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

[galaxyproject/infrastructure-playbook] 346402: Fix squid conf for cvmfs1-psu0 localhost (cvmfs_se...
by GitHub 12 Apr '18

12 Apr '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 346402da28015558326dbb1f8c3ec1ca678538b1 https://github.com/galaxyproject/infrastructure-playbook/commit/346402da280… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M env/galaxy/templates/squid/cvmfs1-psu0_squid.conf.j2 Log Message: ----------- Fix squid conf for cvmfs1-psu0 localhost (cvmfs_server) access

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[galaxyproject/usegalaxy-playbook] a6bd07: Updated plant_tribes_gene_family_classifier for ne...
by GitHub 12 Apr '18

12 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a6bd075e83b667b0f13f1d65531b1870866eff58 https://github.com/galaxyproject/usegalaxy-playbook/commit/a6bd075e83b667b0… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated plant_tribes_gene_family_classifier for new dependencies.

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[galaxyproject/galaxy] fa1231: Minor build fixes.
by GitHub 12 Apr '18

12 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa1231e9ec162df80442432c36ed1cb8b8ab2d42 https://github.com/galaxyproject/galaxy/commit/fa1231e9ec162df80442432c36ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Minor build fixes. Fix qunit issue and linting issue introduced with #5876. Commit: 1583db76ebebbcecf67dbf334dc1b24f5748b382 https://github.com/galaxyproject/galaxy/commit/1583db76ebebbcecf67dbf334dc1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #5878 from jmchilton/fixbuild Minor build fixes. Compare: https://github.com/galaxyproject/galaxy/compare/acff3b2e9555...1583db76ebeb

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[galaxyproject/galaxy] 79f664: More, better workflow editor Selenium tests.
by GitHub 11 Apr '18

11 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79f664aa4e482d81ae3392f6cc0a9c927a144518 https://github.com/galaxyproject/galaxy/commit/79f664aa4e482d81ae3392f6cc0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako M test/base/workflows_format_2/main.py M test/galaxy_selenium/components.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_editor.py Log Message: ----------- More, better workflow editor Selenium tests. - More stuff tested: - Setting input name and annotation, saving, reloading. - Simple tests for collection inputs in addition to data inputs. - A simple workflow renders its connections. - More screenshots. - Expanded use of navigation.yml for abstraction description of elements. - More abstractions for probing the workflow in the editor - should serve as a basis for additional tests. - Decorate editor DOM to allow finding elements in reproducible ways (enables testing, but should help with tours as well). - Make editor tests more robust by: - Doing more appropriate waiting, instead of adding sleeps for jQuery interactions. - Not assuming each test occurs with a fresh user (and hence workflow list). Commit: acff3b2e9555c042cfcaa2e6c798b0ecd74d0449 https://github.com/galaxyproject/galaxy/commit/acff3b2e9555c042cfcaa2e6c798… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako M test/base/workflows_format_2/main.py M test/galaxy_selenium/components.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_editor.py Log Message: ----------- Merge pull request #5876 from jmchilton/editor_tests More, better workflow editor Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/6ee1c44df765...acff3b2e9555

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[galaxyproject/galaxy] 4e8e6a: add link to ftp help to upload modal
by GitHub 11 Apr '18

11 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e8e6a8f01219ef17409a5efe925ca07358939f3 https://github.com/galaxyproject/galaxy/commit/4e8e6a8f01219ef17409a5efe925… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js Log Message: ----------- add link to ftp help to upload modal Commit: aae2f1d85c0b3b81ebdd943685945b4204d6dba8 https://github.com/galaxyproject/galaxy/commit/aae2f1d85c0b3b81ebdd94368594… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M lib/galaxy/managers/configuration.py Log Message: ----------- add note to FTP upload modal when oidc is enabled Commit: fe78b5bd89a90b49de5cd95e7ee660296c95dc16 https://github.com/galaxyproject/galaxy/commit/fe78b5bd89a90b49de5cd95e7ee6… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Some updates to FTP-upload messages w.r.t OIDC-based log-ins. Commit: 6bb404e7a6ff7485bb528f16692d13f916490a3b https://github.com/galaxyproject/galaxy/commit/6bb404e7a6ff7485bb528f16692d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Merge pull request #27 from VJalili/openid-ftp Some updates to FTP-upload messages w.r.t OIDC-based log-ins. Commit: c03b699f66ba0a96e8455cf2ac43f928385d3835 https://github.com/galaxyproject/galaxy/commit/c03b699f66ba0a96e8455cf2ac43… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js Log Message: ----------- reword Commit: 6ee1c44df765c060a8396e14c17639b4bd8d20d9 https://github.com/galaxyproject/galaxy/commit/6ee1c44df765c060a8396e14c176… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M lib/galaxy/managers/configuration.py Log Message: ----------- Merge pull request #5814 from martenson/openid-ftp add note to FTP modal when oidc is enabled Compare: https://github.com/galaxyproject/galaxy/compare/11204b176500...6ee1c44df765

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[galaxyproject/galaxy] 2eca6a: Use `extras` to specify additional social_auth_cor...
by GitHub 11 Apr '18

11 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2eca6a252bfde71c921b24b302a8d1655caac514 https://github.com/galaxyproject/galaxy/commit/2eca6a252bfde71c921b24b302a8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Use `extras` to specify additional social_auth_core dependencies - Fix oscillating environment markers due to slight differences in how packages specify their requirements - Update requirements files with `make update-dependencies` Commit: 11204b17650045d73244d68db3133698b3e96b35 https://github.com/galaxyproject/galaxy/commit/11204b17650045d73244d68db313… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Merge pull request #5877 from nsoranzo/dependencies_update Use `extras` to specify additional social_auth_core dependencies Compare: https://github.com/galaxyproject/galaxy/compare/484f5f6ec1bc...11204b176500

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[galaxyproject/usegalaxy-playbook] 06a4da: Use inheritance vars for directories and links
by GitHub 11 Apr '18

11 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 06a4dad1fa25cfaf9219140015c157753e1ccf3f https://github.com/galaxyproject/usegalaxy-playbook/commit/06a4dad1fa25cfaf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M common_roles M env/test/group_vars/webservers/vars.yml Log Message: ----------- Use inheritance vars for directories and links

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[galaxyproject/infrastructure-playbook] fa3ed8: Use inheritance vars for directories and links.
by GitHub 11 Apr '18

11 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fa3ed84610566507ec0b632dfb3a64c991d01bb3 https://github.com/galaxyproject/infrastructure-playbook/commit/fa3ed846105… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M common_roles M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M taccenv/group_vars/all.yml M taccenv/group_vars/galaxyservers.yml M taccenv/host_vars/galaxy-db-02.tacc.utexas.edu/vars.yml Log Message: ----------- Use inheritance vars for directories and links.

