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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 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 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 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 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 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 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 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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[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 1557: Refactor internals of metadata.
by Nate Coraor 20 Oct '08

20 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/a5831435c654 changeset: 1557:a5831435c654 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Oct 16 14:12:37 2008 -0400 description: Refactor internals of metadata. Significantly reduce the number of objects created during interation (i.e. MetadataParameters are created only once per spec). Some oddness remains until it can be determined to be necessary or not, i.e.: iter( metadata_collection ) != iter( metadata_collection.items() ) 10 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/datatypes/metadata.py lib/galaxy/datatypes/sequence.py lib/galaxy/datatypes/tabular.py lib/galaxy/model/__init__.py lib/galaxy/tools/__init__.py lib/galaxy/tools/parameters/basic.py lib/galaxy/tools/parameters/validation.py lib/galaxy/web/controllers/root.py templates/dataset/edit_attributes.mako diffs (682 lines): diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/datatypes/data.py Thu Oct 16 14:12:37 2008 -0400 @@ -1,9 +1,8 @@ import logging, os, sys, time, sets, tempfile from galaxy import util from cgi import escape -from galaxy.datatypes.metadata import * -from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes import metadata +import metadata +from metadata import MetadataElement #import directly to maintain ease of use in Datatype class definitions log = logging.getLogger(__name__) @@ -17,11 +16,11 @@ Metaclass for Data class. Sets up metadata spec. """ def __init__( cls, name, bases, dict_ ): - cls.metadata_spec = MetadataSpecCollection() - for base in bases: - if hasattr(base, "metadata_spec"): - cls.metadata_spec.update(base.metadata_spec) - Statement.process( cls ) + cls.metadata_spec = metadata.MetadataSpecCollection() + for base in bases: #loop through bases (class/types) of cls + if hasattr( base, "metadata_spec" ): #base of class Data (object) has no metadata + cls.metadata_spec.update( base.metadata_spec ) #add contents of metadata spec of base class to cls + metadata.Statement.process( cls ) class Data( object ): """ diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Thu Oct 16 14:12:37 2008 -0400 @@ -1,296 +1,299 @@ import sys, logging -from galaxy.util.bunch import Bunch +from galaxy.util import string_as_bool from galaxy.util.odict import odict from galaxy.web import form_builder -from types import * log = logging.getLogger( __name__ ) -# Taken in part from Elixir and how they do it: http://elixir.ematia.de - -STATEMENTS = "__galaxy_statements__" +STATEMENTS = "__galaxy_statements__" #this is the name of the property in a Datatype class where new metadata spec element Statements are stored class Statement( object ): - ''' + """ This class inserts its target into a list in the surrounding class. the data.Data class has a metaclass which executes these statements. This is how we shove the metadata element spec into the class. - ''' + """ def __init__( self, target ): self.target = target def __call__( self, *args, **kwargs ): - class_locals = sys._getframe(1).f_locals - statements = class_locals.setdefault(STATEMENTS, []) - statements.append((self, args, kwargs)) + class_locals = sys._getframe( 1 ).f_locals #get the locals dictionary of the frame object one down in the call stack (i.e. the Datatype class calling MetadataElement) + statements = class_locals.setdefault( STATEMENTS, [] ) #get and set '__galaxy_statments__' to an empty list if not in locals dict + statements.append( ( self, args, kwargs ) ) #add Statement containing info to populate a MetadataElementSpec @classmethod def process( cls, element ): for statement, args, kwargs in getattr( element, STATEMENTS, [] ): - statement.target( element, *args, **kwargs ) + statement.target( element, *args, **kwargs ) #statement.target is MetadataElementSpec, element is a Datatype class + + +class MetadataCollection: + """ + MetadataCollection is not a collection at all, but rather a proxy + to the real metadata which is stored as a Dictionary. This class + handles processing the metadata elements when they are set and + retrieved, returning default values in cases when metadata is not set. + """ + def __init__(self, parent ): + self.parent = parent + #initialize dict if needed + if self.parent._metadata is None: + self.parent._metadata = {} + @property + def spec( self ): + return self.parent.datatype.metadata_spec + def __iter__( self ): + return self.parent._metadata.__iter__() + def get( self, key, default=None ): + try: + return self.