Update Phi-Annotator-App to API version 1.2.0

.env.example

@@ -12,6 +12,14 @@ PERSON_NAME_ANNOTATOR_PROTOCOL=http://
 PERSON_NAME_ANNOTATOR_HOST=localhost
 PERSON_NAME_ANNOTATOR_PORT=9001
 
-PHYSICAL_ADDRESS_ANNOTATOR_PROTOCOL=http://
-PHYSICAL_ADDRESS_ANNOTATOR_HOST=localhost
-PHYSICAL_ADDRESS_ANNOTATOR_PORT=9002
+LOCATION_ANNOTATOR_PROTOCOL=http://
+LOCATION_ANNOTATOR_HOST=localhost
+LOCATION_ANNOTATOR_PORT=9002
+
+CONTACT_ANNOTATOR_PROTOCOL=http://
+CONTACT_ANNOTATOR_HOST=localhost
+CONTACT_ANNOTATOR_PORT=9003
+
+ID_ANNOTATOR_PROTOCOL=http://
+ID_ANNOTATOR_HOST=localhost
+ID_ANNOTATOR_PORT=9004

client/Dockerfile

@@ -1,16 +1,17 @@
 # pull official node base image
-FROM node:16.2.0-alpine3.12 as build
+FROM node:16.6.0-alpine3.12 as build
 WORKDIR /app
 ENV PATH /app/node_modules/.bin:$PATH
 COPY package.json ./
 COPY package-lock.json ./
 RUN npm ci --silent
 RUN npm install [email protected] -g --silent
-COPY . ./
+COPY src ./src
+COPY public ./public
 RUN npm run build
 
 # production environment
-FROM nginx:1.21.0-alpine
+FROM nginx:1.21.1-alpine
 COPY --from=build /app/build /usr/share/nginx/html
 COPY nginx/nginx.conf /etc/nginx/conf.d/default.conf
 

client/package.json

@@ -7,15 +7,15 @@
     "@material-ui/data-grid": "^4.0.0-alpha.30",
     "@material-ui/icons": "^4.11.2",
     "@testing-library/jest-dom": "^5.13.0",
-    "@testing-library/react": "^11.2.7",
+    "@testing-library/react": "^12.0.0",
     "@testing-library/user-event": "^13.1.9",
     "prop-types": "^15.7.2",
     "react": "^17.0.2",
     "react-dom": "^17.0.2",
     "react-router-dom": "^5.2.0",
     "react-scripts": "4.0.3",
     "typescript": "^4.3.2",
-    "web-vitals": "^1.1.1"
+    "web-vitals": "^2.0.1"
   },
   "scripts": {
     "start": "chmod +x ./env.sh && ./env.sh && cp env-config.js ./public/ && react-scripts start",
@@ -43,9 +43,9 @@
     ]
   },
   "devDependencies": {
-    "@typescript-eslint/eslint-plugin": "^4.26.0",
-    "@typescript-eslint/parser": "^4.26.0",
-    "eslint": "^7.28.0",
+    "@typescript-eslint/eslint-plugin": "^4.28.5",
+    "@typescript-eslint/parser": "^4.28.5",
+    "eslint": "^7.32.0",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-react": "^7.24.0"
   }

client/src/.openapi-generator/FILES

@@ -20,10 +20,11 @@ models/TextDateAnnotation.ts
 models/TextDateAnnotationAllOf.ts
 models/TextIdAnnotation.ts
 models/TextIdAnnotationAllOf.ts
+models/TextLocationAnnotation.ts
+models/TextLocationAnnotationAllOf.ts
 models/TextPersonNameAnnotation.ts
-models/TextPhysicalAddressAnnotation.ts
-models/TextPhysicalAddressAnnotationAllOf.ts
 models/Tool.ts
 models/ToolDependencies.ts
+models/ToolType.ts
 models/index.ts
 runtime.ts

client/src/.openapi-generator/VERSION

@@ -1 +1 @@
-5.1.1
+5.2.0

client/src/apis/DeidentifiedNoteApi.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/apis/HealthCheckApi.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/apis/ToolApi.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/components/AnnotationView.js

@@ -7,8 +7,7 @@ import PropTypes from 'prop-types';
 function AnnotationView(props) {
   const types = [
     {type: 'text_date', name: 'Date', key: 'textDateAnnotations'},
-    {type: 'text_physical_address', name: 'Physical Address', key:
-    'textPhysicalAddressAnnotations'},
+    {type: 'text_location', name: 'Location', key: 'textLocationAnnotations'},
     {type: 'text_person_name', name: 'Person Name', key:
     'textPersonNameAnnotations'},
     {type: 'text_contact', name: 'Contact Info', key: 'textContactAnnotations'},

client/src/components/App.js

@@ -68,7 +68,7 @@ class App extends React.Component {
           confidenceThreshold: 20,
           maskingCharConfig: {maskingChar: '*'},
           annotationTypes: [
-            'text_person_name', 'text_physical_address', 'text_date'],
+            'text_person_name', 'text_location', 'text_date'],
         }],
         note: {
           text: defaultText,
@@ -167,7 +167,7 @@ class App extends React.Component {
       confidenceThreshold: 20,
       maskingCharConfig: {maskingChar: '*'},
       annotationTypes: [
-        'text_person_name', 'text_physical_address', 'text_date'],
+        'text_person_name', 'text_location', 'text_date'],
       key: this.state.deidentifyRequest.keyMax+1,
     };
     deidentificationSteps.push(newDeidStep);

