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

commit/galaxy-central: dannon: Sanitize output anytime a raw text/html dataset is served via dataset/display.
by Bitbucket 05 Dec '11

05 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/35fee32991ce/ changeset: 35fee32991ce user: dannon date: 2011-12-06 03:57:19 summary: Sanitize output anytime a raw text/html dataset is served via dataset/display. affected #: 1 file diff -r b2bc0629e78176b9cbe34c86a8eb141dfa0c70aa -r 35fee32991ce5463d79ce278cb3a9c1155e8982f lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -317,7 +317,7 @@ trans.response.headers["Content-Type"] = "application/octet-stream" trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, file_ext) return open(data.metadata.get(metadata_name).file_name) - + @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): """Catches the dataset id and displays file contents as directed""" @@ -337,10 +337,9 @@ raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): return trans.show_error_message( "You are not allowed to access this dataset" ) - + if data.state == trans.model.Dataset.states.UPLOAD: return trans.show_error_message( "Please wait until this dataset finishes uploading before attempting to view it." ) - if filename and filename != "index": # For files in extra_files_path file_path = os.path.join( data.extra_files_path, filename ) @@ -357,14 +356,14 @@ return open( file_path ) else: return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) ) - + trans.response.set_content_type(data.get_mime()) trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) - + if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file if data.extension in composite_extensions: return self.archive_composite_dataset( trans, data, **kwd ) - else: + else: trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) if not to_ext: to_ext = data.extension @@ -375,11 +374,13 @@ return open( data.file_name ) if not os.path.exists( data.file_name ): raise paste.httpexceptions.HTTPNotFound( "File Not Found (%s)." % data.file_name ) - max_peek_size = 1000000 # 1 MB if isinstance(data.datatype, datatypes.images.Html): max_peek_size = 10000000 # 10 MB for html if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size: + if trans.response.get_content_type() == "text/html": + # Sanitize anytime we respond with plain text/html content. + return sanitize_html(open( data.file_name ).read()) return open( data.file_name ) else: trans.response.set_content_type( "text/html" ) 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: natefoo: Fedora(/RHEL/SL/CentOS) init script, thanks Brad Chapman!
by Bitbucket 05 Dec '11

05 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b2bc0629e781/ changeset: b2bc0629e781 user: natefoo date: 2011-12-05 20:55:00 summary: Fedora(/RHEL/SL/CentOS) init script, thanks Brad Chapman! affected #: 2 files diff -r 94dc7288f81f61553467e283e2646755312d8a38 -r b2bc0629e78176b9cbe34c86a8eb141dfa0c70aa contrib/README --- a/contrib/README +++ b/contrib/README @@ -19,6 +19,12 @@ paths, and configure for start at boot with `update-rc.d galaxy defaults`. Also written and submitted by James Casbon. +galaxy.fedora-init: + + init script for Fedora/RedHat/Scientific Linux/CentOS. Copy to + /etc/init.d/galaxy, modify paths, and configure for start at boot with + `chkconfig galaxy on`. Written and submitted by Brad Chapman. + galaxy.solaris-smf.xml: SMF Manifest for Solaris 10 and OpenSolaris. Import with `svccfg import diff -r 94dc7288f81f61553467e283e2646755312d8a38 -r b2bc0629e78176b9cbe34c86a8eb141dfa0c70aa contrib/galaxy.fedora-init --- /dev/null +++ b/contrib/galaxy.fedora-init @@ -0,0 +1,105 @@ +#!/bin/bash +# +# Init file for Galaxy (http://galaxyproject.org/) +# Suitable for use on Fedora and derivatives (RedHat Enterprise Linux, Scientific Linux, CentOS) +# +# Contributed by Brad Chapman +# +# chkconfig: 2345 98 20 +# description: Galaxy http://galaxyproject.org/ + +#--- config + +SERVICE_NAME="galaxy" +RUN_AS="galaxy" +RUN_IN="/path/to/galaxy-dist" + +#--- main actions + +start() { + echo "Starting $SERVICE_NAME... " + cmd="cd $RUN_IN && sh run.sh --daemon" + case "$(id -un)" in + $RUN_AS) + eval "$cmd" + ;; + root) + su - $RUN_AS -c "$cmd" + ;; + *) + echo "*** ERROR *** must be $RUN_AS or root in order to control this service" >&2 + exit 1 + esac + echo "...done." +} + +stop() { + echo -n "Stopping $SERVICE_NAME... " + + cmd="cd $RUN_IN && sh run.sh --stop-daemon" + + case "$(id -un)" in + $RUN_AS) + eval "$cmd" + ;; + root) + su - $RUN_AS -c "$cmd" + ;; + *) + echo "*** ERROR *** must be $RUN_AS or root in order to control this service" >&2 + exit 1 + esac + + echo "done." +} + +status() { + echo -n "$SERVICE_NAME status: " + + while read pid; do + if [ "$(readlink -m /proc/$pid/cwd)" = "$(readlink -m $RUN_IN)" ]; then + echo "started" + return 0 + fi + done < <(ps ax -o 'pid cmd' | grep -P '^\s*\d+ python ./scripts/paster.py serve' | awk '{print $1}') + echo "stopped" + return 3 +} + +notsupported() { + echo "*** ERROR*** $SERVICE_NAME: operation [$1] not supported" +} + +usage() { + echo "Usage: $SERVICE_NAME start|stop|restart|status" +} + + +#--- + +case "$1" in + start) + start "$@" + ;; + stop) + stop + ;; + restart|reload) + stop + start + ;; + status) + set +e + status + exit $? + ;; + '') + usage >&2 + exit 1 + ;; + *) + notsupported "$1" >&2 + usage >&2 + exit 1 + ;; +esac 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 tool data tables for GATK.