__getattr__( key ) or default + except: + return default + def items(self): + return iter( [ ( k, self.get( k ) ) for k in self.spec.iterkeys() ] ) + def __str__(self): + return dict( self.items() ).__str__() + def __nonzero__( self ): + return bool( self.parent._metadata ) + def __getattr__( self, name ): + if name in self.spec: + if name in self.parent._metadata: + return self.spec[name].wrap( self.parent._metadata[name] ) + return self.spec[name].wrap( self.spec[name].default ) + if name in self.parent._metadata: + return self.parent._metadata[name] + def __setattr__( self, name, value ): + if name == "parent": + self.__dict__[name] = value + else: + if name in self.spec: + self.parent._metadata[name] = self.spec[name].unwrap( value ) + else: + self.parent._metadata[name] = value + def element_is_set( self, name ): + return bool( self.parent._metadata.get( name, False ) ) + def get_html_by_name( self, name, **kwd ): + if name in self.spec: + return self.spec[name].param.get_html( value=getattr( self, name ), context=self, **kwd ) + class MetadataSpecCollection( odict ): - ''' + """ A simple extension of dict which allows cleaner access to items and allows the values to be iterated over directly as if it were a list. append() is also implemented for simplicity and does not "append". - ''' - def __init__(self, dict = None): - odict.__init__(self, dict = None) + """ + def __init__( self, dict = None ): + odict.__init__( self, dict = None ) def append( self, item ): self[item.name] = item def iter( self ): return self.itervalues() def __getattr__( self, name ): - return self.get(name) + return self.get( name ) class MetadataParameter( object ): - def __init__( self, spec, value, context ): - ''' + def __init__( self, spec ): + self.spec = spec + + def get_html_field( self, value=None, context={}, other_values={}, **kwd ): + return form_builder.TextField( self.spec.name, value=value ) + + def get_html( self, value, context={}, other_values={}, **kwd ): + """ The "context" is simply the metadata collection/bunch holding this piece of metadata. This is passed in to allow for metadata to validate against each other (note: this could turn into a huge, recursive mess if not done with care). For example, a column assignment should validate against the number of columns in the dataset. - ''' - self.spec = spec - """Since strings are stored as unicode, we need to decode them for display""" - if isinstance( value, ListType ): - for i, elem in enumerate( value ): - if type ( elem ) == unicode: - value[i] = elem.decode( 'ascii' ) - elif isinstance ( value, basestring ): - if type( value ) == unicode: - value = value.decode( 'ascii' ) - self.value = value - self.context = context - self.display = True - - def __str__(self): - if self.value is None: - return str(self.spec.no_value) - return str(self.value) + """ + if self.spec.get("readonly"): + return value + if self.spec.get("optional"): + checked = False + if value: checked = "true" + checkbox = form_builder.CheckboxField( "is_" + self.spec.name, checked=checked ) + return checkbox.get_html() + self.get_html_field( value=value, context=context, other_values=other_values, **kwd ).get_html() + else: + return self.get_html_field( value=value, context=context, other_values=other_values, **kwd ).get_html() + + def to_string( self, value ): + return str( value ) @classmethod - def marshal( cls, value ): - ''' + def marshal ( cls, value ): + """ This method should/can be overridden to convert the incoming value to whatever type it is supposed to be. - ''' + """ return value - @classmethod - def validate( cls, value ): - ''' + def validate( self, value ): + """ Throw an exception if the value is invalid. - ''' + """ pass - def get_html_field( self, value=None, other_values={} ): - return form_builder.TextField( self.spec.name, value=value or self.value ) - def get_html( self ): - if self.spec.get("readonly"): - return self.value - if self.spec.get("optional"): - checked = False - if self.value: checked = "true" - checkbox = form_builder.CheckboxField( "is_" + self.spec.name, checked=checked ) - return checkbox.get_html() + self.get_html_field().get_html() - else: - return self.get_html_field().get_html() - - @classmethod - def unwrap( cls, form_value ): - value = cls.marshal(form_value) - cls.validate(value) + def unwrap( self, form_value ): + """ + Turns a value into its storable form. + """ + value = self.marshal( form_value ) + self.validate( value ) return value + def wrap( self, value ): + """ + Turns a value into its usable form. + """ + return value + + class MetadataElementSpec( object ): - ''' + """ Defines a metadata element and adds it to the metadata_spec (which is a MetadataSpecCollection) of datatype. - ''' + """ def __init__( self, datatype, name=None, desc=None, param=MetadataParameter, default=None, no_value = None, visible=True, **kwargs ): self.name = name self.desc = desc or name - self.param = param self.default = default self.no_value = no_value self.visible = visible # Catch-all, allows for extra attributes to be set self.