Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f88c8c3983a07d90363d7656611fe12367876bae https://github.com/galaxyproject/galaxy/commit/f88c8c3983a07d90363d7656611fe... Author: vahid jalili.vahid@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/b593368e0772e49788784cfa6f54c... Author: vahid jalili.vahid@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/6aa59d133e7315d4b3bc8c2188dd7... Author: vahid jalili.vahid@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/fbb28b93bdfa348dca2fd14d33f68... Author: vahid jalili.vahid@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/a9ea8d5621fbf355623fdb2aad42c... Author: vahid jalili.vahid@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/a66bf826fcb14227ef9041cd8572c... Author: vahid jalili.vahid@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/432b551d060ff5dd27416c94f5a2c... Author: vahid jalili.vahid@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/3a90758f62e1b73ba2284e5307319... Author: vahid jalili.vahid@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/57f5a5f645345508f7aac856f7d34... Author: vahid jalili.vahid@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/a8705f9dcd1ca1f7b88fc6d9b58e0... Author: vahid jalili.vahid@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/5f55f561905334f98ca56060dd4ff... Author: vahid jalili.vahid@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/41cc0dcd1bbd448406257cbf184c1... Author: vahid jalili.vahid@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/d355108334c134eba950cac286ce7... Author: vahid jalili.vahid@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/2e4e28e29610c88de21f49805706f... Author: vahid jalili.vahid@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/c027e31a5b4167ac8f3c225f43631... Author: vahid jalili.vahid@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/2326add5023827ff15f38ad97bf7c... Author: vahid jalili.vahid@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/7ba12a1ddc6b5c0fa9c214dc00376... Author: vahid jalili.vahid@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/7c0cc5eac7f851df6e108c94d41db... Author: vahid jalili.vahid@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/9dc040366e8ce0dea72734fae5bae... Author: vahid jalili.vahid@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/734a0058afa2f19990bb903496598... Author: vahid jalili.vahid@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/64d1cd8cab341512c74a47bf92930... Author: vahid jalili.vahid@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/14816031988379ae233f0f7b738f1... Author: vahid jalili.vahid@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/7ae287d884b626d0a6160b2044857... Author: vahid jalili.vahid@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/f622206faadad8916951cf2a19dca... Author: vahid jalili.vahid@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/bd2c30b8173c185eb0c7ede48aab2... Author: vahid jalili.vahid@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/e0199f270082a655f742cc6ca0410... Author: vahid jalili.vahid@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/0e5589776646311e169d85830a6cc... Author: vahid jalili.vahid@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/3714a926ad09c49389bbd7fc4998f... Author: vahid jalili.vahid@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/875a79ae660a3f763040a5216cd9e... Author: vahid jalili.vahid@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/9087debcc4f4f6c39189477bf98c7... Author: vahid jalili.vahid@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/fe41dcb38014c85354db387ce6b0a... Author: vahid jalili.vahid@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/df2cf940c68ae7910faf21f0d308b... Author: vahid jalili.vahid@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/6f50966ec05f3406b398431f666d1... Author: vahid jalili.vahid@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/18c0130df9b589e375cb4faefd879... Author: vahid jalili.vahid@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/80718cdc4d2d5936dc7fcad7bb120... Author: vahid jalili.vahid@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/f2150af7485632a57b725d4943f3d... Author: vahid jalili.vahid@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/4829f2defd217d157298682072433... Author: vahid jalili.vahid@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/55c0b4bc01c724a0350097e382850... Author: vahid jalili.vahid@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/81483754bc3d859f306a012be098f... Author: vahid jalili.vahid@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/9205cf25b7064fcd310b1c229a00e... Author: vahid jalili.vahid@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/5d8b8e1ef306c7ad6d32b42b52ed5... Author: vahid jalili.vahid@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/e6bb39d4492e1cf70e7bbe0dfdce6... Author: vahid jalili.vahid@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/6734638aab3263075c5a664dc9df2... Author: vahid jalili.vahid@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/bef0ad90e8aedc9ed538682ac5a5a... Author: vahid jalili.vahid@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/071e1743edb35d560d2afe0b5216c... Author: vahid jalili.vahid@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/9c3ec350511a33d005480fd50d5b7... Author: vahid jalili.vahid@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/ed0d2d46cbbf5e8c5d7926e051c0b... Author: vahid jalili.vahid@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/3352c3e3b811b170845d2ee3841f0... Author: vahid jalili.vahid@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/6238849f0741e1b15a73686dc18cd... Author: vahid jalili.vahid@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/88dc7e3c9fd43fd8754839c9cf6f0... Author: vahid jalili.vahid@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/7c1a8462e5a4c815286b7756507af... Author: vahid jalili.vahid@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/b8704f8c6e417c7c205e5d6207bba... Author: vahid jalili.vahid@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/cd6b93470ade00025805a56a8ca4a... Author: vahid jalili.vahid@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/04cb179ea5ba055be603ca156e495... Author: vahid jalili.vahid@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/54f3033d8a1c9fe52f37e45d710af... Author: vahid jalili.vahid@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/1a10718e9d07816af6018df639723... Author: vahid jalili.vahid@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/bd46767c77b5b29ff3c18b2c9750a... Author: vahid jalili.vahid@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/6f27d09d69cca11b1873ecbdfad2c... Author: vahid jalili.vahid@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/d39c9c3aca6c4a7ddb07fd139584d... Author: vahid jalili.vahid@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/3cb9fd0f713e8e7984497bacacfc6... Author: vahid jalili.vahid@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/98e840845611d53d1a5e4c34fe0c0... Author: vahid jalili.vahid@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/61bbddefed51aa3cb1e806871b33b... Author: vahid jalili.vahid@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/e290feac4d459e98d83d7a8d1ed11... Author: vahid jalili.vahid@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/8eba74c0cdf849c57b4c910991906... Author: vahid jalili.vahid@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/98d591068960372d8346b363513f0... Author: vahid jalili.vahid@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/2c770323cb328fc5aae9af7704eb9... Author: vahid jalili.vahid@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/5f7206ac2bdec3e4180901302b6c4... Author: vahid jalili.vahid@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/ae0e173ab5910bc65b35178fe4030... Author: vahid jalili.vahid@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/35482fd3f028976810172ca129f28... Author: vahid jalili.vahid@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/55362e46f8f4946a33093651d074a... Author: vahid jalili.vahid@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/b3c1f3cf5180d583552ff95ac24af... Author: vahid jalili.vahid@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/dec858f88a641eae58c633ff31581... Author: vahid jalili.vahid@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/55cb550abf97d0a66e1e85d5bc279... Author: vahid jalili.vahid@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/54374aed02085ade8526f945b5dc8... Author: vahid jalili.vahid@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/9151c0dde211c09e8f537a208545f... Author: vahid jalili.vahid@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/3104ae1443f04c3c0f429e577baf2... Author: vahid jalili.vahid@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/bdb2c3e97a77fea21b4c15c684561... Author: vahid jalili.vahid@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/ba5312f6197a80845923ce590098a... Author: vahid jalili.vahid@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/40609a81f20b179da43021e9e23fc... Author: vahid jalili.vahid@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/0d0493e5b2478c94a56f651181d76... Author: vahid jalili.vahid@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/467467093030b693642815e33f26d... Author: vahid jalili.vahid@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/2e0e049117e42a409e1b794d58e46... Author: vahid jalili.vahid@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/8d6669f36ad1fdd77e3e2e992347f... Author: vahid jalili.vahid@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/d5a295b6883170c9a774462f6bb83... Author: vahid jalili.vahid@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/60d2794f3021457149fda16f4f40b... Author: vahid jalili.vahid@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/ed77f128e34b8ef7d8dacd1c25fdd... Author: vahid