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commit/galaxy-central: dan: One more occurance of fastq_to_fasta that was dropped.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/085454c899af/ Changeset: 085454c899af User: dan Date: 2013-10-10 22:25:43 Summary: One more occurance of fastq_to_fasta that was dropped. Affected #: 1 file diff -r 6621aa022ebad1eee0e808a16137af73aecafd61 -r 085454c899afaaf05a9c17d3818ed2b3029e7210 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -95,6 +95,7 @@ <tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /><tool file="filters/wiggle_to_simple.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/gtf2bedgraph.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Restore the fastq_to_fasta that was not migrated.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6621aa022eba/ Changeset: 6621aa022eba User: Dave Bouvier Date: 2013-10-10 22:16:19 Summary: Restore the fastq_to_fasta that was not migrated. Affected #: 1 file diff -r e66766f18a58e200391f28157d0993b35014b84d -r 6621aa022ebad1eee0e808a16137af73aecafd61 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -258,6 +258,7 @@ <tool file="fastq/fastq_paired_end_interlacer.xml" /><tool file="fastq/fastq_paired_end_deinterlacer.xml" /><tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Remove migrated tools that were somehow restored to tool_conf.xml.sample
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e66766f18a58/ Changeset: e66766f18a58 User: Dave Bouvier Date: 2013-10-10 22:12:52 Summary: Remove migrated tools that were somehow restored to tool_conf.xml.sample Affected #: 1 file diff -r ff76fd33b81cdde1fb270de688ec5e86488ba34d -r e66766f18a58e200391f28157d0993b35014b84d tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -1,12 +1,12 @@ -<?xml version="1.0"?> +<?xml version='1.0' encoding='utf-8'?><toolbox> - <section name="Get Data" id="getext"> - <tool file="data_source/upload.xml"/> + <section id="getext" name="Get Data"> + <tool file="data_source/upload.xml" /><tool file="data_source/ucsc_tablebrowser.xml" /><tool file="data_source/ucsc_tablebrowser_test.xml" /><tool file="data_source/ucsc_tablebrowser_archaea.xml" /><tool file="data_source/bx_browser.xml" /> - <tool file="data_source/ebi_sra.xml"/> + <tool file="data_source/ebi_sra.xml" /><tool file="data_source/microbial_import.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/biomart_test.xml" /> @@ -32,19 +32,19 @@ <tool file="genomespace/genomespace_importer.xml" /><tool file="validation/fix_errors.xml" /></section> - <section name="Send Data" id="send"> + <section id="send" name="Send Data"><tool file="data_destination/epigraph.xml" /><tool file="data_destination/epigraph_test.xml" /><tool file="genomespace/genomespace_exporter.xml" /></section> - <section name="ENCODE Tools" id="EncodeTools"> + <section id="EncodeTools" name="ENCODE Tools"><tool file="encode/gencode_partition.xml" /><tool file="encode/random_intervals.xml" /></section> - <section name="Lift-Over" id="liftOver"> + <section id="liftOver" name="Lift-Over"><tool file="extract/liftOver_wrapper.xml" /></section> - <section name="Text Manipulation" id="textutil"> + <section id="textutil" name="Text Manipulation"><tool file="filters/fixedValueColumn.xml" /><tool file="stats/column_maker.xml" /><tool file="filters/catWrapper.xml" /> @@ -65,25 +65,25 @@ <tool file="stats/dna_filtering.xml" /><tool file="new_operations/tables_arithmetic_operations.xml" /></section> - <section name="Filter and Sort" id="filter"> + <section id="filter" name="Filter and Sort"><tool file="stats/filtering.xml" /><tool file="filters/sorter.xml" /><tool file="filters/grep.xml" /> - <label text="GFF" id="gff" /> + <label id="gff" text="GFF" /><tool file="filters/gff/extract_GFF_Features.xml" /><tool file="filters/gff/gff_filter_by_attribute.xml" /><tool file="filters/gff/gff_filter_by_feature_count.xml" /><tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /></section> - <section name="Join, Subtract and Group" id="group"> + <section id="group" name="Join, Subtract and Group"><tool file="filters/joiner.xml" /> - <tool file="filters/compare.xml"/> - <tool file="new_operations/subtract_query.xml"/> + <tool file="filters/compare.xml" /> + <tool file="new_operations/subtract_query.xml" /><tool file="stats/grouping.xml" /><tool file="new_operations/column_join.xml" /></section> - <section name="Convert Formats" id="convert"> + <section id="convert" name="Convert Formats"><tool file="filters/axt_to_concat_fasta.xml" /><tool file="filters/axt_to_fasta.xml" /><tool file="filters/axt_to_lav.xml" /> @@ -95,39 +95,38 @@ <tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /> - <tool file="fastq/fastq_to_fasta.xml" /><tool file="filters/wiggle_to_simple.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/gtf2bedgraph.xml" /><tool file="filters/wig_to_bigwig.xml" /><tool file="filters/bed_to_bigbed.xml" /></section> - <section name="Extract Features" id="features"> + <section id="features" name="Extract Features"><tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /></section> - <section name="Fetch Sequences" id="fetchSeq"> + <section id="fetchSeq" name="Fetch Sequences"><tool file="extract/extract_genomic_dna.xml" /></section> - <section name="Fetch Alignments" id="fetchAlign"> + <section id="fetchAlign" name="Fetch Alignments"><tool file="maf/interval2maf_pairwise.xml" /><tool file="maf/interval2maf.xml" /> - <tool file="maf/maf_split_by_species.xml"/> + <tool file="maf/maf_split_by_species.xml" /><tool file="maf/interval_maf_to_merged_fasta.xml" /> - <tool file="maf/genebed_maf_to_fasta.xml"/> - <tool file="maf/maf_stats.xml"/> - <tool file="maf/maf_thread_for_species.xml"/> - <tool file="maf/maf_limit_to_species.xml"/> - <tool file="maf/maf_limit_size.xml"/> - <tool file="maf/maf_by_block_number.xml"/> - <tool file="maf/maf_reverse_complement.xml"/> - <tool file="maf/maf_filter.xml"/> + <tool file="maf/genebed_maf_to_fasta.xml" /> + <tool file="maf/maf_stats.xml" /> + <tool file="maf/maf_thread_for_species.xml" /> + <tool file="maf/maf_limit_to_species.xml" /> + <tool file="maf/maf_limit_size.xml" /> + <tool file="maf/maf_by_block_number.xml" /> + <tool file="maf/maf_reverse_complement.xml" /> + <tool file="maf/maf_filter.xml" /></section> - <section name="Get Genomic Scores" id="scores"> + <section id="scores" name="Get Genomic Scores"><tool file="stats/wiggle_to_simple.xml" /><tool file="stats/aggregate_binned_scores_in_intervals.xml" /><tool file="extract/phastOdds/phastOdds_tool.xml" /></section> - <section name="Operate on Genomic Intervals" id="bxops"> + <section id="bxops" name="Operate on Genomic Intervals"><tool file="new_operations/intersect.xml" /><tool file="new_operations/subtract.xml" /><tool file="new_operations/merge.xml" /> @@ -141,21 +140,19 @@ <tool file="new_operations/flanking_features.xml" /><tool file="annotation_profiler/annotation_profiler.xml" /></section> - <section name="Statistics" id="stats"> + <section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /><tool file="stats/cor.xml" /><tool file="stats/generate_matrix_for_pca_lda.xml" /><tool file="stats/lda_analy.xml" /><tool file="stats/plot_from_lda.xml" /> - <tool file="regVariation/t_test_two_samples.xml" /> - <tool file="regVariation/compute_q_values.xml" /><tool file="stats/MINE.xml" /> - <label text="GFF" id="gff" /> + <label id="gff" text="GFF" /><tool file="stats/count_gff_features.xml" /></section> - <section name="Wavelet Analysis" id="dwt"> + <section id="dwt" name="Wavelet Analysis"><tool file="discreteWavelet/execute_dwt_var_perFeature.xml" /></section> - <section name="Graph/Display Data" id="plots"> + <section id="plots" name="Graph/Display Data"><tool file="plotting/histogram2.xml" /><tool file="plotting/scatterplot.xml" /><tool file="plotting/bar_chart.xml" /> - <tool file="plotting/xy_plot.xml" /><tool file="plotting/boxplot.xml" /><tool file="visualization/GMAJ.xml" /><tool file="visualization/LAJ.xml" /> @@ -177,57 +173,48 @@ <tool file="maf/vcf_to_maf_customtrack.xml" /><tool file="mutation/visualize.xml" /></section> - <section name="Regional Variation" id="regVar"> + <section id="regVar" name="Regional Variation"><tool file="regVariation/windowSplitter.xml" /><tool file="regVariation/featureCounter.xml" /><tool file="regVariation/WeightedAverage.xml" /><tool file="regVariation/quality_filter.xml" /><tool file="regVariation/maf_cpg_filter.xml" /><tool file="regVariation/getIndels_2way.xml" /> - <tool file="regVariation/getIndels_3way.xml" /><tool file="regVariation/getIndelRates_3way.xml" /><tool file="regVariation/substitutions.xml" /><tool file="regVariation/substitution_rates.xml" /><tool file="regVariation/microsats_alignment_level.xml" /><tool file="regVariation/microsats_mutability.xml" /> - <tool file="regVariation/delete_overlapping_indels.xml" /> - <tool file="regVariation/compute_motifs_frequency.xml" /> - <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /> - <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s - <tool file="regVariation/draw_stacked_barplots.xml" /> - <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" /> - <tool file="regVariation/microsatellite_birthdeath.xml" /></section> - <section name="Multiple regression" id="multReg"> + <section id="multReg" name="Multiple