May 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 3e799c: Overhaul the stats role, use RPM paths of things, ...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3e799c0971c4be4650a995225adc6f605b600e2d https://github.com/galaxyproject/infrastructure-playbook/commit/3e799c0971c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M common_roles A env/common/files/ssl/stats/ca-key.pem A env/common/files/ssl/stats/ca.pem A env/common/files/ssl/stats/ca.srl A env/common/files/ssl/stats/infrastats.galaxyproject.org/influxdb.pem A env/common/files/ssl/stats/infrastats.galaxyproject.org/influxdb_privatekey… M env/common/group_vars/sslservers/vars.yml A env/galaxy/group_vars/statsservers/vars.yml A env/galaxy/group_vars/statsservers/vault.yml A env/galaxy/host_vars/infrastats.galaxyproject.org.yml M env/galaxy/inventory M env/galaxy/playbook.yml A env/galaxy/templates/nginx/infrastats.j2 M env/tacc/group_vars/statsservers/vars.yml M env/tacc/templates/supervisor/stats.j2 M roles/galaxyproject.nginx/meta/.galaxy_install_info M roles/galaxyproject.nginx/tasks/ssl.yml M roles/postfix/tasks/relay.yml M roles/stats/defaults/main.yml A roles/stats/files/redhat/grafana-server.service A roles/stats/handlers/main.yml M roles/stats/tasks/main.yml A roles/stats/tasks/redhat.yml A roles/stats/tasks/service.yml R roles/stats/templates/grafana.conf.j2 A roles/stats/templates/grafana.ini.j2 M roles/stats/templates/influxdb.conf.j2 A roles/stats/vars/redhat.yml Log Message: ----------- Overhaul the stats role, use RPM paths of things, install infastats.galaxyproject.org for general outside-TACC infrastructure stats **NOTE:** This service 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] fb291e: check memory later
by GitHub 10 May '18

