Changes for release v0.4.6

package.json

@@ -1,7 +1,7 @@
 {
   "name": "@samply/lens",
   "description": "A web component library for clinical data search and visualisation",
-  "version": "0.4.5",
+  "version": "0.4.6",
   "type": "module",
   "module": "dist/lens.js",
   "main": "dist/lens.umd.js",

packages/demo/src/AppCCP.svelte

@@ -21,7 +21,9 @@
     let catalogueUrl: string = "";
     let optionsFilePath: string = "";
 
-    if (import.meta.env.VITE_TARGET_ENVIRONMENT === "production") {
+    let environment = import.meta.env.VITE_TARGET_ENVIRONMENT;
+
+    if (environment === "production") {
         catalogueUrl = "catalogues/catalogue-dktk.json";
         optionsFilePath = "options-ccp-prod.json";
     } else {
@@ -158,10 +160,12 @@
         <div class="charts">
             <div class="chart-wrapper result-summary">
                 <lens-result-summary />
-                <lens-negotiate-button
-                    type={"ccp"}
-                    title={"Daten und Proben Anfragen"}
-                ></lens-negotiate-button>
+                {#if environment !== "production"}
+                    <lens-negotiate-button
+                        type={"ProjectManager"}
+                        title={"Daten und Proben Anfragen"}
+                    ></lens-negotiate-button>
+                {/if}
                 <lens-search-modified-display
                     >Diagramme repräsentieren nicht mehr die aktuelle Suche!</lens-search-modified-display
                 >
@@ -290,7 +294,7 @@
     >
     <a
         class="privacy-policy"
-        href="https://hub.dkfz.de/s/M8Ldxd5GsfrQG9S"
+        href="https://hub.dkfz.de/s/5LPccy6fgRSoD65"
         download="datenschutzerklaerung"
         target="_blank">Datenschutz</a
     >

packages/demo/src/main.ts

@@ -5,9 +5,6 @@
 
 import "../../lib";
 
-// import "./fragment-development.css";
-// import App from "./AppFragmentDevelopment.svelte";
-
 import "./ccp.css";
 import App from "./AppCCP.svelte";
 

packages/demo/src/measures.ts

@@ -64,7 +64,6 @@ First(
 
 define AgeClass:
 if (Patient.birthDate is null) then 'unknown' else ToString((AgeInYears() div 10) * 10)
-if (PrimaryDiagnosis.onset is null) then 'unknown' else ToString((AgeInYearsAt(FHIRHelpers.ToDateTime(PrimaryDiagnosis.onset)) div 10) * 10)
 
 define PatientDeceased:
 First (from [Observation: Code '75186-7' from loinc] O return O.value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/VitalstatusCS').code.first())

packages/lib/index.ts

@@ -13,4 +13,4 @@ export { default as DataPasser } from "./src/components/DataPasser.wc.svelte";
 export { default as ModifiedSearchComponent } from "./src/components/informational/ModifiedSearchComponent.wc.svelte";
 export { default as ErrorToasts } from "./src/components/ErrorToasts.wc.svelte";
 
-export * from "./src/styles/index.css";
+import "./src/styles/index.css";

packages/lib/src/classes/blaze.ts

@@ -25,7 +25,7 @@ export class Blaze {
         try {
             let response: ResponseStore = new Map<string, Site>().set(
                 this.name,
-                { status: "claimed", data: {} as SiteData },
+                { status: "claimed" },
             );
 
             this.updateResponse(response);

packages/lib/src/classes/spot.ts

@@ -2,7 +2,7 @@
  * TODO: document this class
  */
 
-import type { SiteData, Status } from "../types/response";
+import type { SiteData } from "../types/response";
 import type { ResponseStore } from "../types/backend";
 import type { BeamResult } from "../types/spot";
 import { errorChannel } from "../stores/error-channel";
@@ -67,7 +67,7 @@ export class Spot {
                 const response: BeamResult = JSON.parse(message.data);
                 if (response.task !== this.currentTask) return;
                 const site: string = response.from.split(".")[1];
-                const status: Status = response.status;
+                const status = response.status;
                 const body: SiteData =
                     status === "succeeded"
                         ? JSON.parse(atob(response.body))
@@ -80,13 +80,6 @@ export class Spot {
                 updateResponse(parsedResponse);
             });
 
-            // read error events from beam
-            eventSource.addEventListener("error", (message) => {
-                console.error(`Beam returned error ${message}`);
-                errorChannel.set("Fehler von Beam erhalten"); // show user-facing error
-                eventSource.close();
-            });
-
             // event source in javascript throws an error then the event source is closed by backend
             eventSource.onerror = () => {
                 console.info(

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

@@ -6,6 +6,7 @@
 
 <!-- This component offers an api to pass and get data from the stores -->
 <script lang="ts">
+    import { get } from "svelte/store";
     import { catalogue, getCriteria } from "../stores/catalogue";
     import { responseStore, updateResponseStore } from "../stores/response";
     import {
@@ -24,6 +25,7 @@
         RemoveValueFromQueryAPIParams,
     } from "../types/dataPasser";
     import { buildQueryFromAst } from "../helpers/ast-transformer";
+    import type { Category } from "../types/treeData";
 