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[galaxyproject/infrastructure-playbook] 6a60ea: - Serve datacache via HTTP as well as rsync
by GitHub 11 Apr '18

11 Apr '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6a60eaaf69dbeb7cac1c09802990bac1e9bd9474 https://github.com/galaxyproject/infrastructure-playbook/commit/6a60eaaf69d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M common_roles A env/galaxy/files/sites/datacache/index.html M env/galaxy/group_vars/jenkinsslaves/vars.yml M env/galaxy/host_vars/athena.galaxyproject.org/vars.yml M env/galaxy/host_vars/chouffe.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml M env/galaxy/inventory A env/galaxy/templates/nginx/datacache.j2 A env/galaxy/templates/squid/cvmfs1-psu0_squid.conf.j2 M roles/cvmfs/tasks/stratum1.yml Log Message: ----------- - Serve datacache via HTTP as well as rsync - Switch to inheritance chain for directories and files common role tasks

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[galaxyproject/galaxy] f88c8c: OAuth2.0 initial commit.
by GitHub 10 Apr '18

10 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f88c8c3983a07d90363d7656611fe12367876bae https://github.com/galaxyproject/galaxy/commit/f88c8c3983a07d90363d7656611f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- OAuth2.0 initial commit. Commit: b593368e0772e49788784cfa6f54c3a5d7c35106 https://github.com/galaxyproject/galaxy/commit/b593368e0772e49788784cfa6f54… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py A lib/galaxy/authnz/__init__.py M lib/galaxy/config.py Log Message: ----------- Added a sample config file and its related parser and setup. Commit: 6aa59d133e7315d4b3bc8c2188dd78d2a5f3ce5c https://github.com/galaxyproject/galaxy/commit/6aa59d133e7315d4b3bc8c2188dd… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py Log Message: ----------- Added UserOAuth2 class to model, and defined a table in mappings. Commit: fbb28b93bdfa348dca2fd14d33f681ce76692503 https://github.com/galaxyproject/galaxy/commit/fbb28b93bdfa348dca2fd14d33f6… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Formatting ... added an empty line between two classes. Commit: a9ea8d5621fbf355623fdb2aad42c588d19326c4 https://github.com/galaxyproject/galaxy/commit/a9ea8d5621fbf355623fdb2aad42… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- (1) added provider to the OAuth2.0 model, (2) changed endpoints, Commit: a66bf826fcb14227ef9041cd8572c46f8a8fe8d5 https://github.com/galaxyproject/galaxy/commit/a66bf826fcb14227ef9041cd8572… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: A lib/galaxy/model/migrate/versions/0135_add_oauth2_table.py Log Message: ----------- Add migrate script for the OAuth2 table. Commit: 432b551d060ff5dd27416c94f5a2c316322f24a2 https://github.com/galaxyproject/galaxy/commit/432b551d060ff5dd27416c94f5a2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: A config/oauth2_config.xml.sample M lib/galaxy/authnz/__init__.py Log Message: ----------- Add sample OAuth2.0 configuration file, and updated its parser. Commit: 3a90758f62e1b73ba2284e5307319f3850004f7b https://github.com/galaxyproject/galaxy/commit/3a90758f62e1b73ba2284e530731… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Change endpoint: `OAuth2Authenticate`-> `OAuth2Authentication` Commit: 57f5a5f645345508f7aac856f7d34e0e3974003d https://github.com/galaxyproject/galaxy/commit/57f5a5f645345508f7aac856f7d3… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Update OAuth2.0 controller. Commit: a8705f9dcd1ca1f7b88fc6d9b58e0040d44c4a06 https://github.com/galaxyproject/galaxy/commit/a8705f9dcd1ca1f7b88fc6d9b58e… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/model/migrate/versions/0135_add_oauth2_table.py Log Message: ----------- Migration: Removed `nullable` restriction from 3 OAuth2.0 columns. Commit: 5f55f561905334f98ca56060dd4fff4cf4878985 https://github.com/galaxyproject/galaxy/commit/5f55f561905334f98ca56060dd4f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Change `user` to `user_id`, & set some args optional on UserAuth2 init Commit: 41cc0dcd1bbd448406257cbf184c1bf0d955bd35 https://github.com/galaxyproject/galaxy/commit/41cc0dcd1bbd448406257cbf184c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Remove nullable restriction from some fields of galaxy_user_oauth2 table Commit: d355108334c134eba950cac286ce7691341c06cb https://github.com/galaxyproject/galaxy/commit/d355108334c134eba950cac286ce… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Controller now attempts re-authentication upon False reply from callback Commit: 2e4e28e29610c88de21f49805706fdddbfe0ad27 https://github.com/galaxyproject/galaxy/commit/2e4e28e29610c88de21f49805706… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/oidc_idp_google.py Log Message: ----------- Add an interface for IdPs, & separated Google-specific flow from parent class Commit: c027e31a5b4167ac8f3c225f436310b0b09854e9 https://github.com/galaxyproject/galaxy/commit/c027e31a5b4167ac8f3c225f4363… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Change OAuth2.0 endpoints to lower-case (was camel) Commit: 2326add5023827ff15f38ad97bf7c4ad8afbdede https://github.com/galaxyproject/galaxy/commit/2326add5023827ff15f38ad97bf7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Add a `TODO` comment. Commit: 7ba12a1ddc6b5c0fa9c214dc0037642541e5dde8 https://github.com/galaxyproject/galaxy/commit/7ba12a1ddc6b5c0fa9c214dc0037… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/authnz/__init__.py Log Message: ----------- Fix a bug; callback does not need to pass the provider name Commit: 7c0cc5eac7f851df6e108c94d41db6d511a42b38 https://github.com/galaxyproject/galaxy/commit/7c0cc5eac7f851df6e108c94d41d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/authnz/oidc_idp_google.py Log Message: ----------- Fix bugs; no need to `commit`, access_token accessor change, and add missing `()` Commit: 9dc040366e8ce0dea72734fae5bae83813ea1371 https://github.com/galaxyproject/galaxy/commit/9dc040366e8ce0dea72734fae5ba… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/authnz/oidc_idp_google.py Log Message: ----------- rename access_token to access_token_info Commit: 734a0058afa2f19990bb903496598312215e06ef https://github.com/galaxyproject/galaxy/commit/734a0058afa2f19990bb90349659… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/oauth2_config.xml.sample M lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- make sample OAuth2.0 endpoint lowercase, and updated a comment. Commit: 64d1cd8cab341512c74a47bf92930c17f67bc72a https://github.com/galaxyproject/galaxy/commit/64d1cd8cab341512c74a47bf9293… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Remove a `TODO` on Google callback check. Commit: 14816031988379ae233f0f7b738f16058e9187bd https://github.com/galaxyproject/galaxy/commit/14816031988379ae233f0f7b738f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/authnz/oidc_idp_google.py Log Message: ----------- Updated a log message. Commit: 7ae287d884b626d0a6160b2044857799827b9fef https://github.com/galaxyproject/galaxy/commit/7ae287d884b626d0a6160b204485… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Added package requirements Commit: f622206faadad8916951cf2a19dca6f27c6f82ca https://github.com/galaxyproject/galaxy/commit/f622206faadad8916951cf2a19dc… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/oidc_idp_google.