diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4fe9996b9695a1aef92842de301509b4c58556e1 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,7 @@ +- repo: https://github.com/Yelp/detect-secrets.git + #git@github.com:Yelp/detect-secrets + rev: v0.13.0 + hooks: + - id: detect-secrets + args: ['--baseline', '.secrets.baseline'] + # exclude: .*/tests/.* diff --git a/.secrets.baseline b/.secrets.baseline new file mode 100644 index 0000000000000000000000000000000000000000..8637f8a80c4060c5243e95f5a1e09f6896ae9725 --- /dev/null +++ b/.secrets.baseline @@ -0,0 +1,2181 @@ +{ + "exclude": { + "files": "frontend/package-lock.json|^.secrets.baseline$", + "lines": null + }, + "generated_at": "2020-01-10T13:53:44Z", + "plugins_used": [ + { + "name": "AWSKeyDetector" + }, + { + "name": "ArtifactoryDetector" + }, + { + "base64_limit": 3.5, + "name": "Base64HighEntropyString" + }, + { + "name": "BasicAuthDetector" + }, + { + "hex_limit": 3, + "name": "HexHighEntropyString" + }, + { + "name": "JwtTokenDetector" + }, + { + "keyword_exclude": null, + "name": "KeywordDetector" + }, + { + "name": "MailchimpDetector" + }, + { + "name": "PrivateKeyDetector" + }, + { + "name": "SlackDetector" + }, + { + "name": "SoftlayerDetector" + }, + { + "name": "StripeDetector" + } + ], + "results": { + ".gitlab-ci.yml": [ + { + "hashed_secret": "7108e8d092c87038926f21e59c97942d3eb98c63", + "is_secret": false, + "is_verified": false, + "line_number": 29, + "type": "Base64 High Entropy String" + } + ], + ".idea/compiler.xml": [ + { + "hashed_secret": "0b8d01c02f2240b3ee003fad5f363a4fdf43db36", + "is_secret": false, + "is_verified": false, + "line_number": 3, + "type": "Base64 High Entropy String" + } + ], + ".idea/modules.xml": [ + { + "hashed_secret": "e214f6735f68ae8b517a0fb7ea1bcf5999a96cb3", + "is_secret": false, + "is_verified": false, + "line_number": 3, + "type": "Base64 High Entropy String" + } + ], + ".idea/vcs.xml": [ + { + "hashed_secret": "8a5c21bf9d873ea850214c2841dde1c762679fb9", + "is_secret": false, + "is_verified": false, + "line_number": 3, + "type": "Base64 High Entropy String" + } + ], + "CONTRIBUTING.md": [ + { + "hashed_secret": "cd944b0e6673e265b8136de65bc350231cd4ee19", + "is_secret": false, + "is_verified": false, + "line_number": 37, + "type": "Base64 High Entropy String" + } + ], + "backend/build.gradle.kts": [ + { + "hashed_secret": "a8cc3e6575cfcb001213d2d4a539446e338c99f3", + "is_secret": false, + "is_verified": false, + "line_number": 30, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "72f190d7abc405337b349f4d86ce350c5e4527e0", + "is_secret": false, + "is_verified": false, + "line_number": 61, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "30193f9b586d5e62e446374763cc61f7e9cea0cd", + "is_secret": false, + "is_verified": false, + "line_number": 64, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/GermplasmController.java": [ + { + "hashed_secret": "be2d7d4e773b648842c7a3bfd9aceb2eff115a41", + "is_secret": false, + "is_verified": false, + "line_number": 62, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "cd856c7d2fb312ad7f86b753aed6dea369dbfbe6", + "is_secret": false, + "is_verified": false, + "line_number": 87, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/LocationController.java": [ + { + "hashed_secret": "7c8781bb6d329df5d6b4105e6b15d2f223fa9215", + "is_secret": false, + "is_verified": false, + "line_number": 51, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/ObservationVariableController.java": [ + { + "hashed_secret": "b4fda7fe6dab054568e7bef09735e12f78374aa4", + "is_secret": false, + "is_verified": false, + "line_number": 55, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/PhenotypeController.java": [ + { + "hashed_secret": "5d329f70db15153f9b756e1d21eb78bc69690970", + "is_secret": false, + "is_verified": false, + "line_number": 38, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/ProgramController.java": [ + { + "hashed_secret": "558a9d41b9ca2d7971a693a910e573ef841faec5", + "is_secret": false, + "is_verified": false, + "line_number": 63, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/brapi/v1/StudyController.java": [ + { + "hashed_secret": "a894aca407157e8fdf128bd0430a3e95d8b5eafa", + "is_secret": false, + "is_verified": false, + "line_number": 79, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "cbda3d243a0cef3b507c9676b11df75675b74200", + "is_secret": false, + "is_verified": false, + "line_number": 101, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/DataDiscoveryController.java": [ + { + "hashed_secret": "8af6d48a4477835bdc1968cf9af537cee0e160bb", + "is_secret": false, + "is_verified": false, + "line_number": 26, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/GnpISGermplasmController.java": [ + { + "hashed_secret": "bf323cc69121867f99337930dc946edce615f2ab", + "is_secret": false, + "is_verified": false, + "line_number": 28, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/api/faidare/v1/XRefDocumentController.java": [ + { + "hashed_secret": "4bfe834790cf990f01c1f8f482eb8d8e31098781", + "is_secret": false, + "is_verified": false, + "line_number": 32, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/config/MimeMappingServletCustomizer.java": [ + { + "hashed_secret": "3bcfe3365c3b3720606044fefc489c8e0fcaa655", + "is_secret": false, + "is_verified": false, + "line_number": 18, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/config/RestClientConfig.java": [ + { + "hashed_secret": "d62d396f1dc69c7308cba02c0f54a68022e85077", + "is_secret": false, + "is_verified": false, + "line_number": 19, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/GermplasmAttributeCriteria.java": [ + { + "hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825", + "is_secret": false, + "is_verified": false, + "line_number": 19, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/GermplasmAttributeListCriteria.java": [ + { + "hashed_secret": "f9266e68dab0d92d296a03bc40be686705fcddcf", + "is_secret": false, + "is_verified": false, + "line_number": 19, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/GermplasmGETSearchCriteria.java": [ + { + "hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825", + "is_secret": false, + "is_verified": false, + "line_number": 19, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/GermplasmPOSTSearchCriteria.java": [ + { + "hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825", + "is_secret": false, + "is_verified": false, + "line_number": 19, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "38d9070c435d5fc2e1186bf2c4ff4ddd39dc60c7", + "is_secret": false, + "is_verified": false, + "line_number": 34, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/ObservationUnitCriteria.java": [ + { + "hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825", + "is_secret": false, + "is_verified": false, + "line_number": 22, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "921bd972137666fa4e9467b44243e0d5d3cee1fd", + "is_secret": false, + "is_verified": false, + "line_number": 28, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "16446a8fe4999a2dc3381b100b249a63e8bc82af", + "is_secret": false, + "is_verified": false, + "line_number": 38, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "fe4bdf7ff8c0bde6ff4a5fe73c3df64686b59da0", + "is_secret": false, + "is_verified": false, + "line_number": 46, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/criteria/StudySummaryCriteria.java": [ + { + "hashed_secret": "e02307234404d08f6346900b32b17ca90f9c4ed8", + "is_secret": false, + "is_verified": false, + "line_number": 34, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "f98c96dfd0a6ae593449b5dd101af7838d2e4837", + "is_secret": false, + "is_verified": false, + "line_number": 37, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/data/germplasm/GermplasmAttributeValueListVO.java": [ + { + "hashed_secret": "9b4ea0964706f977148ec989e7373d9622613547", + "is_secret": false, + "is_verified": false, + "line_number": 15, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudyDetailVO.java": [ + { + "hashed_secret": "f98c96dfd0a6ae593449b5dd101af7838d2e4837", + "is_secret": false, + "is_verified": false, + "line_number": 27, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/data/study/StudySummaryVO.java": [ + { + "hashed_secret": "e02307234404d08f6346900b32b17ca90f9c4ed8", + "is_secret": false, + "is_verified": false, + "line_number": 24, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "f98c96dfd0a6ae593449b5dd101af7838d2e4837", + "is_secret": false, + "is_verified": false, + "line_number": 24, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/datadiscovery/criteria/DataDiscoveryCriteriaImpl.java": [ + { + "hashed_secret": "d0346392c0a55403e2f845c277b44f3c2dd75356", + "is_secret": false, + "is_verified": false, + "line_number": 29, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/domain/xref/XRefDocumentSearchCriteria.java": [ + { + "hashed_secret": "115a9779753641744ba0e30c3ff8586c823b6f7e", + "is_secret": false, + "is_verified": false, + "line_number": 18, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/repository/es/GermplasmRepositoryImpl.java": [ + { + "hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825", + "is_secret": false, + "is_verified": false, + "line_number": 113, + "type": "Base64 High Entropy String" + } + ], + "backend/src/main/java/fr/inra/urgi/faidare/repository/es/StudyRepositoryImpl.java": [ + { + "hashed_secret": 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"5377075e9f1f3303124270dc429b3592cd642ef8", + "is_secret": false, + "is_verified": false, + "line_number": 95, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "d4e3be43e763c3e766fde194ce789d8737849605", + "is_secret": false, + "is_verified": false, + "line_number": 99, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "dd67dc07fbd13faea9b61655035b2ff0f831dd34", + "is_secret": false, + "is_verified": false, + "line_number": 100, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "649dc3f39fb80e397781867b85350b4c0c943bfa", + "is_secret": false, + "is_verified": false, + "line_number": 118, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "16c8584a6705f6e38f4276ebee046e8c158390c9", + "is_secret": false, + "is_verified": false, + "line_number": 124, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "ef6cb40a0febd446b2cfdfe423f3c21c9928825b", + "is_secret": false, + "is_verified": false, + "line_number": 127, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "2aa4906f7b7b4bd9b89e5968e6e96c6857b1abf0", + "is_secret": false, + "is_verified": false, + "line_number": 128, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "ee2cce11b4c556e7a958eaec001d8d5d646863c9", + "is_secret": false, + "is_verified": false, + "line_number": 130, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "e522b5699211259613ebfbf7a4e2f8c4b98bd197", + "is_secret": false, + "is_verified": false, + "line_number": 131, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "66cae49608281f789250e6bdbd8f1693107591c4", + "is_secret": false, + "is_verified": false, + "line_number": 144, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "2acdddd4d7b888ef8ab0da48dcfefd85bf78ef4d", + "is_secret": false, + "is_verified": false, + "line_number": 147, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": 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"line_number": 164, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "67d30319555e1f5db43ca8fdb1c396764d728f0a", + "is_secret": false, + "is_verified": false, + "line_number": 166, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "af96939de7d02feb09a9c26ba02e0c84bf538dec", + "is_secret": false, + "is_verified": false, + "line_number": 169, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "1b465000db5b4a33305981f63c0aaa66c41ef660", + "is_secret": false, + "is_verified": false, + "line_number": 170, + "type": "Base64 High Entropy String" + } + ] + }, + "version": "0.13.0", + "word_list": { + "file": null, + "hash": null + } +} diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a5d7d2ddaffc191b3ac38931a8a153211cca929d..a304b2e113cef70c1d305120bf2c968d885bb2c5 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -6,50 +6,62 @@ * One stable & protected [master](/) branch * Feature branches for development following the pattern `[dev_type]/[dev_name]` (ie. `chore/explaining_how_to_merge`) where `[dev_type]` can be: - * fix (bug fixes) - * feat (new feature) - * style (style modification) - * refactor (code refactoring) - * chore (base maintenance such as version bump) - * test (for anything related to tests) + * fix (bug fixes) + * feat (new feature) + * style (style modification) + * refactor (code refactoring) + * chore (base maintenance such as version bump) + * test (for anything related to tests) ### Commit & branches merge + * Commit name should follow pattern `[dev_type]: [brief description of the commit, lower than 50 characters]. [JIRA-KEY]` * All branches must be merged via a `merge request` (MR) -* Merge requests should be created at the time of the branch creation in order to allow reviewer to comment and follow the