- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 64652c: Drop wait from cached job tests
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64652c28cf7ea88195b1c9008c46137c3bb3644a https://github.com/galaxyproject/galaxy/commit/64652c28cf7ea88195b1c9008c46… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Drop wait from cached job tests Commit: 31d850b64484dd4f418a27c9313a954f89e37d7d https://github.com/galaxyproject/galaxy/commit/31d850b64484dd4f418a27c9313a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py Log Message: ----------- Make discovery of cachable jobs more robust We update the actually used version once the job inputs are ready. This allows finding jobs when a dataset is being new / being updated while the job is new. This is also more accurate since we record the dataset versino that is actually being used when the tool is being evaluated. This should allow chaching when simultaneously running workflows that share steps. Commit: a0982c1b900111d0b2a4add372f0caef0686a000 https://github.com/galaxyproject/galaxy/commit/a0982c1b900111d0b2a4add372f0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Only create HDA history if HDA columns have changed This creates fewer versions because we ignore relationship changes. Commit: 5c54793ddfbd86875322280ab74041152e6c8a40 https://github.com/galaxyproject/galaxy/commit/5c54793ddfbd86875322280ab740… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6669 from mvdbeek/fix_cache_tests Increase robustness and accuracy of job search / cache use Compare: https://github.com/galaxyproject/galaxy/compare/89405fae9435...5c54793ddfbd **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.

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[galaxyproject/usegalaxy-playbook] 432c0d: Install logflux for nginx rate limit logs
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/swarmscale-2.0 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 432c0d613aeac21334211f28a0ffc7c353231c1f https://github.com/galaxyproject/usegalaxy-playbook/commit/432c0d613aeac213… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M env/common/stack.yml A env/test/group_vars/logfluxservers.yml M env/test/inventory A roles/logflux/defaults/main.yml A roles/logflux/handlers/main.yml A roles/logflux/tasks/main.yml A roles/logflux/templates/logflux.service.j2 A roles/logflux/templates/rsyslog.conf.j2 Log Message: ----------- Install logflux for nginx rate limit logs **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.

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[galaxyproject/galaxy] 9f14fc: Add Seurat datatype: rdata.seurat
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f14fcb1005452bae314eeebb324351a98510204 https://github.com/galaxyproject/galaxy/commit/9f14fcb1005452bae314eeebb324… Author: Maria Doyle <maria.doyle(a)petermac.org> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add Seurat datatype: rdata.seurat Commit: 89405fae9435bfc344f10c4155736d2810df84cd https://github.com/galaxyproject/galaxy/commit/89405fae9435bfc344f10c415573… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6648 from mblue9/add_seurat_datatype Add Seurat datatype: rdata.seurat Compare: https://github.com/galaxyproject/galaxy/compare/6787dbc9ee90...89405fae9435 **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.

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[galaxyproject/galaxy] 51b4de: Allow running scripts/galaxy-main without Galaxy o...
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51b4def4ec005b136707bff38611ed09ba6db2ff https://github.com/galaxyproject/galaxy/commit/51b4def4ec005b136707bff38611… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Allow running scripts/galaxy-main without Galaxy on $PYTHONPATH Commit: 4ed9df9a947563a5fca4e07caad1b6a19cd6a845 https://github.com/galaxyproject/galaxy/commit/4ed9df9a947563a5fca4e07caad1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Set config builder attributes before they're referenced in app_kwds() Commit: 923ed2ed493a9575473b58da52d80de2d58ab41a https://github.com/galaxyproject/galaxy/commit/923ed2ed493a9575473b58da52d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Simplify importing from galaxy lib Commit: e14b871eb9ce577a8ee107728e4acb41028ddaa1 https://github.com/galaxyproject/galaxy/commit/e14b871eb9ce577a8ee107728e4a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Add test for scripts/galaxy-main Commit: 6787dbc9ee90662e2bf52b596d787ea0d66f88bd https://github.com/galaxyproject/galaxy/commit/6787dbc9ee90662e2bf52b596d78… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M scripts/galaxy-main M test/integration/test_scripts.py Log Message: ----------- Merge pull request #6642 from natefoo/galaxy-main-import Allow running scripts/galaxy-main without Galaxy on sys.path Compare: https://github.com/galaxyproject/galaxy/compare/7f1f8a7a4eda...6787dbc9ee90 **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.

