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[hg] galaxy 2383: Accidently commited a testing change, removed
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/656f1df80b46 changeset: 2383:656f1df80b46 user: James Taylor <james(a)jamestaylor.org> date: Wed Apr 29 14:47:18 2009 -0400 description: Accidently commited a testing change, removed 1 file(s) affected in this change: tools/maf/interval2maf.xml diffs (11 lines): diff -r 89541ac4983f -r 656f1df80b46 tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Wed Apr 29 13:56:59 2009 -0400 +++ b/tools/maf/interval2maf.xml Wed Apr 29 14:47:18 2009 -0400 @@ -6,7 +6,6 @@ #end if </command> <inputs> - <param type="text" name="TEST" label="Test" /> <param format="interval" name="input1" type="data" label="Choose intervals"> <validator type="unspecified_build" /> </param>

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[hg] galaxy 2380: Replacing \"qual\" datatype with 3 new datatyp...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/22b08d47f7ba changeset: 2380:22b08d47f7ba user: guru date: Wed Apr 29 11:53:22 2009 -0400 description: Replacing \"qual\" datatype with 3 new datatypes: qualsolid, qual454 and qualsolexa. 10 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml lib/galaxy/datatypes/qualityscore.py lib/galaxy/datatypes/registry.py lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py tools/metag_tools/fastqsolexa_to_fasta_qual.xml tools/metag_tools/rmapq_wrapper.xml tools/metag_tools/short_reads_figure_high_quality_length.xml tools/metag_tools/short_reads_figure_score.xml tools/metag_tools/short_reads_trim_seq.xml diffs (409 lines): diff -r 5a4aac327bad -r 22b08d47f7ba datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Wed Apr 29 10:27:57 2009 -0400 +++ b/datatypes_conf.xml.sample Wed Apr 29 11:53:22 2009 -0400 @@ -19,7 +19,7 @@ </datatype> <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"> <converter file="fastqsolexa_to_fasta_converter.xml" target_datatype="fasta"/> - <converter file="fastqsolexa_to_qual_converter.xml" target_datatype="qual"/> + <converter file="fastqsolexa_to_qual_converter.xml" target_datatype="qualsolexa"/> </datatype> <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/> <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true"> @@ -42,7 +42,9 @@ </datatype> <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/> <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/> - <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" display_in_upload="true"/> + <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> + <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> + <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> <datatype extension="scf" type="galaxy.datatypes.images:Scf" mimetype="application/octet-stream" display_in_upload="true"/> <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/> @@ -186,7 +188,9 @@ <sniffer type="galaxy.datatypes.sequence:Maf"/> <sniffer type="galaxy.datatypes.sequence:Lav"/> <sniffer type="galaxy.datatypes.sequence:csFasta"/> - <sniffer type="galaxy.datatypes.qualityscore:QualityScore"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSolexa"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> + <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> <sniffer type="galaxy.datatypes.sequence:Fasta"/> <sniffer type="galaxy.datatypes.sequence:FastqSolexa"/> <sniffer type="galaxy.datatypes.interval:Wiggle"/> diff -r 5a4aac327bad -r 22b08d47f7ba lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml --- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml Wed Apr 29 10:27:57 2009 -0400 +++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml Wed Apr 29 11:53:22 2009 -0400 @@ -4,7 +4,7 @@ <param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/> </inputs> <outputs> - <data format="qual" name="output1" /> + <data format="qualsolexa" name="output1" /> </outputs> <help> </help> diff -r 5a4aac327bad -r 22b08d47f7ba lib/galaxy/datatypes/qualityscore.py --- a/lib/galaxy/datatypes/qualityscore.py Wed Apr 29 10:27:57 2009 -0400 +++ b/lib/galaxy/datatypes/qualityscore.py Wed Apr 29 11:53:22 2009 -0400 @@ -9,11 +9,11 @@ log = logging.getLogger(__name__) -class QualityScore ( data.Text ): +class QualityScoreSOLiD ( data.Text ): """ until we know more about quality score formats """ - file_ext = "qual" + file_ext = "qualsolid" def set_peek( self, dataset, line_count=None ): if not dataset.dataset.purged: @@ -21,7 +21,7 @@ if line_count is None: dataset.blurb = data.nice_size( dataset.get_size() ) else: - dataset.blurb = "%s lines, Quality score file" % util.commaify( str( line_count ) ) + dataset.blurb = "%s lines, SOLiD Quality score file" % util.commaify( str( line_count ) ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' @@ -30,15 +30,80 @@ try: return dataset.peek except: - return "Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) ) + return "SOLiD Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) ) def sniff( self, filename ): """ >>> fname = get_test_fname( 'sequence.fasta' ) - >>> QualityScore().sniff( fname ) + >>> QualityScoreSOLiD().sniff( fname ) False - >>> fname = get_test_fname( 'sequence.qual' ) - >>> QualityScore().sniff( fname ) + >>> fname = get_test_fname( 'sequence.qualsolid' ) + >>> QualityScoreSOLiD().sniff( fname ) + True + """ + try: + fh = open( filename ) + readlen = None + goodblock = 0 + while True: + line = fh.readline() + if not line: + if goodblock > 0: + return True + else: + break #EOF + line = line.strip() + if line and not line.startswith( '#' ): #first non-empty non-comment line + if line.startswith( '>' ): + line = fh.readline().strip() + if line == '' or line.startswith( '>' ): + break + try: + [ int( x ) for x in line.split() ] + if not(readlen): + readlen = len(line.split()) + assert len(line.split()) == readlen #SOLiD reads should be of the same length + except: + break + goodblock += 1 + if goodblock > 10: + return True + else: + break #we found a non-empty line, but it's not a header + except: + pass + return False + +class QualityScore454 ( data.Text ): + """ + until we know more about quality score formats + """ + file_ext = "qual454" + + def set_peek( self, dataset, line_count=None ): + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name ) + if line_count is None: + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.blurb = "%s lines, 454 Quality score file" % util.commaify( str( line_count ) ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def display_peek(self, dataset): + try: + return dataset.peek + except: + return "454 Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) ) + + def sniff( self, filename ): + """ + >>> fname = get_test_fname( 'sequence.fasta' ) + >>> QualityScore454().sniff( fname ) + False + >>> fname = get_test_fname( 'sequence.qual454' ) + >>> QualityScore454().sniff( fname ) True """ try: @@ -63,3 +128,59 @@ except: pass return False + +class QualityScoreSolexa ( data.Text ): + """ + until we know more about quality score formats + """ + file_ext = "qualsolexa" + + def set_peek( self, dataset, line_count=None ): + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name ) + if line_count is None: + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.blurb = "%s lines, Solexa Quality score file" % util.commaify( str( line_count ) ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def display_peek(self, dataset): + try: + return dataset.peek + except: + return "Solexa Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) ) + + def sniff( self, filename ): + """ + >>> fname = get_test_fname( 'sequence.fasta' ) + >>> QualityScoreSolexa().sniff( fname ) + False + >>> fname = get_test_fname( 'sequence.qualsolexa' ) + >>> QualityScoreSolexa().sniff( fname ) + True + """ + try: + fh = open( filename ) + readlen = None + while True: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line and not line.startswith( '#' ): + if len(line.split('\t')) > 1: + break + try: + [ int( x ) for x in line.split() ] + if not(readlen): + readlen = len(line.split()) + assert len(line.split()) == readlen #Solexa reads should be of the same length + except: + break + + except: + pass + return False + diff -r 5a4aac327bad -r 22b08d47f7ba lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Wed Apr 29 10:27:57 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Wed Apr 29 11:53:22 2009 -0400 @@ -116,7 +116,9 @@ 'laj' : images.Laj(), 'lav' : sequence.Lav(), 'maf' : sequence.Maf(), - 'qual' : qualityscore.QualityScore(), + 'qualsolid' : qualityscore.QualityScoreSOLiD(), + 'qualsolexa' : qualityscore.QualityScoreSolexa(), + 'qual454' : qualityscore.QualityScore454(), 'scf' : images.Scf(), 'tabular' : tabular.Tabular(), 'taxonomy' : tabular.Taxonomy(), @@ -140,7 +142,9 @@ 'laj' : 'text/plain', 'lav' : 'text/plain', 'maf' : 'text/plain', - 'qual' : 'text/plain', + 'qualsolid' : 'text/plain', + 'qualsolexa' : 'text/plain', + 'qual454' : 'text/plain', 'scf' : 'application/octet-stream', 'tabular' : 'text/plain', 'taxonomy' : 'text/plain', diff -r 5a4aac327bad -r 22b08d47f7ba lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Wed Apr 29 11:53:22 2009 -0400 @@ -0,0 +1,47 @@ +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +import sys, logging + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) + +def upgrade(): + # Load existing tables + metadata.reflect() + # Add 2 indexes to the galaxy_user table + i = Index( 'ix_hda_extension', HistoryDatasetAssociation_table.c.extension ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) ) + + # Set the default data in the galaxy_user table, but only for null values + cmd = "UPDATE history_dataset_association SET extension = 'qual454' WHERE extension = 'qual' and peek like \'>%%\'" + try: + db_session.execute( cmd ) + except Exception, e: + log.debug( "Resetting extension qual to qual454 in history_dataset_association failed: %s" % ( str( e ) ) ) + cmd = "UPDATE history_dataset_association SET extension = 'qualsolexa' WHERE extension = 'qual' and peek not like \'>%%\'" + try: + db_session.execute( cmd ) + except Exception, e: + log.debug( "Resetting extension qual to qualsolexa in history_dataset_association failed: %s" % ( str( e ) ) ) + # Add 1 index to the history_dataset_association table + try: + i.drop() + except Exception, e: + log.debug( "Dropping index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) ) + + +def downgrade(): + pass diff -r 5a4aac327bad -r 22b08d47f7ba tools/metag_tools/fastqsolexa_to_fasta_qual.xml --- a/tools/metag_tools/fastqsolexa_to_fasta_qual.xml Wed Apr 29 10:27:57 2009 -0400 +++ b/tools/metag_tools/fastqsolexa_to_fasta_qual.xml Wed Apr 29 11:53:22 2009 -0400 @@ -6,7 +6,7 @@ </inputs> <outputs> <data name="output1" format="fasta"/> - <data name="output2" format="qual"/> + <data name="output2" format="qualsolexa"/> </outputs> <tests>  diff -r 5a4aac327bad -r 22b08d47f7ba tools/metag_tools/rmapq_wrapper.xml --- a/tools/metag_tools/rmapq_wrapper.xml Wed Apr 29 10:27:57 2009 -0400 +++ b/tools/metag_tools/rmapq_wrapper.xml Wed Apr 29 11:53:22 2009 -0400 @@ -13,7 +13,7 @@ </options> </param> <param name="input_seq" type="data" format="fasta" label="Sequence file"/> - <param name="input_score" type="data" format="qual" label="Quality score file"/> + <param name="input_score" type="data" format="qualsolexa" label="Quality score file"/> <param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/> <param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/> <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/> @@ -46,7 +46,7 @@ <test> <param name="database" value="/depot/data2/galaxy/faseq/test" /> <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/> - <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qual" /> + <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" /> <param name="high_score" value="40" /> <param name="high_len" value="36" /> <param name="read_len" value="36" /> diff -r 5a4aac327bad -r 22b08d47f7ba tools/metag_tools/short_reads_figure_high_quality_length.xml --- a/tools/metag_tools/short_reads_figure_high_quality_length.xml Wed Apr 29 10:27:57 2009 -0400 +++ b/tools/metag_tools/short_reads_figure_high_quality_length.xml Wed Apr 29 11:53:22 2009 -0400 @@ -5,7 +5,7 @@ <inputs> <page> - <param name="input1" type="data" format="qual,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/> + <param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/> <param name="input2" type="integer" size="5" value="20" label="Quality score threshold" /> </page> </inputs> @@ -17,12 +17,12 @@ </requirements> <tests> <test> - <param name="input1" value="solexa.qual" ftype="qual" /> + <param name="input1" value="solexa.qual" ftype="qualsolexa" /> <param name="input2" value="5" /> <output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/> </test> <test> - <param name="input1" value="454.qual" ftype="qual" /> + <param name="input1" value="454.qual" ftype="qual454" /> <param name="input2" value="5" /> <output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/> </test> diff -r 5a4aac327bad -r 22b08d47f7ba tools/metag_tools/short_reads_figure_score.xml --- a/tools/metag_tools/short_reads_figure_score.xml Wed Apr 29 10:27:57 2009 -0400 +++ b/tools/metag_tools/short_reads_figure_score.xml Wed Apr 29 11:53:22 2009 -0400 @@ -5,7 +5,7 @@ <inputs> <page> - <param name="input1" type="data" format="qual, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/> + <param name="input1" type="data" format="qualsolexa, qual454, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/> </page> </inputs> @@ -17,11 +17,11 @@ </requirements> <tests> <test> - <param name="input1" value="solexa.qual" ftype="qual" /> + <param name="input1" value="solexa.qual" ftype="qualsolexa" /> <output name="output1" file="solexaScore.png" ftype="png" /> </test> <test> - <param name="input1" value="454.qual" ftype="qual" /> + <param name="input1" value="454.qual" ftype="qual454" /> <output name="output1" file="454Score.png" ftype="png" /> </test> </tests> diff -r 5a4aac327bad -r 22b08d47f7ba tools/metag_tools/short_reads_trim_seq.xml --- a/tools/metag_tools/short_reads_trim_seq.xml Wed Apr 29 10:27:57 2009 -0400 +++ b/tools/metag_tools/short_reads_trim_seq.xml Wed Apr 29 11:53:22 2009 -0400 @@ -7,7 +7,7 @@ <inputs> <page> <param name="input1" type="data" format="fasta,txtseq.zip" label="Reads" /> - <param name="input2" type="data" format="qual,txtseq.zip" label="Quality scores" /> + <param name="input2" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality scores" /> <param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/> <param name="length" type="integer" size="5" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" /> <conditional name="sequencing_method_choice"> @@ -36,7 +36,7 @@ <test> <param name="sequencer" value="454" /> <param name="input1" value="454.fasta" ftype="fasta" /> - <param name="input2" value="454.qual" ftype="qual" /> + <param name="input2" value="454.qual" ftype="qual454" /> <param name="input3" value="no" /> <param name="trim" value="20" /> <param name="length" value="0" /> @@ -45,7 +45,7 @@ <test> <param name="sequencer" value="Solexa" /> <param name="input1" value="solexa.fasta" ftype="fasta" /> - <param name="input2" value="solexa.qual" ftype="qual" /> + <param name="input2" value="solexa.qual" ftype="qualsolexa" /> <param name="input3" value="0" /> <param name="trim" value="20" /> <param name="length" value="0" />

