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[galaxyproject/galaxy] ec320d: Update `cloud` objectstore to adhere with cloudbri...
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ec320d2bad5c327b625e66a13a22c941cac96c5d https://github.com/galaxyproject/galaxy/commit/ec320d2bad5c327b625e66a13a22… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Update `cloud` objectstore to adhere with cloudbridge v1 interface. Commit: d0e2820b4f2e35e5a15c96296c656e7c03ee44df https://github.com/galaxyproject/galaxy/commit/d0e2820b4f2e35e5a15c96296c65… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Log exception message failing to create bucket in cloud objectstore. Commit: a52b8a436523a6de040001d45f9773699e58445b https://github.com/galaxyproject/galaxy/commit/a52b8a436523a6de040001d45f97… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Catch a cloudbridge exception if a given bucket does not exist. Commit: 0956604e557bf1a3857fa870beee7f7f6f36d929 https://github.com/galaxyproject/galaxy/commit/0956604e557bf1a3857fa870beee… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update cloud manager to adhere with v1 cloudbridge interface. Commit: 94fe62803b18151f4aa7830c27704fe6ab65cefb https://github.com/galaxyproject/galaxy/commit/94fe62803b18151f4aa7830c2770… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update cloudbridge version in conditional requirements. Commit: ae41b22113332d7cb11db4d64b9037da473d90ba https://github.com/galaxyproject/galaxy/commit/ae41b22113332d7cb11db4d64b90… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update dependencies using `make update-dependencies`. Commit: c95d995e9d980ced74ef0697b14c786a72369680 https://github.com/galaxyproject/galaxy/commit/c95d995e9d980ced74ef0697b14c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Fix pyinotify environment marker Remove outdated pin on boto. Commit: 11274995ca5a84f750000be724d770e77d9de990 https://github.com/galaxyproject/galaxy/commit/11274995ca5a84f750000be724d7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Rename bucket to bucket_name in cloud API and manager. Commit: 240074224f07d1a047e5560627e3f19fb02ae0e7 https://github.com/galaxyproject/galaxy/commit/240074224f07d1a047e5560627e3… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Rename bucket_obj to bucket. Commit: ebc5858f02e07585860b4adc26ccaff300e1154c https://github.com/galaxyproject/galaxy/commit/ebc5858f02e07585860b4adc26cc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/managers/cloud.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Merge pull request #6660 from VJalili/upgrade_cloudbridge Upgrade CloudBridge to v1.0.1 Compare: https://github.com/galaxyproject/galaxy/compare/b8fe2fe294f1...ebc5858f02e0 **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] c0c587: Add page_to_raw to decode ids in the database.
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0c587abdf23b8d5a01222cace7cc81f4b3d82f4 https://github.com/galaxyproject/galaxy/commit/c0c587abdf23b8d5a01222cace7c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: A scripts/page_to_raw.py Log Message: ----------- Add page_to_raw to decode ids in the database. Commit: a23e5d77a54710662a784d7ec1454e3af54c3097 https://github.com/galaxyproject/galaxy/commit/a23e5d77a54710662a784d7ec145… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Allow pages to read both encoded and unencoded ids out of the database. Always save unencoded version, with the additional benefit of using a simpler, smaller placeholder. Commit: b8fa78358c07fc2b0eaa53f2e02a2674cc522ef1 https://github.com/galaxyproject/galaxy/commit/b8fa78358c07fc2b0eaa53f2e02a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Remove outdated comment; I refactored to handle this. Commit: f9d791c228d1dfafdaaae404ae1ec6fb94f51555 https://github.com/galaxyproject/galaxy/commit/f9d791c228d1dfafdaaae404ae1e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/page_to_raw.py Log Message: ----------- Refactoring, drop BS4. It's faster, for sure, but this leaves us with fewer moving parts and this isn't a script anyone's going to run often. Hopefully. Commit: f01726dc6f27492a20007ca51d4dda82f1eb43c8 https://github.com/galaxyproject/galaxy/commit/f01726dc6f27492a20007ca51d4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Almost there, one more (preexisting) bug to fix. This adds validation on save and correct processing to the page writer. Commit: eb8d80b6d248eaeb7218ce0ad324be93634ca805 https://github.com/galaxyproject/galaxy/commit/eb8d80b6d248eaeb7218ce0ad324… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/page_to_raw.py Log Message: ----------- Handle item name fetching, enforce accessible Commit: 2fa6dedf4e22351b88bb0706992928c306137cea