- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0cf38e: Force window jquery access for charts.mako. This ...
by GitHub 17 Dec '17

17 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0cf38e5d52c9eb9120dcc0e6971355402c95128a https://github.com/galaxyproject/galaxy/commit/0cf38e5d52c9eb9120dcc0e69713… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Force window jquery access for charts.mako. This isn't great, but charts *and* the rest of the viz framework are being refactored into bundles that will avoid this hackery. Commit: 6fc9296d5359afecdfff8c3a3b5af9bace14ac6b https://github.com/galaxyproject/galaxy/commit/6fc9296d5359afecdfff8c3a3b5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-17 (Sun, 17 Dec 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Merge pull request #5210 from dannon/fix_charts_jquery_usage Force window jquery access for charts Compare: https://github.com/galaxyproject/galaxy/compare/02b6ff3492ef...6fc9296d5359

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[galaxyproject/galaxy] f9969e: Remove API scripts for axed APIs.
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9969ee97acfb985c82c98946f08f522c232e654 https://github.com/galaxyproject/galaxy/commit/f9969ee97acfb985c82c98946f08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py Log Message: ----------- Remove API scripts for axed APIs. Commit: 02b6ff3492efca986e34c769cc5a4869167332fb https://github.com/galaxyproject/galaxy/commit/02b6ff3492efca986e34c769cc5a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py Log Message: ----------- Merge pull request #5230 from jmchilton/axed_api_scripts Remove API scripts for axed API (requests, samples...) Compare: https://github.com/galaxyproject/galaxy/compare/94dae3b7de18...02b6ff3492ef

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[galaxyproject/galaxy] d5e39c: Python3: fix list.sort() and sorted() to use `key`...
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5e39c873e9aed6a2b0822b0f7187aa8a73430be https://github.com/galaxyproject/galaxy/commit/d5e39c873e9aed6a2b0822b0f718… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/users.py Log Message: ----------- Python3: fix list.sort() and sorted() to use `key` parameter instead of `cmp` xref. https://github.com/galaxyproject/galaxy/issues/1715 xref. https://github.com/galaxyproject/galaxy/issues/5216 Commit: 94dae3b7de180303427d4bfd0b1cbd4ee183469c https://github.com/galaxyproject/galaxy/commit/94dae3b7de180303427d4bfd0b1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/users.py Log Message: ----------- Merge pull request #5225 from nsoranzo/fix_sort_sorted Python3: fix list.sort() and sorted() to use `key` parameter instead of `cmp` Compare: https://github.com/galaxyproject/galaxy/compare/6d3eadedbd70...94dae3b7de18