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[galaxyproject/galaxy] 8affe2: py3: fix secure_hash_message_digest.py
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8affe206df782658dbc388d5ffe1c5c1d6a136ef https://github.com/galaxyproject/galaxy/commit/8affe206df782658dbc388d5ffe1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/secure_hash_message_digest.py Log Message: ----------- py3: fix secure_hash_message_digest.py Commit: df5cab38ae35a38e1d7486d8c2fc0c8f452ed32e https://github.com/galaxyproject/galaxy/commit/df5cab38ae35a38e1d7486d8c2fc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/wc_gnu.xml Log Message: ----------- Fix wc_gnu test 1; list comprehensions are function objects on py3 and can't access outer local namespace Commit: 6352a0ef3ea5d80771276bcf4b928dda3acdbc08 https://github.com/galaxyproject/galaxy/commit/6352a0ef3ea5d80771276bcf4b92… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/util/ucsc.py Log Message: ----------- Fix wiggle2simple1 Commit: 36c74bbafa972f0e76ad8bf7befa23090eb8d92e https://github.com/galaxyproject/galaxy/commit/36c74bbafa972f0e76ad8bf7befa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- Fix maf_utilities comparison Commit: 6c7203b83d19d1f79bd6b1790ce24e9507931257 https://github.com/galaxyproject/galaxy/commit/6c7203b83d19d1f79bd6b1790ce2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/plotting/boxplot.xml Log Message: ----------- py3: Fix qual_stats_boxplot Commit: 6405aeb86c2240e010fadcd4e4758feccabba218 https://github.com/galaxyproject/galaxy/commit/6405aeb86c2240e010fadcd4e475… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Comment out tests with unavailable test data Commit: 8190c3fc4389299c8d9484bf3b3409b5cea51921 https://github.com/galaxyproject/galaxy/commit/8190c3fc4389299c8d9484bf3b34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/join.py Log Message: ----------- Fix the join1 tool Commit: 3fcf1e336dd2e32b0199388528078ce19ab7d98b https://github.com/galaxyproject/galaxy/commit/3fcf1e336dd2e32b019938852807… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/solid_tools/solid_qual_stats.py Log Message: ----------- Fix solid_qual_stats.py Commit: 2d732715ff50241fcddfab58795306a3880bd3c3 https://github.com/galaxyproject/galaxy/commit/2d732715ff50241fcddfab587953… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/grouping.py Log Message: ----------- Fix grouping tool Commit: 8889bd0a3d93266893a21dedefa9f93b8e51e8ef https://github.com/galaxyproject/galaxy/commit/8889bd0a3d93266893a21dedefa9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/senatag.py Log Message: ----------- Fix various things about the hgv_ldtools tool Unfortnately this doens't produce the test-data output on python 3 and so I added a requiremtn on python 2. (I think the result is probably correct but not deterministic). Commit: 9949053f430fcd44cdff6434f934146eecaa1d1f https://github.com/galaxyproject/galaxy/commit/9949053f430fcd44cdff6434f934… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_limit_to_species.py Log Message: ----------- Fix maf_limit_to_species.py if no species is given Commit: 2827dbf669ff2e9e2a7938aad0b81c94220c813d https://github.com/galaxyproject/galaxy/commit/2827dbf669ff2e9e2a7938aad0b8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_interval.py Log Message: ----------- Fix maf_to_interval.py Commit: 548b9c8c89121935e5557d98e6e8ec87327714bf https://github.com/galaxyproject/galaxy/commit/548b9c8c89121935e5557d98e6e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_bed.py Log Message: ----------- Fix maf_to_bed.py Commit: 2d36e8955e020958334088d6ba5853c1027d8b75 https://github.com/galaxyproject/galaxy/commit/2d36e8955e020958334088d6ba58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 918634f1fbbfafecbe9a25e869f82ea2df7e8edf https://github.com/galaxyproject/galaxy/commit/918634f1fbbfafecbe9a25e869f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Switch rpy2 to 2.9.4, 2.7.8 can't be resolved Commit: 491fe4251e97335505243f460f6a3bdf99df1556 https://github.com/galaxyproject/galaxy/commit/491fe4251e97335505243f460f6a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/uniq.xml Log Message: ----------- Fix uniq tests on OSX Commit: 77b43946f616b2e29b0550a21255a2c970dbd4dc https://github.com/galaxyproject/galaxy/commit/77b43946f616b2e29b0550a21255… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/next_gen_conversion/solid2fastq.xml Log Message: ----------- Fix solid2fastq tests Commit: 18ac62c1fd5952a94e5c6eaf4c3e357335a47ff2 https://github.com/galaxyproject/galaxy/commit/18ac62c1fd5952a94e5c6eaf4c3e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/wig_to_bigwig.xml Log Message: ----------- Fix wig_to_bigwig tool tests Commit: da4906dc56175cabd72a7d4b9b2ecce93bcad740 https://github.com/galaxyproject/galaxy/commit/da4906dc56175cabd72a7d4b9b2e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/functional/known_broken_tools.txt Log Message: ----------- Add GeneBed_Maf_Fasta2 to no test list Commit: c1dffec4ecdda1494a6169e3239c82dadbeda50c https://github.com/galaxyproject/galaxy/commit/c1dffec4ecdda1494a6169e3239c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/tailWrapper.xml Log Message: ----------- Quote tail wrapper inputs and outputs, drop interpreter attribute Commit: 05f18d029bb1308ab37e575f6972e8e18792e8b5 https://github.com/galaxyproject/galaxy/commit/05f18d029bb1308ab37e575f6972… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml Log Message: ----------- Fix linkToGProfile test Commit: 4acfd9a770518b33191a395dc1c606b82b67879a https://github.com/galaxyproject/galaxy/commit/4acfd9a770518b33191a395dc1c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/sff_extractor.xml Log Message: ----------- Fix sffextractor tests by requiring python 2.7 Commit: f22f0ebb2f95415573a42c0b4a783dde8aeb8c04 https://github.com/galaxyproject/galaxy/commit/f22f0ebb2f95415573a42c0b4a78… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_split_by_species.xml Log Message: ----------- Sort maf_split_by_species test output Commit: e8d0ce39cf60b8311d9b749189a29025ad476144 https://github.com/galaxyproject/galaxy/commit/e8d0ce39cf60b8311d9b749189a2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml Log Message: ----------- Fix random order of fasta headers in maf_to_bed Commit: aee261daf7f87289063a91371fd66ffcb3c595b8 https://github.com/galaxyproject/galaxy/commit/aee261daf7f87289063a91371fd6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_fasta_multiple_sets.py Log Message: ----------- Fix random header order in MAF to FASTA Commit: 36196bd2be7b350c0aae85c44cd1fcb8a1b1c737 https://github.com/galaxyproject/galaxy/commit/36196bd2be7b350c0aae85c44cd1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_interval.xml Log Message: ----------- Specify maf ftype in maf_to_interval.xml Commit: 906951f28e075829444c8c222000e4af82a86ef9 https://github.com/galaxyproject/galaxy/commit/906951f28e075829444c8c222000… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/solid_tools/solid_qual_stats.xml Log Message: ----------- Single-quote paths in solid_qual_stats and fix test by using sim_size -- we have different float precision between py2 and py3. Commit: 72f95ba9c4bb940c892b8f6b37a1d91471d013c9 https://github.com/galaxyproject/galaxy/commit/72f95ba9c4bb940c892b8f6b37a1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/bed_to_bigbed.xml Log Message: ----------- Test bed_to_bigbed using compare="sim_size" Commit: 8b757f22d1489deb09a863cfc701f4ce1ea0c1f3 https://github.com/galaxyproject/galaxy/commit/8b757f22d1489deb09a863cfc701… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/functional/known_broken_tools.txt Log Message: ----------- Exclude bed_to_bigbed and wig_to_bigwig from tests They work, but required hg17.len to be present. Commit: 91b02cc6a80ea267743779ffcf4483ada5338cf9 https://github.com/galaxyproject/galaxy/commit/91b02cc6a80ea267743779ffcf44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh Log Message: ----------- Add .ci/jenkins/main* for testing tools in tool_conf.xml.main Commit: 7f220276cc2fb500447b0f320b3d4985855def01 https://github.com/galaxyproject/galaxy/commit/7f220276cc2fb500447b0f320b3d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/joinWrapper.py Log Message: ----------- py3: Fix comp1 tool Commit: c939e7bb616103fb4d79067cf3d8159e276524ea https://github.com/galaxyproject/galaxy/commit/c939e7bb616103fb4d79067cf3d8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Bump version of Summary Statistics for rpy2 version update Commit: 7f1f8a7a4eda4b753bcedcc25b11a9abe34175c6 https://github.com/galaxyproject/galaxy/commit/7f1f8a7a4eda4b753bcedcc25b11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/ucsc.py M test/functional/known_broken_tools.txt M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/secure_hash_message_digest.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/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/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/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/grouping.py M tools/stats/gsummary.xml Log Message: ----------- Merge pull request #6627 from mvdbeek/test_more_tools Test tools shipped with Galaxy Compare: https://github.com/galaxyproject/galaxy/compare/ae7b4fda8976...7f1f8a7a4eda **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.

