details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publi... changeset: 1460:837f8b7698c4 user: James Taylor james@jamestaylor.org date: Thu Jul 31 17:55:41 2008 -0400 description: Fix for preserving values of parameters after a repeat/conditional in Tool.update_state. This should fix the problem reported by Dan with the subject "Re: [galaxy-bugs] Galaxy tool error report from cathy@bx.psu.edu". Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1461: Compensatory bug in conditional parameters that was revealed by previous

details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publi... changeset: 1461:6bbf70be8b03 user: James Taylor james@jamestaylor.org date: Thu Jul 31 20:49:06 2008 -0400 description: Compensatory bug in conditional parameters that was revealed by previous commit. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1462: Fix for JobWrapper.finish, dataset state no longer flushed prior to other attributes ( e.g., metadata) being flushed.

details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publi... changeset: 1462:777d9bdfd7d3 user: greg date: Fri Aug 01 14:25:42 2008 -0400 description: Fix for JobWrapper.finish, dataset state no longer flushed prior to other attributes ( e.g., metadata) being flushed. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1463: Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params.

details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publi... changeset: 1463:66be239241bc user: greg date: Fri Aug 01 14:34:16 2008 -0400 description: Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1464: Fix for the creation of workflows from shared histories.

details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publi... changeset: 1464:c7acaa1bb88f user: dan@scofield.bx.psu.edu date: Fri Aug 01 15:05:54 2008 -0400 description: Fix for the creation of workflows from shared histories.

Added a column 'copied_from_history_dataset_association' to history_dataset_association. This requires a db change. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1465: Remove a couple templates that I missed in the rollback.

details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publi... changeset: 1465:3b35cdf1689a user: Nate Coraor nate@bx.psu.edu date: Fri Aug 01 15:26:02 2008 -0400 description: Remove a couple templates that I missed in the rollback. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1466: Better fix for gops command line parser, now properly handles no strand column.

details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publi... changeset: 1466:91c63a82359a user: greg date: Mon Aug 04 10:20:23 2008 -0400 description: Better fix for gops command line parser, now properly handles no strand column.

diffs (371 lines):

diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml --- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml Mon Aug 04 10:20:23 2008 -0400 @@ -1,5 +1,5 @@ <tool id="CONVERTER_fastqsolexa_to_qual_0" name="Convert Fastqsolexa to Qual"> - <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 $input1.extension</command> + <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 ${input1.extension}</command> <inputs> <param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/> </inputs> diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/interval_to_bed_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Aug 04 10:20:23 2008 -0400 @@ -1,7 +1,7 @@ <tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED"> <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> <!-- Used on the metadata edit page. --> - <command interpreter="python">interval_to_bed_converter.py $output1 $input1 $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol</command> + <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command> <inputs> <page> <param format="interval" name="input1" type="data" label="Choose intervals"/> diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/maf_to_interval_converter.xml --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Mon Aug 04 10:20:23 2008 -0400 @@ -1,6 +1,6 @@ <tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals"> <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> - <command interpreter="python">maf_to_interval_converter.py $output1 $input1 $input1_dbkey</command> + <command interpreter="python">maf_to_interval_converter.py $output1 $input1 ${input1.metadata.dbkey}</command> <inputs> <page> <param format="maf" name="input1" type="data" label="Choose MAF file"/> diff -r b301cae30997 -r 91c63a82359a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Mon Aug 04 10:20:23 2008 -0400 @@ -400,11 +400,6 @@ else: job.state = 'ok' for dataset_assoc in job.output_datasets: - if stderr: - dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR - else: - dataset_assoc.dataset.dataset.state = model.Dataset.states.OK - dataset_assoc.dataset.dataset.flush() for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running dataset.blurb = 'done' dataset.peek = 'no peek' @@ -424,6 +419,11 @@ else: dataset.blurb = "empty" dataset.flush() + if stderr: + dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR + else: + dataset_assoc.dataset.dataset.state = model.Dataset.states.OK + dataset_assoc.dataset.dataset.flush()

# Save stdout and stderr if len( stdout ) > 32768: diff -r b301cae30997 -r 91c63a82359a lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/model/__init__.py Mon Aug 04 10:20:23 2008 -0400 @@ -104,7 +104,7 @@ class HistoryDatasetAssociation( object ): def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, - parent_id=None, validation_errors=None, visible=True, create_dataset = False ): + parent_id=None, copied_from_history_dataset_association = None, validation_errors=None, visible=True, create_dataset = False ): self.name = name or "Unnamed dataset" self.id = id self.hid = hid @@ -125,6 +125,7 @@ self.dataset = dataset self.parent_id = parent_id self.validation_errors = validation_errors + self.copied_from_history_dataset_association = copied_from_history_dataset_association

