Merge pull request #94 from samply/develop

Develop

package.json

@@ -1,7 +1,7 @@
 {
   "name": "@samply/lens",
   "description": "A web component library for clinical data search and visualisation",
-  "version": "0.0.5",
+  "version": "0.1.0",
   "type": "module",
   "module": "dist/lens.js",
   "main": "dist/lens.umd.js",

packages/demo/public/options.json

@@ -1,6 +1,9 @@
 {
     "iconOptions": {
-        "infoUrl": "info-circle-svgrepo-com.svg"
+        "infoUrl": "info-circle-svgrepo-com.svg",
+        "selectAll": {
+            "text": "Add all"
+        }
     },
     "chartOptions": {
         "patients": {

packages/lib/src/components/Options.wc.svelte

@@ -35,6 +35,22 @@
                     ) {
                         store.set("infoUrl", options.iconOptions.infoUrl);
                     }
+                    if (
+                        "selectAll" in options.iconOptions &&
+                        typeof options.iconOptions["selectAll"] === "object" &&
+                        options.iconOptions.selectAll
+                    ) {
+                        // Allow for future possibility of iconUrl instead of text
+                        if (
+                            "text" in options.iconOptions.selectAll &&
+                            typeof options.iconOptions.selectAll["text"] ===
+                                "string"
+                        )
+                            store.set(
+                                "selectAllText",
+                                options.iconOptions.selectAll.text,
+                            );
+                    }
                 }
             }
 

packages/lib/src/components/catalogue/DataTreeElement.svelte

@@ -1,4 +1,5 @@
 <script lang="ts">
+    import { addItemToQuery, activeQueryGroupIndex } from "../../stores/query";
     import type { Category } from "../../types/treeData";
     import DataTreeElement from "./DataTreeElement.svelte";
     import NumberInputComponent from "./NumberInputComponent.svelte";
@@ -37,7 +38,6 @@
      * watches the open tree nodes store to update the open state of the subcategorys
      */
     let open: boolean = false;
-
     $: {
         if (subCategoryName) {
             open = $openTreeNodes
@@ -93,6 +93,13 @@
         });
     };
 
+    let finalParent: boolean =
+        !("childCategories" in element) &&
+        (!("fieldType" in element) ||
+            ("fieldType" in element &&
+                typeof element.fieldType === "string" &&
+                element.fieldType == "single-select"));
+
     /**
      * watches the number input store to update the number input components
      */
@@ -131,6 +138,32 @@
         }
         return store;
     });
+
+    $: selectAllText = $iconStore.get("selectAllText");
+
+    const selectAllOptions = (): void => {
+        if (!("criteria" in element)) return;
+
+        element.criteria.forEach((criterion) => {
+            const queryItem: QueryItem = {
+                id: uuidv4(),
+                key: element.key,
+                name: element.name,
+                system: "system" in element ? element.system : "",
+                type: "type" in element ? element.type : "",
+                values: [
+                    {
+                        name: criterion.name,
+                        value: criterion.aggregatedValue
+                            ? criterion.aggregatedValue
+                            : criterion.key,
+                        queryBindId: uuidv4(),
+                    },
+                ],
+            };
+            addItemToQuery(queryItem, $activeQueryGroupIndex);
+        });
+    };
 </script>
 
 <div part="data-tree-element">
@@ -160,6 +193,12 @@
         <InfoButtonComponent message={element.infoButtonText} />
     {/if}
 
+    {#if finalParent && open}
+        <button part="add-all-options-button" on:click={selectAllOptions}>
+            {selectAllText ? selectAllText : "Add all"}
+        </button>
+    {/if}
+
     {#if open}
         {#if "childCategories" in element}
             {#each element.childCategories as child}

packages/lib/src/components/search-bar/SearchBarMultipleComponent.wc.svelte

@@ -10,17 +10,10 @@
 />
 
 <script lang="ts">
-    import type { Category } from "../../types/treeData";
     import { queryStore } from "../../stores/query";
     import SearchBarComponent from "./SearchBarComponent.wc.svelte";
     import type { QueryItem } from "../../types/queryData";
 
-    /**
-     * props
-     * @param treeData takes a Category tree to build the autocomplete items from
-     * @param noMatchesFoundMessage takes a string to display when no matches are found
-     */
-    export let treeData: Category[] = [];
     export let noMatchesFoundMessage: string = "No matches found";
     export let placeholderText: string = "Type to filter conditions";
 
