From 5658c2fee607b1eaa9b6f2299de9d637451c8147 Mon Sep 17 00:00:00 2001 From: SeriousHorncat Date: Mon, 30 Sep 2024 17:37:59 -0500 Subject: [PATCH 1/4] work in progress for upgrading versions; unit tests are failling for an unknown reason, am investigating --- .gitignore | 1 + backend/requirements.txt | 2 +- backend/src/security/security.py | 13 +- frontend/package.json | 12 +- frontend/test/views/AnnotationView.spec.js | 8 +- frontend/yarn.lock | 1177 +++++++++++--------- 6 files changed, 648 insertions(+), 565 deletions(-) diff --git a/.gitignore b/.gitignore index dc1d1762..e440cc6f 100644 --- a/.gitignore +++ b/.gitignore @@ -21,6 +21,7 @@ rosalution-annotation-log.txt* *.graphql **/node_modules/** +**/.vite/** # e2e run captures /system-tests/cypress/downloads diff --git a/backend/requirements.txt b/backend/requirements.txt index c8ed1a04..faf82857 100644 --- a/backend/requirements.txt +++ b/backend/requirements.txt @@ -7,7 +7,7 @@ jq==1.6.0 python-multipart==0.0.7 PyJWT[crypto]==2.8.0 -passlib[bcrypt]==1.7.4 +bcrypt==4.2.0 # dev pytest-cov==4.0.0 diff --git a/backend/src/security/security.py b/backend/src/security/security.py index b9d1faf0..402be971 100644 --- a/backend/src/security/security.py +++ b/backend/src/security/security.py @@ -14,14 +14,14 @@ from fastapi import Depends, HTTPException, Response, status from fastapi.security import SecurityScopes -from passlib.context import CryptContext +import bcrypt from ..dependencies import oauth2_scheme # from ..models.token import TokenData from ..config import Settings, get_settings -pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto") +# pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto") SECURITY_SCOPES = { "pre-clinical-intake": "Pre-Clinical Intake", @@ -56,12 +56,17 @@ def create_access_token( def get_password_hash(password): """Takes the plain password and makes a hash from it using CryptContext""" - return pwd_context.hash(password) + pwd_bytes = password.encode('utf-8') + salt = bcrypt.gensalt() + hashed_password = bcrypt.hashpw(password=pwd_bytes, salt=salt) + return hashed_password def verify_password(plain_password, hashed_password): """This will use the CryptContext to hash the plain password and check against the stored pass hash to verify""" - return pwd_context.verify(plain_password, hashed_password) + password_byte_encoded = plain_password.encode('utf-8') + hashed_password = hashed_password.encode('utf-8') + return bcrypt.checkpw(password=password_byte_encoded, hashed_password=hashed_password) def authenticate_password(user: Optional[dict], password: str): diff --git a/frontend/package.json b/frontend/package.json index f92e5777..1d416a93 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -25,16 +25,16 @@ "vue-router": "4.2.5" }, "devDependencies": { - "@vitejs/plugin-vue": "5.0.5", - "@vitest/coverage-v8": "1.6.0", - "@vitest/ui": "1.6.0", + "@vitejs/plugin-vue": "5.1.4", + "@vitest/coverage-v8": "2.1.1", + "@vitest/ui": "2.1.1", "@vue/test-utils": "2.4.1", "eslint": "8.50.0", "eslint-config-google": "0.14.0", "eslint-plugin-vue": "9.17.0", "happy-dom": "14.12.3", - "sinon": "16.0.0", - "vite": "5.3.2", - "vitest": "1.6.0" + "sinon": "19.0.2", + "vite": "5.4.8", + "vitest": "2.1.1" } } diff --git a/frontend/test/views/AnnotationView.spec.js b/frontend/test/views/AnnotationView.spec.js index 01e05300..253134fc 100644 --- a/frontend/test/views/AnnotationView.spec.js +++ b/frontend/test/views/AnnotationView.spec.js @@ -236,15 +236,15 @@ describe('AnnotationView', () => { }); describe('when an image section has an image', () => { - const initialImageAnnotation = {'file_id': 'fake-image-id-1', 'created_date': 'fake-date'}; - beforeEach(() => { + + + it('allows user to add an image when an image already exists', async () => { + const initialImageAnnotation = {'file_id': 'fake-image-id-1', 'created_date': 'fake-date'}; const annotationsWithNewEvidence = mockAnnotationsForCPAM0002; annotationsWithNewEvidence['GeneHomology_Multi-SequenceAlignment'] = [initialImageAnnotation]; mockAnnotations.returns(annotationsWithNewEvidence); wrapper = getMountedComponent(); - }); - it('allows user to add an image when an image already exists', async () => { const newImageResult = { file_id: 'fake-image-id-2', section: 'GeneHomology_Multi-SequenceAlignment', diff --git a/frontend/yarn.lock b/frontend/yarn.lock index 07e400bf..0c20bd96 100644 --- a/frontend/yarn.lock +++ b/frontend/yarn.lock @@ -7,18 +7,18 @@ resolved "https://registry.yarnpkg.com/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz#bd9154aec9983f77b3a034ecaa015c2e4201f6cf" integrity sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA== -"@ampproject/remapping@^2.2.1": - version "2.2.1" - resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.2.1.tgz#99e8e11851128b8702cd57c33684f1d0f260b630" - integrity 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"https://registry.yarnpkg.com/@babel/helper-string-parser/-/helper-string-parser-7.24.8.tgz#5b3329c9a58803d5df425e5785865881a81ca48d" + integrity sha512-pO9KhhRcuUyGnJWwyEgnRJTSIZHiT+vMD0kPeD+so0l7mxkMT19g3pjY9GTnHySck/hDzq+dtW/4VgnMkippsQ== "@babel/helper-validator-identifier@^7.24.7": version "7.24.7" @@ -30,17 +30,19 @@ resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.23.0.tgz#da950e622420bf96ca0d0f2909cdddac3acd8719" integrity sha512-vvPKKdMemU85V9WE/l5wZEmImpCtLqbnTvqDS2U1fJ96KrxoW7KrXhNsNCblQlg8Ck4b85yxdTyelsMUgFUXiw== -"@babel/parser@^7.24.4": - version "7.24.7" - resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.24.7.tgz#9a5226f92f0c5c8ead550b750f5608e766c8ce85" - integrity sha512-9uUYRm6OqQrCqQdG1iCBwBPZgN8ciDBro2nIOFaiRz1/BCxaI7CNvQbDHvsArAC7Tw9Hda/B3U+6ui9u4HWXPw== +"@babel/parser@^7.25.4": + version "7.25.6" + resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.25.6.tgz#85660c5ef388cbbf6e3d2a694ee97a38f18afe2f" + integrity sha512-trGdfBdbD0l1ZPmcJ83eNxB9rbEax4ALFTF7fN386TMYbeCQbyme5cOEXQhbGXKebwGaB/J52w1mrklMcbgy6Q== + dependencies: + "@babel/types" "^7.25.6" -"@babel/types@^7.24.0": - version "7.24.7" - resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.24.7.tgz#6027fe12bc1aa724cd32ab113fb7f1988f1f66f2" - integrity sha512-XEFXSlxiG5td2EJRe8vOmRbaXVgfcBlszKujvVmWIK/UpywWljQCfzAv3RQCGujWQ1RD4YYWEAqDXfuJiy8f5Q== +"@babel/types@^7.25.4", "@babel/types@^7.25.6": + version "7.25.6" + resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.25.6.tgz#893942ddb858f32ae7a004ec9d3a76b3463ef8e6" + integrity sha512-/l42B1qxpG6RdfYf343Uw1vmDjeNhneUXtzhojE7pDgfpEypmRhI6j1kr17XCVv4Cgl9HdAiQY2x0GwKm7rWCw== dependencies: - "@babel/helper-string-parser" "^7.24.7" + "@babel/helper-string-parser" "^7.24.8" "@babel/helper-validator-identifier" "^7.24.7" to-fast-properties "^2.0.0" @@ -246,43 +248,53 @@ resolved "https://registry.yarnpkg.com/@humanwhocodes/object-schema/-/object-schema-1.2.1.tgz#b520529ec21d8e5945a1851dfd1c32e94e39ff45" integrity sha512-ZnQMnLV4e7hDlUvw8H+U8ASL02SS2Gn6+9Ac3wGGLIe7+je2AeAOxPY+izIPJDfFDb7eDjev0Us8MO1iFRN8hA== +"@isaacs/cliui@^8.0.2": + version "8.0.2" + resolved "https://registry.yarnpkg.com/@isaacs/cliui/-/cliui-8.0.2.tgz#b37667b7bc181c168782259bab42474fbf52b550" + integrity sha512-O8jcjabXaleOG9DQ0+ARXWZBTfnP4WNAqzuiJK7ll44AmxGKv/J2M4TPjxjY3znBCfvBXFzucm1twdyFybFqEA== + dependencies: + string-width "^5.1.2" + string-width-cjs "npm:string-width@^4.2.0" + strip-ansi "^7.0.1" + strip-ansi-cjs "npm:strip-ansi@^6.0.1" + wrap-ansi "^8.1.0" + wrap-ansi-cjs "npm:wrap-ansi@^7.0.0" + "@istanbuljs/schema@^0.1.2": version "0.1.3" resolved "https://registry.yarnpkg.com/@istanbuljs/schema/-/schema-0.1.3.tgz#e45e384e4b8ec16bce2fd903af78450f6bf7ec98" integrity sha512-ZXRY4jNvVgSVQ8DL3LTcakaAtXwTVUxE81hslsyD2AtoXW/wVob10HkOJ1X/pAlcI7D+2YoZKg5do8G/w6RYgA== -"@jest/schemas@^29.6.3": - version "29.6.3" - resolved "https://registry.yarnpkg.com/@jest/schemas/-/schemas-29.6.3.tgz#430b5ce8a4e0044a7e3819663305a7b3091c8e03" - integrity sha512-mo5j5X+jIZmJQveBKeS/clAueipV7KgiX1vMgCxam1RNYiqE1w62n0/tJJnHtjW8ZHcQco5gY85jA3mi0L+nSA== +"@jridgewell/gen-mapping@^0.3.5": + version "0.3.5" + resolved "https://registry.yarnpkg.com/@jridgewell/gen-mapping/-/gen-mapping-0.3.5.tgz#dcce6aff74bdf6dad1a95802b69b04a2fcb1fb36" + integrity sha512-IzL8ZoEDIBRWEzlCcRhOaCupYyN5gdIK+Q6fbFdPDg6HqX6jpkItn7DFIpW9LQzXG6Df9sA7+OKnq0qlz/GaQg== dependencies: - "@sinclair/typebox" "^0.27.8" - -"@jridgewell/gen-mapping@^0.3.0": - version "0.3.3" - resolved "https://registry.yarnpkg.com/@jridgewell/gen-mapping/-/gen-mapping-0.3.3.tgz#7e02e6eb5df901aaedb08514203b096614024098" - integrity sha512-HLhSWOLRi875zjjMG/r+Nv0oCW8umGb0BgEhyX3dDX3egwZtB8PqLnjz3yedt8R5StBrzcg4aBpnh8UA9D1BoQ== - dependencies: - "@jridgewell/set-array" "^1.0.1" + "@jridgewell/set-array" "^1.2.1" 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"https://registry.yarnpkg.com/@nodelib/fs.stat/-/fs.stat-2.0.5.tgz#5bd262af94e9d25bd1e71b05deed44876a222e8b" integrity sha512-RkhPPp2zrqDAQA/2jNhnztcPAlv64XdhIp7a7454A5ovI7Bukxgt7MX7udwAu3zg1DcpPU0rz3VV1SeaqvY4+A== -"@nodelib/fs.walk@^1.2.3", "@nodelib/fs.walk@^1.2.8": +"@nodelib/fs.walk@^1.2.8": version "1.2.8" resolved "https://registry.yarnpkg.com/@nodelib/fs.walk/-/fs.walk-1.2.8.tgz#e95737e8bb6746ddedf69c556953494f196fe69a" integrity sha512-oGB+UxlgWcgQkgwo8GcEGwemoTFt3FIO9ababBmaGwXIoBKZ+GTy0pP185beGg7Llih/NSHSV2XAs1lnznocSg== @@ -324,6 +328,11 @@ resolved "https://registry.yarnpkg.com/@one-ini/wasm/-/wasm-0.1.1.tgz#6013659736c9dbfccc96e8a9c2b3de317df39323" integrity sha512-XuySG1E38YScSJoMlqovLru4KTUNSjgVTIjyh7qMX6aNN5HY5Ct5LhRJdxO79JtTzKfzV/bnWpz+zquYrISsvw== +"@pkgjs/parseargs@^0.11.0": + version "0.11.0" + resolved "https://registry.yarnpkg.com/@pkgjs/parseargs/-/parseargs-0.11.0.tgz#a77ea742fab25775145434eb1d2328cf5013ac33" + integrity 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isexe@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/isexe/-/isexe-2.0.0.tgz#e8fbf374dc556ff8947a10dcb0572d633f2cfa10" @@ -1327,16 +1380,16 @@ istanbul-lib-report@^3.0.0, istanbul-lib-report@^3.0.1: make-dir "^4.0.0" supports-color "^7.1.0" -istanbul-lib-source-maps@^5.0.4: - version "5.0.4" - resolved "https://registry.yarnpkg.com/istanbul-lib-source-maps/-/istanbul-lib-source-maps-5.0.4.tgz#1947003c72a91b6310efeb92d2a91be8804d92c2" - integrity sha512-wHOoEsNJTVltaJp8eVkm8w+GVkVNHT2YDYo53YdzQEL2gWm1hBX5cGFR9hQJtuGLebidVX7et3+dmDZrmclduw== +istanbul-lib-source-maps@^5.0.6: + version "5.0.6" + resolved "https://registry.yarnpkg.com/istanbul-lib-source-maps/-/istanbul-lib-source-maps-5.0.6.tgz#acaef948df7747c8eb5fbf1265cb980f6353a441" + integrity sha512-yg2d+Em4KizZC5niWhQaIomgf5WlL4vOOjZ5xGCmF8SnPE/mDWWXgvRExdcpCgh9lLRRa1/fSYp2ymmbJ1pI+A== dependencies: "@jridgewell/trace-mapping" "^0.3.23" debug "^4.1.1" istanbul-lib-coverage "^3.0.0" -istanbul-reports@^3.1.6: +istanbul-reports@^3.1.7: version "3.1.7" resolved "https://registry.yarnpkg.com/istanbul-reports/-/istanbul-reports-3.1.7.tgz#daed12b9e1dca518e15c056e1e537e741280fa0b" integrity sha512-BewmUXImeuRk2YY0PVbxgKAysvhRPUQE0h5QRM++nVWyubKGV0l8qQ5op8+B2DOmwSe63Jivj0BjkPQVf8fP5g== @@ -1344,6 +1397,15 @@ istanbul-reports@^3.1.6: html-escaper "^2.0.0" istanbul-lib-report "^3.0.0" +jackspeak@^3.1.2: + version "3.4.3" + resolved "https://registry.yarnpkg.com/jackspeak/-/jackspeak-3.4.3.tgz#8833a9d89ab4acde6188942bd1c53b6390ed5a8a" + integrity sha512-OGlZQpz2yfahA/Rd1Y8Cd9SIEsqvXkLVoSw/cgwhnhFMDbsQFeZYoJJ7bIZBS9BcamUW96asq/npPWugM+RQBw== + dependencies: + "@isaacs/cliui" "^8.0.2" + optionalDependencies: + "@pkgjs/parseargs" "^0.11.0" + js-beautify@1.14.9: version "1.14.9" resolved "https://registry.yarnpkg.com/js-beautify/-/js-beautify-1.14.9.tgz#a5db728bc5a0d84d3b1a597c376b29bd4d39c8e5" @@ -1354,11 +1416,6 @@ js-beautify@1.14.9: glob "^8.1.0" nopt "^6.0.0" -js-tokens@^9.0.0: - version "9.0.0" - 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"https://registry.yarnpkg.com/locate-path/-/locate-path-6.0.0.tgz#55321eb309febbc59c4801d931a72452a681d286" @@ -1436,20 +1480,18 @@ lodash@^4.17.21: resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.21.tgz#679591c564c3bffaae8454cf0b3df370c3d6911c" integrity sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg== -loupe@^2.3.6: - version "2.3.6" - resolved "https://registry.yarnpkg.com/loupe/-/loupe-2.3.6.tgz#76e4af498103c532d1ecc9be102036a21f787b53" - integrity sha512-RaPMZKiMy8/JruncMU5Bt6na1eftNoo++R4Y+N2FrxkDVTrGvcyzFTsaGif4QTeKESheMGegbhw6iUAq+5A8zA== - dependencies: - get-func-name "^2.0.0" - -loupe@^2.3.7: - version "2.3.7" - resolved "https://registry.yarnpkg.com/loupe/-/loupe-2.3.7.tgz#6e69b7d4db7d3ab436328013d37d1c8c3540c697" - integrity sha512-zSMINGVYkdpYSOBmLi0D1Uo7JU9nVdQKrHxC8eYlV+9YKK9WePqAlL7lSlorG/U2Fw1w0hTBmaa/jrQ3UbPHtA== +loupe@^3.1.0, loupe@^3.1.1: + version "3.1.1" + resolved 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@@ -1531,25 +1557,17 @@ minimatch@^5.0.1: dependencies: brace-expansion "^2.0.1" -mlly@^1.2.0: - version "1.4.2" - resolved "https://registry.yarnpkg.com/mlly/-/mlly-1.4.2.tgz#7cf406aa319ff6563d25da6b36610a93f2a8007e" - integrity sha512-i/Ykufi2t1EZ6NaPLdfnZk2AX8cs0d+mTzVKuPfqPKPatxLApaBoxJQ9x1/uckXtrS/U5oisPMDkNs0yQTaBRg== +minimatch@^9.0.4: + version "9.0.5" + resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-9.0.5.tgz#d74f9dd6b57d83d8e98cfb82133b03978bc929e5" + integrity sha512-G6T0ZX48xgozx7587koeX9Ys2NYy6Gmv//P89sEte9V9whIapMNF4idKxnW2QtCcLiTWlb/wfCabAtAFWhhBow== dependencies: - acorn "^8.10.0" - pathe "^1.1.1" - pkg-types "^1.0.3" - ufo "^1.3.0" + brace-expansion "^2.0.1" -mlly@^1.4.2, mlly@^1.7.0: - version "1.7.1" - resolved "https://registry.yarnpkg.com/mlly/-/mlly-1.7.1.tgz#e0336429bb0731b6a8e887b438cbdae522c8f32f" - integrity sha512-rrVRZRELyQzrIUAVMHxP97kv+G786pHmOKzuFII8zDYahFBS7qnHh2AlYSl1GAHhaMPCz6/oHjVMcfFYgFYHgA== - dependencies: - acorn "^8.11.3" - pathe "^1.1.2" - pkg-types "^1.1.1" - ufo "^1.5.3" +"minipass@^5.0.0 || ^6.0.2 || ^7.0.0", minipass@^7.1.2: + version "7.1.2" + resolved "https://registry.yarnpkg.com/minipass/-/minipass-7.1.2.tgz#93a9626ce5e5e66bd4db86849e7515e92340a707" + integrity sha512-qOOzS1cBTWYF4BH8fVePDBOO9iptMnGUEZwNc/cMWnTV2nVLZ7VoNWEPHkYczZA0pdoA7dl6e7FL659nX9S2aw== mrmime@^2.0.0: version "2.0.0" @@ -1561,6 +1579,11 @@ ms@2.1.2: resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.2.tgz#d09d1f357b443f493382a8eb3ccd183872ae6009" integrity sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w== +ms@^2.1.3: + version "2.1.3" + resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.3.tgz#574c8138ce1d2b5861f0b44579dbadd60c6615b2" + integrity sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA== + nanoid@^3.3.6: version "3.3.6" resolved "https://registry.yarnpkg.com/nanoid/-/nanoid-3.3.6.tgz#443380c856d6e9f9824267d960b4236ad583ea4c" @@ -1576,16 +1599,16 @@ natural-compare@^1.4.0: resolved "https://registry.yarnpkg.com/natural-compare/-/natural-compare-1.4.0.tgz#4abebfeed7541f2c27acfb29bdbbd15c8d5ba4f7" integrity sha512-OWND8ei3VtNC9h7V60qff3SVobHr996CTwgxubgyQYEpg290h9J0buyECNNJexkFm5sOajh5G116RYA1c8ZMSw== -nise@^5.1.4: - version "5.1.4" - resolved "https://registry.yarnpkg.com/nise/-/nise-5.1.4.tgz#491ce7e7307d4ec546f5a659b2efe94a18b4bbc0" - integrity sha512-8+Ib8rRJ4L0o3kfmyVCL7gzrohyDe0cMFTBa2d364yIrEGMEoetznKJx899YxjybU6bL9SQkYPSBBs1gyYs8Xg== +nise@^6.1.1: + version "6.1.1" + resolved "https://registry.yarnpkg.com/nise/-/nise-6.1.1.tgz#78ea93cc49be122e44cb7c8fdf597b0e8778b64a" + integrity sha512-aMSAzLVY7LyeM60gvBS423nBmIPP+Wy7St7hsb+8/fc1HmeoHJfLO8CKse4u3BtOZvQLJghYPI2i/1WZrEj5/g== dependencies: - "@sinonjs/commons" "^2.0.0" - "@sinonjs/fake-timers" "^10.0.2" - "@sinonjs/text-encoding" "^0.7.1" - just-extend "^4.0.2" - path-to-regexp "^1.7.0" + "@sinonjs/commons" "^3.0.1" + "@sinonjs/fake-timers" "^13.0.1" + "@sinonjs/text-encoding" "^0.7.3" + just-extend "^6.2.0" + path-to-regexp "^8.1.0" nopt@^6.0.0: version "6.0.0" @@ -1594,13 +1617,6 @@ nopt@^6.0.0: dependencies: abbrev "^1.0.0" -npm-run-path@^5.1.0: - version "5.3.0" - resolved "https://registry.yarnpkg.com/npm-run-path/-/npm-run-path-5.3.0.tgz#e23353d0ebb9317f174e93417e4a4d82d0249e9f" - integrity sha512-ppwTtiJZq0O/ai0z7yfudtBpWIoxM8yE6nHi1X47eFR2EWORqfbu6CnPlNsjeN683eT0qG6H/Pyf9fCcvjnnnQ== - dependencies: - path-key "^4.0.0" - nth-check@^2.1.1: version "2.1.1" resolved "https://registry.yarnpkg.com/nth-check/-/nth-check-2.1.1.tgz#c9eab428effce36cd6b92c924bdb000ef1f1ed1d" @@ -1615,13 +1631,6 @@ once@^1.3.0: dependencies: wrappy "1" -onetime@^6.0.0: - version "6.0.0" - resolved "https://registry.yarnpkg.com/onetime/-/onetime-6.0.0.tgz#7c24c18ed1fd2e9bca4bd26806a33613c77d34b4" - integrity sha512-1FlR+gjXK7X+AsAHso35MnyN5KqGwJRi/31ft6x0M194ht7S+rWAvd7PHss9xSKMzE0asv1pyIHaJYq+BbacAQ== - dependencies: - mimic-fn "^4.0.0" - optionator@^0.9.3: version "0.9.3" resolved "https://registry.yarnpkg.com/optionator/-/optionator-0.9.3.tgz#007397d44ed1872fdc6ed31360190f81814e2c64" @@ -1641,13 +1650,6 @@ p-limit@^3.0.2: dependencies: yocto-queue "^0.1.0" -p-limit@^5.0.0: - version "5.0.0" - resolved "https://registry.yarnpkg.com/p-limit/-/p-limit-5.0.0.tgz#6946d5b7140b649b7a33a027d89b4c625b3a5985" - integrity sha512-/Eaoq+QyLSiXQ4lyYV23f14mZRQcXnxfHrN0vCai+ak9G0pp9iEQukIIZq5NccEvwRB8PUnZT0KsOoDCINS1qQ== - dependencies: - yocto-queue "^1.0.0" - p-locate@^5.0.0: version "5.0.0" resolved "https://registry.yarnpkg.com/p-locate/-/p-locate-5.0.0.tgz#83c8315c6785005e3bd021839411c9e110e6d834" @@ -1655,6 +1657,11 @@ p-locate@^5.0.0: dependencies: p-limit "^3.0.2" +package-json-from-dist@^1.0.0: + version "1.0.1" + resolved "https://registry.yarnpkg.com/package-json-from-dist/-/package-json-from-dist-1.0.1.tgz#4f1471a010827a86f94cfd9b0727e36d267de505" + integrity 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source-map-js "^1.2.1" + prelude-ls@^1.2.1: version "1.2.1" resolved "https://registry.yarnpkg.com/prelude-ls/-/prelude-ls-1.2.1.tgz#debc6489d7a6e6b0e7611888cec880337d316396" integrity sha512-vkcDPrRZo1QZLbn5RLGPpg/WmIQ65qoWWhcGKf/b5eplkkarX0m9z8ppCat4mlOqUsWpyNuYgO3VRyrYHSzX5g== -pretty-format@^29.7.0: - version "29.7.0" - resolved "https://registry.yarnpkg.com/pretty-format/-/pretty-format-29.7.0.tgz#ca42c758310f365bfa71a0bda0a807160b776812" - integrity sha512-Pdlw/oPxN+aXdmM9R00JVC9WVFoCLTKJvDVLgmJ+qAffBMxsV85l/Lu7sNx4zSzPyoL2euImuEwHhOXdEgNFZQ== - dependencies: - "@jest/schemas" "^29.6.3" - ansi-styles "^5.0.0" - react-is "^18.0.0" - proto-list@~1.2.1: version "1.2.4" resolved "https://registry.yarnpkg.com/proto-list/-/proto-list-1.2.4.tgz#212d5bfe1318306a420f6402b8e26ff39647a849" @@ -1787,11 +1782,6 @@ queue-microtask@^1.2.2: resolved "https://registry.yarnpkg.com/queue-microtask/-/queue-microtask-1.2.3.tgz#4929228bbc724dfac43e0efb058caf7b6cfb6243" integrity 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+ version "0.2.7" + resolved "https://registry.yarnpkg.com/tinyglobby/-/tinyglobby-0.2.7.tgz#36f583c166ac2d91f47c799d6e2e256fdcfb3a56" + integrity sha512-qFWYeNxBQxrOTRHvGjlRdBamy8JFqu6c0bwRru9leE+q8J72tLtlT0L3v+2T7fbLXN7FGzDNBhXkWiJqHUHD9g== + dependencies: + fdir "^6.4.0" + picomatch "^4.0.2" + +tinypool@^1.0.0: + version "1.0.1" + resolved "https://registry.yarnpkg.com/tinypool/-/tinypool-1.0.1.tgz#c64233c4fac4304e109a64340178760116dbe1fe" + integrity sha512-URZYihUbRPcGv95En+sz6MfghfIc2OJ1sv/RmhWZLouPY0/8Vo80viwPvg3dlaS9fuq7fQMEfgRRK7BBZThBEA== + +tinyrainbow@^1.2.0: + version "1.2.0" + resolved "https://registry.yarnpkg.com/tinyrainbow/-/tinyrainbow-1.2.0.tgz#5c57d2fc0fb3d1afd78465c33ca885d04f02abb5" + integrity sha512-weEDEq7Z5eTHPDh4xjX789+fHfF+P8boiFB+0vbWzpbnbsEr/GRaohi/uMKxg8RZMXnl1ItAi/IUHWMsjDV7kQ== + +tinyspy@^3.0.0: + version "3.0.2" + resolved "https://registry.yarnpkg.com/tinyspy/-/tinyspy-3.0.2.tgz#86dd3cf3d737b15adcf17d7887c84a75201df20a" + integrity sha512-n1cw8k1k0x4pgA2+9XrOkFydTerNcJ1zWCO5Nn9scWHTD+5tp8dghT2x1uduQePZTZgd3Tupf+x9BxJjeJi77Q== to-fast-properties@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/to-fast-properties/-/to-fast-properties-2.0.0.tgz#dc5e698cbd079265bc73e0377681a4e4e83f616e" integrity sha512-/OaKK0xYrs3DmxRYqL/yDc+FxFUVYhDlXMhRmv3z915w2HF1tnN1omB354j8VUGO/hbRzyD6Y3sA7v7GS/ceog== -to-regex-range@^5.0.1: - version "5.0.1" - resolved "https://registry.yarnpkg.com/to-regex-range/-/to-regex-range-5.0.1.tgz#1648c44aae7c8d988a326018ed72f5b4dd0392e4" - integrity