10 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb291eb530858c79c83be10502d4b78b585d77cb https://github.com/galaxyproject/galaxy/commit/fb291eb530858c79c83be10502d4… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- check memory later Commit: 830561a7bcd18a2aa80b8c0d5e1dc359ea9744ed https://github.com/galaxyproject/galaxy/commit/830561a7bcd18a2aa80b8c0d5e1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Fix nested collection element downloads in UI. Fixes #6035. Commit: 765a834497ebfc555ac0de98cbbae9ad395f1c49 https://github.com/galaxyproject/galaxy/commit/765a834497ebfc555ac0de98cbba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Memory statement and cd both before instrument_pre_commands Commit: 7d4109bac1588cd67cc06b093b1fc18b509a69c9 https://github.com/galaxyproject/galaxy/commit/7d4109bac1588cd67cc06b093b1f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Merge pull request #6073 from jmchilton/fix6035 [18.05] Fix nested collection element downloads in UI. Commit: 483e879ca6fee1e58b6f9c99bf07291064ad5065 https://github.com/galaxyproject/galaxy/commit/483e879ca6fee1e58b6f9c99bf07… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix dropdown zindex handling for history panels Commit: 7cc01380afd017c5cac2af2b2d735b2265774a68 https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Update bs4 style dropdowns, minor cleanup Commit: 1343b04380b048dd75264c2ed9fb2ae7ca820d00 https://github.com/galaxyproject/galaxy/commit/1343b04380b048dd75264c2ed9fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix workflow step cloning Problem one is that passing the tool_state as the input payload doesn't preserve the tool state, adressed with the client-part fix. Then passing the tool state still has no effect since the state is properly recovered in `module_factory.from_dict`, but then overwritten by recovering the state starting with an empty dict. It looks like this isn't necessary as we call populate_state anyway when calling `module.get_config_form()`. Fixes https://github.com/galaxyproject/galaxy/issues/5879. Commit: 7b558ddc5965f6223c862680341e81b345c73d82 https://github.com/galaxyproject/galaxy/commit/7b558ddc5965f6223c862680341e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6079 from dannon/dropdown-zindex-fix [18.05] Dropdown zindex fix Commit: e55cf0114f6f230a1b7935a73336546efd9b57b2 https://github.com/galaxyproject/galaxy/commit/e55cf0114f6f230a1b7935a73336… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- reword text feedback on viz job submission Commit: de5ed28120fdd35495c837148c48526aec7a45d8 https://github.com/galaxyproject/galaxy/commit/de5ed28120fdd35495c837148c48… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Merge pull request #6090 from martenson/text-adjustment reword text feedback on viz job submission Commit: 098f638d26355abe54c83bd43b8daf1078e1ccd3 https://github.com/galaxyproject/galaxy/commit/098f638d26355abe54c83bd43b8d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #5925 from erasche/cd-before-metrics [18.01] jobscript - check memory later Commit: 1083fa4ddb611300892516d1947dfd975e60978e https://github.com/galaxyproject/galaxy/commit/1083fa4ddb611300892516d1947d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- [18.05] Fix sniff validation for dynamic compressed types. This was broken in a bad PR merge/rebase process since the validation mode didn't exist when the initial dynamic compressed types PR was opened. Commit: fba70530abf4470e98fc6f1d56d770f33092530b https://github.com/galaxyproject/galaxy/commit/fba70530abf4470e98fc6f1d56d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #6091 from jmchilton/sniff_prefix_fixes [18.05] Fix sniff validation for dynamic compressed types. Commit: 4f20aee2189218cfead67d0153cd579d5674d3eb https://github.com/galaxyproject/galaxy/commit/4f20aee2189218cfead67d0153cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Rebuild client for workflow step copy fix Commit: 5fa450dc9b9826ffc0bd0a3552a586a2dfcbb859 https://github.com/galaxyproject/galaxy/commit/5fa450dc9b9826ffc0bd0a3552a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore `populate_state`, but only execute if `tool_state` not given Commit: 250973eb46fc69baa6e8018c5f6e6e9552edd877 https://github.com/galaxyproject/galaxy/commit/250973eb46fc69baa6e8018c5f6e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #6085 from mvdbeek/fix_workflow_step_cloning [18.01] Fix workflow step cloning Commit: a7e7ac723ff7379cf201be9b99acae95ebb8851d https://github.com/galaxyproject/galaxy/commit/a7e7ac723ff7379cf201be9b99ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Escape tool names in the onclick event handlers for the workflow editor's toolbox. Commit: 1f608a67de540e657d418ed2abf050c605f5fba1 https://github.com/galaxyproject/galaxy/commit/1f608a67de540e657d418ed2abf0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6099 from dannon/workflow_editor_escape [18.05] Escape tool names in the onclick event handlers for the workflow edit… Commit: 07a34f8c5759fa9d609cd008524aaef473259762 https://github.com/galaxyproject/galaxy/commit/07a34f8c5759fa9d609cd008524a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml Log Message: ----------- Add file missing file required for converting bz2 compressed files. Should have been included with #5794. Commit: 208d1de2e13b84f6a9551cd7ca08b859a16be57e https://github.com/galaxyproject/galaxy/commit/208d1de2e13b84f6a9551cd7ca08… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Set the level for SLOREQs to 'warning' Commit: 9ef3449f174ab6128af3bab8bcde75b4cecdcca8 https://github.com/galaxyproject/galaxy/commit/9ef3449f174ab6128af3bab8bcde… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #6102 from dannon/sentry_add_type_tag [18.05] Set the level for SLOREQs to 'warning' Commit: 63abfd657a38355357b476c044afa05d7d07b594 https://github.com/galaxyproject/galaxy/commit/63abfd657a38355357b476c044af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml Log Message: ----------- Merge pull request #6101 from jmchilton/more_conversion_fixes [18.05] Add file missing file required for converting bz2 compressed files. Commit: ef7d90a3dec1c0e517a196999d892b34af6896d1 https://github.com/galaxyproject/galaxy/commit/ef7d90a3dec1c0e517a196999d89… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 4e65608431279a2c251a0f76817a578a32d10913 https://github.com/galaxyproject/galaxy/commit/4e65608431279a2c251a0f76817a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/style/scss/history.scss A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a53551448b75...4e6560843127 **NOTE:** This service 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] fb291e: check memory later
by GitHub 10 May '18