by Bitbucket 05 Dec '11

05 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/94dc7288f81f/ changeset: 94dc7288f81f user: dan date: 2011-12-05 18:32:02 summary: Update tool data tables for GATK. affected #: 1 file diff -r 46e455a590e5923db81cda0034d6192503ce29a6 -r 94dc7288f81f61553467e283e2646755312d8a38 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -77,8 +77,13 @@ </table><table name="gatk_picard_indexes" comment_char="#"> - <columns>value, dbkey, name, path, tools_valid_for</columns> - <file path="tool-data/picard_index.loc" /> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gatk_sorted_picard_index.loc" /> + </table> +  + <table name="gatk_annotations" comment_char="#"> + <columns>value, name, gatk_value, tools_valid_for</columns> + <file path="tool-data/gatk_annotations.txt" /></table><table name="srma_indexes" comment_char="#"> 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: GATK tools will now use their own .loc file for picard indexes and will also load annotations from an external file.
by Bitbucket 05 Dec '11

05 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/46e455a590e5/ changeset: 46e455a590e5 user: dan date: 2011-12-05 18:27:54 summary: GATK tools will now use their own .loc file for picard indexes and will also load annotations from an external file. affected #: 5 files diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tool-data/gatk_annotations.txt.sample --- /dev/null +++ b/tool-data/gatk_annotations.txt.sample @@ -0,0 +1,30 @@ +#unique_id name gatk_value tools_valid_for +AlleleBalance AlleleBalance AlleleBalance UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +AlleleBalanceBySample AlleleBalanceBySample AlleleBalanceBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +BaseCounts BaseCounts BaseCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +ChromosomeCounts ChromosomeCounts ChromosomeCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +DepthOfCoverage DepthOfCoverage DepthOfCoverage UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +DepthPerAlleleBySample DepthPerAlleleBySample DepthPerAlleleBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +FisherStrand FisherStrand FisherStrand UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +GCContent GCContent GCContent UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +HaplotypeScore HaplotypeScore HaplotypeScore UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +HardyWeinberg HardyWeinberg HardyWeinberg UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +HomopolymerRun HomopolymerRun HomopolymerRun UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +InbreedingCoeff InbreedingCoeff InbreedingCoeff UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +IndelType IndelType IndelType UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +LowMQ LowMQ LowMQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MVLikelihoodRatio MVLikelihoodRatio MVLikelihoodRatio UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MappingQualityZero MappingQualityZero MappingQualityZero UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MappingQualityZeroBySample MappingQualityZeroBySample MappingQualityZeroBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MappingQualityZeroFraction MappingQualityZeroFraction MappingQualityZeroFraction UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +NBaseCount NBaseCount NBaseCount UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +QualByDepth QualByDepth QualByDepth UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +RMSMappingQuality RMSMappingQuality RMSMappingQuality UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +ReadDepthAndAllelicFractionBySample ReadDepthAndAllelicFractionBySample ReadDepthAndAllelicFractionBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +ReadPosRankSumTest ReadPosRankSumTest ReadPosRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +SampleList SampleList SampleList UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +SnpEff SnpEff SnpEff VariantAnnotator,VariantRecalibrator +SpanningDeletions SpanningDeletions SpanningDeletions UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +TechnologyComposition TechnologyComposition TechnologyComposition UnifiedGenotyper,VariantAnnotator,VariantRecalibrator diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tool-data/gatk_sorted_picard_index.loc.sample --- /dev/null +++ b/tool-data/gatk_sorted_picard_index.loc.sample @@ -0,0 +1,26 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Picard dict and associated files. You will need +#to create these data files and then create a picard_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The picard_index.loc +#file has this format (longer white space is the TAB character): +# +#<unique_build_id><dbkey><display_name><fasta_file_path> +# +#So, for example, if you had hg18 indexed and stored in +#/depot/data2/galaxy/srma/hg18/, +#then the srma_index.loc entry would look like this: +# +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +# +#and your /depot/data2/galaxy/srma/hg18/ directory +#would contain the following three files: +#hg18.fa +#hg18.dict +#hg18.fa.fai +# +#The dictionary file for each reference (ex. hg18.dict) must be +#created via Picard (http://picard.sourceforge.net) Note that +#the dict file does not have the .fa extension although the +#path list in the loc file does include it. +# diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -113,7 +113,7 @@ --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}" ${analysis_param_type.doContextDependentGapPenalties} #if str( $analysis_param_type.annotation ) != "None": - #for $annotation in str( $analysis_param_type.annotation ).split( ','): + #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','): --annotation "${annotation}" #end for #end if @@ -123,7 +123,7 @@ #end for #end if #if str( $analysis_param_type.exclude_annotations ) != "None": - #for $annotation in str( $analysis_param_type.exclude_annotations ).split( ','): + #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','): --excludeAnnotation "${annotation}" #end for #end if @@ -366,35 +366,11 @@ <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="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" /> +  + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> + </options></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" /> +  + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> + </options></param></when></conditional> diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -26,13 +26,13 @@ --useAllAnnotations #else: #if str( $annotations_type.annotations ) != "None": - #for $annotation in str( $annotations_type.annotations ).split( ',' ): + #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ): --annotation "${annotation}" #end for #end if #end if #if str( $exclude_annotations ) != "None": - #for $annotation in str( $exclude_annotations ).split( ',' ): + #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ): --excludeAnnotation "${annotation}" #end for #end if @@ -179,36 +179,11 @@ </when><when value="choose"><param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" > -  - <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" /> +  + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/> + </options></param></when></conditional> @@ -388,36 +363,11 @@ <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" /> +  + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/> + </options></param></inputs> diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -100,7 +100,7 @@ ##start analysis specific options -p ' #if str( $annotations ) != "None": - #for $annotation in str( $annotations ).split( ',' ): + #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ): --use_annotation "${annotation}" #end for #end if @@ -337,36 +337,11 @@ </repeat><param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations"> -  - <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"/> +  + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/> + </options></param><param name="mode" type="select" label="Recalibration mode"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Look for datasets/indices in metadata and use if found rather than doing conversion.
