Merge pull request #27 from samply/feature/ffpe-specimen

Feature/ffpe specimen

packages/demo/public/options.json

@@ -115,7 +115,44 @@
             },
             {
                 "title": "Bioproben*",
-                "dataKey": "specimen"
+                "aggregatedDataKeys": [
+                    {
+                        "groupCode": "specimen"
+                    },
+                    {
+                        "stratifierCode": "Histlogoies",
+                        "stratumCode": "1"
+                    },
+                    {
+                    }
+                ]
+            }
+        ]
+    },
+    "resultSummaryOptions": {
+        "title": "Ergebnisse",
+        "dataTypes": [
+            {
+                "title": "Standorte",
+                "dataKey": "collections"
+            },
+            {
+                "title": "Patienten",
+                "dataKey": "patients"
+            },
+            {
+                "title": "Bioproben*",
+                "aggregatedDataKeys": [
+                    {
+                        "groupCode": "specimen"
+                    },
+                    {
+                        "stratifierCode": "Histlogoies",
+                        "stratumCode": "1"
+                    },
+                    {
+                    }
+                ]
             }
         ]
     }

packages/demo/src/AppCCP.svelte

@@ -7,6 +7,7 @@
     dktkPatientsMeasure,
     dktkProceduresMeasure,
     dktkSpecimenMeasure,
+    dktkHistologyMeasure
   } from "./measures";
 
   let mockCatalogueData = "";
@@ -30,6 +31,7 @@
     dktkSpecimenMeasure,
     dktkProceduresMeasure,
     dktkMedicationStatementsMeasure,
+    dktkHistologyMeasure
   ];
 
   const backendMeasures = `DKTK_STRAT_DEF_IN_INITIAL_POPULATION`;
@@ -209,8 +211,6 @@
     <div class="charts">
       <div class="chart-wrapper result-summary">
         <lens-result-summary
-          title="Ergebnisse"
-          resultSummaryDataTypes={JSON.stringify(resultSummaryConfig)}
         />
         <lens-search-modified-display>Diagramme repräsentieren nicht mehr die aktuelle Suche!</lens-search-modified-display>
       </div>

packages/demo/src/measures.ts

@@ -1025,3 +1025,49 @@ export const dktkMedicationStatementsMeasure = {
 DKTK_STRAT_MEDICATION_STRATIFIER
 `,
 };
+
+export const dktkHistologyMeasure = {
+  key: 'Histo',
+  measure: {
+    code: {
+      text: 'Histo',
+    },
+    extension: [
+      {
+        url: 'http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-populationBasis',
+        valueCode: 'Observation',
+      },
+    ],
+    population: [
+      {
+        code: {
+          coding: [
+            {
+              system:
+                'http://terminology.hl7.org/CodeSystem/measure-population',
+              code: 'initial-population',
+            },
+          ],
+        },
+        criteria: {
+          language: 'text/cql-identifier',
+          expression: 'Histo',
+        },
+      },
+    ],
+    stratifier: [
+      {
+        code: {
+          text: 'Histlogoies',
+        },
+        criteria: {
+          language: 'text/cql-identifier',
+          expression: 'Histlogoy',
+        },
+      },
+    ],
+  },
+  cql: `
+  DKTK_STRAT_HISTOLOGY_STRATIFIER
+`,
+};

packages/lib/src/components/results/ResultSummaryComponent.wc.svelte

@@ -8,24 +8,31 @@
 />
 
 <script lang="ts">
-    import { uiSiteMappingsStore } from "../../stores/mappings";
+    import { lensOptions } from "../../stores/options";
     import {
         responseStore,
         getAggregatedPopulation,
+        getAggregatedPopulationForStratumCode,
     } from "../../stores/response";
     import type { ResponseStore } from "../../types/backend";
-    import NegotiateButtonComponent from "../buttons/NegotiateButtonComponent.wc.svelte";
 
-    export let title: string = "";
-    export let resultSummaryDataTypes: { key: string; title: string; population?: string | number }[] = [];
-    export let negotiateButton: boolean = false;
-    export let negotiateButtonText: string = "Negotiate";
 
+    let options: any = {};
+    $: options = $lensOptions.resultSummaryOptions
+
+    let resultSummaryDataTypes: { key: string; title: string; population?: string | number }[]
+    $: resultSummaryDataTypes = options?.dataTypes || [];
+
+    
     /**
      * Extracts the population for each result summary data type and adds it to the type object
      * @param store
      */
     const fillPopulationToSummaryTypes = (store: ResponseStore): void => {
+        if (!options?.dataTypes) {
+            return;
+        }
+        console.log(store);
         
         /**
          * show the number of sites with data and the number of sites claimed/succeeded
@@ -42,34 +49,56 @@
             }
         });
 