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Removed white spaces between parenthesis and arguments. Commit: bd2c30b8173c185eb0c7ede48aab23e2e9fe4cf1 https://github.com/galaxyproject/galaxy/commit/bd2c30b8173c185eb0c7ede48aab… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M config/galaxy.ini.sample A config/oauth2_config.xml.sample M lib/galaxy/app.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/oidc_idp_google.py M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_oauth2_table.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Rebased and merged conflicts. Removed white spaces between parenthesis and arguments. Commit: e0199f270082a655f742cc6ca0410e6a3392afdb https://github.com/galaxyproject/galaxy/commit/e0199f270082a655f742cc6ca041… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge remote-tracking branch 'origin/oauth2-after-rebase' into oauth2-after-rebase # Conflicts: # lib/galaxy/config.py # lib/galaxy/dependencies/pinned-requirements.txt # lib/galaxy/model/__init__.py # lib/galaxy/model/mapping.py Commit: 0e5589776646311e169d85830a6cc471c7d8a355 https://github.com/galaxyproject/galaxy/commit/0e5589776646311e169d85830a6c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: R lib/galaxy/model/migrate/versions/0135_add_oauth2_table.py A lib/galaxy/model/migrate/versions/0136_add_oauth2_table.py Log Message: ----------- Changed migrated code sequence number. Commit: 3714a926ad09c49389bbd7fc4998f3d99e212380 https://github.com/galaxyproject/galaxy/commit/3714a926ad09c49389bbd7fc4998… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/model/migrate/versions/0136_add_oauth2_table.py Log Message: ----------- Removed white space between parenthesis and arguments. Commit: 875a79ae660a3f763040a5216cd9e3d4c6a0d1e5 https://github.com/galaxyproject/galaxy/commit/875a79ae660a3f763040a5216cd9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/oidc_idp_google.py Log Message: ----------- Few more white space removal. Commit: 9087debcc4f4f6c39189477bf98c7951d1ac2565 https://github.com/galaxyproject/galaxy/commit/9087debcc4f4f6c39189477bf98c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/authnz/oidc_idp_google.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Some formatting updates, and one additional endpoint removal Commit: fe41dcb38014c85354db387ce6b0a7b2b6257036 https://github.com/galaxyproject/galaxy/commit/fe41dcb38014c85354db387ce6b0… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/models.py A lib/galaxy/authnz/psa_authnz.py A lib/galaxy/authnz/psa_storage.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0137_psa_tables.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/controllers/authn.py R lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- An alpha version of authentication based on PSA. Commit: df2cf940c68ae7910faf21f0d308b318539a6cc5 https://github.com/galaxyproject/galaxy/commit/df2cf940c68ae7910faf21f0d308… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R lib/galaxy/authnz/psa_storage.py Log Message: ----------- Removed unused PSA storage file. Commit: 6f50966ec05f3406b398431f666d1abd6020059e https://github.com/galaxyproject/galaxy/commit/6f50966ec05f3406b398431f666d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Replaced custom BaseStrategy with PSA Core BaseStrategy. Commit: 18c0130df9b589e375cb4faefd8794046c3c8ae4 https://github.com/galaxyproject/galaxy/commit/18c0130df9b589e375cb4faefd87… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/authnz/oidc_idp_google.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0137_psa_tables.py Log Message: ----------- First efforts in replacing the PSA user with the Galaxy user. Commit: 80718cdc4d2d5936dc7fcad7bb1208f2022ac1fe https://github.com/galaxyproject/galaxy/commit/80718cdc4d2d5936dc7fcad7bb12… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py Log Message: ----------- Deleted PSAUsers class and mapping. Commit: f2150af7485632a57b725d4943f3d4b3db7d63b4 https://github.com/galaxyproject/galaxy/commit/f2150af7485632a57b725d4943f3… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Updates to Galaxy-user and PSA social incorporation. Commit: 4829f2defd217d157298682072433c1579419c29 https://github.com/galaxyproject/galaxy/commit/4829f2defd217d15729868207243… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/authnz/oidc_idp_google.py M lib/galaxy/model/mapping.py R lib/galaxy/model/migrate/versions/0136_add_oauth2_table.py A lib/galaxy/model/migrate/versions/0136_add_oidc_rp_table.py M lib/galaxy/model/migrate/versions/0137_psa_tables.py Log Message: ----------- Renamed `galaxy_user_oauth2` table to 'oidc_rp' Commit: 55c0b4bc01c724a0350097e3828502c294bb37d2 https://github.com/galaxyproject/galaxy/commit/55c0b4bc01c724a0350097e38285… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0137_psa_tables.py Log Message: ----------- extended `social_auth_usersocialauth` table. Commit: 81483754bc3d859f306a012be098f043f0aab464 https://github.com/galaxyproject/galaxy/commit/81483754bc3d859f306a012be098… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0137_psa_tables.py Log Message: ----------- Renamed user authnz table and model. Commit: 9205cf25b7064fcd310b1c229a00e6f227ae5df0 https://github.com/galaxyproject/galaxy/commit/9205cf25b7064fcd310b1c229a00… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Added two methods to return id and access tokens, & updated a comment. Commit: 5d8b8e1ef306c7ad6d32b42b52ed53c0d9410150 https://github.com/galaxyproject/galaxy/commit/5d8b8e1ef306c7ad6d32b42b52ed… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Implemented disconnect endpoint, & updated some comments. Commit: e6bb39d4492e1cf70e7bbe0dfdce6cb6063a489b https://github.com/galaxyproject/galaxy/commit/e6bb39d4492e1cf70e7bbe0dfdce… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Updated the disconnect process, & added some comments. Commit: 6734638aab3263075c5a664dc9df233e0b96e24d https://github.com/galaxyproject/galaxy/commit/6734638aab3263075c5a664dc9df… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Updated flush function. Commit: bef0ad90e8aedc9ed538682ac5a5acad75a77534 