sha512-65P7iz6X5yEr1cwcgvQxbbIw7Uk3gOy5dIdtZ4rDveLqhrdJP+Li/Hx6tyK0NEb+2GCyneCMJiGqrADCSNk8sQ== - dependencies: - is-number "^7.0.0" - totalist@^3.0.0: version "3.0.1" resolved "https://registry.yarnpkg.com/totalist/-/totalist-3.0.1.tgz#ba3a3d600c915b1a97872348f79c127475f6acf8" @@ -1994,26 +2054,21 @@ type-check@^0.4.0, type-check@~0.4.0: dependencies: prelude-ls "^1.2.1" -type-detect@4.0.8, type-detect@^4.0.0, type-detect@^4.0.8: +type-detect@4.0.8: version "4.0.8" resolved "https://registry.yarnpkg.com/type-detect/-/type-detect-4.0.8.tgz#7646fb5f18871cfbb7749e69bd39a6388eb7450c" integrity sha512-0fr/mIH1dlO+x7TlcMy+bIDqKPsw/70tVyeHW787goQjhmqaZe10uwLujubK9q9Lg6Fiho1KUKDYz0Z7k7g5/g== +type-detect@^4.1.0: + version "4.1.0" + resolved "https://registry.yarnpkg.com/type-detect/-/type-detect-4.1.0.tgz#deb2453e8f08dcae7ae98c626b13dddb0155906c" + integrity sha512-Acylog8/luQ8L7il+geoSxhEkazvkslg7PSNKOX59mbB9cOveP5aq9h74Y7YU8yDpJwetzQQrfIwtf4Wp4LKcw== + type-fest@^0.20.2: version "0.20.2" resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-0.20.2.tgz#1bf207f4b28f91583666cb5fbd327887301cd5f4" integrity sha512-Ne+eE4r0/iWnpAxD852z3A+N0Bt5RN//NjJwRd2VFHEmrywxf5vsZlh4R6lixl6B+wz/8d+maTSAkN1FIkI3LQ== -ufo@^1.3.0: - version "1.3.1" - resolved "https://registry.yarnpkg.com/ufo/-/ufo-1.3.1.tgz#e085842f4627c41d4c1b60ebea1f75cdab4ce86b" - integrity sha512-uY/99gMLIOlJPwATcMVYfqDSxUR9//AUcgZMzwfSTJPDKzA1S8mX4VLqa+fiAtveraQUBCz4FFcwVZBGbwBXIw== - -ufo@^1.5.3: - version "1.5.3" - resolved "https://registry.yarnpkg.com/ufo/-/ufo-1.5.3.tgz#3325bd3c977b6c6cd3160bf4ff52989adc9d3344" - integrity sha512-Y7HYmWaFwPUmkoQCUIAYpKqkOf+SbVj/2fJJZ4RJMCfZp0rTGwRbzQD+HghfnhKOjL9E01okqz+ncJskGYfBNw== - uri-js@^4.2.2: version "4.4.1" resolved "https://registry.yarnpkg.com/uri-js/-/uri-js-4.4.1.tgz#9b1a52595225859e55f669d928f88c6c57f2a77e" @@ -2026,18 +2081,28 @@ util-deprecate@^1.0.2: resolved "https://registry.yarnpkg.com/util-deprecate/-/util-deprecate-1.0.2.tgz#450d4dc9fa70de732762fbd2d4a28981419a0ccf" integrity sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw== -vite-node@1.6.0: - version "1.6.0" - resolved "https://registry.yarnpkg.com/vite-node/-/vite-node-1.6.0.tgz#2c7e61129bfecc759478fa592754fd9704aaba7f" - integrity sha512-de6HJgzC+TFzOu0NTC4RAIsyf/DY/ibWDYQUcuEA84EMHhcefTUGkjFHKKEJhQN4A+6I0u++kr3l36ZF2d7XRw== +vite-node@2.1.1: + version "2.1.1" + resolved "https://registry.yarnpkg.com/vite-node/-/vite-node-2.1.1.tgz#7d46f623c04dfed6df34e7127711508a3386fa1c" + integrity sha512-N/mGckI1suG/5wQI35XeR9rsMsPqKXzq1CdUndzVstBj/HvyxxGctwnK6WX43NGt5L3Z5tcRf83g4TITKJhPrA== dependencies: cac "^6.7.14" - debug "^4.3.4" - pathe "^1.1.1" - picocolors "^1.0.0" + debug "^4.3.6" + pathe "^1.1.2" vite "^5.0.0" -vite@5.3.2, vite@^5.0.0: +vite@5.4.8: + version "5.4.8" + resolved "https://registry.yarnpkg.com/vite/-/vite-5.4.8.tgz#af548ce1c211b2785478d3ba3e8da51e39a287e8" + integrity sha512-FqrItQ4DT1NC4zCUqMB4c4AZORMKIa0m8/URVCZ77OZ/QSNeJ54bU1vrFADbDsuwfIPcgknRkmqakQcgnL4GiQ== + dependencies: + esbuild "^0.21.3" + postcss "^8.4.43" + rollup "^4.20.0" + optionalDependencies: + fsevents "~2.3.3" + +vite@^5.0.0: version "5.3.2" resolved "https://registry.yarnpkg.com/vite/-/vite-5.3.2.tgz#2f0a8531c71060467ed3e0a205a203f269b6d9c8" integrity sha512-6lA7OBHBlXUxiJxbO5aAY2fsHHzDr1q7DvXYnyZycRs2Dz+dXBWuhpWHvmljTRTpQC2uvGmUFFkSHF2vGo90MA== @@ -2048,31 +2113,30 @@ vite@5.3.2, vite@^5.0.0: optionalDependencies: fsevents "~2.3.3" -vitest@1.6.0: - version "1.6.0" - resolved "https://registry.yarnpkg.com/vitest/-/vitest-1.6.0.tgz#9d5ad4752a3c451be919e412c597126cffb9892f" - integrity sha512-H5r/dN06swuFnzNFhq/dnz37bPXnq8xB2xB5JOVk8K09rUtoeNN+LHWkoQ0A/i3hvbUKKcCei9KpbxqHMLhLLA== - dependencies: - "@vitest/expect" "1.6.0" - "@vitest/runner" "1.6.0" - "@vitest/snapshot" "1.6.0" - "@vitest/spy" "1.6.0" - "@vitest/utils" "1.6.0" - acorn-walk "^8.3.2" - chai "^4.3.10" - debug "^4.3.4" - execa "^8.0.1" - local-pkg "^0.5.0" - magic-string "^0.30.5" - pathe "^1.1.1" - picocolors "^1.0.0" - std-env "^3.5.0" - strip-literal "^2.0.0" - tinybench "^2.5.1" - tinypool "^0.8.3" +vitest@2.1.1: + version "2.1.1" + resolved "https://registry.yarnpkg.com/vitest/-/vitest-2.1.1.tgz#24a6f6f5d894509f10685b82de008c507faacbb1" + integrity sha512-97We7/VC0e9X5zBVkvt7SGQMGrRtn3KtySFQG5fpaMlS+l62eeXRQO633AYhSTC3z7IMebnPPNjGXVGNRFlxBA== + dependencies: + "@vitest/expect" "2.1.1" + "@vitest/mocker" "2.1.1" + "@vitest/pretty-format" "^2.1.1" + "@vitest/runner" "2.1.1" + "@vitest/snapshot" "2.1.1" + "@vitest/spy" "2.1.1" + "@vitest/utils" "2.1.1" + chai "^5.1.1" + debug "^4.3.6" + magic-string "^0.30.11" + pathe "^1.1.2" + std-env "^3.7.0" + tinybench "^2.9.0" + tinyexec "^0.3.0" + tinypool "^1.0.0" + tinyrainbow "^1.2.0" vite "^5.0.0" - vite-node "1.6.0" - why-is-node-running "^2.2.2" + vite-node "2.1.1" + why-is-node-running "^2.3.0" vue-component-type-helpers@1.8.4: version "1.8.4" @@ -2127,14 +2191,32 @@ which@^2.0.1: dependencies: isexe "^2.0.0" -why-is-node-running@^2.2.2: - version "2.2.2" - resolved "https://registry.yarnpkg.com/why-is-node-running/-/why-is-node-running-2.2.2.tgz#4185b2b4699117819e7154594271e7e344c9973e" - integrity sha512-6tSwToZxTOcotxHeA+qGCq1mVzKR3CwcJGmVcY+QE8SHy6TnpFnh8PAvPNHYr7EcuVeG0QSMxtYCuO1ta/G/oA== +why-is-node-running@^2.3.0: + version "2.3.0" + resolved "https://registry.yarnpkg.com/why-is-node-running/-/why-is-node-running-2.3.0.tgz#a3f69a97107f494b3cdc3bdddd883a7d65cebf04" + integrity sha512-hUrmaWBdVDcxvYqnyh09zunKzROWjbZTiNy8dBEjkS7ehEDQibXJ7XvlmtbwuTclUiIyN+CyXQD4Vmko8fNm8w== dependencies: siginfo "^2.0.0" stackback "0.0.2" +"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0": + version "7.0.0" + resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" + integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q== + dependencies: + ansi-styles "^4.0.0" + string-width "^4.1.0" + strip-ansi "^6.0.0" + +wrap-ansi@^8.1.0: + version "8.1.0" + resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-8.1.0.tgz#56dc22368ee570face1b49819975d9b9a5ead214" + integrity sha512-si7QWI6zUMq56bESFvagtmzMdGOtoxfR+Sez11Mobfc7tm+VkUckk9bW2UeffTGVUbOksxmSw0AA2gs8g71NCQ== + dependencies: + ansi-styles "^6.1.0" + string-width "^5.0.1" + strip-ansi "^7.0.1" + wrappy@1: version "1.0.2" resolved "https://registry.yarnpkg.com/wrappy/-/wrappy-1.0.2.tgz#b5243d8f3ec1aa35f1364605bc0d1036e30ab69f" @@ -2154,8 +2236,3 @@ yocto-queue@^0.1.0: version "0.1.0" resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b" integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q== - -yocto-queue@^1.0.0: - version "1.0.0" - resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-1.0.0.tgz#7f816433fb2cbc511ec8bf7d263c3b58a1a3c251" - integrity sha512-9bnSc/HEW2uRy67wc+T8UwauLuPJVn28jb+GtJY16iiKWyvmYJRXVT4UamsAEGQfPohgr2q4Tq0sQbQlxTfi1g== From 73fa5182dce45addb190b6b414fd8a3f53dfe4cf Mon Sep 17 00:00:00 2001 From: SeriousHorncat Date: Tue, 1 Oct 2024 07:23:29 -0500 Subject: [PATCH 2/4] wip for figuring out whats wrong --- frontend/test/views/AnnotationView.spec.js | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/frontend/test/views/AnnotationView.spec.js b/frontend/test/views/AnnotationView.spec.js index 253134fc..0f3de47c 100644 --- a/frontend/test/views/AnnotationView.spec.js +++ b/frontend/test/views/AnnotationView.spec.js @@ -236,15 +236,15 @@ describe('AnnotationView', () => { }); describe('when an image section has an image', () => { - - - it('allows user to add an image when an image already exists', async () => { - const initialImageAnnotation = {'file_id': 'fake-image-id-1', 'created_date': 'fake-date'}; + const initialImageAnnotation = {'file_id': 'fake-image-id-1', 'created_date': 'fake-date'}; + beforeEach(() => { const annotationsWithNewEvidence = mockAnnotationsForCPAM0002; annotationsWithNewEvidence['GeneHomology_Multi-SequenceAlignment'] = [initialImageAnnotation]; mockAnnotations.returns(annotationsWithNewEvidence); wrapper = getMountedComponent(); + }); + it('allows user to add an image when an image already exists', async () => { const newImageResult = { file_id: 'fake-image-id-2', section: 'GeneHomology_Multi-SequenceAlignment', @@ -252,6 +252,10 @@ describe('AnnotationView', () => { annotationAttachMock.returns([initialImageAnnotation, newImageResult]); + const lookingFor = wrapper.findAllComponents(SectionImage); + + // expect(lookingFor.length).to.equal(1); + const annotationSection = wrapper.findComponent('[id=Gene_Homology]'); annotationSection.vm.