[galaxy-commits] [galaxyproject/galaxy] f88c8c: OAuth2.0 initial commit.

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 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 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 client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.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-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/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M 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 client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.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-button.js A client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.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-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/de/locale.js M client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/polyfills.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js A client/galaxy/scripts/qunit/tests/graph_tests.js A client/galaxy/scripts/qunit/tests/hda_base_tests.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job_dag_tests.js A client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics_logger_tests.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_tests.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/popupmenu.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/levenshtein.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/natural-sort.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.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/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 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 M client/grunt-tasks/install-libs.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 M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M client/toolshed/scripts/mvc/groups/group-model.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 config/plugins/visualizations/charts/static/client/views/editor.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js M config/plugins/visualizations/charts/static/client/views/viewer.js M config/plugins/visualizations/charts/static/client/views/viewport.js M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/charts/webpack.config.js R config/plugins/visualizations/scatterplot/Gruntfile.js R config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js R config/plugins/visualizations/scatterplot/src/scatterplot-display.js R config/plugins/visualizations/scatterplot/src/scatterplot-model.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M 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/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/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 lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py A lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py R lib/galaxy/datatypes/converters/bam_to_bai.xml R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml A lib/galaxy/datatypes/converters/cram_to_bam.py A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml 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/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_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/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/454Score.pdf A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/example.iqtree A lib/galaxy/datatypes/test/github88.v3k.sdf A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map A lib/galaxy/datatypes/test/matrix.cool A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/dependencies/dev-requirements.txt R lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/develop/Pipfile A lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock A lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/flake8/Pipfile A lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock A lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt R lib/galaxy/external_services/__init__.py R lib/galaxy/external_services/actions.py R lib/galaxy/external_services/parameters.py R lib/galaxy/external_services/result_handlers/__init__.py R lib/galaxy/external_services/result_handlers/basic.py R lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py R lib/galaxy/jobs/deferred/__init__.py R lib/galaxy/jobs/deferred/data_transfer.py R lib/galaxy/jobs/deferred/manual_data_transfer.py R lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py A lib/galaxy/managers/jobs.py M lib/galaxy/managers/libraries.py A lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py R lib/galaxy/sample_tracking/__init__.py R lib/galaxy/sample_tracking/data_transfer.py R lib/galaxy/sample_tracking/external_service_types.py R lib/galaxy/sample_tracking/request_types.py R lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.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/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py A 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/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/github.py A lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/locations/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/repositories.py M lib/galaxy/tools/toolbox/__init__.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/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.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/tours/__init__.py M lib/galaxy/util/__init__.py R lib/galaxy/util/backports/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/dictifiable.py A lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/image_util.py M lib/galaxy/util/jstree.py R lib/galaxy/util/log/__init__.py R lib/galaxy/util/log/fluent_log.py A lib/galaxy/util/logging/__init__.py A lib/galaxy/util/logging/fluent_log.py A lib/galaxy/util/monitors.py R lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/util/permutations.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/util/sanitize_html.py A lib/galaxy/util/script.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py A lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py R lib/galaxy/web/base/interactive_environments.py R lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/jobs.py R lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py R lib/galaxy/webapps/galaxy/api/request_types.py R lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py R lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_admin.py R lib/galaxy/webapps/galaxy/controllers/library_common.py R lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/page.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/root.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/mimeparse.py M lib/psyco_full.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M manage_db.sh R manage_tools.sh R openid/yahoo.xml M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/copy_hda_to_library_folder.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py R scripts/api/form_create_from_xml.py M scripts/api/library_upload_dir.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py M scripts/api/search.py R scripts/api/sequencer_configuration_create.py M scripts/api/workflow_import.py R scripts/binary_compatibility.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.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 M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M 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/common_startup_functions.sh M scripts/data_libraries/build_lucene_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/dump_tour.py M scripts/edam_mapping.py M scripts/extract_toolbox_sections.py M scripts/fetch_eggs.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py A scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_tool_dependencies.py R scripts/manage_tools.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py M setup.cfg R static/GruntFile.js.map R static/jqtouch/img/backButton.png R static/jqtouch/img/back_button.png R static/jqtouch/img/back_button_clicked.png R static/jqtouch/img/bg_row.gif R static/jqtouch/img/bg_row_select.gif R static/jqtouch/img/blueButton.png R static/jqtouch/img/button.png R static/jqtouch/img/button_clicked.png R static/jqtouch/img/cancel.png R static/jqtouch/img/chevron.png R static/jqtouch/img/chevron_select.png R static/jqtouch/img/grayButton.png R static/jqtouch/img/header.gif R static/jqtouch/img/listGroup.png R static/jqtouch/img/loading.gif R static/jqtouch/img/pinstripes.png R static/jqtouch/img/selection.png R static/jqtouch/img/thumb.png R static/jqtouch/img/toggle.png R static/jqtouch/img/toggleOn.png R static/jqtouch/img/toolButton.png R static/jqtouch/img/toolbar.gif R static/jqtouch/img/toolbar.png R static/jqtouch/img/whiteButton.png R static/jqtouch/jqtouch.css R static/maps/admin.toolshed.js.map R static/maps/analysis.js.map R static/maps/app.js.map R static/maps/app/analysis.js.map R static/maps/galaxy-app-base.js.map R static/maps/galaxy.interactive_environments.js.map R static/maps/galaxy.js.map R static/maps/galaxy.library.js.map R static/maps/galaxy.menu.js.map R static/maps/galaxy.pages.js.map R static/maps/i18n.js.map R static/maps/layout/generic-nav-view.js.map R static/maps/layout/masthead.js.map R static/maps/layout/menu.js.map R static/maps/layout/modal.js.map R static/maps/layout/page.js.map R static/maps/layout/panel.js.map R static/maps/layout/router.js.map R static/maps/layout/scratchbook.js.map R static/maps/libs/backbone.js.map R static/maps/libs/bbi/bigwig.js.map R static/maps/libs/bbi/jquery-ajax-native.js.map R static/maps/libs/bbi/jszlib.js.map R static/maps/libs/bbi/spans.js.map R static/maps/libs/bibtex.js.map