November 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Updates for GATK tools.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9ee4e2e41fd6/ changeset: 9ee4e2e41fd6 user: dan date: 2011-11-29 22:45:37 summary: Updates for GATK tools. affected #: 2 files diff -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 -r 9ee4e2e41fd60c75c2b87d55648c538438809430 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -1,4 +1,4 @@ -<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.4"> +<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.5"><description>SNP and indel caller</description><requirements><requirement type="package" version="1.3">gatk</requirement> @@ -122,7 +122,18 @@ --group "${group}" #end for #end if + #if str( $analysis_param_type.exclude_annotations ) != "None": + #for $annotation in str( $analysis_param_type.exclude_annotations ).split( ','): + --excludeAnnotation "${annotation}" + #end for + #end if ' +## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': +## -p '--annotation "SnpEff"' +## -d "--snpEffFile:${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod}" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name}" +## #else: +## -p '--excludeAnnotation "SnpEff"' +## #end if #end if </command><inputs> @@ -354,42 +365,91 @@ <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /><param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /><param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> - <option value="ChromosomeCounts"/> - <option value="IndelType"/> - <option value="SpanningDeletions"/> - <option value="HardyWeinberg"/> - <option value="NBaseCount"/> - <option value="MappingQualityZero"/> - <option value="AlleleBalance"/> - <option value="BaseCounts"/> - <option value="LowMQ"/> - <option value="InbreedingCoeff"/> - <option value="RMSMappingQuality"/> - <option value="HaplotypeScore"/> - <option value="TechnologyComposition"/> - <option value="SampleList"/> - <option value="FisherStrand"/> - <option value="HomopolymerRun"/> - <option value="DepthOfCoverage"/> - <option value="SnpEff"/> - <option value="MappingQualityZeroFraction"/> - <option value="GCContent"/> - <option value="MappingQualityRankSumTest"/> - <option value="ReadPosRankSumTest"/> - <option value="BaseQualityRankSumTest"/> - <option value="QualByDepth"/> - <option value="SBByDepth"/> - <option value="ReadDepthAndAllelicFractionBySample"/> - <option value="AlleleBalanceBySample"/> - <option value="DepthPerAlleleBySample"/> - <option value="MappingQualityZeroBySample"/> + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> +  + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /></param> +<param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"> - <option value="Standard">Standard</option> - <option value="Experimental">Experimental</option> - <option value="WorkInProgress">WorkInProgress</option> -  + <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> + <option value="Standard">Standard</option> + <option value="Experimental">Experimental</option> + <option value="WorkInProgress">WorkInProgress</option> + <option value="RankSumTest">RankSumTest</option> + </param> +  + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > +  + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> +  + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /> + </param></when></conditional></inputs> diff -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 -r 9ee4e2e41fd60c75c2b87d55648c538438809430 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -1,4 +1,4 @@ -<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.3"> +<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.4"><description></description><requirements><requirement type="package" version="1.3">gatk</requirement> @@ -13,6 +13,7 @@ -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" + ##--list -T "VariantAnnotator" ##--num_threads 4 ##hard coded, for now -et "NO_ET" ##ET no phone home @@ -30,6 +31,11 @@ #end for #end if #end if + #if str( $exclude_annotations ) != "None": + #for $annotation in str( $exclude_annotations ).split( ',' ): + --excludeAnnotation "${annotation}" + #end for + #end if ## #for $additional_annotation in $additional_annotations: ## --annotation "${additional_annotation.additional_annotation_type.additional_annotation_type_selector}" ## #for $name, $param in $additional_annotation.additional_annotation_type.iteritems(): @@ -55,7 +61,10 @@ #end for #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': - -d "--snpEff:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}" + -p '--annotation "SnpEff"' + -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}" + #else: + -p '--excludeAnnotation "SnpEff"' #end if #for $expression in $expressions: @@ -124,6 +133,10 @@ --group "${group}" #end for #end if + #if str( $family_string ) != "": + --family_string "${family_string}" + #end if + --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}" ' </command><inputs> @@ -166,35 +179,35 @@ <when value="choose"><param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" > - <option value="ChromosomeCounts"/> - <option value="IndelType"/> - <option value="SpanningDeletions"/> - <option value="HardyWeinberg"/> - <option value="NBaseCount"/> - <option value="MappingQualityZero"/> - <option value="AlleleBalance"/> - <option value="BaseCounts"/> - <option value="LowMQ"/> - <option value="InbreedingCoeff"/> - <option value="RMSMappingQuality"/> - <option value="HaplotypeScore"/> - <option value="TechnologyComposition"/> - <option value="SampleList"/> - <option value="FisherStrand"/> - <option value="HomopolymerRun"/> - <option value="DepthOfCoverage"/> - <option value="SnpEff"/> - <option value="MappingQualityZeroFraction"/> - <option value="GCContent"/> - <option value="MappingQualityRankSumTest"/> - <option value="ReadPosRankSumTest"/> - <option value="BaseQualityRankSumTest"/> - <option value="QualByDepth"/> - <option value="SBByDepth"/> - <option value="ReadDepthAndAllelicFractionBySample"/> - <option value="AlleleBalanceBySample"/> - <option value="DepthPerAlleleBySample"/> - <option value="MappingQualityZeroBySample"/> + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> + <option value="SnpEff" /> + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /></param></when></conditional> @@ -371,7 +384,41 @@ <option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option></param> - + <param name="family_string" type="text" value="" label="Family String"/> + <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio."/> + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > +  + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> + <option value="SnpEff" /> + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /> + </param> + </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Updates for 'GenomeSpace import from file browser' tools.