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[hg] galaxy 2381: Handle the addition of new tool parameters bet...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dae0313bf5bb changeset: 2381:dae0313bf5bb user: James Taylor <james(a)jamestaylor.org> date: Wed Apr 29 13:46:02 2009 -0400 description: Handle the addition of new tool parameters better in the workflow editor. Default values will be filled in and a message displayed to the user 7 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/tools/parameters/grouping.py lib/galaxy/web/controllers/workflow.py lib/galaxy/workflow/modules.py static/scripts/galaxy.workflow_editor.canvas.js templates/workflow/editor.mako tools/maf/interval2maf.xml diffs (252 lines): diff -r 22b08d47f7ba -r dae0313bf5bb lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Apr 29 11:53:22 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Apr 29 13:46:02 2009 -0400 @@ -676,25 +676,7 @@ """ context = ExpressionContext( state, context ) for input in inputs.itervalues(): - if isinstance( input, Repeat ): - # Repeat elements are always initialized to have 0 units. - state[ input.name ] = [] - elif isinstance( input, Conditional ): - # State for a conditional is a plain dictionary. - s = state[ input.name ] = {} - # Get the default value for the 'test element' and use it - # to determine the current case - test_value = input.test_param.get_initial_value( trans, context ) - current_case = input.get_current_case( test_value, trans ) - # Store the current case in a special value - s['__current_case__'] = current_case - # Store the value of the test element - s[ input.test_param.name ] = test_value - # Recursively fill in state for selected case - self.fill_in_new_state( trans, input.cases[current_case].inputs, s, context ) - else: - # `input` is just a plain parameter, get its default value - state[ input.name ] = input.get_initial_value( trans, context ) + state[ input.name ] = input.get_initial_value( trans, context ) def get_param_html_map( self, trans, page=0, other_values={} ): """ @@ -1057,6 +1039,41 @@ def params_from_strings( self, params, app, ignore_errors=False ): return params_from_strings( self.inputs, params, app, ignore_errors ) + + + def check_and_update_param_values( self, values, trans ): + """ + Check that all parameters have values, and fill in with default + values where neccesary. This could be called after loading values + from a database in case new parameters have been added. + """ + messages = [] + self.check_and_update_param_values_helper( self.inputs, values, trans, messages ) + return messages + + def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="" ): + """ + Recursive helper for `check_and_update_param_values_helper` + """ + context = ExpressionContext( values, context ) + for input in inputs.itervalues(): + # No value, insert the default + if input.name not in values: + messages.append( prefix + input.label ) + values[input.name] = input.get_initial_value( trans, context ) + # Value, visit recursively as usual + else: + if isinstance( input, Repeat ): + for i, d in enumerate( values[ input.name ] ): + rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 ) + self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix ) + elif isinstance( input, Conditional ): + group_values = values[ input.name ] + current = group_values["__current_case__"] + self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix ) + else: + # Regular tool parameter, no recursion needed + pass def handle_unvalidated_param_values( self, input_values, app ): """ diff -r 22b08d47f7ba -r dae0313bf5bb lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Wed Apr 29 11:53:22 2009 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Apr 29 13:46:02 2009 -0400 @@ -3,6 +3,7 @@ """ from basic import ToolParameter +from galaxy.util.expressions import ExpressionContext class Group( object ): def __init__( self ): @@ -19,6 +20,11 @@ into the preferred value form. """ return value + def get_initial_value( self, trans, context ): + """ + Return the initial state/value for this group + """ + raise TypeError( "Not implemented" ) class Repeat( Group ): type = "repeat" @@ -65,7 +71,9 @@ if isinstance( input, ToolParameter ): callback( new_prefix, input, d[input.name], parent = d ) else: - input.visit_inputs( new_prefix, d[input.name], callback ) + input.visit_inputs( new_prefix, d[input.name], callback ) + def get_initial_value( self, trans, context ): + return [] class Conditional( Group ): type = "conditional" @@ -109,6 +117,22 @@ callback( prefix, input, value[input.name], parent = value ) else: input.visit_inputs( prefix, value[input.name], callback ) + def get_initial_value( self, trans, context ): + # State for a conditional is a plain dictionary. + rval = {} + # Get the default value for the 'test element' and use it + # to determine the current case + test_value = self.test_param.get_initial_value( trans, context ) + current_case = self.get_current_case( test_value, trans ) + # Store the current case in a special value + rval['__current_case__'] = current_case + # Store the value of the test element + rval[ self.test_param.name ] = test_value + # Fill in state for selected case + child_context = ExpressionContext( rval, context ) + for child_input in self.cases[current_case].inputs.itervalues(): + rval[ child_input.name ] = child_input.get_initial_value( trans, child_context ) + return rval class ConditionalWhen( object ): def __init__( self ): diff -r 22b08d47f7ba -r dae0313bf5bb lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Wed Apr 29 11:53:22 2009 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed Apr 29 13:46:02 2009 -0400 @@ -300,9 +300,16 @@ data = {} data['name'] = workflow.name data['steps'] = {} + data['upgrade_messages'] = {} # For each step, rebuild the form and encode the state for step in workflow.steps: + # Load from database representation module = module_factory.from_workflow_step( trans, step ) + # Fix any missing parameters + upgrade_message = module.check_and_update_state() + if upgrade_message: + data['upgrade_messages'][step.order_index] = upgrade_message + # Pack atrributes into plain dictionary step_dict = { 'id': step.order_index, 'type': module.type, @@ -312,7 +319,7 @@ 'tool_errors': module.get_errors(), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), - 'form_html': module.get_config_form() + 'form_html': module.get_config_form(), } # Connections input_conn_dict = {} @@ -324,6 +331,7 @@ step_dict['position'] = step.position # Add to return value data['steps'][step.order_index] = step_dict + print data['upgrade_messages'] return data @web.json diff -r 22b08d47f7ba -r dae0313bf5bb lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py Wed Apr 29 11:53:22 2009 -0400 +++ b/lib/galaxy/workflow/modules.py Wed Apr 29 13:46:02 2009 -0400 @@ -60,6 +60,13 @@ pass def get_config_form( self ): raise TypeError( "Abstract method" ) + + def check_and_update_state( self ): + """ + If the state is not in sync with the current implementation of the + module, try to update. Returns a list of messages to be displayed + """ + pass ## ---- Run time --------------------------------------------------------- @@ -236,7 +243,11 @@ return value, error # Update state using incoming values errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback ) - self.errors = errors or None + self.errors = errors or None + + def check_and_update_state( self ): + return self.tool.check_and_update_param_values( self.state.inputs, self.trans ) + def add_dummy_datasets( self, connections=None): if connections: # Store onnections by input name diff -r 22b08d47f7ba -r dae0313bf5bb static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Apr 29 11:53:22 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Apr 29 13:46:02 2009 -0400 @@ -255,6 +255,7 @@ if ( data.type ) { this.type = data.type; } + this.name = data.name; this.form_html = data.form_html; this.tool_state = data.tool_state; this.tool_errors = data.tool_errors; diff -r 22b08d47f7ba -r dae0313bf5bb templates/workflow/editor.mako --- a/templates/workflow/editor.mako Wed Apr 29 11:53:22 2009 -0400 +++ b/templates/workflow/editor.mako Wed Apr 29 13:46:02 2009 -0400 @@ -78,7 +78,18 @@ workflow.fit_canvas_to_nodes(); scroll_to_nodes(); canvas_manager.draw_overview(); - hide_modal(); + // Determine if any parameters were 'upgraded' and provide message + upgrade_message = "" + $.each( data['upgrade_messages'], function( k, v ) { + upgrade_message += ( "<li>Step " + ( parseInt(k) + 1 ) + ": " + workflow.nodes[k].name + " -- " + v.join( ", " ) ); + }); + if ( upgrade_message ) { + show_modal( "Workflow loaded with changes", + "Values were not found for the following parameters (possibly a result of tool upgrades), <br/> default values have been used. Please review the following parameters and then save.<ul>" + upgrade_message + "</ul>", + { "Continue" : hide_modal } ); + } else { + hide_modal(); + } }, beforeSubmit: function( data ) { show_modal( "Loading workflow", "progress" ); @@ -88,7 +99,9 @@ }); $(document).ajaxError( function ( e, x ) { - show_modal( "Server error", x.responseText, { "Ignore error" : hide_modal } ); + console.log( e, x ); + var message = x.responseText || x.statusText || "Could not connect to server"; + show_modal( "Server error", message, { "Ignore error" : hide_modal } ); return false; }); diff -r 22b08d47f7ba -r dae0313bf5bb tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Wed Apr 29 11:53:22 2009 -0400 +++ b/tools/maf/interval2maf.xml Wed Apr 29 13:46:02 2009 -0400 @@ -6,6 +6,7 @@ #end if </command> <inputs> + <param type="text" name="TEST" label="Test" /> <param format="interval" name="input1" type="data" label="Choose intervals"> <validator type="unspecified_build" /> </param>

