73 schema 1.1.2 (#97)

* Update Annotator & Deidentifier Versions

Also renames docker container networks.

* Add Scripts for Generating Deidentifier Client SDK

* Add Auto-Generated API Client

* Update ToolDependencies Reference

Keeps pace with the schema update.

* Update ToolDependency Member Names

* Update Member Name of Note Type

* Add Contact & ID to Named Annotation Types

* Add New Annotation Types to Annotation Table

* Update Web Client Version Number

client/src/.openapi-generator/FILES

@@ -0,0 +1,29 @@
+apis/DeidentifiedNoteApi.ts
+apis/HealthCheckApi.ts
+apis/ToolApi.ts
+apis/index.ts
+index.ts
+models/AnnotationSet.ts
+models/DateOffsetConfig.ts
+models/DeidentificationStep.ts
+models/DeidentifyRequest.ts
+models/DeidentifyResponse.ts
+models/HealthCheck.ts
+models/License.ts
+models/MaskingCharConfig.ts
+models/ModelError.ts
+models/Note.ts
+models/TextAnnotation.ts
+models/TextContactAnnotation.ts
+models/TextContactAnnotationAllOf.ts
+models/TextDateAnnotation.ts
+models/TextDateAnnotationAllOf.ts
+models/TextIdAnnotation.ts
+models/TextIdAnnotationAllOf.ts
+models/TextPersonNameAnnotation.ts
+models/TextPhysicalAddressAnnotation.ts
+models/TextPhysicalAddressAnnotationAllOf.ts
+models/Tool.ts
+models/ToolDependencies.ts
+models/index.ts
+runtime.ts

client/src/.openapi-generator/VERSION

@@ -1 +1 @@
-5.0.1
+5.1.1

client/src/apis/DeidentifiedNoteApi.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/apis/HealthCheckApi.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/apis/ToolApi.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/components/AnnotationView.js

@@ -11,6 +11,8 @@ function AnnotationView(props) {
     'textPhysicalAddressAnnotations'},
     {type: 'text_person_name', name: 'Person Name', key:
     'textPersonNameAnnotations'},
+    {type: 'text_contact', name: 'Contact Info', key: 'textContactAnnotations'},
+    {type: 'text_id', name: 'Identifier', key: 'textIdAnnotations'},
   ];
 
   let allAnnotations;

client/src/components/App.js

@@ -72,7 +72,7 @@ class App extends React.Component {
         }],
         note: {
           text: defaultText,
-          noteType: '0000', // FIXME: figure out whether and how to get this
+          type: '0000', // FIXME: figure out whether and how to get this
           identifier: '0000',
           patientId: '0000',
         },

client/src/components/DeidentificationConfigForm.js

@@ -16,6 +16,8 @@ const ANNOTATION_TYPE_NAMES = {
   'text_date': 'Date',
   'text_person_name': 'Person Name',
   'text_physical_address': 'Physical Address',
+  'text_contact': 'Contact Info',
+  'text_id': 'Identifier',
 };
 
 export class DeidentificationConfigForm extends React.Component {

client/src/components/InfoDialog.js

@@ -33,10 +33,11 @@ const StyledTableRow = withStyles((theme) => ({
 }))(TableRow);
 
 function ToolDependencyRow(props) {
+  console.log(props.toolDependency);
   return (
     <StyledTableRow maxHeight="100px">
-      <StyledTableCell>{ props.toolDependency.toolType }</StyledTableCell>
-      <StyledTableCell>{ props.toolDependency.toolApiVersion }</StyledTableCell>
+      <StyledTableCell>{ props.toolDependency.type }</StyledTableCell>
+      <StyledTableCell>{ props.toolDependency.apiVersion }</StyledTableCell>
       <StyledTableCell>
         <Link href={ props.toolDependency.url }>
           { props.toolDependency.name }</Link>
@@ -81,7 +82,7 @@ function ToolDependenciesTable(props) {
         </TableHead>
         <TableBody>
           <ToolDependencyRow toolDependency={props.deidentifierInfo} />
-          {props.toolDependencies.map(
+          {props.toolDependencies.tools.map(
             (toolDependency, index) => <ToolDependencyRow
               key={index}
               toolDependency={toolDependency}
@@ -113,7 +114,7 @@ export class InfoDialog extends React.Component {
     this.props.toolApi.getToolDependencies()
       .then((apiResponse) => {
         this.setState({
-          toolDependencies: apiResponse.toolDependencies,
+          toolDependencies: apiResponse,
         });
       })
       .catch((error) => {

