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[hg] galaxy 1569: Fix for mapping unit test. Testing of metadat...
by Nate Coraor 23 Oct '08

23 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/df07d0c2830f changeset: 1569:df07d0c2830f user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Oct 22 14:27:57 2008 -0400 description: Fix for mapping unit test. Testing of metadata elements requires a valid datatype. 1 file(s) affected in this change: lib/galaxy/model/mapping_tests.py diffs (12 lines): diff -r 0b022adfdc34 -r df07d0c2830f lib/galaxy/model/mapping_tests.py --- a/lib/galaxy/model/mapping_tests.py Wed Oct 22 13:49:22 2008 -0400 +++ b/lib/galaxy/model/mapping_tests.py Wed Oct 22 14:27:57 2008 -0400 @@ -16,7 +16,7 @@ #h1.queries.append( model.Query( "h1->q2" ) ) h2 = model.History( name=( "H" * 1024 ) ) #q1 = model.Query( "h2->q1" ) - d1 = model.HistoryDatasetAssociation( metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True ) + d1 = model.HistoryDatasetAssociation( extension="interval", metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True ) #h2.queries.append( q1 ) #h2.queries.append( model.Query( "h2->q2" ) ) model.context.current.flush()

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[hg] galaxy 1565: Fix for fix for unit tests.
by Nate Coraor 21 Oct '08

21 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/4f9042e95e60 changeset: 1565:4f9042e95e60 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Oct 20 16:51:51 2008 -0400 description: Fix for fix for unit tests. 1 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py diffs (12 lines): diff -r eef0fd813076 -r 4f9042e95e60 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Oct 20 15:09:47 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Oct 20 16:51:51 2008 -0400 @@ -1182,7 +1182,7 @@ return [] def converter_safe( self, other_values, trans ): - if not hasattr( trans, 'has_multiple_pages' ) or self.tool.has_multiple_pages or not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: + if self.tool is None or self.tool.has_multiple_pages or not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: return False if other_values is None: return True # we don't know other values, so we can't check, assume ok

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[hg] galaxy 1566: Add the guppy egg
by Nate Coraor 21 Oct '08

21 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/510ff36caaf3 changeset: 1566:510ff36caaf3 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Oct 21 10:40:08 2008 -0400 description: Add the guppy egg 2 file(s) affected in this change: eggs.ini lib/galaxy/eggs/__init__.py diffs (37 lines): diff -r 4f9042e95e60 -r 510ff36caaf3 eggs.ini --- a/eggs.ini Mon Oct 20 16:51:51 2008 -0400 +++ b/eggs.ini Tue Oct 21 10:40:08 2008 -0400 @@ -22,6 +22,7 @@ pysqlite = 2.3.5 python_lzo = 1.08 threadframe = 0.2 +guppy = 0.1.8 [eggs:noplatform] Beaker = 0.5 @@ -70,6 +71,7 @@ pysqlite = http://initd.org/pub/software/pysqlite/releases/2.3/2.3.5/pysqlite-2.3.5.ta… http://www.sqlite.org/sqlite-source-3_5_4.zip python_lzo = http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.tar… http://www.oberhumer.com/opensource/lzo/download/LZO-v1/lzo-1.08.tar.gz threadframe = http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz +guppy = http://pypi.python.org/packages/source/g/guppy/guppy-0.1.8.tar.gz Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-0.5.tar.gz docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz diff -r 4f9042e95e60 -r 510ff36caaf3 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Mon Oct 20 16:51:51 2008 -0400 +++ b/lib/galaxy/eggs/__init__.py Tue Oct 21 10:40:08 2008 -0400 @@ -490,6 +490,14 @@ return False except: return False + elif egg_name == "guppy": + try: + if self.config.get( "app:main", "use_memdump" ) == "True": + return True + else: + return False + except: + return False elif egg_name == "MySQL_python": try: if self.config.get( "app:main", "database_connection" ).startswith( "mysql://" ):