regression"><tool file="regVariation/linear_regression.xml" /><tool file="regVariation/logistic_regression_vif.xml" /><tool file="regVariation/best_regression_subsets.xml" /><tool file="regVariation/rcve.xml" /><tool file="regVariation/partialR_square.xml" /></section> - <section name="Multivariate Analysis" id="multVar"> + <section id="multVar" name="Multivariate Analysis"><tool file="multivariate_stats/pca.xml" /><tool file="multivariate_stats/cca.xml" /><tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section> - <section name="Evolution" id="hyphy"> + <section id="hyphy" name="Evolution"><tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /><tool file="hyphy/hyphy_nj_tree_wrapper.xml" /><tool file="hyphy/hyphy_dnds_wrapper.xml" /> - <tool file="evolution/mutate_snp_codon.xml" /><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /></section> - <section name="Motif Tools" id="motifs"> - <tool file="meme/meme.xml"/> - <tool file="meme/fimo.xml"/> + <section id="motifs" name="Motif Tools"> + <tool file="meme/meme.xml" /> + <tool file="meme/fimo.xml" /><tool file="rgenetics/rgWebLogo3.xml" /></section> - <section name="Multiple Alignments" id="clustal"> + <section id="clustal" name="Multiple Alignments"><tool file="rgenetics/rgClustalw.xml" /></section> - <section name="Metagenomic analyses" id="tax_manipulation"> + <section id="tax_manipulation" name="Metagenomic analyses"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /><tool file="taxonomy/t2ps_wrapper.xml" /> @@ -235,38 +222,35 @@ <tool file="taxonomy/lca.xml" /><tool file="taxonomy/poisson2test.xml" /></section> - <section name="FASTA manipulation" id="fasta_manipulation"> + <section id="fasta_manipulation" name="FASTA manipulation"><tool file="fasta_tools/fasta_compute_length.xml" /><tool file="fasta_tools/fasta_filter_by_length.xml" /><tool file="fasta_tools/fasta_concatenate_by_species.xml" /><tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /> - <tool file="fastx_toolkit/fasta_formatter.xml" /> - <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> - <tool file="fastx_toolkit/fastx_collapser.xml" /></section> - <section name="NGS: QC and manipulation" id="NGS_QC"> + <section id="NGS_QC" name="NGS: QC and manipulation"> - <label text="FastQC: fastq/sam/bam" id="fastqcsambam" /> + <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /><tool file="rgenetics/rgFastQC.xml" /> - <label text="Illumina fastq" id="illumina" /> + <label id="illumina" text="Illumina fastq" /><tool file="fastq/fastq_groomer.xml" /><tool file="fastq/fastq_paired_end_splitter.xml" /><tool file="fastq/fastq_paired_end_joiner.xml" /><tool file="fastq/fastq_stats.xml" /> - <label text="Roche-454 data" id="454" /> + <label id="454" text="Roche-454 data" /><tool file="metag_tools/short_reads_figure_score.xml" /><tool file="metag_tools/short_reads_trim_seq.xml" /><tool file="fastq/fastq_combiner.xml" /> - <label text="AB-SOLiD data" id="solid" /> + <label id="solid" text="AB-SOLiD data" /><tool file="next_gen_conversion/solid2fastq.xml" /><tool file="solid_tools/solid_qual_stats.xml" /><tool file="solid_tools/solid_qual_boxplot.xml" /> - <label text="Generic FASTQ manipulation" id="generic_fastq" /> + <label id="generic_fastq" text="Generic FASTQ manipulation" /><tool file="fastq/fastq_filter.xml" /><tool file="fastq/fastq_trimmer.xml" /><tool file="fastq/fastq_trimmer_by_quality.xml" /> @@ -274,25 +258,10 @@ <tool file="fastq/fastq_paired_end_interlacer.xml" /><tool file="fastq/fastq_paired_end_deinterlacer.xml" /><tool file="fastq/fastq_manipulation.xml" /> - <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /> - <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" /> - <tool file="fastx_toolkit/fastq_quality_converter.xml" /> - <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> - <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> - <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastq_quality_filter.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> - <tool file="fastx_toolkit/fastx_barcode_splitter.xml" /> - <tool file="fastx_toolkit/fastx_clipper.xml" /> - <tool file="fastx_toolkit/fastx_collapser.xml" /> - <tool file="fastx_toolkit/fastx_renamer.xml" /> - <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> - <tool file="fastx_toolkit/fastx_trimmer.xml" /> + <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /></section> - <section name="NGS: Mapping" id="solexa_tools"> + <section id="solexa_tools" name="NGS: Mapping"><tool file="sr_mapping/bowtie2_wrapper.xml" /><tool file="sr_mapping/bfast_wrapper.xml" /><tool file="metag_tools/megablast_wrapper.xml" /><tool file="metag_tools/megablast_xml_parser.xml" /><tool file="sr_mapping/PerM.xml" /><tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml"/> + <tool file="sr_mapping/mosaik.xml" /></section> - <section name="NGS: Indel Analysis" id="indel_analysis"> + <section id="indel_analysis" name="NGS: Indel Analysis"><tool file="indels/sam_indel_filter.xml" /> - <tool file="indels/indel_sam2interval.xml" /><tool file="indels/indel_table.xml" /><tool file="indels/indel_analysis.xml" /></section> - <section name="NGS: RNA Analysis" id="ngs-rna-tools"> + <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - <label text="RNA-seq" id="rna_seq" /> + <label id="rna_seq" text="RNA-seq" /><tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/tophat2_wrapper.xml" /><tool file="ngs_rna/tophat_color_wrapper.xml" /> - <tool file="ngs_rna/cufflinks_wrapper.xml" /> - <tool file="ngs_rna/cuffcompare_wrapper.xml" /> - <tool file="ngs_rna/cuffmerge_wrapper.xml" /> - <tool file="ngs_rna/cuffdiff_wrapper.xml" /><tool file="ngs_rna/express_wrapper.xml" /> - <label text="Filtering" id="filtering" /> + <label id="filtering" text="Filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> - <section name="NGS: SAM Tools" id="samtools"> - <tool file="samtools/sam_bitwise_flag_filter.xml" /> - <tool file="samtools/sam2interval.xml" /> - <tool file="samtools/sam_to_bam.xml" /> - <tool file="samtools/bam_to_sam.xml" /> - <tool file="samtools/sam_merge.xml" /> - <tool file="samtools/samtools_mpileup.xml" /> - <tool file="samtools/sam_pileup.xml" /> - <tool file="samtools/pileup_parser.xml" /> - <tool file="samtools/pileup_interval.xml" /> - <tool file="samtools/samtools_flagstat.xml" /> - <tool file="samtools/samtools_rmdup.xml" /> - <tool file="samtools/samtools_slice_bam.xml" /> + <section id="samtools" name="NGS: SAM Tools"></section> - <section name="NGS: GATK Tools (beta)" id="gatk"> - <label text="Alignment Utilities" id="gatk_bam_utilities"/> + <section id="gatk" name="NGS: GATK Tools (beta)"> + <label id="gatk_bam_utilities" text="Alignment Utilities" /><tool file="gatk/depth_of_coverage.xml" /><tool file="gatk/print_reads.xml" /> - <label text="Realignment" id="gatk_realignment" /> + <label id="gatk_realignment" text="Realignment" /><tool file="gatk/realigner_target_creator.xml" /><tool file="gatk/indel_realigner.xml" /> - <label text="Base Recalibration" id="gatk_recalibration" /> + <label id="gatk_recalibration" text="Base Recalibration" /><tool file="gatk/count_covariates.xml" /><tool file="gatk/table_recalibration.xml" /><tool file="gatk/analyze_covariates.xml" /> - <label text="Genotyping" id="gatk_genotyping" /> + <label id="gatk_genotyping" text="Genotyping" /><tool file="gatk/unified_genotyper.xml" /> - <label text="Annotation" id="gatk_annotation" /> + <label id="gatk_annotation" text="Annotation" /><tool file="gatk/variant_annotator.xml" /> - <label text="Filtration" id="gatk_filtration" /> + <label id="gatk_filtration" text="Filtration" /><tool file="gatk/variant_filtration.xml" /><tool file="gatk/variant_select.xml" /> - <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /> + <label id="gatk_variant_quality_score_recalibration" text="Variant Quality Score Recalibration" /><tool file="gatk/variant_recalibrator.xml" /><tool file="gatk/variant_apply_recalibration.xml" /> - <label text="Variant Utilities" id="gatk_variant_utilities"/> + <label id="gatk_variant_utilities" text="Variant Utilities" /><tool file="gatk/variants_validate.xml" /><tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section name="NGS: Peak Calling" id="peak_calling"> + <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /><tool file="genetrack/genetrack_indexer.xml" /><tool file="genetrack/genetrack_peak_prediction.xml" /></section> - <section name="NGS: Simulation" id="ngs-simulation"> + <section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /></section> - <section name="Phenotype Association" id="hgv"> + <section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /><tool file="phenotype_association/sift.xml" /><tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml"/> - <tool file="phenotype_association/ctd.xml" /> - <tool file="phenotype_association/funDo.xml" /> + <tool file="phenotype_association/linkToDavid.xml" /><tool file="phenotype_association/snpFreq.xml" /><tool file="phenotype_association/ldtools.xml" /><tool file="phenotype_association/pass.xml" /><tool file="phenotype_association/gpass.xml" /><tool file="phenotype_association/beam.xml" /><tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/hilbertvis.xml" /><tool file="phenotype_association/freebayes.xml" /><tool file="phenotype_association/master2pg.xml" /><tool file="phenotype_association/vcf2pgSnp.xml" /> - <tool file="phenotype_association/dividePgSnpAlleles.xml" /></section> - <section name="VCF Tools" id="vcf_tools"> + <section id="vcf_tools" name="VCF Tools"><tool file="vcf_tools/intersect.xml" /><tool file="vcf_tools/annotate.xml" /><tool file="vcf_tools/filter.