https://github.com/galaxyproject/galaxy/commit/2fa6dedf4e22351b88bb07069929… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Only display encoded ids in editor as well. Commit: 4fa1cc38eacbc20622f81bbe7505df0d21480b72 https://github.com/galaxyproject/galaxy/commit/4fa1cc38eacbc20622f81bbe7505… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: R scripts/page_to_raw.py A scripts/pages_identifier_conversion.py Log Message: ----------- Rename page 'fixer' script Commit: f8273572f7aaf08cc94c06d8569b26089c231fa4 https://github.com/galaxyproject/galaxy/commit/f8273572f7aaf08cc94c06d8569b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js Log Message: ----------- Fix (unrelated to the changes in this PR -- bonus bug) name injection for embedded objects. Commit: 5ffff7f1b455a6a0f95377f715421ee8229b56f5 https://github.com/galaxyproject/galaxy/commit/5ffff7f1b455a6a0f95377f71542… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M static/scripts/bundled/extended.bundled.js M static/scripts/galaxy.pages.js Log Message: ----------- Client build. Looks like we accidentally committed the map references? Leaving that in place, but we had agreed to drop them. Commit: eab6dd858168a5a5cf396b79d4415a265082e9d7 https://github.com/galaxyproject/galaxy/commit/eab6dd858168a5a5cf396b79d441… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Add dry run mode for script to test Commit: f2072310afac4ab6052bade41cdadb03210963d4 https://github.com/galaxyproject/galaxy/commit/f2072310afac4ab6052bade41cda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Swap placeholder template string back to a single line. Commit: a3799350ff81d56bcc7db6a5cc8a53470bbe72fe https://github.com/galaxyproject/galaxy/commit/a3799350ff81d56bcc7db6a5cc8a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Fix hda security check. Commit: 4ec42d28362cdc6252206a8b9d2f4cc9361c4def https://github.com/galaxyproject/galaxy/commit/4ec42d28362cdc6252206a8b9d2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Enforce PAGE_MAXRAW, otherwise we have no way to differentiate between potentially all-integer 16 character identifiers. I can't think of a better way to do this, unfortunately. Commit: cf9d7c53f0637425fa3af6153d432aa240838cb2 https://github.com/galaxyproject/galaxy/commit/cf9d7c53f0637425fa3af6153d43… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Restructure to allow individual successful conversions to commit, only rolling back individual fails instead of the entire transaction. This is going to be necessary for complicated deployments like main, where we have ~95% working fine but the otehr 5% were busted to start with (and won't parse), etc. Also swap dryrun to difflib display. Commit: d7a245608ead868c8104f2e6dbbbc9fc9ef20dcc https://github.com/galaxyproject/galaxy/commit/d7a245608ead868c8104f2e6dbbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Fix lint Commit: 3571df4e4d8324a84eaeb16cd840098165fb2ffd https://github.com/galaxyproject/galaxy/commit/3571df4e4d8324a84eaeb16cd840… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Use PAGE_MAXRAW in both places (refactor this after it all works perfectly) Commit: fa64299fd1f32e58185259a35612c0f203accb72 https://github.com/galaxyproject/galaxy/commit/fa64299fd1f32e58185259a35612… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Drop redundant decode; this is handled in either path of the logic above. Commit: eba93525afbfa16234754efee081caf028e0cc0d https://github.com/galaxyproject/galaxy/commit/eba93525afbfa16234754efee081… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Minor refactoring/dedupe Commit: 1ee673306c59f7a97a072b47046151ccd53273a5 https://github.com/galaxyproject/galaxy/commit/1ee673306c59f7a97a072b470461… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Skip the commit attempt, just flush on success Commit: 9217680ab6af2d0d96a1ce8be520ed010767cdfb https://github.com/galaxyproject/galaxy/commit/9217680ab6af2d0d96a1ce8be520… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M lib/galaxy/webapps/galaxy/controllers/page.py A scripts/pages_identifier_conversion.py M static/scripts/bundled/extended.bundled.js M static/scripts/galaxy.pages.js M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6647 from dannon/page_fixes [18.05] Pages - fixes for encoded ids in the database Commit: b8fe2fe294f11f8700cda2dd6bbdd1d796cada2c https://github.com/galaxyproject/galaxy/commit/b8fe2fe294f11f8700cda2dd6bbd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M lib/galaxy/webapps/galaxy/controllers/page.py A scripts/pages_identifier_conversion.py M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3e4bbfbbc29f...b8fe2fe294f1 **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] 9d5146: Expose version parameter for workflows, allows ret...