https://github.com/galaxyproject/galaxy/commit/bef0ad90e8aedc9ed538682ac5a5… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Enabled authenticating an anonymous user. Commit: 071e1743edb35d560d2afe0b5216c64e385af9a3 https://github.com/galaxyproject/galaxy/commit/071e1743edb35d560d2afe0b5216… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Updated the temporary user password to a random string. Commit: 9c3ec350511a33d005480fd50d5b74c2170b2878 https://github.com/galaxyproject/galaxy/commit/9c3ec350511a33d005480fd50d5b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: A =0.6.1 A =1.10.0 A =1.4.0 M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Fixed a bug: cannot disconnect anonymous users. Commit: ed0d2d46cbbf5e8c5d7926e051c0bcd1cb764e65 https://github.com/galaxyproject/galaxy/commit/ed0d2d46cbbf5e8c5d7926e051c0… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Resolved a bug: cannot disconnect if not already authenticated. Commit: 3352c3e3b811b170845d2ee3841f0c66b8f1a668 https://github.com/galaxyproject/galaxy/commit/3352c3e3b811b170845d2ee3841f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Simplified UserAuthnzToken class by flattening unnecessary indirections. Commit: 6238849f0741e1b15a73686dc18cd95a3a0d3e4e https://github.com/galaxyproject/galaxy/commit/6238849f0741e1b15a73686dc18c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Explained the key-value pairs of a static property. Commit: 88dc7e3c9fd43fd8754839c9cf6f00f471377a3a https://github.com/galaxyproject/galaxy/commit/88dc7e3c9fd43fd8754839c9cf6f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Removed some comments and implemented Nonce class. Commit: 7c1a8462e5a4c815286b7756507afc21efea7941 https://github.com/galaxyproject/galaxy/commit/7c1a8462e5a4c815286b7756507a… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Simplified Nonce class. Commit: b8704f8c6e417c7c205e5d6207bbad0d54fd5f5c https://github.com/galaxyproject/galaxy/commit/b8704f8c6e417c7c205e5d6207bb… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0137_psa_tables.py Log Message: ----------- Refactored PSA Nonce table, & removed some unused imports. Commit: cd6b93470ade00025805a56a8ca4adde4c701678 https://github.com/galaxyproject/galaxy/commit/cd6b93470ade00025805a56a8ca4… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Added missing `.table` in mapping.py for the PSA tables. Commit: 04cb179ea5ba055be603ca156e495fbf900be40c https://github.com/galaxyproject/galaxy/commit/04cb179ea5ba055be603ca156e49… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Implemented SocialAuthAssociation class. Commit: 54f3033d8a1c9fe52f37e45d710afae47775b7d1 https://github.com/galaxyproject/galaxy/commit/54f3033d8a1c9fe52f37e45d710a… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Added some missing mappers of the PSA-related tables. Commit: 1a10718e9d07816af6018df639723a12849622c9 https://github.com/galaxyproject/galaxy/commit/1a10718e9d07816af6018df63972… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Implemented PSA partial class. Commit: bd46767c77b5b29ff3c18b2c9750a3ddfabd033a https://github.com/galaxyproject/galaxy/commit/bd46767c77b5b29ff3c18b2c9750… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Implemented PSA Code class. Commit: 6f27d09d69cca11b1873ecbdfad2ca0edbf58025 https://github.com/galaxyproject/galaxy/commit/6f27d09d69cca11b1873ecbdfad2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Some clean-ups in psa_authnz Commit: d39c9c3aca6c4a7ddb07fd139584d7841032d3b5 https://github.com/galaxyproject/galaxy/commit/d39c9c3aca6c4a7ddb07fd139584… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0137_psa_tables.py Log Message: ----------- refactored PSA-related models and tables. Commit: 3cb9fd0f713e8e7984497bacacfc6d73bd652c3a https://github.com/galaxyproject/galaxy/commit/3cb9fd0f713e8e7984497bacacfc… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Removed a solved todo comment. Commit: 98e840845611d53d1a5e4c34fe0c0a3dcf4a75df https://github.com/galaxyproject/galaxy/commit/98e840845611d53d1a5e4c34fe0c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Removed unused parameter provider from PSAAuthnz initialization. Commit: 61bbddefed51aa3cb1e806871b33bf1dcd561d22 https://github.com/galaxyproject/galaxy/commit/61bbddefed51aa3cb1e806871b33… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Made some IdP-specific settings dynamic. Commit: e290feac4d459e98d83d7a8d1ed11fe9b87e278e https://github.com/galaxyproject/galaxy/commit/e290feac4d459e98d83d7a8d1ed1… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Redirect user to main page after a successful authentication. Commit: 8eba74c0cdf849c57b4c910991906f2266ba3e86 https://github.com/galaxyproject/galaxy/commit/8eba74c0cdf849c57b4c91099190… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Added on-the-fly-config function. Commit: 98d591068960372d8346b363513f022f6c2d7a32 https://github.com/galaxyproject/galaxy/commit/98d591068960372d8346b363513f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Login an anonymous user after a successful authn with an IdP. Commit: 2c770323cb328fc5aae9af7704eb9f4cdee6fe6d https://github.com/galaxyproject/galaxy/commit/2c770323cb328fc5aae9af7704eb… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Commented a configuration key. Commit: 5f7206ac2bdec3e4180901302b6c487f05ab9927 https://github.com/galaxyproject/galaxy/commit/5f7206ac2bdec3e4180901302b6c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- disabled consent prompt for Google authn. Commit: ae0e173ab5910bc65b35178fe403076f3cdc9fcd https://github.com/galaxyproject/galaxy/commit/ae0e173ab5910bc65b35178fe403… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Made `prompt` a variable defined in and read from configuration. Commit: 35482fd3f028976810172ca129f28dddbbb81b71 https://github.com/galaxyproject/galaxy/commit/35482fd3f028976810172ca129f2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py Log Message: ----------- Added PSA-level configuration (i.e., applied to all backends). Commit: 55362e46f8f4946a33093651d074a68bbb079cae https://github.com/galaxyproject/galaxy/commit/55362e46f8f4946a33093651d074… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: A config/oidc_rp_config.xml.sample Log Message: ----------- Added `oidc_rp_config.xml.sample` file. Commit: b3c1f3cf5180d583552ff95ac24afd4f1d33fdbf https://github.com/galaxyproject/galaxy/commit/b3c1f3cf5180d583552ff95ac24a… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Capture errors on authnz callback. Commit: dec858f88a641eae58c633ff315811efdb969b36 https://github.com/galaxyproject/galaxy/commit/dec858f88a641eae58c633ff3158… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Added disconnect redirect URL to disconnect function signature. Commit: 55cb550abf97d0a66e1e85d5bc279c1ede0002e4 https://github.com/galaxyproject/galaxy/commit/55cb550abf97d0a66e1e85d5bc27… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M config/oauth2_config.xml.sample Log Message: ----------- Updated OAuth2.0 configuration sample file. Commit: 54374aed02085ade8526f945b5dc8967745a6270 https://github.com/galaxyproject/galaxy/commit/54374aed02085ade8526f945b5dc… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M config/galaxy.ini.sample R config/oauth2_config.xml.sample R config/oidc_rp_config.xml.sample M lib/galaxy/app.py M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/oidc_idp_google.