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[galaxyproject/galaxy] 9b488f: One last Selenium fix for collection interface cha...
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b488ff291a7d5c2204ed20b3f71769fe58d7e30 https://github.com/galaxyproject/galaxy/commit/9b488ff291a7d5c2204ed20b3f71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- One last Selenium fix for collection interface change. Commit: ae7b4fda89764ccae189141c75d1609a751b3add https://github.com/galaxyproject/galaxy/commit/ae7b4fda89764ccae189141c75d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #6672 from jmchilton/selenium_fixes_47 One last Selenium fix for collection interface change. Compare: https://github.com/galaxyproject/galaxy/compare/309c13b5ba42...ae7b4fda8976 **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.

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[galaxyproject/galaxy] d645d8: Update bx-python to 0.8.2
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d645d80443c23d89fc65f3bb33caf4be9c9c7f21 https://github.com/galaxyproject/galaxy/commit/d645d80443c23d89fc65f3bb33ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update bx-python to 0.8.2 to include https://github.com/bxlab/bx-python/pull/35 . Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 . Commit: 309c13b5ba42dc3ee27982202b3ed320d9ecb214 https://github.com/galaxyproject/galaxy/commit/309c13b5ba42dc3ee27982202b3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8e7088b1a074...309c13b5ba42 **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.

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[galaxyproject/galaxy] d645d8: Update bx-python to 0.8.2
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: d645d80443c23d89fc65f3bb33caf4be9c9c7f21 https://github.com/galaxyproject/galaxy/commit/d645d80443c23d89fc65f3bb33ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update bx-python to 0.8.2 to include https://github.com/bxlab/bx-python/pull/35 . Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 . **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.

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[galaxyproject/galaxy] 85cab9: Update bx-python to 0.8.2
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85cab90689f07fd17b15f7d52efc5e0cae720056 https://github.com/galaxyproject/galaxy/commit/85cab90689f07fd17b15f7d52efc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update bx-python to 0.8.2 to include https://github.com/bxlab/bx-python/pull/35 . Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 . Commit: 8e7088b1a0744df3c35871d24b91dfd76fe310c3 https://github.com/galaxyproject/galaxy/commit/8e7088b1a0744df3c35871d24b91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6670 from nsoranzo/release_18.05_bx-python_0.8.2 [18.05] Update bx-python to 0.8.2 Compare: https://github.com/galaxyproject/galaxy/compare/09f6e1f9ee08...8e7088b1a074 **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.

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[galaxyproject/galaxy] 296105: row ids that are all numeric become ints...
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 296105ee395194c48d962671a8c367469ea74907 https://github.com/galaxyproject/galaxy/commit/296105ee395194c48d962671a8c3… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- row ids that are all numeric become ints... Since the "F" prefix is checked with substring, row_id must always be a string Commit: 55d350d015f20afc1c350130caaa0aa9858b7aa0 https://github.com/galaxyproject/galaxy/commit/55d350d015f20afc1c350130caaa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/communication-server-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M 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static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M 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static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-rules-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/collection/rules-input-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-utils.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/chart/chart-client.js M static/scripts/mvc/visualization/chart/components/model.js M static/scripts/mvc/visualization/chart/components/screenshot.js M static/scripts/mvc/visualization/chart/utilities/datasets.js M static/scripts/mvc/visualization/chart/utilities/jobs.js M static/scripts/mvc/visualization/chart/utilities/series.js M static/scripts/mvc/visualization/chart/views/description.js M static/scripts/mvc/visualization/chart/views/editor.js M static/scripts/mvc/visualization/chart/views/groups.js M static/scripts/mvc/visualization/chart/views/menu.js M static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Add static for 2a148ff1ec37c68e280c431fceee88ee0510e017 Commit: 03c485ee45e96784b269896a23223d233c566b89 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static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M 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static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge pull request #6639 from bwlang/patch-2 [18.05] row ids that are all numeric become ints... Commit: 09f6e1f9ee08f4da770d18e2fb33e6434c64ba90 https://github.com/galaxyproject/galaxy/commit/09f6e1f9ee08f4da770d18e2fb33… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8148bd91deb4...09f6e1f9ee08 **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.