by Bitbucket 05 Dec '11

05 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/943855e11c85/ changeset: 943855e11c85 user: jgoecks date: 2011-12-05 18:19:48 summary: Look for datasets/indices in metadata and use if found rather than doing conversion. affected #: 2 files diff -r 5e67b3ddbda241bf8a24969ac6caa47e9cbe5d9b -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -928,7 +928,10 @@ depends_list = trans.app.datatypes_registry.converter_deps[self.extension][target_ext] except KeyError: depends_list = [] - # See if converted dataset already exists + # See if converted dataset already exists, either in metadata in conversions. + converted_dataset = self.get_metadata_dataset( trans, target_ext ) + if converted_dataset: + return converted_dataset converted_dataset = self.get_converted_files_by_type( target_ext ) if converted_dataset: return converted_dataset @@ -958,6 +961,21 @@ session.add( assoc ) session.flush() return None + def get_metadata_dataset( self, trans, dataset_ext ): + """ + Returns an HDA that points to a metadata file which contains a + converted data with the requested extension. + """ + for name, value in self.metadata.items(): + # HACK: MetadataFile objects do not have a type/ext, so need to use metadata name + # to determine type. + if dataset_ext == 'bai' and name == 'bam_index' and isinstance( value, trans.app.model.MetadataFile ): + # HACK: MetadataFile objects cannot be used by tools, so return + # a fake HDA that points to metadata file. + fake_dataset = trans.app.model.Dataset( state=trans.app.model.Dataset.states.OK, + external_filename=value.file_name ) + fake_hda = trans.app.model.HistoryDatasetAssociation( dataset=fake_dataset ) + return fake_hda def clear_associated_files( self, metadata_safe = False, purge = False ): raise 'Unimplemented' def get_child_by_designation(self, designation): diff -r 5e67b3ddbda241bf8a24969ac6caa47e9cbe5d9b -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -546,7 +546,7 @@ valid_chroms = indexer.valid_chroms() else: # Standalone data provider - standalone_provider = get_data_provider(data_sources['data_standalone']['name'])( dataset ) + standalone_provider = get_data_provider( data_sources['data_standalone']['name'] )( dataset ) kwargs = {"stats": True} if not standalone_provider.has_data( chrom ): return messages.NO_DATA @@ -609,16 +609,8 @@ else: tracks_dataset_type = data_sources['data']['name'] data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) - # HACK: Use bai from bam HDA's metadata if available. This saves - # the client from waiting a long time to generate a duplicate - # bam via a converted dataset. - if dataset.ext == "bam" and dataset.metadata.get( "bam_index", None ) is not None: - converted_dataset = dataset.metadata.bam_index - deps = None - else: - # Default behavior. - converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) - deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type ) + converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type ) + deps = dataset.get_converted_dataset_deps( trans, tracks_dataset_type ) data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) # Get and return data from data_provider. @@ -1037,16 +1029,15 @@ data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } return data_sources_dict - + def _convert_dataset( self, trans, dataset, target_type ): """ Converts a dataset to the target_type and returns a message indicating status of the conversion. None is returned to indicate that dataset was converted successfully. """ - - # Get converted dataset; this will start the conversion if - # necessary. + + # Get converted dataset; this will start the conversion if necessary. try: converted_dataset = dataset.get_converted_dataset( trans, target_type ) except NoConverterException: @@ -1063,7 +1054,7 @@ msg = { 'kind': messages.ERROR, 'message': job.stderr } elif not converted_dataset or converted_dataset.state != model.Dataset.states.OK: msg = messages.PENDING - + return msg def _get_highest_priority_msg( message_list ): 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: Allow select_param.fields.name method of accessing additional attributes from dynamic options work for multiple selects.