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[galaxyproject/galaxy] e8a128: [17.09] Deployer doc fixes.
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8a1280f78e1fa19e2173f922f2221ea28279964 https://github.com/galaxyproject/galaxy/commit/e8a1280f78e1fa19e2173f922f22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 42c572f34469ec39a55588504a97f1466c59f332 https://github.com/galaxyproject/galaxy/commit/42c572f34469ec39a55588504a97… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- Merge pull request #5147 from jmchilton/1709_docs_fixes [17.09] Small deployer doc fixes. Commit: 710177f3983d5e66b11c329f699079f67667329c https://github.com/galaxyproject/galaxy/commit/710177f3983d5e66b11c329f6990… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Add API tests for history uploads from URL Commit: a1f399c451715424dcd8d1bc9d9ec804e44de24d https://github.com/galaxyproject/galaxy/commit/a1f399c451715424dcd8d1bc9d9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Read in stderr form galaxy.json before checking whether stderr and exit code combination should result in a failed job. This should fix https://github.com/galaxyproject/galaxy/issues/5214. Commit: 3d2adcd1f310b94d0d6f6e37e71d1ee74da2fb3d https://github.com/galaxyproject/galaxy/commit/3d2adcd1f310b94d0d6f6e37e71d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restrict reading tool provided metadata to tools that actually provide metadata Commit: 62a3ff3562c5b9c534794c2d0bb6320de7747135 https://github.com/galaxyproject/galaxy/commit/62a3ff3562c5b9c534794c2d0bb6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Do not assert dataset state in test_gzipped_html_content_blocked_by_default test Commit: 9ee2a7d4577a715137edcf33fd2b0a474a7a8b8d https://github.com/galaxyproject/galaxy/commit/9ee2a7d4577a715137edcf33fd2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Adjust stderr collection to (Legacy-)ToolProvidedMetadata Commit: b39772011a717dc7c70f1e05dd581b427e33a521 https://github.com/galaxyproject/galaxy/commit/b39772011a717dc7c70f1e05dd58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/base/populators.py Log Message: ----------- Optionally allow dataset populators to fail Commit: 121285b40be5d7233af33b40045a9c2ffb5a9c46 https://github.com/galaxyproject/galaxy/commit/121285b40be5d7233af33b40045a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Let ToolProvidedMetadata interface more directly decide if it has failed outputs. I like this better for three reasons: - Since usually it is scripts producing this JSON - we have the most control at that point for determining the failure and we don't have to deal with an artificial dependency between the tool's stdio and the output. - At some point we could potentially allow some datasets to be ok now even though the job fails. - It is a cleaner interface at the Python level between job finish and output collection IMO (no need for isinstance checking). Commit: d52802d7962c3006b7fe91f43a9d21721187f27c https://github.com/galaxyproject/galaxy/commit/d52802d7962c3006b7fe91f43a9d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6 from jmchilton/fail_if_galaxy_json_tools_write_to_stderr Let ToolProvidedMetadata interface more directly decide if it has failed outputs. Commit: 3f6c45578e2c4e99fa725054c829e03a9c409a1b https://github.com/galaxyproject/galaxy/commit/3f6c45578e2c4e99fa725054c829… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix dataset spelling (thx @nsoranzo) Commit: 44635eae1dc1aeb511f3cf9c6006aff4219de841 https://github.com/galaxyproject/galaxy/commit/44635eae1dc1aeb511f3cf9c6006… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5217 from mvdbeek/fail_if_galaxy_json_tools_write_to_stderr [17.09] Fail job if tools that use galaxy.json write to stderr Commit: 90ba35a9a49f583a1fe2a173c1239be86d71125a https://github.com/galaxyproject/galaxy/commit/90ba35a9a49f583a1fe2a173c123… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_17.09' into merge_1709 Commit: 6d3eadedbd7093fc19553d7812152293960f3f14 https://github.com/galaxyproject/galaxy/commit/6d3eadedbd7093fc19553d781215… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5227 from jmchilton/merge_1709 Merge 17.09. Compare: https://github.com/galaxyproject/galaxy/compare/717b5bbce9c5...6d3eadedbd70

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[galaxyproject/galaxy] 3b9d28: Add check_py3_compatibility Travis job
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b9d2881618ca47f2135e3d226262ff736994260 https://github.com/galaxyproject/galaxy/commit/3b9d2881618ca47f2135e3d22626… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/check_py3_compatibility.sh M .travis.yml M tox.ini Log Message: ----------- Add check_py3_compatibility Travis job Commit: 717b5bbce9c552de5d28d783bc8620c9396f269c https://github.com/galaxyproject/galaxy/commit/717b5bbce9c552de5d28d783bc86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/check_py3_compatibility.sh M .travis.yml M tox.ini Log Message: ----------- Merge pull request #5228 from nsoranzo/add_check_py3_compatibility_travis_job Add check_py3_compatibility Travis job Compare: https://github.com/galaxyproject/galaxy/compare/7e7dc249ab93...717b5bbce9c5

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[galaxyproject/galaxy] 18221a: paster.pid/log to galaxy.pid/log reference update
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18221ae931b22187a5978bd89222a8e84ed400f0 https://github.com/galaxyproject/galaxy/commit/18221ae931b22187a5978bd89222… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/first_startup.sh M contrib/galaxy.fedora-init M doc/source/admin/production.md M scripts/summarize_timings.py Log Message: ----------- paster.pid/log to galaxy.pid/log reference update Fix errors in `first_startup` jobs: https://travis-ci.org/galaxyproject/galaxy/jobs/316342622#L1029 Introduced in https://github.com/galaxyproject/galaxy/pull/4475 Commit: 7e7dc249ab93e66e405abf830782bcf78c0788c5 https://github.com/galaxyproject/galaxy/commit/7e7dc249ab93e66e405abf830782… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M .ci/first_startup.sh M contrib/galaxy.fedora-init M doc/source/admin/production.md M scripts/summarize_timings.py Log Message: ----------- Merge pull request #5226 from nsoranzo/fix_paster.log_pid paster.pid/log to galaxy.pid/log reference update Compare: https://github.com/galaxyproject/galaxy/compare/5b6eaac4a06c...7e7dc249ab93