@property def ext( self ): @@ -252,7 +253,7 @@ return self.datatype.get_converter_types( self, datatypes_registry)

def copy( self, copy_children = False, parent_id = None ): - des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id ) + des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self ) des.flush() if copy_children: for child in self.children: diff -r b301cae30997 -r 91c63a82359a lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/model/mapping.py Mon Aug 04 10:20:23 2008 -0400 @@ -72,6 +72,7 @@ Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), Column( "hid", Integer ), Column( "name", TrimmedString( 255 ) ), Column( "info", TrimmedString( 255 ) ), @@ -250,13 +251,17 @@ history=relation( History, primaryjoin=( History.table.c.id == HistoryDatasetAssociation.table.c.history_id ) ), + copied_to_history_dataset_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), + backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id] ) ), implicitly_converted_datasets=relation( ImplicitlyConvertedDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), children=relation( HistoryDatasetAssociation, primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), - backref=backref( "parent", remote_side=[HistoryDatasetAssociation.table.c.id] ) ) + backref=backref( "parent", primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id] ) ) ) )

assign_mapper( context, Dataset, Dataset.table, diff -r b301cae30997 -r 91c63a82359a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Aug 04 10:20:23 2008 -0400 @@ -731,7 +731,7 @@ for i, rep_state in enumerate( group_state ): rep_index = rep_state['__index__'] max_index = max( max_index, rep_index ) - prefix = "%s_%d|" % ( key, rep_index ) + rep_prefix = "%s_%d|" % ( key, rep_index ) if group_old_errors: rep_old_errors = group_old_errors[i] else: @@ -740,7 +740,7 @@ input.inputs, rep_state, incoming, - prefix=prefix, + prefix=rep_prefix, context=context, update_only=update_only, old_errors=rep_old_errors, @@ -765,9 +765,9 @@ group_state = state[input.name] group_old_errors = old_errors.get( input.name, {} ) old_current_case = group_state['__current_case__'] - prefix = "%s|" % ( key ) + group_prefix = "%s|" % ( key ) # Deal with the 'test' element and see if it's value changed - test_param_key = prefix + input.test_param.name + test_param_key = group_prefix + input.test_param.name test_param_error = None test_incoming = incoming.get( test_param_key, None ) if test_param_key not in incoming \ @@ -797,7 +797,7 @@ input.cases[current_case].inputs, group_state, incoming, - prefix=prefix, + prefix=group_prefix, context=context, update_only=update_only, old_errors=group_old_errors, diff -r b301cae30997 -r 91c63a82359a lib/galaxy/tools/util/galaxyops/__init__.py --- a/lib/galaxy/tools/util/galaxyops/__init__.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/tools/util/galaxyops/__init__.py Mon Aug 04 10:20:23 2008 -0400 @@ -13,13 +13,18 @@ print >> sys.stderr, msg sys.exit( 1 )

-# Default chrom, start, end, stran cols for a bed file +# Default chrom, start, end, strand cols for a bed file BED_DEFAULT_COLS = 0, 1, 2, 5

def parse_cols_arg( cols ): """Parse a columns command line argument into a four-tuple""" if cols: - return map( lambda x: int( x ) - 1, cols.split(",") ) + # Handle case where no strand column included - in this case, cols + # looks something like 1,2,3, + if cols.endswith( ',' ): + cols += '0' + col_list = map( lambda x: int( x ) - 1, cols.split(",") ) + return col_list else: return BED_DEFAULT_COLS