client/src/components/DeidentificationConfigForm.js

@@ -15,7 +15,7 @@ const DEIDENTIFICATION_STRATEGIES = {
 const ANNOTATION_TYPE_NAMES = {
   'text_date': 'Date',
   'text_person_name': 'Person Name',
-  'text_physical_address': 'Physical Address',
+  'text_location': 'Location',
   'text_contact': 'Contact Info',
   'text_id': 'Identifier',
 };

client/src/config.js

@@ -36,7 +36,7 @@ export default class Config {
 
   version() {
     // Version of the web client
-    return '1.1.0';
+    return '1.2.0';
   }
 
   source() {

client/src/models/AnnotationSet.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
@@ -26,14 +26,14 @@ import {
     TextIdAnnotationFromJSON,
     TextIdAnnotationFromJSONTyped,
     TextIdAnnotationToJSON,
+    TextLocationAnnotation,
+    TextLocationAnnotationFromJSON,
+    TextLocationAnnotationFromJSONTyped,
+    TextLocationAnnotationToJSON,
     TextPersonNameAnnotation,
     TextPersonNameAnnotationFromJSON,
     TextPersonNameAnnotationFromJSONTyped,
     TextPersonNameAnnotationToJSON,
-    TextPhysicalAddressAnnotation,
-    TextPhysicalAddressAnnotationFromJSON,
-    TextPhysicalAddressAnnotationFromJSONTyped,
-    TextPhysicalAddressAnnotationToJSON,
 } from './';
 
 /**
@@ -55,11 +55,11 @@ export interface AnnotationSet {
      */
     textPersonNameAnnotations: Array<TextPersonNameAnnotation>;
     /**
-     * Physical address annotations in a text
-     * @type {Array<TextPhysicalAddressAnnotation>}
+     * Location annotations in a text
+     * @type {Array<TextLocationAnnotation>}
      * @memberof AnnotationSet
      */
-    textPhysicalAddressAnnotations: Array<TextPhysicalAddressAnnotation>;
+    textLocationAnnotations: Array<TextLocationAnnotation>;
     /**
      * ID annotations in a text
      * @type {Array<TextIdAnnotation>}
@@ -86,7 +86,7 @@ export function AnnotationSetFromJSONTyped(json: any, ignoreDiscriminator: boole
 
         'textDateAnnotations': ((json['textDateAnnotations'] as Array<any>).map(TextDateAnnotationFromJSON)),
         'textPersonNameAnnotations': ((json['textPersonNameAnnotations'] as Array<any>).map(TextPersonNameAnnotationFromJSON)),
-        'textPhysicalAddressAnnotations': ((json['textPhysicalAddressAnnotations'] as Array<any>).map(TextPhysicalAddressAnnotationFromJSON)),
+        'textLocationAnnotations': ((json['textLocationAnnotations'] as Array<any>).map(TextLocationAnnotationFromJSON)),
         'textIdAnnotations': ((json['textIdAnnotations'] as Array<any>).map(TextIdAnnotationFromJSON)),
         'textContactAnnotations': ((json['textContactAnnotations'] as Array<any>).map(TextContactAnnotationFromJSON)),
     };
@@ -103,7 +103,7 @@ export function AnnotationSetToJSON(value?: AnnotationSet | null): any {
 
         'textDateAnnotations': ((value.textDateAnnotations as Array<any>).map(TextDateAnnotationToJSON)),
         'textPersonNameAnnotations': ((value.textPersonNameAnnotations as Array<any>).map(TextPersonNameAnnotationToJSON)),
-        'textPhysicalAddressAnnotations': ((value.textPhysicalAddressAnnotations as Array<any>).map(TextPhysicalAddressAnnotationToJSON)),
+        'textLocationAnnotations': ((value.textLocationAnnotations as Array<any>).map(TextLocationAnnotationToJSON)),
         'textIdAnnotations': ((value.textIdAnnotations as Array<any>).map(TextIdAnnotationToJSON)),
         'textContactAnnotations': ((value.textContactAnnotations as Array<any>).map(TextContactAnnotationToJSON)),
     };

client/src/models/DateOffsetConfig.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/models/DeidentificationStep.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
@@ -43,7 +43,7 @@ export interface DeidentificationStep {
      */
     maskingCharConfig?: MaskingCharConfig;
     /**
-     * Configuration for the "annotation type" strategy. E.g. "John Smith lives at 123 Main St" -> "[PERSON_NAME] lives at [PHYSICAL_ADDRESS]".
+     * Configuration for the "annotation type" strategy. E.g. "John Smith lives at 123 Main St" -> "[PERSON_NAME] lives at [LOCATION]".
      * @type {object}
      * @memberof DeidentificationStep
      */
@@ -75,7 +75,7 @@ export interface DeidentificationStep {
 export enum DeidentificationStepAnnotationTypesEnum {
     Date = 'text_date',
     PersonName = 'text_person_name',
-    PhysicalAddress = 'text_physical_address',
+    Location = 'text_location',
     Id = 'text_id',
     Contact = 'text_contact'
 }

client/src/models/DeidentifyRequest.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/models/DeidentifyResponse.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/models/HealthCheck.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/models/License.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/models/MaskingCharConfig.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/models/ModelError.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/models/Note.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).

client/src/models/TextAnnotation.ts

@@ -2,9 +2,9 @@
 /* eslint-disable */
 /**
  * NLP Sandbox PHI Deidentifier API
- * # 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) 
+ * # 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) 
  *
- * The version of the OpenAPI document: 1.1.2
+ * The version of the OpenAPI document: 1.2.0
  * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).