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commit/galaxy-central: dannon: Fix for browsing libraries, json2 wasn't being loaded, needed in IE for jstorage to work.
by Bitbucket 30 Nov '11

30 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/de03f821784b/ changeset: de03f821784b user: dannon date: 2011-11-30 13:29:32 summary: Fix for browsing libraries, json2 wasn't being loaded, needed in IE for jstorage to work. affected #: 1 file diff -r b751663f3f64ea794951f57b2ff4686debd1b455 -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -48,6 +48,7 @@ <%def name="javascripts()"> ${parent.javascripts()} + ${h.js("json2")} ${h.js("jstorage")} ${common_javascripts()} ${self.grid_javascripts()} 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: Minor fix for 04e8ed0cd930.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b751663f3f64/ changeset: b751663f3f64 user: dan date: 2011-11-29 23:35:14 summary: Minor fix for 04e8ed0cd930. affected #: 1 file diff -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 -r b751663f3f64ea794951f57b2ff4686debd1b455 tools/sr_mapping/PerM.xml --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -13,7 +13,7 @@ #if $s.space == "color" "${s.sourceOfRef.index.fields.path}" #elif $s.space == "base" - "${s.sourceOfRef.index.fields.path" + "${s.sourceOfRef.index.fields.path}" #end if #end if #if $s.mate.singleOrPairs == "single": 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: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04e8ed0cd930/ changeset: 04e8ed0cd930 user: dan date: 2011-11-29 23:30:14 summary: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools. affected #: 13 files diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml +++ b/tools/metag_tools/megablast_wrapper.xml @@ -2,7 +2,7 @@ <description> compare short reads against htgs, nt, and wgs databases</description><command interpreter="python"> megablast_wrapper.py - --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }" + --db_build="${source_select.fields.path}" --input=$input_query --word_size=$word_size --identity_cutoff=$iden_cutoff diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -19,7 +19,7 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes_color' ].get_fields() )[0][-1] }" + --indexes-path="${refGenomeSource.index.fields.path}" #end if ## Are reads single-end or paired? diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -17,7 +17,7 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" + --indexes-path="${refGenomeSource.index.fields.path}" #end if ## Are reads single-end or paired? diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -4,7 +4,7 @@ <command interpreter="python"> ngs_simulation.py #if $in_type.input_type == "built-in" - --input="${ filter( lambda x: str( x[0] ) == str( $in_type.genome ), $__app__.tool_data_tables[ 'ngs_sim_fasta' ].get_fields() )[0][-1] }" + --input="${in_type.genome.fields.path}" --genome=$in_type.genome #else --input=$in_type.input1 diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -6,7 +6,7 @@ #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else - --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" + --ref "${genomeSource.index.fields.path}" #end if </command><requirements><requirement type="package">picard</requirement></requirements> diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/PerM.xml --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -11,9 +11,9 @@ $s.sourceOfRef.ref #else #if $s.space == "color" - "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_color_indexes' ].get_fields() )[0][-1] }" + "${s.sourceOfRef.index.fields.path}" #elif $s.space == "base" - "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_base_indexes' ].get_fields() )[0][-1] }" + "${s.sourceOfRef.index.fields.path" #end if #end if #if $s.mate.singleOrPairs == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_color_wrapper.xml --- a/tools/sr_mapping/bowtie_color_wrapper.xml +++ b/tools/sr_mapping/bowtie_color_wrapper.xml @@ -58,7 +58,7 @@ #end if #else ##use pre-built index - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }" + --ref="${refGenomeSource.index.fields.path}" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -61,8 +61,7 @@ #end if #else ##use pre-built index - ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" - --ref="${ refGenomeSource.index.fields.path }" + --ref="${refGenomeSource.index.fields.path}" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_color_wrapper.xml --- a/tools/sr_mapping/bwa_color_wrapper.xml +++ b/tools/sr_mapping/bwa_color_wrapper.xml @@ -14,7 +14,7 @@ --dbkey=$dbkey #else: ##use precomputed indexes - --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes_color' ].get_fields() )[0][-1] }" + --ref="${genomeSource.indices.fields.path}" --do_not_build_index #end if diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -17,7 +17,7 @@ --dbkey=$dbkey #else: ##use precomputed indexes - --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" + --ref="${genomeSource.indices.fields.path}" --do_not_build_index #end if diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_paired_reads_wrapper.xml --- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml @@ -12,7 +12,7 @@ --input1=$source.input1 --ref_sequences=$input1.metadata.sequences #else: - --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --input1="${source.input1_2bit.fields.path}" #end if --output=$output1 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR} diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml +++ b/tools/sr_mapping/lastz_wrapper.xml @@ -12,7 +12,7 @@ --input1=$source.input1 --ref_sequences=$input1.metadata.sequences #else: - --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --input1="${source.input1_2bit.fields.path}" --ref_sequences="None" #end if #if $params.source_select=="pre_set": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -13,7 +13,7 @@ #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': - ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } + ${genomeSource.indexReference.fields.path} #else: $genomeSource.historyReference #end if Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix tab to 4 spaces in tool_conf.xml.sample.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0532712a2708/ changeset: 0532712a2708 user: dan date: 2011-11-29 23:07:06 summary: Fix tab to 4 spaces in tool_conf.xml.sample. affected #: 1 file diff -r 9ee4e2e41fd60c75c2b87d55648c538438809430 -r 0532712a2708855e77d1a6a9a1099121983458a4 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -469,7 +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" /> + <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: 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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commit/galaxy-central: greg: Remove the old template_path setting from community_wsgi.ini. since it is set incorrecly and not neede anyway.
by Bitbucket 25 Nov '11

25 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/31932fa8c0e1/ changeset: 31932fa8c0e1 user: greg date: 2011-11-25 15:24:58 summary: Remove the old template_path setting from community_wsgi.ini. since it is set incorrecly and not neede anyway. affected #: 1 file diff -r ab90893a7cf51e272cafa97b4702d32edb44223f -r 31932fa8c0e1e2f84c54107356487ec427d2a521 community_wsgi.ini.sample --- a/community_wsgi.ini.sample +++ b/community_wsgi.ini.sample @@ -26,9 +26,6 @@ # Temporary storage for additional datasets, this should be shared through the cluster new_file_path = database/tmp -# Where templates are stored -template_path = lib/galaxy/webapps/community/templates - # Session support (beaker) use_beaker_session = True session_type = memory 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: Re-engineer the datatypes registry so that it is initialized once when the Galaxy server is started, but data types can continue to be loaded throughout the Galaxy server's session (hopefully this doesn't break anything).
