diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 0000000..2c39c4b --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,34 @@ +name: Deploy to AWS Lambda using Serverless + +on: + push: + branches: + - main + +jobs: + deploy: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v2 + + - name: Set up Node.js + uses: actions/setup-node@v2 + with: + node-version: 18 + + - name: Install dependencies + run: npm ci + + - name: Build and Compile + run: npm build + + - name: Run Tests + run: npm test + + - name: Deploy + run: npx serverless deploy + env: + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} \ No newline at end of file diff --git a/.gitignore b/.gitignore index 811a1a0..52ffcdc 100644 --- a/.gitignore +++ b/.gitignore @@ -9,4 +9,7 @@ test/data/*-out.* test.csv # Serverless artifacts -.serverless \ No newline at end of file +.serverless + +# API uploads +uploads \ No newline at end of file diff --git a/README.md b/README.md index c4d26ea..d9ccab2 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ API and CLI of the Molecular International Prognostic Scoring System (IPSS-M) fo - [📖 IPSS-M Publication](#page_with_curl-ipss-m-publication) - [🚀 API Usage](#rocket-api-usage) -- [👾 CLI Usage](#alien-cli-usage) +- [🤖 CLI Usage](#robot-cli-usage) - [🔥 Using it as a node/javascript package](#fire-using-it-as-a-nodejavascript-package) - [💥 IPSS-M](#boom-ipss-m) - [⚡️ IPSS-R and IPSS-R (Age adjusted)](#zap-ipss-r-and-ipss-r-age-adjusted) @@ -139,7 +139,7 @@ $ curl \ } ``` -## :alien: CLI Usage +## :robot: CLI Usage You can use the command line interface to annotate a file with patients, where each row is a patient and each column is a variable. diff --git a/openapi.yml b/openapi.yml index b218e9e..6b058ea 100644 --- a/openapi.yml +++ b/openapi.yml @@ -47,6 +47,31 @@ paths: $ref: '#/components/schemas/IpssrResponse' '500': description: An error occurred while calculating IPSS-R risk score + /annotateFile: + post: + summary: Annotate a file with patients, with IPSS-M and IPSS-R risk scores. + requestBody: + required: true + content: + multipart/form-data: + schema: + type: object + properties: + file: + type: string + format: binary + description: csv/tsv or excel file to be annotated. One patient per row. + responses: + '200': + description: Successful operation. Stream the annotated file as CSV. + content: + text/plain: + schema: + type: string + '400': + description: Bad request + '500': + description: An error occurred while annotating the file. components: schemas: Clinical: diff --git a/package-lock.json b/package-lock.json index 5d697e0..fca1602 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,10 +9,12 @@ "version": "1.0.4", "license": "MIT", "dependencies": { + "@types/multer": "^1.4.11", "exceljs": "^4.3.0", "express": "^4.18.2", "ipssm": "^1.0.4", "joi": "^17.11.0", + "multer": "^1.4.5-lts.1", "papaparse": "^5.4.1", "serverless-http": "^3.2.0", "yargs": "^17.7.2" @@ -2593,7 +2595,6 @@ "version": "1.19.5", "resolved": "https://registry.npmjs.org/@types/body-parser/-/body-parser-1.19.5.tgz", "integrity": "sha512-fB3Zu92ucau0iQ0JMCFQE7b/dv8Ot07NI3KaZIkIUNXq82k4eBAqUaneXfleGY9JWskeS9y+u0nXMyspcuQrCg==", - "dev": true, "dependencies": { "@types/connect": "*", "@types/node": "*" @@ -2630,7 +2631,6 @@ "version": "3.4.38", "resolved": "https://registry.npmjs.org/@types/connect/-/connect-3.4.38.tgz", "integrity": "sha512-K6uROf1LD88uDQqJCktA4yzL1YYAK6NgfsI0v/mTgyPKWsX1CnJ0XPSDhViejru1GcRkLWb8RlzFYJRqGUbaug==", - 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"dev": true, "dependencies": { "undici-types": "~5.26.4" } @@ -2720,14 +2723,12 @@ "node_modules/@types/qs": { "version": "6.9.10", "resolved": "https://registry.npmjs.org/@types/qs/-/qs-6.9.10.tgz", - "integrity": "sha512-3Gnx08Ns1sEoCrWssEgTSJs/rsT2vhGP+Ja9cnnk9k4ALxinORlQneLXFeFKOTJMOeZUFD1s7w+w2AphTpvzZw==", - "dev": true + "integrity": "sha512-3Gnx08Ns1sEoCrWssEgTSJs/rsT2vhGP+Ja9cnnk9k4ALxinORlQneLXFeFKOTJMOeZUFD1s7w+w2AphTpvzZw==" }, "node_modules/@types/range-parser": { "version": "1.2.7", "resolved": "https://registry.npmjs.org/@types/range-parser/-/range-parser-1.2.7.tgz", - "integrity": "sha512-hKormJbkJqzQGhziax5PItDUTMAM9uE2XXQmM37dyd4hVM+5aVl7oVxMVUiVQn2oCQFN/LKCZdvSM0pFRqbSmQ==", - "dev": true + "integrity": "sha512-hKormJbkJqzQGhziax5PItDUTMAM9uE2XXQmM37dyd4hVM+5aVl7oVxMVUiVQn2oCQFN/LKCZdvSM0pFRqbSmQ==" }, "node_modules/@types/responselike": { "version": "1.0.3", @@ -2748,7 +2749,6 @@ "version": "0.17.4", "resolved": "https://registry.npmjs.org/@types/send/-/send-0.17.4.tgz", "integrity": "sha512-x2EM6TJOybec7c52BX0ZspPodMsQUd5L6PRwOunVyVUhXiBSKf3AezDL8Dgvgt5o0UfKNfuA0eMLr2wLT4AiBA==", - "dev": true, "dependencies": { "@types/mime": "^1", "@types/node": "*" @@ -2758,7 +2758,6 @@ "version": "1.15.5", "resolved": "https://registry.npmjs.org/@types/serve-static/-/serve-static-1.15.5.tgz", "integrity": "sha512-PDRk21MnK70hja/YF8AHfC7yIsiQHn1rcXx7ijCFBX/k+XQJhQT/gw3xekXKJvx+5SXaMMS8oqQy09Mzvz2TuQ==", - "dev": true, "dependencies": { "@types/http-errors": "*", "@types/mime": "*", @@ -3021,6 +3020,11 @@ "node": ">= 8" } }, + "node_modules/append-field": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/append-field/-/append-field-1.0.0.tgz", + "integrity": "sha512-klpgFSWLW1ZEs8svjfb7g4qWY0YS5imI82dTg+QahUvJ8YqAY0P10Uk8tTyh9ZGuYEZEMaeJYCF5BFuX552hsw==" + }, "node_modules/archive-type": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/archive-type/-/archive-type-4.0.0.tgz", @@ -3572,6 +3576,11 @@ "integrity": "sha512-T7zexNBwiiaCOGDg9xNX9PBmjrubblRkENuptryuI64URkXDFum9il/JGL8Lm8wYfAXpredVXXZz7eMHilimiQ==", "dev": true }, + "node_modules/buffer-from": { + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/buffer-from/-/buffer-from-1.1.2.tgz", + "integrity": "sha512-E+XQCRwSbaaiChtv6k6Dwgc+bx+Bs6vuKJHHl5kox/BaKbhiXzqQOwK4cO22yElGp2OCmjwVhT3HmxgyPGnJfQ==" + }, "node_modules/buffer-indexof-polyfill": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/buffer-indexof-polyfill/-/buffer-indexof-polyfill-1.0.2.tgz", @@ -3607,6 +3616,17 @@ "dev": true, "peer": true }, + "node_modules/busboy": { + "version": "1.6.0", + "resolved": "https://registry.npmjs.org/busboy/-/busboy-1.6.0.tgz", + "integrity": "sha512-8SFQbg/0hQ9xy3UNTB0YEnsNBbWfhf7RtnzpL7TkBiTBRfrQ9Fxcnz7VJsleJpyp6rVLvXiuORqjlHi5q+PYuA==", + "dependencies": { + "streamsearch": "^1.1.0" + }, + "engines": { + "node": ">=10.16.0" + } + }, "node_modules/bytes": { "version": "3.1.2", "resolved": "https://registry.npmjs.org/bytes/-/bytes-3.1.2.tgz", @@ -4072,6 +4092,47 @@ "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz", "integrity": "sha512-/Srv4dswyQNBfohGpz9o6Yb3Gz3SrUDqBH5rTuhGR7ahtlbYKnVxw2bCFMRljaA7EXHaXZ8wsHdodFvbkhKmqg==" }, + "node_modules/concat-stream": { + "version": "1.6.2", + "resolved": "https://registry.npmjs.org/concat-stream/-/concat-stream-1.6.2.tgz", + "integrity": "sha512-27HBghJxjiZtIk3Ycvn/4kbJk/1uZuJFfuPEns6LaEvpvG1f0hTea8lilrouyo9mVc2GWdcEZ8OLoGmSADlrCw==", + "engines": [ + "node >= 0.8" + ], + "dependencies": { + "buffer-from": "^1.0.0", + "inherits": "^2.0.3", + "readable-stream": "^2.2.2", + "typedarray": "^0.0.6" + } + }, + "node_modules/concat-stream/node_modules/readable-stream": { + "version": "2.3.8", + "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-2.3.8.tgz", + "integrity": "sha512-8p0AUk4XODgIewSi0l8Epjs+EVnWiK7NoDIEGU0HhE7+ZyY8D1IMY7odu5lRrFXGg71L15KG8QrPmum45RTtdA==", + "dependencies": { + "core-util-is": "~1.0.0", + "inherits": "~2.0.3", + "isarray": "~1.0.0", + "process-nextick-args": "~2.0.0", + "safe-buffer": "~5.1.1", + "string_decoder": "~1.1.1", + "util-deprecate": "~1.0.1" + } + }, + "node_modules/concat-stream/node_modules/safe-buffer": { + "version": "5.1.2", + "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.2.tgz", + "integrity": "sha512-Gd2UZBJDkXlY7GbJxfsE8/nvKkUEU1G38c1siN6QP6a9PT9MmHB8GnpscSmMJSoF8LOIrt8ud/wPtojys4G6+g==" + }, + "node_modules/concat-stream/node_modules/string_decoder": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz", + "integrity": "sha512-n/ShnvDi6FHbbVfviro+WojiFzv+s8MPMHBczVePfUpDJLwoLT0ht1l4YwBCbi8pJAveEEdnkHyPyTP/mzRfwg==", + "dependencies": { + "safe-buffer": "~5.1.0" + } + }, "node_modules/content-disposition": { "version": "0.5.4", "resolved": "https://registry.npmjs.org/content-disposition/-/content-disposition-0.5.4.tgz", @@ -7053,6 +7114,23 @@ "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==", "dev": true }, + "node_modules/multer": { + "version": "1.4.5-lts.1", + "resolved": "https://registry.npmjs.org/multer/-/multer-1.4.5-lts.1.tgz", + "integrity": "sha512-ywPWvcDMeH+z9gQq5qYHCCy+ethsk4goepZ45GLD63fOu0YcNecQxi64nDs3qluZB+murG3/D4dJ7+dGctcCQQ==", + "dependencies": { + "append-field": "^1.0.0", + "busboy": "^1.0.0", + "concat-stream": "^1.5.2", + "mkdirp": "^0.5.4", + "object-assign": "^4.1.1", + "type-is": "^1.6.4", + "xtend": "^4.0.0" + }, + "engines": { + "node": ">= 