R static/maps/libs/bootstrap-tour.js.map R static/maps/libs/bootstrap.js.map R static/maps/libs/common-libs.js.map R static/maps/libs/d3.js.map R static/maps/libs/farbtastic.js.map R static/maps/libs/jquery.complexify.js.map R static/maps/libs/jquery.sparklines.js.map R static/maps/libs/jquery/jqtouch.js.map R static/maps/libs/jquery/jquery-ui.js.map R static/maps/libs/jquery/jquery.autocomplete.js.map R static/maps/libs/jquery/jquery.cookie.js.map R static/maps/libs/jquery/jquery.dynatree.js.map R static/maps/libs/jquery/jquery.event.drag.js.map R static/maps/libs/jquery/jquery.event.drop.js.map R static/maps/libs/jquery/jquery.event.hover.js.map R static/maps/libs/jquery/jquery.form.js.map R static/maps/libs/jquery/jquery.js.map R static/maps/libs/jquery/jquery.migrate.js.map R static/maps/libs/jquery/jquery.mousewheel.js.map R static/maps/libs/jquery/jquery.rating.js.map R static/maps/libs/jquery/jquery.wymeditor.js.map R static/maps/libs/jquery/jstorage.js.map R static/maps/libs/jquery/jstree.js.map R static/maps/libs/jquery/select2.js.map R static/maps/libs/raven.js.map R static/maps/libs/require.js.map R static/maps/libs/showdown.js.map R static/maps/libs/toastr.js.map R static/maps/libs/underscore.js.map R static/maps/mvc/annotation.js.map R static/maps/mvc/base-mvc.js.map R static/maps/mvc/base/controlled-fetch-collection.js.map R static/maps/mvc/citation/citation-model.js.map R static/maps/mvc/citation/citation-view.js.map R static/maps/mvc/collection/base-creator.js.map R static/maps/mvc/collection/collection-li-edit.js.map R static/maps/mvc/collection/collection-li.js.map R static/maps/mvc/collection/collection-model.js.map R static/maps/mvc/collection/collection-view-edit.js.map R static/maps/mvc/collection/collection-view.js.map R static/maps/mvc/collection/list-collection-creator.js.map R static/maps/mvc/collection/list-of-pairs-collection-creator.js.map R static/maps/mvc/collection/pair-collection-creator.js.map R static/maps/mvc/collection/paired-collection-creator.js.map R static/maps/mvc/dataset/data.js.map R static/maps/mvc/dataset/dataset-choice.js.map R static/maps/mvc/dataset/dataset-edit-attributes.js.map R static/maps/mvc/dataset/dataset-error.js.map R static/maps/mvc/dataset/dataset-li-edit.js.map R static/maps/mvc/dataset/dataset-li.js.map R static/maps/mvc/dataset/dataset-list.js.map R static/maps/mvc/dataset/dataset-model.js.map R static/maps/mvc/dataset/states.js.map R static/maps/mvc/form/form-data.js.map R static/maps/mvc/form/form-input.js.map R static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-repeat.js.map R static/maps/mvc/form/form-section.js.map R static/maps/mvc/form/form-view.js.map R static/maps/mvc/form/form-wrapper.js.map R static/maps/mvc/grid/grid-model.js.map R static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/grid/grid-template.js.map R static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/groups/group-detail-view.js.map R static/maps/mvc/groups/group-groupdetail-view.js.map R static/maps/mvc/groups/group-grouprow-view.js.map R static/maps/mvc/groups/group-list-view.js.map R static/maps/mvc/groups/group-listrow-view.js.map R static/maps/mvc/groups/group-model.js.map R static/maps/mvc/groups/group.model.js.map R static/maps/mvc/history/copy-dialog.js.map R static/maps/mvc/history/hda-li-edit.js.map R static/maps/mvc/history/hda-li.js.map R static/maps/mvc/history/hda-model.js.map R static/maps/mvc/history/hdca-li-edit.js.map R static/maps/mvc/history/hdca-li.js.map R static/maps/mvc/history/hdca-model.js.map R static/maps/mvc/history/history-content-model.js.map R static/maps/mvc/history/history-contents.js.map R static/maps/mvc/history/history-list.js.map R static/maps/mvc/history/history-model.js.map R static/maps/mvc/history/history-preferences.js.map R static/maps/mvc/history/history-structure-view.js.map R static/maps/mvc/history/history-view-annotated.js.map R static/maps/mvc/history/history-view-edit-current.js.map R static/maps/mvc/history/history-view-edit.js.map R static/maps/mvc/history/history-view.js.map R static/maps/mvc/history/job-dag.js.map R static/maps/mvc/history/multi-panel.js.map R static/maps/mvc/history/options-menu.js.map R static/maps/mvc/job/job-li.js.map R static/maps/mvc/job/job-model.js.map R static/maps/mvc/job/job-params.js.map R static/maps/mvc/library/library-dataset-view.js.map R static/maps/mvc/library/library-folder-view.js.map R static/maps/mvc/library/library-folderlist-view.js.map R static/maps/mvc/library/library-folderrow-view.js.map R static/maps/mvc/library/library-foldertoolbar-view.js.map R static/maps/mvc/library/library-library-view.js.map R static/maps/mvc/library/library-librarylist-view.js.map R static/maps/mvc/library/library-libraryrow-view.js.map R static/maps/mvc/library/library-librarytoolbar-view.js.map R static/maps/mvc/library/library-model.js.map R static/maps/mvc/list/list-item.js.map R static/maps/mvc/list/list-panel.js.map R static/maps/mvc/list/list-view.js.map R static/maps/mvc/tag.js.map R static/maps/mvc/tool/tool-form-base.js.map R static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form.js.map R static/maps/mvc/tool/tool-genomespace.js.map R static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tool-webhooks.js.map R static/maps/mvc/tool/tools.js.map R static/maps/mvc/toolshed/categories-view.js.map R static/maps/mvc/toolshed/repo-queue-view.js.map R static/maps/mvc/toolshed/repo-status-view.js.map R static/maps/mvc/toolshed/repositories-view.js.map R static/maps/mvc/toolshed/repository-queue-view.js.map R static/maps/mvc/toolshed/repository-view.js.map R static/maps/mvc/toolshed/shed-category-view.js.map R static/maps/mvc/toolshed/shed-list-view.js.map R static/maps/mvc/toolshed/shed-repo-details-view.js.map R static/maps/mvc/toolshed/shed-repo-list-view.js.map R static/maps/mvc/toolshed/sheds-list-view.js.map R static/maps/mvc/toolshed/toolshed-model.js.map R static/maps/mvc/toolshed/util.js.map R static/maps/mvc/toolshed/workflows-view.js.map R static/maps/mvc/tours.js.map R static/maps/mvc/ui/error-modal.js.map R static/maps/mvc/ui/icon-button.js.map R static/maps/mvc/ui/popup-menu.js.map R static/maps/mvc/ui/ui-buttons.js.map R static/maps/mvc/ui/ui-color-picker.js.map R static/maps/mvc/ui/ui-drilldown.js.map R static/maps/mvc/ui/ui-frames.js.map R static/maps/mvc/ui/ui-list.js.map R static/maps/mvc/ui/ui-misc.js.map R static/maps/mvc/ui/ui-modal.js.map R static/maps/mvc/ui/ui-options.js.map R static/maps/mvc/ui/ui-popover.js.map R static/maps/mvc/ui/ui-portlet.js.map R static/maps/mvc/ui/ui-select-content.js.map R static/maps/mvc/ui/ui-select-default.js.map R static/maps/mvc/ui/ui-select-ftp.js.map R static/maps/mvc/ui/ui-select-genomespace.js.map R static/maps/mvc/ui/ui-select-library.js.map R static/maps/mvc/ui/ui-select.js.map R static/maps/mvc/ui/ui-slider.js.map R static/maps/mvc/ui/ui-table.js.map R static/maps/mvc/ui/ui-tabs.js.map R static/maps/mvc/ui/ui-thumbnails.js.map R static/maps/mvc/upload/collection/collection-row.js.map R static/maps/mvc/upload/collection/collection-view.js.map R static/maps/mvc/upload/composite/composite-row.js.map R static/maps/mvc/upload/composite/composite-view.js.map R static/maps/mvc/upload/default/default-row.js.map R static/maps/mvc/upload/default/default-view.js.map R static/maps/mvc/upload/upload-button.js.map R static/maps/mvc/upload/upload-ftp.js.map R static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-settings.js.map R static/maps/mvc/upload/upload-view.js.map R static/maps/mvc/user/change-password.js.map R static/maps/mvc/user/extra-information.js.map R static/maps/mvc/user/manage-user-information.js.map R static/maps/mvc/user/user-custom-builds.js.map R static/maps/mvc/user/user-model.js.map R static/maps/mvc/user/user-preferences.js.map R static/maps/mvc/user/user-quotameter.js.map R static/maps/mvc/visualization/visualization-model.js.map R static/maps/mvc/webhooks.js.map R static/maps/mvc/workflow/workflow-canvas.js.map R static/maps/mvc/workflow/workflow-configure-menu.js.map R static/maps/mvc/workflow/workflow-connector.js.map R static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow-icons.js.map R static/maps/mvc/workflow/workflow-manager.js.map R static/maps/mvc/workflow/workflow-node.js.map R static/maps/mvc/workflow/workflow-terminals.js.map R static/maps/mvc/workflow/workflow-view-data.js.map R static/maps/mvc/workflow/workflow-view-node.js.map R static/maps/mvc/workflow/workflow-view-terminals.js.map R static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map R static/maps/nls/de/locale.js.map R static/maps/nls/es/locale.js.map R static/maps/nls/fr/locale.js.map R static/maps/nls/ja/locale.js.map R static/maps/nls/locale.js.map R static/maps/nls/zh/locale.js.map R static/maps/onload.js.map R static/maps/polyfills.js.map R static/maps/reports_webapp/run_stats.js.map R static/maps/templates/compiled/panel_section.js.map R static/maps/templates/compiled/tool_form.js.map R static/maps/templates/compiled/tool_link.js.map R static/maps/templates/compiled/tool_search.js.map R static/maps/toolshed.groups.js.map R static/maps/ui/autocom_tagging.js.map R static/maps/ui/editable-text.js.map R static/maps/ui/fa-icon-button.js.map R static/maps/ui/filter-control.js.map R static/maps/ui/hoverhighlight.js.map R static/maps/ui/loading-indicator.js.map R static/maps/ui/mode-button.js.map R static/maps/ui/pagination.js.map R static/maps/ui/peek-column-selector.js.map R static/maps/ui/popupmenu.js.map R static/maps/ui/scroll-panel.js.map R static/maps/ui/search-input.js.map R static/maps/utils/add-logging.js.map R