by Bitbucket 23 Nov '11

23 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ab90893a7cf5/ changeset: ab90893a7cf5 user: greg date: 2011-11-23 22:16:15 summary: Re-engineer the datatypes registry so that it is initialized once when the Galaxy server is started, but data types can continue to be loaded throughout the Galaxy server's session (hopefully this doesn't break anything). Add support for a single "import_module" to be passed to the new load_datatypes() method in the datatypes registry. This provides the ability to load a single class module from an installed tool shed repository along with a datatypes_conf.xml file included in the installed repository and pass them to the new load_datatypes() method. In the future, multiple imported modules may be allowed. The datatypes_conf.xml file included in the repository must conform to a slightly different definition than the same named file that comes with the distribution. This new definition will be documented in the Galaxy tool shed wiki. We now have the ability to load new data types into the Galaxy server from an installed tool shed repository without restarting the Galaxy server. affected #: 12 files diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -22,7 +22,8 @@ self.config.check() config.configure_logging( self.config ) # Set up datatypes registry - self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config ) + self.datatypes_registry = galaxy.datatypes.registry.Registry() + self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) galaxy.model.set_datatypes_registry( self.datatypes_registry ) # Set up the tool sheds registry if os.path.isfile( self.config.tool_sheds_config ): diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -12,7 +12,7 @@ pass class Registry( object ): - def __init__( self, root_dir=None, config=None ): + def __init__( self ): self.log = logging.getLogger(__name__) self.log.addHandler( logging.NullHandler() ) self.datatypes_by_extension = {} @@ -27,21 +27,33 @@ self.sniff_order = [] self.upload_file_formats = [] self.display_applications = odict() #map a display application id to a display application - inherit_display_application_by_class = [] + self.datatype_converters_path = None + self.datatype_indexers_path = None + self.display_applications_path = None + def load_datatypes( self, root_dir=None, config=None, imported_module=None ): if root_dir and config: + inherit_display_application_by_class = [] # Parse datatypes_conf.xml tree = galaxy.util.parse_xml( config ) root = tree.getroot() # Load datatypes and converters from config self.log.debug( 'Loading datatypes from %s' % config ) registration = root.find( 'registration' ) - self.datatype_converters_path = os.path.join( root_dir, registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' ) ) - self.datatype_indexers_path = os.path.join( root_dir, registration.get( 'indexers_path', 'lib/galaxy/datatypes/indexers' ) ) - self.display_applications_path = os.path.join( root_dir, registration.get( 'display_path', 'display_applications' ) ) - if not os.path.isdir( self.datatype_converters_path ): - raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path ) - if not os.path.isdir( self.datatype_indexers_path ): - raise ConfigurationError( "Directory does not exist: %s" % self.datatype_indexers_path ) + # The following implementation implies that only the first datatypes_conf.xml parsed will + # define the various paths. This is probably ok, since we can justifiably require that the + # local datatypes_conf.xml file sets the standard, and all additional datatypes_conf.xml + # files installed with repositories from tool sheds must use the same paths. However, we + # may discover at some future time that allowing for multiple paths is more optimal. + if not self.datatype_converters_path: + self.datatype_converters_path = os.path.join( root_dir, registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' ) ) + if not os.path.isdir( self.datatype_converters_path ): + raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path ) + if not self.datatype_indexers_path: + self.datatype_indexers_path = os.path.join( root_dir, registration.get( 'indexers_path', 'lib/galaxy/datatypes/indexers' ) ) + if not os.path.isdir( self.datatype_indexers_path ): + raise ConfigurationError( "Directory does not exist: %s" % self.datatype_indexers_path ) + if not self.display_applications_path: + self.display_applications_path = os.path.join( root_dir, registration.get( 'display_path', 'display_applications' ) ) for elem in registration.findall( 'datatype' ): try: extension = elem.get( 'extension', None ) @@ -55,11 +67,14 @@ fields = dtype.split( ':' ) datatype_module = fields[0] datatype_class_name = fields[1] - fields = datatype_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - datatype_class = getattr( module, datatype_class_name ) + if imported_module: + datatype_class = getattr( imported_module, datatype_class_name ) + else: + fields = datatype_module.split( '.' ) + module = __import__( fields.pop(0) ) + for mod in fields: + module = getattr( module, mod ) + datatype_class = getattr( module, datatype_class_name ) elif type_extension: datatype_class = self.datatypes_by_extension[type_extension].__class__ if make_subclass: @@ -252,10 +267,8 @@ if not included: self.sniff_order.append(datatype) append_to_sniff_order() - def get_available_tracks(self): return self.available_tracks - def get_mimetype_by_extension(self, ext, default = 'application/octet-stream' ): """Returns a mimetype based on an extension""" try: @@ -265,7 +278,6 @@ mimetype = default self.log.warning('unknown mimetype in data factory %s' % ext) return mimetype - def get_datatype_by_extension(self, ext ): """Returns a datatype based on an extension""" try: @@ -273,7 +285,6 @@ except KeyError: builder = data.Text() return builder - def change_datatype(self, data, ext, set_meta = True ): data.extension = ext # call init_meta and copy metadata from itself. The datatype @@ -287,7 +298,6 @@ data.set_meta( overwrite = False ) data.set_peek() return data - def old_change_datatype(self, data, ext): """Creates and returns a new datatype based on an existing data and an extension""" newdata = factory(ext)(id=data.id) @@ -295,7 +305,6 @@ setattr(newdata, key, value) newdata.ext = ext return newdata - def load_datatype_converters( self, toolbox ): """Adds datatype converters from self.converters to the calling app's toolbox""" for elem in self.converters: @@ -312,7 +321,6 @@ self.log.debug( "Loaded converter: %s", converter.id ) except: self.log.exception( "error reading converter from path: %s" % converter_path ) - def load_external_metadata_tool( self, toolbox ): """Adds a tool which is used to set external metadata""" #we need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated tool. @@ -337,7 +345,6 @@ toolbox.tools_by_id[ set_meta_tool.id ] = set_meta_tool self.set_external_metadata_tool = set_meta_tool self.log.debug( "Loaded external metadata tool: %s", self.set_external_metadata_tool.id ) - def load_datatype_indexers( self, toolbox ): """Adds indexers from self.indexers to the toolbox from app""" for elem in self.indexers: @@ -347,7 +354,6 @@ toolbox.tools_by_id[indexer.id] = indexer self.datatype_indexers[datatype] = indexer self.log.debug( "Loaded indexer: %s", indexer.id ) - def get_converters_by_datatype(self, ext): """Returns available converters by source type""" converters = odict() @@ -360,7 +366,6 @@ if ext in self.datatype_converters.keys(): converters.update(self.datatype_converters[ext]) return converters - def get_indexers_by_datatype( self, ext ): """Returns indexers based on datatype""" class_chain = list() @@ -373,14 +378,12 @@ ext2type = lambda x: self.get_datatype_by_extension(x) class_chain = sorted(class_chain, lambda x,y: issubclass(ext2type(x),ext2type(y)) and -1 or 1) return [self.datatype_indexers[x] for x in class_chain] - def get_converter_by_target_type(self, source_ext, target_ext): """Returns a converter based on source and target datatypes""" converters = self.get_converters_by_datatype(source_ext) if target_ext in converters.keys(): return converters[target_ext] return None - def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): """Returns ( target_ext, existing converted dataset )""" for convert_ext in self.get_converters_by_datatype( dataset.ext ): @@ -394,10 +397,8 @@ ret_data = None return ( convert_ext, ret_data ) return ( None, None ) - def get_composite_extensions( self ): return [ ext for ( ext, d_type ) in self.datatypes_by_extension.iteritems() if d_type.composite_type is not None ] - def get_upload_metadata_params( self, context, group, tool ): """Returns dict of case value:inputs for metadata conditional for upload tool""" rval = {} @@ -413,4 +414,3 @@ if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype rval[ 'auto' ] = rval[ 'txt' ] return rval - diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -280,6 +280,7 @@ """ if sniff_order is None: datatypes_registry = registry.Registry() + datatypes_registry.load_datatypes() sniff_order = datatypes_registry.sniff_order for datatype in sniff_order: """ diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -25,7 +25,9 @@ log = logging.getLogger( __name__ ) -datatypes_registry = galaxy.datatypes.registry.Registry() #Default Value Required for unit tests +datatypes_registry = galaxy.datatypes.registry.Registry() +# Default Value Required for unit tests +datatypes_registry.load_datatypes() class NoConverterException(Exception): def __init__(self, value): diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1307,7 +1307,9 @@ if tool is None: #This occurs for things such as unit tests import galaxy.datatypes.registry - formats.append( galaxy.datatypes.registry.Registry().get_datatype_by_extension( extension.lower() ).