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[galaxyproject/galaxy] 0b6444: Skip tool tests in test/functional/known_broken_to...
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b64442ed3d06bd7fdf9f0fbb53520d28e9332b9 https://github.com/galaxyproject/galaxy/commit/0b64442ed3d06bd7fdf9f0fbb535… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py Log Message: ----------- Skip tool tests in test/functional/known_broken_tools.txt Commit: 300ab73c10332968a98eb5f77a85abc66a3f4686 https://github.com/galaxyproject/galaxy/commit/300ab73c10332968a98eb5f77a85… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M pytest.ini M test/functional/test_toolbox_pytest.py Log Message: ----------- Mark skipped tests instead of not collecting them Also marks tests as tool or data_manager, so `pytest -m <tool|data_manager>` can be used to select a subset of tests. Commit: 6f299202313c3b40d357468e9ba0e9b32f858038 https://github.com/galaxyproject/galaxy/commit/6f299202313c3b40d357468e9ba0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use pytest for -framework, -installed, -data_manager, -migrated tests Commit: 546b90a6985cc6a8e4d87482778c8ac275c9903f https://github.com/galaxyproject/galaxy/commit/546b90a6985cc6a8e4d87482778c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Add additional test target for tools in tool_conf.xml.main Commit: e73257f8ed2556a94a6e58efff62ed1873709f42 https://github.com/galaxyproject/galaxy/commit/e73257f8ed2556a94a6e58efff62… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M test/functional/test_toolbox_pytest.py Log Message: ----------- Set conda_auto_init and conda_auto_install to true for pytest driver Commit: 7f807ce971e8d743dca0f0438e5ce078f742ec65 https://github.com/galaxyproject/galaxy/commit/7f807ce971e8d743dca0f0438e5c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix shell syntax Commit: 9099e73a3e00658082891fae7ea3de0774cce2ad https://github.com/galaxyproject/galaxy/commit/9099e73a3e00658082891fae7ea3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M .coveragerc Log Message: ----------- Add include-ignored, otherwise spams stderr out Commit: d476fcc072dbcb8e3b19f511dc43ae731e7c97e0 https://github.com/galaxyproject/galaxy/commit/d476fcc072dbcb8e3b19f511dc43… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M lib/galaxy/jobs/runners/util/kill.py Log Message: ----------- Fix LocalShell on python3 Commit: 1c64cdd674fcbfc0f077f5d31947dd9b6c6e9149 https://github.com/galaxyproject/galaxy/commit/1c64cdd674fcbfc0f077f5d31947… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M pytest.ini M run_tests.sh M tox.ini Log Message: ----------- Use pytest to run unit and doctests Commit: 1152a19fd2cd5d6589becde3c7ebdd6435a33cff https://github.com/galaxyproject/galaxy/commit/1152a19fd2cd5d6589becde3c7eb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use pytest-cov for testing coverage Commit: 66c64ccfe46cfd91bcffabaf2b4bddd7b86cef91 https://github.com/galaxyproject/galaxy/commit/66c64ccfe46cfd91bcffabaf2b4b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Adapt dynamic_tool_destination unit tests to pytest as driver The log capturing seems to be a bit different Commit: d9a2c5a970aafabe101842991a34074701f8854c https://github.com/galaxyproject/galaxy/commit/d9a2c5a970aafabe101842991a34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Don't test tools in tool_conf.xml.sample as part of -framework This replicates what the FrameworkToolsGalaxyTestDriver does. Commit: aa0becad0be33ee7fe1d430c64f1d89f475ca6e2 https://github.com/galaxyproject/galaxy/commit/aa0becad0be33ee7fe1d430c64f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Simplify tool_conf selection in run_tests.sh Drops -with_framework_test_tools altogether. Thanks @nsoranzo. Commit: 8148bd91deb4d4f9b621b6e3097ae0f01ba81abd https://github.com/galaxyproject/galaxy/commit/8148bd91deb4d4f9b621b6e3097a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M .coveragerc M lib/galaxy/jobs/runners/util/kill.py M pytest.ini M run_tests.sh A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M tox.ini Log Message: ----------- Merge pull request #6638 from mvdbeek/move_tests_to_pytest_setup Move tests to pytest setup Compare: https://github.com/galaxyproject/galaxy/compare/bc1526ab2dd5...8148bd91deb4 **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.

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[galaxyproject/galaxy] 73b6e8: Eliminate more queries in history.add_dataset(s) b...
by GitHub 04 Sep '18

04 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73b6e81a0ab2f646de7d3709bcbf9e4284a1c439 https://github.com/galaxyproject/galaxy/commit/73b6e81a0ab2f646de7d3709bcbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py Log Message: ----------- Eliminate more queries in history.add_dataset(s) by using cached IDs. Commit: 74bb5434a0e9020673f1d4acaab98a6bd9865268 https://github.com/galaxyproject/galaxy/commit/74bb5434a0e9020673f1d4acaab9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Eliminate old and invalid tool optimization comment. Commit: b2fe48a6be69bd5c05357ae0a8a7fe07f8d314db https://github.com/galaxyproject/galaxy/commit/b2fe48a6be69bd5c05357ae0a8a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Allow history_id to be specified instead of history in check_elements. Commit: bc1526ab2dd5044f3ea274c176fcb43b490b0c63 https://github.com/galaxyproject/galaxy/commit/bc1526ab2dd5044f3ea274c176fc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6644 from jmchilton/add_datasets Small Optimizations to Adding Datasets to History Compare: https://github.com/galaxyproject/galaxy/compare/3ca449fa73fc...bc1526ab2dd5 **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.

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[galaxyproject/galaxy] 3c5991: Allow group tag selection also for multiple="true"...
by GitHub 04 Sep '18

04 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c5991632246d5fd404b269507642f819abf7d68 https://github.com/galaxyproject/galaxy/commit/3c5991632246d5fd404b26950764… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Allow group tag selection also for multiple="true" inputs Commit: 3ca449fa73fcc18389876756814fdaa5bb6e2aed https://github.com/galaxyproject/galaxy/commit/3ca449fa73fcc18389876756814f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #6661 from mvdbeek/group_tags_for_multiple_true_inputs Allow group tag selection also for multiple="true" inputs Compare: https://github.com/galaxyproject/galaxy/compare/b9d07aed22c5...3ca449fa73fc **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.