client/src/config.js

@@ -36,7 +36,7 @@ export default class Config {
 
   version() {
     // Version of the web client
-    return '1.0.0';
+    return '1.1.0';
   }
 
   source() {

client/src/models/AnnotationSet.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech
@@ -14,10 +14,18 @@
 
 import { exists, mapValues } from '../runtime';
 import {
+    TextContactAnnotation,
+    TextContactAnnotationFromJSON,
+    TextContactAnnotationFromJSONTyped,
+    TextContactAnnotationToJSON,
     TextDateAnnotation,
     TextDateAnnotationFromJSON,
     TextDateAnnotationFromJSONTyped,
     TextDateAnnotationToJSON,
+    TextIdAnnotation,
+    TextIdAnnotationFromJSON,
+    TextIdAnnotationFromJSONTyped,
+    TextIdAnnotationToJSON,
     TextPersonNameAnnotation,
     TextPersonNameAnnotationFromJSON,
     TextPersonNameAnnotationFromJSONTyped,
@@ -52,6 +60,18 @@ export interface AnnotationSet {
      * @memberof AnnotationSet
      */
     textPhysicalAddressAnnotations: Array<TextPhysicalAddressAnnotation>;
+    /**
+     * ID annotations in a text
+     * @type {Array<TextIdAnnotation>}
+     * @memberof AnnotationSet
+     */
+    textIdAnnotations: Array<TextIdAnnotation>;
+    /**
+     * Contact annotations in a text
+     * @type {Array<TextContactAnnotation>}
+     * @memberof AnnotationSet
+     */
+    textContactAnnotations: Array<TextContactAnnotation>;
 }
 
 export function AnnotationSetFromJSON(json: any): AnnotationSet {
@@ -67,6 +87,8 @@ 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)),
+        'textIdAnnotations': ((json['textIdAnnotations'] as Array<any>).map(TextIdAnnotationFromJSON)),
+        'textContactAnnotations': ((json['textContactAnnotations'] as Array<any>).map(TextContactAnnotationFromJSON)),
     };
 }
 
@@ -82,6 +104,8 @@ 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)),
+        'textIdAnnotations': ((value.textIdAnnotations as Array<any>).map(TextIdAnnotationToJSON)),
+        'textContactAnnotations': ((value.textContactAnnotations as Array<any>).map(TextContactAnnotationToJSON)),
     };
 }
 

client/src/models/DateOffsetConfig.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/models/DeidentificationStep.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech
@@ -73,9 +73,11 @@ export interface DeidentificationStep {
 * @enum {string}
 */
 export enum DeidentificationStepAnnotationTypesEnum {
-    PhysicalAddress = 'text_physical_address',
     Date = 'text_date',
-    PersonName = 'text_person_name'
+    PersonName = 'text_person_name',
+    PhysicalAddress = 'text_physical_address',
+    Id = 'text_id',
+    Contact = 'text_contact'
 }
 
 export function DeidentificationStepFromJSON(json: any): DeidentificationStep {

client/src/models/DeidentifyRequest.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/models/DeidentifyResponse.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/models/HealthCheck.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/models/License.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/models/MaskingCharConfig.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/models/ModelError.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech

client/src/models/Note.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech
@@ -36,7 +36,7 @@ export interface Note {
      * @type {string}
      * @memberof Note
      */
-    noteType: string;
+    type: string;
     /**
      * The ID of the FHIR patient
      * @type {string}
@@ -57,7 +57,7 @@ export function NoteFromJSONTyped(json: any, ignoreDiscriminator: boolean): Note
 
         'identifier': json['identifier'],
         'text': json['text'],
-        'noteType': json['noteType'],
+        'type': json['type'],
         'patientId': json['patientId'],
     };
 }
@@ -73,7 +73,7 @@ export function NoteToJSON(value?: Note | null): any {
 
         'identifier': value.identifier,
         'text': value.text,
-        'noteType': value.noteType,
+        'type': value.type,
         'patientId': value.patientId,
     };
 }

client/src/models/TextAnnotation.ts

@@ -4,8 +4,8 @@
  * 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) 
  *
- * The version of the OpenAPI document: 1.0.1
- * Contact: [email protected]
+ * The version of the OpenAPI document: 1.1.2
+ * Contact: [email protected]
  *
  * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
  * https://openapi-generator.tech