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Update Phi-Annotator-App to API version 1.2.0 (#99)
* Update Example Env File * Update `physical-annotator` to `location-annotator` * Update `phi-deidentifier` to `phi-deidentifier-example` * Point phi-deidentifier Image Link to Correct URL * Bump eslint from 7.28.0 to 7.32.0 in /client Bumps [eslint](https://github.com/eslint/eslint) from 7.28.0 to 7.32.0. - [Release notes](https://github.com/eslint/eslint/releases) - [Changelog](https://github.com/eslint/eslint/blob/master/CHANGELOG.md) - [Commits](eslint/eslint@v7.28.0...v7.32.0) --- updated-dependencies: - dependency-name: eslint dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * Bump eslint from 7.28.0 to 7.32.0 in /client Bumps [eslint](https://github.com/eslint/eslint) from 7.28.0 to 7.32.0. - [Release notes](https://github.com/eslint/eslint/releases) - [Changelog](https://github.com/eslint/eslint/blob/master/CHANGELOG.md) - [Commits](eslint/eslint@v7.28.0...v7.32.0) --- updated-dependencies: - dependency-name: eslint dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * PHYSICAL_ADDRESS -> LOCATION * Regenerate Client from updated API Spec * "Physical Address" -> "Location" in Web Client * "Physical Address" -> "Location" in docker-compose.yml * Bump Web Client Version Number * Copy Just Necessary Files in Dockerfile * Bump @typescript-eslint/eslint-plugin from 4.26.0 to 4.28.5 in /client (#110) Bumps [@typescript-eslint/eslint-plugin](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/eslint-plugin) from 4.26.0 to 4.28.5. - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/master/packages/eslint-plugin/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v4.28.5/packages/eslint-plugin) --- updated-dependencies: - dependency-name: "@typescript-eslint/eslint-plugin" dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump @openapitools/openapi-generator-cli from 2.3.3 to 2.3.9 (#108) Bumps [@openapitools/openapi-generator-cli](https://github.com/OpenAPITools/openapi-generator-cli) from 2.3.3 to 2.3.9. - [Release notes](https://github.com/OpenAPITools/openapi-generator-cli/releases) - [Changelog](https://github.com/OpenAPITools/openapi-generator-cli/blob/master/.releaserc) - [Commits](OpenAPITools/openapi-generator-cli@v2.3.3...v2.3.9) --- updated-dependencies: - dependency-name: "@openapitools/openapi-generator-cli" dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump node from 16.2.0-alpine3.12 to 16.6.0-alpine3.12 in /client (#107) Bumps node from 16.2.0-alpine3.12 to 16.6.0-alpine3.12. --- updated-dependencies: - dependency-name: node dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump @testing-library/react from 11.2.7 to 12.0.0 in /client (#105) Bumps [@testing-library/react](https://github.com/testing-library/react-testing-library) from 11.2.7 to 12.0.0. - [Release notes](https://github.com/testing-library/react-testing-library/releases) - [Changelog](https://github.com/testing-library/react-testing-library/blob/main/CHANGELOG.md) - [Commits](testing-library/react-testing-library@v11.2.7...v12.0.0) --- updated-dependencies: - dependency-name: "@testing-library/react" dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump nginx from 1.21.0-alpine to 1.21.1-alpine in /client (#106) Bumps nginx from 1.21.0-alpine to 1.21.1-alpine. --- updated-dependencies: - dependency-name: nginx dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump @typescript-eslint/parser from 4.26.0 to 4.28.5 in /client (#111) Bumps [@typescript-eslint/parser](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/parser) from 4.26.0 to 4.28.5. - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/master/packages/parser/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v4.28.5/packages/parser) --- updated-dependencies: - dependency-name: "@typescript-eslint/parser" dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Connor Boyle <[email protected]> * Bump web-vitals from 1.1.1 to 2.0.1 in /client (#87) Bumps [web-vitals](https://github.com/GoogleChrome/web-vitals) from 1.1.1 to 2.0.1. - [Release notes](https://github.com/GoogleChrome/web-vitals/releases) - [Changelog](https://github.com/GoogleChrome/web-vitals/blob/main/CHANGELOG.md) - [Commits](GoogleChrome/web-vitals@v1.1.1...v2.0.1) --- updated-dependencies: - dependency-name: web-vitals dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Thomas Schaffter <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Thomas Schaffter <[email protected]>
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‎.env.example‎

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PERSON_NAME_ANNOTATOR_HOST=localhost
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PERSON_NAME_ANNOTATOR_PORT=9001
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PHYSICAL_ADDRESS_ANNOTATOR_PROTOCOL=http://
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PHYSICAL_ADDRESS_ANNOTATOR_HOST=localhost
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PHYSICAL_ADDRESS_ANNOTATOR_PORT=9002
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LOCATION_ANNOTATOR_PROTOCOL=http://
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LOCATION_ANNOTATOR_HOST=localhost
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LOCATION_ANNOTATOR_PORT=9002
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CONTACT_ANNOTATOR_PROTOCOL=http://
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CONTACT_ANNOTATOR_HOST=localhost
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CONTACT_ANNOTATOR_PORT=9003
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ID_ANNOTATOR_PROTOCOL=http://
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ID_ANNOTATOR_HOST=localhost
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ID_ANNOTATOR_PORT=9004