1 0

[hg] galaxy 2384: Added functional tests for testing sniffing an...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cd1bcec32519 changeset: 2384:cd1bcec32519 user: guru date: Wed Apr 29 16:32:23 2009 -0400 description: Added functional tests for testing sniffing and metadata settings of qual454 and qualsolid datatypes. 6 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/datatypes/qualityscore.py lib/galaxy/datatypes/registry.py test-data/qualscores.qual454 test-data/qualscores.qualsolid test/functional/test_sniffing_and_metadata_settings.py diffs (194 lines): diff -r 656f1df80b46 -r cd1bcec32519 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Wed Apr 29 14:47:18 2009 -0400 +++ b/datatypes_conf.xml.sample Wed Apr 29 16:32:23 2009 -0400 @@ -188,7 +188,6 @@ <sniffer type="galaxy.datatypes.sequence:Maf"/> <sniffer type="galaxy.datatypes.sequence:Lav"/> <sniffer type="galaxy.datatypes.sequence:csFasta"/> - <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSolexa"/> <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/> <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/> <sniffer type="galaxy.datatypes.sequence:Fasta"/> diff -r 656f1df80b46 -r cd1bcec32519 lib/galaxy/datatypes/qualityscore.py --- a/lib/galaxy/datatypes/qualityscore.py Wed Apr 29 14:47:18 2009 -0400 +++ b/lib/galaxy/datatypes/qualityscore.py Wed Apr 29 16:32:23 2009 -0400 @@ -152,35 +152,4 @@ except: return "Solexa Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) ) - def sniff( self, filename ): - """ - >>> fname = get_test_fname( 'sequence.fasta' ) - >>> QualityScoreSolexa().sniff( fname ) - False - >>> fname = get_test_fname( 'sequence.qualsolexa' ) - >>> QualityScoreSolexa().sniff( fname ) - True - """ - try: - fh = open( filename ) - readlen = None - while True: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line and not line.startswith( '#' ): - if len(line.split('\t')) > 1: - break - try: - [ int( x ) for x in line.split() ] - if not(readlen): - readlen = len(line.split()) - assert len(line.split()) == readlen #Solexa reads should be of the same length - except: - break - - except: - pass - return False - + \ No newline at end of file diff -r 656f1df80b46 -r cd1bcec32519 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Wed Apr 29 14:47:18 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Wed Apr 29 16:32:23 2009 -0400 @@ -159,6 +159,9 @@ xml.BlastXml(), sequence.Maf(), sequence.Lav(), + sequence.csFasta(), + qualityscore.QualityScoreSOLiD(), + qualityscore.QualityScore454(), sequence.Fasta(), sequence.FastqSolexa(), interval.Wiggle(), diff -r 656f1df80b46 -r cd1bcec32519 test-data/qualscores.qual454 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qualscores.qual454 Wed Apr 29 16:32:23 2009 -0400 @@ -0,0 +1,49 @@ +>EYKX4VC04IWAEA length=68 xy=3531_0528 region=4 run=R_2007_11_07_16_15_57_ +22 13 9 6 4 3 2 2 1 1 1 1 24 44 33 23 16 11 7 2 28 33 23 18 28 27 27 28 20 21 42 35 21 6 24 25 31 21 28 27 41 34 15 28 28 27 28 28 33 24 27 28 28 24 27 36 27 28 28 28 +28 28 36 30 8 34 25 18 +>EYKX4VC04JKOGH length=48 xy=3808_3903 region=4 run=R_2007_11_07_16_15_57_ +28 28 27 28 38 31 10 28 28 27 27 34 25 28 24 26 27 28 27 37 29 34 25 31 21 28 21 36 28 31 20 24 27 37 28 28 34 27 3 34 25 24 28 28 26 28 35 28 +>EYKX4VC04JIUVK length=84 xy=3788_0830 region=4 run=R_2007_11_07_16_15_57_ +29 20 14 11 8 6 3 1 25 27 25 28 28 27 28 27 28 28 36 28 27 28 36 29 7 28 28 28 27 27 27 35 26 35 26 27 36 28 28 28 38 32 11 28 36 28 27 26 35 25 28 38 31 11 27 28 37 28 27 27 +28 36 29 8 33 24 41 34 19 3 26 28 28 28 35 26 36 29 8 38 32 11 28 28 +>EYKX4VC04JWDRY length=78 xy=3942_1068 region=4 run=R_2007_11_07_16_15_57_ +36 24 14 5 27 20 28 27 28 32 22 28 27 43 36 23 11 27 28 28 28 32 23 36 27 28 28 26 38 32 11 34 25 27 43 36 23 11 38 31 11 37 28 28 28 27 28 30 20 28 32 22 28 36 27 37 30 9 27 28 +28 27 28 42 35 20 5 28 28 28 35 26 27 27 26 39 32 12 +>EYKX4VC04JWMUW length=55 xy=3945_0550 region=4 run=R_2007_11_07_16_15_57_ +36 24 14 4 28 17 34 25 35 25 31 20 28 28 36 27 28 28 24 27 28 28 37 28 27 27 35 25 31 21 27 39 32 12 28 36 28 28 26 27 28 27 26 28 42 35 20 6 28 27 28 28 28 28 28 +>EYKX4VC04JH4RG length=85 xy=3779_3850 region=4 run=R_2007_11_07_16_15_57_ +37 28 35 26 38 31 10 27 37 28 28 38 31 10 27 35 25 25 28 28 28 28 28 28 28 28 27 28 33 23 28 32 22 35 25 31 20 34 25 31 21 26 28 27 26 26 15 36 29 7 27 27 24 36 27 28 37 28 36 28 +27 28 28 28 37 28 28 40 34 14 37 28 28 26 28 36 28 26 28 37 28 28 28 28 27 +>EYKX4VC04JDAWO length=117 xy=3724_3814 region=4 run=R_2007_11_07_16_15_57_ +25 28 28 28 34 25 28 28 28 28 28 28 28 27 27 30 19 28 28 34 25 28 28 26 32 23 28 28 27 28 28 34 25 28 27 28 25 25 36 27 36 29 7 36 27 33 23 28 28 36 27 31 21 28 30 20 28 34 24 28 +27 34 25 28 28 28 28 28 28 27 28 27 37 30 9 28 28 27 28 27 28 28 28 27 33 23 28 28 28 17 28 31 20 28 21 26 28 33 23 26 28 27 26 28 35 26 28 28 21 28 26 28 33 23 36 27 27 +>EYKX4VC04JEY0S length=57 xy=3743_3898 region=4 run=R_2007_11_07_16_15_57_ +23 28 35 28 6 26 24 27 33 23 26 28 28 28 28 33 27 3 27 30 19 28 28 36 27 33 24 24 32 23 25 26 27 28 31 21 34 27 5 28 22 27 28 24 26 28 28 27 28 24 37 29 26 35 26 26 15 +>EYKX4VC04JKOGB length=68 xy=3808_3897 region=4 run=R_2007_11_07_16_15_57_ +28 34 27 4 27 28 24 28 28 28 28 27 27 31 20 28 27 27 26 28 35 26 37 28 28 28 28 28 41 34 19 4 35 26 27 32 22 28 25 36 28 26 28 28 25 36 29 8 28 28 28 27 24 28 41 34 16 27 21 28 +21 26 33 26 21 40 34 14 +>EYKX4VC04JOZA4 length=160 xy=3857_3886 region=4 run=R_2007_11_07_16_15_57_ +35 24 15 7 1 26 28 41 34 15 28 28 28 28 28 27 25 40 34 14 28 28 44 35 24 15 8 2 27 24 27 27 35 26 28 27 36 27 26 36 28 24 27 37 29 27 28 26 35 26 28 28 28 27 26 35 26 37 29 36 +28 28 26 36 28 28 28 37 28 28 28 28 28 28 28 28 36 28 43 36 22 10 19 37 28 27 37 28 24 27 37 28 38 32 11 28 37 29 26 25 34 25 36 27 24 25 24 36 27 23 27 28 39 32 12 39 32 12 28 37 +29 25 27 27 27 24 28 39 32 12 28 26 44 36 24 14 5 33 26 2 33 24 26 24 28 28 27 35 25 34 25 26 41 34 16 43 36 22 8 28 +>EYKX4VC04JLDPN length=75 xy=3816_3865 region=4 run=R_2007_11_07_16_15_57_ +28 28 36 27 28 28 36 27 28 27 28 28 28 27 26 36 27 28 28 27 28 28 28 28 28 28 28 28 27 28 40 33 14 28 28 28 40 33 13 24 27 28 28 28 27 23 32 22 25 18 26 21 24 36 27 26 24 25 28 26 +27 37 28 22 28 28 34 24 28 25 23 26 23 25 27 +>EYKX4VC04IEKBT length=167 xy=3329_0983 region=4 run=R_2007_11_07_16_15_57_ +26 17 12 9 7 5 4 2 1 28 44 31 21 15 11 8 5 2 34 25 44 35 24 15 7 1 35 26 37 29 28 36 27 37 28 28 27 36 27 27 39 32 12 36 27 28 37 28 28 35 26 36 27 28 28 24 27 27 28 28 +28 36 27 40 33 14 27 28 43 36 23 12 2 28 27 27 36 27 43 36 22 8 27 37 28 35 25 28 28 28 28 36 27 41 35 16 39 32 12 28 36 28 28 27 28 38 31 11 28 27 28 28 28 37 28 35 25 28 39 33 +13 28 28 28 28 28 26 26 28 28 27 27 28 27 25 39 32 12 28 28 35 25 25 27 28 28 28 26 36 27 28 28 35 25 28 28 34 25 28 27 36 28 26 28 28 28 28 +>EYKX4VC04H76LH length=104 xy=3256_2259 region=4 run=R_2007_11_07_16_15_57_ +20 12 7 5 3 2 2 1 1 1 1 1 1 28 30 19 26 28 33 23 27 37 28 28 36 28 28 37 28 28 36 28 27 42 35 21 7 27 27 30 19 31 21 28 27 33 23 28 28 28 27 35 25 28 35 26 27 36 27 28 +36 27 28 36 27 28 36 27 28 36 28 28 36 28 28 36 27 27 35 25 27 33 23 28 36 27 28 31 21 28 35 25 27 34 25 28 33 23 28 32 22 26 34 24 +>EYKX4VC04I6APD length=156 xy=3645_0543 region=4 run=R_2007_11_07_16_15_57_ +21 12 8 5 4 2 2 1 1 1 1 1 1 28 38 32 11 28 44 36 24 14 5 24 28 28 28 21 27 42 35 21 7 27 28 27 24 26 28 37 28 35 26 28 26 28 27 24 28 28 27 28 44 18 9 5 3 2 1 1 +1 1 1 1 1 1 1 1 1 35 26 41 34 17 25 24 12 28 28 27 38 32 11 28 28 23 28 27 28 27 20 39 32 12 22 26 36 27 27 27 24 36 28 28 36 27 35 26 40 33 18 1 26 34 27 28 24 22 40 34 +15 26 32 22 28 28 28 25 28 28 39 33 13 27 28 32 22 32 23 42 35 21 7 28 43 36 23 10 27 43 36 23 10 36 28 25 +>EYKX4VC04IPT6U length=143 xy=3457_2692 region=4 run=R_2007_11_07_16_15_57_ +30 20 15 11 8 5 3 1 28 19 27 34 24 44 36 23 13 3 28 35 25 28 27 28 28 28 28 27 35 25 28 36 27 27 28 28 28 28 36 27 36 28 28 42 35 21 6 28 28 27 27 44 35 24 15 8 1 27 27 28 +36 27 28 28 27 28 28 35 26 43 36 23 12 2 28 36 27 26 28 28 36 27 28 28 36 27 41 34 16 25 28 41 34 16 36 28 40 34 14 39 33 13 36 27 40 34 18 2 28 40 34 18 2 35 25 28 27 41 34 19 +4 26 27 28 27 28 28 34 25 36 27 28 28 28 36 27 37 28 28 27 28 27 28 +>EYKX4VC04JX6Y2 length=68 xy=3962_3644 region=4 run=R_2007_11_07_16_15_57_ +28 28 28 27 35 28 6 27 28 27 36 27 28 25 37 28 33 26 2 28 27 28 24 28 37 29 28 28 28 28 28 23 28 32 22 28 36 27 28 26 34 25 28 28 35 26 28 28 26 27 25 28 28 24 28 28 27 27 28 28 +28 28 33 23 28 40 34 14 \ No newline at end of file diff -r 656f1df80b46 -r cd1bcec32519 test-data/qualscores.qualsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qualscores.qualsolid Wed Apr 29 16:32:23 2009 -0400 @@ -0,0 +1,48 @@ +>946_21_302_F3 +2 10 2 2 4 2 21 2 2 4 4 17 5 2 5 2 11 4 2 2 2 10 7 3 15 2 2 2 3 19 3 2 6 3 2 +>946_21_659_F3 +3 31 3 2 2 2 34 3 2 2 2 31 2 2 3 4 31 8 3 2 2 30 4 8 3 3 2 2 6 9 4 4 6 2 2 +>946_21_1071_F3 +5 5 2 2 2 8 5 3 2 3 7 7 2 3 4 6 5 2 2 2 5 5 2 2 2 3 8 2 3 3 3 8 2 3 2 +>946_21_1115_F3 +21 5 2 8 13 31 6 2 17 24 10 27 4 21 29 8 20 2 11 21 13 24 5 5 6 24 31 2 13 6 22 17 6 27 10 +>946_21_1218_F3 +11 21 2 13 13 16 27 16 19 27 22 28 14 26 24 23 29 10 15 13 6 4 7 16 26 22 11 6 16 22 21 6 4 7 21 +>946_21_1232_F3 +17 16 2 28 21 31 15 16 10 11 8 20 6 5 18 6 13 23 7 13 4 12 19 8 6 9 10 19 7 10 6 10 20 14 8 +>946_21_1368_F3 +28 30 31 31 31 20 29 24 27 31 31 31 24 26 31 31 26 15 27 31 27 30 29 27 30 27 30 21 23 26 24 31 17 30 19 +>946_21_1406_F3 +4 29 3 2 4 5 34 8 2 2 3 29 4 2 8 2 11 4 2 2 2 28 8 5 3 4 31 2 2 2 2 28 5 2 2 +>946_21_1695_F3 +25 31 8 29 19 31 19 12 16 31 30 13 16 21 31 22 13 13 19 23 32 16 6 14 16 24 13 6 6 14 8 8 5 11 6 +>946_21_1945_F3 +23 27 14 10 17 31 29 31 10 13 31 29 23 8 24 30 31 28 10 20 26 28 31 5 22 31 24 28 9 7 15 7 20 5 4 +>946_21_2013_F3 +2 26 2 2 2 2 2 2 9 2 2 2 2 2 2 2 2 4 2 2 2 2 3 2 2 2 2 2 2 2 2 2 4 2 2 +>946_22_108_F3 +17 14 12 28 12 17 18 28 19 13 14 6 17 5 3 6 2 7 6 12 16 7 13 9 11 8 2 5 5 6 6 7 20 11 19 +>946_22_1241_F3 +16 8 5 20 11 6 13 5 19 13 8 9 17 31 8 17 2 6 31 21 12 11 8 12 5 8 15 8 5 5 7 5 11 6 10 +>946_22_1296_F3 +10 8 33 31 27 31 26 5 17 11 6 23 8 24 6 8 14 14 27 11 16 8 8 29 5 21 8 5 14 8 7 16 4 5 5 +>946_22_1356_F3 +2 31 4 3 2 6 31 4 2 2 4 2 3 8 2 2 2 3 4 8 2 2 3 3 11 2 2 2 4 2 2 2 9 2 2 +>946_22_1520_F3 +8 11 12 21 13 15 16 25 20 21 14 23 31 23 30 18 25 23 27 30 21 30 15 14 25 22 22 21 21 22 16 23 26 13 21 +>946_22_1532_F3 +27 30 34 26 25 29 31 31 24 29 29 33 28 22 24 31 30 30 24 22 25 31 19 9 26 29 23 22 13 28 30 31 24 7 29 +>946_22_1582_F3 +28 19 4 5 6 25 30 4 5 8 15 19 5 9 8 29 27 4 4 2 27 17 2 2 5 30 22 2 11 6 26 16 3 2 2 +>946_22_1598_F3 +23 5 33 6 19 8 13 4 30 17 11 13 6 16 8 8 27 5 24 8 8 26 16 8 17 2 23 25 4 23 10 16 10 7 13 +>946_22_1834_F3 +31 28 30 31 31 34 27 29 31 28 31 29 16 31 31 25 31 11 27 21 26 29 16 18 21 19 29 13 24 24 27 24 8 24 10 +>946_22_1939_F3 +30 29 31 31 25 31 33 24 31 30 25 31 27 33 31 27 31 26 30 19 16 27 29 31 21 25 27 9 26 27 23 15 20 27 27 +>946_23_975_F3 +31 31 3 3 2 32 29 3 3 4 28 27 2 4 4 30 24 3 7 3 28 24 5 7 8 29 22 2 6 6 2 24 2 2 2 +>946_23_1133_F3 +19 28 22 31 25 14 28 30 32 27 10 33 26 31 31 14 30 30 16 30 10 28 23 16 6 14 17 10 6 8 18 5 8 9 5 +>946_23_1221_F3 +30 26 30 32 23 29 29 27 28 20 26 23 14 29 27 29 28 29 23 14 30 27 30 27 8 24 13 26 11 12 20 17 15 5 21 \ No newline at end of file diff -r 656f1df80b46 -r cd1bcec32519 test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Wed Apr 29 14:47:18 2009 -0400 +++ b/test/functional/test_sniffing_and_metadata_settings.py Wed Apr 29 16:32:23 2009 -0400 @@ -114,6 +114,18 @@ self.check_history_for_string( 'NCBI Blast XML data' ) self.check_history_for_string( 'format: <span class="blastxml">blastxml</span>' ) self.delete_history_item( 1 ) + def test_65_qualsolid_datatype( self ): + """Testing correctly sniffing qualsolid data type upon upload""" + self.upload_file( 'qualscores.qualsolid' ) + self.verify_dataset_correctness('qualscores.qualsolid') + self.check_history_for_string('qualscores.qualsolid format: <span class="qualsolid">qualsolid</span>, database: \? Info: uploaded qualsolid file') + self.delete_history_item( 1 ) + def test_70_qual454_datatype( self ): + """Testing correctly sniffing qual454 data type upon upload""" + self.upload_file( 'qualscores.qual454' ) + self.verify_dataset_correctness('qualscores.qual454') + self.check_history_for_string('qualscores.qual454 format: <span class="qual454">qual454</span>, database: \? Info: uploaded qual454 file') + self.delete_history_item( 1 ) def test_9999_clean_up( self ): self.delete_history() self.logout()