static/maps/utils/ajax-queue.js.map R static/maps/utils/async-save-text.js.map R static/maps/utils/config.js.map R static/maps/utils/deferred.js.map R static/maps/utils/graph.js.map R static/maps/utils/levenshtein.js.map R static/maps/utils/localization.js.map R static/maps/utils/metrics-logger.js.map R static/maps/utils/natural-sort.js.map R static/maps/utils/query-string-parsing.js.map R static/maps/utils/uploadbox.js.map R static/maps/utils/utils.js.map R static/maps/viz/bbi-data-manager.js.map R static/maps/viz/circster.js.map R static/maps/viz/phyloviz.js.map R static/maps/viz/sweepster.js.map R static/maps/viz/trackster.js.map R static/maps/viz/trackster/filters.js.map R static/maps/viz/trackster/painters.js.map R static/maps/viz/trackster/slotting.js.map R static/maps/viz/trackster/tracks.js.map R static/maps/viz/trackster/util.js.map R static/maps/viz/visualization.js.map R static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js R static/scripts/analysis.js R static/scripts/app.js R static/scripts/app/analysis.js M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/admin.bundled.js.map A static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/extended.bundled.js A static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js R static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js R static/scripts/bundled/login.bundled.js.map A static/scripts/bundled/masthead.bundled.js A static/scripts/bundled/viz.bundled.js A static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js R static/scripts/galaxy.menu.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/libs/backbone.js M static/scripts/libs/bbi/bigwig.js M static/scripts/libs/bbi/jquery-ajax-native.js M static/scripts/libs/bbi/jszlib.js M static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/bootstrap.js R static/scripts/libs/common-libs.js M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/jquery/jquery-ui.js M static/scripts/libs/jquery/jquery.autocomplete.js A static/scripts/libs/jquery/jquery.complexify.js M static/scripts/libs/jquery/jquery.cookie.js M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/libs/jquery/jquery.event.drag.js M static/scripts/libs/jquery/jquery.event.drop.js M static/scripts/libs/jquery/jquery.event.hover.js M static/scripts/libs/jquery/jquery.form.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/jquery/jquery.mousewheel.js M static/scripts/libs/jquery/jquery.rating.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/libs/jquery/jstorage.js M static/scripts/libs/jquery/jstree.js M static/scripts/libs/jquery/select2.js M static/scripts/libs/raven.js M static/scripts/libs/require.js R static/scripts/libs/showdown.js M static/scripts/libs/toastr.js M static/scripts/libs/underscore.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js R static/scripts/mvc/citation/citation-model.js R static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.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/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js A static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js A static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js A static/scripts/mvc/library/library-util.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-genomespace.js R static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tool-webhooks.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-queue-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js R static/scripts/mvc/toolshed/shed-category-view.js M static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/shed-repo-details-view.js R static/scripts/mvc/toolshed/shed-repo-list-view.js R static/scripts/mvc/toolshed/sheds-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js A static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/change-password.js R static/scripts/mvc/user/extra-information.js R static/scripts/mvc/user/manage-user-information.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/packed M static/scripts/polyfills.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js M static/style/blue/base.css R static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/maps/mvc/groups/group-model.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/forms/create_form.mako R templates/admin/forms/edit_form_definition.mako R templates/admin/forms/grid.mako R templates/admin/forms/view_form_definition.mako R templates/admin/library/grid.mako R templates/admin/library/new_library.mako R templates/admin/package_tool.mako R templates/admin/reload_tool.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako R templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako R templates/admin/tool_shed_repository/initiate_repository_installation.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako A templates/admin/tool_shed_repository/monitor_repository_installation.mako R templates/admin/tool_shed_repository/repair_repository.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako R templates/admin/tool_shed_repository/repository_installation_grid.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/admin/tool_shed_repository/tool_dependencies_grid.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_base.mako M templates/display_common.mako R templates/export_base.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako M templates/js-app.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako R templates/rss.mako R templates/search/index.mako M templates/sharing_base.mako M templates/show_params.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako R templates/webapps/galaxy/admin/toolsheds.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako R templates/webapps/galaxy/external_services/generic_jquery_grid.mako R templates/webapps/galaxy/external_services/generic_json.mako R templates/webapps/galaxy/external_services/json_common.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/citations.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako R templates/webapps/galaxy/history/permissions.mako R templates/webapps/galaxy/history/rename.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R templates/webapps/galaxy/library/common/library_dataset_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_search_results.mako R templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako R templates/webapps/galaxy/mobile/dataset/detail.mako R templates/webapps/galaxy/mobile/dataset/peek.mako R templates/webapps/galaxy/mobile/form.mako R templates/webapps/galaxy/mobile/history/detail.mako R templates/webapps/galaxy/mobile/history/list.mako R templates/webapps/galaxy/mobile/index.mako R templates/webapps/galaxy/mobile/manage_library.mako R templates/webapps/galaxy/mobile/settings.mako R templates/webapps/galaxy/page/create.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako R templates/webapps/galaxy/user/list_users.mako R templates/webapps/galaxy/visualization/create.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/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test-data/1.fastqsanger M test-data/1.fastqsolexa A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab A test-data/selenium-test-notebook.ipynb M test-data/simple_line_alternative.txt M test-data/simple_lines_interleaved.txt M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_configuration.py M test/api/test_dataset_collections.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tools.py A test/api/test_tools_upload.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api.py M test/base/api_util.py A test/base/constants.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/bibtex.xml A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml M test/functional/tools/collection_split_on_column.xml M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml A test/functional/tools/config_vars.xml M test/functional/tools/create_2.xml A test/functional/tools/data_source.py A test/functional/tools/empty_datasets.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/identifier_in_actions.xml M test/functional/tools/metadata.xml A test/functional/tools/output_filter_with_input.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml A test/functional/twilltestcase.py M test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/tour_generator A test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml M test/galaxy_selenium/sizzle.py A test/galaxy_selenium/smart_components.py A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py A test/integration/test_data_manager_table_reload.py M test/integration/test_job_resubmission.py A test/integration/test_local_job_cancellation.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_mules_as_job_handlers.py M test/integration/test_resolvers.py M test/integration/test_upload_configuration_options.py M test/integration/test_workflow_handler_configuration.py A test/integration/test_workflow_scheduling_options.py A test/integration/tool_sheds_conf.xml M test/manual/workflows_scaling.py R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-qunit-1.0.0.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py A test/selenium_tests/test_custom_builds.py A test/selenium_tests/test_history_copy_elements.py M test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_multi_view.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_panel_collections.py A test/selenium_tests/test_history_panel_pagination.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py M test/selenium_tests/test_login.py A test/selenium_tests/test_navigates_galaxy.py A test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py A test/selenium_tests/test_saved_histories.py A test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/shed_functional/functional_tests.