6.0.0" + } + }, "node_modules/mute-stream": { "version": "0.0.8", "resolved": "https://registry.npmjs.org/mute-stream/-/mute-stream-0.0.8.tgz", @@ -7238,7 +7316,6 @@ "version": "4.1.1", "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz", "integrity": "sha512-rJgTQnkUnH1sFw8yT6VSU3zD3sWmu6sZhIseY8VX+GRu3P6F7Fu+JNDoXfklElbLJSnc3FUQHVe4cU5hj+BcUg==", - "dev": true, "engines": { "node": ">=0.10.0" } @@ -8593,6 +8670,14 @@ "is-stream": "^1.1.0" } }, + "node_modules/streamsearch": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/streamsearch/-/streamsearch-1.1.0.tgz", + "integrity": "sha512-Mcc5wHehp9aXz1ax6bZUyY5afg9u2rv5cqQI3mRrYkGC8rW2hM02jWuwjtL++LS5qinSyhj2QfLyNsuc+VsExg==", + "engines": { + "node": ">=10.0.0" + } + }, "node_modules/string_decoder": { "version": "1.3.0", "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz", @@ -8964,6 +9049,11 @@ "node": ">= 0.6" } }, + "node_modules/typedarray": { + "version": "0.0.6", + "resolved": "https://registry.npmjs.org/typedarray/-/typedarray-0.0.6.tgz", + "integrity": "sha512-/aCDEGatGvZ2BIk+HmLf4ifCJFwvKFNb9/JeZPMulfgFracn9QFcAf5GO8B/mweUjSoblS5In0cWhqpfs/5PQA==" + }, "node_modules/typescript": { "version": "5.3.3", "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.3.3.tgz", @@ -8996,8 +9086,7 @@ "node_modules/undici-types": { "version": "5.26.5", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz", - "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==", - "dev": true + "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==" }, "node_modules/uni-global": { "version": "1.0.0", @@ -9583,7 +9672,6 @@ "version": "4.0.2", "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==", - "dev": true, "engines": { "node": ">=0.4" } diff --git a/package.json b/package.json index 7b0e783..97b0e2c 100644 --- a/package.json +++ b/package.json @@ -43,10 +43,12 @@ "vitest": "^0.34.4" }, "dependencies": { + "@types/multer": "^1.4.11", "exceljs": "^4.3.0", "express": "^4.18.2", "ipssm": "^1.0.4", "joi": "^17.11.0", + "multer": "^1.4.5-lts.1", "papaparse": "^5.4.1", "serverless-http": "^3.2.0", "yargs": "^17.7.2" diff --git a/redoc-static.html b/redoc-static.html index a1c4a9b..8d9c585 100644 --- a/redoc-static.html +++ b/redoc-static.html @@ -340,7 +340,7 @@ -
MDS Foundation
API docs by Redocly
MDS Foundation
API docs by Redocly

Successful operation

Request samples

Content type
application/json
{
  • "BM_BLAST": 30,
  • "HB": 4,
  • "PLT": 2000,
  • "ANC": 15,
  • "AGE": 18,
  • "CYTO_IPSSR": "Very Good"
}

Response samples

Content type
application/json
{
  • "patient": {
    },
  • "ipssr": {
    }
}
+

Request samples

Content type
application/json
{
  • "BM_BLAST": 30,
  • "HB": 4,
  • "PLT": 2000,
  • "ANC": 15,
  • "AGE": 18,
  • "CYTO_IPSSR": "Very Good"
}

Response samples

Content type
application/json
{
  • "patient": {
    },
  • "ipssr": {
    }
}

Annotate a patient file

Request Body schema: multipart/form-data
required
file
string <binary>

Responses