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_add_oidc_rp_table.py M lib/galaxy/model/migrate/versions/0137_psa_tables.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Some refactoring. Commit: 9151c0dde211c09e8f537a208545f436cb36153e https://github.com/galaxyproject/galaxy/commit/9151c0dde211c09e8f537a208545… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: A config/oidc_config.xml.sample Log Message: ----------- Added a description for the attribute-value pairs of OIDC config file. Commit: 3104ae1443f04c3c0f429e577baf2186a65c944a https://github.com/galaxyproject/galaxy/commit/3104ae1443f04c3c0f429e577baf… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- updated redirect uri, now it is read from config. Commit: bdb2c3e97a77fea21b4c15c684561c8854faeffc https://github.com/galaxyproject/galaxy/commit/bdb2c3e97a77fea21b4c15c68456… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Switched strategy and backend to local variables. Commit: ba5312f6197a80845923ce590098ab3c0ca5d751 https://github.com/galaxyproject/galaxy/commit/ba5312f6197a80845923ce590098… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Replaced multiple local backend name variables, with a static dict. Commit: 40609a81f20b179da43021e9e23fc3b54106bac8 https://github.com/galaxyproject/galaxy/commit/40609a81f20b179da43021e9e23f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Removed the temporary global variable _trans. Commit: 0d0493e5b2478c94a56f651181d767689989dc8c https://github.com/galaxyproject/galaxy/commit/0d0493e5b2478c94a56f651181d7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Removed the temporary global variable _user. Commit: 467467093030b693642815e33f26d086ec25927d https://github.com/galaxyproject/galaxy/commit/467467093030b693642815e33f26… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Replaced local url variable with a config key. Commit: 2e0e049117e42a409e1b794d58e464eb25ddd211 https://github.com/galaxyproject/galaxy/commit/2e0e049117e42a409e1b794d58e4… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Re-arch: parse all config at init time, and create backends on the fly. Commit: 8d6669f36ad1fdd77e3e2e992347f50c17cf670f https://github.com/galaxyproject/galaxy/commit/8d6669f36ad1fdd77e3e2e992347… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Removed unused configuration in user login function, and saved the info of the just logged in user in a local config rather than session (through strategy). Commit: d5a295b6883170c9a774462f6bb8348ec3492aa0 https://github.com/galaxyproject/galaxy/commit/d5a295b6883170c9a774462f6bb8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fixed a typo. Commit: 60d2794f3021457149fda16f4f40b85b29cad90e https://github.com/galaxyproject/galaxy/commit/60d2794f3021457149fda16f4f40… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Refactored backend and strategy variables scope in callback to be local. Commit: ed77f128e34b8ef7d8dacd1c25fdd942f1780355 https://github.com/galaxyproject/galaxy/commit/ed77f128e34b8ef7d8dacd1c25fd… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Extended the signature of login_user function. Commit: 7249a1c10a13a42d71bd103b5b12c8726caadd52 https://github.com/galaxyproject/galaxy/commit/7249a1c10a13a42d71bd103b5b12… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Updated get_current_user function to rely only on Galaxy Trans. Commit: a1b9842d5ffcc8bf84746e55864668f895eca907 https://github.com/galaxyproject/galaxy/commit/a1b9842d5ffcc8bf84746e558646… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Made dynamic the backend name part of a state token config key. Commit: 794746e5d4f4de73d36e84b9c169dca2c36daac0 https://github.com/galaxyproject/galaxy/commit/794746e5d4f4de73d36e84b9c169… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Removed an unused trans assignment. Commit: e168eaf9e3ce796f2eb5cca252acd5e261828a2f https://github.com/galaxyproject/galaxy/commit/e168eaf9e3ce796f2eb5cca252ac… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- A line break. Commit: 009248b583b131232d863120c34d145afbc29b78 https://github.com/galaxyproject/galaxy/commit/009248b583b131232d863120c34d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Replaced a temporary redirect URI assignment with a config kvp. Commit: d2ad5692f4573826e8386d25c44297513cc6eb1c https://github.com/galaxyproject/galaxy/commit/d2ad5692f4573826e8386d25c442… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Refactored the scope of strategy & backend variables of disconnect func. Commit: 0623793d71b03e0c097d4018480a8e9a4dfd1b4f https://github.com/galaxyproject/galaxy/commit/0623793d71b03e0c097d4018480a… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Removed an unused trans variable assignment in disconnect function. Commit: 0663e570789b354850585d7d7bc3ecf51784d15d https://github.com/galaxyproject/galaxy/commit/0663e570789b354850585d7d7bc3… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Now authnz callback receives login_redirect_url from controller. Commit: e9ba0b9f3cb27a6afecb5d506361b4f9173cc65b https://github.com/galaxyproject/galaxy/commit/e9ba0b9f3cb27a6afecb5d506361… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Refactored disconnect redirect url. Commit: aa076533459b3a2b9e58b471a9a56a1b6ad288a9 https://github.com/galaxyproject/galaxy/commit/aa076533459b3a2b9e58b471a9a5… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M config/oidc_config.xml.sample M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Some updates to config parameters. Commit: ba05d28a07c8c59a229dd812d61f92e0577c86f9 https://github.com/galaxyproject/galaxy/commit/ba05d28a07c8c59a229dd812d61f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Changed the scope of config variable. Commit: 33f2a8f0eab2233ba6550d90ccd7eaa857843560 https://github.com/galaxyproject/galaxy/commit/33f2a8f0eab2233ba6550d90ccd7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Fixed a bug with disconnect redirect url. Commit: ab130f73719f235e1e45b76431c24792fcc7aa7c https://github.com/galaxyproject/galaxy/commit/ab130f73719f235e1e45b76431c2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-16 (Sat, 16 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Updated