     /**
      * Getters
@@ -65,11 +67,20 @@
      * returns the catalogue to the library user
      * @param category the category name (e.g. "diagnosis")
      * @returns array of strings containing the bottom level items' keys
+     * @deprecated Marked for deletion in v0.4.7. You may use getCatalogueAPI() and extract the criteria yourself.
      */
     export const getCriteriaAPI = (category: string): string[] => {
         return getCriteria(category);
     };
 
+    /**
+     * Get the catalogue
+     * @returns The catalogue
+     */
+    export const getCatalogueAPI = (): Category[] => {
+        return get(catalogue);
+    };
+
     /**
      * Setters
      */

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

@@ -8,30 +8,56 @@
     import { fade } from "svelte/transition";
     import { errorChannel } from "../stores/error-channel";
 
-    let toasts: { uuid: string; message: string }[] = [];
+    // Each toast has a unique id that maps to the error message
+    let toasts: Map<string, string> = new Map();
 
     /**
      * @param message user-facing error message
      */
     function showToast(message: string): void {
-        toasts.push({ uuid: crypto.randomUUID(), message });
+        const uuid = crypto.randomUUID();
+        toasts.set(uuid, message);
         toasts = toasts; // update
 
         setTimeout(() => {
-            toasts.shift();
+            toasts.delete(uuid);
             toasts = toasts; // update
         }, 8000);
     }
 
     // subscribe to error channel
-    $: if ($errorChannel) {
+    $: if ($errorChannel !== "") {
         showToast($errorChannel);
         errorChannel.set("");
     }
 </script>
 
 <div part="flex-container">
-    {#each toasts as toast (toast.uuid)}
-        <div out:fade part="toast">{toast.message}</div>
+    {#each toasts as [uuid, message] (uuid)}
+        <div out:fade part="toast">
+            <div part="message">{message}</div>
+            <button
+                part="close-button"
+                on:click={() => {
+                    toasts.delete(uuid);
+                    toasts = toasts; // update
+                }}
+            >
+                <svg
+                    xmlns="http://www.w3.org/2000/svg"
+                    fill="none"
+                    viewBox="0 0 24 24"
+                    stroke-width="1.5"
+                    stroke="currentColor"
+                    style="height: 24px; width: 24px; display: block;"
+                >
+                    <path
+                        stroke-linecap="round"
+                        stroke-linejoin="round"
+                        d="M6 18 18 6M6 6l12 12"
+                    />
+                </svg>
+            </button>
+        </div>
     {/each}
 </div>

packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte

@@ -7,7 +7,7 @@
 <script lang="ts">
     import { datarequestsStore } from "../../stores/datarequests";
     import { negotiate } from "../../services/ccpProjectManager";
-    import { bbmrinegotiate } from "../../services/bbmriNegotiate";
+    import { bbmriNegotiate } from "../../services/bbmriNegotiate";
 
     export let title: string = "Negotiate with biobanks";
     export let type: string;
@@ -16,9 +16,9 @@
      *
      */
     function exec(): void {
-        if (type == "bbmri") {
-            bbmrinegotiate($datarequestsStore);
-        } else if (type == "ccp") {
+        if (type == "Negotiator") {
+            bbmriNegotiate($datarequestsStore);
+        } else if (type == "ProjectManager") {
             negotiate($datarequestsStore);
         }
     }

packages/lib/src/components/buttons/SearchButtonComponenet.wc.svelte

@@ -23,7 +23,7 @@
     } from "../../types/backend";
     import type { BlazeOption } from "../../types/blaze";
     import type { SpotOption } from "../../types/spot";
-    import type { AstTopLayer } from "../../types/ast";
+    import { isTopLayer, type AstTopLayer } from "../../types/ast";
     import type { Site } from "../../types/response";
 
     export let title: string = "Search";
@@ -54,12 +54,10 @@
         // If one of the AND nodes has no children that means the corresponding search bar is empty.
         if (
             ast.children.some(
-                (child) =>
-                    child.nodeType === "branch" && child.children.length === 0,
+                (child) => isTopLayer(child) && child.children.length === 0,
             ) &&
             ast.children.some(
-                (child) =>
-                    child.nodeType === "branch" && child.children.length !== 0,
+                (child) => isTopLayer(child) && child.children.length !== 0,
             )
         ) {
             console.error(

packages/lib/src/components/buttons/StoreDeleteButtonComponent.svelte

@@ -3,6 +3,7 @@
         queryStore,
         removeItemFromQuery,
         removeValueFromQuery,
+        queryModified,
     } from "../../stores/query";
     import { iconStore } from "../../stores/icons";
     import type { QueryItem } from "../../types/queryData";
@@ -23,6 +24,7 @@
         dispatch("clear-search");
 
         if (type === "group") {
+            queryModified.set(true);
             queryStore.update((query) => {
                 query = query.filter((group, i) => i !== index);
                 if (query.length === 0) {