__class__ ) + datatypes_registry = galaxy.datatypes.registry.Registry() + datatypes_registry.load_datatypes() + formats.append( datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) else: formats.append( tool.app.datatypes_registry.get_datatype_by_extension( extension.lower() ).__class__ ) self.formats = tuple( formats ) diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f lib/galaxy/util/none_like.py --- a/lib/galaxy/util/none_like.py +++ b/lib/galaxy/util/none_like.py @@ -20,7 +20,9 @@ def __init__( self, datatypes_registry = None, ext = 'data', dbkey = '?' ): self.ext = self.extension = ext self.dbkey = dbkey - if datatypes_registry is None: datatypes_registry = Registry() + if datatypes_registry is None: + datatypes_registry = Registry() + datatypes_registry.load_datatypes() self.datatype = datatypes_registry.get_datatype_by_extension( ext ) self._metadata = None self.metadata = MetadataCollection( self ) diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -4,7 +4,7 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.tools.search import ToolBoxSearch from galaxy.tools import ToolSection, json_fix -from galaxy.util import inflector +from galaxy.util import parse_xml, inflector import logging log = logging.getLogger( __name__ ) @@ -874,8 +874,7 @@ tmp_stderr.close() if returncode == 0: # Load data types required by tools. - # TODO: uncomment the following when we're ready... - #self.__load_datatypes( trans, repo_files_dir ) + self.__load_datatypes( trans, repo_files_dir ) # Load tools and tool data files required by them. sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) if repository_tools_tups: @@ -898,9 +897,8 @@ persisted_new_tool_section.write( new_tool_section ) persisted_new_tool_section.close() # Parse the persisted tool panel section - tree = ElementTree.parse( tmp_name ) + tree = parse_xml( tmp_name ) root = tree.getroot() - ElementInclude.include( root ) # Load the tools in the section into the tool panel. trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path ) # Remove the temporary file @@ -1186,35 +1184,49 @@ datatypes_config = os.path.abspath( os.path.join( root, name ) ) break if datatypes_config: + imported_module = None # Parse datatypes_config. - tree = ElementTree.parse( datatypes_config ) - root = tree.getroot() - ElementInclude.include( root ) - datatype_files = root.find( 'datatype_files' ) + tree = parse_xml( datatypes_config ) + datatypes_config_root = tree.getroot() + relative_path_to_datatype_file_name = None + datatype_files = datatypes_config_root.find( 'datatype_files' ) + # Currently only a single datatype_file is supported. For example: + # <datatype_files> + # <datatype_file name="gmap.py"/> + # </datatype_files> for elem in datatype_files.findall( 'datatype_file' ): datatype_file_name = elem.get( 'name', None ) if datatype_file_name: # Find the file in the installed repository. - relative_path = None for root, dirs, files in os.walk( repo_files_dir ): if root.find( '.hg' ) < 0: for name in files: if name == datatype_file_name: - relative_path = os.path.join( root, name ) + relative_path_to_datatype_file_name = os.path.join( root, name ) break - relative_head, relative_tail = os.path.split( relative_path ) - # TODO: get the import_module by parsing the <registration><datatype> tags - if datatype_file_name.find( '.' ) > 0: - import_module = datatype_file_name.split( '.' )[ 0 ] - else: - import_module = datatype_file_name - try: - sys.path.insert( 0, relative_head ) - module = __import__( import_module ) - sys.path.pop( 0 ) - except Exception, e: - log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) ) - trans.app.datatypes_registry = galaxy.datatypes.registry.Registry( trans.app.config.root, datatypes_config ) + break + if relative_path_to_datatype_file_name: + relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name ) + registration = datatypes_config_root.find( 'registration' ) + # Get the module by parsing the <datatype> tag. + for elem in registration.findall( 'datatype' ): + # A 'type' attribute is currently required. The attribute + # should be something like: type="gmap:GmapDB". + dtype = elem.get( 'type', None ) + if dtype: + fields = dtype.split( ':' ) + datatype_module = fields[0] + datatype_class_name = fields[1] + # Since we currently support only a single datatype_file, + # we have what we need. + break + try: + sys.path.insert( 0, relative_head ) + imported_module = __import__( datatype_module ) + sys.path.pop( 0 ) + except Exception, e: + log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) ) + trans.app.datatypes_registry.load_datatypes( root_dir=trans.app.config.root, config=datatypes_config, imported_module=imported_module ) def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ): # The sample_files list contains all files whose name ends in .sample sample_files = [] diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -15,7 +15,8 @@ self.config.check() config.configure_logging( self.config ) # Set up datatypes registry - self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config ) + self.datatypes_registry = galaxy.datatypes.registry.Registry() + self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -244,7 +244,9 @@ else: # FIXME: This doesn't work at all now that toolbox requires an 'app' instance # (to get at datatypes, might just pass a datatype registry directly) - my_app = bunch.Bunch( datatypes_registry = galaxy.datatypes.registry.Registry() ) + datatypes_registry = galaxy.datatypes.registry.Registry() + datatypes_registry.load_datatypes() + my_app = bunch.Bunch( datatypes_registry ) test_toolbox.toolbox = tools.ToolBox( 'tool_conf.xml.test', 'tools', my_app ) # ---- Find tests --------------------------------------------------------- diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f scripts/set_metadata.py --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -37,7 +37,9 @@ # Set up datatypes registry config_root = sys.argv.pop( 1 ) datatypes_config = sys.argv.pop( 1 ) - galaxy.model.set_datatypes_registry( galaxy.datatypes.registry.Registry( config_root, datatypes_config ) ) + datatypes_registry = galaxy.datatypes.registry.Registry() + datatypes_registry.load_datatypes( root_dir=config_root, config=datatypes_config ) + galaxy.model.set_datatypes_registry( datatypes_registry ) job_metadata = sys.argv.pop( 1 ) ext_override = dict() diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f tools/data_source/data_source.py --- a/tools/data_source/data_source.py +++ b/tools/data_source/data_source.py @@ -57,7 +57,8 @@ enhanced_handling = True json_file = open( job_params[ 'job_config' ][ 'TOOL_PROVIDED_JOB_METADATA_FILE' ], 'w' ) #specially named file for output junk to pass onto set metadata - datatypes_registry = Registry( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] ) + datatypes_registry = Registry() + datatypes_registry.load_datatypes( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] ) URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded URL_method = params.get( 'URL_method', None ) diff -r 856aac70b018de6a748cf49355677d4dbe27ddf6 -r ab90893a7cf51e272cafa97b4702d32edb44223f tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -369,7 +369,8 @@ output_paths = parse_outputs( sys.argv[4:] ) json_file = open( 'galaxy.json', 'w' ) - registry = Registry( sys.argv[1], sys.argv[2] ) + registry = Registry() + registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) for line in open( sys.argv[3], 'r' ): dataset = from_json_string( line ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: refactor action icon creation and initialization.
