emboss_5/emboss_vectorstrip.xml" id="EMBOSS: vectorstrip106" version="5.0.0" /> - <tool file="emboss_5/emboss_water.xml" id="EMBOSS: water107" version="5.0.0" /> - <tool file="emboss_5/emboss_wobble.xml" id="EMBOSS: wobble108" version="5.0.0" /> - <tool file="emboss_5/emboss_wordcount.xml" id="EMBOSS: wordcount109" version="5.0.0" /> - <tool file="emboss_5/emboss_wordmatch.xml" id="EMBOSS: wordmatch110" version="5.0.0" /> + <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="b94ca591877b"> + <tool id="EMBOSS: antigenic1" version="5.0.0" /> + <tool id="EMBOSS: backtranseq2" version="5.0.0" /> + <tool id="EMBOSS: banana3" version="5.0.0" /> + <tool id="EMBOSS: biosed4" version="5.0.0" /> + <tool id="EMBOSS: btwisted5" version="5.0.0" /> + <tool id="EMBOSS: cai_custom6" version="5.0.0" /> + <tool id="EMBOSS: cai6" version="5.0.0" /> + <tool id="EMBOSS: chaos7" version="5.0.0" /> + <tool id="EMBOSS: charge8" version="5.0.0" /> + <tool id="EMBOSS: checktrans9" version="5.0.0" /> + <tool id="EMBOSS: chips10" version="5.0.0" /> + <tool id="EMBOSS: cirdna11" version="5.0.0" /> + <tool id="EMBOSS: codcmp12" version="5.0.0" /> + <tool id="EMBOSS: coderet13" version="5.0.0" /> + <tool id="EMBOSS: compseq14" version="5.0.0" /> + <tool id="EMBOSS: cpgplot15" version="5.0.0" /> + <tool id="EMBOSS: cpgreport16" version="5.0.0" /> + <tool id="EMBOSS: cusp17" version="5.0.0" /> + <tool id="EMBOSS: cutseq18" version="5.0.0" /> + <tool id="EMBOSS: dan19" version="5.0.0" /> + <tool id="EMBOSS: degapseq20" version="5.0.0" /> + <tool id="EMBOSS: descseq21" version="5.0.0" /> + <tool id="EMBOSS: diffseq22" version="5.0.0" /> + <tool id="EMBOSS: digest23" version="5.0.0" /> + <tool id="EMBOSS: dotmatcher24" version="5.0.0" /> + <tool id="EMBOSS: dotpath25" version="5.0.0" /> + <tool id="EMBOSS: dottup26" version="5.0.0" /> + <tool id="EMBOSS: dreg27" version="5.0.0" /> + <tool id="EMBOSS: einverted28" version="5.0.0" /> + <tool id="EMBOSS: epestfind29" version="5.0.0" /> + <tool id="EMBOSS: equicktandem31" version="5.0.0" /> + <tool id="EMBOSS: est2genome32" version="5.0.0" /> + <tool id="EMBOSS: etandem33" version="5.0.0" /> + <tool id="EMBOSS: extractfeat34" version="5.0.0" /> + <tool id="EMBOSS: extractseq35" version="5.0.0" /> + <tool id="EMBOSS: freak36" version="5.0.0" /> + <tool id="EMBOSS: fuzznuc37" version="5.0.0" /> + <tool id="EMBOSS: fuzzpro38" version="5.0.0" /> + <tool id="EMBOSS: fuzztran39" version="5.0.0" /> + <tool id="EMBOSS: garnier40" version="5.0.0" /> + <tool id="EMBOSS: geecee41" version="5.0.0" /> + <tool id="EMBOSS: getorf42" version="5.0.0" /> + <tool id="EMBOSS: helixturnhelix43" version="5.0.0" /> + <tool id="EMBOSS: hmoment44" version="5.0.0" /> + <tool id="EMBOSS: iep45" version="5.0.0" /> + <tool id="EMBOSS: infoseq46" version="5.0.0" /> + <tool id="EMBOSS: isochore47" version="5.0.0" /> + <tool id="EMBOSS: lindna48" version="5.0.0" /> + <tool id="EMBOSS: marscan49" version="5.0.0" /> + <tool id="EMBOSS: maskfeat50" version="5.0.0" /> + <tool id="EMBOSS: maskseq51" version="5.0.0" /> + <tool id="EMBOSS: matcher52" version="5.0.0" /> + <tool id="EMBOSS: megamerger53" version="5.0.0" /> + <tool id="EMBOSS: merger54" version="5.0.0" /> + <tool id="EMBOSS: msbar55" version="5.0.0" /> + <tool id="EMBOSS: needle56" version="5.0.0" /> + <tool id="EMBOSS: newcpgreport57" version="5.0.0" /> + <tool id="EMBOSS: newcpgseek58" version="5.0.0" /> + <tool id="EMBOSS: newseq59" version="5.0.0" /> + <tool id="EMBOSS: noreturn60" version="5.0.0" /> + <tool id="EMBOSS: notseq61" version="5.0.0" /> + <tool id="EMBOSS: nthseq62" version="5.0.0" /> + <tool id="EMBOSS: octanol63" version="5.0.0" /> + <tool id="EMBOSS: oddcomp64" version="5.0.0" /> + <tool id="EMBOSS: palindrome65" version="5.0.0" /> + <tool id="EMBOSS: pasteseq66" version="5.0.0" /> + <tool id="EMBOSS: patmatdb67" version="5.0.0" /> + <tool id="EMBOSS: pepcoil68" version="5.0.0" /> + <tool id="EMBOSS: pepinfo69" version="5.0.0" /> + <tool id="EMBOSS: pepnet70" version="5.0.0" /> + <tool id="EMBOSS: pepstats71" version="5.0.0" /> + <tool id="EMBOSS: pepwheel72" version="5.0.0" /> + <tool id="EMBOSS: pepwindow73" version="5.0.0" /> + <tool id="EMBOSS: pepwindowall74" version="5.0.0" /> + <tool id="EMBOSS: plotcon75" version="5.0.0" /> + <tool id="EMBOSS: plotorf76" version="5.0.0" /> + <tool id="EMBOSS: polydot77" version="5.0.0" /> + <tool id="EMBOSS: preg78" version="5.0.0" /> + <tool id="EMBOSS: prettyplot79" version="5.0.0" /> + <tool id="EMBOSS: prettyseq80" version="5.0.0" /> + <tool id="EMBOSS: primersearch81" version="5.0.0" /> + <tool id="EMBOSS: revseq82" version="5.0.0" /> + <tool id="EMBOSS: seqmatchall83" version="5.0.0" /> + <tool id="EMBOSS: seqret84" version="5.0.0" /> + <tool id="EMBOSS: showfeat85" version="5.0.0" /> + <tool id="EMBOSS: shuffleseq87" version="5.0.0" /> + <tool id="EMBOSS: sigcleave88" version="5.0.0" /> + <tool id="EMBOSS: sirna89" version="5.0.0" /> + <tool id="EMBOSS: sixpack90" version="5.0.0" /> + <tool id="EMBOSS: skipseq91" version="5.0.0" /> + <tool id="EMBOSS: splitter92" version="5.0.0" /> + <tool id="EMBOSS: supermatcher95" version="5.0.0" /> + <tool id="EMBOSS: syco96" version="5.0.0" /> + <tool id="EMBOSS: tcode97" version="5.0.0" /> + <tool id="EMBOSS: textsearch98" version="5.0.0" /> + <tool id="EMBOSS: tmap99" version="5.0.0" /> + <tool id="EMBOSS: tranalign100" version="5.0.0" /> + <tool id="EMBOSS: transeq101" version="5.0.0" /> + <tool id="EMBOSS: trimest102" version="5.0.0" /> + <tool id="EMBOSS: trimseq103" version="5.0.0" /> + <tool id="EMBOSS: twofeat104" version="5.0.0" /> + <tool id="EMBOSS: union105" version="5.0.0" /> + <tool id="EMBOSS: vectorstrip106" version="5.0.0" /> + <tool id="EMBOSS: water107" version="5.0.0" /> + <tool id="EMBOSS: wobble108" version="5.0.0" /> + <tool id="EMBOSS: wordcount109" version="5.0.0" /> + <tool id="EMBOSS: wordmatch110" version="5.0.0" /></repository></section></toolshed> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Ensure that the integrated datatypes registry configs exist when needed.