the build_absolute_uri function of the Strategy. Commit: cb4645fd198073fc408b6513cac2caba5ab6ad66 https://github.com/galaxyproject/galaxy/commit/cb4645fd198073fc408b6513cac2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-17 (Sun, 17 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Some cleanup. Commit: cd9783e9f15d1e476bcc2e5462644d331d8ecead https://github.com/galaxyproject/galaxy/commit/cd9783e9f15d1e476bcc2e546264… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-17 (Sun, 17 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Removed the unused function `create_user`. Commit: b086802f22ddcaa090edfdb677e8a18408402bda https://github.com/galaxyproject/galaxy/commit/b086802f22ddcaa090edfdb677e8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Now get IdP names from buildapp/router; previously it was hard-code. Commit: 10e805328341a4e3755ff3a994f97ad70e9f80fa https://github.com/galaxyproject/galaxy/commit/10e805328341a4e3755ff3a994f9… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Added some authnz front-end components. 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'remotes/upstream/dev' into psaAlpha # Conflicts: # client/galaxy/scripts/apps/analysis.js # lib/galaxy/dependencies/pinned-requirements.txt # lib/galaxy/model/__init__.py # lib/galaxy/webapps/galaxy/buildapp.py Commit: 0b1219692d58c44a9c50be887c7161c12207ae71 https://github.com/galaxyproject/galaxy/commit/0b1219692d58c44a9c50be887c71… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: R lib/galaxy/model/migrate/versions/0136_add_oidc_rp_table.py A lib/galaxy/model/migrate/versions/0137_add_oidc_rp_table.py R lib/galaxy/model/migrate/versions/0137_psa_tables.py A lib/galaxy/model/migrate/versions/0138_psa_tables.py Log Message: ----------- Incremented migration scripts number. Commit: ba18313ae333e5c8c9f343bafab6688904b96639 https://github.com/galaxyproject/galaxy/commit/ba18313ae333e5c8c9f343bafab6… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fixed some bugs: some imports were removed as a result of last merge. Commit: 74b27d22176a8c78019c6a5fee841110b20cf1d5 https://github.com/galaxyproject/galaxy/commit/74b27d22176a8c78019c6a5fee84… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Extended login, callback, and disconnect functions to return success, message and redirect uri. Commit: 294bdf421ffb0f8b0b5076663b357d006f4ec064 https://github.com/galaxyproject/galaxy/commit/294bdf421ffb0f8b0b5076663b35… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py Log Message: ----------- Updated a dictionary init/update to dict literal values. Commit: b4bdfe5930f7128bb3bb3b7d870ce1c91b66b1f9 https://github.com/galaxyproject/galaxy/commit/b4bdfe5930f7128bb3bb3b7d870c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Refactored internal functions of Authn to adhere with private methods naming convention. Commit: 969a2e44dcb01c4518d037c70a73436d2e135dc8 https://github.com/galaxyproject/galaxy/commit/969a2e44dcb01c4518d037c70a73… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/authnz/__init__.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/webapps/galaxy/controllers/authn.py Log Message: ----------- Updated disconnect function to return `success`, `message` & `response`. Commit: 6935adc85b870cba7233bc0aeca35d2070ccf7a8 https://github.com/galaxyproject/galaxy/commit/6935adc85b870cba7233bc0aeca3… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: R lib/galaxy/authnz/oidc_idp_google.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py R lib/galaxy/model/migrate/versions/0137_add_oidc_rp_table.py A lib/galaxy/model/migrate/versions/0137_add_oidc_tables.py R lib/galaxy/model/migrate/versions/0138_psa_tables.py Log Message: ----------- Removed the non-PSA-based authnz code. Commit: 7552952140e1f064aac80eb729fedaa6bd250ac3 https://github.com/galaxyproject/galaxy/commit/7552952140e1f064aac80eb729fe… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py Log Message: ----------- Moved AuthnzManager to another module than init to avoid cyclic imports. Commit: 0b3b7564cf9061e486a09eef56e7863aed6d7008 https://github.com/galaxyproject/galaxy/commit/0b3b7564cf9061e486a09eef56e7… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: R lib/galaxy/authnz/models.py Log Message: ----------- Removed temporary class User, and temporary models module. Commit: 22b4859dff4834950b0b9ac20817e8a529c09dee https://github.com/galaxyproject/galaxy/commit/22b4859dff4834950b0b9ac20817… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/authn.py A lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Fixed a typo. Commit: 3ae155241629f66060a59b77f3d330ebf7e99f79 https://github.com/galaxyproject/galaxy/commit/3ae155241629f66060a59b77f3d3… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M templates/user/login.mako Log Message: ----------- Added the "Login with Google" button. Commit: a17d8ddc15768353a581fd23110fde458f92d834 https://github.com/galaxyproject/galaxy/commit/a17d8ddc15768353a581fd23110f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Fixed a bug redirecting after successfully handling a call-back. Commit: 8385954e9d164d3d8a89e979ab236d7179afd305 https://github.com/galaxyproject/galaxy/commit/8385954e9d164d3d8a89e979ab23… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Capture callback errors, and inform the user and log the error. Commit: 2165447f3653ff1235714b123407db68d9c34d61 https://github.com/galaxyproject/galaxy/commit/2165447f3653ff1235714b123407… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Updated callback error handling. Commit: be1acdc6b6554a2de3ef21551bf4b6a1c47f40c3 https://github.com/galaxyproject/galaxy/commit/be1acdc6b6554a2de3ef21551bf4… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Fixed a bug capturing some errors raised when handling authnz callbacks. Commit: 0c85d9030dd65bffe9e118dbede4ee60808ff009 https://github.com/galaxyproject/galaxy/commit/0c85d9030dd65bffe9e118dbede4… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Some refactoring and updates to authnz error/exception handling. Commit: bc854b0471590c41d348714b69a86197865e8f0d https://github.com/galaxyproject/galaxy/commit/bc854b0471590c41d348714b69a8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add dependencies required for a PSA-based Authnz. 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templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/group/index.mako M test-data/neostore.zip A test-data/new_element_sort_order.txt M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_1.ga M test/base/interactor.py M test/base/populators.py A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_parsing.