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[hg] galaxy 1561: Fix the use_heartbeat check in config.py
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d3a267ac124b changeset: 1561:d3a267ac124b user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Oct 20 09:25:38 2008 -0400 description: Fix the use_heartbeat check in config.py 1 file(s) affected in this change: lib/galaxy/config.py diffs (12 lines): diff -r 0a0045644219 -r d3a267ac124b lib/galaxy/config.py --- a/lib/galaxy/config.py Fri Oct 17 13:31:17 2008 -0400 +++ b/lib/galaxy/config.py Mon Oct 20 09:25:38 2008 -0400 @@ -55,7 +55,7 @@ self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "" ) self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "" ) self.pbs_stage_path = kwargs.get('pbs_stage_path', "" ) - self.use_heartbeat = kwargs.get( 'use_heartbeat', False ) + self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', "False" ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,flybase,elegans" ).lower().split(",") self.brand = kwargs.get( 'brand', None )

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[hg] galaxy 1560: Fix for optional datasets to work with metadat...
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/0a0045644219 changeset: 1560:0a0045644219 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Oct 17 13:31:17 2008 -0400 description: Fix for optional datasets to work with metadata changes. 1 file(s) affected in this change: lib/galaxy/util/none_like.py diffs (12 lines): diff -r f802eb92a49a -r 0a0045644219 lib/galaxy/util/none_like.py --- a/lib/galaxy/util/none_like.py Fri Oct 17 13:02:26 2008 -0400 +++ b/lib/galaxy/util/none_like.py Fri Oct 17 13:31:17 2008 -0400 @@ -23,7 +23,7 @@ if datatypes_registry is None: datatypes_registry = Registry() self.datatype = datatypes_registry.get_datatype_by_extension( ext ) self._metadata = None - self.metadata = MetadataCollection( self, self.datatype.metadata_spec ) + self.metadata = MetadataCollection( self ) def __getattr__( self, name ): return "None" def missing_meta( self ):

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[hg] galaxy 1562: Fix for implicit conversion checking on multip...
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/26ae03082033 changeset: 1562:26ae03082033 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Oct 20 12:44:33 2008 -0400 description: Fix for implicit conversion checking on multiple paged tools. Conversion is never allowed on multi-paged tools. 1 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py diffs (34 lines): diff -r d3a267ac124b -r 26ae03082033 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Oct 20 09:25:38 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Oct 20 12:44:33 2008 -0400 @@ -1006,7 +1006,8 @@ def __init__( self, tool, elem ): ToolParameter.__init__( self, tool, elem ) # Add metadata validator - self.validators.append( validation.MetadataValidator() ) + if not str_bool( elem.get( 'no_validation', False ) ): + self.validators.append( validation.MetadataValidator() ) # Build tuple of classes for supported data formats formats = [] self.extensions = elem.get( 'format', 'data' ).split( "," ) @@ -1107,7 +1108,7 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = True ) #need to assume converter_safe = True, since we don't know about other parameter values here + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( None, trans ) ) if target_ext is not None: return True return False @@ -1180,8 +1181,10 @@ return [] def converter_safe( self, other_values, trans ): - if not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: + if self.tool.has_multiple_pages or not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: return False + if other_values is None: + return True # we don't know other values, so we can't check, assume ok converter_safe = [True] def visitor( prefix, input, value, parent = None ): if isinstance( input, SelectToolParameter ) and self.name in input.get_dependencies():

