Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 13995757f26a8819638332b3541fa68811c86cfe https://github.com/galaxyproject/galaxy/commit/13995757f26a8819638332b3541fa... Author: Zipho Mashologu <zipho.m@gmail.com> Date: 2017-06-10 (Sat, 10 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/neo4j.py Log Message: ----------- added the zip format (datatype) for neostore. Commit: 58f93d3663953239b30d2fbb05b3f3a49829452d https://github.com/galaxyproject/galaxy/commit/58f93d3663953239b30d2fbb05b3f... Author: Zipho Mashologu <zipho.m@gmail.com> Date: 2017-06-10 (Sat, 10 Jun 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js 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tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'dev' into neo_datatype Commit: 6e9a66556f0e172eb0cace2cf7266525880e587c https://github.com/galaxyproject/galaxy/commit/6e9a66556f0e172eb0cace2cf7266... Author: Zipho Mashologu <zipho.m@gmail.com> Date: 2017-06-11 (Sun, 11 Jun 2017) Changed paths: M lib/galaxy/datatypes/neo4j.py Log Message: ----------- fixing unit test failure Commit: 013b03ab76e7b45d6cd5779fa196e64c2f086a82 https://github.com/galaxyproject/galaxy/commit/013b03ab76e7b45d6cd5779fa196e... Author: Zipho Mashologu <zipho.m@gmail.com> Date: 2017-06-11 (Sun, 11 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/neo4j.py Log Message: ----------- fixing travis build failures Commit: 8731ec764635afa9fdb831d5829b1825424eec76 https://github.com/galaxyproject/galaxy/commit/8731ec764635afa9fdb831d5829b1... Author: Zipho Mashologu <zipho.m@gmail.com> Date: 2017-06-11 (Sun, 11 Jun 2017) Changed paths: M lib/galaxy/datatypes/neo4j.py Log Message: ----------- making neostore.counts.db.a and neostore.counts.db.b optional Commit: 40edf26ceba2e6484e3b856cfd0487b9b728a8c4 https://github.com/galaxyproject/galaxy/commit/40edf26ceba2e6484e3b856cfd048... Author: Zipho Mashologu <zipho.m@gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/neo4j.py M tools/data_source/upload.py Log Message: ----------- changes to the version Commit: 791a746934ee90f41779f34c3a4afb7edfb1a3a4 https://github.com/galaxyproject/galaxy/commit/791a746934ee90f41779f34c3a4af... Author: Zipho Mashologu <zipho.m@gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/datatypes/neo4j.py M test-data/neostore.zip A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml Log Message: ----------- added tests Commit: ad47d781b1cbef4d89e12ba8e70820f0ad85deca https://github.com/galaxyproject/galaxy/commit/ad47d781b1cbef4d89e12ba8e7082... Author: Zipho Mashologu <zipho.m@gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- removing the import logging as not used on the tool Commit: dc67206b216ab5295751090cd88077dcdec87de6 https://github.com/galaxyproject/galaxy/commit/dc67206b216ab5295751090cd8807... Author: John Chilton <jmchilton@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: A .ci/autopep8.sh R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh R .ci/flake8_wrapper_imports.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M Makefile M README.rst A SECURITY_POLICY.md A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/bibtex.js R 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client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js A 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test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import.xml M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/joiner.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/wc_gnu.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into neo_datatype Commit: 590c19cfaae965569c26fe65d6b088606a2a89b1 https://github.com/galaxyproject/galaxy/commit/590c19cfaae965569c26fe65d6b08... Author: John Chilton <jmchilton@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Remove no longer needed binary registeration for new neo4j datatype. Commit: b2e7af4e34d15515647ebb671c220cf05e84749d https://github.com/galaxyproject/galaxy/commit/b2e7af4e34d15515647ebb671c220... Author: John Chilton <jmchilton@gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Fix import linting for neo4j datatype. Commit: 75283c7b6c2dc4e602fef67d5f4c68204e661e37 https://github.com/galaxyproject/galaxy/commit/75283c7b6c2dc4e602fef67d5f4c6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-01-02 (Tue, 02 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/neo4j.py M test-data/neostore.zip A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml Log Message: ----------- Merge pull request #4178 from zipho/neo_datatype Neostore Zip datatype support Compare: https://github.com/galaxyproject/galaxy/compare/cc18db4e4917...75283c7b6c2d