1 0

[hg] galaxy 2385: PyTables and GeneTrack eggs. Still need to bu...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/add0911007d9 changeset: 2385:add0911007d9 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Apr 29 17:37:22 2009 -0400 description: PyTables and GeneTrack eggs. Still need to bundle up pychartdir. 2 file(s) affected in this change: dist-eggs.ini eggs.ini diffs (55 lines): diff -r cd1bcec32519 -r add0911007d9 dist-eggs.ini --- a/dist-eggs.ini Wed Apr 29 16:32:23 2009 -0400 +++ b/dist-eggs.ini Wed Apr 29 17:37:22 2009 -0400 @@ -24,9 +24,15 @@ py2.5-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.5 [groups] -py2.4-linux = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 -py2.5-linux = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 -linux = py2.4-linux py2.5-linux +py2.4-linux-i686 = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 +py2.4-linux-x86_64 = py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 +py2.5-linux-i686 = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 +py2.5-linux-x86_64 = py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 +py2.4-linux = py2.4-linux-i686 py2.4-linux-x86_64 +py2.5-linux = py2.5-linux-i686 py2.5-linux-x86_64 +linux-i686 = py2.4-linux-i686 py2.5-linux-i686 +linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 +linux = linux-i686 linux-x86_64 py2.4-macosx = py2.4-macosx-10.3-fat-ucs2 py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.5-macosx-10.5-i386-ucs2 macosx = py2.4-macosx py2.5-macosx diff -r cd1bcec32519 -r add0911007d9 eggs.ini --- a/eggs.ini Wed Apr 29 16:32:23 2009 -0400 +++ b/eggs.ini Wed Apr 29 17:37:22 2009 -0400 @@ -24,6 +24,7 @@ threadframe = 0.2 guppy = 0.1.8 numpy = 1.2.1 +tables = 2.1.1 [eggs:noplatform] Beaker = 0.5 @@ -51,6 +52,7 @@ wsgiref = 0.1.2 Babel = 0.9.4 wchartype = 0.1 +GeneTrack = 1.0.3 ; extra version information [tags] @@ -61,6 +63,7 @@ flup = .dev_r2311 bx_python = _dev_r4bf1f32e6b76 nose = .dev_r101 +tables = _hdf5_1.8.2_lzo_2.03_bzip2_1.0.5_static ; source location, necessary for scrambling [source] @@ -100,3 +103,5 @@ wsgiref = http://pypi.python.org/packages/source/w/wsgiref/wsgiref-0.1.2.zip Babel = http://ftp.edgewall.com/pub/babel/Babel-0.9.4.zip wchartype = http://ginstrom.com/code/wchartype-0.1.zip +tables = http://www.pytables.org/download/stable/tables-2.1.1.tar.gz ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.2.tar.gz http://www.oberhumer.com/opensource/lzo/download/lzo-2.03.tar.gz http://www.bzip.org/1.0.5/bzip2-1.0.5.tar.gz +GeneTrack = http://genetrack.googlecode.com/files/GeneTrack-1.0.3.zip http://dalchemy.com/opensource/formkit/FormKit_0.9b2.tar.gz