by Bitbucket 05 Dec '11

05 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5e67b3ddbda2/ changeset: 5e67b3ddbda2 user: dan date: 2011-12-05 17:37:46 summary: Allow select_param.fields.name method of accessing additional attributes from dynamic options work for multiple selects. affected #: 2 files diff -r 52de9815a7c4438c03daaa478df29c037e18f2a1 -r 5e67b3ddbda241bf8a24969ac6caa47e9cbe5d9b lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2190,11 +2190,14 @@ Only applicable for dynamic_options selects, which have more than simple 'options' defined (name, value, selected). """ def __init__( self, input, value, other_values ): - self.input = input - self.value = value - self.other_values = other_values + self._input = input + self._value = value + self._other_values = other_values + self._fields = {} def __getattr__( self, name ): - return self.input.options.get_field_by_name_for_value( name, self.value, None, self.other_values ) + if name not in self._fields: + self._fields[ name ] = self._input.options.get_field_by_name_for_value( name, self._value, None, self._other_values ) + return self._input.separator.join( map( str, self._fields[ name ] ) ) def __init__( self, input, value, app, other_values={} ): self.input = input diff -r 52de9815a7c4438c03daaa478df29c037e18f2a1 -r 5e67b3ddbda241bf8a24969ac6caa47e9cbe5d9b lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -525,13 +525,18 @@ """ Get contents of field by name for specified value. """ + rval = [] if isinstance( field_name, int ): field_index = field_name else: assert field_name in self.columns, "Requested '%s' column missing from column def" % field_name field_index = self.columns[ field_name ] - for fields in self.get_fields_by_value( value, trans, other_values ): - return fields[ field_index ] + if not isinstance( value, list ): + value = [value] + for val in value: + for fields in self.get_fields_by_value( val, trans, other_values ): + rval.append( fields[ field_index ] ) + return rval def get_options( self, trans, other_values ): rval = [] 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: dannon: Fix for workflow multiple input regression from 6185:07f3f601d645.
by Bitbucket 05 Dec '11

05 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/52de9815a7c4/ changeset: 52de9815a7c4 user: dannon date: 2011-12-05 17:29:31 summary: Fix for workflow multiple input regression from 6185:07f3f601d645. affected #: 1 file diff -r e69c868b6891ccf6deabcba8a767cdf31593d1be -r 52de9815a7c4438c03daaa478df29c037e18f2a1 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1432,7 +1432,7 @@ step.upgrade_messages = {} # Connections by input name step.input_connections_by_name = \ - dict( ( conn.input_name, conn ) for conn in step.input_connections ) + dict( ( conn.input_name, conn ) for conn in step.input_connections ) # Extract just the arguments for this step by prefix p = "%s|" % step.id l = len(p) @@ -1446,7 +1446,7 @@ has_upgrade_messages = True # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) - module.add_dummy_datasets( connections=step.input_connections ) + module.add_dummy_datasets( connections=step.input_connections ) # Get the tool tool = module.tool # Get the state @@ -1462,7 +1462,7 @@ state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) ) step_errors = module.update_runtime_state( trans, state, step_args ) if step_errors: - errors[step.id] = state.inputs["__errors__"] = step_errors + errors[step.id] = state.inputs["__errors__"] = step_errors if 'run_workflow' in kwargs and not errors: new_history = None if 'new_history' in kwargs: @@ -1486,7 +1486,7 @@ tool = trans.app.toolbox.tools_by_id[ step.tool_id ] except KeyError, e: # Handle the case where the workflow requires a tool not available in the local Galaxy instance. - # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id + # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id # attribute should contain what we're looking for. for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): if step.tool_id == available_tool.old_id: @@ -1528,7 +1528,8 @@ invocations.append({'outputs': outputs, 'new_history': new_history}) trans.sa_session.flush() - return trans.fill_template( "workflow/run_complete.mako", + if invocations: + return trans.fill_template( "workflow/run_complete.mako", workflow=stored, invocations=invocations ) else: @@ -1549,7 +1550,7 @@ has_upgrade_messages = True # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) - step.module.add_dummy_datasets( connections=step.input_connections ) + step.module.add_dummy_datasets( connections=step.input_connections ) # Store state with the step step.state = step.module.state # Error dict @@ -1568,7 +1569,7 @@ # Render the form stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) return trans.fill_template( - "workflow/run.mako", + "workflow/run.mako", steps=workflow.steps, workflow=stored, has_upgrade_messages=has_upgrade_messages, @@ -1580,8 +1581,8 @@ finally: # restore the active history if saved_history is not None: - trans.set_history(saved_history) - + trans.set_history(saved_history) + def get_item( self, trans, id ): return self.get_stored_workflow( trans, id ) 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: Fix some broken functional tests and fixes for deleting multiple data libraries and resetting the password for multiple users. Fixes issue # 678.