by Bitbucket 23 Nov '11

23 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/856aac70b018/ changeset: 856aac70b018 user: jgoecks date: 2011-11-23 22:11:39 summary: Trackster: refactor action icon creation and initialization. affected #: 1 file diff -r 255f4bde822b4b9b36c1a9074cc6063a47127ff2 -r 856aac70b018de6a748cf49355677d4dbe27ddf6 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -677,6 +677,7 @@ this.prefs = this.config.values; this.drag_handle_class = drag_handle_class; this.is_overview = false; + this.action_icons = {}; // FIXME: this should be a saved setting this.content_visible = true; @@ -688,8 +689,10 @@ if (this.header_div) { this.container_div.append(this.header_div); - this.icons_div = this.build_icons_div().hide(); - this.header_div.append(this.icons_div); + this.icons_div = $("<div/>").css("float", "left").hide().appendTo(this.header_div); + this.build_action_icons(this.action_icons_def); + this.header_div.append( $("<div style='clear: both'/>") ); + // Suppress double clicks in header so that they do not impact viz. this.header_div.dblclick( function(e) { e.stopPropagation(); } ); @@ -706,6 +709,64 @@ } }; +Drawable.prototype.action_icons_def = [ + // Hide/show drawable content. + { + name: "toggle_icon", + title: "Hide/show content", + css_class: "toggle", + on_click_fn: function(drawable) { + if ( drawable.content_visible ) { + drawable.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle"); + drawable.hide_contents(); + drawable.content_visible = false; + } else { + drawable.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand"); + drawable.content_visible = true; + drawable.show_contents(); + } + } + }, + // Edit settings. + { + name: "settings_icon", + title: "Edit settings", + css_class: "settings-icon", + on_click_fn: function(drawable) { + var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, + ok_fn = function() { + drawable.config.update_from_form( $(".dialog-box") ); + hide_modal(); + $(window).unbind("keypress.check_enter_esc"); + }, + check_enter_esc = function(e) { + if ((e.keyCode || e.which) === 27) { // Escape key + cancel_fn(); + } else if ((e.keyCode || e.which) === 13) { // Enter key + ok_fn(); + } + }; + + $(window).bind("keypress.check_enter_esc", check_enter_esc); + show_modal("Configure", drawable.config.build_form(), { + "Cancel": cancel_fn, + "OK": ok_fn + }); + } + }, + // Remove. + { + name: "remove_icon", + title: "Remove", + css_class: "remove-icon", + on_click_fn: function(drawable) { + // Tipsy for remove icon must be deleted when drawable is deleted. + $(".tipsy").remove(); + drawable.remove(); + } + } +]; + extend(Drawable.prototype, { init: function() {}, request_draw: function() {}, @@ -749,9 +810,27 @@ */ build_header_div: function() {}, /** - * Build drawable's icons div. + * Add an action icon to this object. Appends icon unless prepend flag is specified. */ - build_icons_div: function() {}, + add_action_icon: function(name, title, css_class, on_click_fn, prepend) { + var drawable = this; + this.action_icons[name] = $("<a/>").attr("href", "javascript:void(0);").attr("title", title) + .addClass("icon-button").addClass(css_class).tipsy( {gravity: 's'} ) + .click( function() { on_click_fn(drawable); } ) + .appendTo(this.icons_div); + }, + /** + * Build drawable's icons div from object's icons_dict. + */ + build_action_icons: function(action_icons_def) { + // Create icons. + var icon_dict; + for (var i = 0; i < action_icons_def.length; i++) { + icon_dict = action_icons_def[i]; + this.add_action_icon(icon_dict.name, icon_dict.title, icon_dict.css_class, + icon_dict.on_click_fn, icon_dict.prepend); + } + }, /** * Update icons. */ @@ -880,65 +959,6 @@ this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div); return header_div; }, - build_icons_div: function() { - var icons_div = $("<div/>").css("float", "left"); - - this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show group content") - .addClass("icon-button toggle").tipsy( {gravity: 's'} ) - .appendTo(icons_div); - this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") - .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) - .appendTo(icons_div); - this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove") - .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) - .appendTo(icons_div); - var group = this; - - // Toggle icon hides or shows the group content. - this.toggle_icon.click( function() { - if ( group.content_visible ) { - group.toggle_icon.addClass("toggle-expand").removeClass("toggle"); - group.hide_contents(); - group.content_visible = false; - } else { - group.toggle_icon.addClass("toggle").removeClass("toggle-expand"); - group.content_visible = true; - group.show_contents(); - } - }); - - // Clicking on settings icon opens group config. - this.settings_icon.click( function() { - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - group.config.update_from_form( $(".dialog-box") ); - hide_modal(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - show_modal("Configure Group", group.config.build_form(), { - "Cancel": cancel_fn, - "OK": ok_fn - }); - }); - - // Clicking on remove icon removes group. - this.remove_icon.click( function() { - // Tipsy for remove icon must be deleted when group is deleted. - $(".tipsy").remove(); - group.remove(); - }); - - return icons_div; - }, hide_contents : function () { this.content_div.hide(); }, @@ -2493,7 +2513,64 @@ this.content_div = $("<div class='track-content'>").appendTo(this.container_div); this.container.content_div.append(this.container_div); }; + extend(Track.prototype, Drawable.prototype, { + action_icons_def: [ + // Change track mode. + { + name: "mode_icon", + title: "Set display mode", + css_class: "chevron-expand", + on_click_fn: function() {} + }, + // Hide/show content. + Drawable.prototype.action_icons_def[0], + // Set track as overview. + { + name: "overview_icon", + title: "Set as overview", + css_class: "overview-icon", + on_click_fn: function() { + track.view.set_overview(track); + } + }, + // Edit config. + Drawable.prototype.action_icons_def[1], + // Toggle track filters. + { + name: "filters_icon", + title: "Filters", + css_class: "filters-icon", + on_click_fn: function(track) { + // TODO: update tipsy text. + track.filters_div.toggle(); + track.filters_manager.reset_filters(); + } + }, + // Toggle track tool. + { + name: "tools_icon", + title: "Tools", + css_class: "tools-icon", + on_click_fn: function(track) { + // TODO: update tipsy text. + + track.dynamic_tool_div.toggle(); + + // Update track name. + if (track.dynamic_tool_div.is(":visible")) { + track.set_name(track.name + track.tool_region_and_parameters_str()); + } + else { + track.revert_name(); + } + // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed. + $(".tipsy").remove(); + } + }, + // Remove track. + Drawable.prototype.action_icons_def[2] + ], build_container_div: function () { return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); }, @@ -2504,38 +2581,17 @@ .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); return header_div; }, - build_icons_div: function() { - var icons_div = $("<div/>").css("float", "left"); - - // Track icons. - this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode") - .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(icons_div); - this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content") - .addClass("icon-button toggle").tipsy( {gravity: 's'} ) - .appendTo(icons_div); - this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") - .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) - .appendTo(icons_div); - this.overview_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set as overview") - .addClass("icon-button overview-icon").tipsy( {gravity: 's'} ) - .appendTo(icons_div); - this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters") - .addClass("icon-button filters-icon").tipsy( {gravity: 's'} ) - .appendTo(icons_div).hide(); - this.tools_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Tools") - .addClass("icon-button tools-icon").tipsy( {gravity: 's'} ) - .appendTo(icons_div).hide(); - this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove") - .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) - .appendTo(icons_div); + build_action_icons: function() { + Drawable.prototype.build_action_icons.call(this, this.action_icons_def); + + // Set up behavior for modes popup. var track = this; - - // Set up behavior for modes popup. if (track.display_modes !== undefined) { var init_mode = (track.config && track.config.values['mode'] ? track.config.values['mode'] : track.display_modes[0]); track.mode = init_mode; - this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); + + this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); var mode_mapping = {}; for (var i = 0, len = track.display_modes.length; i < len; i++) { @@ -2550,79 +2606,8 @@ }(mode); } - make_popupmenu(this.mode_icon, mode_mapping); + make_popupmenu(this.action_icons.mode_icon, mode_mapping); } - - // Toggle icon hides or shows the track content. - this.toggle_icon.click( function() { - if ( track.content_visible ) { - track.toggle_icon.addClass("toggle-expand").removeClass("toggle"); - track.hide_contents(); - track.content_visible = false; - } else { - track.toggle_icon.addClass("toggle").removeClass("toggle-expand"); - track.content_visible = true; - track.show_contents(); - } - }); - - // Clicking on settings icon opens track config. - this.settings_icon.click( function() { - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - track.config.update_from_form( $(".dialog-box") ); - hide_modal(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - show_modal("Configure Track", track.config.build_form(), { - "Cancel": cancel_fn, - "OK": ok_fn - }); - }); - - this.overview_icon.click( function() { - track.view.set_overview(track); - }); - - this.filters_icon.click( function() { - // TODO: update tipsy text. - track.filters_div.toggle(); - track.filters_manager.reset_filters(); - }); - - this.tools_icon.click( function() { - // TODO: update tipsy text. - - track.dynamic_tool_div.toggle(); - - // Update track name. - if (track.dynamic_tool_div.is(":visible")) { - track.set_name(track.name + track.tool_region_and_parameters_str()); - } - else { - track.revert_name(); - } - // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed. - $(".tipsy").remove(); - }); - - // Clicking on remove icon removes track. - this.remove_icon.click( function() { - // Tipsy for remove icon must be deleted when track is deleted. - $(".tipsy").remove(); - track.remove(); - }); - - return icons_div; }, /** * Hide any elements that are part of the tracks contents area. Should @@ -2808,7 +2793,7 @@ track.config.values['mode'] = name; track.tile_cache.clear(); track.request_draw(); - this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); + this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); return track; }, /** @@ -2821,20 +2806,20 @@ // Show/hide filter icon. // if (track.filters_available > 0) { - track.filters_icon.show(); + track.action_icons.filters_icon.show(); } else { - track.filters_icon.hide(); + track.action_icons.filters_icon.hide(); } // // Show/hide tool icon. // if (track.tool) { - track.tools_icon.show(); + track.action_icons.tools_icon.show(); } else { - track.tools_icon.hide(); + track.action_icons.tools_icon.hide(); } // @@ -3506,7 +3491,7 @@ } else if ( mode == "summary_tree" ) { mode = "coverage histogram"; } - this.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")"); + this.action_icons.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")"); } }, /** 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.

