Merge pull request #68 from samply/feature/aggregate-ffpe-tissue-in-c…

…atalogue-and-chart Feature/aggregate ffpe tissue in catalogue and chart
samply · Mar 20, 2024 · aa14d2e · aa14d2e
2 parents 537c9c0 + 40214f6
commit aa14d2e
Show file tree

Hide file tree

Showing 4 changed files with 109 additions and 8 deletions.
diff --git a/packages/demo/public/catalogues/catalogue-dktk.json b/packages/demo/public/catalogues/catalogue-dktk.json
@@ -20181,14 +20181,46 @@
                                 {
                                     "value": "histology",
                                     "name": "tumor-tissue-ffpe"
+                                },
+                                {
+                                    "value": "sample_kind",
+                                    "name": "tissue-ffpe"
+                                },
+                                {
+                                    "value": "sample_kind",
+                                    "name": "normal-tissue-ffpe"
+                                },
+                                {
+                                    "value": "sample_kind",
+                                    "name": "other-tissue-ffpe"
                                 }
                             ]
                         ]
                     },
                     {
                         "key": "tumor-tissue-frozen",
                         "name": "Gewebe schockgefroren",
-                        "description": "Tumorgewebe (Kryo/Frisch)"
+                        "description": "Tumorgewebe (Kryo/Frisch)",
+                        "aggregatedValue": [
+                            [
+                                {
+                                    "value": "sample_kind",
+                                    "name": "tissue-frozen"
+                                },
+                                {
+                                    "value": "sample_kind",
+                                    "name": "tumor-tissue-frozen"
+                                },
+                                {
+                                    "value": "sample_kind",
+                                    "name": "normal-tissue-frozen"
+                                },
+                                {
+                                    "value": "sample_kind",
+                                    "name": "other-tissue-frozen"
+                                }
+                            ]
+                        ]
                     },
                     {
                         "key": "tissue-other",

diff --git a/packages/demo/public/options.json b/packages/demo/public/options.json
@@ -83,9 +83,29 @@
             "hintText": [
                 "Verteilung der Probentypen die mit den identifizierten Patienten verbunden sind."
             ],
+            "accumulatedValues": [
+                {
+                    "name": "ffpe-tissue",
+                    "values": [
+                        "tissue-ffpe",
+                        "tumor-tissue-ffpe",
+                        "normal-tissue-ffpe",
+                        "other-tissue-ffpe"
+                    ]
+                },
+                {
+                    "name": "frozen-tissue",
+                    "values": [
+                        "tissue-frozen",
+                        "tumor-tissue-frozen",
+                        "normal-tissue-frozen",
+                        "other-tissue-frozen"
+                    ]
+                }
+            ],
             "tooltips": {
-                "tissue-ffpe": "Gewebe FFPE",
-                "tissue-frozen": "Gewebe schockgefroren",
+                "ffpe-tissue": "Gewebe FFPE",
+                "frozen-tissue": "Gewebe schockgefroren",
                 "tissue-other": "Gewebe, Andere Konservierungsart",
                 "whole-blood": "Vollblut",
                 "blood-serum": "Serum",
@@ -106,8 +126,8 @@
                 "derivative-other": "Derivat, Andere"
             },
             "legendMapping":{
-                "tissue-ffpe": "Gewebe FFPE",
-                "tissue-frozen": "Gewebe schockgefroren",
+                "ffpe-tissue": "Gewebe FFPE",
+                "frozen-tissue": "Gewebe schockgefroren",
                 "tissue-other": "Gewebe, Andere Konservierungsart",
                 "whole-blood": "Vollblut",
                 "blood-serum": "Serum",

diff --git a/packages/lib/src/components/results/ChartComponent.wc.svelte b/packages/lib/src/components/results/ChartComponent.wc.svelte
@@ -52,7 +52,6 @@
     export let filterRegex: string = "";
     export let groupingLabel: string = "";
     export let viewScales: boolean = chartType !== "pie" ? true : false;
-
     let options: ChartOption;
     $: options =
         ($lensOptions?.chartOptions &&
@@ -171,6 +170,23 @@
         },
     };
 
+    const accumulateValues = (
+        responseStore: ResponseStore,
+        valuesToAccumulate: string[],
+        catalogueGroupCode: string,
+    ): number => {
+        let aggregatedData = 0;
+
+        valuesToAccumulate.forEach((value: string) => {
+            aggregatedData += getAggregatedPopulationForStratumCode(
+                responseStore,
+                value,
+                catalogueGroupCode,
+            );
+        });
+        return aggregatedData;
+    };
+
     /**
      * gets the aggregated population for a given stratum code
      * @param responseStore - the response store
@@ -242,6 +258,36 @@
             });
         }
 
+        /**
+         * if accumulated values are set, accumulate the values of the given stratum codes and adds them to the chart
+         * e.g. {name: "frozen-tissue", values: ["tissue-frozen","tissue-ffpe"]}
+         * will remove the values from the chart and add their accumulated value to "frozen-tissue"
+         */
+        if (
+            options.accumulatedValues !== undefined &&
+            options.accumulatedValues.length > 0
+        ) {
+            options.accumulatedValues.forEach((valueToAccumulate) => {
+                const aggregationCount: number = accumulateValues(
+                    responseStore,
+                    valueToAccumulate.values,
+                    catalogueGroupCode,
+                );
+
+                combinedSubGroupData.data.push(aggregationCount);
+                combinedSubGroupData.labels.push(valueToAccumulate.name);
+
+                for (let i = 0; i < combinedSubGroupData.labels.length; i++) {
+                    const element: string = combinedSubGroupData.labels[i];
+                    if (valueToAccumulate.values.includes(element)) {
+                        combinedSubGroupData.labels.splice(i, 1);
+                        combinedSubGroupData.data.splice(i, 1);
+                        i--;
+                    }
+                }
+            });
+        }
+
         return {
             labels: combinedSubGroupData.labels,
             data: [
@@ -384,7 +430,11 @@
          * will be aggregated in groups if a divider is set
          * eg. 'C30', 'C31.1', 'C31.2' -> 'C31' when divider is '.'
          */
-        let chartData = getChartDataSets(responseStore, chartLabels);
+        let chartData: ChartDataSets = getChartDataSets(
+            responseStore,
+            chartLabels,
+        );
+
         chart.data.datasets = chartData.data;
         chartLabels = chartData.labels;
 

diff --git a/packages/lib/src/stores/query.ts b/packages/lib/src/stores/query.ts
@@ -219,7 +219,6 @@ export const addStratifier = ({
     groupRange,
 }): void => {
     let queryItem: QueryItem;
-    console.log(catalogue);
     catalogue.forEach((parentCategory: Category) => {
         if ("childCategories" in parentCategory) {
             parentCategory.childCategories.forEach(