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/__init__.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/dataset_collections/test_matching.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M 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 client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.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-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/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M 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 client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.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-button.js A client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.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-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/de/locale.js M client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/polyfills.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js A client/galaxy/scripts/qunit/tests/graph_tests.js A client/galaxy/scripts/qunit/tests/hda_base_tests.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job_dag_tests.js A client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics_logger_tests.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_tests.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/ui/popupmenu.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/levenshtein.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/natural-sort.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.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/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 config/plugins/visualizations/charts/static/client/views/editor.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js M config/plugins/visualizations/charts/static/client/views/viewer.js M config/plugins/visualizations/charts/static/client/views/viewport.js M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/charts/webpack.config.js R config/plugins/visualizations/scatterplot/Gruntfile.js R config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js R config/plugins/visualizations/scatterplot/src/scatterplot-display.js R config/plugins/visualizations/scatterplot/src/scatterplot-model.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M 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 lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py A lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py R lib/galaxy/datatypes/converters/bam_to_bai.xml R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml A lib/galaxy/datatypes/converters/cram_to_bam.py A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml 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/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/454Score.pdf A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/example.iqtree A lib/galaxy/datatypes/test/github88.v3k.sdf A lib/galaxy/datatypes/test/infernal_model.cm A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map A lib/galaxy/datatypes/test/matrix.cool A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/dependencies/dev-requirements.txt R lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/develop/Pipfile A lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock A lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/flake8/Pipfile A lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock A lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt R lib/galaxy/external_services/__init__.py R lib/galaxy/external_services/actions.py R lib/galaxy/external_services/parameters.py R lib/galaxy/external_services/result_handlers/__init__.py R lib/galaxy/external_services/result_handlers/basic.py R lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py R lib/galaxy/jobs/deferred/__init__.py R lib/galaxy/jobs/deferred/data_transfer.py R lib/galaxy/jobs/deferred/manual_data_transfer.py R lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py A lib/galaxy/managers/jobs.py M lib/galaxy/managers/libraries.py A lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py R lib/galaxy/sample_tracking/__init__.py R lib/galaxy/sample_tracking/data_transfer.py R lib/galaxy/sample_tracking/external_service_types.py R lib/galaxy/sample_tracking/request_types.py R lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.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/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py A 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/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/github.py A lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/locations/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/repositories.py M lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/__init__.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/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.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/tours/__init__.py M lib/galaxy/util/__init__.py R lib/galaxy/util/backports/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/dictifiable.py A lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/image_util.py M lib/galaxy/util/jstree.py R lib/galaxy/util/log/__init__.py R lib/galaxy/util/log/fluent_log.py A lib/galaxy/util/logging/__init__.py A lib/galaxy/util/logging/fluent_log.py A lib/galaxy/util/monitors.py R lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/util/permutations.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/util/sanitize_html.py A lib/galaxy/util/script.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py A lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py R lib/galaxy/web/base/interactive_environments.py R lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/jobs.py R lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py R lib/galaxy/webapps/galaxy/api/request_types.py R lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py R lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py R lib/galaxy/webapps/galaxy/controllers/external_service.py R lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_admin.py R lib/galaxy/webapps/galaxy/controllers/library_common.py R lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/page.py R lib/galaxy/webapps/galaxy/controllers/request_type.py R lib/galaxy/webapps/galaxy/controllers/requests.py R lib/galaxy/webapps/galaxy/controllers/requests_admin.py R lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/root.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/mimeparse.py M lib/psyco_full.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M manage_db.sh R manage_tools.sh R openid/yahoo.xml M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/copy_hda_to_library_folder.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py R scripts/api/form_create_from_xml.py M scripts/api/library_upload_dir.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py M scripts/api/search.py R scripts/api/sequencer_configuration_create.py M scripts/api/workflow_import.py R scripts/binary_compatibility.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.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 M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M 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/common_startup_functions.sh M scripts/data_libraries/build_lucene_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/dump_tour.py M scripts/edam_mapping.py M scripts/extract_toolbox_sections.py M scripts/fetch_eggs.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py A scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_tool_dependencies.py R scripts/manage_tools.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py M setup.cfg R static/GruntFile.js.map R static/jqtouch/img/backButton.png R static/jqtouch/img/back_button.png R static/jqtouch/img/back_button_clicked.png R static/jqtouch/img/bg_row.gif R static/jqtouch/img/bg_row_select.gif R static/jqtouch/img/blueButton.png R static/jqtouch/img/button.png R static/jqtouch/img/button_clicked.png R static/jqtouch/img/cancel.png R static/jqtouch/img/chevron.png R static/jqtouch/img/chevron_select.png R static/jqtouch/img/grayButton.png R static/jqtouch/img/header.gif R static/jqtouch/img/listGroup.png R static/jqtouch/img/loading.gif R static/jqtouch/img/pinstripes.png R static/jqtouch/img/selection.png R static/jqtouch/img/thumb.png R static/jqtouch/img/toggle.png R static/jqtouch/img/toggleOn.png R static/jqtouch/img/toolButton.png R static/jqtouch/img/toolbar.gif R static/jqtouch/img/toolbar.png R static/jqtouch/img/whiteButton.png R static/jqtouch/jqtouch.css R static/maps/admin.toolshed.js.map R static/maps/analysis.js.map R static/maps/app.js.map R static/maps/app/analysis.js.map R static/maps/galaxy-app-base.js.map R static/maps/galaxy.interactive_environments.js.map R static/maps/galaxy.js.map R static/maps/galaxy.library.js.map R static/maps/galaxy.menu.js.map R static/maps/galaxy.pages.js.map R static/maps/i18n.js.map R static/maps/layout/generic-nav-view.js.map R static/maps/layout/masthead.js.map R static/maps/layout/menu.js.map R static/maps/layout/modal.js.map R static/maps/layout/page.js.map R static/maps/layout/panel.js.map R static/maps/layout/router.js.map R static/maps/layout/scratchbook.js.map R static/maps/libs/backbone.js.map R static/maps/libs/bbi/bigwig.js.map R static/maps/libs/bbi/jquery-ajax-native.js.map R static/maps/libs/bbi/jszlib.js.map R static/maps/libs/bbi/spans.js.map R static/maps/libs/bibtex.js.map R