developments, specify the `WIP` tag in the MR name (go further: *[feature highlight WIP](https://about.gitlab.com/2016/01/08/feature-highlight-wip/)*). - Example: - ``` - git checkout -b chore/explaining_how_to_merge - git push --set-upstram origin chore/explaining_how_to_merge - ``` - Returns a link for creating the merge request easily: - ``` - Total 0 (delta 0), reused 0 (delta 0) - remote: - remote: To create a merge request for chore/explaining_how_to_merge, visit: - remote:   https://forgemia.inra.fr/urgi-is/faidare/merge_requests/new?merge_request%5Bsource_branch%5D=chore/explaining_how_to_merge - remote: - To forgemia.inra.fr:urgi-is/faidare.git - * [new branch]      chore/explaining_how_to_merge -> chore/explaining_how_to_merge - La branche 'chore/explaining_how_to_merge' est paramétrée pour suivre la branche distante 'chore/explaining_how_to_merge' depuis 'origin'. - ``` +* Merge requests should be created at the time of the branch creation in order to allow reviewer to comment and follow the developments, specify the `WIP` tag in the MR name (go further: *[feature highlight WIP](https://about.gitlab.com/2016/01/08/feature-highlight-wip/)*). Example: + + ```sh + git checkout -b chore/explaining_how_to_merge + git push --set-upstram origin chore/explaining_how_to_merge + ``` + + Returns a link for creating the merge request easily: + + ```sh + Total 0 (delta 0), reused 0 (delta 0) + remote: + remote: To create a merge request for chore/explaining_how_to_merge, visit: + remote:   https://forgemia.inra.fr/urgi-is/faidare/merge_requests/new?merge_request%5Bsource_branch%5D=chore/explaining_how_to_merge + remote: + To forgemia.inra.fr:urgi-is/faidare.git + * [new branch]      chore/explaining_how_to_merge -> chore/explaining_how_to_merge + La branche 'chore/explaining_how_to_merge' est paramétrée pour suivre la branche distante 'chore/explaining_how_to_merge' depuis 'origin'. + ``` * A `git rebase` is strongly recommanded before merging a MR - * [Git rebase official documentation](https://git-scm.com/book/en/v2/Git-Branching-Rebasing) - * [How to keep a clean history](https://about.gitlab.com/2018/06/07/keeping-git-commit-history-clean/) + * [Git rebase official documentation](https://git-scm.com/book/en/v2/Git-Branching-Rebasing) + * [How to keep a clean history](https://about.gitlab.com/2018/06/07/keeping-git-commit-history-clean/) * Merge requests should be reviewed by at least 2 colleagues * Continuous Integration is launched automatically by Gitlab on each commit push or merge request creation. ## Data management + * Git LFS (look at [how to install](https://git-lfs.github.com/)) feature is enabled on this project in order to store JSON test data * Another dedicated Git LFS project (internal only) will be created to handle all private + public JSON files * **TODO**: refer to the good Git LFS project in the CI settings for indexing the relevant data into the relevant Elasticsearch indices/instances * the JSON files generation will be handled by an external ET (extract/transform) tool. ## Development environment + * Look at the [README.md](README.md) for installation and execution instructions. * Recommanded IDE is [Intellij IDEA](https://www.jetbrains.com/idea/) * Use linting to apply code standards within the team: - * Use `ng lint` (for frontend code only) - * Use [Checkstyle](https://checkstyle.org/) and [PMD](https://pmd.github.io/) (**TODO**: implement) for backend (+frontend?) code + * Use `ng lint` (for frontend code only) + * Use [Checkstyle](https://checkstyle.org/) and [PMD](https://pmd.github.io/) (**TODO**: implement) for backend (+frontend?) code * All runtime variables should be externalized from the code in order to facilitate the CI management (database host/port, application name, public URL, JSON location...) and the adoption by partners +* Configure [Yelp's detect-secrets](https://github.com/Yelp/detect-secrets) pre-commit hook to track any high entropy strings, which could possibly be leaked secrets. + * Run: `pip3 install pre-commit detect-secrets --user && pre-commit install` to configure you dev environment. + * If a secret is detected: + * either fix it (because it must not be committed) + * or run: + * `detect-secrets scan --update .secrets.baseline` to update the secret baseline, then + * `detect-secrets audit .secrets.baseline` to tag it as a false positive if relevant.