10 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: fb291eb530858c79c83be10502d4b78b585d77cb https://github.com/galaxyproject/galaxy/commit/fb291eb530858c79c83be10502d4… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- check memory later Commit: 765a834497ebfc555ac0de98cbbae9ad395f1c49 https://github.com/galaxyproject/galaxy/commit/765a834497ebfc555ac0de98cbba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Memory statement and cd both before instrument_pre_commands Commit: 1343b04380b048dd75264c2ed9fb2ae7ca820d00 https://github.com/galaxyproject/galaxy/commit/1343b04380b048dd75264c2ed9fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix workflow step cloning Problem one is that passing the tool_state as the input payload doesn't preserve the tool state, adressed with the client-part fix. Then passing the tool state still has no effect since the state is properly recovered in `module_factory.from_dict`, but then overwritten by recovering the state starting with an empty dict. It looks like this isn't necessary as we call populate_state anyway when calling `module.get_config_form()`. Fixes https://github.com/galaxyproject/galaxy/issues/5879. Commit: 098f638d26355abe54c83bd43b8daf1078e1ccd3 https://github.com/galaxyproject/galaxy/commit/098f638d26355abe54c83bd43b8d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #5925 from erasche/cd-before-metrics [18.01] jobscript - check memory later Commit: 4f20aee2189218cfead67d0153cd579d5674d3eb https://github.com/galaxyproject/galaxy/commit/4f20aee2189218cfead67d0153cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Rebuild client for workflow step copy fix Commit: 5fa450dc9b9826ffc0bd0a3552a586a2dfcbb859 https://github.com/galaxyproject/galaxy/commit/5fa450dc9b9826ffc0bd0a3552a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore `populate_state`, but only execute if `tool_state` not given Commit: 250973eb46fc69baa6e8018c5f6e6e9552edd877 https://github.com/galaxyproject/galaxy/commit/250973eb46fc69baa6e8018c5f6e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #6085 from mvdbeek/fix_workflow_step_cloning [18.01] Fix workflow step cloning Commit: ef7d90a3dec1c0e517a196999d892b34af6896d1 https://github.com/galaxyproject/galaxy/commit/ef7d90a3dec1c0e517a196999d89… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/63abfd657a38...ef7d90a3dec1 **NOTE:** This service 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] 07a34f: Add file missing file required for converting bz2 ...
by GitHub 09 May '18

09 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 07a34f8c5759fa9d609cd008524aaef473259762 https://github.com/galaxyproject/galaxy/commit/07a34f8c5759fa9d609cd008524a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml Log Message: ----------- Add file missing file required for converting bz2 compressed files. Should have been included with #5794. Commit: 63abfd657a38355357b476c044afa05d7d07b594 https://github.com/galaxyproject/galaxy/commit/63abfd657a38355357b476c044af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml Log Message: ----------- Merge pull request #6101 from jmchilton/more_conversion_fixes [18.05] Add file missing file required for converting bz2 compressed files. Compare: https://github.com/galaxyproject/galaxy/compare/9ef3449f174a...63abfd657a38 **NOTE:** This service 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] 1ac321: raise sloreq threshold from 1 to 3
by GitHub 09 May '18