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d5146017c77f3a2c29bb4c7dec5885849f67c66 https://github.com/galaxyproject/galaxy/commit/9d5146017c77f3a2c29bb4c7dec5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Expose version parameter for workflows, allows retrieving non-latest versions Commit: f49da14e45feed1273c705112a6d75a484ba9548 https://github.com/galaxyproject/galaxy/commit/f49da14e45feed1273c705112a6d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Move recovery functionality for getting perticular workflow versions into StoredWorkflow Commit: e18433127f244b332325e6a7bf9e914f9e0391e6 https://github.com/galaxyproject/galaxy/commit/e18433127f244b332325e6a7bf9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Order list of workflows related to a StoredWorkflow This will put the newest workflows first. Commit: c652cf4b078ae69e36292f1ba1ef72a899ff0b4f https://github.com/galaxyproject/galaxy/commit/c652cf4b078ae69e36292f1ba1ef… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Allow loading non-latest workflows into editor There is no UI-element so far, but you can append &version=<N> to the editor URL to load any arbitrary version of a workflow. Commit: 3d8db3a91f9b5dff0b5940fc0f40f5d5b19f051a https://github.com/galaxyproject/galaxy/commit/3d8db3a91f9b5dff0b5940fc0f40… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Inform user that workflow loading has failed This sends the user back to the worflow index page. Commit: 56411c3c116d160fc4c95b718e52a27b13c5bd98 https://github.com/galaxyproject/galaxy/commit/56411c3c116d160fc4c95b718e52… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Hack around routes returning 'None' for parameter Commit: f1e94f84739c929429c0079f245baa10afacc155 https://github.com/galaxyproject/galaxy/commit/f1e94f84739c929429c0079f245b… Author: charesredhat <cstrittmatter(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Added Workflow version change control to the top bar Commit: 98a2526cec43129e143c3201e908dee943194353 https://github.com/galaxyproject/galaxy/commit/98a2526cec43129e143c3201e908… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Show current version in version selection Commit: 85d80ec20ba7bf9985c3139aa47a75e974aafa5d https://github.com/galaxyproject/galaxy/commit/85d80ec20ba7bf9985c3139aa47a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Always pass in a version when loading the wf-editor Commit: 85adb0a371b0079b929e360e7fa35e97b2cd09d8 https://github.com/galaxyproject/galaxy/commit/85adb0a371b0079b929e360e7fa3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move version selection to right-hand most location Commit: d377b00388f8c8060853ef77f8be6187968e78b4 https://github.com/galaxyproject/galaxy/commit/d377b00388f8c8060853ef77f8be… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Indicate which version is currently on display Commit: efec721676d2b27c91afb655c7c6630ed838a39e https://github.com/galaxyproject/galaxy/commit/efec721676d2b27c91afb655c7c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move version selection out of editor.mako Also adds an API that lists workflow versions for a workflow id. Commit: 3e4bbfbbc29f84ae30cd5905e7a43376915cbf47 https://github.com/galaxyproject/galaxy/commit/3e4bbfbbc29f84ae30cd5905e7a4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6683 from mvdbeek/expose_workflow_versions Expose workflow versions Compare: https://github.com/galaxyproject/galaxy/compare/d349d4763d61...3e4bbfbbc29f **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] c0c587: Add page_to_raw to decode ids in the database.