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into psaAlpha Commit: 3afc67d3b4ffe214659262a8a0d6e2b900b80887 https://github.com/galaxyproject/galaxy/commit/3afc67d3b4ffe214659262a8a0d6… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: A config/oauth2_config.xml.sample M lib/galaxy/app.py A lib/galaxy/authnz/oidc_idp_google.py M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/model/migrate/versions/0136_add_oauth2_table.py A lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Merge branch 'oauth2-after-rebase' into psaAlpha Commit: cd924854a888bf4fce2208247e8cce98d633002a https://github.com/galaxyproject/galaxy/commit/cd924854a888bf4fce2208247e8c… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: A =0.6.1 A =1.10.0 A =1.4.0 M config/galaxy.ini.sample A config/oidc_config.xml.sample M lib/galaxy/app.py M lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0137_add_oidc_tables.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/galaxy/controllers/authnz.py M templates/user/login.mako Log Message: ----------- Merge pull request #4 from VJalili/psaAlpha PSA-based authnz Commit: 1502e0dabd9321d9cfa5345820ec7a11d86e5504 https://github.com/galaxyproject/galaxy/commit/1502e0dabd9321d9cfa5345820ec… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: R lib/galaxy/model/migrate/versions/0136_add_oauth2_table.py R lib/galaxy/model/migrate/versions/0137_add_oidc_tables.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Remove OAuth2.0 migration script, & update OIDC migration script number. Commit: d85c35456012eae9b31bcfa7c29d9f9f844ff57a https://github.com/galaxyproject/galaxy/commit/d85c35456012eae9b31bcfa7c29d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: R config/oauth2_config.xml.sample Log Message: ----------- Remove old OAuth2.0 configuration file. Commit: f06d79355aa8ebba7814ca418b186495c719ce44 https://github.com/galaxyproject/galaxy/commit/f06d79355aa8ebba7814ca418b18… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: A config/oidc_backends_config.xml.sample Log Message: ----------- Add missing oidc_backends_config.xml.sample. Commit: b88339e74f2133a3b94cc99a76886cae4e429f52 https://github.com/galaxyproject/galaxy/commit/b88339e74f2133a3b94cc99a7688… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- obfuscate client id and secret in oidc backend config sample. Commit: 2a6f6e18812b23b5d00f8fd68dafdd43bce19f87 https://github.com/galaxyproject/galaxy/commit/2a6f6e18812b23b5d00f8fd68daf… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Add a sample of redirect URL to oidc_backends_config.xml.sample. Commit: 0f4ec2ffc5e3a5ba7650ef438f3046284f5de167 https://github.com/galaxyproject/galaxy/commit/0f4ec2ffc5e3a5ba7650ef438f30… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Fix a line indentation issue. Commit: cab0b48be397d2326b5c98d1c763cf7f6e1e7ed4 https://github.com/galaxyproject/galaxy/commit/cab0b48be397d2326b5c98d1c763… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Set optional parameter username as last argument of `User` constructor. Commit: 8980e82a6d29c7051ad97777fd0c3a2fa298f4be https://github.com/galaxyproject/galaxy/commit/8980e82a6d29c7051ad97777fd0c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M templates/user/login.mako Log Message: ----------- Check for missing `enable_oidc` in login mako. Commit: 26c91f2d3a3dd01925cd56565e515c8bca53c16e https://github.com/galaxyproject/galaxy/commit/26c91f2d3a3dd01925cd56565e51… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: R lib/galaxy/webapps/galaxy/controllers/oauth2.py Log Message: ----------- Remove unused OAuth2 controller. Commit: 218b88e02e8939fd1c85813aa9e8552b38557d81 https://github.com/galaxyproject/galaxy/commit/218b88e02e8939fd1c85813aa9e8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: R lib/galaxy/authnz/oidc_idp_google.py Log Message: ----------- Remove the unused google oidc implementation. Commit: 4e7b39e7a4c46e6b60bf24575d6df88ad5638615 https://github.com/galaxyproject/galaxy/commit/4e7b39e7a4c46e6b60bf24575d6d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Some sorts on imports and adding new lines. Commit: b951bb2a7b2d7ec0ea89e792bd7ab9937e4c596a https://github.com/galaxyproject/galaxy/commit/b951bb2a7b2d7ec0ea89e792bd7a… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: R =0.6.1 R =1.10.0 R =1.4.0 M lib/galaxy/authnz/managers.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Some ordering to imports; remove `socket` & `codecs` imports. Commit: 3c4ceb02a217b0bc2468cb36e3562788323cafe8 https://github.com/galaxyproject/galaxy/commit/3c4ceb02a217b0bc2468cb36e356… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Replaced `unicode` with `str`. Commit: a992d1f306b655145de123b6b28d620415230ca7 https://github.com/galaxyproject/galaxy/commit/a992d1f306b655145de123b6b28d… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M config/oidc_backends_config.xml.sample Log Message: ----------- Update a comment. Commit: d1ac81983bf37f04d91202d945c3591d84c6a637 https://github.com/galaxyproject/galaxy/commit/d1ac81983bf37f04d91202d945c3… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- cross-python 2/3 assertion if object is of string type. Commit: c7ab4e2213a19b14604fd58c8842278cc90e8120 https://github.com/galaxyproject/galaxy/commit/c7ab4e2213a19b14604fd58c8842… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Fix a bug with disconnect. Commit: 362cfcad4045dc582fd036e659cb263d1783d4a7 https://github.com/galaxyproject/galaxy/commit/362cfcad4045dc582fd036e659cb… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Remove additional new line. Commit: 68acf98919efa77612232ee4016a0426523f7868 https://github.com/galaxyproject/galaxy/commit/68acf98919efa77612232ee4016a… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Fixed a bug re-associating a disconnected OIDC identity with a user. 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Commit: 5c13e50e93e22d6ca16288045bba9dceb1606896 https://github.com/galaxyproject/galaxy/commit/5c13e50e93e22d6ca16288045bba… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Set PSA to persist ID and refresh tokens. Commit: ba3eaec96ab2038021a45bc6decf8be8026dad6c https://github.com/galaxyproject/galaxy/commit/ba3eaec96ab2038021a45bc6decf… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Update PSA setting to persist `id_token`. 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static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M static/style/blue/base.css M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M 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test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/galaxy_selenium/navigation.yml A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/manual/launch_and_run.sh M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_describing_tours.