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[galaxyproject/galaxy] 710177: Add API tests for history uploads from URL
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 710177f3983d5e66b11c329f699079f67667329c https://github.com/galaxyproject/galaxy/commit/710177f3983d5e66b11c329f6990… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Add API tests for history uploads from URL Commit: a1f399c451715424dcd8d1bc9d9ec804e44de24d https://github.com/galaxyproject/galaxy/commit/a1f399c451715424dcd8d1bc9d9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Read in stderr form galaxy.json before checking whether stderr and exit code combination should result in a failed job. This should fix https://github.com/galaxyproject/galaxy/issues/5214. Commit: 3d2adcd1f310b94d0d6f6e37e71d1ee74da2fb3d https://github.com/galaxyproject/galaxy/commit/3d2adcd1f310b94d0d6f6e37e71d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restrict reading tool provided metadata to tools that actually provide metadata Commit: 62a3ff3562c5b9c534794c2d0bb6320de7747135 https://github.com/galaxyproject/galaxy/commit/62a3ff3562c5b9c534794c2d0bb6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Do not assert dataset state in test_gzipped_html_content_blocked_by_default test Commit: 9ee2a7d4577a715137edcf33fd2b0a474a7a8b8d https://github.com/galaxyproject/galaxy/commit/9ee2a7d4577a715137edcf33fd2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Adjust stderr collection to (Legacy-)ToolProvidedMetadata Commit: b39772011a717dc7c70f1e05dd581b427e33a521 https://github.com/galaxyproject/galaxy/commit/b39772011a717dc7c70f1e05dd58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/base/populators.py Log Message: ----------- Optionally allow dataset populators to fail Commit: 121285b40be5d7233af33b40045a9c2ffb5a9c46 https://github.com/galaxyproject/galaxy/commit/121285b40be5d7233af33b40045a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Let ToolProvidedMetadata interface more directly decide if it has failed outputs. I like this better for three reasons: - Since usually it is scripts producing this JSON - we have the most control at that point for determining the failure and we don't have to deal with an artificial dependency between the tool's stdio and the output. - At some point we could potentially allow some datasets to be ok now even though the job fails. - It is a cleaner interface at the Python level between job finish and output collection IMO (no need for isinstance checking). Commit: d52802d7962c3006b7fe91f43a9d21721187f27c https://github.com/galaxyproject/galaxy/commit/d52802d7962c3006b7fe91f43a9d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6 from jmchilton/fail_if_galaxy_json_tools_write_to_stderr Let ToolProvidedMetadata interface more directly decide if it has failed outputs. Commit: 3f6c45578e2c4e99fa725054c829e03a9c409a1b https://github.com/galaxyproject/galaxy/commit/3f6c45578e2c4e99fa725054c829… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix dataset spelling (thx @nsoranzo) Commit: 44635eae1dc1aeb511f3cf9c6006aff4219de841 https://github.com/galaxyproject/galaxy/commit/44635eae1dc1aeb511f3cf9c6006… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5217 from mvdbeek/fail_if_galaxy_json_tools_write_to_stderr [17.09] Fail job if tools that use galaxy.json write to stderr Compare: https://github.com/galaxyproject/galaxy/compare/42c572f34469...44635eae1dc1

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[galaxyproject/galaxy] 6f7228: Python3: fix moved imports
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f722861cfd4c36f93348048fe6e6c83305fcc9f https://github.com/galaxyproject/galaxy/commit/6f722861cfd4c36f93348048fe6e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: A .ci/check_py3_compatibility.sh M contrib/nagios/check_galaxy.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/util/biostar.py M test/base/driver_util.py M test/functional/webhooks/phdcomics/helper/__init__.py Log Message: ----------- Python3: fix moved imports Add `.ci/check_py3_compatibility.sh` script to find library modules that have been moved in Python3. Fix errors found by the script. Commit: 5b6eaac4a06cfcd714dd4b578cdbf3239868ca28 https://github.com/galaxyproject/galaxy/commit/5b6eaac4a06cfcd714dd4b578cdb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: A .ci/check_py3_compatibility.sh M contrib/nagios/check_galaxy.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/util/biostar.py M test/base/driver_util.py M test/functional/webhooks/phdcomics/helper/__init__.py Log Message: ----------- Merge pull request #5221 from nsoranzo/python3 Python3: fix moved imports Compare: https://github.com/galaxyproject/galaxy/compare/ad0459d81840...5b6eaac4a06c

