- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Set message type to error when history deletion fails due to sharing. Fixes #477
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/70a9d3998da6/ changeset: r5162:70a9d3998da6 user: jgoecks date: 2011-03-02 23:31:09 summary: Set message type to error when history deletion fails due to sharing. Fixes #477 affected #: 1 file (31 bytes) --- a/lib/galaxy/web/controllers/history.py Wed Mar 02 17:15:08 2011 -0500 +++ b/lib/galaxy/web/controllers/history.py Wed Mar 02 17:31:09 2011 -0500 @@ -250,9 +250,11 @@ n_deleted = 0 deleted_current = False message_parts = [] + status = SUCCESS for history in histories: if history.users_shared_with: message_parts.append( "History (%s) has been shared with others, unshare it before deleting it. " % history.name ) + status = ERROR elif not history.deleted: # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later history.deleted = True @@ -262,7 +264,6 @@ trans.new_history() trans.log_event( "History (%s) marked as deleted" % history.name ) n_deleted += 1 - status = SUCCESS if n_deleted: message_parts.append( "Deleted %d %s. " % ( n_deleted, iff( n_deleted != 1, "histories", "history" ) ) ) if deleted_current: 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: jgoecks: Trackster: make visual analytics code compatible with HDA/LDDA changes.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2728b804c2ed/ changeset: r5161:2728b804c2ed user: jgoecks date: 2011-03-02 23:15:08 summary: Trackster: make visual analytics code compatible with HDA/LDDA changes. affected #: 1 file (46 bytes) --- a/static/scripts/trackster.js Wed Mar 02 16:21:36 2011 -0500 +++ b/static/scripts/trackster.js Wed Mar 02 17:15:08 2011 -0500 @@ -1640,7 +1640,7 @@ // TODO: add support for other kinds of tool data tracks. if (current_track.track_type === 'FeatureTrack') { - new_track = new ToolDataFeatureTrack(track_name, view, undefined, {}, {}, current_track); + new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); } this.add_track(new_track); @@ -2964,7 +2964,7 @@ track.data_url = default_data_url; track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; track.dataset_state_url = converted_datasets_state_url; - $.getJSON(track.dataset_state_url, { dataset_id : track.dataset_id }, function(track_data) {}); + $.getJSON(track.dataset_state_url, { dataset_id : track.dataset_id, hda_ldda: track.hda_ldda }, function(track_data) {}); } }; post_init(); 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: natefoo: Generalize setup of chrom length files for buildbot.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/defc14c13e9f/ changeset: r5160:defc14c13e9f user: natefoo date: 2011-03-02 22:21:36 summary: Generalize setup of chrom length files for buildbot. affected #: 4 files (73 bytes) --- a/buildbot_setup.sh Wed Mar 02 16:20:16 2011 -0500 +++ b/buildbot_setup.sh Wed Mar 02 16:21:36 2011 -0500 @@ -112,10 +112,13 @@ done # for wig_to_bigWig and bed_to_bigBed -if [ ! -f "tool-data/shared/ucsc/chrom/hg17.len" -a -f "test-data/wig_to_bigwig_hg17.len" ]; then - mkdir -p tool-data/shared/ucsc/chrom - cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len -fi +for build in hg17 hg18; do + if [ -f "test-data/chrom/$build.len" ]; then + echo "Copying test-data/chrom/$build.len to tool-data/shared/ucsc/chrom/" + mkdir -p tool-data/shared/ucsc/chrom + cp test-data/chrom/$build.len tool-data/shared/ucsc/chrom/$build.len + fi +done if [ -d "test-data-repo" ]; then echo "Updating test data repository" --- a/test-data/wig_to_bigwig_hg17.len Wed Mar 02 16:20:16 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -chr10 135413628 -chr10_random 113275 -chr11 134452384 -chr12 132449811 -chr12_random 466818 -chr13 114142980 -chr13_random 186858 -chr14 106368585 -chr15 100338915 -chr15_random 784346 -chr16 88827254 -chr16_random 105485 -chr17 78774742 -chr17_random 2618010 -chr18 76117153 -chr18_random 4262 -chr19 63811651 -chr19_random 301858 -chr1 245522847 -chr1_random 3897131 -chr20 62435964 -chr21 46944323 -chr22 49554710 -chr22_random 257318 -chr2 243018229 -chr2_random 418158 -chr3 199505740 -chr3_random 970716 -chr4 191411218 -chr4_random 1030282 -chr5 180857866 -chr5_random 143687 -chr6 170975699 -chr6_random 1875562 -chr6_hla_hap1 139182 -chr6_hla_hap2 150447 -chr7 158628139 -chr7_random 778964 -chr8 146274826 -chr8_random 943810 -chr9 138429268 -chr9_random 1312665 -chrM 16571 -chrX 154824264 -chrX_random 1719168 -chrY 57701691 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: natefoo: Fix symlink to microbial_data.loc in buildbot setup.