static/maps/libs/bootstrap-tour.js.map R static/maps/libs/bootstrap.js.map R static/maps/libs/common-libs.js.map R static/maps/libs/d3.js.map R static/maps/libs/farbtastic.js.map R static/maps/libs/jquery.complexify.js.map R static/maps/libs/jquery.sparklines.js.map R static/maps/libs/jquery/jqtouch.js.map R static/maps/libs/jquery/jquery-ui.js.map R static/maps/libs/jquery/jquery.autocomplete.js.map R static/maps/libs/jquery/jquery.cookie.js.map R static/maps/libs/jquery/jquery.dynatree.js.map R static/maps/libs/jquery/jquery.event.drag.js.map R static/maps/libs/jquery/jquery.event.drop.js.map R static/maps/libs/jquery/jquery.event.hover.js.map R static/maps/libs/jquery/jquery.form.js.map R static/maps/libs/jquery/jquery.js.map R static/maps/libs/jquery/jquery.migrate.js.map R static/maps/libs/jquery/jquery.mousewheel.js.map R static/maps/libs/jquery/jquery.rating.js.map R static/maps/libs/jquery/jquery.wymeditor.js.map R static/maps/libs/jquery/jstorage.js.map R static/maps/libs/jquery/jstree.js.map R static/maps/libs/jquery/select2.js.map R static/maps/libs/raven.js.map R static/maps/libs/require.js.map R static/maps/libs/showdown.js.map R static/maps/libs/toastr.js.map R static/maps/libs/underscore.js.map R static/maps/mvc/annotation.js.map R static/maps/mvc/base-mvc.js.map R static/maps/mvc/base/controlled-fetch-collection.js.map R static/maps/mvc/citation/citation-model.js.map R static/maps/mvc/citation/citation-view.js.map R static/maps/mvc/collection/base-creator.js.map R static/maps/mvc/collection/collection-li-edit.js.map R static/maps/mvc/collection/collection-li.js.map R static/maps/mvc/collection/collection-model.js.map R static/maps/mvc/collection/collection-view-edit.js.map R static/maps/mvc/collection/collection-view.js.map R static/maps/mvc/collection/list-collection-creator.js.map R static/maps/mvc/collection/list-of-pairs-collection-creator.js.map R static/maps/mvc/collection/pair-collection-creator.js.map R static/maps/mvc/collection/paired-collection-creator.js.map R static/maps/mvc/dataset/data.js.map R static/maps/mvc/dataset/dataset-choice.js.map R static/maps/mvc/dataset/dataset-edit-attributes.js.map R static/maps/mvc/dataset/dataset-error.js.map R static/maps/mvc/dataset/dataset-li-edit.js.map R static/maps/mvc/dataset/dataset-li.js.map R static/maps/mvc/dataset/dataset-list.js.map R static/maps/mvc/dataset/dataset-model.js.map R static/maps/mvc/dataset/states.js.map R static/maps/mvc/form/form-data.js.map R static/maps/mvc/form/form-input.js.map R static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-repeat.js.map R static/maps/mvc/form/form-section.js.map R static/maps/mvc/form/form-view.js.map R static/maps/mvc/form/form-wrapper.js.map R static/maps/mvc/grid/grid-model.js.map R static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/grid/grid-template.js.map R static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/groups/group-detail-view.js.map R static/maps/mvc/groups/group-groupdetail-view.js.map R static/maps/mvc/groups/group-grouprow-view.js.map R static/maps/mvc/groups/group-list-view.js.map R static/maps/mvc/groups/group-listrow-view.js.map R static/maps/mvc/groups/group-model.js.map R static/maps/mvc/groups/group.model.js.map R static/maps/mvc/history/copy-dialog.js.map R static/maps/mvc/history/hda-li-edit.js.map R static/maps/mvc/history/hda-li.js.map R static/maps/mvc/history/hda-model.js.map R static/maps/mvc/history/hdca-li-edit.js.map R static/maps/mvc/history/hdca-li.js.map R static/maps/mvc/history/hdca-model.js.map R static/maps/mvc/history/history-content-model.js.map R static/maps/mvc/history/history-contents.js.map R static/maps/mvc/history/history-list.js.map R static/maps/mvc/history/history-model.js.map R static/maps/mvc/history/history-preferences.js.map R static/maps/mvc/history/history-structure-view.js.map R static/maps/mvc/history/history-view-annotated.js.map R static/maps/mvc/history/history-view-edit-current.js.map R static/maps/mvc/history/history-view-edit.js.map R static/maps/mvc/history/history-view.js.map R static/maps/mvc/history/job-dag.js.map R static/maps/mvc/history/multi-panel.js.map R static/maps/mvc/history/options-menu.js.map R static/maps/mvc/job/job-li.js.map R static/maps/mvc/job/job-model.js.map R static/maps/mvc/job/job-params.js.map R static/maps/mvc/library/library-dataset-view.js.map R static/maps/mvc/library/library-folder-view.js.map R static/maps/mvc/library/library-folderlist-view.js.map R static/maps/mvc/library/library-folderrow-view.js.map R static/maps/mvc/library/library-foldertoolbar-view.js.map R static/maps/mvc/library/library-library-view.js.map R static/maps/mvc/library/library-librarylist-view.js.map R static/maps/mvc/library/library-libraryrow-view.js.map R static/maps/mvc/library/library-librarytoolbar-view.js.map R static/maps/mvc/library/library-model.js.map R static/maps/mvc/list/list-item.js.map R static/maps/mvc/list/list-panel.js.map R static/maps/mvc/list/list-view.js.map R static/maps/mvc/tag.js.map R static/maps/mvc/tool/tool-form-base.js.map R static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form.js.map R static/maps/mvc/tool/tool-genomespace.js.map R static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tool-webhooks.js.map R static/maps/mvc/tool/tools.js.map R static/maps/mvc/toolshed/categories-view.js.map R static/maps/mvc/toolshed/repo-queue-view.js.map R static/maps/mvc/toolshed/repo-status-view.js.map R static/maps/mvc/toolshed/repositories-view.js.map R static/maps/mvc/toolshed/repository-queue-view.js.map R static/maps/mvc/toolshed/repository-view.js.map R static/maps/mvc/toolshed/shed-category-view.js.map R static/maps/mvc/toolshed/shed-list-view.js.map R static/maps/mvc/toolshed/shed-repo-details-view.js.map R static/maps/mvc/toolshed/shed-repo-list-view.js.map R static/maps/mvc/toolshed/sheds-list-view.js.map R static/maps/mvc/toolshed/toolshed-model.js.map R static/maps/mvc/toolshed/util.js.map R static/maps/mvc/toolshed/workflows-view.js.map R static/maps/mvc/tours.js.map R static/maps/mvc/ui/error-modal.js.map R static/maps/mvc/ui/icon-button.js.map R static/maps/mvc/ui/popup-menu.js.map R static/maps/mvc/ui/ui-buttons.js.map R static/maps/mvc/ui/ui-color-picker.js.map R static/maps/mvc/ui/ui-drilldown.js.map R static/maps/mvc/ui/ui-frames.js.map R static/maps/mvc/ui/ui-list.js.map R static/maps/mvc/ui/ui-misc.js.map R static/maps/mvc/ui/ui-modal.js.map R static/maps/mvc/ui/ui-options.js.map R static/maps/mvc/ui/ui-popover.js.map R static/maps/mvc/ui/ui-portlet.js.map R static/maps/mvc/ui/ui-select-content.js.map R static/maps/mvc/ui/ui-select-default.js.map R static/maps/mvc/ui/ui-select-ftp.js.map R static/maps/mvc/ui/ui-select-genomespace.js.map R static/maps/mvc/ui/ui-select-library.js.map R static/maps/mvc/ui/ui-select.js.map R static/maps/mvc/ui/ui-slider.js.map R static/maps/mvc/ui/ui-table.js.map R static/maps/mvc/ui/ui-tabs.js.map R static/maps/mvc/ui/ui-thumbnails.js.map R static/maps/mvc/upload/collection/collection-row.js.map R static/maps/mvc/upload/collection/collection-view.js.map R static/maps/mvc/upload/composite/composite-row.js.map R static/maps/mvc/upload/composite/composite-view.js.map R static/maps/mvc/upload/default/default-row.js.map R static/maps/mvc/upload/default/default-view.js.map R static/maps/mvc/upload/upload-button.js.map R static/maps/mvc/upload/upload-ftp.js.map R static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-settings.js.map R static/maps/mvc/upload/upload-view.js.map R static/maps/mvc/user/change-password.js.map R static/maps/mvc/user/extra-information.js.map R static/maps/mvc/user/manage-user-information.js.map R static/maps/mvc/user/user-custom-builds.js.map R static/maps/mvc/user/user-model.js.map R static/maps/mvc/user/user-preferences.js.map R static/maps/mvc/user/user-quotameter.js.map R static/maps/mvc/visualization/visualization-model.js.map R static/maps/mvc/webhooks.js.map R static/maps/mvc/workflow/workflow-canvas.js.map R static/maps/mvc/workflow/workflow-configure-menu.js.map R static/maps/mvc/workflow/workflow-connector.js.map R static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow-icons.js.map R static/maps/mvc/workflow/workflow-manager.js.map R static/maps/mvc/workflow/workflow-node.js.map R static/maps/mvc/workflow/workflow-terminals.js.map R static/maps/mvc/workflow/workflow-view-data.js.map R static/maps/mvc/workflow/workflow-view-node.js.map R static/maps/mvc/workflow/workflow-view-terminals.js.map R static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map R static/maps/nls/de/locale.js.map R static/maps/nls/es/locale.js.map R static/maps/nls/fr/locale.js.map R static/maps/nls/ja/locale.js.map R static/maps/nls/locale.js.map R static/maps/nls/zh/locale.js.map R static/maps/onload.js.map R static/maps/polyfills.js.map R static/maps/reports_webapp/run_stats.js.map R static/maps/templates/compiled/panel_section.js.map R static/maps/templates/compiled/tool_form.js.map R static/maps/templates/compiled/tool_link.js.map R static/maps/templates/compiled/tool_search.js.map R static/maps/toolshed.groups.js.map R static/maps/ui/autocom_tagging.js.map R static/maps/ui/editable-text.js.map R static/maps/ui/fa-icon-button.js.map R static/maps/ui/filter-control.js.map R static/maps/ui/hoverhighlight.js.map R static/maps/ui/loading-indicator.js.map R static/maps/ui/mode-button.js.map R static/maps/ui/pagination.js.map R static/maps/ui/peek-column-selector.js.map R static/maps/ui/popupmenu.js.map R static/maps/ui/scroll-panel.js.map R static/maps/ui/search-input.js.map R static/maps/utils/add-logging.js.map R static/maps/utils/ajax-queue.js.map R static/maps/utils/async-save-text.js.map R static/maps/utils/config.js.map R static/maps/utils/deferred.js.map R static/maps/utils/graph.js.map R static/maps/utils/levenshtein.js.map R static/maps/utils/localization.js.map R static/maps/utils/metrics-logger.js.map R static/maps/utils/natural-sort.js.map R static/maps/utils/query-string-parsing.js.map R static/maps/utils/uploadbox.js.map R static/maps/utils/utils.js.map R static/maps/viz/bbi-data-manager.js.map R static/maps/viz/circster.js.map R static/maps/viz/phyloviz.js.map R static/maps/viz/sweepster.js.map R static/maps/viz/trackster.js.map R static/maps/viz/trackster/filters.js.map R static/maps/viz/trackster/painters.js.map R static/maps/viz/trackster/slotting.js.map R static/maps/viz/trackster/tracks.js.map R static/maps/viz/trackster/util.js.map R static/maps/viz/visualization.js.map R static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js R static/scripts/analysis.js R static/scripts/app.js R static/scripts/app/analysis.js M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js R static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js R static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js R static/scripts/galaxy.menu.