@@ -40,7 +33,6 @@
     {#each $queryStore as _, index}
         <div part="search-bar-wrapper">
             <SearchBarComponent
-                {treeData}
                 {noMatchesFoundMessage}
                 {placeholderText}
                 {index}

packages/lib/src/cql-translator-service/ast-to-cql-translator.ts

@@ -119,8 +119,11 @@ const getSingleton = (criterion: AstBottomLayerValue): string => {
         if (myCQL) {
             switch (myCriterion.type) {
                 case "gender":
+                case "BBMRI_gender":
                 case "histology":
                 case "conditionValue":
+                case "BBMRI_conditionValue":
+                case "BBMRI_conditionSampleDiagnosis":
                 case "conditionBodySite":
                 case "conditionLocalization":
                 case "observation":
@@ -131,6 +134,8 @@ const getSingleton = (criterion: AstBottomLayerValue): string => {
                 case "procedureResidualstatus":
                 case "medicationStatement":
                 case "specimen":
+                case "BBMRI_specimen":
+                case "BBMRI_hasSpecimen":
                 case "hasSpecimen":
                 case "Organization":
                 case "observationMolecularMarkerName":

packages/lib/src/cql-translator-service/cqlquery-mappings.ts

@@ -63,6 +63,21 @@ export const alias = new Map<string, string>([
         "http://dktk.dkfz.de/fhir/onco/core/CodeSystem/TNMmSymbolCS",
     ],
     ["molecularMarker", "http://www.genenames.org"],
+
+    ["BBMRI_icd10", "http://hl7.org/fhir/sid/icd-10"],
+    ["BBMRI_icd10gm", "http://fhir.de/CodeSystem/dimdi/icd-10-gm"],
+    [
+        "BBMRI_SampleMaterialType",
+        "https://fhir.bbmri.de/CodeSystem/SampleMaterialType",
+    ], //specimentype
+    [
+        "BBMRI_StorageTemperature",
+        "https://fhir.bbmri.de/CodeSystem/StorageTemperature",
+    ],
+    [
+        "BBMRI_SmokingStatus",
+        "http://hl7.org/fhir/uv/ips/ValueSet/current-smoking-status-uv-ips",
+    ],
 ]);
 
 export const cqltemplate = new Map<string, string>([
@@ -192,6 +207,69 @@ export const cqltemplate = new Map<string, string>([
         "(exists ([Observation: Code '21908-9' from loinc] O where O.value.coding.code contains '{{C}}')) or (exists ([Observation: Code '21902-2' from loinc] O where O.value.coding.code contains '{{C}}'))",
     ],
     ["histology", "exists from [Observation: Code '59847-4' from loinc] O\n"],
+
+    ["BBMRI_gender", "Patient.gender"],
+    [
+        "BBMRI_conditionSampleDiagnosis",
+        "((exists[Condition: Code '{{C}}' from {{A1}}]) or (exists[Condition: Code '{{C}}' from {{A2}}])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains '{{C}}'))",
+    ],
+    ["BBMRI_conditionValue", "exists [Condition: Code '{{C}}' from {{A1}}]"],
+    [
+        "BBMRI_conditionRangeDate",
+        "exists from [Condition] C\nwhere FHIRHelpers.ToDateTime(C.onset) between {{D1}} and {{D2}}",
+    ],
+    [
+        "BBMRI_conditionRangeAge",
+        "exists from [Condition] C\nwhere AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) between Ceiling({{D1}}) and Ceiling({{D2}})",
+    ],
+    ["BBMRI_age", "AgeInYears() between Ceiling({{D1}}) and Ceiling({{D2}})"],
+    [
+        "BBMRI_observation",
+        "exists from [Observation: Code '{{K}}' from {{A1}}] O\nwhere O.value.coding.code contains '{{C}}'",
+    ],
+    [
+        "BBMRI_observationSmoker",
+        "exists from [Observation: Code '72166-2' from {{A1}}] O\nwhere O.value.coding.code contains '{{C}}'",
+    ],
+    [
+        "BBMRI_observationRange",
+        "exists from [Observation: Code '{{K}}' from {{A1}}] O\nwhere O.value between {{D1}} and {{D2}}",
+    ],
+    [
+        "BBMRI_observationBodyWeight",
+        "exists from [Observation: Code '29463-7' from {{A1}}] O\nwhere ((O.value as Quantity) < {{D1}} 'kg' and (O.value as Quantity) > {{D2}} 'kg')",
+    ],
+    [
+        "BBMRI_observationBMI",
+        "exists from [Observation: Code '39156-5' from {{A1}}] O\nwhere ((O.value as Quantity) < {{D1}} 'kg/m2' and (O.value as Quantity) > {{D2}} 'kg/m2')",
+    ],
+    ["BBMRI_hasSpecimen", "exists [Specimen]"],
+    ["BBMRI_specimen", "exists [Specimen: Code '{{C}}' from {{A1}}]"],
+    ["BBMRI_retrieveSpecimenByType", "(S.type.coding.code contains '{{C}}')"],
+    [
+        "BBMRI_retrieveSpecimenByTemperature",
+        "(S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding.code contains '{{C}}')",
+    ],
+    [
+        "BBMRI_retrieveSpecimenBySamplingDate",
+        "(FHIRHelpers.ToDateTime(S.collection.collected) between {{D1}} and {{D2}})",
+    ],
+    [
+        "BBMRI_retrieveSpecimenByFastingStatus",
+        "(S.collection.fastingStatus.coding.code contains '{{C}}')",
+    ],
+    [
+        "BBMRI_samplingDate",
+        "exists from [Specimen] S\nwhere FHIRHelpers.ToDateTime(S.collection.collected) between {{D1}} and {{D2}}",
+    ],
+    [
+        "BBMRI_fastingStatus",
+        "exists from [Specimen] S\nwhere S.collection.fastingStatus.coding.code contains '{{C}}'",
+    ],
+    [
+        "BBMRI_storageTemperature",
+        "exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding contains Code '{{C}}' from {{A1}})",
+    ],
 ]);
 
