Merge pull request #395 from inowas/t15-more-fixes

T15 more fixes

Author: Roschl

src/core/model/qmra/DoseResponse.ts

@@ -87,25 +87,6 @@ class DoseResponse extends GenericObject<IDoseResponse> {
     });
   }
 
-  public static fromDefaults(pathogenId: number) {
-    return new DoseResponse({
-      id: uuid.v4(),
-      pathogenId: pathogenId,
-      pathogenName: '',
-      pathogenGroup: '',
-      bestFitModel: '',
-      hostType: '',
-      doseUnits: '',
-      k: null,
-      alpha: null,
-      n50: null,
-      route: '',
-      response: '',
-      reference: '',
-      link: '',
-    });
-  }
-
   public static fromObject(obj: IDoseResponse) {
     return new DoseResponse(obj);
   }

src/core/model/qmra/DoseResponse.type.ts

@@ -4,9 +4,9 @@ export default interface IDoseResponse {
   pathogenName: string;
   pathogenGroup: string;
   bestFitModel: string;
-  k: number;
-  alpha: number;
-  n50: number;
+  k: number | null;
+  alpha: number | null;
+  n50: number | null;
   hostType: string;
   doseUnits: string;
   route: string;
@@ -20,9 +20,9 @@ export interface IDoseResponsePayload {
   PathogenName: string;
   PathogenGroup: string;
   'Best fit model*': string;
-  alpha: number;
-  k: number;
-  N50: number;
+  alpha?: number | null;
+  k?: number | null;
+  N50?: number | null;
   'Host type': string;
   'Dose units': string;
   Route: string;

src/core/model/qmra/Qmra.ts

@@ -237,9 +237,9 @@ class Qmra extends GenericObject<IQmra> {
   }
 
   public fromPayload(obj: IQmraRequest) {
-    const eventsPerYear = obj.config.exposure.filter((e) => e.name === 'number_of_exposures');
-    const litresPerEvent = obj.config.exposure.filter((e) => e.name === 'volume_perEvent');
-    const numberOfRepeatings = obj.config.exposure.filter((e) => e.name === 'number_of_repeatings')
+    const eventsPerYear = obj.exposure.filter((e) => e.name === 'number_of_exposures');
+    const litresPerEvent = obj.exposure.filter((e) => e.name === 'volume_perEvent');
+    const numberOfRepeatings = obj.exposure.filter((e) => e.name === 'number_of_repeatings')
 
     let litresPerEventValue: IValue = {type: 'value', min: 0, max: 1, mode: 1, value: 365};
 
@@ -275,26 +275,24 @@ class Qmra extends GenericObject<IQmra> {
         litresPerEvent: litresPerEventValue
       })
     ];
-    this.inflow = obj.config.inflow.map((p) => Pathogen.fromPayload(p));
-    this.treatmentProcesses = obj.config.treatment.processes.map((tp) => TreatmentProcess.fromPayload(tp));
-    this.treatmentSchemes = obj.config.treatment.schemes.map((ts) => TreatmentScheme.fromPayload(ts));
-    this.health = obj.config.health.map((h) => Health.fromPayload(h));
-    this.doseResponse = obj.config.doseresponse.map((dr) => DoseResponse.fromPayload(dr));
+    this.inflow = obj.inflow.map((p) => Pathogen.fromPayload(p));
+    this.treatmentProcesses = obj.treatment.processes.map((tp) => TreatmentProcess.fromPayload(tp));
+    this.treatmentSchemes = obj.treatment.schemes.map((ts) => TreatmentScheme.fromPayload(ts));
+    this.health = obj.health.map((h) => Health.fromPayload(h));
+    this.doseResponse = obj.doseresponse.map((dr) => DoseResponse.fromPayload(dr));
     return this;
   }
 