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[hg] galaxy 2379: Fix for issubtype in workflow editor, would ca...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5a4aac327bad changeset: 2379:5a4aac327bad user: James Taylor <james(a)jamestaylor.org> date: Wed Apr 29 10:27:57 2009 -0400 description: Fix for issubtype in workflow editor, would cause problems drawing connections for types with no inheritence relationships 1 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js diffs (12 lines): diff -r e0534b25c282 -r 5a4aac327bad static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Tue Apr 28 15:32:44 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Apr 29 10:27:57 2009 -0400 @@ -645,7 +645,7 @@ function issubtype( child, parent ) { child = ext_to_type[child]; parent = ext_to_type[parent]; - return ( parent in type_to_type[child] ); + return ( type_to_type[child] ) && ( parent in type_to_type[child] ); }; function populate_datatype_info( data ) {

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[hg] galaxy 2374: Display only the number of associations on the...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d0c905db68db changeset: 2374:d0c905db68db user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Apr 27 16:03:44 2009 -0400 description: Display only the number of associations on the main users, groups, roles pages rather than the associated objects - much faster display times. Also a tweek to my last fix for the column_maker tool. 6 file(s) affected in this change: lib/galaxy/web/controllers/admin.py templates/admin/dataset_security/groups.mako templates/admin/dataset_security/roles.mako templates/admin/dataset_security/users.mako test/base/twilltestcase.py tools/stats/column_maker.py diffs (483 lines): diff -r 22118cf46b0a -r d0c905db68db lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Apr 27 13:33:47 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Apr 27 16:03:44 2009 -0400 @@ -280,23 +280,12 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - # Build a list of tuples which are groups followed by lists of members and roles - # [ ( group, [ member, member, member ], [ role, role ] ), ( group, [ member, member ], [ role ] ) ] - groups_members_roles = [] groups = trans.app.model.Group.query() \ .filter( trans.app.model.Group.table.c.deleted==False ) \ .order_by( trans.app.model.Group.table.c.name ) \ .all() - for group in groups: - members = [] - for uga in group.members: - members.append( trans.app.model.User.get( uga.user_id ) ) - roles = [] - for gra in group.roles: - roles.append( trans.app.model.Role.get( gra.role_id ) ) - groups_members_roles.append( ( group, members, roles ) ) return trans.fill_template( '/admin/dataset_security/groups.mako', - groups_members_roles=groups_members_roles, + groups=groups, msg=msg, messagetype=messagetype ) @web.expose @@ -647,20 +636,9 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - # Build a list of tuples which are users followed by lists of groups and roles - # [ ( user, [ group, group, group ], [ role, role ] ), ( user, [ group, group ], [ role ] ) ] - users_groups_roles = [] users = trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all() - for user in users: - groups = [] - for uga in user.groups: - groups.append( trans.app.model.Group.get( uga.group_id ) ) - roles = [] - for ura in user.non_private_roles: - roles.append( trans.app.model.Role.get( ura.role_id ) ) - users_groups_roles.append( ( user, groups, roles ) ) return trans.fill_template( '/admin/dataset_security/users.mako', - users_groups_roles=users_groups_roles, + users=users, allow_user_deletion=trans.app.config.allow_user_deletion, msg=msg, messagetype=messagetype ) @@ -702,91 +680,6 @@ out_groups=out_groups, msg=msg, messagetype=messagetype ) - # Utility methods to enable removal of associations - redirects are key - @web.expose - @web.require_admin - def remove_group_from_role( self, trans, **kwd ): - params = util.Params( kwd ) - group_id = int( params.group_id ) - group = trans.app.model.Group.get( group_id ) - role_id = int( params.role_id ) - role = trans.app.model.Role.get( role_id ) - gra = trans.app.model.GroupRoleAssociation.filter( and_( trans.app.model.GroupRoleAssociation.table.c.group_id==group_id, - trans.app.model.GroupRoleAssociation.table.c.role_id==role_id ) ).first() - gra.delete() - gra.flush() - msg = "Group '%s' removed from role '%s'" % ( group.name, role.name ) - trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_group_from_user( self, trans, **kwd ): - params = util.Params( kwd ) - group_id = int( params.group_id ) - group = trans.app.model.Group.get( group_id ) - user_id = int( params.user_id ) - user = trans.app.model.User.get( user_id ) - uga = trans.app.model.UserGroupAssociation.filter( and_( trans.app.model.UserGroupAssociation.table.c.group_id==group_id, - trans.app.model.UserGroupAssociation.table.c.user_id==user_id ) ).first() - uga.delete() - uga.flush() - msg = "Group '%s' removed from user '%s'" % ( group.name, user.email ) - trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_role_from_group( self, trans, **kwd ): - params = util.Params( kwd ) - role_id = int( params.role_id ) - role = trans.app.model.Role.get( role_id ) - group_id = int( params.group_id ) - group = trans.app.model.Group.get( group_id ) - gra = trans.app.model.GroupRoleAssociation.filter( and_( trans.app.model.GroupRoleAssociation.table.c.role_id==role_id, - trans.app.model.GroupRoleAssociation.table.c.group_id==group_id ) ).first() - gra.delete() - gra.flush() - msg = "Role '%s' removed from group '%s'" % ( role.name, group.name ) - trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_role_from_user( self, trans, **kwd ): - params = util.Params( kwd ) - user_id = int( params.user_id ) - user = trans.app.model.User.get( user_id ) - role_id = int( params.role_id ) - role = trans.app.model.Role.get( role_id ) - ura = trans.app.model.UserRoleAssociation.filter( and_( trans.app.model.UserRoleAssociation.table.c.user_id==user_id, - trans.app.model.UserRoleAssociation.table.c.role_id==role_id ) ).first() - ura.delete() - ura.flush() - msg = "Role '%s' removed from user '%s'" % ( role.name, user.email ) - trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_user_from_group( self, trans, **kwd ): - params = util.Params( kwd ) - user_id = int( params.user_id ) - user = trans.app.model.User.get( user_id ) - group_id = int( params.group_id ) - group = trans.app.model.Group.get( group_id ) - uga = trans.app.model.UserGroupAssociation.filter( and_( trans.app.model.UserGroupAssociation.table.c.user_id==user_id, - trans.app.model.UserGroupAssociation.table.c.group_id==group_id ) ).first() - uga.delete() - uga.flush() - msg = "User '%s' removed from group '%s'" % ( user.email, group.name ) - trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_user_from_role( self, trans, **kwd ): - params = util.Params( kwd ) - user_id = int( params.user_id ) - user = trans.app.model.User.get( user_id ) - role_id = int( params.role_id ) - role = trans.app.model.Role.get( role_id ) - ura = trans.app.model.UserRoleAssociation.filter( and_( trans.app.model.UserRoleAssociation.table.c.user_id==user_id, - trans.app.model.UserRoleAssociation.table.c.role_id==role_id ) ).first() - ura.delete() - ura.flush() - msg = "User '%s' removed from role '%s'" % ( user.email, role.name ) - trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) # Galaxy Library Stuff @web.expose diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/groups.mako --- a/templates/admin/dataset_security/groups.mako Mon Apr 27 13:33:47 2009 -0400 +++ b/templates/admin/dataset_security/groups.mako Mon Apr 27 16:03:44 2009 -0400 @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> ## Render a row -<%def name="render_row( group, members, roles, ctr, anchored, curr_anchor )"> +<%def name="render_row( group, ctr, anchored, curr_anchor )"> %if ctr % 2 == 1: <tr class="odd_row"> %else: @@ -18,34 +18,10 @@ </div> </td> <td> - <ul> - %for user in members: - <li> - <a href="${h.url_for( controller='admin', action='user', user_id=user.id )}">${user.email}</a> - <a id="user-${user.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="user-${user.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_user_from_group', group_id=group.id, user_id=user.id )}">Remove user from group</a> - </div> - </li> - %endfor - </ul> + ${len( group.members )} </td> <td> - <ul> - %for role in roles: - <li> - %if not role.type == trans.app.model.Role.types.PRIVATE: - <a href="${h.url_for( controller='admin', action='role', role_id=role.id )}">${role.name}</a> - <a id="role-${role.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="role-${role.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_group', group_id=group.id, role_id=role.id )}">Remove role from group</a> - </div> - %else: - ${role.name} - %endif - </li> - %endfor - </ul> + ${len( group.roles )} %if not anchored: <a name="${curr_anchor}"></a> <div style="float: right;"><a href="#TOP">top</a></div> @@ -65,12 +41,12 @@ ${render_msg( msg, messagetype )} %endif -%if len( groups_members_roles ) == 0: +%if len( groups ) == 0: There are no Galaxy groups %else: <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <% - render_quick_find = len( groups_members_roles ) > 50 + render_quick_find = len( groups ) > 50 ctr = 0 %> %if render_quick_find: @@ -91,34 +67,29 @@ %endif <tr class="header"> <td>Name</td> - <td>Associated Users</td> - <td>Associated Roles</td> + <td>Users</td> + <td>Roles</td> </tr> - %for ctr, group_tuple in enumerate( groups_members_roles ): - <% - group = group_tuple[0] - members = group_tuple[1] - roles = group_tuple[2] - %> + %for ctr, group in enumerate( groups ): %if render_quick_find and not group.name.upper().startswith( curr_anchor ): <% anchored = False %> %endif %if render_quick_find and group.name.upper().startswith( curr_anchor ): %if not anchored: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} %endif %elif render_quick_find: %for anchor in anchors[ anchor_loc: ]: %if group.name.upper().startswith( anchor ): %if not anchored: <% curr_anchor = anchor %> - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} %endif <% anchor_loc = anchors.index( anchor ) @@ -127,7 +98,7 @@ %endif %endfor %else: - ${render_row( group, members, roles, ctr, True, '' )} + ${render_row( group, ctr, True, '' )} %endif %endfor </table> diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/roles.mako --- a/templates/admin/dataset_security/roles.mako Mon Apr 27 13:33:47 2009 -0400 +++ b/templates/admin/dataset_security/roles.mako Mon Apr 27 16:03:44 2009 -0400 @@ -20,30 +20,10 @@ <td>${role.description}</td> <td>${role.type}</td> <td> - <ul> - %for ura in role.users: - <li> - <a href="${h.url_for( controller='admin', action='user', user_id=ura.user.id )}">${ura.user.email}</a> - <a id="user-${ura.user.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="user-${ura.user.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_user', role_id=role.id, user_id=ura.user.id )}">Remove user from role</a> - </div> - </li> - %endfor - </ul> + ${len( role.users )} </td> <td> - <ul> - %for gra in role.groups: - <li> - <a href="${h.url_for( controller='admin', action='group', group_id=gra.group.id )}">${gra.group.name}</a> - <a id="group-${gra.group.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="group-${gra.group.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_group_from_role', role_id=role.id, group_id=gra.group.id )}">Remove group from role</a> - </div> - </li> - %endfor - </ul> + ${len( role.groups )} %if not anchored: <a name="${curr_anchor}"></a> <div style="float: right;"><a href="#TOP">top</a></div> @@ -91,8 +71,8 @@ <td>Name</td> <td>Description</td> <td>Type</td> - <td>Associated Users</td> - <td>Associated Groups</td> + <td>Users</td> + <td>Groups</td> </tr> %for ctr, role in enumerate( roles ): %if render_quick_find and not role.name.upper().startswith( curr_anchor ): diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/users.mako --- a/templates/admin/dataset_security/users.mako Mon Apr 27 13:33:47 2009 -0400 +++ b/templates/admin/dataset_security/users.mako Mon Apr 27 16:03:44 2009 -0400 @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> ## Render a row -<%def name="render_row( user, groups, roles, ctr, anchored, curr_anchor )"> +<%def name="render_row( user, ctr, anchored, curr_anchor )"> %if ctr % 2 == 1: <tr class="odd_row"> %else: @@ -20,30 +20,10 @@ </div> </td> <td> - <ul> - %for group in groups: - <li> - <a href="${h.url_for( controller='admin', action='group', group_id=group.id )}">${group.name}</a> - <a id="group-${group.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="group-${group.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_group_from_user', user_id=user.id, group_id=group.id )}">Remove group from user</a> - </div> - </li> - %endfor - </ul> + ${len( user.groups )} </td> <td> - <ul> - %for role in roles: - <li> - <a href="${h.url_for( controller='admin', action='role', role_id=role.id )}">${role.name}</a> - <a id="role-${role.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="role-${role.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_user', user_id=user.id, role_id=role.id )}">Remove role from user</a> - </div> - </li> - %endfor - </ul> + ${len( user.roles )} %if not anchored: <a name="${curr_anchor}"></a> <div style="float: right;"><a href="#TOP">top</a></div> @@ -65,12 +45,12 @@ ${render_msg( msg, messagetype )} %endif -%if len( users_groups_roles ) == 0: +%if len( users ) == 0: There are no Galaxy users %else: <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <% - render_quick_find = len( users_groups_roles ) > 50 + render_quick_find = len( users ) > 50 ctr = 0 %> %if render_quick_find: @@ -91,34 +71,29 @@ %endif <tr class="header"> <td>Email</td> - <td>Associated Groups</td> - <td>Associated Roles</td> + <td>Groups</td> + <td>Roles</td> </tr> - %for ctr, user_tuple in enumerate( users_groups_roles ): - <% - user = user_tuple[0] - groups = user_tuple[1] - roles = user_tuple[2] - %> + %for ctr, user in enumerate( users ): %if render_quick_find and not user.email.upper().startswith( curr_anchor ): <% anchored = False %> %endif %if render_quick_find and user.email.upper().startswith( curr_anchor ): %if not anchored: - ${render_row( user, groups, roles, ctr, anchored, curr_anchor )} + ${render_row( user, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( user, groups, roles, ctr, anchored, curr_anchor )} + ${render_row( user, ctr, anchored, curr_anchor )} %endif %elif render_quick_find: %for anchor in anchors[ anchor_loc: ]: %if user.email.upper().startswith( anchor ): %if not anchored: <% curr_anchor = anchor %> - ${render_row( user, groups, roles, ctr, anchored, curr_anchor )} + ${render_row( user, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( user, groups, roles, ctr, anchored, curr_anchor )} + ${render_row( user, ctr, anchored, curr_anchor )} %endif <% anchor_loc = anchors.index( anchor ) @@ -127,7 +102,7 @@ %endif %endfor %else: - ${render_row( user, groups, roles, ctr, True, '' )} + ${render_row( user, ctr, True, '' )} %endif %endfor </table> diff -r 22118cf46b0a -r d0c905db68db test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Apr 27 13:33:47 2009 -0400 +++ b/test/base/twilltestcase.py Mon Apr 27 16:03:44 2009 -0400 @@ -787,29 +787,6 @@ self.check_page_for_string( check_str ) self.home() - # Utility methods to test removal of associations - def remove_role_from_group( self, role_id, role_name, group_id, group_name ): - """Remove a role from a group""" - self.home() - self.visit_url( "%s/admin/remove_role_from_group?role_id=%s&group_id=%s" % ( self.url, role_id, group_id ) ) - check_str = "Role '%s' removed from group '%s'" % ( role_name, group_name ) - self.check_page_for_string( check_str ) - self.home() - def remove_user_from_group( self, user_id, email, group_id, group_name ): - """Remove a user from a group""" - self.home() - self.visit_url( "%s/admin/remove_user_from_group?user_id=%s&group_id=%s" % ( self.url, user_id, group_id ) ) - check_str = "User '%s' removed from group '%s'" % ( email, group_name ) - self.check_page_for_string( check_str ) - self.home() - def remove_user_from_role( self, user_id, email, role_id, role_name ): - """Remove a user from a role""" - self.home() - self.visit_url( "%s/admin/remove_user_from_role?user_id=%s&role_id=%s" % ( self.url, user_id, role_id ) ) - check_str = "User '%s' removed from role '%s'" % ( email, role_name ) - self.check_page_for_string( check_str ) - self.home() - # Library stuff def create_library( self, name='Library One', description='This is Library One' ): """Create a new library""" diff -r 22118cf46b0a -r d0c905db68db tools/stats/column_maker.py --- a/tools/stats/column_maker.py Mon Apr 27 13:33:47 2009 -0400 +++ b/tools/stats/column_maker.py Mon Apr 27 16:03:44 2009 -0400 @@ -13,10 +13,6 @@ sys.stderr.write( msg ) sys.exit() -data_err = "This tool can only be used with tab-delimited data." -columns_err = "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. " -column_types_err = "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. " -invalid_metadata_err = "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. " inp_file = sys.argv[1] out_file = sys.argv[2] expr = sys.argv[3] @@ -24,16 +20,16 @@ try: in_columns = int( sys.argv[5] ) except: - stop_err( columns_err + data_err ) + stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." ) if in_columns < 2: # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method. - stop_err( columns_err + data_err ) + stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." ) try: in_column_types = sys.argv[6].split( ',' ) except: - stop_err( column_types_err + data_err ) + stop_err( "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." ) if len( in_column_types ) != in_columns: - stop_err( invalid_metadata_err + data_err ) + stop_err( "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." ) # Unescape if input has been escaped mapped_str = {