‎client/Dockerfile‎

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# pull official node base image
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FROM node:16.2.0-alpine3.12 as build
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FROM node:16.6.0-alpine3.12 as build
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WORKDIR /app
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ENV PATH /app/node_modules/.bin:$PATH
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COPY package.json ./
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COPY package-lock.json ./
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RUN npm ci --silent
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RUN npm install [email protected] -g --silent
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COPY . ./
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COPY src ./src
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COPY public ./public
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RUN npm run build
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# production environment
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FROM nginx:1.21.0-alpine
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FROM nginx:1.21.1-alpine
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COPY --from=build /app/build /usr/share/nginx/html
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COPY nginx/nginx.conf /etc/nginx/conf.d/default.conf
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‎client/package-lock.json‎

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‎client/package.json‎

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"@material-ui/data-grid": "^4.0.0-alpha.30",
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"@material-ui/icons": "^4.11.2",
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"@testing-library/jest-dom": "^5.13.0",
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"@testing-library/react": "^11.2.7",
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"@testing-library/react": "^12.0.0",
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"@testing-library/user-event": "^13.1.9",
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"prop-types": "^15.7.2",
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"react": "^17.0.2",
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"react-dom": "^17.0.2",
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"react-router-dom": "^5.2.0",
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"react-scripts": "4.0.3",
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"typescript": "^4.3.2",
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"web-vitals": "^1.1.1"
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"web-vitals": "^2.0.1"
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},
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"scripts": {
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"start": "chmod +x ./env.sh && ./env.sh && cp env-config.js ./public/ && react-scripts start",
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]
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},
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"devDependencies": {
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"@typescript-eslint/eslint-plugin": "^4.26.0",
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"@typescript-eslint/parser": "^4.26.0",
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"eslint": "^7.28.0",
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"@typescript-eslint/eslint-plugin": "^4.28.5",
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"@typescript-eslint/parser": "^4.28.5",
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"eslint": "^7.32.0",
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"eslint-config-google": "^0.14.0",
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"eslint-plugin-react": "^7.24.0"
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}

‎client/src/.openapi-generator/FILES‎

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models/TextDateAnnotationAllOf.ts
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models/TextIdAnnotation.ts
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models/TextIdAnnotationAllOf.ts
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models/TextLocationAnnotation.ts
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models/TextLocationAnnotationAllOf.ts
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models/TextPersonNameAnnotation.ts
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models/TextPhysicalAddressAnnotation.ts
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models/TextPhysicalAddressAnnotationAllOf.ts
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models/Tool.ts
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models/ToolDependencies.ts
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models/ToolType.ts
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models/index.ts
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runtime.ts

‎client/src/.openapi-generator/VERSION‎

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5.1.1
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5.2.0

‎client/src/apis/DeidentifiedNoteApi.ts‎

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/* eslint-disable */
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/**
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* NLP Sandbox PHI Deidentifier API
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* # Introduction This NLP tool takes as input a clinical note and returned a de-identified version of the note. This design of this API is a work in progress. # Examples - [NLP Sandbox PHI Deidentifier](https://github.com/nlpsandbox/phi-deidentifier)
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* # Introduction This NLP tool takes as input a clinical note and returned a de-identified version of the note. This design of this API is a work in progress. # Examples - [NLP Sandbox PHI Deidentifier Example](https://github.com/nlpsandbox/phi-deidentifier-example)
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*
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* The version of the OpenAPI document: 1.1.2
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* The version of the OpenAPI document: 1.2.0
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* Contact: [email protected]
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*
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‎client/src/apis/HealthCheckApi.ts‎

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/* eslint-disable */
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/**
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* NLP Sandbox PHI Deidentifier API
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* # Introduction This NLP tool takes as input a clinical note and returned a de-identified version of the note. This design of this API is a work in progress. # Examples - [NLP Sandbox PHI Deidentifier](https://github.com/nlpsandbox/phi-deidentifier)
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* # Introduction This NLP tool takes as input a clinical note and returned a de-identified version of the note. This design of this API is a work in progress. # Examples - [NLP Sandbox PHI Deidentifier Example](https://github.com/nlpsandbox/phi-deidentifier-example)
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* The version of the OpenAPI document: 1.2.0
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‎client/src/apis/ToolApi.ts‎

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/* eslint-disable */
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/**
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* # Introduction This NLP tool takes as input a clinical note and returned a de-identified version of the note. This design of this API is a work in progress. # Examples - [NLP Sandbox PHI Deidentifier](https://github.com/nlpsandbox/phi-deidentifier)
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* # Introduction This NLP tool takes as input a clinical note and returned a de-identified version of the note. This design of this API is a work in progress. # Examples - [NLP Sandbox PHI Deidentifier Example](https://github.com/nlpsandbox/phi-deidentifier-example)
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* The version of the OpenAPI document: 1.2.0
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‎client/src/components/AnnotationView.js‎

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function AnnotationView(props) {
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const types = [
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{type: 'text_date', name: 'Date', key: 'textDateAnnotations'},
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{type: 'text_physical_address', name: 'Physical Address', key:
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'textPhysicalAddressAnnotations'},
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{type: 'text_location', name: 'Location', key: 'textLocationAnnotations'},
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{type: 'text_person_name', name: 'Person Name', key:
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'textPersonNameAnnotations'},
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{type: 'text_contact', name: 'Contact Info', key: 'textContactAnnotations'},

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