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Fix exception class name bug I introduced in the last change to the drmaa runner.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff76fd33b81c/ Changeset: ff76fd33b81c User: natefoo Date: 2013-10-10 21:17:13 Summary: Fix exception class name bug I introduced in the last change to the drmaa runner. Affected #: 1 file diff -r 60a1b0fdccd252c406d8b92ab60005456afe6e7c -r ff76fd33b81cdde1fb270de688ec5e86488ba34d lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -214,7 +214,7 @@ state = self.ds.jobStatus( external_job_id ) # TODO: probably need to keep track of InvalidJobException count and remove after it exceeds some configurable except ( drmaa.DrmCommunicationException, drmaa.InternalException, drmaa.InvalidJobException ), e: - log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.name, e ) + log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.__name__, e ) new_watched.append( ajs ) continue except Exception, e: 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: guerler: Connect upload front end to upload tool via tools api
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/60a1b0fdccd2/ Changeset: 60a1b0fdccd2 User: guerler Date: 2013-10-10 20:41:47 Summary: Connect upload front end to upload tool via tools api Affected #: 3 files diff -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 -r 60a1b0fdccd252c406d8b92ab60005456afe6e7c lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -214,69 +214,6 @@ trans.sa_session.flush() return hda.to_dict() - # copy from upload - if source == 'upload': - - # get upload specific features - dbkey = payload.get('dbkey', None) - extension = payload.get('extension', None) - space_to_tabs = payload.get('space_to_tabs', False) - - # check for filename - if content.filename is None: - trans.response.status = 400 - return "history_contents:create() : The contents parameter needs to contain the uploaded file content." - - # create a dataset - dataset = trans.app.model.Dataset() - trans.sa_session.add(dataset) - trans.sa_session.flush() - - # get file destination - file_destination = dataset.get_file_name() - - # check if the directory exists - dn = os.path.dirname(file_destination) - if not os.path.exists(dn): - os.makedirs(dn) - - # get file and directory names - fn = os.path.basename(content.filename) - - # save file locally - open(file_destination, 'wb').write(content.file.read()) - - # log - log.info ('The file "' + fn + '" was uploaded successfully.') - - # replace separation with tabs - if space_to_tabs: - log.info ('Replacing spaces with tabs.') - sniff.convert_newlines_sep2tabs(file_destination) - - # guess extension - if extension is None: - log.info ('Guessing extension.') - extension = sniff.guess_ext(file_destination) - - # create hda - hda = trans.app.model.HistoryDatasetAssociation(dataset = dataset, name = content.filename, - extension = extension, dbkey = dbkey, history = history, sa_session = trans.sa_session) - - # add status ok - hda.state = hda.states.OK - - # add dataset to history - history.add_dataset(hda, genome_build = dbkey) - permissions = trans.app.security_agent.history_get_default_permissions( history ) - trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) - - # add to session - trans.sa_session.add(hda) - trans.sa_session.flush() - - # get name - return hda.to_dict() else: # other options trans.response.status = 501 diff -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 -r 60a1b0fdccd252c406d8b92ab60005456afe6e7c static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -38,10 +38,12 @@ this.$body.css('max-height', maxHeight); // fix height if available - if (this.options.height < maxHeight) - this.$body.css('height', this.options.height); - else - this.$body.css('height', maxHeight); + if (this.options.height) { + if (this.options.height < maxHeight) + this.$body.css('height', this.options.height); + else + this.$body.css('height', maxHeight); + } // remove scroll bar if (this.options.height) diff -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 -r 60a1b0fdccd252c406d8b92ab60005456afe6e7c static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -19,9 +19,7 @@ // extension types select_extension : { - 'auto' : 'Auto-detect', - 'bed' : 'bed', - 'ab1' : 'ab1' + 'auto' : 'Auto-detect' }, // states @@ -134,18 +132,31 @@ // get element var it = this.get_upload_item(index); + + // get current history + var current_history = Galaxy.currHistoryPanel.model.get('id'); - // read in configuration - var data = { - source : "upload", - space_to_tabs : it.find('#space_to_tabs').is(':checked'), - extension : it.find('#extension').val() - } + // configure tool + this.uploadbox.configure({url : galaxy_config.root + "api/tools/", paramname : "files_0|file_data"}); - // configure url - var current_history = Galaxy.currHistoryPanel.model.get('id'); - this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"}); + // get + var file_type = it.find('#extension').val(); + var space_to_tabs = it.find('#space_to_tabs').is(':checked'); + // configure tool + tool_input = {}; + tool_input['dbkey'] = '?'; + tool_input['file_type'] = file_type; + tool_input['files_0|NAME'] = file.name; + tool_input['files_0|type'] = 'upload_dataset'; + tool_input['space_to_tabs'] = space_to_tabs; + + // setup data + data = {}; + data['history_id'] = current_history; + data['tool_id'] = 'upload1'; + data['inputs'] = JSON.stringify(tool_input); + // return additional data to be send with file return data; }, 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: Filter tool dependency installation to only those that were checked when installing them from the Manage tool dependencies page for an installed tool shed repository.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8/ Changeset: ab9f5cb3acd8 User: greg Date: 2013-10-10 20:11:09 Summary: Filter tool dependency installation to only those that were checked when installing them from the Manage tool dependencies page for an installed tool shed repository. Affected #: 3 files diff -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -701,11 +701,11 @@ installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, tool_shed_repository=tool_shed_repository, name='inst_td_ids', - uninstalled=False ) + uninstalled_only=False ) uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, tool_shed_repository=tool_shed_repository, name='uninstalled_tool_dependency_ids', - uninstalled=True ) + uninstalled_only=True ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako', repository=tool_shed_repository, installed_tool_dependencies_select_field=installed_tool_dependencies_select_field, diff -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -429,6 +429,10 @@ will be installed in: ~/<app.config.tool_dependency_dir>/<package_name>/<package_version>/<repo_owner>/<repo_name>/<repo_installed_changeset_revision> """ + # The received list of tool_dependencies are the database records for those dependencies defined in the received tool_dependencies_config + # that should be installed. This allows for filtering out dependencies that have not been checked for installation on the 'Manage tool + # dependencies' page for an installed tool shed repository. + attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] sa_session = app.model.context.current installed_tool_dependencies = [] # Parse the tool_dependencies.xml config. @@ -439,19 +443,43 @@ fabric_version_checked = False for elem in root: if elem.tag == 'package': - # Only install the tool_dependency if it is not already installed. + # Only install the tool_dependency if it is not already installed and it is associated with a database record in the received + # tool_dependencies. package_name = elem.get( 'name', None ) package_version = elem.get( 'version', None ) if package_name and package_version: - for tool_dependency in tool_dependencies: - if tool_dependency.name==package_name and tool_dependency.version==package_version: - break - if tool_dependency.can_install: + attr_tup = ( package_name, package_version, 'package' ) + try: + index = attr_tups_of_dependencies_for_install.index( attr_tup ) + except Exception, e: + index = None + if index is not None: + tool_dependency = tool_dependencies[ index ] + if tool_dependency.can_install: + try: + tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) + except Exception, e: + error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) ) + log.exception( error_message ) + if tool_dependency: + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message + sa_session.add( tool_dependency ) + sa_session.flush() + if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, + app.model.ToolDependency.installation_status.ERROR ]: + installed_tool_dependencies.append( tool_dependency ) + elif elem.tag == 'set_environment': + env_var_name = env_var_elem.get( 'name', None ) + if env_var_name: + # Tool dependencies of type "set_environmnet" always have the version attribute set to