by Bitbucket 05 Dec '11

05 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e69c868b6891/ changeset: e69c868b6891 user: greg date: 2011-12-05 15:58:36 summary: Fix some broken functional tests and fixes for deleting multiple data libraries and resetting the password for multiple users. Fixes issue # 678. affected #: 7 files diff -r 627260f26eba2116bc6bfecf285d7d04d12a912b -r e69c868b6891ccf6deabcba8a767cdf31593d1be lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -5,6 +5,7 @@ from datetime import date, datetime, timedelta from time import strftime from galaxy import config, tools, web, util +from galaxy.util import inflector from galaxy.util.hash_util import * from galaxy.util.json import json_fix from galaxy.web import error, form, url_for @@ -2030,28 +2031,28 @@ @web.require_admin def reset_user_password( self, trans, **kwd ): webapp = kwd.get( 'webapp', 'galaxy' ) - id = kwd.get( 'id', None ) - if not id: - message = "No user ids received for resetting passwords" + user_id = kwd.get( 'id', None ) + if not user_id: + message = "No users received for resetting passwords." trans.response.send_redirect( web.url_for( controller='admin', action='users', webapp=webapp, message=message, status='error' ) ) - ids = util.listify( id ) + user_ids = util.listify( user_id ) if 'reset_user_password_button' in kwd: message = '' status = '' - for user_id in ids: + for user_id in user_ids: user = get_user( trans, user_id ) password = kwd.get( 'password', None ) confirm = kwd.get( 'confirm' , None ) if len( password ) < 6: - message = "Please use a password of at least 6 characters" + message = "Use a password of at least 6 characters." status = 'error' break elif password != confirm: - message = "Passwords do not match" + message = "Passwords do not match." status = 'error' break else: @@ -2059,18 +2060,18 @@ trans.sa_session.add( user ) trans.sa_session.flush() if not message and not status: - message = "Passwords reset for %d users" % len( ids ) + message = "Passwords reset for %d %s." % ( len( user_ids ), inflector.cond_plural( len( user_ids ), 'user' ) ) status = 'done' trans.response.send_redirect( web.url_for( controller='admin', action='users', webapp=webapp, message=util.sanitize_text( message ), status=status ) ) - users = [ get_user( trans, user_id ) for user_id in ids ] - if len( ids ) > 1: - id=','.join( id ) + users = [ get_user( trans, user_id ) for user_id in user_ids ] + if len( user_ids ) > 1: + user_id = ','.join( user_ids ) return trans.fill_template( '/admin/user/reset_password.mako', - id=id, + id=user_id, users=users, password='', confirm='', @@ -2435,13 +2436,11 @@ # overwrite it in case it contains stuff proprietary to the local instance. if not os.path.exists( os.path.join( tool_data_path, loc_file ) ): shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, loc_file ) ) -def get_user( trans, id ): +def get_user( trans, user_id ): """Get a User from the database by id.""" - # Load user from database - id = trans.security.decode_id( id ) - user = trans.sa_session.query( trans.model.User ).get( id ) + user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) if not user: - return trans.show_error_message( "User not found for id (%s)" % str( id ) ) + return trans.show_error_message( "User not found for id (%s)" % str( user_id ) ) return user def get_user_by_username( trans, username ): """Get a user from the database by username""" diff -r 627260f26eba2116bc6bfecf285d7d04d12a912b -r e69c868b6891ccf6deabcba8a767cdf31593d1be lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -2250,6 +2250,7 @@ # contents will be purged. The association between this method and the cleanup_datasets.py script # enables clean maintenance of libraries and library dataset disk files. This is also why the item_types # are not any of the associations ( the cleanup_datasets.py script handles everything ). + status = kwd.get( 'status', 'done' ) show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) item_types = { 'library': trans.app.model.Library, 'folder': trans.app.model.LibraryFolder, @@ -2264,22 +2265,36 @@ item_desc = 'Dataset' else: item_desc = item_type.capitalize() - try: - library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) ) - except: - library_item = None - if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ): - message = 'Invalid %s id ( %s ) specifield.' % ( item_desc, item_id ) + library_item_ids = util.listify( item_id ) + valid_items = 0 + invalid_items = 0 + not_authorized_items = 0 + flush_needed = False + message = '' + for library_item_id in library_item_ids: + try: + library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( library_item_id ) ) + except: + library_item = None + if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ): + invalid_items += 1 + elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ): + not_authorized_items += 1 + else: + valid_items += 1 + library_item.deleted = True + trans.sa_session.add( library_item ) + flush_needed = True + if flush_needed: + trans.sa_session.flush() + if valid_items: + message += "%d %s marked deleted. " % ( valid_items, inflector.cond_plural( valid_items, item_desc ) ) + if invalid_items: + message += '%d invalid %s specifield. ' % ( invalid_items, inflector.cond_plural( invalid_items, item_desc ) ) status = 'error' - elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ): - message = "You are not authorized to delete %s '%s'." % ( item_desc, library_item.name ) + if not_authorized_items: + message += 'You are not authorized to delete %d %s. ' % ( not_authorized_items, inflector.cond_plural( not_authorized_items, item_desc ) ) status = 'error' - else: - library_item.deleted = True - trans.sa_session.add( library_item ) - trans.sa_session.flush() - message = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) ) - status = 'done' if item_type == 'library': return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_libraries', @@ -2296,6 +2311,7 @@ @web.expose def undelete_library_item( self, trans, cntrller, library_id, item_id, item_type, **kwd ): # This action will handle undeleting all types of library items + status = kwd.get( 'status', 'done' ) show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) item_types = { 'library': trans.app.model.Library, 'folder': trans.app.model.LibraryFolder, @@ -2304,31 +2320,49 @@ current_user_roles = trans.get_current_user_roles() if item_type not in item_types: message = 'Bad item_type specified: %s' % str( item_type ) - status = ERROR + status = 'error' else: if item_type == 'library_dataset': item_desc = 'Dataset' else: item_desc = item_type.capitalize() - try: - library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) ) - except: - library_item = None - if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ): - message = 'Invalid %s id ( %s ) specifield.' % ( item_desc, item_id ) + + library_item_ids = util.listify( item_id ) + valid_items = 0 + invalid_items = 0 + purged_items = 0 + not_authorized_items = 0 + flush_needed = False + message = '' + for library_item_id in library_item_ids: + try: + library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( library_item_id ) ) + except: + library_item = None + if not library_item or not ( is_admin or trans.app.security_agent.can_access_library_item( current_user_roles, library_item, trans.user ) ): + invalid_items += 1 + elif library_item.purged: + purged_items += 1 + elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ): + not_authorized_items += 1 + else: + valid_items += 1 + library_item.deleted = False + trans.sa_session.add( library_item ) + flush_needed = True + if flush_needed: + trans.sa_session.flush() + if valid_items: + message += "%d %s marked undeleted. " % ( valid_items, inflector.cond_plural( valid_items, item_desc ) ) + if invalid_items: + message += '%d invalid %s specifield. ' % ( invalid_items, inflector.cond_plural( invalid_items, item_desc ) ) status = 'error' - elif library_item.purged: - message = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name ) - status = ERROR - elif not ( is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, library_item ) ): - message = "You are not authorized to delete %s '%s'." % ( item_desc, library_item.name ) - status = 'error' - else: - library_item.deleted = False - trans.sa_session.add( library_item ) - trans.sa_session.flush() - message = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) ) - status = SUCCESS + if not_authorized_items: + message += 'You are not authorized to undelete %d %s. ' % ( not_authorized_items, inflector.cond_plural( not_authorized_items, item_desc ) ) + status = 'error' + if purged_items: + message += '%d %s marked purged, so cannot be undeleted. ' % ( purged_items, inflector.cond_plural( purged_items, item_desc ) ) + status = 'error' if item_type == 'library': return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_libraries', diff -r 627260f26eba2116bc6bfecf285d7d04d12a912b -r e69c868b6891ccf6deabcba8a767cdf31593d1be test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1224,7 +1224,7 @@ tc.fv( "1", "password", password ) tc.fv( "1", "confirm", password ) tc.submit( "reset_user_password_button" ) - self.check_page_for_string( "Passwords reset for 1 users" ) + self.check_page_for_string( "Passwords reset for 1 user." ) self.home() def mark_user_deleted( self, user_id, email='' ): """Mark a user as deleted""" @@ -2278,7 +2278,7 @@ item_desc = 'Dataset' else: item_desc = item_type.capitalize() - check_str = "%s '%s' has been marked deleted" % ( item_desc, item_name ) + check_str = "marked deleted" self.check_page_for_string( check_str ) self.home() def undelete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): @@ -2290,7 +2290,7 @@ item_desc = 'Dataset' else: item_desc = item_type.capitalize() - check_str = "%s '%s' has been marked undeleted" % ( item_desc, item_name ) + check_str = "marked undeleted" self.check_page_for_string( check_str ) self.home() def purge_library( self, library_id, library_name ): diff -r 627260f26eba2116bc6bfecf285d7d04d12a912b -r e69c868b6891ccf6deabcba8a767cdf31593d1be test/functional/test_library_features.py --- a/test/functional/test_library_features.py +++ b/test/functional/test_library_features.py @@ -137,7 +137,7 @@ assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] ) + strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] ) def test_050_add_2nd_public_dataset_to_folder2( self ): """Testing adding a 2nd public dataset folder2""" # Logged in as admin_user @@ -156,7 +156,7 @@ assert ldda3 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda3 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda3.name, ldda3.message, admin_user.email ] ) + strings_displayed=[ ldda3.name, ldda3.message, 'bed' ] ) def test_055_copy_dataset_from_history_to_subfolder( self ): """Testing copying a dataset from the current history to a subfolder""" # logged in as admin_user @@ -176,7 +176,7 @@ assert ldda4 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda4 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda4.name, ldda4.message, admin_user.email ] ) + strings_displayed=[ ldda4.name, ldda4.message, 'bed' ] ) def test_060_editing_dataset_attribute_info( self ): """Testing editing a library dataset's attribute information""" # logged in as admin_user @@ -299,11 +299,11 @@ ldda_message = 'Uploaded all files in test-data/users/test1...' self.browse_library( 'library', self.security.encode_id( library1.id ), - strings_displayed=[ regular_user1.email, ldda_message, '1.fasta' ] ) + strings_displayed=[ 'fasta', ldda_message, '1.fasta' ] ) ldda_message = 'Uploaded all files in test-data/users/test3.../run1' self.browse_library( 'library', self.security.encode_id( library1.id ), - strings_displayed=[ regular_user3.email, ldda_message, '2.fasta' ] ) + strings_displayed=[ 'fasta', ldda_message, '2.fasta' ] ) def test_085_mark_ldda2_deleted( self ): """Testing marking ldda2 as deleted""" # Logged in as admin_user diff -r 627260f26eba2116bc6bfecf285d7d04d12a912b -r e69c868b6891ccf6deabcba8a767cdf31593d1be test/functional/test_library_security.py --- a/test/functional/test_library_security.py +++ b/test/functional/test_library_security.py @@ -157,7 +157,7 @@ assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] ) + strings_displayed=[ ldda1.name, ldda1.message, 'bed' ] ) def test_030_access_ldda1_with_private_role_restriction( self ): """Testing accessing ldda1 with a private role restriction""" # Logged in as admin_user @@ -262,20 +262,20 @@ assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database' self.browse_library( cntrller='library', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] ) + strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] ) def test_045_accessing_ldda2_with_role_associated_with_group_and_users( self ): """Testing accessing ldda2 with a role that is associated with a group and users""" # Logged in as admin_user # admin_user should be able to see 2.bed since she is associated with role2 self.browse_library( cntrller='library', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] ) + strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] ) self.logout() # regular_user1 should be able to see 2.bed since she is associated with group_two self.login( email = regular_user1.email ) self.browse_library( cntrller='library', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ folder1.name, ldda2.name, ldda2.message, admin_user.email ] ) + strings_displayed=[ folder1.name, ldda2.name, ldda2.message, 'bed' ] ) # Check the permissions on the dataset 2.bed - they are as folows: # DATASET_MANAGE_PERMISSIONS = test(a)bx.psu.edu # DATASET_ACCESS = Role2 @@ -356,7 +356,7 @@ strings_displayed=[ "Upload a directory of files" ] ) self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ admin_user.email, ldda_message ] ) + strings_displayed=[ 'bed', ldda_message ] ) def test_055_change_permissions_on_datasets_uploaded_from_library_dir( self ): """Testing changing the permissions on datasets uploaded from a directory from the Admin view""" # logged in as admin_user diff -r 627260f26eba2116bc6bfecf285d7d04d12a912b -r e69c868b6891ccf6deabcba8a767cdf31593d1be test/functional/test_library_templates.py --- a/test/functional/test_library_templates.py +++ b/test/functional/test_library_templates.py @@ -181,7 +181,7 @@ assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] ) + strings_displayed=[ ldda1.name, ldda1.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library1.id ), @@ -308,7 +308,7 @@ assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library2.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library2.id ), @@ -363,8 +363,7 @@ 'Option1' ] ) def test_100_add_ldda_to_folder3( self ): """ - Testing adding a new library dataset to library3's folder, - making sure the SelectField setting is correct on the upload form. + Testing adding a new library dataset to library3's folder, making sure the SelectField setting is correct on the upload form. """ filename = '3.bed' ldda_message = '3.bed message' @@ -381,7 +380,7 @@ assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library3.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library3.id ), @@ -453,8 +452,7 @@ 'This text should be inherited' ] ) def test_120_add_ldda_to_folder4( self ): """ - Testing adding a new library dataset to library4's folder, - making sure the TextArea setting is correct on the upload form. + Testing adding a new library dataset to library4's folder, making sure the TextArea setting is correct on the upload form. """ filename = '4.bed' ldda_message = '4.bed message' @@ -471,7 +469,7 @@ assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library4.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library4.id ), @@ -519,8 +517,7 @@ 'This text should be inherited' ] ) def test_140_add_ldda_to_folder5( self ): """ - Testing adding a new library dataset to library5's folder, - making sure the TextField setting is correct on the upload form. + Testing adding a new library dataset to library5's folder, making sure the TextField setting is correct on the upload form. """ # Logged in as admin_user filename = '5.bed' @@ -537,7 +534,7 @@ assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library5.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library5.id ), @@ -558,9 +555,7 @@ field_default_1='%s default' % TextArea_form.name ) def test_150_add_ldda_to_library5( self ): """ - Testing adding a new library dataset to library5's folder, - making sure the TextField and new TextArea settings are - correct on the upload form. + Testing adding a new library dataset to library5's folder, making sure the TextField and new TextArea settings are correct on the upload form. """ filename = '6.bed' ldda_message = '6.bed message' @@ -579,7 +574,7 @@ assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library5.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library5.id ), @@ -626,8 +621,7 @@ 'none' ] ) def test_170_add_ldda_to_folder6( self ): """ - Testing adding a new library dataset to library6's folder, - making sure the WorkflowField setting is correct on the upload form. + Testing adding a new library dataset to library6's folder, making sure the WorkflowField setting is correct on the upload form. """ # Logged in as admin_user filename = '7.bed' @@ -644,7 +638,7 @@ assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library6.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library6.id ), diff -r 627260f26eba2116bc6bfecf285d7d04d12a912b -r e69c868b6891ccf6deabcba8a767cdf31593d1be test/functional/test_user_info.py --- a/test/functional/test_user_info.py +++ b/test/functional/test_user_info.py @@ -206,7 +206,7 @@ self.edit_user_info( cntrller='user', password='testuser', new_password='testuser#',\ - strings_displayed_after_submit=[ 'The password has been changed.' ] ) + strings_displayed_after_submit=[ 'The password has been changed' ] ) self.logout() refresh( regular_user12 ) # Test logging in with new email and password 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: Trackster: decode dbkey when adding tracks.