   public toPayload() {
     return {
-      config: {
-        exposure: this.generateExposure(),
-        inflow: this.inflow.map((p) => p.toPayload()),
-        treatment: {
-          processes: this.treatmentProcesses.map((p) => p.toPayload()),
-          schemes: this.treatmentSchemes.map((s) => s.toPayload())
-        },
-        doseresponse: this.doseResponse.map((r) => r.toPayload()),
-        health: this.health.map((h) => h.toPayload())
-      }
+      exposure: this.generateExposure(),
+      inflow: this.inflow.map((p) => p.toPayload()),
+      treatment: {
+        processes: this.treatmentProcesses.map((p) => p.toPayload()),
+        schemes: this.treatmentSchemes.map((s) => s.toPayload())
+      },
+      doseresponse: this.doseResponse.map((r) => r.toPayload()),
+      health: this.health.map((h) => h.toPayload())
     };
   }
 

src/core/model/qmra/Qmra.type.ts

@@ -24,16 +24,14 @@ interface IQmraData {
 }
 
 export interface IQmraRequest {
-  config: {
-    exposure: IExposure[];
-    inflow: IPathogenPayload[];
-    treatment: {
-      processes: ITreatmentProcessPayload[];
-      schemes: ITreatmentSchemePayload[];
-    };
-    doseresponse: IDoseResponsePayload[];
-    health: IHealthPayload[];
+  exposure: IExposure[];
+  inflow: IPathogenPayload[];
+  treatment: {
+    processes: ITreatmentProcessPayload[];
+    schemes: ITreatmentSchemePayload[];
   };
+  doseresponse: IDoseResponsePayload[];
+  health: IHealthPayload[];
 }
 
 export default IQmra;

src/scenes/t15/components/DoseResponse/DoseResponseForm.tsx

@@ -53,16 +53,16 @@ const DoseResponseForm = ({onChange, readOnly, selectedDoseResponse}: IProps) =>
 
     if (value === 'beta-Poisson') {
       cItem.bestFitModel = 'beta-Poisson';
-      cItem.k = NaN;
+      cItem.k = null;
       cItem.n50 = 0;
       cItem.alpha = 0;
     }
 
     if (value === 'exponential') {
       cItem.bestFitModel = 'exponential';
       cItem.k = 0;
-      cItem.n50 = NaN;
-      cItem.alpha = NaN;
+      cItem.n50 = null;
+      cItem.alpha = null;
     }
 
     setElement(cItem);
@@ -100,7 +100,7 @@ const DoseResponseForm = ({onChange, readOnly, selectedDoseResponse}: IProps) =>
             placeholder="alpha"
             readOnly={readOnly}
             type="number"
-            value={activeInput === 'alpha' ? activeValue : element.alpha}
+            value={activeInput === 'alpha' ? activeValue : element.alpha || 0}
           />
         </Form.Field>
         <Form.Field>
@@ -112,7 +112,7 @@ const DoseResponseForm = ({onChange, readOnly, selectedDoseResponse}: IProps) =>
             placeholder="N50"
             readOnly={readOnly}
             type="number"
-            value={activeInput === 'n50' ? activeValue : element.n50}
+            value={activeInput === 'n50' ? activeValue : element.n50 || 0}
           />
         </Form.Field>
       </Form.Group>
@@ -127,7 +127,7 @@ const DoseResponseForm = ({onChange, readOnly, selectedDoseResponse}: IProps) =>
           placeholder="k"
           readOnly={readOnly}
           type="number"
-          value={activeInput === 'k' ? activeValue : element.k}
+          value={activeInput === 'k' ? activeValue : element.k || 0}
         />
       </Form.Field>
       }

src/scenes/t15/components/JsonUpload.tsx

@@ -1,15 +1,15 @@
-import { Button, Icon, Message, Modal } from 'semantic-ui-react';
-import { JSON_SCHEMA_URL } from '../../../services/api';
+import {Button, Icon, Message, Modal} from 'semantic-ui-react';
+import {JSON_SCHEMA_URL} from '../../../services/api';
 import {validate as jsonSchemaValidate} from '../../../services/jsonSchemaValidator';
 import Qmra from '../../../core/model/qmra/Qmra';
-import React, { ChangeEvent, useState } from 'react';
+import React, {ChangeEvent, useState} from 'react';
 