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[hg] galaxy 1558: Fixes for data_source tools, data.name, data.i...
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f5b051c51295 changeset: 1558:f5b051c51295 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Oct 17 10:46:29 2008 -0400 description: Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type. 6 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/tools/__init__.py tools/data_source/flymine.xml tools/data_source/ucsc_tablebrowser.xml tools/data_source/ucsc_tablebrowser_archaea.xml tools/data_source/ucsc_tablebrowser_test.xml diffs (119 lines): diff -r a5831435c654 -r f5b051c51295 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Thu Oct 16 14:12:37 2008 -0400 +++ b/datatypes_conf.xml.sample Fri Oct 17 10:46:29 2008 -0400 @@ -150,7 +150,6 @@ <sniffer order="05" type="galaxy.datatypes.sequence:Maf"/> <sniffer order="10" type="galaxy.datatypes.sequence:Lav"/> <sniffer order="15" type="galaxy.datatypes.sequence:Fasta"/> - <sniffer order="20" type="galaxy.datatypes.sequence:Fastq"/> <sniffer order="25" type="galaxy.datatypes.sequence:FastqSolexa"/> <sniffer order="30" type="galaxy.datatypes.interval:Wiggle"/> <sniffer order="35" type="galaxy.datatypes.images:Html"/> diff -r a5831435c654 -r f5b051c51295 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Oct 16 14:12:37 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Oct 17 10:46:29 2008 -0400 @@ -23,6 +23,7 @@ from galaxy.tools.actions import DefaultToolAction from galaxy.model import directory_hash_id from galaxy.util.none_like import NoneDataset +from galaxy.datatypes import sniff log = logging.getLogger( __name__ ) @@ -1143,22 +1144,21 @@ description = param_dict.get( 'position', '' ) if not description: description = 'unknown position' - data_type = param_dict.get( 'data_type ') + data_type = param_dict.get( 'data_type' ) items = out_data.items() for name, data in items: if organism and table and description: data.name = '%s on %s: %s (%s)' % ( data.name, organism, table, description ) data.info = info data.dbkey = dbkey - ext = data_type - try: - ext = data_type_to_ext[ data_type ] + try: + data_type = data_type_to_ext[ data_type ] except: pass - if ext not in app.datatypes_registry.datatypes_by_extension: - ext = 'interval' - data = app.datatypes_registry.change_datatype( data, ext ) - # store external data source's request parameters temporarily in output file + if data_type not in app.datatypes_registry.datatypes_by_extension: + data_type = 'interval' + data = app.datatypes_registry.change_datatype( data, data_type ) + # Store external data source's request parameters temporarily in output file out = open( data.file_name, 'w' ) for key, value in param_dict.items(): print >> out, '%s\t%s' % ( key, value ) @@ -1171,9 +1171,15 @@ # tag set in the tool config. if self.tool_type == 'data_source': name, data = out_data.items()[0] - if data.state == data.states.OK and not data.info: - data.info = data.name - if not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ): + if data.state == data.states.OK: + data.name = param_dict.get( 'name', data.name ) + data.info = param_dict.get( 'info', data.name ) + data.dbkey = param_dict.get( 'dbkey', data.dbkey ) + data.extension = param_dict.get( 'data_type', data.extension ) + if data.extension == 'txt': + data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order ) + data = app.datatypes_registry.change_datatype( data, data_type ) + elif not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ): data.set_meta() if data.missing_meta(): data = app.datatypes_registry.change_datatype( data, 'tabular' ) diff -r a5831435c654 -r f5b051c51295 tools/data_source/flymine.xml --- a/tools/data_source/flymine.xml Thu Oct 16 14:12:37 2008 -0400 +++ b/tools/data_source/flymine.xml Fri Oct 17 10:46:29 2008 -0400 @@ -14,7 +14,7 @@ <request_param galaxy_name="description" remote_name="description" missing="" /> <request_param galaxy_name="name" remote_name="name" missing="FlyMine query" /> <request_param galaxy_name="info" remote_name="info" missing="" /> - <request_param galaxy_name="data_type" remote_name="data_type" missing="interval" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> </request_param_translation> <uihints minwidth="800"/> <outputs> diff -r a5831435c654 -r f5b051c51295 tools/data_source/ucsc_tablebrowser.xml --- a/tools/data_source/ucsc_tablebrowser.xml Thu Oct 16 14:12:37 2008 -0400 +++ b/tools/data_source/ucsc_tablebrowser.xml Fri Oct 17 10:46:29 2008 -0400 @@ -16,7 +16,7 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="unknown table" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> </request_param_translation> <uihints minwidth="800"/> <outputs> diff -r a5831435c654 -r f5b051c51295 tools/data_source/ucsc_tablebrowser_archaea.xml --- a/tools/data_source/ucsc_tablebrowser_archaea.xml Thu Oct 16 14:12:37 2008 -0400 +++ b/tools/data_source/ucsc_tablebrowser_archaea.xml Fri Oct 17 10:46:29 2008 -0400 @@ -16,7 +16,7 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> </request_param_translation> <uihints minwidth="800"/> <outputs> diff -r a5831435c654 -r f5b051c51295 tools/data_source/ucsc_tablebrowser_test.xml --- a/tools/data_source/ucsc_tablebrowser_test.xml Thu Oct 16 14:12:37 2008 -0400 +++ b/tools/data_source/ucsc_tablebrowser_test.xml Fri Oct 17 10:46:29 2008 -0400 @@ -16,7 +16,7 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> </request_param_translation> <uihints minwidth="800"/> <outputs>