jalili.vahid@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/7249a1c10a13a42d71bd103b5b12c... Author: vahid jalili.vahid@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/a1b9842d5ffcc8bf84746e5586466... Author: vahid jalili.vahid@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/794746e5d4f4de73d36e84b9c169d... Author: vahid jalili.vahid@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/e168eaf9e3ce796f2eb5cca252acd... Author: vahid jalili.vahid@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/009248b583b131232d863120c34d1... Author: vahid jalili.vahid@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/d2ad5692f4573826e8386d25c4429... Author: vahid jalili.vahid@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/0623793d71b03e0c097d4018480a8... Author: vahid jalili.vahid@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/0663e570789b354850585d7d7bc3e... Author: vahid jalili.vahid@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/e9ba0b9f3cb27a6afecb5d506361b... Author: vahid jalili.vahid@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/aa076533459b3a2b9e58b471a9a56... Author: vahid jalili.vahid@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/ba05d28a07c8c59a229dd812d61f9... Author: vahid jalili.vahid@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/33f2a8f0eab2233ba6550d90ccd7e... Author: vahid jalili.vahid@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/ab130f73719f235e1e45b76431c24... Author: vahid jalili.vahid@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/cb4645fd198073fc408b6513cac2c... Author: vahid jalili.vahid@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/cd9783e9f15d1e476bcc2e5462644... Author: vahid jalili.vahid@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/b086802f22ddcaa090edfdb677e8a... Author: vahid jalili.vahid@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/10e805328341a4e3755ff3a994f97... Author: vahid jalili.vahid@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.
Commit: c05c3c1c2325a2c51db3d194b6b7f34d999bfe89 https://github.com/galaxyproject/galaxy/commit/c05c3c1c2325a2c51db3d194b6b7f... Author: vahid jalili.vahid@gmail.com Date: 2017-12-18 (Mon, 18 Dec 2017)
Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh R .ci/flake8_wrapper_imports.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M Makefile M README.rst A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M 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test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/test_security_helper.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py A test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools_support.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 R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import.xml M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joiner.xml M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini
Log Message: ----------- Merge remote-tracking branch '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/0b1219692d58c44a9c50be887c716... Author: vahid jalili.vahid@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/ba18313ae333e5c8c9f343bafab66... Author: vahid jalili.vahid@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/74b27d22176a8c78019c6a5fee841... Author: vahid jalili.vahid@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/294bdf421ffb0f8b0b5076663b357... Author: vahid jalili.vahid@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/b4bdfe5930f7128bb3bb3b7d870ce... Author: vahid jalili.vahid@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/969a2e44dcb01c4518d037c70a734... Author: vahid jalili.vahid@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/6935adc85b870cba7233bc0aeca35... Author: vahid jalili.vahid@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/7552952140e1f064aac80eb729fed... Author: vahid jalili.vahid@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/0b3b7564cf9061e486a09eef56e78... Author: vahid jalili.vahid@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/22b4859dff4834950b0b9ac20817e... Author: vahid jalili.vahid@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/3ae155241629f66060a59b77f3d33... Author: vahid jalili.vahid@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/a17d8ddc15768353a581fd23110fd... Author: vahid jalili.vahid@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/8385954e9d164d3d8a89e979ab236... Author: vahid jalili.vahid@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/2165447f3653ff1235714b123407d... Author: vahid jalili.vahid@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/be1acdc6b6554a2de3ef21551bf4b... Author: vahid jalili.vahid@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/0c85d9030dd65bffe9e118dbede4e... Author: vahid jalili.vahid@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/bc854b0471590c41d348714b69a86... Author: vahid jalili.vahid@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.