__dict__.update(kwargs) - datatype.metadata_spec.append( self ) + #set up param last, as it uses values set above + self.param = param( self ) + datatype.metadata_spec.append( self ) #add spec element to the spec def get( self, name ): return self.__dict__.get(name, None) - def hasAttribute( self, attribute ): - return ((self.permission & attribute) == attribute) - def wrap( self, value, context ): - return self.param( self, value, context ) - def unwrap( self, form_value, context ): - return self.param.unwrap( form_value ) - + def wrap( self, value ): + """ + Turns a stored value into its usable form. + """ + return self.param.wrap( value ) + def unwrap( self, value ): + """ + Turns an incoming value into its storable form. + """ + return self.param.unwrap( value ) -# Basic attributes for describing metadata elements -MetadataAttributes = Bunch( - READONLY = 1, - OPTIONAL = 2 - ) - - -class MetadataCollection: - """ - MetadataCollection is not a collection at all, but rather a proxy - to the real metadata which is stored as a Bunch. This class - handles updating the reference to the Bunch when it is changed (so - that SQLAlchemy knows to update it) as well as returning default - values in cases when metadata is not set. - """ - def __init__(self, parent, spec): - self.parent = parent - if spec is None: self.spec = MetadataSpecCollection() - else: self.spec = spec - - #set default metadata values - if self.parent._metadata is None: - self.parent._metadata = {} - - def __iter__(self): - return self.bunch.__iter__() - def get( self, key, default=None ): - try: - return self.bunch.get( key, default ) or self.spec[key].default - except: - return default - def items(self): - return iter( [(k, self.get(k)) for k in self.spec.iterkeys() ] ) - def __str__(self): - return dict( self.items() ).__str__() - def __nonzero__(self): - return self.bunch.__nonzero__() - def __getattr__(self, name): - if name == "bunch": - return self.parent._metadata - if name in self.bunch: - return self.bunch[name] - if name in self.spec: - return self.spec[name].default - def __setattr__(self, name, value): - if name in ["parent","spec"]: - self.__dict__[name] = value - elif name == "bunch": - self.parent._metadata = value - else: - self.bunch[name] = value - def element_is_set( self, name ): - return bool( self.bunch.get( name, False ) ) - -MetadataElement = Statement(MetadataElementSpec) - +MetadataElement = Statement( MetadataElementSpec ) """ MetadataParameter sub-classes. """ class SelectParameter( MetadataParameter ): - def __init__( self, spec, value, context ): - MetadataParameter.__init__( self, spec, value, context ) - self.values = spec.get("values") + def __init__( self, spec ): + MetadataParameter.__init__( self, spec ) + self.values = self.spec.get( "values" ) + self.multiple = string_as_bool( self.spec.get( "multiple" ) ) - def __setattr__(self, name, value): - MetadataParameter.__setattr__(self, name, value) - if name in ['value']: - if value is None: - MetadataParameter.__setattr__(self, name, []) - elif not isinstance(value, list): - MetadataParameter.__setattr__(self, name, [value]) + def to_string( self, value ): + if value in [ None, [] ]: + return str( self.spec.no_value ) + if not isinstance( value, list ): + value = [value] + return ",".join( map( str, value ) ) - def __iter__( self ): - return iter( self.value ) - - def __str__(self): - if self.value in [None, []]: - return str(self.spec.no_value) - return ",".join(map(str,self.value)) - - def get_html_field( self, value=None, other_values={} ): - field = form_builder.SelectField( self.spec.name, multiple=self.spec.get("multiple"), display=self.spec.get("display") ) - for value, label in self.values or [(value, value) for value in self.value]: + def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): + field = form_builder.SelectField( self.spec.name, multiple=self.multiple, display=self.spec.get("display") ) + for val, label in self.values or values or [(val2, val2) for val2 in value]: try: - if value in self.value: - field.add_option( label, value, selected=True ) + if ( self.multiple and val in value ) or ( not self.multiple and val == value ): + field.add_option( label, val, selected=True ) else: - field.add_option( label, value, selected=False ) + field.add_option( label, val, selected=False ) except TypeError: - field.add_option( value, label, selected=False ) + field.add_option( val, label, selected=False ) return field - def get_html( self ): + def get_html( self, value, context={}, other_values={}, values=None, **kwd ): if self.spec.get("readonly"): - if self.value in [None, [] ]: - return str(self.spec.no_value) - return ", ".join(map(str,self.value)) - return MetadataParameter.get_html(self) + if value in [ None, [] ]: + return str( self.spec.no_value ) + return ", ".join( map( str, value ) ) + return MetadataParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) + + def wrap( self, value ): + value = self.marshal( value ) #do we really need this (wasteful)? - yes because we are not sure that all existing selects have been stored previously as lists. Also this will handle the case where defaults/no_values are specified and are single non-list values. + if self.multiple: + return value + elif value: + return value[0] #single select, only return the first value + return None @classmethod def marshal( cls, value ): # Store select as list, even if single item if value is None: return [] - if not isinstance(value, list): return [value] + if not isinstance( value, list ): return [value] return value class RangeParameter( SelectParameter ): - def __init__( self, spec, value, context ): - SelectParameter.