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/347cd30ff32f/ changeset: 347cd30ff32f user: dan date: 2011-11-29 19:41:40 summary: Updates for 'GenomeSpace import from file browser' tools. affected #: 2 files diff -r 9301e65263cf292d2f047b075aaf067444f60c73 -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 tools/data_source/genomespace_file_browser_prod.xml --- a/tools/data_source/genomespace_file_browser_prod.xml +++ b/tools/data_source/genomespace_file_browser_prod.xml @@ -4,7 +4,7 @@ <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "prod"</command><inputs action="https://dm.genomespace.org/datamanager/defaultdirectory" check_values="False" method="post"><display>go to GenomeSpace Data Manager </display> - <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&runtool_btn=Execute" /> + <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_prod&runtool_btn=Execute" /><param name="appName" type="hidden" value="Galaxy" /></inputs><uihints minwidth="800"/> diff -r 9301e65263cf292d2f047b075aaf067444f60c73 -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 tools/data_source/genomespace_file_browser_test.xml --- a/tools/data_source/genomespace_file_browser_test.xml +++ b/tools/data_source/genomespace_file_browser_test.xml @@ -4,7 +4,7 @@ <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "test"</command><inputs action="https://dmtest.genomespace.org:8444/datamanager/defaultdirectory" check_values="False" method="post"><display>go to GenomeSpace Data Manager </display> - <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&runtool_btn=Execute" /> + <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_test&runtool_btn=Execute" /><param name="appName" type="hidden" value="Galaxy" /></inputs><uihints minwidth="800"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhance the process for displaying a workflow in a tool shed repository so that workflows in change sets other than the repository tip can be viewed.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9301e65263cf/ changeset: 9301e65263cf user: greg date: 2011-11-29 17:15:10 summary: Enhance the process for displaying a workflow in a tool shed repository so that workflows in change sets other than the repository tip can be viewed. affected #: 3 files diff -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 -r 9301e65263cf292d2f047b075aaf067444f60c73 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -765,6 +765,48 @@ ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None +def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ): + repository = get_repository( trans, repository_id ) + repo = hg.repository( get_configured_ui(), repository.repo_path ) + tool = None + message = '' + if changeset_revision == repository.tip: + try: + tool = load_tool( trans, os.path.abspath( tool_config ) ) + except Exception, e: + tool = None + message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + else: + # Get the tool config file name from the hgweb url, something like: + # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml + old_tool_config_file_name = tool_config.split( '/' )[ -1 ] + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + fctx = None + for filename in ctx: + filename_head, filename_tail = os.path.split( filename ) + if filename_tail == old_tool_config_file_name: + fctx = ctx[ filename ] + break + if fctx: + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + try: + tool = load_tool( trans, tmp_filename ) + except Exception, e: + tool = None + message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + try: + os.unlink( tmp_filename ) + except: + pass + else: + tool = None + return tool, message def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True ): """ Build a SelectField whose options are the changeset_revision diff -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 -r 9301e65263cf292d2f047b075aaf067444f60c73 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1905,46 +1905,7 @@ status = params.get( 'status', 'done' ) webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, repository_id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) - valid = True - if changeset_revision == repository.tip: - try: - tool = load_tool( trans, os.path.abspath( tool_config ) ) - except Exception, e: - tool = None - valid = False - message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) - else: - # Get the tool config file name from the hgweb url, something like: - # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml - old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - fctx = None - for filename in ctx: - filename_head, filename_tail = os.path.split( filename ) - if filename_tail == old_tool_config_file_name: - fctx = ctx[ filename ] - break - if fctx: - # Write the contents of the old tool config to a temporary file. - fh = tempfile.NamedTemporaryFile( 'w' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'w' ) - fh.write( fctx.data() ) - fh.close() - try: - tool = load_tool( trans, tmp_filename ) - except Exception, e: - tool = None - valid = False - message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) - try: - os.unlink( tmp_filename ) - except: - pass - else: - tool = None + tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) try: diff -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 -r 9301e65263cf292d2f047b075aaf067444f60c73 lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -22,13 +22,13 @@ module.state = dict( name="Input Dataset" ) return module @classmethod - def from_dict( Class, trans, d, tools_metadata=None, secure=True ): + def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ): module = Class( trans ) - state = from_json_string( d[ "tool_state" ] ) + state = from_json_string( step_dict[ "tool_state" ] ) module.state = dict( name=state.get( "name", "Input Dataset" ) ) return module @classmethod - def from_workflow_step( Class, trans, tools_metadata, step ): + def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): module = Class( trans ) module.state = dict( name="Input Dataset" ) if step.tool_inputs and "name" in step.tool_inputs: @@ -39,35 +39,38 @@ type = "tool" - def __init__( self, trans, tools_metadata, tool_id ): + def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ): self.trans = trans self.tools_metadata = tools_metadata self.tool_id = tool_id self.tool = None + self.errors = None for tool_dict in tools_metadata: if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: - self.tool = load_tool( trans, os.path.abspath( tool_dict[ 'tool_config' ] ) ) + self.tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] ) + if message and self.tool is None: + self.errors = 'unavailable' + break self.post_job_actions = {} self.workflow_outputs = [] self.state = None - self.errors = None @classmethod - def new( Class, trans, tools_metadata, tool_id=None ): - module = Class( trans, tools_metadata, tool_id ) + def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ): + module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) module.state = module.tool.new_state( trans, all_pages=True ) return module @classmethod - def from_dict( Class, trans, d, tools_metadata, secure=True ): - tool_id = d[ 'tool_id' ] - module = Class( trans, tools_metadata, tool_id ) + def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ): + tool_id = step_dict[ 'tool_id' ] + module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) module.state = DefaultToolState() if module.tool is not None: - module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) - module.errors = d.get( "tool_errors", None ) + module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure ) + module.errors = step_dict.get( "tool_errors", None ) return module @classmethod - def from_workflow_step( Class, trans, tools_metadata, step ): - module = Class( trans, tools_metadata, step.tool_id ) + def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id ) module.state = DefaultToolState() if module.tool: module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) @@ -115,18 +118,18 @@ def __init__( self, module_types ): self.module_types = module_types def new( self, trans, type, tools_metadata=None, tool_id=None ): - """Return module for type and (optional) tool_id intialized with new / default state.""" + """Return module for type and (optional) tool_id initialized with new / default state.""" assert type in self.module_types return self.module_types[type].new( trans, tool_id ) - def from_dict( self, trans, d, **kwargs ): - """Return module initialized from the data in dictionary `d`.""" - type = d[ 'type' ] + def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): + """Return module initialized from the data in dictionary `step_dict`.""" + type = step_dict[ 'type' ] assert type in self.module_types - return self.module_types[ type ].from_dict( trans, d, **kwargs ) - def from_workflow_step( self, trans, tools_metadata, step ): + return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd ) + def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): """Return module initialized from the WorkflowStep object `step`.""" type = step.type - return self.module_types[ type ].from_workflow_step( trans, tools_metadata, step ) + return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) @@ -153,6 +156,8 @@ @web.expose def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ): repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata workflow_name = decode( workflow_name ) for workflow_dict in metadata[ 'workflows' ]: @@ -162,7 +167,7 @@ tools_metadata = metadata[ 'tools' ] else: tools_metadata = [] - workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata ) + workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ) data = [] canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) text = svgfig.SVG( "g" ) @@ -179,7 +184,7 @@ max_width, max_x, max_y = 0, 0, 0 for step in workflow.steps: step.upgrade_messages = {} - module = module_factory.from_workflow_step( trans, tools_metadata, step ) + module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) tool_errors = module.type == 'tool' and not module.tool module_data_inputs = self.__get_data_inputs( step, module ) module_data_outputs = self.__get_data_outputs( step, module, workflow.steps ) @@ -308,11 +313,11 @@ data_outputs.append( data_outputs_dict ) return data_outputs return module.get_data_outputs() - def __workflow_from_dict( self, trans, data, tools_metadata ): + def __workflow_from_dict( self, trans, workflow_dict, tools_metadata, repository_id, changeset_revision ): """Creates and returns workflow object from a dictionary.""" trans.workflow_building_mode = True workflow = model.Workflow() - workflow.name = data[ 'name' ] + workflow.name = workflow_dict[ 'name' ] workflow.has_errors = False steps = [] # Keep ids for each step that we need to use to make connections. @@ -322,12 +327,12 @@ # will be ( tool_id, tool_name, tool_version ). missing_tool_tups = [] # First pass to build step objects and populate basic values - for key, step_dict in data[ 'steps' ].iteritems(): + for key, step_dict in workflow_dict[ 'steps' ].iteritems(): # Create the model class for the step step = model.WorkflowStep() step.name = step_dict[ 'name' ] step.position = step_dict[ 'position' ] - module = module_factory.from_dict( trans, step_dict, tools_metadata=tools_metadata, secure=False ) + module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False ) if module.type == 'tool' and module.tool is None: # A required tool is not available in the current repository. step.tool_errors = 'unavailable' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Make the use of the 'require_login' config setting functionally correct for the tool shed, and debug it's use in the Galaxy framework as well.
by Bitbucket 28 Nov '11

28 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5db0da0007fc/ changeset: 5db0da0007fc user: greg date: 2011-11-28 22:31:04 summary: Make the use of the 'require_login' config setting functionally correct for the tool shed, and debug it's use in the Galaxy framework as well. affected #: 5 files diff -r 3ee9430186fbe87dd2053b0d4efdc00e70a04b45 -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -15,15 +15,11 @@ log = logging.getLogger( __name__ ) require_login_template = """ -<h1>Welcome to Galaxy</h1> - <p> - This installation of Galaxy has been configured such that only users who are logged in may use it.%s + This %s has been configured such that only users who are logged in may use it.%s </p><p/> """ -require_login_nocreation_template = require_login_template % "" -require_login_creation_template = require_login_template % " If you don't already have an account, <a href='%s'>you may create one</a>." OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id', 'Yahoo!' : 'http://yahoo.com', @@ -362,15 +358,23 @@ else: refresh_frames = [ 'masthead', 'history' ] message, status, user, success = self.