Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 60d0d9d5ec36fb1e6a79a4f51ab919325687b10d https://github.com/galaxyproject/galaxy/commit/60d0d9d5ec36fb1e6a79a4f51ab91... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Add grooming for composite files. Add call to groom_dataset_content() for composite files. Commit: 665e11facbf0b9b86fbcde04593fcd49ebe96777 https://github.com/galaxyproject/galaxy/commit/665e11facbf0b9b86fbcde04593fc... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add ISA composite data type. Add new data types isa-tab and isa-json. Add isa-rwval library (isatools Python 2 version) in requirements. Commit: 1fb63a1369e8fa75b1f7825693ef286682659a64 https://github.com/galaxyproject/galaxy/commit/1fb63a1369e8fa75b1f7825693ef2... Author: Pablo Moreno <pcm32@users.noreply.github.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- [ISA datatype] adds logger setting for isatools.isatab to avoid failing uploads when no pandas (#31) * [ISA datatype] adds logger setting for isatools.isatab to avoid failing uploads when no pandas. * Update isa.py Commit: fe139ad8dfe6c83188c33498d8d2854b33670c04 https://github.com/galaxyproject/galaxy/commit/fe139ad8dfe6c83188c33498d8d28... Author: Pablo Moreno <pcm32@users.noreply.github.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Installs isa-rwval from develop Otherwise failing currently when building in the container. Commit: 06c57810d9050ffd4c81ce8e189741f255d6eafc https://github.com/galaxyproject/galaxy/commit/06c57810d9050ffd4c81ce8e18974... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct linting issues detected by Travis-CI run. Commit: 5babb80fc24febbbbed1af5b0bf56c84f16ab8a4 https://github.com/galaxyproject/galaxy/commit/5babb80fc24febbbbed1af5b0bf56... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct again lint errors for Travis-CI. Commit: 84c002283209a5717682c31d1013034e9cfc828b https://github.com/galaxyproject/galaxy/commit/84c002283209a5717682c31d10130... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct some more lint errors for Travis-CI. Commit: b9c63df60e12b6220f088645c17bf6d8bd68ab1b https://github.com/galaxyproject/galaxy/commit/b9c63df60e12b6220f088645c17bf... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Change ISA Tools web site link. Replace ISA Tools .org web site that has just been hacked, by the GitHub page of the organization. Commit: cf7034399083c77d38e29c2832339776df103983 https://github.com/galaxyproject/galaxy/commit/cf7034399083c77d38e29c2832339... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Escape filename in primary file. Commit: a50537cd5a2cb1039bcc7b0fa215d523c6e97499 https://github.com/galaxyproject/galaxy/commit/a50537cd5a2cb1039bcc7b0fa215d... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Escape assay information in ISA display_data(). Commit: 86de0d3bc431404d6fca26e7506ec11415411788 https://github.com/galaxyproject/galaxy/commit/86de0d3bc431404d6fca26e7506ec... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove unused method _list_archive_files(). Commit: 62ff476a7c3eeaca51147b5ae0cac753b71ba9ee https://github.com/galaxyproject/galaxy/commit/62ff476a7c3eeaca51147b5ae0cac... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Use CompressedFile class. Replace unzip custom code by Galaxy call to CompressedFile class. Commit: abd22c12f22b15c010bcfe6b7dca63d1c2135d18 https://github.com/galaxyproject/galaxy/commit/abd22c12f22b15c010bcfe6b7dca6... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove logger configuration. Commit: 55bae21f77c03ebb1d114e9dbe593490b3e07993 https://github.com/galaxyproject/galaxy/commit/55bae21f77c03ebb1d114e9dbe593... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Comment out raw files listing in ISA type. Commit: e9f00065ee190ebdeca5c02d21c068d815674999 https://github.com/galaxyproject/galaxy/commit/e9f00065ee190ebdeca5c02d21c06... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove dynamical setting of study name for ISA. Commit: 2be9e1f637180d04d4e085b1c91292df3e09c72e https://github.com/galaxyproject/galaxy/commit/2be9e1f637180d04d4e085b1c9129... Author: djcomlab <djcomlab@gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Add new lazy table parsing for isa-tab datatype and reintroduce data files Commit: 87cdd2156d46036807134f8d91fde4fcc2ac10de https://github.com/galaxyproject/galaxy/commit/87cdd2156d46036807134f8d91fde... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A test-data/MTBLS6.zip M test/api/test_tools_upload.py Log Message: ----------- Start writing upload test for isa-tab. Do not know how to read zip file content and submit it to uploader for a composite type. Commit: 08ce54fe6e0f3cc178ad41a6fa3c00177cfbfef1 https://github.com/galaxyproject/galaxy/commit/08ce54fe6e0f3cc178ad41a6fa3c0... Author: djcomlab <djcomlab@gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Introduce new table parsers to get data files back; temporarily puts dependency back to Git repo to test against (updated PyPI package for isa-rwval will be pushed soon). Commit: eac29d55f9567b68ca94b3c2e468c380a64261ba https://github.com/galaxyproject/galaxy/commit/eac29d55f9567b68ca94b3c2e468c... Author: djcomlab <djcomlab@gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Fix requirements again for isa-rwval==0.10.1 Commit: b4fa3d28064e1c527a3b1a3232d10873490b6825 https://github.com/galaxyproject/galaxy/commit/b4fa3d28064e1c527a3b1a3232d10... Author: djcomlab <djcomlab@gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Cleanup presentation of data files (unused rendering using datafile id) Commit: 832f51b5168cc9751eecb77a62ff7a06807f92ed https://github.com/galaxyproject/galaxy/commit/832f51b5168cc9751eecb77a62ff7... Author: Pierrick Roger <pk.roger@icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pinned requirements as a symbolic link as done in dev branch. Commit: 39d4447a97ab8fe8359d3fd2a1df2815014570ea https://github.com/galaxyproject/galaxy/commit/39d4447a97ab8fe8359d3fd2a1df2... Author: djcomlab <djcomlab@gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Add check so that empty filenames not added to file list. Commit: a98cc55db25492217ff5cb6d91716122e39347fb https://github.com/galaxyproject/galaxy/commit/a98cc55db25492217ff5cb6d91716... Author: djcomlab <djcomlab@gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Fix upload test for isa-tab datatype Commit: f2176d395478fe4c4ad41ae3f03747b3967abc6d https://github.com/galaxyproject/galaxy/commit/f2176d395478fe4c4ad41ae3f0374... Author: djcomlab <djcomlab@gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update isa-rwval version as new update fixes a bug Commit: efc7864cabb0f7adc65929f3bff2f56c3ef14041 https://github.com/galaxyproject/galaxy/commit/efc7864cabb0f7adc65929f3bff2f... 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test/unit/visualizations/plugins/test_VisualizationsRegistry.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_workflow_progress.py A tool-data/intermine_simple_display.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample A tools/data_source/intermine.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge branch 'dev' into feature/isa_data_type Commit: 35093e38fcfe4f9efc3a2914d694cf4a11f24ace https://github.com/galaxyproject/galaxy/commit/35093e38fcfe4f9efc3a2914d694c... Author: Pierrick ROGER <pk.roger@icloud.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Remove spaces in blank line. Commit: a9eb587a3e38849c5044700f9f01c47d53f55a87 https://github.com/galaxyproject/galaxy/commit/a9eb587a3e38849c5044700f9f01c... Author: Pierrick ROGER <pk.roger@icloud.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Various corrections for py34-lint Add second blank line. Remove useless imports. Commit: 99bc4b33d2fa14a42f9ee7f4a9afe4dcf867c851 https://github.com/galaxyproject/galaxy/commit/99bc4b33d2fa14a42f9ee7f4a9afe... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-10-19 (Fri, 19 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt A test-data/MTBLS6.zip M test/api/test_tools_upload.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5787 from phnmnl/feature/isa_data_type Feature/isa data type Compare: https://github.com/galaxyproject/galaxy/compare/81f31d1a29e1...99bc4b33d2fa **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.