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/libs/backbone.js M static/scripts/libs/bbi/bigwig.js M static/scripts/libs/bbi/jquery-ajax-native.js M static/scripts/libs/bbi/jszlib.js M static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/bootstrap.js R static/scripts/libs/common-libs.js M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/jquery/jquery-ui.js M static/scripts/libs/jquery/jquery.autocomplete.js A static/scripts/libs/jquery/jquery.complexify.js M static/scripts/libs/jquery/jquery.cookie.js M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/libs/jquery/jquery.event.drag.js M static/scripts/libs/jquery/jquery.event.drop.js M static/scripts/libs/jquery/jquery.event.hover.js M static/scripts/libs/jquery/jquery.form.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/jquery/jquery.mousewheel.js M static/scripts/libs/jquery/jquery.rating.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/libs/jquery/jstorage.js M static/scripts/libs/jquery/jstree.js M static/scripts/libs/jquery/select2.js M static/scripts/libs/raven.js M static/scripts/libs/require.js R static/scripts/libs/showdown.js M static/scripts/libs/toastr.js M static/scripts/libs/underscore.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js R static/scripts/mvc/citation/citation-model.js R static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.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/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js A static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js A static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js A static/scripts/mvc/library/library-util.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-genomespace.js R static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tool-webhooks.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-queue-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js R static/scripts/mvc/toolshed/shed-category-view.js M static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/shed-repo-details-view.js R static/scripts/mvc/toolshed/shed-repo-list-view.js R static/scripts/mvc/toolshed/sheds-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js A static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/change-password.js R static/scripts/mvc/user/extra-information.js R static/scripts/mvc/user/manage-user-information.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/packed M static/scripts/polyfills.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.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/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js M static/style/blue/base.css R static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/maps/mvc/groups/group-model.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js R templates/admin/external_service/common.mako R templates/admin/external_service/create_external_service.mako R templates/admin/external_service/edit_external_service.mako R templates/admin/external_service/grid.mako R templates/admin/external_service/reload_external_service_types.mako R templates/admin/external_service/view_external_service.mako R templates/admin/forms/create_form.mako R templates/admin/forms/edit_form_definition.mako R templates/admin/forms/grid.mako R templates/admin/forms/view_form_definition.mako R templates/admin/library/grid.mako R templates/admin/library/new_library.mako R templates/admin/package_tool.mako R templates/admin/reload_tool.mako R templates/admin/request_type/common.mako R templates/admin/request_type/create_request_type.mako R templates/admin/request_type/edit_request_type.mako R templates/admin/request_type/grid.mako R templates/admin/request_type/request_type_permissions.mako R templates/admin/request_type/view_request_type.mako R templates/admin/requests/grid.mako R templates/admin/requests/reject.mako R templates/admin/requests/rename_datasets.mako R templates/admin/requests/sample_datasets_grid.mako R templates/admin/requests/view_sample_dataset.mako R templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako R templates/admin/tool_shed_repository/initiate_repository_installation.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako A templates/admin/tool_shed_repository/monitor_repository_installation.mako R templates/admin/tool_shed_repository/repair_repository.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako R templates/admin/tool_shed_repository/repository_installation_grid.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/admin/tool_shed_repository/tool_dependencies_grid.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_base.mako M templates/display_common.mako R templates/export_base.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako M templates/js-app.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako R templates/rss.mako R templates/search/index.mako M templates/sharing_base.mako M templates/show_params.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako R templates/webapps/galaxy/admin/toolsheds.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako R templates/webapps/galaxy/external_services/generic_jquery_grid.mako R templates/webapps/galaxy/external_services/generic_json.mako R templates/webapps/galaxy/external_services/json_common.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/citations.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako R templates/webapps/galaxy/history/permissions.mako R templates/webapps/galaxy/history/rename.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R templates/webapps/galaxy/library/common/library_dataset_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_search_results.mako R templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako R templates/webapps/galaxy/mobile/dataset/detail.mako R templates/webapps/galaxy/mobile/dataset/peek.mako R templates/webapps/galaxy/mobile/form.mako R templates/webapps/galaxy/mobile/history/detail.mako R templates/webapps/galaxy/mobile/history/list.mako R templates/webapps/galaxy/mobile/index.mako R templates/webapps/galaxy/mobile/manage_library.mako R templates/webapps/galaxy/mobile/settings.mako R templates/webapps/galaxy/page/create.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/requests/common/add_samples.mako R templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/requests/common/create_request.mako R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako R templates/webapps/galaxy/requests/common/edit_samples.mako R templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/requests/common/index.mako R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako R templates/webapps/galaxy/requests/common/sample_datasets.mako R templates/webapps/galaxy/requests/common/sample_state.mako R templates/webapps/galaxy/requests/common/view_request.mako R templates/webapps/galaxy/requests/common/view_request_history.mako R templates/webapps/galaxy/requests/common/view_sample.mako R templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/requests/common/view_sample_history.mako R templates/webapps/galaxy/requests/find_samples_index.mako R templates/webapps/galaxy/requests/grid.mako R templates/webapps/galaxy/requests/index.mako R templates/webapps/galaxy/user/list_users.mako R templates/webapps/galaxy/visualization/create.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/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test-data/1.fastqsanger M test-data/1.fastqsolexa A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test-data/neostore.zip A test-data/new_element_sort_order.txt A test-data/selenium-test-notebook.ipynb M test-data/simple_line_alternative.txt M test-data/simple_lines_interleaved.txt M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_configuration.py M test/api/test_dataset_collections.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tools.py A test/api/test_tools_upload.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api.py M test/base/api_util.py A test/base/constants.py M test/base/data/test_workflow_1.ga M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/bibtex.xml A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml M test/functional/tools/collection_split_on_column.xml M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/config_vars.xml M test/functional/tools/create_2.xml A test/functional/tools/data_source.py A test/functional/tools/empty_datasets.