by Bitbucket 03 Dec '11

03 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/627260f26eba/ changeset: 627260f26eba user: jgoecks date: 2011-12-04 00:05:58 summary: Trackster: decode dbkey when adding tracks. affected #: 1 file diff -r 7e5b7ae22a29ec69cbcfb28c8820e70b6d2ca89c -r 627260f26eba2116bc6bfecf285d7d04d12a912b lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -30,6 +30,13 @@ OK = "ok" ) +def _decode_dbkey( dbkey ): + """ Decodes dbkey and returns tuple ( username, dbkey )""" + if ':' in dbkey: + return dbkey.split( ':' ) + else: + return None, dbkey + class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, history ): return history.get_display_name() @@ -92,6 +99,7 @@ def filter( self, trans, user, query, dbkey ): """ Filter by dbkey; datasets without a dbkey are returned as well. """ # use raw SQL b/c metadata is a BLOB + dbkey_user, dbkey = _decode_dbkey( dbkey ) dbkey = dbkey.replace("'", "\\'") return query.filter( or_( \ or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ), \ @@ -213,13 +221,6 @@ return True return False - - def _decode_dbkey( self, dbkey ): - """ Decodes dbkey and returns tuple ( username, dbkey )""" - if ':' in dbkey: - return dbkey.split( ':' ) - else: - return None, dbkey @web.expose @web.require_login() @@ -323,7 +324,7 @@ low = 0 # If there is no dbkey owner, default to current user. - dbkey_owner, dbkey = self._decode_dbkey( dbkey ) + dbkey_owner, dbkey = _decode_dbkey( dbkey ) if dbkey_owner: dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first() else: @@ -429,7 +430,7 @@ """ # If there is no dbkey owner, default to current user. - dbkey_owner, dbkey = self._decode_dbkey( dbkey ) + dbkey_owner, dbkey = _decode_dbkey( dbkey ) if dbkey_owner: dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first() else: 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: Remove unneeded vis_id parameter from tracks/chroms method.
by Bitbucket 03 Dec '11

03 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7e5b7ae22a29/ changeset: 7e5b7ae22a29 user: jgoecks date: 2011-12-03 23:06:33 summary: Remove unneeded vis_id parameter from tracks/chroms method. affected #: 2 files diff -r 866567627a0f78ee78fe443c65a43a86229802b4 -r 7e5b7ae22a29ec69cbcfb28c8820e70b6d2ca89c lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -293,7 +293,7 @@ return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset ) @web.json - def chroms( self, trans, vis_id=None, dbkey=None, num=None, chrom=None, low=None ): + def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ): """ Returns a naturally sorted list of chroms/contigs for either a given visualization or a given dbkey. Use either chrom or low to specify the starting chrom in the return list. @@ -322,25 +322,12 @@ else: low = 0 - # - # Get viz, dbkey. - # - - # Must specify either vis_id or dbkey. - if not vis_id and not dbkey: - return trans.show_error_message("No visualization id or dbkey specified.") - - # Need to get user and dbkey in order to get chroms data. - if vis_id: - # Use user, dbkey from viz. - visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True ) - visualization.config = self.get_visualization_config( trans, visualization ) - vis_user = visualization.user - vis_dbkey = visualization.dbkey + # If there is no dbkey owner, default to current user. + dbkey_owner, dbkey = self._decode_dbkey( dbkey ) + if dbkey_owner: + dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first() else: - # No vis_id, so visualization is new. User is current user, dbkey must be given. - vis_user = trans.user - vis_dbkey = dbkey + dbkey_user = trans.user # # Get len file. @@ -348,21 +335,21 @@ len_file = None len_ds = None user_keys = {} - if 'dbkeys' in vis_user.preferences: - user_keys = from_json_string( vis_user.preferences['dbkeys'] ) - if vis_dbkey in user_keys: - dbkey_attributes = user_keys[ vis_dbkey ] + if 'dbkeys' in dbkey_user.preferences: + user_keys = from_json_string( dbkey_user.preferences['dbkeys'] ) + if dbkey in user_keys: + dbkey_attributes = user_keys[ dbkey ] if 'fasta' in dbkey_attributes: build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] ) len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name # Backwards compatibility: look for len file directly. elif 'len' in dbkey_attributes: - len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ vis_dbkey ][ 'len' ] ).file_name + len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name if not len_file: len_ds = trans.db_dataset_for( dbkey ) if not len_ds: - len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % vis_dbkey ) + len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % dbkey ) else: len_file = len_ds.file_name @@ -432,7 +419,7 @@ to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()] to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) )) - return { 'reference': self._has_reference_data( trans, vis_dbkey, vis_user ), 'chrom_info': to_sort, + return { 'reference': self._has_reference_data( trans, dbkey, dbkey_user ), 'chrom_info': to_sort, 'prev_chroms' : prev_chroms, 'next_chroms' : next_chroms, 'start_index' : start_index } @web.json diff -r 866567627a0f78ee78fe443c65a43a86229802b4 -r 7e5b7ae22a29ec69cbcfb28c8820e70b6d2ca89c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1195,7 +1195,8 @@ */ load_chroms: function(url_parms) { url_parms['num'] = MAX_CHROMS_SELECTABLE; - $.extend( url_parms, (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey } ) ); + url_parms['dbkey'] = this.dbkey; + var view = this, chrom_data = $.Deferred(); 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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