diff -r b301cae30997 -r 91c63a82359a lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Mon Aug 04 10:20:23 2008 -0400 @@ -676,9 +676,16 @@ if dataset.state in ( 'new', 'running', 'queued' ): warnings.add( "Some datasets still queued or running were ignored" ) continue - if not dataset.creating_job_associations: - jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] - for assoc in dataset.creating_job_associations: + + #if this hda was copied from another, we need to find the job that created the origial hda + job_hda = dataset + while job_hda.copied_from_history_dataset_association: + job_hda = job_hda.copied_from_history_dataset_association + + if not job_hda.creating_job_associations: + jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] + + for assoc in job_hda.creating_job_associations: job = assoc.job if job in jobs: jobs[ job ].append( ( assoc.name, dataset ) ) diff -r b301cae30997 -r 91c63a82359a templates/history/permissions.mako --- a/templates/history/permissions.mako Wed Jul 30 17:15:40 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">Change Default History Permissions</%def> - -%if trans.user: - <div class="toolForm"> - <div class="toolFormTitle">Change Default History Permissions</div> - <div class="toolFormBody"> - <form name="set_permissions" method="post"> - <div class="form-row"> - <% user_groups = [ assoc.group for assoc in trans.user.groups ] %> - <% cur_groups = [ assoc.group for assoc in trans.get_history().default_groups ] %> - <div style="float: left; width: 250px; margin-right: 10px;"> - <table> - <tr><th>Group</th><th>In</th><th>Out</th></tr> - %for group in user_groups: - <tr><td>${group.name}</td><td><input type="radio" name="group_${group.id}" value="in" - %if group in cur_groups: - checked - %endif - ></td><td><input type="radio" name="group_${group.id}" value="out" - %if group not in cur_groups: - checked - %endif - ></td></tr> - %endfor - </table> - </div> - - <div style="clear: both"></div> - - <div class="toolParamHelp" style="clear: both;"> - This will change the default permissions assigned to new datasets for your current history. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="set_permissions" value="Save"> - </div> - </form> - </div> - </div> -%endif \ No newline at end of file diff -r b301cae30997 -r 91c63a82359a templates/tool_form.tmpl --- a/templates/tool_form.tmpl Wed Jul 30 17:15:40 2008 -0400 +++ b/templates/tool_form.tmpl Mon Aug 04 10:20:23 2008 -0400 @@ -57,9 +57,9 @@ #set group_state = $tool_state[$input.name] #set group_errors = $errors.get( $input.name, {} ) #set current_case = $group_state['__current_case__'] - #set prefix = $prefix + $input.name + "|" - $row_for_param( $prefix, $input.test_param, $group_state, $group_errors, $context ) - $do_inputs( $input.cases[$current_case].inputs, $group_state, $group_errors, $prefix, $context ) + #set group_prefix = $prefix + $input.name + "|" + $row_for_param( $group_prefix, $input.test_param, $group_state, $group_errors, $context ) + $do_inputs( $input.cases[$current_case].inputs, $group_state, $group_errors, $group_prefix, $context ) #else $row_for_param( $prefix, $input, $tool_state, $errors, $context ) #end if diff -r b301cae30997 -r 91c63a82359a templates/user/permissions.mako --- a/templates/user/permissions.mako Wed Jul 30 17:15:40 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">Change Default History Permissions</%def> - -%if trans.user: - <div class="toolForm"> - <div class="toolFormTitle">Change Default Permissions for new Histories </div> - <div class="toolFormBody"> - <form name="set_permissions" method="post"> - <div class="form-row"> - <% user_groups = [ assoc.group for assoc in trans.user.groups ] %> - <% cur_groups = [ assoc.group for assoc in trans.user.default_groups ] %> - <div style="float: left; width: 250px; margin-right: 10px;"> - <table> - <tr><th>Group</th><th>In</th><th>Out</th></tr> - %for group in user_groups: - <tr><td>${group.name}</td><td><input type="radio" name="group_${group.id}" value="in" - %if group in cur_groups: - checked - %endif - ></td><td><input type="radio" name="group_${group.id}" value="out" - %if group not in cur_groups: - checked - %endif - ></td></tr> - %endfor - </table> - </div> - - <div style="clear: both"></div> - - <div class="toolParamHelp" style="clear: both;"> - This will change the default permissions assigned to new datasets for new histories. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="set_permissions" value="Save"> - </div> - </form> - </div> - </div> -%endif \ No newline at end of file diff -r b301cae30997 -r 91c63a82359a templates/workflow/editor_tool_form.mako --- a/templates/workflow/editor_tool_form.mako Wed Jul 30 17:15:40 2008 -0400 +++ b/templates/workflow/editor_tool_form.mako Mon Aug 04 10:20:23 2008 -0400 @@ -23,10 +23,10 @@ %elif input.type == "conditional": <% group_values = values[input.name] %> <% current_case = group_values['__current_case__'] %> - <% prefix = prefix + input.name + "|" %> + <% group_prefix = prefix + input.name + "|" %> <% group_errors = errors.get( input.name, {} ) %> - ${row_for_param( input.test_param, group_values[ input.test_param.name ], group_errors, prefix )} - ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, prefix )} + ${row_for_param( input.test_param, group_values[ input.test_param.name ], group_errors, group_prefix )} + ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, group_prefix )} %else: ${row_for_param( input, values[ input.name ], errors, prefix )} %endif diff -r b301cae30997 -r 91c63a82359a test-data/12.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12.bed Mon Aug 04 10:20:23 2008 -0400 @@ -0,0 +1,10 @@ +chr1 147962192 147962580 +chr1 115468538 115468624 +chr1 115483024 115483277 +chr1 115484165 115484501 +chr1 115485764 115485980 +chr1 115486322 115486481 +chr1 115491298 115491487 +chr1 115468538 115468624 +chr1 115483024 115483277 +chr1 115484165 115484501 diff -r b301cae30997 -r 91c63a82359a test-data/gops_intersect_no_strand_out.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_intersect_no_strand_out.bed Mon Aug 04 10:20:23 2008 -0400 @@ -0,0 +1,1 @@ +chr1 147962192 147962580 diff -r b301cae30997 -r 91c63a82359a tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml Wed Jul 30 17:15:40 2008 -0400 +++ b/tools/new_operations/intersect.xml Mon Aug 04 10:20:23 2008 -0400 @@ -50,6 +50,13 @@ <param name="returntype" value="" /> <output name="output" file="gops_intersect_bigint_out.interval" /> </test> + <test> + <param name="input1" value="12.bed" ftype="bed" /> + <param name="input2" value="1.bed" ftype="bed" /> + <param name="min" value="1" /> + <param name="returntype" value="" /> + <output name="output" file="gops_intersect_no_strand_out.bed" /> + </test> </tests> <help>