by Bitbucket 20 Dec '11

20 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0497ba5576fa/ changeset: 0497ba5576fa user: greg date: 2011-12-20 15:38:15 summary: Ensure that the integrated datatypes registry configs exist when needed. affected #: 5 files diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -126,7 +126,7 @@ try: # If the datatypes registry was persisted, attempt to # remove the temporary file in which it was written. - if self.datatypes_registry.xml_filename is not None: - os.unlink( self.datatypes_registry.xml_filename ) + if self.datatypes_registry.integrated_datatypes_configs is not None: + os.unlink( self.datatypes_registry.integrated_datatypes_configs ) except: pass diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -434,6 +434,12 @@ if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype rval[ 'auto' ] = rval[ 'txt' ] return rval + @property + def integrated_datatypes_configs( self ): + if self.xml_filename and os.path.isfile( self.xml_filename ): + return self.xml_filename + self.to_xml_file() + return self.xml_filename def to_xml_file( self ): if self.xml_filename is not None: # If persisted previously, attempt to remove diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -868,7 +868,7 @@ if config_root is None: config_root = self.app.config.root if datatypes_config is None: - datatypes_config = self.app.datatypes_registry.xml_filename + datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], self.sa_session, exec_dir = exec_dir, diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1674,7 +1674,7 @@ # For the upload tool, we need to know the root directory and the # datatypes conf path, so we can load the datatypes registry param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) - param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.xml_filename + param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.integrated_datatypes_configs # Return the dictionary of parameters return param_dict diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -51,7 +51,7 @@ dataset_files_path = trans.app.model.Dataset.file_path, output_fnames = None, config_root = None, - datatypes_config = trans.app.datatypes_registry.xml_filename, + datatypes_config = trans.app.datatypes_registry.integrated_datatypes_configs, job_metadata = None, kwds = { 'overwrite' : overwrite } ) incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Clean up implementation in 303741fda0ec
by Bitbucket 19 Dec '11

19 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/166ea1ba55cb/ changeset: 166ea1ba55cb user: jgoecks date: 2011-12-19 21:00:53 summary: Clean up implementation in 303741fda0ec affected #: 1 file diff -r 303741fda0ec4ce0fc7b42a0334a6c84f44c7a1f -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -678,7 +678,7 @@ output.count = int( data_elem.get("count", 1) ) output.filters = data_elem.findall( 'filter' ) output.from_work_dir = data_elem.get("from_work_dir", None) - output.hidden = data_elem.get("hidden", None) in [ 'true', 'True' ] + output.hidden = util.string_as_bool( data_elem.get("hidden", "") ) output.tool = self output.actions = ToolOutputActionGroup( output, data_elem.find( 'actions' ) ) self.outputs[ output.name ] = output Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Add hidden attribute to tool outputs so that an output can be hidden by default.
by Bitbucket 19 Dec '11

19 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/303741fda0ec/ changeset: 303741fda0ec user: jgoecks date: 2011-12-19 19:40:18 summary: Add hidden attribute to tool outputs so that an output can be hidden by default. affected #: 2 files diff -r 10e0d2765f24c32f840be414d88bf813321e41b5 -r 303741fda0ec4ce0fc7b42a0334a6c84f44c7a1f lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -316,7 +316,7 @@ """ def __init__( self, name, format=None, format_source=None, metadata_source=None, - parent=None, label=None, filters = None, actions = None ): + parent=None, label=None, filters = None, actions = None, hidden=False ): self.name = name self.format = format self.format_source = format_source @@ -325,6 +325,7 @@ self.label = label self.filters = filters or [] self.actions = actions + self.hidden = hidden # Tuple emulation @@ -677,6 +678,7 @@ output.count = int( data_elem.get("count", 1) ) output.filters = data_elem.findall( 'filter' ) output.from_work_dir = data_elem.get("from_work_dir", None) + output.hidden = data_elem.get("hidden", None) in [ 'true', 'True' ] output.tool = self output.actions = ToolOutputActionGroup( output, data_elem.find( 'actions' ) ) self.outputs[ output.name ] = output diff -r 10e0d2765f24c32f840be414d88bf813321e41b5 -r 303741fda0ec4ce0fc7b42a0334a6c84f44c7a1f lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -286,6 +286,8 @@ if str( getattr( check, when_elem.get( 'attribute' ) ) ) == when_elem.get( 'value', None ): ext = when_elem.get( 'format', ext ) data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True, sa_session=trans.sa_session ) + if output.hidden: + data.visible = False # Commit the dataset immediately so it gets database assigned unique id trans.sa_session.add( data ) trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Only persist the datatypes registry when the load_datatypes() method is called. Tools and metadata setting processes that create their own datatypes registry will use the existing temporary file rather than persisting the registry themselves.