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c0c587abdf23b8d5a01222cace7cc81f4b3d82f4 https://github.com/galaxyproject/galaxy/commit/c0c587abdf23b8d5a01222cace7c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: A scripts/page_to_raw.py Log Message: ----------- Add page_to_raw to decode ids in the database. Commit: a23e5d77a54710662a784d7ec1454e3af54c3097 https://github.com/galaxyproject/galaxy/commit/a23e5d77a54710662a784d7ec145… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Allow pages to read both encoded and unencoded ids out of the database. Always save unencoded version, with the additional benefit of using a simpler, smaller placeholder. Commit: b8fa78358c07fc2b0eaa53f2e02a2674cc522ef1 https://github.com/galaxyproject/galaxy/commit/b8fa78358c07fc2b0eaa53f2e02a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Remove outdated comment; I refactored to handle this. Commit: f9d791c228d1dfafdaaae404ae1ec6fb94f51555 https://github.com/galaxyproject/galaxy/commit/f9d791c228d1dfafdaaae404ae1e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/page_to_raw.py Log Message: ----------- Refactoring, drop BS4. It's faster, for sure, but this leaves us with fewer moving parts and this isn't a script anyone's going to run often. Hopefully. Commit: f01726dc6f27492a20007ca51d4dda82f1eb43c8 https://github.com/galaxyproject/galaxy/commit/f01726dc6f27492a20007ca51d4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Almost there, one more (preexisting) bug to fix. This adds validation on save and correct processing to the page writer. Commit: eb8d80b6d248eaeb7218ce0ad324be93634ca805 https://github.com/galaxyproject/galaxy/commit/eb8d80b6d248eaeb7218ce0ad324… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/page_to_raw.py Log Message: ----------- Handle item name fetching, enforce accessible Commit: 2fa6dedf4e22351b88bb0706992928c306137cea https://github.com/galaxyproject/galaxy/commit/2fa6dedf4e22351b88bb07069929… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Only display encoded ids in editor as well. Commit: 4fa1cc38eacbc20622f81bbe7505df0d21480b72 https://github.com/galaxyproject/galaxy/commit/4fa1cc38eacbc20622f81bbe7505… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: R scripts/page_to_raw.py A scripts/pages_identifier_conversion.py Log Message: ----------- Rename page 'fixer' script Commit: f8273572f7aaf08cc94c06d8569b26089c231fa4 https://github.com/galaxyproject/galaxy/commit/f8273572f7aaf08cc94c06d8569b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js Log Message: ----------- Fix (unrelated to the changes in this PR -- bonus bug) name injection for embedded objects. Commit: 5ffff7f1b455a6a0f95377f715421ee8229b56f5 https://github.com/galaxyproject/galaxy/commit/5ffff7f1b455a6a0f95377f71542… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M static/scripts/bundled/extended.bundled.js M static/scripts/galaxy.pages.js Log Message: ----------- Client build. Looks like we accidentally committed the map references? Leaving that in place, but we had agreed to drop them. Commit: eab6dd858168a5a5cf396b79d4415a265082e9d7 https://github.com/galaxyproject/galaxy/commit/eab6dd858168a5a5cf396b79d441… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Add dry run mode for script to test Commit: f2072310afac4ab6052bade41cdadb03210963d4 https://github.com/galaxyproject/galaxy/commit/f2072310afac4ab6052bade41cda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Swap placeholder template string back to a single line. Commit: a3799350ff81d56bcc7db6a5cc8a53470bbe72fe https://github.com/galaxyproject/galaxy/commit/a3799350ff81d56bcc7db6a5cc8a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Fix hda security check. Commit: 4ec42d28362cdc6252206a8b9d2f4cc9361c4def https://github.com/galaxyproject/galaxy/commit/4ec42d28362cdc6252206a8b9d2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Enforce PAGE_MAXRAW, otherwise we have no way to differentiate between potentially all-integer 16 character identifiers. I can't think of a better way to do this, unfortunately. Commit: cf9d7c53f0637425fa3af6153d432aa240838cb2 https://github.com/galaxyproject/galaxy/commit/cf9d7c53f0637425fa3af6153d43… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Restructure to allow individual successful conversions to commit, only rolling back individual fails instead of the entire transaction. This is going to be necessary for complicated deployments like main, where we have ~95% working fine but the otehr 5% were busted to start with (and won't parse), etc. Also swap dryrun to difflib display. Commit: d7a245608ead868c8104f2e6dbbbc9fc9ef20dcc https://github.com/galaxyproject/galaxy/commit/d7a245608ead868c8104f2e6dbbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Fix lint Commit: 3571df4e4d8324a84eaeb16cd840098165fb2ffd https://github.com/galaxyproject/galaxy/commit/3571df4e4d8324a84eaeb16cd840… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Use