Commit: 596ef2755bc08262d30c623fb2993b6fab8aa019 https://github.com/galaxyproject/galaxy/commit/596ef2755bc08262d30c623fb2993... Author: vahid jalili.vahid@gmail.com Date: 2018-01-15 (Mon, 15 Jan 2018)
Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh R .ci/flake8_wrapper_imports.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M Makefile M README.rst A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js R client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/bibtex.js R client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/jquery.complexify.js R client/galaxy/scripts/libs/jquery/jqtouch.js R client/galaxy/scripts/libs/jquery/jquery.cookie.js R client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/jquery/jquery.migrate.js R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js R client/galaxy/scripts/libs/raven.js R client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.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-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M 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client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.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/job-dag.js A client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js A client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js A client/galaxy/scripts/mvc/library/library-util.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M 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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/trackster/util.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/scripts/viz/viz_views.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less M client/galaxy/style/less/history.less R client/galaxy/style/less/iphone.less M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less A client/galaxy/style/less/theme/plain.less M client/galaxy/style/less/trackster.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js M client/grunt-tasks/style.js R client/grunt-tasks/webpack.js A client/gulpfile.js A client/karma.config.js R client/package-lock.json M client/package.json R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M client/webpack.config.js A client/yarn.lock M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/error_report.yml.sample R config/external_service_types_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/lmod_modules_mapping.yml.sample M config/local_conda_mapping.yml.sample M config/object_store_conf.xml.sample M config/openid_conf.xml.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/components/model.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/client/views/description.js M 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config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot-edit.js A config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js M config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/plugins/visualizations/scatterplot/webpack.config.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M config/user_preferences_extra_conf.yml.sample M config/workflow_schedulers_conf.xml.sample M contrib/galaxy.fedora-init M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M create_db.sh M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/schema_template.md A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md M doc/source/admin/reports.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/api/quickstart.rst M doc/source/conf.py A doc/source/dev/finding_and_improving_slow_code.rst M doc/source/project/issues.rst A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst M doc/source/releases/index.rst M doc/source/slideshow/architecture/galaxy_architecture.md R external_service_types/454_life_sciences.xml R external_service_types/applied_biosystems_solid.xml R external_service_types/pacific_biosciences_smrt_portal.xml R external_service_types/simple_unknown_sequencer.xml M extract_dataset_parts.sh M lib/galaxy/__init__.py A lib/galaxy/actions/library.py M lib/galaxy/app.py M 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Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase
# Conflicts: # lib/galaxy/dependencies/pinned-requirements.txt
Commit: 1e8e60a54596ed5be398321f33479d5a6ef502b8 https://github.com/galaxyproject/galaxy/commit/1e8e60a54596ed5be398321f33479... Author: vahid jalili.vahid@gmail.com Date: 2018-01-15 (Mon, 15 Jan 2018)
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static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/router.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/zh/locale.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/style/blue/base.css M static/style/blue/library.css M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M 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/3afc67d3b4ffe214659262a8a0d6e... Author: Vahid VJalili@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/cd924854a888bf4fce2208247e8cc... Author: Vahid VJalili@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/1502e0dabd9321d9cfa5345820ec7... Author: vahid jalili.vahid@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/d85c35456012eae9b31bcfa7c29d9... Author: vahid jalili.vahid@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/f06d79355aa8ebba7814ca418b186... Author: vahid jalili.vahid@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/b88339e74f2133a3b94cc99a76886... Author: vahid jalili.vahid@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/2a6f6e18812b23b5d00f8fd68dafd... Author: vahid jalili.vahid@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/0f4ec2ffc5e3a5ba7650ef438f304... Author: vahid jalili.vahid@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/cab0b48be397d2326b5c98d1c763c... Author: vahid jalili.vahid@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/8980e82a6d29c7051ad97777fd0c3... Author: vahid jalili.vahid@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/26c91f2d3a3dd01925cd56565e515... Author: vahid jalili.vahid@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/218b88e02e8939fd1c85813aa9e85... Author: vahid jalili.vahid@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/4e7b39e7a4c46e6b60bf24575d6df... Author: vahid jalili.vahid@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/b951bb2a7b2d7ec0ea89e792bd7ab... Author: vahid jalili.vahid@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/3c4ceb02a217b0bc2468cb36e3562... Author: vahid jalili.vahid@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/a992d1f306b655145de123b6b28d6... Author: vahid jalili.vahid@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/d1ac81983bf37f04d91202d945c35... Author: vahid jalili.vahid@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/c7ab4e2213a19b14604fd58c88422... Author: vahid jalili.vahid@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/362cfcad4045dc582fd036e659cb2... Author: Vahid VJalili@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/68acf98919efa77612232ee4016a0... Author: vahid jalili.vahid@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.