__validate_login( trans, webapp, **kwd ) - if success and referer and not referer.startswith( trans.request.base + url_for( controller='user', action='logout' ) ): + if success and referer and not referer.startswith( url_for( trans.request.base + url_for( controller='user', action='logout' ) ) ): redirect_url = referer elif success: redirect_url = url_for( '/' ) if not user and trans.app.config.require_login: if trans.app.config.allow_user_creation: - header = require_login_creation_template % web.url_for( action='create', cntrller='user' ) + create_account_str = " If you don't already have an account, <a href='%s'>you may create one</a>." % \ + web.url_for( action='create', cntrller='user', webapp=webapp ) + if webapp == 'galaxy': + header = require_login_template % ( "Galaxy instance", create_account_str ) + else: + header = require_login_template % ( "Galaxy tool shed", create_account_str ) else: - header = require_login_nocreation_template + if webapp == 'galaxy': + header = require_login_template % ( "Galaxy instance", "" ) + else: + header = require_login_template % ( "Galaxy tool shed", "" ) return trans.fill_template( '/user/login.mako', webapp=webapp, email=email, @@ -405,11 +409,12 @@ status = 'error' else: trans.handle_user_login( user, webapp ) - trans.log_event( "User logged in" ) - message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ - ( user.email, referer, url_for( '/' ) ) - if trans.app.config.require_login: - message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) + if webapp == 'galaxy': + trans.log_event( "User logged in" ) + message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ + ( user.email, referer, url_for( '/' ) ) + if trans.app.config.require_login: + message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) success = True return ( message, status, user, success ) @web.expose @@ -419,10 +424,10 @@ refresh_frames = [ 'masthead', 'history', 'tools' ] else: refresh_frames = [ 'masthead', 'history' ] + # Since logging an event requires a session, we'll log prior to ending the session + trans.log_event( "User logged out" ) else: refresh_frames = [ 'masthead' ] - # Since logging an event requires a session, we'll log prior to ending the session - trans.log_event( "User logged out" ) trans.handle_user_logout( logout_all=logout_all ) message = 'You have been logged out.<br>You can log in again, <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ ( trans.request.referer, url_for( '/' ) ) @@ -471,10 +476,8 @@ cntrller, subscribe_checked, **kwd ) - if success and not is_admin and webapp != 'galaxy': - # Must be logging into the community space webapp - trans.handle_user_login( user, webapp ) - redirect_url = referer + if webapp == 'community': + redirect_url = url_for( '/' ) if success and not is_admin: # The handle_user_login() method has a call to the history_set_default_permissions() method # (needed when logging in with a history), user needs to have default permissions set before logging in diff -r 3ee9430186fbe87dd2053b0d4efdc00e70a04b45 -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -404,26 +404,38 @@ # If the old session was invalid, get a new history with our new session if invalidate_existing_session: self.new_history() - def _ensure_logged_in_user( self, environ ): - allowed_paths = ( - url_for( controller='root', action='index' ), - url_for( controller='root', action='tool_menu' ), - url_for( controller='root', action='masthead' ), - url_for( controller='root', action='history' ), - url_for( controller='user', action='login' ), - url_for( controller='user', action='create' ), - url_for( controller='user', action='reset_password' ), - url_for( controller='library', action='browse' ) - ) - display_as = url_for( controller='root', action='display_as' ) - if self.galaxy_session.user is None: - if self.app.config.ucsc_display_sites and self.request.path == display_as: - try: - host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0] - except( socket.error, socket.herror, socket.gaierror, socket.timeout ): - host = None - if host in UCSC_SERVERS: - return + def _ensure_logged_in_user( self, environ, session_cookie ): + # The value of session_cookie can be one of + # 'galaxysession' or 'galaxycommunitysession' + if session_cookie == 'galaxysession': + # TODO: re-engineer to eliminate the use of allowed_paths + # as maintenance overhead is far too high. + allowed_paths = ( + url_for( controller='root', action='index' ), + url_for( controller='root', action='tool_menu' ), + url_for( controller='root', action='masthead' ), + url_for( controller='root', action='history' ), + url_for( controller='user', action='api_keys' ), + url_for( controller='user', action='create' ), + url_for( controller='user', action='index' ), + url_for( controller='user', action='login' ), + url_for( controller='user', action='logout' ), + url_for( controller='user', action='manage_user_info' ), + url_for( controller='user', action='set_default_permissions' ), + url_for( controller='user', action='reset_password' ), + url_for( controller='library', action='browse' ), + url_for( controller='history', action='list' ), + url_for( controller='dataset', action='list' ) + ) + display_as = url_for( controller='root', action='display_as' ) + if self.galaxy_session.user is None: + if self.app.config.ucsc_display_sites and self.request.path == display_as: + try: + host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0] + except( socket.error, socket.herror, socket.gaierror, socket.timeout ): + host = None + if host in UCSC_SERVERS: + return if self.request.path not in allowed_paths: self.response.send_redirect( url_for( controller='root', action='index' ) ) def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ): @@ -857,7 +869,7 @@ if self.app.config.use_remote_user and self.galaxy_session.user.deleted: self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) if self.app.config.require_login: - self._ensure_logged_in_user( environ ) + self._ensure_logged_in_user( environ, session_cookie ) def get_user( self ): """Return the current user if logged in or None.""" return self.galaxy_session.user diff -r 3ee9430186fbe87dd2053b0d4efdc00e70a04b45 -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -10,25 +10,25 @@ <p>You are currently logged in as ${trans.user.email}.</p><ul> %if webapp == 'galaxy': - <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li> - <li><a href="${h.url_for( controller='user', action='set_default_permissions', cntrller=cntrller )}">${_('Change default permissions')}</a> for new histories</li> + <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, webapp=webapp )}">${_('Manage your information')}</a></li> + <li><a href="${h.url_for( controller='user', action='set_default_permissions', cntrller=cntrller, webapp=webapp )}">${_('Change default permissions')}</a> for new histories</li> %if trans.app.config.enable_api: - <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li> + <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller, webapp=webapp )}">${_('Manage your API keys')}</a></li> %endif %if trans.app.config.enable_openid: - <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${_('Manage OpenIDs')}</a> linked to your account</li> + <li><a href="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller, webapp=webapp )}">${_('Manage OpenIDs')}</a> linked