None. + attr_tup = ( env_var_name, None, 'set_environment' ) + if attr_tup in attr_tups_of_dependencies_for_install: try: - tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) + tool_dependency = set_environment( app, elem, tool_shed_repository ) except Exception, e: - error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) + error_message = "Error setting environment for tool dependency: %s" % str( e ) + log.debug( error_message ) if tool_dependency: tool_dependency.status = app.model.ToolDependency.installation_status.ERROR tool_dependency.error_message = error_message @@ -460,20 +488,6 @@ if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) - elif elem.tag == 'set_environment': - try: - tool_dependency = set_environment( app, elem, tool_shed_repository ) - except Exception, e: - error_message = "Error setting environment for tool dependency: %s" % str( e ) - log.debug( error_message ) - if tool_dependency: - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = error_message - sa_session.add( tool_dependency ) - sa_session.flush() - if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, - app.model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) return installed_tool_dependencies def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ): diff -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -144,13 +144,18 @@ repositories_select_field.add_option( option_label, option_value ) return repositories_select_field -def build_tool_dependencies_select_field( trans, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled=False ): +def build_tool_dependencies_select_field( trans, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled_only=False ): """Method called from Galaxy to generate the current list of tool dependency ids for an installed tool shed repository.""" tool_dependencies_select_field = SelectField( name=name, multiple=multiple, display=display ) for tool_dependency in tool_shed_repository.tool_dependencies: - if uninstalled and tool_dependency.status not in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, - trans.model.ToolDependency.installation_status.UNINSTALLED ]: - continue + if uninstalled_only: + if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, + trans.model.ToolDependency.installation_status.UNINSTALLED ]: + continue + else: + if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, + trans.model.ToolDependency.installation_status.UNINSTALLED ]: + continue option_label = '%s version %s' % ( str( tool_dependency.name ), str( tool_dependency.version ) ) option_value = trans.security.encode_id( tool_dependency.id ) tool_dependencies_select_field.add_option( option_label, option_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.

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commit/galaxy-central: guerler: Update of the new upload front end, fix data viewer
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/450c04224d6c/ Changeset: 450c04224d6c User: guerler Date: 2013-10-10 19:34:36 Summary: Update of the new upload front end, fix data viewer Affected #: 6 files diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -11,13 +11,16 @@ // base element elMain: '#everything', - // defaults inputs + // defaults options optionsDefault: { title : "galaxy-modal", body : "", backdrop : true }, + // options + options : {}, + // initialize initialize : function(options) { // create @@ -31,16 +34,18 @@ this.initialize(options); // fix height - this.$body.css('max-height', $(document).height() / 2); + var maxHeight = $(document).height() / 2; + this.$body.css('max-height', maxHeight); - // set max-height so that modal does not exceed window size and is in middle of page. - /*/ TODO: this could perhaps be handled better using CSS. - this.$body.css( "max-height", - $(window).height() - - this.$footer.outerHeight() - - this.$header.outerHeight() - - parseInt( this.$dialog.css( "padding-top" ), 10 ) - - parseInt( this.$dialog.css( "padding-bottom" ), 10 ));*/ + // fix height if available + if (this.options.height < maxHeight) + this.$body.css('height', this.options.height); + else + this.$body.css('height', maxHeight); + + // remove scroll bar + if (this.options.height) + this.$body.css('overflow', 'hidden'); // show if (this.visible) @@ -64,18 +69,18 @@ // create create: function(options) { // configure options - options = _.defaults(options, this.optionsDefault); + this.options = _.defaults(options, this.optionsDefault); // check for progress bar request - if (options.body == 'progress') - options.body = $('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'); + if (this.options.body == 'progress') + this.options.body = $('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'); // remove former element if (this.$el) this.$el.remove(); // create new element - this.setElement(this.template(options.title)); + this.setElement(this.template(this.options.title)); // link elements this.$body = (this.$el).find('.modal-body'); @@ -84,24 +89,20 @@ this.$backdrop = (this.$el).find('.modal-backdrop'); // append body - this.$body.html(options.body); - - // fix height if available - if (options.height) - this.$body.css('height', options.height); + this.$body.html(this.options.body); // fix min-width so that modal cannot shrink considerably if new content is loaded. this.$body.css('min-width', this.$body.width()); // configure background - if (!options.backdrop) + if (!this.options.backdrop) this.$backdrop.removeClass('in'); // append buttons - if (options.buttons) { + if (this.options.buttons) { // link functions var self = this; - $.each(options.buttons, function(name, value) { + $.each(this.options.buttons, function(name, value) { self.$buttons.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); }); } else diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -19,15 +19,16 @@ // extension types select_extension : { - '' : 'Auto-detect', + 'auto' : 'Auto-detect', 'bed' : 'bed', 'ab1' : 'ab1' }, // states state : { - init : 'fa-icon-trash', - done : 'fa-icon-caret-down' + init : 'fa-icon-trash', + success : 'fa-icon-ok', + error : 'fa-icon-warning-sign' }, // counter @@ -94,7 +95,7 @@ var id = '#upload-' + index; // add upload item - $(this.el).append(this.template_file(id, this.select_extension)); + $(this.el).find('tbody:last').append(this.template_row(id, this.select_extension)); // scroll to bottom //$(this.el).scrollTop($(this.el).prop('scrollHeight')); @@ -106,15 +107,15 @@ it.fadeIn(); // update title - it.find('.title').html(file.name); - - // configure select field - //it.find('#extension').select2(); + it.find('#title').html(file.name); + + // update info + it.find('#size').html(this.size_to_string (file.size)); // add functionality to remove button var self = this; - it.find('.symbol').on('click', function() { self.event_remove (index) }); - + it.find('#symbol').on('click', function() { self.event_remove (index) }); + // initialize progress this.event_progress(index, file, 0); @@ -141,6 +142,10 @@ extension : it.find('#extension').val() } + // configure url + var current_history = Galaxy.currHistoryPanel.model.get('id'); + this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"}); + // return additional data to be send with file return data; }, @@ -157,8 +162,8 @@ // update progress it.find('.progress-bar').css({ width : percentage + '%' }); - // update info - it.find('.info').html(percentage + '% of ' + this.size_to_string (file.size)); + // update value + it.find('#percentage').html(percentage + '%'); }, // success @@ -184,16 +189,15 @@ var it = this.get_upload_item(index); // update progress frame - it.addClass('panel-success'); - it.removeClass('panel-default'); + it.addClass('success'); // update icon - var sy = it.find('.symbol'); + var sy = it.find('#symbol'); sy.removeClass('fa-icon-spin'); sy.removeClass('fa-icon-spinner'); // set status - sy.addClass(this.state.done); + sy.addClass(this.state.success); }, // error @@ -216,22 +220,21 @@ var it = this.get_upload_item(index); // update progress frame - it.addClass('panel-danger'); - it.removeClass('panel-default'); + it.addClass('danger'); // remove progress bar it.find('.progress').remove(); // write error message - it.find('.error').html('<strong>Failed:</strong> ' + message); + it.find('#info').html('<strong>Failed: </strong>' + message).show(); // update icon - var sy = it.find('.symbol'); + var sy = it.find('#symbol'); sy.removeClass('fa-icon-spin'); sy.removeClass('fa-icon-spinner'); // set status - sy.addClass(this.state.done); + sy.addClass(this.state.error); }, // start upload process @@ -242,27 +245,22 @@ return; // switch icons for new uploads + var items = $(this.el).find('.upload-item'); var self = this; - $(this.el).find('.symbol').each(function() + items.each(function() { - if($(this).hasClass(self.state.init)) + var symbol = $(this).find('#symbol'); + if(symbol.hasClass(self.state.init)) { - $(this).removeClass(self.state.init); - $(this).addClass('fa-icon-spinner'); - $(this).addClass('fa-icon-spin'); + symbol.removeClass(self.state.init); + symbol.addClass('fa-icon-spinner'); + symbol.addClass('fa-icon-spin'); } }); - // hide configuration - $(this.el).find('.panel-body').hide(); - // update running this.counter.running = this.counter.announce; this.update_screen(); - - // configure url - var