Commit: 2f479e17da67ab71e646d66c06f200c814ca33d9 https://github.com/galaxyproject/galaxy/commit/2f479e17da67ab71e646d66c06f20... Author: vahid jalili.vahid@gmail.com Date: 2018-01-18 (Thu, 18 Jan 2018)
Changed paths: M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/tool/tool-form.js R config/galaxy.ini.sample A config/galaxy.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M templates/webapps/galaxy/history/display_structured.mako M test/base/driver_util.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/multi_output_recurse.xml M test/functional/tools/samples_tool_conf.xml A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/tools/test_collect_primary_datasets.py M tools/data_source/microbial_import_code.py
Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase
# Conflicts: # config/galaxy.ini.sample
Commit: 181d86f3bd97317b260d54861b758c63e3f01f37 https://github.com/galaxyproject/galaxy/commit/181d86f3bd97317b260d54861b758... Author: vahid jalili.vahid@gmail.com Date: 2018-01-18 (Thu, 18 Jan 2018)
Changed paths: M config/galaxy.yml.sample
Log Message: ----------- Add OIDC configuration to the new galaxy.yml.sample file.
Commit: 5c13e50e93e22d6ca16288045bba9dceb1606896 https://github.com/galaxyproject/galaxy/commit/5c13e50e93e22d6ca16288045bba9... Author: vahid jalili.vahid@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/ba3eaec96ab2038021a45bc6decf8... Author: vahid jalili.vahid@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`.
Commit: 6ea87b5d064763f28ef66d83a8a59c3176f4a03f https://github.com/galaxyproject/galaxy/commit/6ea87b5d064763f28ef66d83a8a59... Author: Vahid VJalili@users.noreply.github.com Date: 2018-02-21 (Wed, 21 Feb 2018)
Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/menu.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js A client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/utils/localization.js M client/galaxy/style/less/base.less A client/galaxy/style/less/charts.less M 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test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/fail_writing_work_dir_file.xml A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R 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/654206ec9dd1133c6f455b0efedc8... Author: vjalili jalili.vahid@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/6dcdcc40d59f10778a4dd7f2e93a3... Author: vjalili jalili.vahid@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/730b931b871d447d9bc4ebe465a0e... Author: vjalili jalili.vahid@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/ea0ebd849f3c62806dff9499ebd16... Author: vjalili jalili.vahid@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/f634c40ad480775f56029290ce618... Author: vjalili jalili.vahid@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 config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_metrics_conf.xml.sample A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/tour_generator/__init__.py M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/galaxy_options.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/model/orm/engine_factory.py 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 lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py A lib/galaxy/util/create_history_template.py M lib/galaxy/util/inflection.py M lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/resource_parser.py M 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/320cf473662af7e9a11b40aca160e... Author: vjalili jalili.vahid@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/6b998e66fdc4d4d482b05e2304067... Author: vjalili jalili.vahid@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/60e936cf426bfc729693cb76d310e... Author: vjalili jalili.vahid@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/5ffaf9fae546957ec0ebdd634ee0b... Author: vjalili jalili.vahid@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/259daf1749cd202da233e568e7621... Author: vjalili jalili.vahid@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 client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/charts.less M client/galaxy/style/less/upload.less M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M 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/86e13a51c552abda08b2e2fd4022b... Author: vjalili jalili.vahid@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/1263161e8292f5c494f0236dbf41b... Author: vjalili jalili.vahid@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/7f1e07b19f5a59a801d7f9df0084e... Author: vjalili jalili.vahid@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/cd7e0b1eeef4b07ff21e3dce244b3... Author: vjalili jalili.vahid@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/1ed2b8f34e00295f1228650fec879... Author: vjalili jalili.vahid@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/00d48f0814f1893a2da31738f24fb... Author: vjalili jalili.vahid@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/d01be5d51d266c2afae729ad41bfa... Author: vjalili jalili.vahid@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/484f5f6ec1bc44077fac4291d4868... Author: Martin Cech marten@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