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/identifier_in_actions.xml M test/functional/tools/job_properties.xml M test/functional/tools/metadata.xml A test/functional/tools/output_filter_with_input.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml A test/functional/twilltestcase.py M test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/tour_generator A test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml M test/galaxy_selenium/sizzle.py A test/galaxy_selenium/smart_components.py A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml A test/integration/test_data_manager_table_reload.py M test/integration/test_job_resubmission.py A test/integration/test_local_job_cancellation.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_mules_as_job_handlers.py M test/integration/test_resolvers.py M test/integration/test_upload_configuration_options.py M test/integration/test_workflow_handler_configuration.py A test/integration/test_workflow_scheduling_options.py A test/integration/tool_sheds_conf.xml M test/manual/workflows_scaling.py R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-qunit-1.0.0.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py A test/selenium_tests/test_custom_builds.py A test/selenium_tests/test_history_copy_elements.py M test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_multi_view.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_panel_collections.py A test/selenium_tests/test_history_panel_pagination.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_login.py A test/selenium_tests/test_navigates_galaxy.py A test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py A test/selenium_tests/test_saved_histories.py A test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/shed_functional/functional_tests.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/__init__.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/dataset_collections/test_matching.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M 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 '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) Changed paths: M .gitignore M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.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/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.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/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/zh/locale.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js 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 M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/user_preferences_extra_conf.yml.sample M doc/source/admin/production.md M doc/source/admin/special_topics/nginx.md M doc/source/api/quickstart.rst M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M scripts/common_startup.sh M scripts/db_shell.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M 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 client/galaxy/style/less/dataset.less M client/galaxy/style/less/galaxy_variables.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/icon-btn.less M client/package.json M client/webpack.config.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced R config/plugins/visualizations/charts/config/charts.xml R config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/client/app.css R config/plugins/visualizations/charts/static/client/app.js R config/plugins/visualizations/charts/static/client/components/model.js R config/plugins/visualizations/charts/static/client/components/screenshot.js R config/plugins/visualizations/charts/static/client/views/description.js R config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/groups.js R config/plugins/visualizations/charts/static/client/views/settings.js R config/plugins/visualizations/charts/static/client/views/viewer.js R config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map R config/plugins/visualizations/charts/static/repository/build/others_example.js R config/plugins/visualizations/charts/static/repository/build/others_example.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/registry.js R config/plugins/visualizations/charts/static/repository/build/registry.js.map R config/plugins/visualizations/charts/static/repository/build/registry.tmp.js R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js R config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js R config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js R config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js R config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/utilities/jobs.js R config/plugins/visualizations/charts/static/repository/utilities/sifjson.js R config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/templates/charts.mako R config/plugins/visualizations/charts/webpack.config.js A config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/common/templates/script_entry_point.mako A config/plugins/visualizations/cytoscape/config/cytoscape.xml A config/plugins/visualizations/cytoscape/package.json A config/plugins/visualizations/cytoscape/src/script.js A config/plugins/visualizations/cytoscape/static/logo.png A config/plugins/visualizations/cytoscape/static/script.js A config/plugins/visualizations/drawrna/config/drawrna.xml A config/plugins/visualizations/drawrna/package.json A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js A config/plugins/visualizations/drawrna/src/script.js A config/plugins/visualizations/drawrna/static/logo.png A config/plugins/visualizations/drawrna/static/script.js A config/plugins/visualizations/example/config/example.xml A config/plugins/visualizations/example/package.json A config/plugins/visualizations/example/src/script.js A config/plugins/visualizations/example/static/logo.png A config/plugins/visualizations/example/static/script.js R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js M config/plugins/visualizations/graphviz/templates/graphviz.mako A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml A config/plugins/visualizations/heatmap/heatmap_default/package.json A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js A config/plugins/visualizations/heatmap/heatmap_default/src/script.js A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/static/script.js A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml A config/plugins/visualizations/jqplot/jqplot_bar/package.json A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png A config/plugins/visualizations/msa/config/msa.xml A config/plugins/visualizations/msa/package.json A config/plugins/visualizations/msa/src/msa.js A config/plugins/visualizations/msa/static/logo.png A config/plugins/visualizations/msa/static/script.js A config/plugins/visualizations/ngl/config/ngl.xml A config/plugins/visualizations/ngl/package.json A config/plugins/visualizations/ngl/src/ngl.js A config/plugins/visualizations/ngl/src/viewer.js A config/plugins/visualizations/ngl/static/logo.png A config/plugins/visualizations/ngl/static/ngl.js A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3/nvd3_bar/package.json A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml A config/plugins/visualizations/phylocanvas/package.json A config/plugins/visualizations/phylocanvas/src/script.js A config/plugins/visualizations/phylocanvas/static/logo.png A config/plugins/visualizations/phylocanvas/static/script.js A config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/pv/package.json A config/plugins/visualizations/pv/src/pv.js A config/plugins/visualizations/pv/static/logo.png A config/plugins/visualizations/pv/static/pv.js M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/visualizations/scatterplot/webpack.config.js A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M config/reports.yml.sample M config/tool_conf.xml.sample M config/tool_shed.yml.sample M config/user_preferences_extra_conf.yml.sample M doc/Makefile M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/webhooks.rst M doc/source/conf.py A doc/source/conf.versioning.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/converters/sam_to_bam.py A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py A lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.phylip M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/merge_collection.xml 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/parameters/sanitize.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/repositories.py A lib/galaxy/tools/tag_collection_from_file.xml 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/xsd/galaxy.xsd M lib/galaxy/util/dictifiable.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/logging/__init__.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.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/base.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py A lib/galaxy/web/framework/helpers/tags.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.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/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.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/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/xml_util.