to your account</li> %endif %if trans.app.config.use_remote_user: %if trans.app.config.remote_user_logout_href: <li><a href="${trans.app.config.remote_user_logout_href}" target="_top">${_('Logout')}</a></li> %endif %else: - <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> + <li><a href="${h.url_for( controller='user', action='logout', webapp=webapp, logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> %endif %else: - <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, webapp='community' )}">${_('Manage your information')}</a></li> - <li><a href="${h.url_for( controller='repository', action='manage_email_alerts', cntrller=cntrller, webapp='community' )}">${_('Manage your email alerts')}</a></li> - <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> + <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, webapp=webapp )}">${_('Manage your information')}</a></li> + <li><a href="${h.url_for( controller='repository', action='manage_email_alerts', cntrller=cntrller, webapp=webapp )}">${_('Manage your email alerts')}</a></li> + <li><a href="${h.url_for( controller='user', action='logout', webapp=webapp, logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> %endif </ul> %if webapp == 'galaxy': @@ -44,7 +44,7 @@ <p>${n_('You are currently not logged in.')}</p> %endif <ul> - <li><a href="${h.url_for( action='login' )}">${_('Login')}</li> - <li><a href="${h.url_for( action='create', cntrller='user' )}">${_('Register')}</a></li> + <li><a href="${h.url_for( action='login', webapp=webapp )}">${_('Login')}</li> + <li><a href="${h.url_for( action='create', cntrller='user', webapp=webapp )}">${_('Register')}</a></li></ul> %endif diff -r 3ee9430186fbe87dd2053b0d4efdc00e70a04b45 -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -74,12 +74,7 @@ %else: <li>Logged in as <span id="user-email">${user_email}</span></li><li><a target="galaxy_main" href="${h.url_for( controller='/user', action='index', cntrller='user', webapp='community' )}">Preferences</a></li> - <% - if app.config.require_login: - logout_url = h.url_for( controller='/root', action='index', webapp='community', m_c='user', m_a='logout' ) - else: - logout_url = h.url_for( controller='/user', action='logout', webapp='community' ) - %> + <% logout_url = h.url_for( controller='/user', action='logout', webapp='community' ) %><li><a target="_top" href="${logout_url}">Logout</a></li> %endif </ul> diff -r 3ee9430186fbe87dd2053b0d4efdc00e70a04b45 -r 5db0da0007fcc59bb23f0e0ae2edb1e961702f14 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -124,7 +124,7 @@ # Menu for user who is not logged in. menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) extra_class = "loggedout-only" visible = ( trans.user == None ) tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) @@ -139,23 +139,19 @@ if app.config.remote_user_logout_href: menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) if app.config.get_bool( 'enable_tracks', False ): menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - if app.config.require_login: - logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout' ) - else: - logout_url = h.url_for( controller='/user', action='logout' ) - menu_options.append( [ 'Logout', logout_url, "_top" ] ) + menu_options.append( [ 'Logout', h.url_for( controller='/user', action='logout', webapp='galaxy' ), "_top" ] ) menu_options.append( None ) menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) if app.config.get_bool( 'enable_pages', False ): menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) if app.config.enable_api: - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) extra_class = "loggedin-only" visible = ( trans.user != None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 28 Nov '11

28 Nov '11

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4dc5538c0a85/ changeset: 4dc5538c0a85 user: natefoo date: 2011-11-28 21:36:58 summary: Merged a closed branch that doesn't show up under newer versions of mercurial. affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/changeset/3ee9430186fb/ changeset: 3ee9430186fb user: natefoo date: 2011-11-28 21:37:23 summary: Merge another closed branch. affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Support display of extra files/composite types in published items. Fixes #628
by Bitbucket 28 Nov '11

28 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c8493a61bbea/ changeset: c8493a61bbea user: jgoecks date: 2011-11-28 20:37:57 summary: Support display of extra files/composite types in published items. Fixes #628 affected #: 3 files diff -r e539a8940288d068ca431b36acf1360910e71050 -r c8493a61bbeabc8a2f254fa77e1a9b7d4d551a12 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -98,7 +98,7 @@ webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', controller='dataset', action='display_application', dataset_id=None, user_id=None, app_name = None, link_name = None, app_action = None, action_param = None ) - webapp.add_route( '/u/:username/d/:slug', controller='dataset', action='display_by_username_and_slug' ) + webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None ) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/w/:slug', controller='workflow', action='display_by_username_and_slug' ) diff -r e539a8940288d068ca431b36acf1360910e71050 -r c8493a61bbeabc8a2f254fa77e1a9b7d4d551a12 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -683,10 +683,14 @@ return self.get_ave_item_rating_data( trans.sa_session, dataset ) @web.expose - def display_by_username_and_slug( self, trans, username, slug, preview=True ): + def display_by_username_and_slug( self, trans, username, slug, filename=None, preview=True ): """ Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id. """ dataset = self.get_dataset( trans, slug, False, True ) if dataset: + # Filename used for composite types. + if filename: + return self.display( trans, dataset_id=slug, filename=filename) + truncated, dataset_data = self.get_data( dataset, preview ) dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset ) diff -r e539a8940288d068ca431b36acf1360910e71050 -r c8493a61bbeabc8a2f254fa77e1a9b7d4d551a12 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -87,7 +87,7 @@ # Get URL for display only. if data.history.user and data.history.user.username: display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', - username=data.history.user.username, slug=dataset_id ) + username=data.history.user.username, slug=dataset_id, filename='' ) else: # HACK: revert to for_editing display URL when there is no user/username. This should only happen when # there's no user/username because dataset is being displayed by history/view after error reported. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update Yogeshwar Kelkar's microsatellite tools.