__init__( self, spec, value, context ) + def __init__( self, spec ): + SelectParameter.__init__( self, spec ) # The spec must be set with min and max values - _min = spec.get("min") or 1 - _max = spec.get("max") or 1 - step = self.spec.get("step") or 1 - self.values = zip(range( _min, _max, step ), range( _min, _max, step )) + self.min = spec.get( "min" ) or 1 + self.max = spec.get( "max" ) or 1 + self.step = self.spec.get( "step" ) or 1 + def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): + if values is None: + values = zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step )) + return SelectParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) + + def get_html( self, value, context={}, other_values={}, values=None, **kwd ): + if values is None: + values = zip( range( self.min, self.max, self.step ), range( self.min, self.max, self.step )) + return SelectParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) + @classmethod def marshal( cls, value ): - values = [int(x) for x in value] + value = SelectParameter.marshal( value ) + values = [ int(x) for x in value ] return values class ColumnParameter( RangeParameter ): - def __init__( self, spec, value, context ): - RangeParameter.__init__( self, spec, value, context ) - column_range = range( 1, context.metadata.columns+1, 1 ) - self.values = zip( column_range, column_range ) - - @classmethod - def marshal( cls, value ): - return int(value) - + + def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): + if values is None and context: + column_range = range( 1, context.columns+1, 1 ) + values = zip( column_range, column_range ) + return RangeParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) + + def get_html( self, value, context={}, other_values={}, values=None, **kwd ): + if values is None and context: + column_range = range( 1, context.columns+1, 1 ) + values = zip( column_range, column_range ) + return RangeParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) + class ColumnTypesParameter( MetadataParameter ): - def __init__( self, spec, value, context ): - MetadataParameter.__init__( self, spec, value, context ) - def __str__(self): - return ",".join( map( str, self.value ) ) + + def to_string( self, value ): + return ",".join( map( str, value ) ) class PythonObjectParameter( MetadataParameter ): - def __init__( self, spec, value, context ): - MetadataParameter.__init__( self, spec, value, context ) - self.value = value - self.display = False + def __init__( self, spec ): + MetadataParameter.__init__( self, spec ) - def __str__(self): - if not self.value: + def to_string( self, value ): + if not value: return self.spec.to_string( self.spec.no_value ) - return self.spec.to_string( self.value ) + return self.spec.to_string( value ) - def get_html_field( self, value=None, other_values={} ): - return form_builder.TextField( self.spec.name, value=str( self ) ) + def get_html_field( self, value=None, context={}, other_values={}, **kwd ): + return form_builder.TextField( self.spec.name, value=self.to_string( value ) ) - def get_html( self ): + def get_html( self, value=None, context={}, other_values={}, **kwd ): return str( self ) @classmethod def marshal( cls, value ): return value - diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/datatypes/sequence.py Thu Oct 16 14:12:37 2008 -0400 @@ -24,7 +24,7 @@ """Add metadata elements""" MetadataElement( name="species", desc="Species", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None ) - MetadataElement( name="species_chromosomes", desc="Species Chromosomes", value={}, param=metadata.PythonObjectParameter, readonly=True, no_value={}, to_string=str ) + MetadataElement( name="species_chromosomes", desc="Species Chromosomes", value={}, param=metadata.PythonObjectParameter, readonly=True, no_value={}, to_string=str, visible=False ) class Fasta( Sequence ): """Class representing a FASTA sequence""" diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/datatypes/tabular.py Thu Oct 16 14:12:37 2008 -0400 @@ -11,7 +11,6 @@ from cgi import escape from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes.metadata import MetadataAttributes log = logging.getLogger(__name__) diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/model/__init__.py Thu Oct 16 14:12:37 2008 -0400 @@ -161,7 +161,7 @@ def get_metadata( self ): if not hasattr( self, '_metadata_collection' ): - self._metadata_collection = MetadataCollection( self, self.datatype.metadata_spec ) + self._metadata_collection = MetadataCollection( self ) return self._metadata_collection def set_metadata( self, bunch ): # Needs to accept a MetadataCollection, a bunch, or a dict @@ -192,8 +192,6 @@ def change_datatype( self, new_ext ): self.clear_associated_files() - if hasattr( self, '_metadata_collection' ): - del self._metadata_collection datatypes_registry.change_datatype( self, new_ext ) def get_size( self ): """Returns the size of the data on disk""" diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Oct 16 14:12:37 2008 -0400 @@ -1313,7 +1313,8 @@ if name in self.metadata.spec: if rval is None: rval = self.metadata.spec[name].no_value - rval = self.metadata.spec[name].wrap( rval, self.metadata.parent ) + rval = self.metadata.spec[name].param.to_string( rval ) + setattr( self, name, rval ) #lets store this value, so we don't need to recalculate if needed again return rval def __nonzero__( self ): return self.metadata.__nonzero__() diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Thu Oct 16 14:12:37 2008 -0400 @@ -830,7 +830,7 @@ dataset = other_values[filter_key] if dataset: for meta_key, meta_dict in filter_value.iteritems(): - if ",".join( dataset.metadata.get( meta_key ) ) == meta_dict['value']: + if dataset.metadata.spec[meta_key].param.to_string( dataset.metadata.get( meta_key ) ) == meta_dict['value']: options.extend( meta_dict['options'] ) return options return self.options diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/tools/parameters/validation.py --- a/lib/galaxy/tools/parameters/validation.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/tools/parameters/validation.py Thu Oct 16 14:12:37 2008 -0400 @@ -251,7 +251,7 @@ def validate( self, value, history = None ): if not value: return if hasattr( value, "metadata" ): - if str( getattr( value.datatype.metadata_spec, self.metadata_name ).wrap( value.metadata.get( self.metadata_name ), value ) ) in self.valid_values: + if value.metadata.spec[self.metadata_name].param.to_string( value.metadata.get( self.metadata_name ) ) in self.valid_values: return raise ValueError( self.message ) diff -r 97a8f6f5ba00 -r a5831435c654 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Wed Oct 15 15:51:13 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 16 14:12:37 2008 -0400 @@ -219,26 +219,26 @@ data.info = p.info # The following for loop will save all metadata_spec items - for name, spec in data.datatype.metadata_spec.items(): + for name, spec in data.metadata.spec.items(): if spec.get("readonly"): continue optional = p.get("is_"+name, None) if optional and optional == 'true': # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr(data.metadata,name,None) + setattr(data.metadata, name, None) else: - setattr(data.metadata,name,spec.unwrap(p.get(name, None), p)) + setattr( data.metadata, name, spec.unwrap( p.get (name, None) ) ) data.datatype.after_edit( data ) trans.app.model.flush() return trans.show_ok_message( "Attributes updated", refresh_frames=['history'] ) elif p.detect: # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in data.datatype.metadata_spec.items(): + for name, spec in data.metadata.spec.items(): # We need to be careful about the attributes we are resetting - if name != 'name' and name != 'info' and name != 'dbkey': + if name not in [ 'name', 'info', 'dbkey' ]: if spec.get( 'default' ): - setattr( data.metadata,name,spec.unwrap( spec.get( 'default' ), spec )) + setattr( data.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) data.datatype.set_meta( data ) data.datatype.after_edit( data ) trans.app.model.flush() @@ -258,16 +258,12 @@ # case it resorts to the old dbkey. Setting the dbkey # sets it properly in the metadata data.metadata.dbkey = data.dbkey - metadata = list() - # a list of MetadataParemeters - for name, spec in data.datatype.metadata_spec.items(): - if spec.visible: - metadata.append( spec.wrap( data.metadata.get(name), data ) ) # let's not overwrite the imported datatypes module with the variable datatypes? + ### the built-in 'id' is overwritten in lots of places as well ldatatypes = [x for x in trans.app.datatypes_registry.datatypes_by_extension.iterkeys()] ldatatypes.sort() trans.log_event( "Opened edit view on dataset %s" % str(id) ) - return trans.fill_template( "/dataset/edit_attributes.mako", data=data, metadata=metadata, + return trans.fill_template( "/dataset/edit_attributes.mako", data=data, datatypes=ldatatypes, err=None ) @web.expose diff -r 97a8f6f5ba00 -r a5831435c654 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Wed Oct 15 15:51:13 2008 -0400 +++ b/templates/dataset/edit_attributes.mako Thu Oct 16 14:12:37 2008 -0400 @@ -38,14 +38,14 @@ </div> <div style="clear: both"></div> </div> - %for element in metadata: - %if element.display: + %for name, spec in data.metadata.spec.items(): + %if spec.visible: <div class="form-row"> <label> - ${element.spec.desc}: + ${spec.desc}: </label> <div style="float: left; width: 250px; margin-right: 10px;"> - ${element.get_html()} + ${data.metadata.get_html_by_name( name )} </div> <div style="clear: both"></div> </div>

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