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_tool_validation.py M tox.ini Log Message: ----------- Merge branch 'dev' into oauth2-after-rebase Commit: 654206ec9dd1133c6f455b0efedc8e571d2abf4d https://github.com/galaxyproject/galaxy/commit/654206ec9dd1133c6f455b0efedc… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add OIDC and OAuth2.0 pinned requirements to `requirements.txt`. Commit: 6dcdcc40d59f10778a4dd7f2e93a33edfe9dc618 https://github.com/galaxyproject/galaxy/commit/6dcdcc40d59f10778a4dd7f2e93a… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- When OIDC is not enabled and user manually reaches its endpoint, Galaxy now informs the user that OIDC is not enabled on that instance. Commit: 730b931b871d447d9bc4ebe465a0e68bacf48baa https://github.com/galaxyproject/galaxy/commit/730b931b871d447d9bc4ebe465a0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 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: ----------- OIDC config in galaxy.yml.sample is now set via config_schema. Commit: ea0ebd849f3c62806dff9499ebd16f777ebd07ce https://github.com/galaxyproject/galaxy/commit/ea0ebd849f3c62806dff9499ebd1… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py M static/style/blue/base.css Log Message: ----------- Replace static redirect and username with proper variables. Commit: f634c40ad480775f56029290ce618fa411bde1ec https://github.com/galaxyproject/galaxy/commit/f634c40ad480775f56029290ce61… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.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/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/ui.less M client/package.json M 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M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M 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lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/config_manage.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.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/tag.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/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/common_startup.sh R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py M static/style/blue/base.css R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako A test-data/1.csv A test-data/example-bag.zip A test-data/qname_sorted.bam A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/tools/multi_output_recurse.xml R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase # Conflicts: # static/style/blue/base.css Commit: 320cf473662af7e9a11b40aca160eccce8ec8842 https://github.com/galaxyproject/galaxy/commit/320cf473662af7e9a11b40aca160… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Encrypt random password of a user who is logged-in using OIDC. Commit: 6b998e66fdc4d4d482b05e230406764a2461d8e9 https://github.com/galaxyproject/galaxy/commit/6b998e66fdc4d4d482b05e230406… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M config/oidc_backends_config.xml.sample M config/oidc_config.xml.sample Log Message: ----------- Add a missing blank line at the end of OIDC config samples. Commit: 60e936cf426bfc729693cb76d310e1c641c602a8 https://github.com/galaxyproject/galaxy/commit/60e936cf426bfc729693cb76d310… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M config/oidc_config.xml.sample Log Message: ----------- Add a comment to OIDC config explaining the unit of settings. Commit: 5ffaf9fae546957ec0ebdd634ee0baaea6bbca3c https://github.com/galaxyproject/galaxy/commit/5ffaf9fae546957ec0ebdd634ee0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- use `random.sample` to generate random password for a user. Commit: 259daf1749cd202da233e568e7621cae2b5c3ffe https://github.com/galaxyproject/galaxy/commit/259daf1749cd202da233e568e762… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/README.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.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/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M 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config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py M static/style/blue/base.css R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_tools.py M test/base/populators.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_scripts.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_uploads.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase # Conflicts: # lib/galaxy/dependencies/pinned-requirements.txt # lib/galaxy/dependencies/requirements.txt Commit: 86e13a51c552abda08b2e2fd4022bb9d3648e5b5 https://github.com/galaxyproject/galaxy/commit/86e13a51c552abda08b2e2fd4022… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add OIDC requirements to pipfiles/default/pinned-requirements.txt Commit: 1263161e8292f5c494f0236dbf41bc338afb9e64 https://github.com/galaxyproject/galaxy/commit/1263161e8292f5c494f0236dbf41… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Remove changes to pinned-requirements.txt Commit: 7f1e07b19f5a59a801d7f9df0084e9bce18b8ebf https://github.com/galaxyproject/galaxy/commit/7f1e07b19f5a59a801d7f9df0084… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add PSA requirement to pipfile and run `make update-dependencies`. Commit: cd7e0b1eeef4b07ff21e3dce244b3e5611b352d6 https://github.com/galaxyproject/galaxy/commit/cd7e0b1eeef4b07ff21e3dce244b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase Commit: 1ed2b8f34e00295f1228650fec879df7535b828c https://github.com/galaxyproject/galaxy/commit/1ed2b8f34e00295f1228650fec87… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- replaced pinned-requirements file with s symlink. Commit: 00d48f0814f1893a2da31738f24fb0161e54c1a7 https://github.com/galaxyproject/galaxy/commit/00d48f0814f1893a2da31738f24f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add the missing pyjwkest requirement to pipfile. Commit: d01be5d51d266c2afae729ad41bfaecc566e74cf https://github.com/galaxyproject/galaxy/commit/d01be5d51d266c2afae729ad41bf… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Create `set_random_password` function in galaxy user. Commit: 484f5f6ec1bc44077fac4291d4868bb871a2392a https://github.com/galaxyproject/galaxy/commit/484f5f6ec1bc44077fac4291d486… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/galaxy.yml.sample A config/oidc_backends_config.xml.sample A config/oidc_config.xml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt A lib/galaxy/dependencies/requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml A lib/galaxy/webapps/galaxy/controllers/authnz.py M templates/user/login.mako Log Message: ----------- Merge pull request #4474 from VJalili/oauth2-after-rebase User authentication using OpenID Connect protocol Compare: https://github.com/galaxyproject/galaxy/compare/ed72b94e1e3a...484f5f6ec1bc

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