1 0

[hg] galaxy 2378: Updated bx-python.
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e0534b25c282 changeset: 2378:e0534b25c282 user: guru date: Tue Apr 28 15:32:44 2009 -0400 description: Updated bx-python. 1 file(s) affected in this change: eggs.ini diffs (19 lines): diff -r 635d97a3a228 -r e0534b25c282 eggs.ini --- a/eggs.ini Tue Apr 28 14:18:21 2009 -0400 +++ b/eggs.ini Tue Apr 28 15:32:44 2009 -0400 @@ -59,13 +59,13 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r130f083b56b9 +bx_python = _dev_r4bf1f32e6b76 nose = .dev_r101 ; source location, necessary for scrambling [source] numpy = http://downloads.sourceforge.net/numpy/numpy-1.2.1.tar.gz -bx_python = http://bitbucket.org/james_taylor/bx-python/get/130f083b56b9.bz2 +bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz

1 0

[hg] galaxy 2377: Fix a problem with dynamic selects depending o...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/635d97a3a228 changeset: 2377:635d97a3a228 user: James Taylor <james(a)jamestaylor.org> date: Tue Apr 28 14:18:21 2009 -0400 description: Fix a problem with dynamic selects depending on other dynamic selects when setting values at runtime in workflows 2 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/tools/parameters/basic.py diffs (43 lines): diff -r 87885ab394a0 -r 635d97a3a228 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue Apr 28 09:44:35 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Tue Apr 28 14:18:21 2009 -0400 @@ -686,12 +686,12 @@ # to determine the current case test_value = input.test_param.get_initial_value( trans, context ) current_case = input.get_current_case( test_value, trans ) - # Recursively fill in state for selected case - self.fill_in_new_state( trans, input.cases[current_case].inputs, s, context ) # Store the current case in a special value s['__current_case__'] = current_case # Store the value of the test element s[ input.test_param.name ] = test_value + # Recursively fill in state for selected case + self.fill_in_new_state( trans, input.cases[current_case].inputs, s, context ) else: # `input` is just a plain parameter, get its default value state[ input.name ] = input.get_initial_value( trans, context ) diff -r 87885ab394a0 -r 635d97a3a228 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Tue Apr 28 09:44:35 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Tue Apr 28 14:18:21 2009 -0400 @@ -569,6 +569,11 @@ def value_to_basic( self, value, app ): if isinstance( value, UnvalidatedValue ): return { "__class__": "UnvalidatedValue", "value": value.value } + elif isinstance( value, RuntimeValue ): + # Need to handle runtime value's ourself since delegating to the + # parent method causes the value to be turned into a string, which + # breaks multiple selection + return { "__class__": "RuntimeValue" } return value def value_from_basic( self, value, app, ignore_errors=False ): if isinstance( value, dict ) and value["__class__"] == "UnvalidatedValue": @@ -598,6 +603,9 @@ dep_value = context[ dep_name ] # Dependency on a dataset that does not yet exist if isinstance( dep_value, DummyDataset ): + return True + # Dependency on a value that has not been checked + if isinstance( dep_value, UnvalidatedValue ): return True # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ):