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e5c0e7205ae2/ changeset: r5159:e5c0e7205ae2 user: natefoo date: 2011-03-02 22:20:16 summary: Fix symlink to microbial_data.loc in buildbot setup. affected #: 1 file (9 bytes) --- a/buildbot_setup.sh Wed Mar 02 13:46:07 2011 -0500 +++ b/buildbot_setup.sh Wed Mar 02 16:20:16 2011 -0500 @@ -48,7 +48,7 @@ /galaxy/data/location/liftOver.loc /galaxy/data/location/maf_index.loc /galaxy/data/location/maf_pairwise.loc -/galaxy/data/location/microbes/microbial_data.loc +/galaxy/data/location/microbial_data.loc /galaxy/data/location/mosaik_index.loc /galaxy/data/location/perm_base_index.loc /galaxy/data/location/perm_color_index.loc 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: natefoo: Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/db8c44cdd4d9/ changeset: r5158:db8c44cdd4d9 user: natefoo date: 2011-03-02 19:46:07 summary: Fix the qual_stats_boxplot and quality_score_distribution tests again, hopefully affected #: 3 files (1.2 KB) Binary file test-data/454Score.png has changed Binary file test-data/boxplot_summary_statistics_out.png has changed Binary file test-data/solexaScore.png has changed 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: dan: Enhance Bowtie wrapper to accept non-sanger variant FASTQ files.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7a9476924daf/ changeset: r5157:7a9476924daf user: dan date: 2011-03-02 17:40:58 summary: Enhance Bowtie wrapper to accept non-sanger variant FASTQ files. affected #: 10 files (7.5 KB) --- a/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_color_wrapper.xml Wed Mar 02 11:40:58 2011 -0500 @@ -7,7 +7,7 @@ --threads="4" ## Outputs --output=$output - #if $singlePaired == "single" + #if str( $singlePaired.sPaired ) == "single" #if $output_unmapped_reads_l --output_unmapped_reads=$output_unmapped_reads_l #end if --- a/tools/sr_mapping/bowtie_wrapper.py Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.py Wed Mar 02 11:40:58 2011 -0500 @@ -67,6 +67,11 @@ import optparse, os, shutil, subprocess, sys, tempfile +#Allow more than Sanger encoded variants +DEFAULT_ASCII_ENCODING = '--phred33-quals' +GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' } +#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config + def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) sys.exit() @@ -131,6 +136,7 @@ parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' ) parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) + parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' ) parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' ) (options, args) = parser.parse_args() stdout = '' @@ -255,9 +261,10 @@ mateOrient = '--%s' % options.mateOrient else: mateOrient = '' + quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING ) if options.params == 'preSet': - aligning_cmds = '-q %s %s -p %s -S %s %s ' % \ - ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace ) + aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \ + ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding ) else: try: if options.skip and int( options.skip ) > 0: @@ -386,14 +393,15 @@ else: keepends = '' aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \ - '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % \ + '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \ ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign, mismatchSeed, mismatchQual, seedLen, rounding, minInsert, maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks, tryHard, valAlign, allValAligns, suppressAlign, best, strata, offrate, seed, snpphred, snpfrac, keepends, - output_unmapped_reads, output_suppressed_reads ) + output_unmapped_reads, output_suppressed_reads, + quality_score_encoding ) except ValueError, e: # clean up temp dir if os.path.exists( tmp_index_dir ): --- a/tools/sr_mapping/bowtie_wrapper.xml Wed Mar 02 11:34:36 2011 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.xml Wed Mar 02 11:40:58 2011 -0500 @@ -8,13 +8,14 @@ --threads="4" ## Outputs --output=$output - #if $singlePaired == "single" + #if str( $singlePaired.sPaired ) == "single" #if $output_unmapped_reads_l --output_unmapped_reads=$output_unmapped_reads_l #end if #if $output_suppressed_reads_l --output_suppressed_reads=$output_suppressed_reads_l #end if + --galaxy_input_format="${singlePaired.sInput1.ext}" #else #if $output_unmapped_reads_l and $output_unmapped_reads_r --output_unmapped_reads_l=$output_unmapped_reads_l @@ -24,9 +25,10 @@ --output_suppressed_reads_l=$output_suppressed_reads_l --output_suppressed_reads_r=$output_suppressed_reads_r #end if + --galaxy_input_format="${singlePaired.pInput1.ext}" #end if ## Inputs - --dataType="solexa" + --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper --suppressHeader=$suppressHeader --genomeSource=$refGenomeSource.genomeSource #if $refGenomeSource.genomeSource == "history": @@ -59,7 +61,8 @@ #end if #else ##use pre-built index - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" + ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" + --ref="${ refGenomeSource.index.fields.path }" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": @@ -191,7 +194,7 @@ <option value="paired">Paired-end</option></param><when value="single"> - <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/><conditional name="sParams"><param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"><option value="preSet">Commonly used</option> @@ -245,8 +248,14 @@ </conditional></when><when value="paired"> - <param name="pInput1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> + <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> + <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">> + <column name="name" index="0"/> + <column name="value" index="0"/> + <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> + </options> + </param><param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /><param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"><option value="fr">FR (for Illumina)</option> @@ -333,7 +342,7 @@ </conditional></actions></data> - <data format="fastqsanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> + <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"><filter>(( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and @@ -344,13 +353,41 @@ singlePaired['pParams']['pMaxFile'] is True )) </filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> + <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"><filter>singlePaired['sPaired'] == "paired"</filter><filter>singlePaired['pParams']['pSettingsType'] == "full"</filter><filter>singlePaired['pParams']['pMaxFile'] is True</filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> + <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"><filter> (( singlePaired['sPaired'] == "single" and @@ -362,11 +399,39 @@ singlePaired['pParams']['pUnmappedFile'] is True )) </filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data> - <data format="fastqsanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> + <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"><filter>singlePaired['sPaired'] == "paired"</filter><filter>singlePaired['pParams']['pSettingsType'] == "full"</filter><filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> + <actions> + <conditional name="singlePaired.sPaired"> + <when value="single"> + <action type="format"> + <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions></data></outputs><tests> @@ -379,6 +444,7 @@ chrM_base needs to be the base location/name of the index files. --><param name="genomeSource" value="indexed" /> + <param name="index" value="equCab2chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> @@ -437,6 +503,86 @@ <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" /><output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" /></test> +  + <test> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="phiX.fasta" /> + <param name="indexSettings" value="indexPreSet" /> + <param name="sPaired" value="paired" /> + <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" /> + <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" /> + <param name="pMaxInsert" value="1000" /> + <param name="pMateOrient" value="ff" /> + <param name="pSettingsType" value="full" /> + <param name="pSkip" value="0" /> + <param name="pAlignLimit" value="-1" /> + <param name="pTrimH" value="0" /> + <param name="pTrimL" value="0" /> + <param name="pMismatchSeed" value="2" /> + <param name="pMismatchQual" value="70" /> + <param name="pSeedLen" value="28" /> + <param name="pRounding" value="round" /> + <param name="pMaqSoapAlign" value="-1" /> + <param name="pMinInsert" value="0" /> + <param name="pMaxAlignAttempt" value="100" /> + <param name="pForwardAlign" value="forward" /> + <param name="pReverseAlign" value="reverse" /> + <param name="pTryHard" value="noTryHard" /> + <param name="pValAlign" value="1" /> + <param name="pAllValAligns" value="noAllValAligns" /> + <param name="pSuppressAlign" value="-1" /> + <param name="pUnmappedFile" value="true" /> + <param name="pMaxFile" value="false" /> + <param name="pBest" value="doBest" /> + <param name="pdMaxBacktracks" value="800" /> + <param name="pdStrata" value="noStrata" /> + <param name="pOffrate" value="-1" /> + <param name="pSeed" value="-1" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> + <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> + <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> + </test> + <test> + <param name="genomeSource" value="history" /> + <param