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[galaxyproject/galaxy] 77706a: Update application documentation
by GitHub 03 Sep '18

03 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77706a8e62f6c7ffafc923b9f94f3359089e8ee9 https://github.com/galaxyproject/galaxy/commit/77706a8e62f6c7ffafc923b9f94f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst Log Message: ----------- Update application documentation With ``` make -C doc/ updaterst ``` Commit: ad02c53154a3d3046a814b838cffdf0a79ac9a13 https://github.com/galaxyproject/galaxy/commit/ad02c53154a3d3046a814b838cff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Fix many links Commit: 59c1ed2266504a2bd03e80e9f4ec72664148524f https://github.com/galaxyproject/galaxy/commit/59c1ed2266504a2bd03e80e9f4ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/galaxy.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Various doc fixes Commit: b9d07aed22c59c2aeb92e30d18953bc6fecea0a6 https://github.com/galaxyproject/galaxy/commit/b9d07aed22c59c2aeb92e30d1895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Merge pull request #6662 from nsoranzo/doc_fixes2 Various link and documentation fixes Compare: https://github.com/galaxyproject/galaxy/compare/76d89d020f56...b9d07aed22c5 **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.

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[galaxyproject/galaxy] ea34aa: adding 4 new GROMACS datatypes: cpt, xtc, top, and...
by GitHub 03 Sep '18

03 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea34aa84be9be03489e541b928ea57adfb087e80 https://github.com/galaxyproject/galaxy/commit/ea34aa84be9be03489e541b928ea… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/datatypes/test/em.trr A lib/galaxy/datatypes/test/md.cpt A lib/galaxy/datatypes/test/md.trr A lib/galaxy/datatypes/test/md.xtc M lib/galaxy/datatypes/text.py Log Message: ----------- adding 4 new GROMACS datatypes: cpt, xtc, top, and gro shrinking test files Commit: 6a730bc5821c94d25411cb51a7033ab56064617b https://github.com/galaxyproject/galaxy/commit/6a730bc5821c94d25411cb51a703… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- linting Commit: 3c7d7d9d49d49781f822a36c3bdbd860ddc0e8f0 https://github.com/galaxyproject/galaxy/commit/3c7d7d9d49d49781f822a36c3bdb… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- tightening up the sniffer functions Commit: 0d97c55cc7256ccff7285d57dd5ed3ec64616887 https://github.com/galaxyproject/galaxy/commit/0d97c55cc7256ccff7285d57dd5e… Author: sb635 <sb635(a)bmd6.physik.privat> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add refs for trr/xtc/cpt binary magic numbers Commit: 56d55399ebe2ecd614a7ba5a146739f58e917541 https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467… Author: sb635 <sb635(a)bmd6.physik.privat> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- removing top and gro sniffers, at least for now Commit: e59219deabe89cbf3a98f984bf54d314157d6599 https://github.com/galaxyproject/galaxy/commit/e59219deabe89cbf3a98f984bf54… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- created new GmxBinary class from which xtc, trr, cpt inherit Commit: 5d15063f7de0b7b07f7bad5d7dbbb31f5e872855 https://github.com/galaxyproject/galaxy/commit/5d15063f7de0b7b07f7bad5d7dbb… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove __init__() from GmxBinary subclasses Commit: 09d349cbfff5623a52f23ccd480b4975759f8d8b https://github.com/galaxyproject/galaxy/commit/09d349cbfff5623a52f23ccd480b… Author: Simon Bray <32272674+simonbray(a)users.noreply.github.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- default for magic_number None not 0 Commit: ed641aceb9d117aee7a83de9bbcd7a7876d20703 https://github.com/galaxyproject/galaxy/commit/ed641aceb9d117aee7a83de9bbcd… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove __init__ from GmxBinary Commit: 76d89d020f56e202939a26b06972e3bce489dd3b https://github.com/galaxyproject/galaxy/commit/76d89d020f56e202939a26b06972… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/test/em.trr A lib/galaxy/datatypes/test/md.cpt A lib/galaxy/datatypes/test/md.trr A lib/galaxy/datatypes/test/md.xtc Log Message: ----------- Merge pull request #6655 from simonbray/dev Adding 4 new GROMACS datatypes: cpt, xtc, top, and gro Compare: https://github.com/galaxyproject/galaxy/compare/410ec1927c34...76d89d020f56 **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.

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[galaxyproject/galaxy] dd0a68: Fixes...
by GitHub 31 Aug '18

31 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd0a6884ba7b20788fdec5b38e3715596b2ac177 https://github.com/galaxyproject/galaxy/commit/dd0a6884ba7b20788fdec5b38e37… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: 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/history/history-contents.js M lib/galaxy/managers/collections.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Fixes... Commit: 5d22d73f303298fdef98c5ab8c8e8e91bae65bb3 https://github.com/galaxyproject/galaxy/commit/5d22d73f303298fdef98c5ab8c8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- client-format Commit: 410ec1927c34fbb4a61969e1fe188babd9a8f82b https://github.com/galaxyproject/galaxy/commit/410ec1927c34fbb4a61969e1fe18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue 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/history/history-contents.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/upload-view.js M lib/galaxy/managers/collections.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #6656 from jmchilton/collect_builder_fixes Assorted fixes for #6572 Compare: https://github.com/galaxyproject/galaxy/compare/3a77b64aeb71...410ec1927c34 **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.