1 0

commit/galaxy-central: greg: More fixes for Galaxy <-> tool shed communication.
by Bitbucket 23 Nov '11

23 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/255f4bde822b/ changeset: 255f4bde822b user: greg date: 2011-11-23 17:24:53 summary: More fixes for Galaxy <-> tool shed communication. affected #: 3 files diff -r af8f5887b97768777be91dab8df40bbcd8b8d3c8 -r 255f4bde822b4b9b36c1a9074cc6063a47127ff2 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -986,12 +986,11 @@ @web.expose @web.require_admin def check_for_updates( self, trans, **kwd ): + # Send a request to the relevant tool shed to see if there are any updates. repository = get_repository( trans, kwd[ 'id' ] ) - galaxy_url = url_for( '', qualified=True ) - # Send a request to the relevant tool shed to see if there are any updates. - # TODO: Fix this to use url_for to support locally hosted tool sheds. - url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision ) + tool_shed_url = get_url_from_repository_tool_shed( trans, repository ) + url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_url, url_for( '', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -1405,3 +1404,17 @@ trans.model.ToolShedRepository.table.c.owner == owner, trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ .first() +def get_url_from_repository_tool_shed( trans, repository ): + # The stored value of repository.tool_shed is something like: + # toolshed.g2.bx.psu.edu + # We need the URL to this tool shed, which is something like: + # http://toolshed.g2.bx.psu.edu/ + for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if shed_url.find( repository.tool_shed ) >= 0: + if shed_url.endswith( '/' ): + shed_url = shed_url.rstrip( '/' ) + return shed_url + # The tool shed from which the repository was originally + # installed must no longer be configured in tool_sheds_conf.xml. + return None + \ No newline at end of file diff -r af8f5887b97768777be91dab8df40bbcd8b8d3c8 -r 255f4bde822b4b9b36c1a9074cc6063a47127ff2 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1125,7 +1125,7 @@ import_button = True if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. - workflow_url = 'http://%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ + workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) response = urllib2.urlopen( workflow_url ) workflow_text = response.read() @@ -1197,7 +1197,7 @@ for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, url_for( '', qualified=True ), webapp ) if missing_tool_tups: url += '&tool_id=' for missing_tool_tup in missing_tool_tups: @@ -1224,8 +1224,7 @@ if tool_shed_url: # We've received the textual representation of a workflow from a Galaxy tool shed. message = "Workflow <b>%s</b> imported successfully." % workflow.name - # TODO: support https in the following url. - url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ + url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) return trans.response.send_redirect( url ) elif installed_repository_file: diff -r af8f5887b97768777be91dab8df40bbcd8b8d3c8 -r 255f4bde822b4b9b36c1a9074cc6063a47127ff2 lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -379,9 +379,8 @@ to_file.write( to_json_string( workflow_data ) ) return open( tmp_fname ) galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - # TODO: support https in the following url. - url = 'http://%s/workflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ - ( galaxy_url, trans.request.host, repository_metadata_id, encode( workflow_name ), webapp ) + url = '%s/workflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ + ( galaxy_url, url_for( '', qualified=True ), repository_metadata_id, encode( workflow_name ), webapp ) return trans.response.send_redirect( url ) return trans.response.send_redirect( web.url_for( controller='workflow', action='view_workflow', 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: Fixes for Galaxy / tool shed communication.
by Bitbucket 22 Nov '11

22 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/af8f5887b977/ changeset: af8f5887b977 user: greg date: 2011-11-22 23:09:14 summary: Fixes for Galaxy / tool shed communication. affected #: 2 files diff -r 9d6a9963b0da21fe3139fcefbd11c1ec6290a529 -r af8f5887b97768777be91dab8df40bbcd8b8d3c8 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -774,21 +774,21 @@ @web.require_admin def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = trans.request.host + galaxy_url = url_for( '', qualified=True ) url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = trans.request.host + galaxy_url = url_for( '', qualified=True ) url = '%s/repository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = trans.request.host + galaxy_url = url_for( '', qualified=True ) url = '%s/repository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @@ -986,11 +986,10 @@ @web.expose @web.require_admin def check_for_updates( self, trans, **kwd ): - params = util.Params( kwd ) repository = get_repository( trans, kwd[ 'id' ] ) - galaxy_url = trans.request.host + galaxy_url = url_for( '', qualified=True ) # Send a request to the relevant tool shed to see if there are any updates. - # TODO: support https in the following url. + # TODO: Fix this to use url_for to support locally hosted tool sheds. url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision ) return trans.response.send_redirect( url ) @@ -1215,7 +1214,7 @@ module = __import__( import_module ) sys.path.pop( 0 ) except Exception, e: - log.debug( "Execption importing datatypes code file included in installed repository: %s" % str( e ) ) + log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) ) trans.app.datatypes_registry = galaxy.datatypes.registry.Registry( trans.app.config.root, datatypes_config ) def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ): # The sample_files list contains all files whose name ends in .sample @@ -1398,10 +1397,11 @@ trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ .first() def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ): + if tool_shed.find( '//' ) > 0: + tool_shed = tool_shed.split( '//' )[1] return trans.sa_session.query( trans.model.ToolShedRepository ) \ .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed, trans.model.ToolShedRepository.table.c.name == name, trans.model.ToolShedRepository.table.c.owner == owner, trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ .first() - diff -r 9d6a9963b0da21fe3139fcefbd11c1ec6290a529 -r af8f5887b97768777be91dab8df40bbcd8b8d3c8 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -437,9 +437,8 @@ if operation == "install": galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) - # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ - ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict ) + url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ + ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict ) return trans.response.send_redirect( url ) else: # This can only occur when there is a multi-select grid with check boxes and an operation, @@ -514,9 +513,8 @@ if operation == "install": galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) - # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ - ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict ) + url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ + ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict ) return trans.response.send_redirect( url ) else: # This can only occur when there is a multi-select grid with check boxes and an operation, @@ -761,9 +759,8 @@ repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) encoded_repo_info_dict = encode( repo_info_dict ) # Redirect back to local Galaxy to perform install. - # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \ - ( galaxy_url, trans.request.host, encoded_repo_info_dict ) + url = '%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \ + ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict ) return trans.response.send_redirect( url ) @web.expose def check_for_updates( self, trans, **kwd ): @@ -776,8 +773,7 @@ changeset_revision = params.get( 'changeset_revision', None ) webapp = params.get( 'webapp', 'community' ) # Start building up the url to redirect back to the calling Galaxy instance. - # TODO: support https in the following url. - url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, trans.request.host ) + url = '%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '', qualified=True ) ) repository = get_repository_by_name_and_owner( trans, name, owner ) url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( repository.name, repository.user.username, changeset_revision ) 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: Have fimo.xml use fields.path approach instead of directly filtering on data table.