current_history = Galaxy.currHistoryPanel.model.get('id'); - this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"}); // initiate upload procedure in plugin this.uploadbox.upload(); @@ -283,9 +281,9 @@ if (this.counter.running == 0) { // remove from screen - var panels = $(this.el).find('.panel'); - panels.fadeOut({complete: function() { panels.remove(); }}); - + var items = $(this.el).find('.upload-item'); + $(this.el).find('table').fadeOut({ complete : function() { items.remove(); }}); + // reset counter this.counter.reset(); @@ -302,18 +300,18 @@ { // get item var it = this.get_upload_item(index); - var sy = it.find('.symbol'); + var sy = it.find('#symbol'); // only remove from queue if not in processing line - if (sy.hasClass(this.state.init) || sy.hasClass(this.state.done)) + if (sy.hasClass(this.state.init) || sy.hasClass(this.state.success) || sy.hasClass(this.state.error)) { // reduce counter - if (it.hasClass('panel-default')) + if (it.hasClass('success')) + this.counter.success--; + else if (it.hasClass('danger')) + this.counter.error--; + else this.counter.announce--; - else if (it.hasClass('panel-success')) - this.counter.success--; - else if (it.hasClass('panel-danger')) - this.counter.error--; // show on screen info this.update_screen(); @@ -340,14 +338,14 @@ this.modal = new mod_modal.GalaxyModal( { title : 'Upload files from your local drive', - body : this.template('upload-box'), + body : this.template('upload-box', 'upload-info'), buttons : { 'Select' : function() {self.uploadbox.select()}, 'Upload' : function() {self.event_upload()}, 'Reset' : function() {self.event_reset()}, 'Close' : function() {self.modal.hide()} }, - height : '250px' + height : '350' }); // set element @@ -441,45 +439,61 @@ this.modal.enableButton('Select'); else this.modal.disableButton('Select'); + + // table visibility + if (this.counter.announce + this.counter.success + this.counter.error > 0) + $(this.el).find('table').show(); + else + $(this.el).find('table').hide(); }, // load html template - template: function(id) + template: function(id, idInfo) { - return '<div id="' + id + '" class="upload-box"></div><h6 id="upload-info" class="upload-info"></h6>'; + return '<div id="' + id + '" class="upload-box">' + + '<table class="table table-striped" style="display: none;">' + + '<thead>' + + '<tr>' + + '<th>Name</th>' + + '<th>Size</th>' + + '<th>Type</th>' + + '<th>Space→Tab</th>' + + '<th>Progress</th>' + + '<th></th>' + + '</tr>' + + '</thead>' + + '<tbody></tbody>' + + '</table>' + + '</div>' + + '<h6 id="' + idInfo + '" class="upload-info"></h6>'; }, - // load html template - template_file: function(id, select_extension) + template_row: function(id, select_extension) { - // start template - var tmpl = '<div id="' + id.substr(1) + '" class="panel panel-default">' + - '<div class="panel-heading">' + - '<h5 class="title"></h5>' + - '<h5 class="info"></h5>' + - '<div class="symbol ' + this.state.init + '"></div>' + - '</div>' + - '<div class="panel-body">' + - '<div class="menu">' + - 'Select file type: ' + - '<select id="extension">'; - + // construct template + var tmpl = '<tr id="' + id.substr(1) + '" class="upload-item">' + + '<td><div id="title" class="title"></div></td>' + + '<td><div id="size" class="size"></div></td>' + + '<td>' + + '<select id="extension">'; + // add file types to selection for (key in select_extension) - tmpl += '<option value="' + key + '">' + select_extension[key] + '</option>'; - - // continue template - tmpl += '</select>, ' + - '<span>Convert space to tabs: <input id="space_to_tabs" type="checkbox"></input></span>' + + tmpl += '<option value="' + key + '">' + select_extension[key] + '</option>'; + + tmpl += '</select>' + + '</td>' + + '<td><input id="space_to_tabs" type="checkbox"></input></td>' + + '<td>' + + '<div id="info" class="info">' + + '<div class="progress">' + + '<div class="progress-bar progress-bar-success"></div>' + + '<div id="percentage" class="percentage">0%</div>' + + '</div>' + '</div>' + - '</div>' + - '<div class="panel-footer">' + - '<div class="progress">' + - '<div class="progress-bar progress-bar-success"></div>' + - '</div>' + - '<h6 class="error"></h6>' + - '</div>' + - '</div>'; + '</td>' + + '<td><div id="symbol" class="symbol ' + this.state.init + '"></div></td>' + + '</tr>'; // return html string return tmpl; diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -183,10 +183,12 @@ var column_types = this.model.get_metadata('column_types'); if (colspan !== undefined) { $cell.attr('colspan', colspan).addClass('stringalign'); - } else if (column_types !== undefined && index < column_types.length) { - if (column_types[index] === 'str' || column_types === 'list') { - /* Left align all str columns, right align the rest */ - $cell.addClass('stringalign'); + } else if (column_types) { + if (index < column_types.length) { + if (column_types[index] === 'str' || column_types === 'list') { + /* Left align all str columns, right align the rest */ + $cell.addClass('stringalign'); + } } } return $cell; diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -20,8 +20,7 @@ success : function() {}, error : function(index, file, message) { alert(message); }, complete : function() {}, - error_browser : "Your browser does not support drag-and-drop file uploads.", - error_filesize : "This file is too large (>250MB). Please use an FTP client to upload it.", + error_filesize : "File exceeds 250MB. Please use an FTP client.", error_default : "Please make sure the file is available." } diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1125,12 +1125,14 @@ .galaxy-frame .frame .f-pin{left:6px;top:1px} .galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px} .upload-info{font-weight:normal;text-align:center} -.upload-box{width:100%;height:95%;max-height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden} -.upload-box .panel .panel-heading .info{position:absolute;top:3px;font-weight:normal;right:20px;text-align:right;margin:0px} -.upload-box .panel .panel-heading .symbol{position:absolute;cursor:pointer;top:0px;right:3px} -.upload-box .panel .panel-body{position:relative;padding:5px} -.upload-box .panel .panel-footer{position:relative;height:20px;padding:0px}.upload-box .panel .panel-footer .progress{height:10px;margin:5px} -.upload-box .panel .panel-footer .error{font-weight:normal;margin:2px} +.upload-box{width:100%;height:90%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px}.upload-box .table{width:100%} +.upload-box .table th{text-align:center;white-space:nowrap} +.upload-box .table td{margin:0px;paddign:0px} +.upload-box .title{width:150px;word-wrap:break-word;font-size:11px} +.upload-box .size{white-space:nowrap} +.upload-box .info{width:130px;font-size:11px}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit} +.upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff} +.upload-box .symbol{cursor:pointer} .unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none} .parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%} .clear:before,.clear:after{content:" ";display:table;} diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -7,8 +7,7 @@ .upload-box { width : 100%; - height : 95%; - max-height : 95%; + height : 90%; text-align : center; overflow : scroll; font-size : @font-size-base; @@ -16,71 +15,58 @@ -moz-border-radius: @border-radius-large; border-radius : @border-radius-large; border : 1px dashed @btn-default-border; - padding : 20px; + padding : 10px; + + .table { + width : 100%; + } + + .table th { + text-align: center; + white-space: nowrap; + } + + .table td { + margin: 0px; + paddign: 0px; + } + + .title { + width: 150px; + word-wrap: break-word; + font-size : @font-size-small; + } + + .size { + white-space: nowrap; + } + + .info { + width: 130px; + font-size : @font-size-small; - .panel - { - display: none; - - .panel-heading - { + .progress { + top:1px; position: relative; - height: 19px; - padding: 5px; - - .title - { - position: absolute; - top: 2px; - font-weight: normal; - text-align: left; - margin: 0px; - max-width: 300px; - overflow: hidden; - } - - .info - { - position: absolute; - top: 3px; - font-weight: normal; - right: 20px; - text-align: right; - margin: 0px; - } - - .symbol - { - position: absolute; - cursor: pointer; - top: 0px; - right: 3px; - } - } - - .panel-body - { - position: relative; - padding: 5px; - } - - .panel-footer - { - position:relative; - height: 20px; + width: 100%; padding: 0px; + margin: 0px; - .progress - { - height: 10px; - margin: 5px; + .progress-bar { + border-radius: inherit; + -moz-border-radius: inherit; } - .error - { - font-weight: normal; - margin: 2px; + .percentage { + position: absolute; + text-align: center; + width: 100%; + color: @white; } } } + + .symbol { + cursor: pointer; + } } \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d2ca877e2c4/ Changeset: 3d2ca877e2c4 User: natefoo Date: 2013-10-10 18:48:07 Summary: Convert DOS line endings. Affected #: 1 file diff -r 1706b14098fc7e88e9aa1c54f28857a818beec4d -r 3d2ca877e2c4d7a17c4113be333ec2431b066a7c tools/data_source/microbial_import_code.py --- a/tools/data_source/microbial_import_code.py +++ b/tools/data_source/microbial_import_code.py @@ -1,154 +1,154 @@ - -def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ): - # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to - # set data.name in exec_after_process(). - microbe_info= {} - orgs = {} - - filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR - for i, line in enumerate( open( filename ) ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - fields = line.split( sep ) - #read each line, if not enough fields, go to next line - try: - info_type = fields.pop(0) - if info_type.upper() == "ORG": - #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dop… - org_num = fields.pop(0) - name = fields.pop(0) - kingdom = fields.pop(0) - group = fields.pop(0) - chromosomes = fields.pop(0) - info_url = fields.pop(0) - link_site = fields.pop(0) - if org_num not in orgs: - orgs[ org_num ] = {} - orgs[ org_num ][ 'chrs' ] = {} - orgs[ org_num ][ 'name' ] = name - orgs[ org_num ][ 'kingdom' ] = kingdom - orgs[ org_num ][ 'group' ] = group - orgs[ org_num ][ 'chromosomes' ] = chromosomes - orgs[ org_num ][ 'info_url' ] = info_url - orgs[ org_num ][ 'link_site' ] = link_site - elif info_type.upper() == "CHR": - #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1 - org_num = fields.pop(0) - chr_acc = fields.pop(0) - name = fields.pop(0) - length = fields.pop(0) - gi = fields.pop(0) - gb = fields.pop(0) - info_url = fields.pop(0) - chr = {} - chr[ 'name' ] = name - chr[ 'length' ] = length - chr[ 'gi' ] = gi - chr[ 'gb' ] = gb - chr[ 'info_url' ] = info_url - if org_num not in orgs: - orgs[ org_num ] = {} - orgs[ org_num ][ 'chrs' ] = {} - orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr - elif info_type.upper() == "DATA": - #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed - uid = fields.pop(0) - org_num = fields.pop(0) - chr_acc = fields.pop(0) - feature = fields.pop(0) - filetype = fields.pop(0) - path = fields.pop(0) - data = {} - data[ 'filetype' ] = filetype - data[ 'path' ] = path - data[ 'feature' ] = feature - - if org_num not in orgs: - orgs[ org_num ] = {} - orgs[ org_num ][ 'chrs' ] = {} - if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]: - orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {} - orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data - else: continue - except: continue - for org_num in orgs: - org = orgs[ org_num ] - if org[ 'kingdom' ] not in microbe_info: - microbe_info[ org[ 'kingdom' ] ] = {} - if org_num not in microbe_info[ org[ 'kingdom' ] ]: - microbe_info[ org[ 'kingdom' ] ][org_num] = org - return microbe_info - -#post processing, set build for data and add additional data to history -from galaxy import datatypes, config, jobs, tools -from shutil import copyfile - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - base_dataset = out_data.items()[0][1] - history = base_dataset.history - if history == None: - print "unknown history!" - return - kingdom = param_dict.get( 'kingdom', None ) - #group = param_dict.get( 'group', None ) - org = param_dict.get( 'org', None ) - - #if not (kingdom or group or org): - if not (kingdom or org): - print "Parameters are not available." + +def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ): + # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to + # set data.name in exec_after_process(). + microbe_info= {} + orgs = {} + + filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR + for i, line in enumerate( open( filename ) ): + line = line.rstrip( '\r\n' ) + if line and not line.startswith( '#' ): + fields = line.split( sep ) + #read each line, if not enough fields, go to next line + try: + info_type = fields.pop(0) + if info_type.upper() == "ORG": + #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dop… + org_num = fields.pop(0) + name = fields.pop(0) + kingdom = fields.pop(0) + group = fields.pop(0) + chromosomes = fields.pop(0) + info_url = fields.pop(0) + link_site = fields.pop(0) + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + orgs[ org_num ][ 'name' ] = name + orgs[ org_num ][ 'kingdom' ] = kingdom + orgs[ org_num ][ 'group' ] = group + orgs[ org_num ][ 'chromosomes' ] = chromosomes + orgs[ org_num ][ 'info_url' ] = info_url + orgs[ org_num ][ 'link_site' ] = link_site + elif info_type.upper() == "CHR": + #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1 + org_num = fields.pop(0) + chr_acc = fields.pop(0) + name = fields.pop(0) + length = fields.pop(0) + gi = fields.pop(0) + gb = fields.pop(0) + info_url = fields.pop(0) + chr = {} + chr[ 'name' ] = name + chr[ 'length' ] = length + chr[ 'gi' ] = gi + chr[ 'gb' ] = gb + chr[ 'info_url' ] = info_url + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr + elif info_type.upper() == "DATA": + #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed + uid = fields.pop(0) + org_num = fields.pop(0) + chr_acc = fields.pop(0) + feature = fields.pop(0) + filetype = fields.pop(0) + path = fields.pop(0) + data = {} + data[ 'filetype' ] = filetype + data[ 'path' ] = path + data[ 'feature' ] = feature + + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]: + orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {} + orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data + else: continue + except: continue + for org_num in orgs: + org = orgs[ org_num ] + if org[ 'kingdom' ] not in microbe_info: + microbe_info[ org[ 'kingdom' ] ] = {} + if org_num not in microbe_info[ org[ 'kingdom' ] ]: + microbe_info[ org[ 'kingdom' ] ][org_num] = org + return microbe_info + +#post processing, set build for data and add additional data to history +from galaxy import datatypes, config, jobs, tools +from shutil import copyfile + +def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): + base_dataset = out_data.items()[0][1] + history = base_dataset.history + if history == None: + print "unknown history!" + return + kingdom = param_dict.get( 'kingdom', None ) + #group = param_dict.get( 'group', None ) + org = param_dict.get( 'org', None ) + + #if not (kingdom or group or org): + if not (kingdom or org): + print "Parameters are not available." #workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values if isinstance( kingdom, tools.parameters.basic.UnvalidatedValue ): - kingdom = kingdom.value + kingdom = kingdom.value if isinstance( org, tools.parameters.basic.UnvalidatedValue ): org = org.value - GALAXY_DATA_INDEX_DIR = app.config.tool_data_path - microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ) - new_stdout = "" - split_stdout = stdout.split("\n") - basic_name = "" - for line in split_stdout: - fields = line.split("\t") - if fields[0] == "#File1": - description = fields[1] - chr = fields[2] - dbkey = fields[3] - file_type = fields[4] - name, data = out_data.items()[0] - data.set_size() - basic_name = data.name - data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")" - data.dbkey = dbkey - data.info = data.name - data = app.datatypes_registry.change_datatype( data, file_type ) - data.init_meta() - data.set_peek() - app.model.context.add( data ) - app.model.context.flush() - elif fields[0] == "#NewFile": - description = fields[1] - chr = fields[2] - dbkey = fields[3] - filepath = fields[4] - file_type = fields[5] - newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library - newdata.set_size() - newdata.extension = file_type - newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")" - app.model.context.add( newdata ) - app.model.context.flush() - app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) - history.add_dataset( newdata ) - app.model.context.add( history ) - app.model.context.flush() - try: - copyfile(filepath,newdata.file_name) - newdata.info = newdata.name - newdata.state = jobs.JOB_OK - except: - newdata.info = "The requested file is missing from the system." - newdata.state = jobs.JOB_ERROR - newdata.dbkey = dbkey - newdata.init_meta() - newdata.set_peek() - app.model.context.flush() + GALAXY_DATA_INDEX_DIR = app.config.tool_data_path + microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ) + new_stdout = "" + split_stdout = stdout.split("\n") + basic_name = "" + for line in split_stdout: + fields = line.split("\t") + if fields[0] == "#File1": + description = fields[1] + chr = fields[2] + dbkey = fields[3] + file_type = fields[4] + name, data = out_data.items()[0] + data.set_size() + basic_name = data.name + data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")" + data.dbkey = dbkey + data.info = data.name + data = app.datatypes_registry.change_datatype( data, file_type ) + data.init_meta() + data.set_peek() + app.model.context.add( data ) + app.model.context.flush() + elif fields[0] == "#NewFile": + description = fields[1] + chr = fields[2] + dbkey = fields[3] + filepath = fields[4] + file_type = fields[5] + newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library + newdata.set_size() + newdata.extension = file_type + newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")" + app.model.context.add( newdata ) + app.model.context.flush() + app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) + history.add_dataset( newdata ) + app.model.context.add( history ) + app.model.context.flush() + try: + copyfile(filepath,newdata.file_name) + newdata.info = newdata.name + newdata.state = jobs.JOB_OK + except: + newdata.info = "The requested file is missing from the system." + newdata.state = jobs.JOB_ERROR + newdata.dbkey = dbkey + newdata.init_meta() + newdata.set_peek() + app.model.context.flush() https://bitbucket.org/galaxy/galaxy-central/commits/33af3a5b36df/ Changeset: 33af3a5b36df User: natefoo Date: 2013-10-10 18:53:10 Summary: Fix outdated usage of states in microbial dataset post-job hook. Affected #: 1 file diff -r 3d2ca877e2c4d7a17c4113be333ec2431b066a7c -r 33af3a5b36df7207ec469d635779329a73117f73 tools/data_source/microbial_import_code.py --- a/tools/data_source/microbial_import_code.py +++ b/tools/data_source/microbial_import_code.py @@ -80,7 +80,7 @@ return microbe_info #post processing, set build for data and add additional data to history -from galaxy import datatypes, config, jobs, tools +from galaxy import datatypes, config, tools from shutil import copyfile def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): @@ -144,10 +144,10 @@ try: copyfile(filepath,newdata.file_name) newdata.info = newdata.name - newdata.state = jobs.JOB_OK + newdata.state = newdata.states.OK except: newdata.info = "The requested file is missing from the system." - newdata.state = jobs.JOB_ERROR + newdata.state = newdata.states.ERROR newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Backout of c78f3f687fbc. I'm sure it is fine, but @natefoo got in my head and I don't want to break anything.