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[galaxyproject/galaxy] 25ae4e: Fix get_fileobj() call in Eland.set_meta()
by GitHub 31 Aug '18

31 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25ae4e6e26a27696fa47ea656fa36889f435e2f2 https://github.com/galaxyproject/galaxy/commit/25ae4e6e26a27696fa47ea656fa3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix get_fileobj() call in Eland.set_meta() Broken in commit 59f44cf2be48abd4bed0f7c6ddf7cc0aee5ad1f5 . Commit: 3a77b64aeb71c027d8f8d7ca56574b63ff83afb3 https://github.com/galaxyproject/galaxy/commit/3a77b64aeb71c027d8f8d7ca5657… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #6659 from nsoranzo/fix_Eland_set_meta Fix get_fileobj() call in Eland.set_meta() Compare: https://github.com/galaxyproject/galaxy/compare/bb9545288272...3a77b64aeb71 **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.

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[galaxyproject/galaxy] feaaec: Strip API keys option from admin panel left side -...
by GitHub 30 Aug '18

30 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: feaaecf2199f78e42668418ab4eb5c8f68ff0e8d https://github.com/galaxyproject/galaxy/commit/feaaecf2199f78e42668418ab4eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Strip API keys option from admin panel left side -- this is all in the user management grid now. I don't know if this got added back in a bad merge or if it was erroneously left in. Commit: 223c3988083c5397626bd33908376bc007bc28bc https://github.com/galaxyproject/galaxy/commit/223c3988083c5397626bd3390837… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- drop admin api keys navigator from selenium configs (which may break other tests, we should wait to see) Commit: bb95452882726e4f6c3f26c76abfe7b22bafadb4 https://github.com/galaxyproject/galaxy/commit/bb95452882726e4f6c3f26c76abf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M test/galaxy_selenium/navigation.yml Log Message: ----------- Merge pull request #6651 from dannon/admin_apikeys_fixup Strip API keys option from admin panel left side Compare: https://github.com/galaxyproject/galaxy/compare/2adae6c4ca77...bb9545288272 **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.

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[galaxyproject/galaxy] 85751e: Add tag and group tag rule to history level rule b...
by GitHub 28 Aug '18

28 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85751ebb163eb5474d6ba18b7bf9d75097d53e15 https://github.com/galaxyproject/galaxy/commit/85751ebb163eb5474d6ba18b7bf9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Add tag and group tag rule to history level rule builder Commit: 1e7ce13b4773ffeaea169b03963a2a252187dfee https://github.com/galaxyproject/galaxy/commit/1e7ce13b4773ffeaea169b03963a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py Log Message: ----------- Reuse HDA copy method in HDAManager Should benefit from smarter flush strategy in HDA.copy() Commit: d1f9ab88e4637d00c6c5c3c2290f6a19dd369456 https://github.com/galaxyproject/galaxy/commit/d1f9ab88e4637d00c6c5c3c2290f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Always copy HDAs when creating a new collection from exisitng datasets, and allow setting tags Commit: 91438996df29caac56bb7a6fe8dc25e52815caf8 https://github.com/galaxyproject/galaxy/commit/91438996df29caac56bb7a6fe8dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Test creation of collection from existing dataset, with a new tag Commit: eb4b878f3f5e9a898d5048c917ce2d379d7bf20f https://github.com/galaxyproject/galaxy/commit/eb4b878f3f5e9a898d5048c917ce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdas.py Log Message: ----------- Simplify hda manager usage Commit: 5dd63dd6d077e9836f126d97a3c50b8a25ea66cc https://github.com/galaxyproject/galaxy/commit/5dd63dd6d077e9836f126d97a3c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Include tags in element_identifier when building collection from datasets Commit: ce892a028cb9d65aa19f8a4333626b421a184ec9 https://github.com/galaxyproject/galaxy/commit/ce892a028cb9d65aa19f8a433362… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Restore hiding of dataset instances Commit: d4a80e61e13fbeeda43a65874910d85cfc1c8b29 https://github.com/galaxyproject/galaxy/commit/d4a80e61e13fbeeda43a65874910… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Adapt unit tests to copying HDAs when creating collections Commit: a9cb290754f09a1ea3073e8858df6f9a9e45b147 https://github.com/galaxyproject/galaxy/commit/a9cb290754f09a1ea3073e8858df… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflows.py Log Message: ----------- Adjust API tests to copying HDAs when creating collection Commit: 711016ab9aac78c96fa65cd04f9421fbb6473b49 https://github.com/galaxyproject/galaxy/commit/711016ab9aac78c96fa65cd04f94… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Treat LDDA as HDA when creating collection This avoids copying the LDDA to HDA and then copying the HDA again. Commit: 34cfdcac6a583c84c8641ac8e26243769d09598d https://github.com/galaxyproject/galaxy/commit/34cfdcac6a583c84c8641ac8e262… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Test for proper 403 response Coincidentally fixed by e013f2fbd1596b103ef195afcba8cbd787c49b33. Commit: c00ae9f81b953df7909aa591e411ebd6298a6f7c https://github.com/galaxyproject/galaxy/commit/c00ae9f81b953df7909aa591e411… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Default to not copying source HDAs when creating new collections via API Commit: 9409322a730d431344d4438e379e61559632812d https://github.com/galaxyproject/galaxy/commit/9409322a730d431344d4438e379e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Revert "Adapt unit tests to copying HDAs when creating collections" This reverts commit 408a003f171be73e4b347579ee6f662a18fc1990. Commit: b13cce0a1340a5f9b7a77ab7eda1ceb0930ed161 https://github.com/galaxyproject/galaxy/commit/b13cce0a1340a5f9b7a77ab7eda1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflows.py Log Message: ----------- Revert "Adjust API tests to copying HDAs when creating collection" This reverts commit f120390a63700ff0ec6c09185aad26b91ad8f842. Commit: cfd8379917703ce03b631fd48b5a2bcecc30bbea https://github.com/galaxyproject/galaxy/commit/cfd8379917703ce03b631fd48b5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Send copy_elements=True in new create collection test Commit: 43ee13a0ce43ae5b29ffa1e317df1db645cb93a8 https://github.com/galaxyproject/galaxy/commit/43ee13a0ce43ae5b29ffa1e317df… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Default to copying HDAs when creating collections via the UI Commit: 50a524496a4ed52184967ede53094e5c8243d93d https://github.com/galaxyproject/galaxy/commit/50a524496a4ed52184967ede5309… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Add unit test for copy_element option Commit: ddb0c74b9bd9f534691a93911f10903da3609927 https://github.com/galaxyproject/galaxy/commit/ddb0c74b9bd9f534691a93911f10… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Original HDA must be owned by user if hiding source elements Commit: 366701cfb23d8de31eac3c4312c6accca2e74ef1 https://github.com/galaxyproject/galaxy/commit/366701cfb23d8de31eac3c4312c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/util/__init__.py A test/unit/managers/test_TagManager.py Log Message: ----------- Strip unicode control characters from tags Leaving them in can trip up postgresql: ``` Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 283, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 396, in create return self.__create_dataset_collection(trans, history, payload, **kwd) File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 525, in __create_dataset_collection **create_params File "lib/galaxy/managers/collections.py", line 108, in create copy_elements=copy_elements, File "lib/galaxy/managers/collections.py", line 181, in create_dataset_collection copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 217, in _element_identifiers_to_elements copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 389, in __load_elements copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 434, in __load_element self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str) File "lib/galaxy/managers/tags.py", line 182, in apply_item_tags self.apply_item_tag(user, item, name, value) File "lib/galaxy/managers/tags.py", line 154, in apply_item_tag tag = self._get_or_create_tag(lc_name) File "lib/galaxy/managers/tags.py", line 233, in _get_or_create_tag tag = self.get_tag_by_name(scrubbed_tag_str) File "lib/galaxy/managers/tags.py", line 205, in get_tag_by_name return self.sa_session.query(galaxy.model.Tag).filter_by(name=tag_name.lower()).first() File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2789, in first ret = list(self[0:1]) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2581, in __getitem__ return list(res) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1416, in _handle_dbapi_exception util.reraise(*exc_info) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) ValueError: A string literal cannot contain NUL (0x00) characters. ``` Commit: 2adae6c4ca77067f2f45f3f101218d411fec7e25 https://github.com/galaxyproject/galaxy/commit/2adae6c4ca77067f2f45f3f10121… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py M test/unit/managers/test_HistoryContentsManager.py A test/unit/managers/test_TagManager.py Log Message: ----------- Merge pull request #6572 from mvdbeek/add_group_tags_to_history_rule_builder Add tagging rule to history level rule builder, copy HDAs when building collection Compare: https://github.com/galaxyproject/galaxy/compare/3121d9f0a468...2adae6c4ca77 **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.