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[hg] galaxy 1559: Added Validator to a bunch of tools..
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f802eb92a49a changeset: 1559:f802eb92a49a user: guru date: Fri Oct 17 13:02:26 2008 -0400 description: Added Validator to a bunch of tools.. 3 file(s) affected in this change: tools/extract/liftOver_wrapper.xml tools/extract/phastOdds/phastOdds_tool.xml tools/stats/aggregate_binned_scores_in_intervals.xml diffs (58 lines): diff -r f5b051c51295 -r f802eb92a49a tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml Fri Oct 17 10:46:29 2008 -0400 +++ b/tools/extract/liftOver_wrapper.xml Fri Oct 17 13:02:26 2008 -0400 @@ -3,7 +3,8 @@ <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey</command> <inputs> <param format="interval" name="input" type="data" label="Convert coordinates of"> - <validator type="unspecified_build" /> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." /> </param> <param name="to_dbkey" type="select" label="To"> <options from_file="liftOver.loc"> @@ -11,7 +12,7 @@ <column name="value" index="2"/> <column name="dbkey" index="0"/> <filter type="data_meta" ref="input" key="dbkey" column="0" /> - </options> + </options> </param> </inputs> <outputs> @@ -39,11 +40,7 @@ .. class:: warningmark -The **To** list will be empty if we don't carry any liftover mappings corresponding to the genome build of the input dataset. - -.. class:: warningmark - -This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case, it will return empty output datasets. +This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case with any line of the input dataset, the tool will return empty output datasets. ----- diff -r f5b051c51295 -r f802eb92a49a tools/extract/phastOdds/phastOdds_tool.xml --- a/tools/extract/phastOdds/phastOdds_tool.xml Fri Oct 17 10:46:29 2008 -0400 +++ b/tools/extract/phastOdds/phastOdds_tool.xml Fri Oct 17 13:02:26 2008 -0400 @@ -4,6 +4,7 @@ <inputs> <param format="interval" name="input" type="data" label="Interval file"> <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/> + <validator type="dataset_metadata_in_file" filename="phastOdds.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." /> </param> <param name="score_file" type="select" label="Available datasets"> <options from_file="phastOdds.loc"> diff -r f5b051c51295 -r f802eb92a49a tools/stats/aggregate_binned_scores_in_intervals.xml --- a/tools/stats/aggregate_binned_scores_in_intervals.xml Fri Oct 17 10:46:29 2008 -0400 +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml Fri Oct 17 13:02:26 2008 -0400 @@ -8,6 +8,8 @@ <inputs> <param format="interval" name="input1" type="data" label="Interval file"> <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16, hg17 or hg18. Click the pencil icon in your history item to set the genome build."/> + <validator type="dataset_metadata_in_file" filename="binned_scores.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build." /> + </param> <conditional name="score_source_type"> <param name="score_source" type="select" label="Score Source">