by Bitbucket 28 Nov '11

28 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e539a8940288/ changeset: e539a8940288 user: dan date: 2011-11-28 19:37:10 summary: Update Yogeshwar Kelkar's microsatellite tools. affected #: 8 files Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: "Convert CG MasterVar file to pgSnp format" tool and test data
by Bitbucket 28 Nov '11

28 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3733a5846207/ changeset: 3733a5846207 user: richard_burhans date: 2011-11-28 19:15:08 summary: "Convert CG MasterVar file to pgSnp format" tool and test data affected #: 4 files Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: Added "Convert CG MasterVar file to pgSnp format" tool to the Human Genome Variation section
by Bitbucket 28 Nov '11

28 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3f0c16a3cafc/ changeset: 3f0c16a3cafc user: richard_burhans date: 2011-11-28 19:13:39 summary: Added "Convert CG MasterVar file to pgSnp format" tool to the Human Genome Variation section affected #: 1 file diff -r bb2494ca739df975e4ac81e9d7b6135931bc37ae -r 3f0c16a3cafcc5849f035df69ed57587b6d291ac tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -469,6 +469,7 @@ <tool file="human_genome_variation/lps.xml" /><tool file="human_genome_variation/hilbertvis.xml" /><tool file="human_genome_variation/freebayes.xml" /> + <tool file="human_genome_variation/master2pg.xml" /></section><section name="Genome Diversity" id="gd"><tool file="genome_diversity/extract_primers.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: hanfeisun: Modify some string in Mako templetes for complete i18n support.
by Bitbucket 28 Nov '11

28 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9c1b9d5f3ac4/ changeset: 9c1b9d5f3ac4 user: hanfeisun date: 2011-11-24 16:56:36 summary: Modify some string in Mako templetes for complete i18n support. affected #: 5 files diff -r ab90893a7cf51e272cafa97b4702d32edb44223f -r 9c1b9d5f3ac4e287c5f8f622a63755568dfb9d03 locale/zh/LC_MESSAGES/ginga.mo Binary file locale/zh/LC_MESSAGES/ginga.mo has changed diff -r ab90893a7cf51e272cafa97b4702d32edb44223f -r 9c1b9d5f3ac4e287c5f8f622a63755568dfb9d03 locale/zh/LC_MESSAGES/ginga.po --- a/locale/zh/LC_MESSAGES/ginga.po +++ b/locale/zh/LC_MESSAGES/ginga.po @@ -33,12 +33,10 @@ msgid "Are you sure you want to delete the current history?" msgstr "确认要删除当前的历史记录吗？" - #: templates/root/history.mako:38 msgid "collapse all" msgstr "全部收缩" - #: templates/root/index.mako:5 msgid "Tools" msgstr "工具" @@ -57,7 +55,6 @@ msgid "Lift-Over" msgstr "版本转换" - msgid "Text Manipulation" msgstr "文本操作" @@ -134,7 +131,7 @@ msgstr "历史项目属性" #: templates/dataset/edit_attributes.mako:19 -msgid "Edit Attributes" +msgid "Edit attributes" msgstr "编辑属性" #: templates/dataset/edit_attributes.mako:64 @@ -148,21 +145,21 @@ "Required metadata values are missing. Some of these values may not be " "editable by the user. Selecting \"Auto-detect\" will attempt to fix these " "values." -msgstr "所需元数据值缺失。其中一些值可能无法被用户编辑。选择“自动检测”将修正这些值。" +msgstr "缺少所需的metadata的值。用户可能无法对这些值进行编辑。选择“自动检测”来尝试修正这些值。" #: templates/dataset/edit_attributes.mako:78 msgid "Convert to new format" -msgstr "转换成新格式" +msgstr "转换为新格式" #: templates/dataset/edit_attributes.mako:84 msgid "Convert to" -msgstr "转换" +msgstr "转换为" #: templates/dataset/edit_attributes.mako:95 msgid "" "This will create a new dataset with the contents of this dataset converted " "to a new format." -msgstr "这将创建一个新的数据集，内容是转换后的数据集。" +msgstr "这将产生一个转换格式后的新数据集，" #: templates/dataset/edit_attributes.mako:111 msgid "Change data type" @@ -177,7 +174,7 @@ "This will change the datatype of the existing dataset but <i>not</i> modify " "its contents. Use this if Galaxy has incorrectly guessed the type of your " "dataset." -msgstr "这将改变已有数据集的数据类型，但是<i>不</i>改变其内容。当Galaxy不能正确判断你的数据类型时，设置该参数。" +msgstr "这将改变已有数据集的数据类型，但<i>不</i>改变其内容。当Galaxy不能正确判断你的数据类型时，设置该参数。" #: templates/dataset/edit_attributes.mako:137 msgid "Copy History Item" @@ -185,19 +182,16 @@ #: templates/history/list.mako:3 msgid "Saved Histories" -msgstr "保存的历史记录" +msgstr "已保存的历史" -#: templates/history/list.mako:19 -msgid "Stored Histories" -msgstr "存储的历史记录" #: templates/history/list.mako:21 templates/root/history.mako:239 msgid "hide deleted" -msgstr "隐藏已删除" +msgstr "隐藏已删除的数据" #: templates/history/list.mako:23 msgid "show deleted" -msgstr "显示已删除" +msgstr "显示已删除的数据" #: templates/history/list.mako:27 msgid "Name" @@ -209,7 +203,7 @@ #: templates/history/list.mako:27 msgid "Last modified" -msgstr "最后修改" +msgstr "最后修改时间" #: templates/history/list.mako:27 msgid "Actions" @@ -229,7 +223,7 @@ #: templates/history/list.mako:49 msgid "undelete" -msgstr "取消删除" +msgstr "还原" #: templates/history/list.mako:55 msgid "Action" @@ -249,7 +243,7 @@ #: templates/history/list.mako:58 msgid "Undelete" -msgstr "取消删除" +msgstr "还原" #: templates/history/list.mako:65 msgid "You have no stored histories" @@ -261,7 +255,7 @@ #: templates/history/options.mako:9 msgid "You must be " -msgstr "你必须" +msgstr "你必须成为" #: templates/history/options.mako:9 msgid "logged in" @@ -290,7 +284,7 @@ #: templates/history/options.mako:18 msgid " a new empty history" -msgstr " 一个新的空历史记录" +msgstr " 一个新的空白历史记录" #: templates/history/options.mako:20 msgid "Construct workflow" @@ -550,10 +544,10 @@ msgid "Show Deleted Datasets" -msgstr "显示已删除数据" +msgstr "显示已删除的数据" msgid "Show Hidden Datasets" -msgstr "显示隐藏数据" +msgstr "显示隐藏的数据" msgid "Show Structure" msgstr "显示结构" @@ -594,4 +588,16 @@ msgid "Register" -msgstr "注册" \ No newline at end of file +msgstr "注册" + +msgid "Support" +msgstr "技术支持" + +msgid "Galaxy Wiki" +msgstr "Galaxy百科" + +msgid "Video tutorials (screencasts)" +msgstr "视频教程（动画演示）" + +msgid "How to Cite Galaxy" +msgstr "如何引用Galaxy" diff -r ab90893a7cf51e272cafa97b4702d32edb44223f -r 9c1b9d5f3ac4e287c5f8f622a63755568dfb9d03 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -19,7 +19,7 @@ </div><div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> %endif - <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Download" class="icon-button disk tooltip"></a> + <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title='${_("Download")}' class="icon-button disk tooltip"></a> %if meta_files: </div> %endif @@ -75,7 +75,7 @@ ## TODO: Make these CSS, just adding a "disabled" class to the normal ## links should be enough. However the number of datasets being uploaded ## at a time is usually small so the impact of these images is also small. - <span title='Display Data' class='icon-button display_disabled