 interface IProps {
   onChange: (response: Qmra) => void;
   qmra: Qmra;
 }
 
-const JsonUpload = ({ onChange, qmra }: IProps) => {
+const JsonUpload = ({onChange, qmra}: IProps) => {
   const [data, setData] = useState<any>();
   const [errors, setErrors] = useState<string[]>([]);
   const [isLoading, setIsLoading] = useState<boolean>(false);
@@ -22,17 +22,23 @@ const JsonUpload = ({ onChange, qmra }: IProps) => {
     }
   };
 
+  const checkFile = (data: any) => Array.isArray(data.inflow) && Array.isArray(data.exposure) &&
+    Array.isArray(data.doseresponse) && Array.isArray(data.health) && data.treatment &&
+    Array.isArray(data.treatment.processes) && Array.isArray(data.treatment.schemes);
+
   const handleConfirm = () => {
     let q = Qmra.fromDefaults();
-    if ('config' in data) {
-      q = qmra.fromPayload(data);
+
+    if ('config' in data && checkFile(data.config)) {
+      q = qmra.fromPayload(data.config);
     }
-    if ('data' in data) {
+    if ('data' in data && checkFile(data.data)) {
       q = Qmra.fromObject(data);
     }
-    if ('inflow' in data) {
+    if ('inflow' in data && checkFile(data)) {
       q = qmra.fromPayload(data);
     }
+
     setShowModal(false);
     onChange(q);
   };
@@ -54,27 +60,30 @@ const JsonUpload = ({ onChange, qmra }: IProps) => {
 
     if (!checkPassed) {
       setData(undefined);
+      setShowModal(true);
       e.push('Invalid JSON');
+      setErrors(e);
     }
 
     const d = JSON.parse(text);
 
-    // TODO: JSON SCHEME VALIDATION
-
     jsonSchemaValidate(
       d,
       JSON_SCHEMA_URL + '/qmra/qmra.payload.json'
     ).then((r) => {
-      console.log(r);
+      if (r[0]) {
+        setErrors([]);
+        setIsLoading(false);
+        setShowModal(true);
+        setData(d);
+      } else {
+        if (Array.isArray(r[1]) && 'message' in r[1][0]) {
+          setErrors(r[1].map((e) => e.message));
+        }
+        setIsLoading(false);
+        setShowModal(true);
+      }
     });
-
-    if (checkPassed && e.length === 0) {
-      setData(d);
-    }
-
-    setErrors(e);
-    setIsLoading(false);
-    setShowModal(true);
   };
 
   const handleUploadFile = (e: ChangeEvent<HTMLInputElement>) => {
@@ -97,7 +106,7 @@ const JsonUpload = ({ onChange, qmra }: IProps) => {
         labelPosition="left"
         loading={isLoading}
       />
-      <input hidden={true} type="file" id="inputField" onChange={handleUploadFile} />
+      <input hidden={true} type="file" id="inputField" onChange={handleUploadFile}/>
       <Modal onClose={handleTriggerModal} open={showModal} size="small">
         <Modal.Header>Upload Json</Modal.Header>
         <Modal.Content>
@@ -111,17 +120,17 @@ const JsonUpload = ({ onChange, qmra }: IProps) => {
         {errors.length > 0 && (
           <Modal.Actions>
             <Button color="grey" onClick={handleTriggerModal}>
-              <Icon name="remove" /> Close
+              <Icon name="remove"/> Close
             </Button>
           </Modal.Actions>
         )}
         {errors.length < 1 && (
           <Modal.Actions>
             <Button color="red" onClick={handleTriggerModal}>
-              <Icon name="remove" /> No
+              <Icon name="remove"/> No
             </Button>
             <Button color="green" onClick={handleConfirm}>
-              <Icon name="checkmark" /> Yes
+              <Icon name="checkmark"/> Yes
             </Button>
           </Modal.Actions>
         )}