1 0

[hg] galaxy 2375: Remove direct references of the model from the...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7fd4f748b0ca changeset: 2375:7fd4f748b0ca user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Apr 27 16:30:08 2009 -0400 description: Remove direct references of the model from the the cleanup_datasets_fix migration script. 1 file(s) affected in this change: lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py diffs (709 lines): diff -r d0c905db68db -r 7fd4f748b0ca lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Mon Apr 27 16:30:08 2009 -0400 @@ -0,0 +1,705 @@ +import sys, logging, os, time, datetime, errno + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +from migrate import migrate_engine +from sqlalchemy import and_ + +from sqlalchemy import * +now = datetime.datetime.utcnow +from sqlalchemy.orm import * + +from galaxy.model.orm.ext.assignmapper import assign_mapper + +from galaxy.model.custom_types import * + +from galaxy.util.bunch import Bunch + + +metadata = MetaData( migrate_engine ) +context = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) + + +## classes +def get_permitted_actions( **kwds ): + return Bunch() + +def directory_hash_id( id ): + s = str( id ) + l = len( s ) + # Shortcut -- ids 0-999 go under ../000/ + if l < 4: + return [ "000" ] + # Pad with zeros until a multiple of three + padded = ( ( 3 - len( s ) % 3 ) * "0" ) + s + # Drop the last three digits -- 1000 files per directory + padded = padded[:-3] + # Break into chunks of three + return [ padded[i*3:(i+1)*3] for i in range( len( padded ) // 3 ) ] + + +class Dataset( object ): + states = Bunch( NEW = 'new', + UPLOAD = 'upload', + QUEUED = 'queued', + RUNNING = 'running', + OK = 'ok', + EMPTY = 'empty', + ERROR = 'error', + DISCARDED = 'discarded' ) + permitted_actions = get_permitted_actions( filter='DATASET' ) + file_path = "/tmp/" + engine = None + def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True ): + self.id = id + self.state = state + self.deleted = False + self.purged = False + self.purgable = purgable + self.external_filename = external_filename + self._extra_files_path = extra_files_path + self.file_size = file_size + def get_file_name( self ): + if not self.external_filename: + assert self.id is not None, "ID must be set before filename used (commit the object)" + # First try filename directly under file_path + filename = os.path.join( self.file_path, "dataset_%d.dat" % self.id ) + # Only use that filename if it already exists (backward compatibility), + # otherwise construct hashed path + if not os.path.exists( filename ): + dir = os.path.join( self.file_path, *directory_hash_id( self.id ) ) + # Create directory if it does not exist + try: + os.makedirs( dir ) + except OSError, e: + # File Exists is okay, otherwise reraise + if e.errno != errno.EEXIST: + raise + # Return filename inside hashed directory + return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) ) + else: + filename = self.external_filename + # Make filename absolute + return os.path.abspath( filename ) + def set_file_name ( self, filename ): + if not filename: + self.external_filename = None + else: + self.external_filename = filename + file_name = property( get_file_name, set_file_name ) + @property + def extra_files_path( self ): + if self._extra_files_path: + path = self._extra_files_path + else: + path = os.path.join( self.file_path, "dataset_%d_files" % self.id ) + #only use path directly under self.file_path if it exists + if not os.path.exists( path ): + path = os.path.join( os.path.join( self.file_path, *directory_hash_id( self.id ) ), "dataset_%d_files" % self.id ) + # Make path absolute + return os.path.abspath( path ) + def get_size( self ): + """Returns the size of the data on disk""" + if self.file_size: + return self.file_size + else: + try: + return os.path.getsize( self.file_name ) + except OSError: + return 0 + def set_size( self ): + """Returns the size of the data on disk""" + try: + if not self.file_size: + self.file_size = os.path.getsize( self.file_name ) + except OSError: + self.file_size = 0 + def has_data( self ): + """Detects whether there is any data""" + return self.get_size() > 0 + def mark_deleted( self, include_children=True ): + self.deleted = True + # FIXME: sqlalchemy will replace this + def _delete(self): + """Remove the file that corresponds to this data""" + try: + os.remove(self.data.file_name) + except OSError, e: + log.critical('%s delete error %s' % (self.__class__.__name__, e)) + +class DatasetInstance( object ): + """A base class for all 'dataset instances', HDAs, LDAs, etc""" + states = Dataset.states + permitted_actions = Dataset.permitted_actions + 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 ): + self.name = name or "Unnamed dataset" + self.id = id + self.info = info + self.blurb = blurb + self.peek = peek + self.extension = extension + self.designation = designation + self.metadata = metadata or dict() + if dbkey: #dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata' + self.dbkey = dbkey + self.deleted = deleted + self.visible = visible + # Relationships + if not dataset and create_dataset: + dataset = Dataset( state=Dataset.states.NEW ) + dataset.flush() + self.dataset = dataset + self.parent_id = parent_id + self.validation_errors = validation_errors + @property + def ext( self ): + return self.extension + def get_dataset_state( self ): + return self.dataset.state + def set_dataset_state ( self, state ): + self.dataset.state = state + self.dataset.flush() #flush here, because hda.flush() won't flush the Dataset object + state = property( get_dataset_state, set_dataset_state ) + def get_file_name( self ): + return self.dataset.get_file_name() + def set_file_name (self, filename): + return self.dataset.set_file_name( filename ) + file_name = property( get_file_name, set_file_name ) + @property + def extra_files_path( self ): + return self.dataset.extra_files_path + @property + def datatype( self ): + return datatypes_registry.get_datatype_by_extension( self.extension ) + def get_metadata( self ): + if not hasattr( self, '_metadata_collection' ) or self._metadata_collection.parent != self: #using weakref to store parent (to prevent circ ref), does a context.clear() cause parent to be invalidated, while still copying over this non-database attribute? + self._metadata_collection = MetadataCollection( self ) + return self._metadata_collection + def set_metadata( self, bunch ): + # Needs to accept a MetadataCollection, a bunch, or a dict + self._metadata = self.metadata.make_dict_copy( bunch ) + metadata = property( get_metadata, set_metadata ) + # This provide backwards compatibility with using the old dbkey + # field in the database. That field now maps to "old_dbkey" (see mapping.py). + def get_dbkey( self ): + dbkey = self.metadata.dbkey + if not isinstance(dbkey, list): dbkey = [dbkey] + if dbkey in [[None], []]: return "?" + return dbkey[0] + def set_dbkey( self, value ): + if "dbkey" in self.datatype.metadata_spec: + if not isinstance(value, list): + self.metadata.dbkey = [value] + else: + self.metadata.dbkey = value + dbkey = property( get_dbkey, set_dbkey ) + def change_datatype( self, new_ext ): + self.clear_associated_files() + datatypes_registry.change_datatype( self, new_ext ) + def get_size( self ): + """Returns the size of the data on disk""" + return self.dataset.get_size() + def set_size( self ): + """Returns the size of the data on disk""" + return self.dataset.set_size() + def has_data( self ): + """Detects whether there is any data""" + return self.dataset.has_data() + def get_raw_data( self ): + """Returns the full data. To stream it open the file_name and read/write as needed""" + return self.datatype.get_raw_data( self ) + def write_from_stream( self, stream ): + """Writes data from a stream""" + self.datatype.write_from_stream(self, stream) + def set_raw_data( self, data ): + """Saves the data on the disc""" + self.datatype.set_raw_data(self, data) + def get_mime( self ): + """Returns the mime type of the data""" + return datatypes_registry.get_mimetype_by_extension( self.extension.lower() ) + def set_peek( self ): + return self.datatype.set_peek( self ) + def set_multi_byte_peek( self ): + return self.datatype.set_multi_byte_peek( self ) + def init_meta( self, copy_from=None ): + return self.datatype.init_meta( self, copy_from=copy_from ) + def set_meta( self, **kwd ): + self.clear_associated_files( metadata_safe = True ) + return self.datatype.set_meta( self, **kwd ) + def set_readonly_meta( self, **kwd ): + return self.datatype.set_readonly_meta( self, **kwd ) + def missing_meta( self, **kwd ): + return self.datatype.missing_meta( self, **kwd ) + def as_display_type( self, type, **kwd ): + return self.datatype.as_display_type( self, type, **kwd ) + def display_peek( self ): + return self.datatype.display_peek( self ) + def display_name( self ): + return self.datatype.display_name( self ) + def display_info( self ): + return self.datatype.display_info( self ) + def get_converted_files_by_type( self, file_type ): + valid = [] + for assoc in self.implicitly_converted_datasets: + if not assoc.deleted and assoc.type == file_type: + valid.append( assoc.dataset ) + return valid + def clear_associated_files( self, metadata_safe = False, purge = False ): + raise 'Unimplemented' + def get_child_by_designation(self, designation): + for child in self.children: + if child.designation == designation: + return child + return None + def get_converter_types(self): + return self.datatype.get_converter_types( self, datatypes_registry) + def find_conversion_destination( self, accepted_formats, **kwd ): + """Returns ( target_ext, exisiting converted dataset )""" + return self.datatype.find_conversion_destination( self, accepted_formats, datatypes_registry, **kwd ) + def add_validation_error( self, validation_error ): + self.validation_errors.append( validation_error ) + def extend_validation_errors( self, validation_errors ): + self.validation_errors.extend(validation_errors) + def mark_deleted( self, include_children=True ): + self.deleted = True + if include_children: + for child in self.children: + child.mark_deleted() + def mark_undeleted( self, include_children=True ): + self.deleted = False + if include_children: + for child in self.children: + child.mark_undeleted() + def undeletable( self ): + if self.purged: + return False + return True + @property + def source_library_dataset( self ): + def get_source( dataset ): + if isinstance( dataset, LibraryDatasetDatasetAssociation ): + if dataset.library_dataset: + return ( dataset, dataset.library_dataset ) + if dataset.copied_from_library_dataset_dataset_association: + source = get_source( dataset.copied_from_library_dataset_dataset_association ) + if source: + return source + if dataset.copied_from_history_dataset_association: + source = get_source( dataset.copied_from_history_dataset_association ) + if source: + return source + return ( None, None ) + return get_source( self ) + + +class HistoryDatasetAssociation( DatasetInstance ): + def __init__( self, + hid = None, + history = None, + copied_from_history_dataset_association = None, + copied_from_library_dataset_dataset_association = None, + **kwd ): + DatasetInstance.__init__( self, **kwd ) + self.hid = hid + # Relationships + self.history = history + self.copied_from_history_dataset_association = copied_from_history_dataset_association + self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association + def copy( self, copy_children = False, parent_id = None, target_history = None ): + hda = HistoryDatasetAssociation( hid=self.hid, + name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + extension=self.extension, + dbkey=self.dbkey, + dataset = self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, + copied_from_history_dataset_association=self, + history = target_history ) + hda.flush() + hda.set_size() + # Need to set after flushed, as MetadataFiles require dataset.id + hda.metadata = self.metadata + if copy_children: + for child in self.children: + child_copy = child.copy( copy_children = copy_children, parent_id = hda.id ) + if not self.datatype.copy_safe_peek: + # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs + hda.set_peek() + hda.flush() + return hda + def to_library_dataset_dataset_association( self, target_folder, replace_dataset=None, parent_id=None ): + if replace_dataset: + # The replace_dataset param ( when not None ) refers to a LibraryDataset that is being replaced with a new version. + library_dataset = replace_dataset + else: + # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new + # LibraryDataset, and the current user's DefaultUserPermissions will be applied to the associated Dataset. + library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info ) + library_dataset.flush() + ldda = LibraryDatasetDatasetAssociation( name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, + library_dataset=library_dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, + copied_from_history_dataset_association=self, + user=self.history.user ) + ldda.flush() + # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset + # Must set metadata after ldda flushed, as MetadataFiles require ldda.id + ldda.metadata = self.metadata + if not replace_dataset: + target_folder.add_library_dataset( library_dataset, genome_build=ldda.dbkey ) + target_folder.flush() + library_dataset.library_dataset_dataset_association_id = ldda.id + library_dataset.flush() + for child in self.children: + child_copy = child.to_library_dataset_dataset_association( target_folder=target_folder, replace_dataset=replace_dataset, parent_id=ldda.id ) + if not self.datatype.copy_safe_peek: + # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs + ldda.set_peek() + ldda.flush() + return ldda + def clear_associated_files( self, metadata_safe = False, purge = False ): + # metadata_safe = True means to only clear when assoc.metadata_safe == False + for assoc in self.implicitly_converted_datasets: + if not metadata_safe or not assoc.metadata_safe: + assoc.clear( purge = purge ) + + + +class LibraryDatasetDatasetAssociation( DatasetInstance ): + def __init__( self, + copied_from_history_dataset_association=None, + copied_from_library_dataset_dataset_association=None, + library_dataset=None, + user=None, + **kwd ): + DatasetInstance.