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1706b14098fc/ Changeset: 1706b14098fc User: jmchilton Date: 2013-10-10 18:16:20 Summary: Backout of c78f3f687fbc. I'm sure it is fine, but @natefoo got in my head and I don't want to break anything. Affected #: 5 files diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -25,7 +25,6 @@ from galaxy.util.bunch import Bunch from galaxy.util.expressions import ExpressionContext from galaxy.util.json import from_json_string -from .output_checker import check_output log = logging.getLogger( __name__ ) @@ -1080,7 +1079,158 @@ self.cleanup() def check_tool_output( self, stdout, stderr, tool_exit_code, job ): - return check_output( self.tool, stdout, stderr, tool_exit_code, job ) + """ + Check the output of a tool - given the stdout, stderr, and the tool's + exit code, return True if the tool exited succesfully and False + otherwise. No exceptions should be thrown. If this code encounters + an exception, it returns True so that the workflow can continue; + otherwise, a bug in this code could halt workflow progress. + Note that, if the tool did not define any exit code handling or + any stdio/stderr handling, then it reverts back to previous behavior: + if stderr contains anything, then False is returned. + Note that the job id is just for messages. + """ + # By default, the tool succeeded. This covers the case where the code + # has a bug but the tool was ok, and it lets a workflow continue. + success = True + + try: + # Check exit codes and match regular expressions against stdout and + # stderr if this tool was configured to do so. + # If there is a regular expression for scanning stdout/stderr, + # then we assume that the tool writer overwrote the default + # behavior of just setting an error if there is *anything* on + # stderr. + if ( len( self.tool.stdio_regexes ) > 0 or + len( self.tool.stdio_exit_codes ) > 0 ): + # Check the exit code ranges in the order in which + # they were specified. Each exit_code is a StdioExitCode + # that includes an applicable range. If the exit code was in + # that range, then apply the error level and add a message. + # If we've reached a fatal error rule, then stop. + max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR + if tool_exit_code != None: + for stdio_exit_code in self.tool.stdio_exit_codes: + if ( tool_exit_code >= stdio_exit_code.range_start and + tool_exit_code <= stdio_exit_code.range_end ): + # Tack on a generic description of the code + # plus a specific code description. For example, + # this might prepend "Job 42: Warning (Out of Memory)\n". + code_desc = stdio_exit_code.desc + if ( None == code_desc ): + code_desc = "" + tool_msg = ( "%s: Exit code %d (%s)" % ( + galaxy.tools.StdioErrorLevel.desc( stdio_exit_code.error_level ), + tool_exit_code, + code_desc ) ) + log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) ) + stderr = tool_msg + "\n" + stderr + max_error_level = max( max_error_level, + stdio_exit_code.error_level ) + if ( max_error_level >= + galaxy.tools.StdioErrorLevel.FATAL ): + break + + if max_error_level < galaxy.tools.StdioErrorLevel.FATAL: + # We'll examine every regex. Each regex specifies whether + # it is to be run on stdout, stderr, or both. (It is + # possible for neither stdout nor stderr to be scanned, + # but those regexes won't be used.) We record the highest + # error level, which are currently "warning" and "fatal". + # If fatal, then we set the job's state to ERROR. + # If warning, then we still set the job's state to OK + # but include a message. We'll do this if we haven't seen + # a fatal error yet + for regex in self.tool.stdio_regexes: + # If ( this regex should be matched against stdout ) + # - Run the regex's match pattern against stdout + # - If it matched, then determine the error level. + # o If it was fatal, then we're done - break. + # Repeat the stdout stuff for stderr. + # TODO: Collapse this into a single function. + if ( regex.stdout_match ): + regex_match = re.search( regex.match, stdout, + re.IGNORECASE ) + if ( regex_match ): + rexmsg = self.regex_err_msg( regex_match, regex) + log.info( "Job %s: %s" + % ( job.get_id_tag(), rexmsg ) ) + stdout = rexmsg + "\n" + stdout + max_error_level = max( max_error_level, + regex.error_level ) + if ( max_error_level >= + galaxy.tools.StdioErrorLevel.FATAL ): + break + + if ( regex.stderr_match ): + regex_match = re.search( regex.match, stderr, + re.IGNORECASE ) + if ( regex_match ): + rexmsg = self.regex_err_msg( regex_match, regex) + log.info( "Job %s: %s" + % ( job.get_id_tag(), rexmsg ) ) + stderr = rexmsg + "\n" + stderr + max_error_level = max( max_error_level, + regex.error_level ) + if ( max_error_level >= + galaxy.tools.StdioErrorLevel.FATAL ): + break + + # If we encountered a fatal error, then we'll need to set the + # job state accordingly. Otherwise the job is ok: + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + success = False + else: + success = True + + # When there are no regular expressions and no exit codes to check, + # default to the previous behavior: when there's anything on stderr + # the job has an error, and the job is ok otherwise. + else: + # TODO: Add in the tool and job id: + # log.debug( "Tool did not define exit code or stdio handling; " + # + "checking stderr for success" ) + if stderr: + success = False + else: + success = True + + # On any exception, return True. + except: + tb = traceback.format_exc() + log.warning( "Tool check encountered unexpected exception; " + + "assuming tool was successful: " + tb ) + success = True + + # Store the modified stdout and stderr in the job: + if None != job: + job.stdout = stdout + job.stderr = stderr + + return success + + def regex_err_msg( self, match, regex ): + """ + Return a message about the match on tool output using the given + ToolStdioRegex regex object. The regex_match is a MatchObject + that will contain the string matched on. + """ + # Get the description for the error level: + err_msg = galaxy.tools.StdioErrorLevel.desc( regex.error_level ) + ": " + # If there's a description for the regular expression, then use it. + # Otherwise, we'll take the first 256 characters of the match. + if None != regex.desc: + err_msg += regex.desc + else: + mstart = match.start() + mend = match.end() + err_msg += "Matched on " + # TODO: Move the constant 256 somewhere else besides here. + if mend - mstart > 256: + err_msg += match.string[ mstart : mstart+256 ] + "..." + else: + err_msg += match.string[ mstart: mend ] + return err_msg def cleanup( self ): # remove temporary files diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d lib/galaxy/jobs/error_level.py --- a/lib/galaxy/jobs/error_level.py +++ /dev/null @@ -1,25 +0,0 @@ - - -# These determine stdio-based error levels from matching on regular expressions -# and exit codes. They are meant to be used comparatively, such as showing -# that warning < fatal. This is really meant to just be an enum. -class StdioErrorLevel( object ): - NO_ERROR = 0 - LOG = 1 - WARNING = 2 - FATAL = 3 - MAX = 3 - descs = { - NO_ERROR: 'No error', - LOG: 'Log', - WARNING: 'Warning', - FATAL: 'Fatal error', - } - - @staticmethod - def desc( error_level ): - err_msg = "Unknown error" - if ( error_level > 0 and - error_level <= StdioErrorLevel.MAX ): - err_msg = StdioErrorLevel.descs[ error_level ] - return err_msg diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d lib/galaxy/jobs/output_checker.py --- a/lib/galaxy/jobs/output_checker.py +++ /dev/null @@ -1,164 +0,0 @@ -import re -from .error_level import StdioErrorLevel -import traceback - -from logging import getLogger -log = getLogger( __name__ ) - - -def check_output( tool, stdout, stderr, tool_exit_code, job ): - """ - Check the output of a tool - given the stdout, stderr, and the tool's - exit code, return True if the tool exited succesfully and False - otherwise. No exceptions should be thrown. If this code encounters - an exception, it returns True so that the workflow can continue; - otherwise, a bug in this code could halt workflow progress. - - Note that, if the tool