by Bitbucket 22 Nov '11

22 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9d6a9963b0da/ changeset: 9d6a9963b0da user: dan date: 2011-11-22 18:21:05 summary: Have fimo.xml use fields.path approach instead of directly filtering on data table. affected #: 1 file diff -r 49c48236f6ae2d8557420b1393fd763ce5f28889 -r 9d6a9963b0da21fe3139fcefbd11c1ec6290a529 tools/meme/fimo.xml --- a/tools/meme/fimo.xml +++ b/tools/meme/fimo.xml @@ -32,7 +32,7 @@ #if str( $fasta_type.fasta_type_selector ) == 'history': "${fasta_type.input_database}" #else: - "${ filter( lambda x: str( x[0] ) == str( $fasta_type.input_database ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][3] }" + "${fasta_type.input_database.fields.path}" #end if ' 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: Have rgPicardGCBiasMetrics.xml use fields.path approach instead of directly filtering on data table.
by Bitbucket 22 Nov '11

22 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/49c48236f6ae/ changeset: 49c48236f6ae user: dan date: 2011-11-22 17:56:53 summary: Have rgPicardGCBiasMetrics.xml use fields.path approach instead of directly filtering on data table. affected #: 1 file diff -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 -r 49c48236f6ae2d8557420b1393fd763ce5f28889 tools/picard/rgPicardGCBiasMetrics.xml --- a/tools/picard/rgPicardGCBiasMetrics.xml +++ b/tools/picard/rgPicardGCBiasMetrics.xml @@ -4,9 +4,9 @@ --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectGcBiasMetrics.jar #if $genomeSource.refGenomeSource == "history": - --ref-file "$genomeSource.ownFile" + --ref-file "${genomeSource.ownFile}" #else: - --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" + --ref "${genomeSource.index.fields.path}" #end if </command><requirements><requirement type="package">picard</requirement></requirements> 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 User preferences within a Galaxy tool shed to enable users to elect to receive email when content is first uploaded to a new repository. Also add a new grid interface to enable users to easily manage registering with any tool shed respositories to receive email when changes are made to the selected repositories.
by Bitbucket 22 Nov '11

22 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/84187b357d0c/ changeset: 84187b357d0c user: greg date: 2011-11-22 17:05:38 summary: Enhance User preferences within a Galaxy tool shed to enable users to elect to receive email when content is first uploaded to a new repository. Also add a new grid interface to enable users to easily manage registering with any tool shed respositories to receive email when changes are made to the selected repositories. affected #: 11 files diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -166,7 +166,7 @@ """Factory method to create parameter of correct type""" param_name = param.get( "name" ) if not param_name: - raise ValueError( "Tool parameters require a 'name'" ) + raise ValueError( "Tool parameter '%s' requires a 'name'" % (param_name ) ) param_type = param.get("type") if not param_type: raise ValueError( "Tool parameter '%s' requires a 'type'" % ( param_name ) ) diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -475,6 +475,7 @@ kwd[ 'f-Category.name' ] = category.name elif operation == "receive email alerts": if kwd[ 'id' ]: + kwd[ 'caller' ] = 'browse_repositories' return trans.response.send_redirect( web.url_for( controller='repository', action='set_email_alerts', **kwd ) ) diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -12,6 +12,28 @@ log = logging.getLogger( __name__ ) +new_repo_email_alert_template = """ +GALAXY TOOL SHED NEW REPOSITORY ALERT +----------------------------------------------------------------------------- +You received this alert because you registered to receive email when +new repositories were created in the Galaxy tool shed named "${host}". +----------------------------------------------------------------------------- + +Repository name: ${repository_name} +Date content uploaded: ${display_date} +Uploaded by: ${username} + +Revision: ${revision} +Change description: +${description} + +${content_alert_str} + +----------------------------------------------------------------------------- +This change alert was sent from the Galaxy tool shed hosted on the server +"${host}" +""" + email_alert_template = """ GALAXY TOOL SHED REPOSITORY UPDATE ALERT ----------------------------------------------------------------------------- @@ -464,7 +486,7 @@ except Exception, e: invalid_files.append( ( name, str( e ) ) ) return metadata_dict, invalid_files -def set_repository_metadata( trans, id, changeset_revision, **kwd ): +def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """Set repository metadata""" message = '' status = 'done' @@ -484,6 +506,9 @@ repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() + # If this is the first record stored for this repository, see if we need to send any email alerts. + if len( repository.downloadable_revisions ) == 1: + handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: # Update the last saved repository_metadata table row. repository_metadata = get_latest_repository_metadata( trans, id ) @@ -557,11 +582,31 @@ def get_user( trans, id ): """Get a user from the database by id""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) -def handle_email_alerts( trans, repository, content_alert_str='' ): +def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ): + # There are 2 complementary features that enable a tool shed user to receive email notification: + # 1. Within User Preferences, they can elect to receive email when the first (or first valid) + # change set is produced for a new repository. + # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" + # which caused them to receive email alerts when updates to the repository occur. This same feature + # is available on a per-repository basis on the repository grid within the tool shed. + # + # There are currently 4 scenarios for sending email notification when a change is made to a repository: + # 1. An admin user elects to receive email when the first change set is produced for a new repository + # from User Preferences. The change set does not have to include any valid content. This allows for + # the capture of inappropriate content being uploaded to new repositories. + # 2. A regular user elects to receive email when the first valid change set is produced for a new repository + # from User Preferences. This differs from 1 above in that the user will not receive email until a + # change set tha tincludes valid content is produced. + # 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the + # user is an admin user, the email will include information about both HTML and image content that was + # included in the change set. + # 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the + # user is not an admin user, the email will not include any information about both HTML and image content + # that was included in the change set. repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) smtp_server = trans.app.config.smtp_server - if smtp_server and repository.email_alerts: + if smtp_server and ( new_repo_alert or repository.email_alerts ): # Send email alert to users that want them. if trans.app.config.email_from is not None: email_from = trans.app.config.email_from @@ -580,26 +625,40 @@ username = ctx.user() # We'll use 2 template bodies because we only want to send content # alerts to tool shed admin users. - admin_body = string.Template( email_alert_template ) \ - .safe_substitute( host=trans.request.host, - repository_name=repository.name, - revision='%s:%s' %( str( ctx.rev() ), ctx ), - display_date=display_date, - description=ctx.description(), - username=username, - content_alert_str=content_alert_str ) - body = string.Template( email_alert_template ) \ - .safe_substitute( host=trans.request.host, - repository_name=repository.name, - revision='%s:%s' %( str( ctx.rev() ), ctx ), - display_date=display_date, - description=ctx.description(), - username=username, - content_alert_str='' ) + if new_repo_alert: + template = new_repo_email_alert_template + else: + template = email_alert_template + admin_body = string.Template( template ).safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str=content_alert_str ) + body = string.Template( template ).safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str='' ) admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) frm = email_from - subject = "Galaxy tool shed repository update alert" - email_alerts = from_json_string( repository.email_alerts ) + if new_repo_alert: + subject = "New Galaxy tool shed repository alert" + email_alerts = [] + for user in trans.sa_session.query( trans.model.User ) \ + .filter( and_( trans.model.User.table.c.deleted == False, + trans.model.User.table.c.new_repo_alert == True ) ): + if admin_only: + if user.email in admin_users: + email_alerts.append( user.email ) + else: + email_alerts.append( user.email ) + else: + subject = "Galaxy tool shed repository update alert" + email_alerts = from_json_string( repository.email_alerts ) for email in email_alerts: to = email.strip() # Send it diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -182,6 +182,37 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) +class EmailAlertsRepositoryListGrid( RepositoryListGrid ): + columns = [ + RepositoryListGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.id, + webapp="community" ) ), + attach_popup=False ), + RepositoryListGrid.DescriptionColumn( "Synopsis", + key="description", + attach_popup=False ), + RepositoryListGrid.UserColumn( "Owner", + model_class=model.User, + link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), + attach_popup=False, + key="User.username" ), + RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) + ] + operations = [ grids.GridOperation( "Receive email alerts", + allow_multiple=True, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ] + global_actions = [ + grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository', webapp='community' ) ) + ] + class ValidRepositoryListGrid( RepositoryListGrid ): class RevisionColumn( grids.GridColumn ): def __init__( self, col_name ): @@ -290,6 +321,7 @@ matched_repository_list_grid = MatchedRepositoryListGrid() valid_repository_list_grid = ValidRepositoryListGrid() repository_list_grid = RepositoryListGrid() + email_alerts_repository_list_grid = EmailAlertsRepositoryListGrid() category_list_grid = CategoryListGrid() @web.expose @@ -876,6 +908,7 @@ elif operation == "receive email alerts": if trans.user: if kwd[ 'id' ]: + kwd[ 'caller' ] = 'browse_repositories' return trans.response.send_redirect( web.url_for( controller='repository', action='set_email_alerts', **kwd ) ) @@ -1550,7 +1583,9 @@ @web.require_login( "set email alerts" ) def set_email_alerts( self, trans, **kwd ): # Set email alerts for selected repositories - params = util.Params( kwd ) + # This method is called from multiple grids, so + # the caller must be passed. + caller = kwd[ 'caller' ] user = trans.user if user: repository_ids = util.listify( kwd.get( 'id', '' ) ) @@ -1582,9 +1617,63 @@ kwd[ 'status' ] = 'done' del kwd[ 'operation' ] return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', + action=caller, **kwd ) ) @web.expose + @web.require_login( "manage email alerts" ) + def manage_email_alerts( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + new_repo_alert = params.get( 'new_repo_alert', '' ) + new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert ) + user = trans.user + if params.get( 'new_repo_alert_button', False ): + user.new_repo_alert = new_repo_alert_checked + trans.sa_session.add( user ) + trans.sa_session.flush() + if new_repo_alert_checked: + message = 'You will receive email alerts for all new valid tool shed repositories.' + else: + message = 'You will not receive any email alerts for new valid tool shed repositories.' + checked = new_repo_alert_checked or ( user and user.new_repo_alert ) + new_repo_alert_check_box = CheckboxField( 'new_repo_alert', checked=checked ) + email_alert_repositories = [] + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.email_alerts != None ) ) \ + .order_by( trans.model.Repository.table.c.name ): + if user.email in repository.email_alerts: + email_alert_repositories.append( repository ) + return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", + webapp='community', + new_repo_alert_check_box=new_repo_alert_check_box, + email_alert_repositories=email_alert_repositories, + message=message, + status=status ) + @web.expose + @web.require_login( "manage email alerts" ) + def multi_select_email_alerts( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if 'webapp' not in kwd: + kwd[ 'webapp' ] = 'community' + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "receive email alerts": + if trans.user: + if kwd[ 'id' ]: + kwd[ 'caller' ] = 'multi_select_email_alerts' + return trans.response.send_redirect( web.url_for( controller='repository', + action='set_email_alerts', + **kwd ) ) + else: + kwd[ 'message' ] = 'You must be logged in to set email alerts.' + kwd[ 'status' ] = 'error' + del kwd[ 'operation' ] + return self.email_alerts_repository_list_grid( trans, **kwd ) + @web.expose @web.require_login( "set repository metadata" ) def set_metadata( self, trans, id, ctx_str, **kwd ): malicious = kwd.get( 'malicious', '' ) diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -32,6 +32,10 @@ tip = repository.tip file_data = params.get( 'file_data', '' ) url = params.get( 'url', '' ) + # Part of the upload process is sending email notification to those that have registered to + # receive them. One scenario occurs when the first change set is produced for the repository. + # See the handle_email_alerts() method for the definition of the scenarios. + new_repo_alert = repository.is_new if params.get( 'upload_button', False ): current_working_dir = os.getcwd() if file_data == '' and url == '': @@ -87,13 +91,14 @@ tar = None istar = False if istar: - ok, message, files_to_remove = self.upload_tar( trans, - repository, - tar, - uploaded_file, - upload_point, - remove_repo_files_not_in_tar, - commit_message ) + ok, message, files_to_remove, content_alert_str = self.upload_tar( trans, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert ) else: if ( isgzip or isbz2 ) and uncompress_file: uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) @@ -131,7 +136,9 @@ # Handle the special case where a xxx.loc.sample file is # being uploaded by copying it to ~/tool-data/xxx.loc. copy_sample_loc_file( trans, full_path ) - handle_email_alerts( trans, repository, content_alert_str=content_alert_str ) + # See if the content of the change set was valid. + admin_only = len( repository.downloadable_revisions ) != 1 + handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) if ok: # Update the repository files for browsing. update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) @@ -150,7 +157,7 @@ else: message = 'No changes to repository.' # Set metadata on the repository tip - error_message, status = set_repository_metadata( trans, repository_id, repository.tip, **kwd ) + error_message, status = set_repository_metadata( trans, repository_id, repository.tip, content_alert_str=content_alert_str, **kwd ) if error_message: message = '%s<br/>%s' % ( message, error_message ) return trans.response.send_redirect( web.url_for( controller='repository', @@ -176,16 +183,17 @@ remove_repo_files_not_in_tar=remove_repo_files_not_in_tar, message=message, status=status ) - def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message ): + def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) files_to_remove = [] + content_alert_str = '' ok, message = self.__check_archive( tar ) if not ok: tar.close() uploaded_file.close() - return ok, message, files_to_remove + return ok, message, files_to_remove, content_alert_str else: if upload_point is not None: full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) @@ -197,7 +205,6 @@ tar.extractall( path=full_path ) tar.close() uploaded_file.close() - content_alert_str = '' if remove_repo_files_not_in_tar and not repository.is_new: # We have a repository that is not new (it contains files), so discover # those files that are in the repository, but not in the uploaded archive. @@ -256,7 +263,7 @@ # appending them to the shed's tool_data_table_conf.xml file on disk. error, message = handle_sample_tool_data_table_conf_file( trans, filename_in_archive ) if error: - return False, message, files_to_remove + return False, message, files_to_remove, content_alert_str if filename_in_archive.endswith( '.loc.sample' ): # Handle the special case where a xxx.loc.sample file is # being uploaded by copying it to ~/tool-data/xxx.loc. @@ -269,8 +276,10 @@ # exception. If this happens, we'll try the following. repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) - handle_email_alerts( trans, repository, content_alert_str ) - return True, '', files_to_remove + # See if the content of the change set was valid. + admin_only = len( repository.downloadable_revisions ) != 1 + handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) + return True, '', files_to_remove, content_alert_str def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: self.__handle_gzip( repository, uploaded_file_name ) diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -20,6 +20,7 @@ self.deleted = False self.purged = False self.username = None + self.new_repo_alert = False def set_password_cleartext( self, cleartext ): """Set 'self.password' to the digest of 'cleartext'.""" self.password = new_secure_hash( text_type=cleartext ) diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -45,6 +45,7 @@ Column( "username", String( 255 ), index=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), + Column( "new_repo_alert", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py --- /dev/null +++ b/lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py @@ -0,0 +1,50 @@ +""" +Migration script to add the new_repo_alert column to the galaxy_user table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset 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, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + # Create and initialize imported column in job table. + User_table = Table( "galaxy_user", metadata, autoload=True ) + c = Column( "new_repo_alert", Boolean, default=False, index=True ) + try: + # Create + c.create( User_table ) + assert c is User_table.c.new_repo_alert + # Initialize. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE galaxy_user SET new_repo_alert=%s" % default_false ) + except Exception, e: + print "Adding new_repo_alert column to the galaxy_user table failed: %s" % str( e ) + log.debug( "Adding new_repo_alert column to the galaxy_user table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + # Drop new_repo_alert column from galaxy_user table. + User_table = Table( "galaxy_user", metadata, autoload=True ) + try: + User_table.c.new_repo_alert.drop() + except Exception, e: + print "Dropping column new_repo_alert from the galaxy_user table failed: %s" % str( e ) + log.debug( "Dropping column new_repo_alert from the galaxy_user table failed: %s" % str( e ) ) diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -16,7 +16,7 @@ <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('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="${h.url_for( controller='user', action='openid_manage', cntrller=cntrller )}">${_('Manage OpenIDs')}</a> linked to your account</li> %endif %if trans.app.config.use_remote_user: %if trans.app.config.remote_user_logout_href: @@ -27,14 +27,18 @@ %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> ${_('of all user sessions')}</li> %endif </ul> - <p> - You are using <strong>${trans.user.get_disk_usage( nice_size=True )}</strong> of disk space in this Galaxy instance. - %if trans.app.config.enable_quotas: - Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>. - %endif - </p> + %if webapp == 'galaxy': + <p> + You are using <strong>${trans.user.get_disk_usage( nice_size=True )}</strong> of disk space in this Galaxy instance. + %if trans.app.config.enable_quotas: + Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>. + %endif + </p> + %endif %else: %if not message: <p>${n_('You are currently not logged in.')}</p> diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -67,9 +67,6 @@ <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a></div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', webapp='community' )}">Browse all repositories</a> - </div> %if trans.user: <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a> diff -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 templates/webapps/community/user/manage_email_alerts.mako --- /dev/null +++ b/templates/webapps/community/user/manage_email_alerts.mako @@ -0,0 +1,54 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<br/><br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='repository', action='multi_select_email_alerts', cntrller='repository', webapp=webapp )}">Manage repository alerts</a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='user', action='index', cntrller='repository', webapp=webapp )}">User preferences</a> + </li> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Email alerts for new repositories</div> + <form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts', webapp=webapp )}" method="post" > + <div class="form-row"> + <label>New repository alert:</label> + ${new_repo_alert_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Check the box and click <b>Save</b> to receive email when the first change set is created for a new repository. + </div> + </div> + <div class="form-row"> + <input type="submit" name="new_repo_alert_button" value="Save"/> + </div> + </form> +</div> +<p/> +%if email_alert_repositories: + <div class="toolForm"> + <div class="toolFormTitle">You are registered to receive email alerts for changes to the following repositories</div> + <div class="form-row"> + <table class="grid"> + <tr> + <th>Name</th> + <th>Description</th> + </tr> + %for repository in email_alert_repositories: + <tr> + <td>${repository.name}</td> + <td>${repository.description}</td> + </tr> + %endfor + </table> + </div> + </div> + <p/> +%endif + 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 file browser importer.
by Bitbucket 21 Nov '11

21 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/843fdc5e0ebd/ changeset: 843fdc5e0ebd user: dan date: 2011-11-21 23:12:07 summary: Updates for GenomeSpace file browser importer. affected #: 3 files diff -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -26,7 +26,9 @@ <tool file="data_source/epigraph_import.xml" /><tool file="data_source/epigraph_import_test.xml" /><tool file="data_source/hbvar.xml" /> - <tool file="data_source/genomespace_file_browser_dev.xml" /> + <tool file="data_source/genomespace_file_browser_prod.xml" /> + <tool file="validation/fix_errors.xml" /></section><section name="Send Data" id="send"> diff -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 tools/data_source/genomespace_file_browser_prod.xml --- /dev/null +++ b/tools/data_source/genomespace_file_browser_prod.xml @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<tool name="GenomeSpace import" id="genomespace_file_browser_prod" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1"> + <description>from file browser</description> + <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "prod"</command> + <inputs action="https://dm.genomespace.org/datamanager/defaultdirectory" check_values="False" method="post"> + <display>go to GenomeSpace Data Manager </display> + <param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&runtool_btn=Execute" /> + <param name="appName" type="hidden" value="Galaxy" /> + </inputs> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="auto" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> diff -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 -r 843fdc5e0ebdc2eafcf97b64c8191b5564ea1836 tools/data_source/genomespace_file_browser_test.xml --- /dev/null +++ b/tools/data_source/genomespace_file_browser_test.xml @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<tool name="GenomeSpace import" id="genomespace_file_browser_test" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1"> + <description>from file browser (test)</description> + <command interpreter="python">genomespace_file_browser.py --json_parameter_file "${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="appName" type="hidden" value="Galaxy" /> + </inputs> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="auto" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> 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 help for some SAMTools.
by Bitbucket 21 Nov '11

21 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/52ce5e6950b7/ changeset: 52ce5e6950b7 user: dan date: 2011-11-21 22:55:16 summary: Update help for some SAMTools. affected #: 5 files diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/bam_to_sam.xml --- a/tools/samtools/bam_to_sam.xml +++ b/tools/samtools/bam_to_sam.xml @@ -56,5 +56,11 @@ .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + </help></tool> diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -177,6 +177,12 @@ .. _consensus: http://samtools.sourceforge.net/cns0.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + </help></tool> diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml +++ b/tools/samtools/sam_to_bam.xml @@ -87,5 +87,11 @@ .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + </help></tool> diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/samtools_flagstat.xml --- a/tools/samtools/samtools_flagstat.xml +++ b/tools/samtools/samtools_flagstat.xml @@ -25,5 +25,13 @@ .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/samtools_rmdup.xml --- a/tools/samtools/samtools_rmdup.xml +++ b/tools/samtools/samtools_rmdup.xml @@ -57,5 +57,13 @@ .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> 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: Remove no longer supported ROD datatypes from GATK tools (version 1.3).
by Bitbucket 21 Nov '11

21 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/945c7a47755f/ changeset: 945c7a47755f user: dan date: 2011-11-21 22:41:19 summary: Remove no longer supported ROD datatypes from GATK tools (version 1.3). affected #: 2 files diff -r 88afa15e556dfea22d34b0a78ffc3ebe162b64f7 -r 945c7a47755f4c468d0742ad02d43647a300565c tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -147,17 +147,17 @@ <option value="custom">Custom</option></param><when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /></when><when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /></when><when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /></when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /></when></conditional></repeat> diff -r 88afa15e556dfea22d34b0a78ffc3ebe162b64f7 -r 945c7a47755f4c468d0742ad02d43647a300565c tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -179,7 +179,7 @@ <option value="custom">Custom</option></param><when value="variant"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="Variant ROD file" /> + <param name="input_rod" type="data" format="vcf" label="Variant ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -198,7 +198,7 @@ </conditional></when><when value="comp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><param name="custom_rod_name" type="text" value="Unnamed" label="ROD Name"/><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> @@ -218,7 +218,7 @@ </conditional></when><when value="dbsnp"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -237,7 +237,7 @@ </conditional></when><when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -256,7 +256,7 @@ </conditional></when><when value="hapmap"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -275,7 +275,7 @@ </conditional></when><when value="omni"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -294,7 +294,7 @@ </conditional></when><when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> @@ -314,7 +314,7 @@ </when><when value="custom"><param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> + <param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"><param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"><option value="is_training_truth_known">Set training/truth/known sites</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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