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[galaxyproject/galaxy] 167ab6: Fix color of workflow panel background
by GitHub 28 Aug '18

28 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 167ab6b54eb330ad44b8c7900d52514a1c90d1cb https://github.com/galaxyproject/galaxy/commit/167ab6b54eb330ad44b8c7900d52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix color of workflow panel background Commit: 3121d9f0a468d23f6619e3496cf46c627560d90c https://github.com/galaxyproject/galaxy/commit/3121d9f0a468d23f6619e3496cf4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6643 from guerler/fix_panel_background Fix color of workflow panel background Compare: https://github.com/galaxyproject/galaxy/compare/7fa539162791...3121d9f0a468 **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.

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[galaxyproject/galaxy] 982e87: Allow supplying name of pasted data, issue #4162
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 982e878f8e5903b42df291015522c6b3334f6035 https://github.com/galaxyproject/galaxy/commit/982e878f8e5903b42df291015522… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Allow supplying name of pasted data, issue #4162 Commit: 163018c35177a9356a7e6f789ee719f3be5d861e https://github.com/galaxyproject/galaxy/commit/163018c35177a9356a7e6f789ee7… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- keep default Galaxy dataset name of pasted content to Pasted Entry Commit: 7fa539162791e5e1eca836616b31381f2ad62b05 https://github.com/galaxyproject/galaxy/commit/7fa539162791e5e1eca836616b31… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Merge pull request #6415 from FredericBGA/supplying_name_pasted_data Allow supplying name of pasted data Compare: https://github.com/galaxyproject/galaxy/compare/660a51495b52...7fa539162791 **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.

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[galaxyproject/galaxy] 51c6e2: Add a step in PSA pipeline to determine if ID toke...
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51c6e2f6ba6b654b7f234c0440cfaa95ac2735b4 https://github.com/galaxyproject/galaxy/commit/51c6e2f6ba6b654b7f234c0440cf… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a step in PSA pipeline to determine if ID token exists. Commit: 405a08522e8f54341478dde5c88868e33ed55ec7 https://github.com/galaxyproject/galaxy/commit/405a08522e8f54341478dde5c888… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- check for missing ID and refresh tokens. Commit: 0ed0bdf203c6d088487c24e42fd50951039f7e74 https://github.com/galaxyproject/galaxy/commit/0ed0bdf203c6d088487c24e42fd5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add some comments explaining when some OIDC-related errors can happen. Commit: 3e6fa40ec84206558aa11679170fd747ff2f20b3 https://github.com/galaxyproject/galaxy/commit/3e6fa40ec84206558aa11679170f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Fix some lint issues in psa_authnz.py. Commit: b29311fdab1a08a70eee7fad69f77bc72d8e88bc https://github.com/galaxyproject/galaxy/commit/b29311fdab1a08a70eee7fad69f7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Get ID token, if expired, refresh it. Commit: 27db877816bdba5f91ada327c63b7a7717341e18 https://github.com/galaxyproject/galaxy/commit/27db877816bdba5f91ada327c63b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove the `get_access_token` as it hides a base method. Commit: f0a8c541d8c83e6e6bbd7731ba4197cae549b47a https://github.com/galaxyproject/galaxy/commit/f0a8c541d8c83e6e6bbd7731ba41… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a comment explaining a PSA pipeline step. Commit: 9d7f50c6c074a9d3e39763180d6e270f7290164f https://github.com/galaxyproject/galaxy/commit/9d7f50c6c074a9d3e39763180d6e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add doc string for `contains_required_data` function. Commit: 660a51495b52cf886db31dbcc807e54c5b787469 https://github.com/galaxyproject/galaxy/commit/660a51495b52cf886db31dbcc807… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6606 from VJalili/refresh_token Refresh an expired OIDC ID token Compare: https://github.com/galaxyproject/galaxy/compare/af99f49d82d9...660a51495b52 **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.