name="ownFile" value="phiX.fasta" /> + <param name="indexSettings" value="indexPreSet" /> + <param name="sPaired" value="paired" /> + <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" /> + <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" /> + <param name="pMaxInsert" value="1000" /> + <param name="pMateOrient" value="ff" /> + <param name="pSettingsType" value="full" /> + <param name="pSkip" value="0" /> + <param name="pAlignLimit" value="-1" /> + <param name="pTrimH" value="0" /> + <param name="pTrimL" value="0" /> + <param name="pMismatchSeed" value="2" /> + <param name="pMismatchQual" value="70" /> + <param name="pSeedLen" value="28" /> + <param name="pRounding" value="round" /> + <param name="pMaqSoapAlign" value="-1" /> + <param name="pMinInsert" value="0" /> + <param name="pMaxAlignAttempt" value="100" /> + <param name="pForwardAlign" value="forward" /> + <param name="pReverseAlign" value="reverse" /> + <param name="pTryHard" value="noTryHard" /> + <param name="pValAlign" value="1" /> + <param name="pAllValAligns" value="noAllValAligns" /> + <param name="pSuppressAlign" value="-1" /> + <param name="pUnmappedFile" value="true" /> + <param name="pMaxFile" value="false" /> + <param name="pBest" value="doBest" /> + <param name="pdMaxBacktracks" value="800" /> + <param name="pdStrata" value="noStrata" /> + <param name="pOffrate" value="-1" /> + <param name="pSeed" value="-1" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> + <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" /> + <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" /> + </test> + <test><!-- Bowtie command: 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: dan: Allow FromParamToolOutputActionOption and ParamValueToolOutputActionOptionFilter to access attributes of parameter values.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/be70b8497349/ changeset: r5156:be70b8497349 user: dan date: 2011-03-02 17:34:36 summary: Allow FromParamToolOutputActionOption and ParamValueToolOutputActionOptionFilter to access attributes of parameter values. affected #: 1 file (532 bytes) --- a/lib/galaxy/tools/parameters/output.py Wed Mar 02 11:34:03 2011 -0500 +++ b/lib/galaxy/tools/parameters/output.py Wed Mar 02 11:34:36 2011 -0500 @@ -179,11 +179,16 @@ self.column = int( self.column ) self.offset = elem.get( 'offset', -1 ) self.offset = int( self.offset ) + self.param_attribute = elem.get( 'param_attribute', [] ) + if self.param_attribute: + self.param_attribute = self.param_attribute.split( '.' ) def get_value( self, other_values ): value = other_values for ref_name in self.name: assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name value = value.get( ref_name ) + for attr_name in self.param_attribute: + value = getattr( value, attr_name ) options = [ [ str( value ) ] ] for filter in self.filters: options = filter.filter_options( options, other_values ) @@ -276,6 +281,9 @@ self.keep = util.string_as_bool( elem.get( "keep", 'True' ) ) self.compare = parse_compare_type( elem.get( 'compare', None ) ) self.cast = parse_cast_attribute( elem.get( "cast", None ) ) + self.param_attribute = elem.get( 'param_attribute', [] ) + if self.param_attribute: + self.param_attribute = self.param_attribute.split( '.' ) def filter_options( self, options, other_values ): if self.ref: #find ref value @@ -283,6 +291,8 @@ for ref_name in self.ref: assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name value = value.get( ref_name ) + for attr_name in self.param_attribute: + value = getattr( value, attr_name ) value = str( value ) else: value = self.value 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: dan: Allow DataToolParameter to be filtered on attributes other than dbkey.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f1495dd691c2/ changeset: r5155:f1495dd691c2 user: dan date: 2011-03-02 17:34:03 summary: Allow DataToolParameter to be filtered on attributes other than dbkey. affected #: 1 file (1.3 KB) --- a/lib/galaxy/tools/parameters/basic.py Wed Mar 02 09:59:24 2011 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Wed Mar 02 11:34:03 2011 -0500 @@ -1256,8 +1256,14 @@ options = elem.find( 'options' ) if options is None: self.options = None + self.options_filter_attribute = None else: self.options = dynamic_options.DynamicOptions( options, self ) + + #HACK to get around current hardcoded limitation of when a set of dynamic options is defined for a DataToolParameter + #it always causes available datasets to be filtered by dbkey + #this behavior needs to be entirely reworked (in a backwards compatible manner) + self.options_filter_attribute = options.get( 'options_filter_attribute', None ) self.is_dynamic = self.options is not None # Load conversions