 export const criterionMap = new Map<string, { type: string; alias?: string[] }>(
@@ -309,5 +387,43 @@ export const criterionMap = new Map<string, { type: string; alias?: string[] }>(
         ["75186-7", { type: "observation", alias: ["loinc", "vitalstatuscs"] }], //Vitalstatus
         //["Organization", {type: "Organization"}],
         ["Organization", { type: "department" }],
+
+        ["BBMRI_gender", { type: "BBMRI_gender" }],
+        [
+            "BBMRI_diagnosis",
+            {
+                type: "BBMRI_conditionSampleDiagnosis",
+                alias: ["BBMRI_icd10", "BBMRI_icd10gm"],
+            },
+        ],
+        [
+            "BBMRI_body_weight",
+            { type: "BBMRI_observationBodyWeight", alias: ["loinc"] },
+        ], //Body weight
+        ["BBMRI_bmi", { type: "BBMRI_observationBMI", alias: ["loinc"] }], //BMI
+        [
+            "BBMRI_smoking_status",
+            { type: "BBMRI_observationSmoker", alias: ["loinc"] },
+        ], //Smoking habit
+        ["BBMRI_donor_age", { type: "BBMRI_age" }],
+        ["BBMRI_date_of_diagnosis", { type: "BBMRI_conditionRangeDate" }],
+        [
+            "BBMRI_sample_kind",
+            { type: "BBMRI_specimen", alias: ["BBMRI_SampleMaterialType"] },
+        ],
+        [
+            "BBMRI_storage_temperature",
+            {
+                type: "BBMRI_storageTemperature",
+                alias: ["BBMRI_StorageTemperature"],
+            },
+        ],
+        ["BBMRI_pat_with_samples", { type: "BBMRI_hasSpecimen" }],
+        ["BBMRI_diagnosis_age_donor", { type: "BBMRI_conditionRangeAge" }],
+        [
+            "BBMRI_fasting_status",
+            { type: "BBMRI_fastingStatus", alias: ["loinc"] },
+        ],
+        ["BBMRI_sampling_date", { type: "BBMRI_samplingDate" }],
     ],
 );

packages/lib/src/styles/catalogue.css

@@ -52,6 +52,17 @@ lens-catalogue::part(data-tree-element-toggle-icon) {
   transition: all 0.1s ease-in-out;
 }
 
+lens-catalogue::part(add-all-options-button) {
+  background-color: var(--button-background-color);
+  border-radius: var(--border-radius-small);
+  color: var(--button-color);
+  position: relative;
+  padding: 3px 8px;
+  cursor: pointer;
+  border: none;
+  left: +15px;
+}
+
 lens-catalogue::part(data-tree-element-toggle-icon-open) {
   transform: rotate(0deg);
 }