did not define any exit code handling or - any stdio/stderr handling, then it reverts back to previous behavior: - if stderr contains anything, then False is returned. - - Note that the job id is just for messages. - """ - # By default, the tool succeeded. This covers the case where the code - # has a bug but the tool was ok, and it lets a workflow continue. - success = True - - try: - # Check exit codes and match regular expressions against stdout and - # stderr if this tool was configured to do so. - # If there is a regular expression for scanning stdout/stderr, - # then we assume that the tool writer overwrote the default - # behavior of just setting an error if there is *anything* on - # stderr. - if ( len( tool.stdio_regexes ) > 0 or - len( tool.stdio_exit_codes ) > 0 ): - # Check the exit code ranges in the order in which - # they were specified. Each exit_code is a StdioExitCode - # that includes an applicable range. If the exit code was in - # that range, then apply the error level and add a message. - # If we've reached a fatal error rule, then stop. - max_error_level = StdioErrorLevel.NO_ERROR - if tool_exit_code != None: - for stdio_exit_code in tool.stdio_exit_codes: - if ( tool_exit_code >= stdio_exit_code.range_start and - tool_exit_code <= stdio_exit_code.range_end ): - # Tack on a generic description of the code - # plus a specific code description. For example, - # this might prepend "Job 42: Warning (Out of Memory)\n". - code_desc = stdio_exit_code.desc - if ( None == code_desc ): - code_desc = "" - tool_msg = ( "%s: Exit code %d (%s)" % ( - StdioErrorLevel.desc( stdio_exit_code.error_level ), - tool_exit_code, - code_desc ) ) - log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) ) - stderr = tool_msg + "\n" + stderr - max_error_level = max( max_error_level, - stdio_exit_code.error_level ) - if ( max_error_level >= - StdioErrorLevel.FATAL ): - break - - if max_error_level < StdioErrorLevel.FATAL: - # We'll examine every regex. Each regex specifies whether - # it is to be run on stdout, stderr, or both. (It is - # possible for neither stdout nor stderr to be scanned, - # but those regexes won't be used.) We record the highest - # error level, which are currently "warning" and "fatal". - # If fatal, then we set the job's state to ERROR. - # If warning, then we still set the job's state to OK - # but include a message. We'll do this if we haven't seen - # a fatal error yet - for regex in tool.stdio_regexes: - # If ( this regex should be matched against stdout ) - # - Run the regex's match pattern against stdout - # - If it matched, then determine the error level. - # o If it was fatal, then we're done - break. - # Repeat the stdout stuff for stderr. - # TODO: Collapse this into a single function. - if ( regex.stdout_match ): - regex_match = re.search( regex.match, stdout, - re.IGNORECASE ) - if ( regex_match ): - rexmsg = __regex_err_msg( regex_match, regex) - log.info( "Job %s: %s" - % ( job.get_id_tag(), rexmsg ) ) - stdout = rexmsg + "\n" + stdout - max_error_level = max( max_error_level, - regex.error_level ) - if ( max_error_level >= - StdioErrorLevel.FATAL ): - break - - if ( regex.stderr_match ): - regex_match = re.search( regex.match, stderr, - re.IGNORECASE ) - if ( regex_match ): - rexmsg = __regex_err_msg( regex_match, regex) - log.info( "Job %s: %s" - % ( job.get_id_tag(), rexmsg ) ) - stderr = rexmsg + "\n" + stderr - max_error_level = max( max_error_level, - regex.error_level ) - if ( max_error_level >= - StdioErrorLevel.FATAL ): - break - - # If we encountered a fatal error, then we'll need to set the - # job state accordingly. Otherwise the job is ok: - if max_error_level >= StdioErrorLevel.FATAL: - success = False - else: - success = True - - # When there are no regular expressions and no exit codes to check, - # default to the previous behavior: when there's anything on stderr - # the job has an error, and the job is ok otherwise. - else: - # TODO: Add in the tool and job id: - # log.debug( "Tool did not define exit code or stdio handling; " - # + "checking stderr for success" ) - if stderr: - success = False - else: - success = True - - # On any exception, return True. - except: - tb = traceback.format_exc() - log.warning( "Tool check encountered unexpected exception; " - + "assuming tool was successful: " + tb ) - success = True - - # Store the modified stdout and stderr in the job: - if None != job: - job.stdout = stdout - job.stderr = stderr - - return success - - -def __regex_err_msg( match, regex ): - """ - Return a message about the match on tool output using the given - ToolStdioRegex regex object. The regex_match is a MatchObject - that will contain the string matched on. - """ - # Get the description for the error level: - err_msg = StdioErrorLevel.desc( regex.error_level ) + ": " - # If there's a description for the regular expression, then use it. - # Otherwise, we'll take the first 256 characters of the match. - if None != regex.desc: - err_msg += regex.desc - else: - mstart = match.start() - mend = match.end() - err_msg += "Matched on " - # TODO: Move the constant 256 somewhere else besides here. - if mend - mstart > 256: - err_msg += match.string[ mstart : mstart + 256 ] + "..." - else: - err_msg += match.string[ mstart: mend ] - return err_msg diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -34,7 +34,6 @@ from sqlalchemy import and_ from galaxy import jobs, model -from galaxy.jobs.error_level import StdioErrorLevel from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.jobs import ParallelismInfo from galaxy.tools.actions import DefaultToolAction @@ -65,11 +64,33 @@ from tool_shed.util import shed_util_common from .loader import load_tool, template_macro_params - log = logging.getLogger( __name__ ) WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' ) +# These determine stdio-based error levels from matching on regular expressions +# and exit codes. They are meant to be used comparatively, such as showing +# that warning < fatal. This is really meant to just be an enum. +class StdioErrorLevel( object ): + NO_ERROR = 0 + LOG = 1 + WARNING = 2 + FATAL = 3 + MAX = 3 + descs = { + NO_ERROR : 'No error', + LOG: 'Log', + WARNING : 'Warning', + FATAL : 'Fatal error' + } + @staticmethod + def desc( error_level ): + err_msg = "Unknown error" + if ( error_level > 0 and + error_level <= StdioErrorLevel.MAX ): + err_msg = StdioErrorLevel.descs[ error_level ] + return err_msg + class ToolNotFoundException( Exception ): pass diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d test/unit/test_job_output_checker.py --- a/test/unit/test_job_output_checker.py +++ /dev/null @@ -1,62 +0,0 @@ -from unittest import TestCase -from galaxy.util.bunch import Bunch -from galaxy.jobs.output_checker import check_output -from galaxy.jobs.error_level import StdioErrorLevel - - -class OutputCheckerTestCase( TestCase ): - - def setUp( self ): - self.tool = Bunch( - stdio_regexes=[], - stdio_exit_codes=[], - ) - self.job = Bunch( - stdout=None, - stderr=None, - get_id_tag=lambda: "test_id", - ) - self.stdout = '' - self.stderr = '' - self.tool_exit_code = None - - def test_default_no_stderr_success( self ): - self.__assertSuccessful() - - def test_default_stderr_failure( self ): - self.stderr = 'foo' - self.__assertNotSuccessful() - - def test_exit_code_error( self ): - mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_exit_codes.append( mock_exit_code ) - self.tool_exit_code = 1 - self.__assertNotSuccessful() - - def test_exit_code_success( self ): - mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_exit_codes.append( mock_exit_code ) - self.tool_exit_code = 0 - self.__assertSuccessful() - - def test_problematic_strings( self ): - problematic_str = '\x80abc' - regex_rule = Bunch( match=r'.abc', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_regexes = [ regex_rule ] - self.stderr = problematic_str - self.__assertNotSuccessful() - - problematic_str = '\x80abc' - regex_rule = Bunch( match=r'.abcd', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_regexes = [ regex_rule ] - self.stderr = problematic_str - self.__assertSuccessful() - - def __assertSuccessful( self ): - self.assertTrue( self.__check_output() ) - - def __assertNotSuccessful( self ): - self.assertFalse( self.__check_output() ) - - def __check_output( self ): - return check_output( self.tool, self.stdout, self.stderr, self.tool_exit_code, self.job ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add status code 404 to response in tool_runner when a tool does not exist.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0f9ac20283c6/ Changeset: 0f9ac20283c6 User: dan Date: 2013-10-10 17:45:42 Summary: Add status code 404 to response in tool_runner when a tool does not exist. Affected #: 1 file diff -r 0226b3a74e2a64ddca1ce166de3d7c491315c4a5 -r 0f9ac20283c65288daa887508594ae67049047d0 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -61,6 +61,7 @@ if not tool: log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) + trans.response.status = 404 return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) if tool.require_login and not trans.user: message = "You must be logged in to use this tool." Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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