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[hg] galaxy 1563: Fix for unit test for DataTool Parameter
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/98867708d5ae changeset: 1563:98867708d5ae user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Oct 20 14:16:38 2008 -0400 description: Fix for unit test for DataTool Parameter 1 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py diffs (12 lines): diff -r 26ae03082033 -r 98867708d5ae lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Oct 20 12:44:33 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Oct 20 14:16:38 2008 -0400 @@ -1181,7 +1181,7 @@ return [] def converter_safe( self, other_values, trans ): - if self.tool.has_multiple_pages or not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: + if not hasattr( trans, 'has_multiple_pages' ) or self.tool.has_multiple_pages or not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: return False if other_values is None: return True # we don't know other values, so we can't check, assume ok

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[hg] galaxy 1564: Add a Heapy-based memdump module. Send the Ga...
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/eef0fd813076 changeset: 1564:eef0fd813076 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Oct 20 15:09:47 2008 -0400 description: Add a Heapy-based memdump module. Send the Galaxy process SIGUSR1 and output of a few (hopefully) useful views of the heap is written to memdump.log. 4 file(s) affected in this change: lib/galaxy/app.py lib/galaxy/config.py lib/galaxy/tools/parameters/basic.py lib/galaxy/util/memdump.py diffs (84 lines): diff -r 98867708d5ae -r eef0fd813076 lib/galaxy/app.py --- a/lib/galaxy/app.py Mon Oct 20 14:16:38 2008 -0400 +++ b/lib/galaxy/app.py Mon Oct 20 15:09:47 2008 -0400 @@ -41,6 +41,11 @@ if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat() self.heartbeat.start() + # Enable the memdump signal catcher if configured and available + if self.config.use_memdump: + from galaxy.util import memdump + if memdump.Memdump: + self.memdump = memdump.Memdump() def shutdown( self ): self.job_stop_queue.shutdown() self.job_queue.shutdown() diff -r 98867708d5ae -r eef0fd813076 lib/galaxy/config.py --- a/lib/galaxy/config.py Mon Oct 20 14:16:38 2008 -0400 +++ b/lib/galaxy/config.py Mon Oct 20 15:09:47 2008 -0400 @@ -56,6 +56,7 @@ self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "" ) self.pbs_stage_path = kwargs.get('pbs_stage_path', "" ) self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', "False" ) ) + self.use_memdump = kwargs.get( 'use_memdump', False ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,flybase,elegans" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) diff -r 98867708d5ae -r eef0fd813076 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Oct 20 14:16:38 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Oct 20 15:09:47 2008 -0400 @@ -29,6 +29,7 @@ self.type = param.get("type") self.label = util.xml_text(param, "label") self.help = util.xml_text(param, "help") + self.unsanitize = param.get( "unsanitize", None ) self.html = "no html set" self.repeat = param.get("repeat", None) self.condition = param.get( "condition", None ) diff -r 98867708d5ae -r eef0fd813076 lib/galaxy/util/memdump.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/util/memdump.py Mon Oct 20 15:09:47 2008 -0400 @@ -0,0 +1,43 @@ + +# Attempt to load guppy module, and only define Memdump class +# if available + +try: + + import pkg_resources + pkg_resources.require( "guppy" ) + +except: + + import sys + print >> sys.stderr, "No guppy module, Memdump not available" + Memdump = None + +else: + + import os, sys, signal, time, guppy + + class Memdump( object ): + def __init__( self, signum=signal.SIGUSR1, fname="memdump.log" ): + self.fname = fname + signal.signal( signum, self.dump ) + self.heapy = guppy.hpy() + def dump( self, signum, stack ): + file = open( self.fname, "a" ) + print >> file, "Memdump for pid %d at %s" % ( os.getpid(), time.asctime() ) + print >> file + try: + h = self.heapy.heap() + print >> file, "heap():" + print >> file, h + print >> file, "\nbyrcs:" + print >> file, h.byrcs + print >> file, "\nbyrcs[0].byid:" + print >> file, h.byrcs[0].byid + print >> file, "\nget_rp():" + print >> file, h.get_rp() + self.heapy.setref() + except AssertionError: + pass + print >> file, "\nEnd dump\n" + file.close()

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