PAGE_MAXRAW in both places (refactor this after it all works perfectly) Commit: fa64299fd1f32e58185259a35612c0f203accb72 https://github.com/galaxyproject/galaxy/commit/fa64299fd1f32e58185259a35612… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Drop redundant decode; this is handled in either path of the logic above. Commit: eba93525afbfa16234754efee081caf028e0cc0d https://github.com/galaxyproject/galaxy/commit/eba93525afbfa16234754efee081… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Minor refactoring/dedupe Commit: 1ee673306c59f7a97a072b47046151ccd53273a5 https://github.com/galaxyproject/galaxy/commit/1ee673306c59f7a97a072b470461… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Skip the commit attempt, just flush on success Commit: 9217680ab6af2d0d96a1ce8be520ed010767cdfb https://github.com/galaxyproject/galaxy/commit/9217680ab6af2d0d96a1ce8be520… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M lib/galaxy/webapps/galaxy/controllers/page.py A scripts/pages_identifier_conversion.py M static/scripts/bundled/extended.bundled.js M static/scripts/galaxy.pages.js M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6647 from dannon/page_fixes [18.05] Pages - fixes for encoded ids in the database Compare: https://github.com/galaxyproject/galaxy/compare/d645d80443c2...9217680ab6af **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] 8f979b: Workflow replacement parameters polish.
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8f979b4da16ff4e1498aa1110b45dbb8d62921f1 https://github.com/galaxyproject/galaxy/commit/8f979b4da16ff4e1498aa1110b45… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflow_fixtures.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Workflow replacement parameters polish. - Selenium test case demonstrating their use in simple workflows. - API test demonstrating they work with nested workflows from the run perspective. - Update run variant of workflow to_dict to parse out replacement parameters to display on the backend and tweak the client to just accept these. - Parse out replacement parameters for subworkflows recursively, include in new run output attribute - nested workflow replacement parameters work now. - Selenium test case demosntrating subworkflow replacement parameters are rendered and used when submitted. Commit: d349d4763d61d540a9704ba5b184189fa0fb2d1e https://github.com/galaxyproject/galaxy/commit/d349d4763d61d540a9704ba5b184… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflow_fixtures.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #6678 from jmchilton/subworkflow_parameters Workflow replacement parameters polish. Compare: https://github.com/galaxyproject/galaxy/compare/d42fb41cb059...d349d4763d61 **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] b9fdc1: Install cutadapt version 1.16
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b9fdc182abaef5430a5b50b0efc107614f33705e https://github.com/galaxyproject/usegalaxy-playbook/commit/b9fdc182abaef543… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Install cutadapt version 1.16 **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] 8695a0: Keep newly broken tool in toolbox
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8695a0d9bc4481ebf49ec9fc13db1c066243b12c https://github.com/galaxyproject/galaxy/commit/8695a0d9bc4481ebf49ec9fc13db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Keep newly broken tool in toolbox That's handy when developing tools and you messed up something so bad the tool isn't valid anymore. We retrieve the non-broken previous version from the tool cache. Commit: 947389887b011fc277ac776b3f6c21c3dd6df96d https://github.com/galaxyproject/galaxy/commit/947389887b011fc277ac776b3f6c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Add unit test that exercises reloading for broken tools Commit: dc49c3ea0ebd64ac2d1b51a67e7c18df06255804 https://github.com/galaxyproject/galaxy/commit/dc49c3ea0ebd64ac2d1b51a67e7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Provide visual feedback if tool is broken Commit: d42fb41cb0599488b17008849b79dc064f7e54f9 https://github.com/galaxyproject/galaxy/commit/d42fb41cb0599488b17008849b79… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6681 from mvdbeek/continue_reloading_if_tool_is_broken Keep newly broken tool in toolbox Compare: https://github.com/galaxyproject/galaxy/compare/64bb339a31e8...d42fb41cb059 **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] 8b8806: update Test, remove gccbosc slide
by GitHub 10 Sep '18