required for the dataset input self.conversions = [] @@ -1302,7 +1308,7 @@ # associated with the dataset that restrict it's access from "public". if self.tool and self.tool.tool_type == 'data_destination' and not trans.app.security_agent.dataset_is_public( hda.dataset ): continue - if self.options and hda.get_dbkey() != filter_value: + if self.options and self._options_filter_attribute( hda ) != filter_value: continue if isinstance( hda.datatype, self.formats): selected = ( value and ( hda in value ) ) @@ -1363,7 +1369,7 @@ return False for i, data in enumerate( datasets ): if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): - if self.options and data.get_dbkey() != filter_value: + if self.options and self._options_filter_attribute( data ) != filter_value: continue most_recent_dataset[0] = data # Also collect children via association object @@ -1437,6 +1443,25 @@ self.tool.visit_inputs( other_values, visitor ) return False not in converter_safe + def _options_filter_attribute( self, value ): + #HACK to get around current hardcoded limitation of when a set of dynamic options is defined for a DataToolParameter + #it always causes available datasets to be filtered by dbkey + #this behavior needs to be entirely reworked (in a backwards compatible manner) + options_filter_attribute = self.options_filter_attribute + if options_filter_attribute is None: + return value.get_dbkey() + if options_filter_attribute.endswith( "()" ): + call_attribute = True + options_filter_attribute = options_filter_attribute[:-2] + else: + call_attribute = False + ref = value + for attribute in options_filter_attribute.split( '.' ): + ref = getattr( ref, attribute ) + if call_attribute: + ref = ref() + return ref + # class RawToolParameter( ToolParameter ): # """ # Completely nondescript parameter, HTML representation is provided as text 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: Clarify what's being searched in the tool shed.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a5cfff74d467/ changeset: r5154:a5cfff74d467 user: greg date: 2011-03-02 15:59:24 summary: Clarify what's being searched in the tool shed. affected #: 1 file (24 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Wed Mar 02 09:40:10 2011 -0500 +++ b/lib/galaxy/webapps/community/controllers/common.py Wed Mar 02 09:59:24 2011 -0500 @@ -30,6 +30,7 @@ # User has previously rated item; update rating. item_rating.rating = rating item_rating.comment = comment + trans.sa_session.add( item_rating ) trans.sa_session.flush() return item_rating @@ -85,12 +86,10 @@ NameColumn( "Name", key="Tool.name", link=( lambda item: dict( operation="view_tool", id=item.id, webapp="community" ) ), - attach_popup=False - ), + attach_popup=False ), DescriptionColumn( "Description", key="description", - attach_popup=False - ), + attach_popup=False ), VersionColumn( "Version", key="version", attach_popup=False, @@ -119,7 +118,7 @@ key="Category.name", visible=False ) ] - columns.append( grids.MulticolFilterColumn( "Search", + columns.append( grids.MulticolFilterColumn( "Search tool name, description, version", cols_to_filter=[ columns[0], columns[1], columns[2] ], key="free-text-search", visible=False, @@ -165,13 +164,11 @@ key="name", link=( lambda item: dict( operation="tools_by_category", id=item.id, webapp="community" ) ), attach_popup=False, - filterable="advanced" - ), + filterable="advanced" ), DescriptionColumn( "Description", key="description", attach_popup=False, - filterable="advanced" - ), + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", @@ -181,7 +178,7 @@ model_class=model.Tool, attach_popup=False ) ] - columns.append( grids.MulticolFilterColumn( "Search", + columns.append( grids.MulticolFilterColumn( "Search category name, description", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, 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: rc: Fix for vcf_extract tool test
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/69552e72d144/ changeset: r5153:69552e72d144 user: rc date: 2011-03-02 15:40:10 summary: Fix for vcf_extract tool test affected #: 1 file (15 bytes) --- a/tools/vcf_tools/extract.xml Wed Mar 02 08:38:19 2011 -0500 +++ b/tools/vcf_tools/extract.xml Wed Mar 02 09:40:10 2011 -0500 @@ -40,7 +40,7 @@ <param name="keep_info" value='' /><param name="discard_info" value='' /><param name="pass_filter" value='true' /> - <output name="output" file="test_extract_pass_filter_quality_9_DP_2000_lt.vcf" ftype="vcf" /> + <output name="output" file="test_extract_pass_filter_quality_9_DP_2000_lt.vcf" lines_diff="6" ftype="vcf" /></test><test><param name="input1" value="test.small.vcf" ftype="vcf" /> 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