__init__( self, **kwd ) + self.copied_from_history_dataset_association = copied_from_history_dataset_association + self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association + self.library_dataset = library_dataset + self.user = user + def to_history_dataset_association( self, target_history, parent_id=None ): + hid = target_history._next_hid() + hda = HistoryDatasetAssociation( name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, + copied_from_library_dataset_dataset_association=self, + history=target_history, + hid=hid ) + hda.flush() + hda.metadata = self.metadata #need to set after flushed, as MetadataFiles require dataset.id + for child in self.children: + child_copy = child.to_history_dataset_association( target_history=target_history, parent_id=hda.id ) + if not self.datatype.copy_safe_peek: + hda.set_peek() #in some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs + hda.flush() + return hda + def copy( self, copy_children = False, parent_id = None, target_folder = None ): + ldda = LibraryDatasetDatasetAssociation( name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, + copied_from_library_dataset_dataset_association=self, + folder=target_folder ) + ldda.flush() + # Need to set after flushed, as MetadataFiles require dataset.id + ldda.metadata = self.metadata + if copy_children: + for child in self.children: + child_copy = child.copy( copy_children = copy_children, parent_id = ldda.id ) + if not self.datatype.copy_safe_peek: + # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs + ldda.set_peek() + ldda.flush() + return ldda + def clear_associated_files( self, metadata_safe = False, purge = False ): + return + def get_library_item_info_templates( self, template_list=[], restrict=False ): + # If restrict is True, we'll return only those templates directly associated with this LibraryDatasetDatasetAssociation + if self.library_dataset_dataset_info_template_associations: + template_list.extend( [ lddita.library_item_info_template for lddita in self.library_dataset_dataset_info_template_associations if lddita.library_item_info_template not in template_list ] ) + self.library_dataset.get_library_item_info_templates( template_list, restrict ) + return template_list + + + +class LibraryDataset( object ): + # This class acts as a proxy to the currently selected LDDA + def __init__( self, folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd ): + self.folder = folder + self.order_id = order_id + self.name = name + self.info = info + self.library_dataset_dataset_association = library_dataset_dataset_association + def set_library_dataset_dataset_association( self, ldda ): + self.library_dataset_dataset_association = ldda + ldda.library_dataset = self + ldda.flush() + self.flush() + def get_info( self ): + if self.library_dataset_dataset_association: + return self.library_dataset_dataset_association.info + elif self._info: + return self._info + else: + return 'no info' + def set_info( self, info ): + self._info = info + info = property( get_info, set_info ) + def get_name( self ): + if self.library_dataset_dataset_association: + return self.library_dataset_dataset_association.name + elif self._name: + return self._name + else: + return 'Unnamed dataset' + def set_name( self, name ): + self._name = name + name = property( get_name, set_name ) + def display_name( self ): + self.library_dataset_dataset_association.display_name() + def get_purged( self ): + return self.library_dataset_dataset_association.dataset.purged + def set_purged( self, purged ): + if purged: + raise Exception( "Not implemented" ) + if not purged and self.purged: + raise Exception( "Cannot unpurge once purged" ) + purged = property( get_purged, set_purged ) + def get_library_item_info_templates( self, template_list=[], restrict=False ): + # If restrict is True, we'll return only those templates directly associated with this LibraryDataset + if self.library_dataset_info_template_associations: + template_list.extend( [ ldita.library_item_info_template for ldita in self.library_dataset_info_template_associations if ldita.library_item_info_template not in template_list ] ) + if restrict not in [ 'True', True ]: + self.folder.get_library_item_info_templates( template_list, restrict ) + return template_list + +##tables + + +Dataset.table = Table( "dataset", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "state", TrimmedString( 64 ) ), + Column( "deleted", Boolean, index=True, default=False ), + Column( "purged", Boolean, index=True, default=False ), + Column( "purgable", Boolean, default=True ), + Column( "external_filename" , TEXT ), + Column( "_extra_files_path", TEXT ), + Column( 'file_size', Numeric( 15, 0 ) ) ) + + + +HistoryDatasetAssociation.table = Table( "history_dataset_association", metadata, + Column( "id", Integer, primary_key=True ), + 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( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), + Column( "hid", Integer ), + Column( "name", TrimmedString( 255 ) ), + Column( "info", TrimmedString( 255 ) ), + Column( "blurb", TrimmedString( 255 ) ), + Column( "peek" , TEXT ), + Column( "extension", TrimmedString( 64 ) ), + Column( "metadata", MetadataType(), key="_metadata" ), + Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), + Column( "designation", TrimmedString( 255 ) ), + Column( "deleted", Boolean, index=True, default=False ), + Column( "visible", Boolean ) ) + + +LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), index=True ), + 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", use_alter=True, name='history_dataset_association_dataset_id_fkey' ), nullable=True ), + Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name='library_dataset_dataset_association_id_fkey' ), nullable=True ), + Column( "name", TrimmedString( 255 ) ), + Column( "info", TrimmedString( 255 ) ), + Column( "blurb", TrimmedString( 255 ) ), + Column( "peek" , TEXT ), + Column( "extension", TrimmedString( 64 ) ), + Column( "metadata", MetadataType(), key="_metadata" ), + Column( "parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), + Column( "designation", TrimmedString( 255 ) ), + Column( "deleted", Boolean, index=True, default=False ), + Column( "visible", Boolean ), + Column( "message", TrimmedString( 255 ) ) ) + +LibraryDataset.table = Table( "library_dataset", metadata, + Column( "id", Integer, primary_key=True ), + Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk" ), nullable=True, index=True ),#current version of dataset, if null, there is not a current version selected + Column( "order_id", Integer ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "name", TrimmedString( 255 ), key="_name" ), #when not None/null this will supercede display in library (but not when imported into user's history?) + Column( "info", TrimmedString( 255 ), key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?) + Column( "deleted", Boolean, index=True, default=False ) ) + + + +##mappers + + +assign_mapper( context, Dataset, Dataset.table, + properties=dict( + history_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ) ), + active_history_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( ( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ) & ( HistoryDatasetAssociation.table.c.deleted == False ) ) ), + library_associations=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) ), + active_library_associations=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( ( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) & ( LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) ) + ) ) + + +assign_mapper( context, HistoryDatasetAssociation, HistoryDatasetAssociation.table, + properties=dict( + dataset=relation( + Dataset, + primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ), + # .history defined in History mapper + 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], uselist=False ) ), + copied_to_library_dataset_dataset_associations=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + children=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), + backref=backref( "parent", primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id], uselist=False ) ), + visible_children=relation( + HistoryDatasetAssociation, + primaryjoin=( ( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ) & ( HistoryDatasetAssociation.table.c.visible == True ) ) ) + ) ) + +assign_mapper( context, LibraryDatasetDatasetAssociation, LibraryDatasetDatasetAssociation.table, + properties=dict( + dataset=relation( Dataset ), + library_dataset = relation( LibraryDataset, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.library_dataset_id == LibraryDataset.table.c.id ) ), + copied_to_library_dataset_dataset_associations=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), + copied_to_history_dataset_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + children=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ), + backref=backref( "parent", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), + visible_children=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ) + ) ) + +assign_mapper( context, LibraryDataset, LibraryDataset.table, + properties=dict( + library_dataset_dataset_association=relation( LibraryDatasetDatasetAssociation, primaryjoin=( LibraryDataset.table.c.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), + expired_datasets = relation( LibraryDatasetDatasetAssociation, foreign_keys=[LibraryDataset.table.c.id,LibraryDataset.table.c.library_dataset_dataset_association_id ], primaryjoin=( ( LibraryDataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.library_dataset_id ) & ( not_( LibraryDataset.table.c.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ) ), viewonly=True, uselist=True ) + ) ) + + +def __guess_dataset_by_filename( filename ): + """Return a guessed dataset by filename""" + try: + fields = os.path.split( filename ) + if fields: + if fields[-1].startswith( 'dataset_' ) and fields[-1].endswith( '.dat' ): #dataset_%d.dat + return Dataset.get( int( fields[-1][ len( 'dataset_' ): -len( '.dat' ) ] ) ) + except: + pass #some parsing error, we can't guess Dataset + return None + +def upgrade(): + log.debug( "Fixing a discrepancy concerning deleted shared history items." ) + affected_items = 0 + start_time = time.time() + for dataset in Dataset.filter( and_( Dataset.c.deleted == True, Dataset.c.purged == False ) ).all(): + for dataset_instance in dataset.history_associations + dataset.library_associations: + if not dataset_instance.deleted: + dataset.deleted = False + if dataset.file_size in [ None, 0 ]: + dataset.set_size() #Restore filesize + affected_items += 1 + break + context.flush() + log.debug( "%i items affected, and restored." % ( affected_items ) ) + log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) + + #fix share before hda + log.debug( "Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs." ) + dataset_by_filename = {} + changed_associations = 0 + start_time = time.time() + for dataset in Dataset.filter( Dataset.external_filename.like( '%dataset_%.dat' ) ).all(): + if dataset.file_name in dataset_by_filename: + guessed_dataset = dataset_by_filename[ dataset.file_name ] + else: + guessed_dataset = __guess_dataset_by_filename( dataset.file_name ) + if guessed_dataset and dataset.file_name != guessed_dataset.file_name:#not os.path.samefile( dataset.file_name, guessed_dataset.file_name ): + guessed_dataset = None + dataset_by_filename[ dataset.file_name ] = guessed_dataset + + if guessed_dataset is not None and guessed_dataset.id != dataset.id: #could we have a self referential dataset? + for dataset_instance in dataset.history_associations + dataset.library_associations: + dataset_instance.dataset = guessed_dataset + changed_associations += 1 + #mark original Dataset as deleted and purged, it is no longer in use, but do not delete file_name contents + dataset.deleted = True + dataset.external_filename = "Dataset was result of share before HDA, and has been replaced: %s mapped to Dataset %s" % ( dataset.external_filename, guessed_dataset.id ) + dataset.purged = True #we don't really purge the file here, but we mark it as purged, since this dataset is now defunct + context.flush() + log.debug( "%i items affected, and restored." % ( changed_associations ) ) + log.debug( "Time elapsed: %s" % ( time.time() - start_time ) ) + +def downgrade(): + log.debug( "Downgrade is not possible." ) +

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