10 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8b88069457747738c9f06f1865ec2a4096902061 https://github.com/galaxyproject/usegalaxy-playbook/commit/8b88069457747738… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update Test, remove gccbosc slide **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] e0d120: document the sniff_compressed_dynamic_datatypes_de...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0d1208834deb7762564d5ae1cdc84da682dde5f https://github.com/galaxyproject/galaxy/commit/e0d1208834deb7762564d5ae1cdc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- document the sniff_compressed_dynamic_datatypes_default config and include in sample Commit: b34414adc8a5afad30d4822dfbc794cfc3bad9ff https://github.com/galaxyproject/galaxy/commit/b34414adc8a5afad30d4822dfbc7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- switch the default to sniff compressed datatypes Commit: 0acdc8a1a3eecae23b1dfe0876cf15d0ab41aa05 https://github.com/galaxyproject/galaxy/commit/0acdc8a1a3eecae23b1dfe0876cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- adjust test definitions for compressed handling so it tests the new defaults Commit: 7c339c9bffb58a71053e8d6dd20122498061f7ec https://github.com/galaxyproject/galaxy/commit/7c339c9bffb58a71053e8d6dd201… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Use uses_test_history for selected upload tests Commit: d437875513c4d88f5096952a63eca62a96ed68bb https://github.com/galaxyproject/galaxy/commit/d437875513c4d88f5096952a63ec… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #29 from mvdbeek/martenson-rename-and-document-config-value Use uses_test_history for selected upload tests Commit: e1b32368028cf9360ecef6400c6ce26f1bb0adc8 https://github.com/galaxyproject/galaxy/commit/e1b32368028cf9360ecef6400c6c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- fix tests for the bed.gz dtaatype compressed beds are not part of the datatypes_conf.xml.sample Commit: 4a21ac30ea51aba6df2d98076a67caaa2e3feed0 https://github.com/galaxyproject/galaxy/commit/4a21ac30ea51aba6df2d98076a67… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Merge branch 'rename-and-document-config-value' of github.com:martenson/galaxy into rename-and-document-config-value Commit: 9b5724d62d614d8f1e721f169ed76d0c5c6a789c https://github.com/galaxyproject/galaxy/commit/9b5724d62d614d8f1e721f169ed7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- add back the unstable flags for bed.gz datasets I expect the datatypes_conf.xml bed compress default will change in near future Commit: 64bb339a31e8e2559bbb4ba81e8f27f65d1fe412 https://github.com/galaxyproject/galaxy/commit/64bb339a31e8e2559bbb4ba81e8f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6641 from martenson/rename-and-document-config-value document config for sniffing compressed files, enable by default Compare: https://github.com/galaxyproject/galaxy/compare/f5194910f724...64bb339a31e8 **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] d6f017: Escape parenthesis in output names
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6f01741a111180f5a4f3a4af56d017250dca124 https://github.com/galaxyproject/galaxy/commit/d6f01741a111180f5a4f3a4af56d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Escape parenthesis in output names Otherwise this leads to: ``` webpack-internal:///0:1468 Uncaught Error: Syntax error, unrecognized expression: .callout.with (parenthesis) at Function.Sizzle.error (webpack-internal:///0:1468) at Sizzle.tokenize (webpack-internal:///0:2125) at Function.Sizzle (webpack-internal:///0:838) at Function.jQuery.find (webpack-internal:///453:290) at jQuery.fn.init.find (webpack-internal:///0:2792) at jQuery.fn.init.jQuery.fn.find (webpack-internal:///453:677) at child.eval (webpack-internal:///760:322) at Function.each (webpack-internal:///0:371) at Object.eval (webpack-internal:///760:319) at Function.each (webpack-internal:///0:371) ``` Commit: f5194910f724554df3b2ac17ff489c0c986cc1ac https://github.com/galaxyproject/galaxy/commit/f5194910f724554df3b2ac17ff48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Merge pull request #6680 from mvdbeek/subworkflow_escape_names Fix wf-editor when loading subworkflow with parenthesis in label Compare: https://github.com/galaxyproject/galaxy/compare/95462754c09f...f5194910f724 **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] e110c8: Use the error severity to send fewer messages to l...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e110c831b2694088b19cfb35a8ca9d876431b381 https://github.com/galaxyproject/usegalaxy-playbook/commit/e110c831b2694088… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Use the error severity to send fewer messages to logflux Commit: 8bb9241f6b6de6a2f1bedad5bece5521203abb2b https://github.com/galaxyproject/usegalaxy-playbook/commit/8bb9241f6b6de6a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: A env/common/templates/nginx/default.j2 M env/test/group_vars/webservers/vars.yml A env/test/templates/nginx/default.j2 Log Message: ----------- Default nginx server for Galaxy servers w/ the status module enabled. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/828cac65b3e7...… **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/infrastructure-playbook] d45011: Configure telegraf on Galaxy servers to log nginx.