-        resultSummaryDataTypes = resultSummaryDataTypes.map((type) => {  
+        resultSummaryDataTypes = options.dataTypes.map((type) => {
+            console.log(getAggregatedPopulationForStratumCode(store, '1', "Histlogoies"));
             /**
-             * If the type is sites, the population is the length of the store
-             * TODO: very specific. this should be more generic
+             * If the type is collections, the population is the length of the store
              */
-            if (type.key === "sites") {
+            if (type.dataKey === "collections") {
                 type.population =`${sitesWithData} / ${sitesClaimed}`;
                 return type;
             }
 
             /**
-             * otherwise, get the population from the store
+             * if the type has only one dataKey, the population is the aggregated population of that dataKey
+             */
+
+            if(type.dataKey) {
+                type.population = getAggregatedPopulation(store, type.dataKey);
+                return type;
+            }
+
+            /**
+             * if the type has multiple dataKeys to aggregate, the population is the aggregated population of all dataKeys
              */
-            type.population = getAggregatedPopulation(store, type.key);
+
+            let aggregatedPopulation: number = 0;
+
+            type.aggregatedDataKeys.forEach((dataKey) => {
+                if(dataKey.groupCode){
+                    aggregatedPopulation += getAggregatedPopulation(store, dataKey.groupCode);
+                } else if(dataKey.stratifierCode && dataKey.stratumCode) {
+                    aggregatedPopulation += getAggregatedPopulationForStratumCode(store, dataKey.stratumCode, dataKey.stratifierCode);
+                }
+                /**
+                 * TODO: add support for stratifiers if needed?
+                 * needs to be implemented in response.ts
+                */
+            });
+
+            type.population = aggregatedPopulation;
             return type;
         });
     };
 
-    responseStore.subscribe((store: ResponseStore): void => {
-        fillPopulationToSummaryTypes(store);
-    });
+    $: fillPopulationToSummaryTypes($responseStore);
 
 </script>
 
-{#if title}
+{#if options?.title}
     <div part="result-summary-header">
         <h4 part="result-summary-header-title">
-            {title}
+            {options.title}
         </h4>
     </div>
 {/if}
@@ -80,8 +109,4 @@
         </div>
     {/each}
 </div>
-{#if negotiateButton}
-    <div part="result-summary-footer">
-        <NegotiateButtonComponent title={negotiateButtonText} />
-    </div>
-{/if}
+

packages/lib/src/components/results/ResultTableComponent.wc.svelte

@@ -10,6 +10,7 @@
     import { negotiateStore } from "../../stores/negotiate";
     import {
         getSitePopulationForCode,
+        getSitePopulationForStratumCode,
         responseStore,
     } from "../../stores/response";
     import TableItemComponent from "./TableItemComponent.svelte";
@@ -26,7 +27,7 @@
      */
     let options: any;
     $: options = ($lensOptions?.tableOptions && $lensOptions?.tableOptions) || {
-        headerData: [{ title: "", dataKey: "" }],
+        headerData: [{ title: "", dataKey: "", aggregatedDataKeys: []}],
     };
 
     $: options?.headerData?.forEach(
@@ -49,16 +50,40 @@
 
             let tableRow: (string | number)[] = [];
 
+
+            /**
+             * builds the table items for each row
+             * the first item is the name of the collection
+             * the following items are the population for each data type (single or aggregated)
+            */
             options.headerData.forEach(
                 (header: HeaderData, index: number): void => {
                     if (index === 0) {
                         const name = $uiSiteMappingsStore.get(key);
                         tableRow.push(name);
-                    } else {
-                        tableRow.push(
-                            getSitePopulationForCode(value.data, header.dataKey)
-                        );
+                        return;
+                    }
+                    if(header.dataKey) {
+                        tableRow.push(getSitePopulationForCode(value.data, header.dataKey));
+                        return;
                     }
+
+                    let aggregatedPopulation: number = 0;
+
+                    header.aggregatedDataKeys.forEach((dataKey) => {
+                        if(dataKey.groupCode){
+                            aggregatedPopulation += getSitePopulationForCode(value.data, dataKey.groupCode);
+                        } else if(dataKey.stratifierCode && dataKey.stratumCode) {
+                            aggregatedPopulation += getSitePopulationForStratumCode(value.data, dataKey.stratumCode, dataKey.stratifierCode);
+                        }
+                        /**
+                         * TODO: add support for stratifiers if needed?
+                         * needs to be implemented in response.ts
+                        */
+                    });
+
+                    tableRow.push(aggregatedPopulation);
+
                 }
             );
 

packages/lib/src/stores/options.ts

@@ -1,4 +1,4 @@
 import { writable } from "svelte/store";
 
 
-export const lensOptions = writable<any>()
+export const lensOptions = writable<any>({})

packages/lib/src/types/biobanks.ts

@@ -1,7 +1,12 @@
 
 export type HeaderData = {
     title: string;
-    dataKey: string;
+    dataKey?: string;
+    aggregatedDataKeys?: {
+        groupCode?: string;
+        stratifierCode?: string;
+        stratumCode?: string;
+    }[];
     ascending?: boolean;
     hintText?: string[];
 };