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[galaxyproject/galaxy] 296105: row ids that are all numeric become ints...
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 296105ee395194c48d962671a8c367469ea74907 https://github.com/galaxyproject/galaxy/commit/296105ee395194c48d962671a8c3… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- row ids that are all numeric become ints... Since the "F" prefix is checked with substring, row_id must always be a string Commit: 55d350d015f20afc1c350130caaa0aa9858b7aa0 https://github.com/galaxyproject/galaxy/commit/55d350d015f20afc1c350130caaa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/communication-server-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M 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static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-utils.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/chart/chart-client.js M static/scripts/mvc/visualization/chart/components/model.js M static/scripts/mvc/visualization/chart/components/screenshot.js M static/scripts/mvc/visualization/chart/utilities/datasets.js M static/scripts/mvc/visualization/chart/utilities/jobs.js M static/scripts/mvc/visualization/chart/utilities/series.js M static/scripts/mvc/visualization/chart/views/description.js M static/scripts/mvc/visualization/chart/views/editor.js M static/scripts/mvc/visualization/chart/views/groups.js M static/scripts/mvc/visualization/chart/views/menu.js M static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Add static for 2a148ff1ec37c68e280c431fceee88ee0510e017 Commit: 03c485ee45e96784b269896a23223d233c566b89 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static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/library/library-util.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/rules/rule-definitions.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/tool/tools.js M 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static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-rules-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/collection/rules-input-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-utils.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/chart/chart-client.js M static/scripts/mvc/visualization/chart/components/model.js M static/scripts/mvc/visualization/chart/components/screenshot.js M static/scripts/mvc/visualization/chart/utilities/datasets.js M static/scripts/mvc/visualization/chart/utilities/jobs.js M static/scripts/mvc/visualization/chart/utilities/series.js M static/scripts/mvc/visualization/chart/views/description.js M static/scripts/mvc/visualization/chart/views/editor.js M static/scripts/mvc/visualization/chart/views/groups.js M static/scripts/mvc/visualization/chart/views/menu.js M static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge pull request #6639 from bwlang/patch-2 [18.05] row ids that are all numeric become ints... Compare: https://github.com/galaxyproject/galaxy/compare/709e49f104e2...03c485ee45e9 **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.

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[galaxyproject/galaxy] 49eae7: Fix for workflow extraction cleanup routine.
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49eae728916af02a6fbd3ce9d69599c08d4e58b9 https://github.com/galaxyproject/galaxy/commit/49eae728916af02a6fbd3ce9d695… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fix for workflow extraction cleanup routine. Workflow extraction would be incorrect if you had parameters ordered and named as e.g. "somename" and "somename_2" in the input root. When these parameters are both dataset inputs, this would cause a server error. Commit: af99f49d82d917b681157ec8f5a4506c6a37cab6 https://github.com/galaxyproject/galaxy/commit/af99f49d82d917b681157ec8f5a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #6636 from blankenberg/11yowffix Fix for workflow extraction cleanup routine. Compare: https://github.com/galaxyproject/galaxy/compare/0e69ca8bfbc3...af99f49d82d9 **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.

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[galaxyproject/galaxy] 6e8a7f: Fix empty handling rule.
by GitHub 26 Aug '18

26 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e8a7fddb1727a7b6f4c3ae4817d38fe73f2079b https://github.com/galaxyproject/galaxy/commit/6e8a7fddb1727a7b6f4c3ae4817d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Fix empty handling rule. Commit: 42ddfbde4c429b6bd3a19f901f0f3bf7db1d85ba https://github.com/galaxyproject/galaxy/commit/42ddfbde4c429b6bd3a19f901f0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M test/base/data/rules_dsl_spec.yml Log Message: ----------- Fill out, polish the rule spec a little more. Drop use of startsWith in favor of indexOf for PhantomJS testing. Commit: 6cd8650b5a5530835e6d396e81d6f481ca6b141a https://github.com/galaxyproject/galaxy/commit/6cd8650b5a5530835e6d396e81d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove stray debug statement left in 18.05. Commit: 4d83746cc2f83c1208abcefbce3e66a00f01076a https://github.com/galaxyproject/galaxy/commit/4d83746cc2f83c1208abcefbce3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Allow loading tag metadata from existing objects in rule builder. This should allow nesting and filtering from tags - including group tags. Commit: 58072302539dd7c5283ee11c13512a19a9bf99fb https://github.com/galaxyproject/galaxy/commit/58072302539dd7c5283ee11c1351… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-27 (Fri, 27 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/util/rules_dsl.py M test/api/test_tools.py M test/base/data/rules_dsl_spec.yml M test/base/populators.py M test/base/rules_test_data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Implement rule builder rule to quickly grab group tag value. Should make it a lot easier to nested and filter on group tag values. Commit: 0e69ca8bfbc3c93bd18a22a32cd77494d55e915e https://github.com/galaxyproject/galaxy/commit/0e69ca8bfbc3c93bd18a22a32cd7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/rules_dsl.py M test/api/test_tools.py M test/base/data/rules_dsl_spec.yml M test/base/populators.py M test/base/rules_test_data.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #6545 from jmchilton/rule_builder_use_group_tags Allow Consuming Tags in the Apply Rules Tool Compare: https://github.com/galaxyproject/galaxy/compare/a3fc0b9f324f...0e69ca8bfbc3 **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.

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