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d45011459599ad8d6985b8d891113ae6463f73a7 https://github.com/galaxyproject/infrastructure-playbook/commit/d4501145959… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/tacc/group_vars/galaxyservers.yml Log Message: ----------- Configure telegraf on Galaxy servers to log nginx. **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] 384a16: Allow schema to validate
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Compare: https://github.com/galaxyproject/galaxy/compare/6d9df51f36e2...7d7a875af398 **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] 828cac: Set data type for logflux
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 828cac65b3e7d6ec6960cc2c649e940da4841383 https://github.com/galaxyproject/usegalaxy-playbook/commit/828cac65b3e7d6ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/test/group_vars/logfluxservers.yml Log Message: ----------- Set data type for logflux **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] ee0c83: Serialize select field options
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee0c8327e4b2f848c9f9d3c0003cc49781c149f4 https://github.com/galaxyproject/galaxy/commit/ee0c8327e4b2f848c9f9d3c0003c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Serialize select field options This fixes the empty select list in the beta install interface. Commit: 95462754c09facf8ae767b88767003b2d00c1da1 https://github.com/galaxyproject/galaxy/commit/95462754c09facf8ae767b887670… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Merge pull request #6677 from mvdbeek/fix_shed_tool_conf_selection Serialize select field options, fixes beta install Compare: https://github.com/galaxyproject/galaxy/compare/ba22818ff45e...95462754c09f **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/infrastructure-playbook] 933fc3: Try using slurmd -b to prevent permanent node fail...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 933fc3603339cf58082a3094dbf94780649938e0 https://github.com/galaxyproject/infrastructure-playbook/commit/933fc360333… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M roles/slurmscale/files/resume.yml Log Message: ----------- Try using slurmd -b to prevent permanent node failure **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] cef8f1: Install logflux for nginx rate limit logs
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cef8f1beb4139a2939f9e92c1462315a73a0f870 https://github.com/galaxyproject/usegalaxy-playbook/commit/cef8f1beb4139a29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 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 Commit: 2c8b698a762a0dba51321f2d0b6dad97f78fd7a5 https://github.com/galaxyproject/usegalaxy-playbook/commit/2c8b698a762a0dba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Fix Main version number (it was updated to this version on 2018-07-18, not sure why it wasn't committed) Commit: b278079d0e2cdb3e3a94e741ee8d622e648818d5 https://github.com/galaxyproject/usegalaxy-playbook/commit/b278079d0e2cdb3e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/main/group_vars/cvmfsstratum0servers.yml Log Message: ----------- Build client on Main Commit: c05443511ed2ec153a4930130e789096c9a71d75 https://github.com/galaxyproject/usegalaxy-playbook/commit/c05443511ed2ec15… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/test/group_vars/logfluxservers.yml M env/test/templates/nginx/galaxy_test.j2 M roles/logflux/defaults/main.yml M roles/logflux/tasks/main.yml M roles/logflux/templates/rsyslog.conf.j2 Log Message: ----------- Fixes for logflux Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3ebe796f2020...… **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] c867c6: Upgraded genomespaceclient to newer version
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c867c6863fbbb75f473f209fea7a805e2da63a47 https://github.com/galaxyproject/galaxy/commit/c867c6863fbbb75f473f209fea7a… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M tools/genomespace/genomespace_importer.py Log Message: ----------- Upgraded genomespaceclient to newer version This fixes issue reported in: https://github.com/galaxyproject/usegalaxy-playbook/issues/100 Also related to PR: https://github.com/galaxyproject/galaxy/pull/6660 Commit: ba22818ff45ee639fb1a199a6dff5085a28f8365 https://github.com/galaxyproject/galaxy/commit/ba22818ff45ee639fb1a199a6dff… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #6668 from gvlproject/genomespaceclient_upgrade Upgraded genomespaceclient to newer version Compare: https://github.com/galaxyproject/galaxy/compare/1ba4b47d7335...ba22818ff45e **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] 3ebe79: Install multigps 0.74 wrapper by Greg.