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M scripts/common_startup.sh A scripts/common_startup_variables.sh M scripts/db_shell.py A scripts/dump_library_paths.py M scripts/functional_tests.py A scripts/maintenance.sh R static/scripts/admin.toolshed.js R static/scripts/bundled/admin.bundled.js R static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/extended.bundled.js R static/scripts/bundled/libs.bundled.js R static/scripts/bundled/login.bundled.js R static/scripts/galaxy.interactive_environments.js R static/scripts/galaxy.js R static/scripts/galaxy.library.js R static/scripts/galaxy.pages.js R static/scripts/i18n.js R static/scripts/layout/generic-nav-view.js R static/scripts/layout/masthead.js R static/scripts/layout/menu.js R static/scripts/layout/modal.js R static/scripts/layout/page.js R static/scripts/layout/panel.js R static/scripts/layout/router.js R static/scripts/layout/scratchbook.js R static/scripts/legacy/grid/grid-model.js R static/scripts/legacy/grid/grid-template.js R static/scripts/legacy/grid/grid-view.js R static/scripts/libs/backbone.js R static/scripts/libs/bbi/bigwig.js R static/scripts/libs/bbi/jquery-ajax-native.js R static/scripts/libs/bbi/jszlib.js R static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtexParse.js R static/scripts/libs/bootstrap-tour.js R static/scripts/libs/bootstrap.js R static/scripts/libs/d3.js R static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jquery-ui.js R static/scripts/libs/jquery/jquery.autocomplete.js R static/scripts/libs/jquery/jquery.complexify.js R static/scripts/libs/jquery/jquery.cookie.js R static/scripts/libs/jquery/jquery.dynatree.js R static/scripts/libs/jquery/jquery.event.drag.js R static/scripts/libs/jquery/jquery.event.drop.js R static/scripts/libs/jquery/jquery.event.hover.js R static/scripts/libs/jquery/jquery.form.js R static/scripts/libs/jquery/jquery.js R static/scripts/libs/jquery/jquery.migrate.js R static/scripts/libs/jquery/jquery.mousewheel.js R static/scripts/libs/jquery/jquery.rating.js R static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/jquery/jstorage.js R static/scripts/libs/jquery/jstree.js R static/scripts/libs/jquery/select2.js R static/scripts/libs/raven.js R static/scripts/libs/require.js R static/scripts/libs/toastr.js R static/scripts/libs/underscore.js R static/scripts/mvc/annotation.js R static/scripts/mvc/base-mvc.js R static/scripts/mvc/base/controlled-fetch-collection.js R static/scripts/mvc/collection/base-creator.js R static/scripts/mvc/collection/collection-li-edit.js R static/scripts/mvc/collection/collection-li.js R static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-view-edit.js R static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/collection/list-collection-creator.js R static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/pair-collection-creator.js R static/scripts/mvc/dataset/data.js R static/scripts/mvc/dataset/dataset-choice.js R static/scripts/mvc/dataset/dataset-edit-attributes.js R static/scripts/mvc/dataset/dataset-error.js R static/scripts/mvc/dataset/dataset-li-edit.js R static/scripts/mvc/dataset/dataset-li.js R static/scripts/mvc/dataset/dataset-list.js R static/scripts/mvc/dataset/dataset-model.js R static/scripts/mvc/dataset/states.js R static/scripts/mvc/form/form-data.js R static/scripts/mvc/form/form-input.js R static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-repeat.js R static/scripts/mvc/form/form-section.js R static/scripts/mvc/form/form-view.js R static/scripts/mvc/form/form-wrapper.js R static/scripts/mvc/grid/grid-model.js R static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/grid/grid-template.js R static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/history/copy-dialog.js R static/scripts/mvc/history/hda-li-edit.js R static/scripts/mvc/history/hda-li.js R static/scripts/mvc/history/hda-model.js R static/scripts/mvc/history/hdca-li-edit.js R static/scripts/mvc/history/hdca-li.js R static/scripts/mvc/history/hdca-model.js R static/scripts/mvc/history/history-content-model.js R static/scripts/mvc/history/history-contents.js R static/scripts/mvc/history/history-item-li.js R static/scripts/mvc/history/history-list.js R static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-preferences.js R static/scripts/mvc/history/history-structure-view.js R static/scripts/mvc/history/history-view-annotated.js R static/scripts/mvc/history/history-view-edit-current.js R static/scripts/mvc/history/history-view-edit.js R static/scripts/mvc/history/history-view.js R static/scripts/mvc/history/job-dag.js R static/scripts/mvc/history/job-states-model.js R static/scripts/mvc/history/multi-panel.js R static/scripts/mvc/history/options-menu.js R static/scripts/mvc/job/job-li.js R static/scripts/mvc/job/job-model.js R static/scripts/mvc/job/job-params.js R static/scripts/mvc/lazy/lazy-limited.js R static/scripts/mvc/library/library-dataset-view.js R static/scripts/mvc/library/library-folder-view.js R static/scripts/mvc/library/library-folderlist-view.js R static/scripts/mvc/library/library-folderrow-view.js R static/scripts/mvc/library/library-foldertoolbar-view.js R static/scripts/mvc/library/library-library-view.js R static/scripts/mvc/library/library-librarylist-view.js R static/scripts/mvc/library/library-libraryrow-view.js R static/scripts/mvc/library/library-librarytoolbar-view.js R static/scripts/mvc/library/library-model.js R static/scripts/mvc/library/library-util.js R static/scripts/mvc/list/list-item.js R static/scripts/mvc/list/list-view.js R static/scripts/mvc/tag.js R static/scripts/mvc/tool/tool-form-base.js R static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form.js R static/scripts/mvc/tool/tool-genomespace.js R static/scripts/mvc/tool/tools.js R static/scripts/mvc/toolshed/categories-view.js R static/scripts/mvc/toolshed/repo-queue-view.js R static/scripts/mvc/toolshed/repo-status-view.js R static/scripts/mvc/toolshed/repositories-view.js R static/scripts/mvc/toolshed/repository-queue-view.js R static/scripts/mvc/toolshed/repository-view.js R static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/toolshed-model.js R static/scripts/mvc/toolshed/util.js R static/scripts/mvc/toolshed/workflows-view.js R static/scripts/mvc/tours.js R static/scripts/mvc/ui/error-modal.js R static/scripts/mvc/ui/icon-button.js R static/scripts/mvc/ui/popup-menu.js R static/scripts/mvc/ui/ui-buttons.js R static/scripts/mvc/ui/ui-color-picker.js R static/scripts/mvc/ui/ui-drilldown.js R static/scripts/mvc/ui/ui-frames.js R static/scripts/mvc/ui/ui-list.js R static/scripts/mvc/ui/ui-misc.js R static/scripts/mvc/ui/ui-modal.js R static/scripts/mvc/ui/ui-options.js R static/scripts/mvc/ui/ui-popover.js R static/scripts/mvc/ui/ui-portlet.js R static/scripts/mvc/ui/ui-select-content.js R static/scripts/mvc/ui/ui-select-default.js R static/scripts/mvc/ui/ui-select-ftp.js R static/scripts/mvc/ui/ui-select-genomespace.js R static/scripts/mvc/ui/ui-select-library.js R static/scripts/mvc/ui/ui-select.js R static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/ui/ui-table.js R static/scripts/mvc/ui/ui-tabs.js R static/scripts/mvc/ui/ui-thumbnails.js R static/scripts/mvc/upload/collection/collection-row.js R static/scripts/mvc/upload/collection/collection-view.js R static/scripts/mvc/upload/composite/composite-row.js R static/scripts/mvc/upload/composite/composite-view.js R static/scripts/mvc/upload/default/default-row.js R static/scripts/mvc/upload/default/default-view.js R static/scripts/mvc/upload/upload-button.js R static/scripts/mvc/upload/upload-extension.js R static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-settings.js R static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/user-custom-builds.js R static/scripts/mvc/user/user-model.js R static/scripts/mvc/user/user-preferences.js R static/scripts/mvc/user/user-quotameter.js R static/scripts/mvc/visualization/visualization-model.js R static/scripts/mvc/webhooks.js R static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-connector.js R static/scripts/mvc/workflow/workflow-forms.js R static/scripts/mvc/workflow/workflow-icons.js R static/scripts/mvc/workflow/workflow-manager.js R static/scripts/mvc/workflow/workflow-model.js R static/scripts/mvc/workflow/workflow-node.js R static/scripts/mvc/workflow/workflow-terminals.js R static/scripts/mvc/workflow/workflow-view-data.js R static/scripts/mvc/workflow/workflow-view-node.js R static/scripts/mvc/workflow/workflow-view-terminals.js R static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js R static/scripts/nls/de/locale.js R static/scripts/nls/es/locale.js R static/scripts/nls/fr/locale.js R static/scripts/nls/ja/locale.js R static/scripts/nls/locale.js R static/scripts/nls/zh/locale.js R static/scripts/onload.js R static/scripts/packed R static/scripts/polyfills.js R static/scripts/reports/run_stats.js R static/scripts/toolshed/groups/group-detail-view.js R static/scripts/toolshed/groups/group-list-view.js R static/scripts/toolshed/groups/group-listrow-view.js R static/scripts/toolshed/groups/group-model.js R static/scripts/toolshed/toolshed.groups.js R static/scripts/ui/autocom_tagging.js R static/scripts/ui/editable-text.js R static/scripts/ui/fa-icon-button.js R static/scripts/ui/filter-control.js R static/scripts/ui/hoverhighlight.js R static/scripts/ui/loading-indicator.js R static/scripts/ui/mode-button.js R static/scripts/ui/pagination.js R static/scripts/ui/peek-column-selector.js R static/scripts/ui/popupmenu.js R static/scripts/ui/scroll-panel.js R static/scripts/ui/search-input.js R static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M static/style/blue/base.css M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/user/register.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/bam_native_from_sam.bam A test-data/new_tags_1.txt M test-data/sam_with_header.sam M test/api/test_tools.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/workflows_format_2/converter.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R 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