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[galaxyproject/galaxy] d1be0a: Allow shells with different parameters to co-exist
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d1be0a20eded8a31d5c514fcc7e370a96d0a01e9 https://github.com/galaxyproject/galaxy/commit/d1be0a20eded8a31d5c514fcc7e3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/__init__.py Log Message: ----------- Allow shells with different parameters to co-exist Commit: 86d9b64ec88a601f51607f09b4363cfe02388328 https://github.com/galaxyproject/galaxy/commit/86d9b64ec88a601f51607f09b436… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use absolute import for Bunch Commit: ad0459d81840464a03730f1cad90a860416e51c4 https://github.com/galaxyproject/galaxy/commit/ad0459d81840464a03730f1cad90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Merge pull request #5223 from mvdbeek/fix_second_submit_host Allow shell plugins with different parameters to co-exist Compare: https://github.com/galaxyproject/galaxy/compare/0d8520fe2df1...ad0459d81840

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[galaxyproject/galaxy] ab4db8: rewrite Admin/DataTables with Vue
by GitHub 15 Dec '17

15 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab4db8925cc895e90972de8b22f1919d25423a12 https://github.com/galaxyproject/galaxy/commit/ab4db8925cc895e90972de8b22f1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/admin/base-grid.vue A client/galaxy/scripts/components/admin/data-manager-grid.vue A client/galaxy/scripts/components/admin/data-tables-grid.vue A client/galaxy/scripts/components/admin/data-tables.vue A client/galaxy/scripts/components/message.vue M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py Log Message: ----------- rewrite Admin/DataTables with Vue Commit: 4516958e9d56ae78fbb606dbeb7664f57cf242b6 https://github.com/galaxyproject/galaxy/commit/4516958e9d56ae78fbb606dbeb76… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js Log Message: ----------- Minor formatting. Commit: 44a1c0bcbcf51dff72d3132f36e2ab106a121ad0 https://github.com/galaxyproject/galaxy/commit/44a1c0bcbcf51dff72d3132f36e2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js A client/galaxy/scripts/components/Message.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue R client/galaxy/scripts/components/admin/base-grid.vue R client/galaxy/scripts/components/admin/data-manager-grid.vue R client/galaxy/scripts/components/admin/data-tables-grid.vue R client/galaxy/scripts/components/admin/data-tables.vue R client/galaxy/scripts/components/message.vue Log Message: ----------- Rename new .vue components. Commit: fe8c009f48d9ed39bd8a7af41d26dc61b1219717 https://github.com/galaxyproject/galaxy/commit/fe8c009f48d9ed39bd8a7af41d26… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue Log Message: ----------- Move UserAPIKeys to components/admin Commit: 0e13c14e9ebca17c385f09df977cb58653be424e https://github.com/galaxyproject/galaxy/commit/0e13c14e9ebca17c385f09df977c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js A static/scripts/libs/bibtex.js M static/scripts/mvc/tours.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M templates/webapps/galaxy/workflow/editor.mako A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into admin_data_tables_vue Commit: 203630c509be0eca1fb150bfa680b8c0b152aa11 https://github.com/galaxyproject/galaxy/commit/203630c509be0eca1fb150bfa680… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: R .ci/py3_sources.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/openid/providers.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py R openid/yahoo.xml M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/galaxy.pages.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js R static/scripts/libs/bibtex.js R static/scripts/libs/vue.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/history-list.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into admin_data_tables_vue Commit: f9d84f876f1c782b0d1580c23aea3b8465ed826c https://github.com/galaxyproject/galaxy/commit/f9d84f876f1c782b0d1580c23aea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js Log Message: ----------- Build client. Commit: 0d8520fe2df1c24c625d27ee8308b4daff0565dc https://github.com/galaxyproject/galaxy/commit/0d8520fe2df1c24c625d27ee8308… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js Log Message: ----------- Merge pull request #5191 from dannon/admin_data_tables_vue Admin data tables vue Compare: https://github.com/galaxyproject/galaxy/compare/9aa596df8b68...0d8520fe2df1

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