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3ebe796f2020f47eedd043519c51789ae003c9f5 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ebe796f2020f47e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Install multigps 0.74 wrapper by Greg. **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] 69252d: Tell pytest not to execute Python code in node_mod...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69252d711a1d7112e3340a25d5b3b821cb027e39 https://github.com/galaxyproject/galaxy/commit/69252d711a1d7112e3340a25d5b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M run_tests.sh Log Message: ----------- Tell pytest not to execute Python code in node_modules for web proxy. Causes test execution to fail for me. Commit: 1ba4b47d7335c097a189a15859c58ddac1e2dadd https://github.com/galaxyproject/galaxy/commit/1ba4b47d7335c097a189a15859c5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6676 from jmchilton/pytest_fix Tell pytest not to execute Python code in node_modules for web proxy. Compare: https://github.com/galaxyproject/galaxy/compare/3824a8948a43...1ba4b47d7335 **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] 5e7415: Optimize initial validation of collection input pa...
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e74154c930326f4c7a69f7dbd33ea88189fb257 https://github.com/galaxyproject/galaxy/commit/5e74154c930326f4c7a69f7dbd33… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Optimize initial validation of collection input parameters. Commit: ca26c3d5aff4d92192bfef744348c94b6e41ea7e https://github.com/galaxyproject/galaxy/commit/ca26c3d5aff4d92192bfef744348… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py Log Message: ----------- Optimize permission loading and checking collection parameters. We were checking permissions twice it seems like to me, only do it once. Avoid loading dataset permissions for each individual dataset in a collection - work with summary sets of role ids. Commit: 3824a8948a43a8a0def879df73087ce190182b3f https://github.com/galaxyproject/galaxy/commit/3824a8948a43a8a0def879df7308… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #6635 from jmchilton/permission_opts Optimize tool execution permission checking Compare: https://github.com/galaxyproject/galaxy/compare/da18624067c8...3824a8948a43 **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] 6a266a: More tests for runtime workflow parameters.
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a266a19a947e853b37ce20eee9fc1f775b5f550 https://github.com/galaxyproject/galaxy/commit/6a266a19a947e853b37ce20eee9f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- More tests for runtime workflow parameters. Commit: 7806a84d1c22ba6f8b580fee78cb6bf594967936 https://github.com/galaxyproject/galaxy/commit/7806a84d1c22ba6f8b580fee78cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/base/workflow_fixtures.py M test/selenium_tests/test_workflow_run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Implement runtime parameters in nested workflows. Commit: fc75d4f9fbf8c6406d80873570392e925e40f56c https://github.com/galaxyproject/galaxy/commit/fc75d4f9fbf8c6406d8087357039… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/api/test_workflows.py M test/base/workflow_fixtures.py Log Message: ----------- Test case - verify step parameters replace after workflow invoke pauses. Commit: da18624067c819d4940658d9a5675c84977a2b3d https://github.com/galaxyproject/galaxy/commit/da18624067c819d4940658d9a567… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_workflow_run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #6664 from jmchilton/runtime_parameters Implement runtime parameters for subworkflows. Compare: https://github.com/galaxyproject/galaxy/compare/5c54793ddfbd...da18624067c8 **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] 03f124: Update Test
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 03f1247cf1dcf1bcf38608323d9aa7fed0206b86 https://github.com/galaxyproject/usegalaxy-playbook/commit/03f1247cf1dcf1bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Conflicts: env/test/files/galaxy/galaxy_version.yml **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] a4495c: Update Test
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/swarmscale-2.0 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4495ccc4a809d6247edd1c4137b26d8d3f191a3 https://github.com/galaxyproject/usegalaxy-playbook/commit/a4495ccc4a809d62… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test **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/infrastructure-playbook] 81dc9b: Update Jetstream image
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 81dc9b98f0c5bf6ccb8521c6aa959d1c1124c917 https://github.com/galaxyproject/infrastructure-playbook/commit/81dc9b98f0c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M roles/slurmscale/files/group_vars/all/spawn.yml Log Message: ----------- Update Jetstream image **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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