tooltip'></span> + <span title='${_("Display Data")}' class='icon-button display_disabled tooltip'></span> %if for_editing: <span title='Edit Attributes' class='icon-button edit_disabled tooltip'></span> %endif @@ -98,7 +98,7 @@ %if data.purged: <span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span> %else: - <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}" + <a class="icon-button display tooltip" title='${_("Display data in browser")}' href="${display_url}" %if for_editing: target="galaxy_main" %endif @@ -110,13 +110,13 @@ %elif data.purged: <span title="Cannot edit attributes of datasets removed from disk" class="icon-button edit_disabled tooltip"></span> %else: - <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a> + <a class="icon-button edit tooltip" title='${_("Edit attributes")}' href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a> %endif %endif %endif %if for_editing: %if can_edit: - <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a> + <a class="icon-button delete tooltip" title='${_("Delete")}' href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a> %else: <span title="Dataset is already deleted" class="icon-button delete_disabled tooltip"></span> %endif @@ -136,17 +136,17 @@ %elif data_state == "queued": <div>${_('Job is waiting to run')}</div><div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> + <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a> %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> + <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> %endif </div> %elif data_state == "running": <div>${_('Job is currently running')}</div><div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> + <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a> %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> + <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> %endif </div> %elif data_state == "error": @@ -163,9 +163,9 @@ %if data.has_data(): ${render_download_links( data, dataset_id )} %endif - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> + <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a> %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> + <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> %endif </div> %elif data_state == "discarded": @@ -177,9 +177,9 @@ %elif data_state == "empty": <div>${_('No data: ')}<i>${data.display_info()}</i></div><div> - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> + <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a> %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> + <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> %endif </div> %elif data_state in [ "ok", "failed_metadata" ]: @@ -193,8 +193,8 @@ %endif <div> ${data.blurb}<br /> - format: <span class="${data.ext}">${data.ext}</span>, - database: + ${_("format: ")} <span class="${data.ext}">${data.ext}</span>, + ${_("database: ")} %if data.dbkey == '?' and can_edit: <a href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main">${_(data.dbkey)}</a> %else: @@ -208,10 +208,10 @@ %if data.has_data(): ${render_download_links( data, dataset_id )} - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> + <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a> %if for_editing: - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> + <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks(): <% if data.dbkey != '?': @@ -266,8 +266,8 @@ <br /> %endfor %elif for_editing: - <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title="View Details" class="icon-button information tooltip"></a> - <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> + <a href="${h.url_for( controller='dataset', action='show_params', dataset_id=dataset_id )}" target="galaxy_main" title='${_("View Details")}' class="icon-button information tooltip"></a> + <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> %endif </div> diff -r ab90893a7cf51e272cafa97b4702d32edb44223f -r 9c1b9d5f3ac4e287c5f8f622a63755568dfb9d03 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -11,71 +11,71 @@ // Init history options. $("#history-options-button").css( "position", "relative" ); make_popupmenu( $("#history-options-button"), { - "History Lists": null, - "Saved Histories": function() { + "${_("History Lists")}": null, + "${_("Saved Histories")}": function() { galaxy_main.location = "${h.url_for( controller='history', action='list')}"; }, - "Histories Shared with Me": function() { + "${_("Histories Shared with Me")}": function() { galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}"; }, - "Current History": null, - "Create New": function() { + "${_("Current History")}": null, + "${_("Create New")}": function() { galaxy_history.location = "${h.url_for( controller='root', action='history_new' )}"; }, - "Clone": function() { + "${_("Clone")}": function() { galaxy_main.location = "${h.url_for( controller='history', action='clone')}"; }, - "Copy Datasets": function() { + "${_("Copy Datasets")}": function() { galaxy_main.location = "${h.url_for( controller='dataset', action='copy_datasets' )}"; }, - "Share or Publish": function() { + "${_("Share or Publish")}": function() { galaxy_main.location = "${h.url_for( controller='history', action='sharing' )}"; }, - "Extract Workflow": function() { + "${_("Extract Workflow")}": function() { galaxy_main.location = "${h.url_for( controller='workflow', action='build_from_current_history' )}"; }, - "Dataset Security": function() { + "${_("Dataset Security")}": function() { galaxy_main.location = "${h.url_for( controller='root', action='history_set_default_permissions' )}"; }, - "Show Deleted Datasets": function() { + "${_("Show Deleted Datasets")}": function() { galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; }, - "Show Hidden Datasets": function() { + "${_("Show Hidden Datasets")}": function() { galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}"; }, - "Purge Deleted Datasets": function() { + "${_("Purge Deleted Datasets")}": function() { if ( confirm( "Really delete all deleted datasets permanently? This cannot be undone." ) ) { galaxy_main.location = "${h.url_for( controller='history', action='purge_deleted_datasets' )}"; } }, - "Show Structure": function() { + "${_("Show Structure")}": function() { galaxy_main.location = "${h.url_for( controller='history', action='display_structured' )}"; }, - "Export to File": function() { + "${_("Export to File")}": function() { galaxy_main.location = "${h.url_for( controller='history', action='export_archive' )}"; }, - "Delete": function() { + "${_("Delete")}": function() { if ( confirm( "Really delete the current history?" ) ) { galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}"; } }, - "Delete Permanently": function() { + "${_("Delete Permanently")}": function() { if ( confirm( "Really delete the current history permanently? This cannot be undone." ) ) { galaxy_main.location = "${h.url_for( controller='history', action='delete_current', purge=True )}"; } }, - "Other Actions": null, - "Import from File": function() { + "${_("Other Actions")}": null, + "${_("Import from File")}": function() { galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; } }); var menu_options = {}; // Holds dictionary of { label: toggle_fn } - SHOW_TOOL = "Show Tool Search"; - HIDE_TOOL = "Hide Tool Search"; - SHOW_RECENT = "Show Recently Used"; - HIDE_RECENT = "Hide Recently Used"; + SHOW_TOOL = "${_("Show Tool Search")}"; + HIDE_TOOL = "${_("Hide Tool Search")}"; + SHOW_RECENT = "${_("Show Recently Used")}"; + HIDE_RECENT = "${_("Hide Recently Used")}"; var toggle_tool_search_fn = function() { // Show/hide menu and update vars, user preferences. diff -r ab90893a7cf51e272cafa97b4702d32edb44223f -r 9c1b9d5f3ac4e287c5f8f622a63755568dfb9d03 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -64,32 +64,32 @@ ## Analyze data tab. - ${tab( "analysis", "Analyze Data", h.url_for( controller='/root', action='index' ) )} + ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )} ## Workflow tab. - ${tab( "workflow", "Workflow", h.url_for( controller='/workflow', action='index' ) )} + ${tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) )} ## 'Shared Items' or Libraries tab. <% menu_options = [ - [ 'Data Libraries', h.url_for( controller='/library', action='index') ], + [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], None, - [ 'Published Histories', h.url_for( controller='/history', action='list_published' ) ], - [ 'Published Workflows', h.url_for( controller='/workflow', action='list_published' ) ] + [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], + [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ] ] if app.config.get_bool( 'enable_tracks', False ): - menu_options.append( [ 'Published Visualizations', h.url_for( controller='/visualization', action='list_published' ) ] ) + menu_options.append( [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ] ) if app.config.get_bool( 'enable_pages', False ): - menu_options.append( [ 'Published Pages', h.url_for( controller='/page', action='list_published' ) ] ) - tab( "shared", "Shared Data", h.url_for( controller='/library', action='index'), menu_options=menu_options ) + menu_options.append( [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] ) + tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options ) %> ## Lab menu. <% menu_options = [ - [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ], - [ 'Find Samples', h.url_for( controller='/requests', action='find_samples_index' ) ], - [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] + [ _('Sequencing Requests'), h.url_for( controller='/requests', action='index' ) ], + [ _('Find Samples'), h.url_for( controller='/requests', action='find_samples_index' ) ], + [ _('Help'), app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) %> @@ -98,10 +98,10 @@ %if app.config.get_bool( 'enable_tracks', False ): <% menu_options = [ - ['New Track Browser', h.url_for( controller='/tracks', action='index' ) ], - ['Saved Visualizations', h.url_for( controller='/visualization', action='list' ) ] + [_('New Track Browser'), h.url_for( controller='/tracks', action='index' ) ], + [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] ] - tab( "visualization", "Visualization", h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) + tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) %> %endif @@ -111,23 +111,23 @@ ## Help tab. <% menu_options = [ - ['Support', app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - ['Galaxy Wiki', app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - ['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - ['How to Cite Galaxy', app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], + [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], + [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], + [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] ] - tab( "help", "Help", None, menu_options=menu_options) + tab( "help", _("Help"), None, menu_options=menu_options) %> ## User tabs. <% # Menu for user who is not logged in. - menu_options = [ [ "Login", h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] + menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] if app.config.allow_user_creation: - menu_options.append( [ "Register", h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedout-only" visible = ( trans.user == None ) - tab( "user", "User", None, visible=visible, menu_options=menu_options ) + tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) # Menu for user who is logged in. if trans.user: @@ -137,9 +137,9 @@ menu_options = [ [ '<li>Logged in as <span id="user-email">%s</span></li>' % email ] ] if app.config.use_remote_user: if app.config.remote_user_logout_href: - menu_options.append( [ 'Logout', app.config.remote_user_logout_href, "_top" ] ) + menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) else: - menu_options.append( [ 'Preferences', h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) if app.config.get_bool( 'enable_tracks', False ): menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) if app.config.require_login: @@ -148,14 +148,14 @@ logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) - menu_options.append( [ 'Saved Histories', h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) - menu_options.append( [ 'Saved Datasets', h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) + menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) + menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) if app.config.get_bool( 'enable_pages', False ): - menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] ) + menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) if app.config.enable_api: - menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) if app.config.use_remote_user: - menu_options.append( [ 'Public Name', h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedin-only" visible = ( trans.user != None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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