$emit('attach-image', 'GeneHomology_Multi-SequenceAlignment', 'hgvs_variant'); From d2d52bb7585217e11917570ebc8965364c9491c2 Mon Sep 17 00:00:00 2001 From: SeriousHorncat Date: Tue, 1 Oct 2024 09:54:46 -0500 Subject: [PATCH 3/4] Fixed the unit tests by adding the changed default for test configuration due to a major version release --- backend/src/security/security.py | 3 --- frontend/test/views/AnnotationView.spec.js | 4 ---- frontend/vite.config.js | 3 +++ frontend/yarn.lock | 6 +++--- 4 files changed, 6 insertions(+), 10 deletions(-) diff --git a/backend/src/security/security.py b/backend/src/security/security.py index 402be971..90e3ea13 100644 --- a/backend/src/security/security.py +++ b/backend/src/security/security.py @@ -18,11 +18,8 @@ from ..dependencies import oauth2_scheme -# from ..models.token import TokenData from ..config import Settings, get_settings -# pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto") - SECURITY_SCOPES = { "pre-clinical-intake": "Pre-Clinical Intake", "bioinformatics-section-user": "Bioinformatics Section User", diff --git a/frontend/test/views/AnnotationView.spec.js b/frontend/test/views/AnnotationView.spec.js index 0f3de47c..01e05300 100644 --- a/frontend/test/views/AnnotationView.spec.js +++ b/frontend/test/views/AnnotationView.spec.js @@ -252,10 +252,6 @@ describe('AnnotationView', () => { annotationAttachMock.returns([initialImageAnnotation, newImageResult]); - const lookingFor = wrapper.findAllComponents(SectionImage); - - // expect(lookingFor.length).to.equal(1); - const annotationSection = wrapper.findComponent('[id=Gene_Homology]'); annotationSection.vm.$emit('attach-image', 'GeneHomology_Multi-SequenceAlignment', 'hgvs_variant'); diff --git a/frontend/vite.config.js b/frontend/vite.config.js index e6919205..b481aa93 100644 --- a/frontend/vite.config.js +++ b/frontend/vite.config.js @@ -16,6 +16,9 @@ export default defineConfig({ functions: 80, branches: 80, }, + sequence: { + hooks: 'parallel', + }, }, resolve: { alias: { diff --git a/frontend/yarn.lock b/frontend/yarn.lock index 0c20bd96..327a14a5 100644 --- a/frontend/yarn.lock +++ b/frontend/yarn.lock @@ -2015,9 +2015,9 @@ tinyexec@^0.3.0: integrity sha512-tVGE0mVJPGb0chKhqmsoosjsS+qUnJVGJpZgsHYQcGoPlG3B51R3PouqTgEGH2Dc9jjFyOqOpix6ZHNMXp1FZg== tinyglobby@^0.2.6: - version "0.2.7" - resolved "https://registry.yarnpkg.com/tinyglobby/-/tinyglobby-0.2.7.tgz#36f583c166ac2d91f47c799d6e2e256fdcfb3a56" - integrity sha512-qFWYeNxBQxrOTRHvGjlRdBamy8JFqu6c0bwRru9leE+q8J72tLtlT0L3v+2T7fbLXN7FGzDNBhXkWiJqHUHD9g== + version "0.2.9" + resolved "https://registry.yarnpkg.com/tinyglobby/-/tinyglobby-0.2.9.tgz#6baddd1b0fe416403efb0dd40442c7d7c03c1c66" + integrity sha512-8or1+BGEdk1Zkkw2ii16qSS7uVrQJPre5A9o/XkWPATkk23FZh/15BKFxPnlTy6vkljZxLqYCzzBMj30ZrSvjw== dependencies: fdir "^6.4.0" picomatch "^4.0.2" From e85567c01bb9baf3060962baee68ee21e1d0cb9a Mon Sep 17 00:00:00 2001 From: SeriousHorncat Date: Tue, 1 Oct 2024 10:44:59 -0500 Subject: [PATCH 4/4] Updated the changelog to include updates from the last year --- CHANGELOG.md | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b949761e..16288d49 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,17 @@ # Changelog -## 0.7.0 - latest +## 0.7.0 ### Features -### Bug Fixes +- Support for attaching documents, URLs, and Images to fields on an Analysis landing page. +- HTTPs by default for deployments +- Versioning for Annotations as dictated by configuration +- Analyses have a version manifest of annotation's dataset, source, and version +- Render's annotations for an analysis according to it's version manifest +- Timestamped discussions for analyses to which allow users to create, update, and remove text-based + messages to each other within an analysis. ## 0.6.0