09 May '18

Branch: refs/heads/sloreq Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1ac321f78dc7339ccce5d3965b65249fe15c609d https://github.com/galaxyproject/usegalaxy-playbook/commit/1ac321f78dc7339c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- raise sloreq threshold from 1 to 3 **NOTE:** This service 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] 208d1d: Set the level for SLOREQs to 'warning'
by GitHub 09 May '18

09 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 208d1de2e13b84f6a9551cd7ca08b859a16be57e https://github.com/galaxyproject/galaxy/commit/208d1de2e13b84f6a9551cd7ca08… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Set the level for SLOREQs to 'warning' Commit: 9ef3449f174ab6128af3bab8bcde75b4cecdcca8 https://github.com/galaxyproject/galaxy/commit/9ef3449f174ab6128af3bab8bcde… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #6102 from dannon/sentry_add_type_tag [18.05] Set the level for SLOREQs to 'warning' Compare: https://github.com/galaxyproject/galaxy/compare/1f608a67de54...9ef3449f174a **NOTE:** This service 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.

1 0

[galaxyproject/usegalaxy-playbook] 770f83: update Main
by GitHub 09 May '18

09 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 770f83edec684dc3eefe56939cc0c38639f667fc https://github.com/galaxyproject/usegalaxy-playbook/commit/770f83edec684dc3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- update Main **NOTE:** This service 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] a7e7ac: Escape tool names in the onclick event handlers fo...
by GitHub 09 May '18

09 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: a7e7ac723ff7379cf201be9b99acae95ebb8851d https://github.com/galaxyproject/galaxy/commit/a7e7ac723ff7379cf201be9b99ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Escape tool names in the onclick event handlers for the workflow editor's toolbox. Commit: 1f608a67de540e657d418ed2abf050c605f5fba1 https://github.com/galaxyproject/galaxy/commit/1f608a67de540e657d418ed2abf0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6099 from dannon/workflow_editor_escape [18.05] Escape tool names in the onclick event handlers for the workflow edit… Compare: https://github.com/galaxyproject/galaxy/compare/fba70530abf4...1f608a67de54 **NOTE:** This service 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] 1343b0: Fix workflow step cloning
by GitHub 09 May '18

09 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 1343b04380b048dd75264c2ed9fb2ae7ca820d00 https://github.com/galaxyproject/galaxy/commit/1343b04380b048dd75264c2ed9fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix workflow step cloning Problem one is that passing the tool_state as the input payload doesn't preserve the tool state, adressed with the client-part fix. Then passing the tool state still has no effect since the state is properly recovered in `module_factory.from_dict`, but then overwritten by recovering the state starting with an empty dict. It looks like this isn't necessary as we call populate_state anyway when calling `module.get_config_form()`. Fixes https://github.com/galaxyproject/galaxy/issues/5879. Commit: 4f20aee2189218cfead67d0153cd579d5674d3eb https://github.com/galaxyproject/galaxy/commit/4f20aee2189218cfead67d0153cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Rebuild client for workflow step copy fix Commit: 5fa450dc9b9826ffc0bd0a3552a586a2dfcbb859 https://github.com/galaxyproject/galaxy/commit/5fa450dc9b9826ffc0bd0a3552a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore `populate_state`, but only execute if `tool_state` not given Commit: 250973eb46fc69baa6e8018c5f6e6e9552edd877 https://github.com/galaxyproject/galaxy/commit/250973eb46fc69baa6e8018c5f6e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #6085 from mvdbeek/fix_workflow_step_cloning [18.01] Fix workflow step cloning Compare: https://github.com/galaxyproject/galaxy/compare/098f638d2635...250973eb46fc **NOTE:** This service 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] d89c5a: Load tools from /cvmfs/sandbox.galaxyproject.org/
by GitHub 09 May '18

09 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d89c5a1d0597dfe4bad487d39da099c87eb306a7 https://github.com/galaxyproject/usegalaxy-playbook/commit/d89c5a1d0597dfe4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Load tools from /cvmfs/sandbox.galaxyproject.org/ **NOTE:** This service 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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