by Bitbucket 18 Dec '11

18 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/10e0d2765f24/ changeset: 10e0d2765f24 user: greg date: 2011-12-18 19:49:26 summary: Only persist the datatypes registry when the load_datatypes() method is called. Tools and metadata setting processes that create their own datatypes registry will use the existing temporary file rather than persisting the registry themselves. affected #: 4 files diff -r 4ee7b5f6b23db6f92bfe6b895bb6db5f4cf4d7b1 -r 10e0d2765f24c32f840be414d88bf813321e41b5 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -174,6 +174,9 @@ self.log.debug( 'Loaded sniffer for datatype: %s' % dtype ) except Exception, exc: self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) ) + # Persist the xml form of the registry into a temporary file so that it + # can be loaded from the command line by tools and set_metadata processing. + self.to_xml_file() # Default values. if not self.datatypes_by_extension: self.datatypes_by_extension = { @@ -466,4 +469,3 @@ os.write( fd, '</sniffers>\n' ) os.write( fd, '</datatypes>\n' ) os.close( fd ) - return os.path.abspath( filename ) diff -r 4ee7b5f6b23db6f92bfe6b895bb6db5f4cf4d7b1 -r 10e0d2765f24c32f840be414d88bf813321e41b5 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -868,7 +868,7 @@ if config_root is None: config_root = self.app.config.root if datatypes_config is None: - datatypes_config = self.app.datatypes_registry.to_xml_file() + datatypes_config = self.app.datatypes_registry.xml_filename return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], self.sa_session, exec_dir = exec_dir, diff -r 4ee7b5f6b23db6f92bfe6b895bb6db5f4cf4d7b1 -r 10e0d2765f24c32f840be414d88bf813321e41b5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1672,8 +1672,7 @@ # For the upload tool, we need to know the root directory and the # datatypes conf path, so we can load the datatypes registry param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) - datatypes_config = self.app.datatypes_registry.to_xml_file() - param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = datatypes_config + param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.xml_filename # Return the dictionary of parameters return param_dict diff -r 4ee7b5f6b23db6f92bfe6b895bb6db5f4cf4d7b1 -r 10e0d2765f24c32f840be414d88bf813321e41b5 lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -51,7 +51,7 @@ dataset_files_path = trans.app.model.Dataset.file_path, output_fnames = None, config_root = None, - datatypes_config = trans.app.datatypes_registry.to_xml_file(), + datatypes_config = trans.app.datatypes_registry.xml_filename, job_metadata = None, kwds = { 'overwrite' : overwrite } ) incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Always set / return the absolute path of the file to which the datatypes registry is persisted.
by Bitbucket 18 Dec '11

18 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4ee7b5f6b23d/ changeset: 4ee7b5f6b23d user: greg date: 2011-12-18 16:52:02 summary: Always set / return the absolute path of the file to which the datatypes registry is persisted. affected #: 2 files diff -r da4342bc04c779a50f50431fbec87d3d0c56576b -r 4ee7b5f6b23db6f92bfe6b895bb6db5f4cf4d7b1 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -441,7 +441,7 @@ pass self.xml_filename = None fd, filename = tempfile.mkstemp() - self.xml_filename = filename + self.xml_filename = os.path.abspath( filename ) if self.converters_path_attr: converters_path_str = ' converters_path="%s"' % self.converters_path_attr else: @@ -466,4 +466,4 @@ os.write( fd, '</sniffers>\n' ) os.write( fd, '</datatypes>\n' ) os.close( fd ) - return filename + return os.path.abspath( filename ) diff -r da4342bc04c779a50f50431fbec87d3d0c56576b -r 4ee7b5f6b23db6f92bfe6b895bb6db5f4cf4d7b1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1673,7 +1673,7 @@ # datatypes conf path, so we can load the datatypes registry param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) datatypes_config = self.app.datatypes_registry.to_xml_file() - param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.abspath( datatypes_config ) + param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = datatypes_config # Return the dictionary of parameters return param_dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0