From 95741dcd3ebaf430c5e6b9be832123930212eff7 Mon Sep 17 00:00:00 2001
From: Patrick Skowronek <patrick.skowronek@dkfz-heidelberg.de>
Date: Tue, 29 Oct 2024 15:53:48 +0100
Subject: [PATCH 1/5] feat: implement bbmri negotiator

---
 .../NegotiateButtonComponent.wc.svelte        |   5 +-
 packages/lib/src/stores/negotiate.ts          | 470 +++++++++---------
 packages/lib/src/types/options.ts             |  14 +
 3 files changed, 255 insertions(+), 234 deletions(-)

diff --git a/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte b/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte
index a9066b9..d1c20e6 100644
--- a/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte
+++ b/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte
@@ -8,15 +8,14 @@
     import { negotiate, negotiateStore } from "../../stores/negotiate";
 
     export let title: string = "Negotiate with biobanks";
-    let disabled: boolean = false;
 </script>
 
 <button
     part={`lens-negotiate-button lens-negotiate-button-${
-        disabled ? "disabled" : "active"
+        $negotiateStore.length === 0 ? "disabled" : "active"
     }`}
     on:click={() => negotiate($negotiateStore)}
-    {disabled}
+    disabled={$negotiateStore.length === 0}
 >
     <div part="lens-negotiate-button-title">
         {title}
diff --git a/packages/lib/src/stores/negotiate.ts b/packages/lib/src/stores/negotiate.ts
index 0e06c3c..01517e5 100644
--- a/packages/lib/src/stores/negotiate.ts
+++ b/packages/lib/src/stores/negotiate.ts
@@ -5,20 +5,16 @@ import { buildAstFromQuery } from "../helpers/ast-transformer";
 import type { AstElement, AstTopLayer } from "../types/ast";
 import { lensOptions } from "./options";
 import { v4 as uuidv4 } from "uuid";
-import type { Collection } from "../types/collection";
 import type { SendableQuery } from "../types/queryData";
-import { translateAstToCql } from "../cql-translator-service/ast-to-cql-translator";
-import { buildLibrary, buildMeasure } from "../helpers/cql-measure";
-import type { MeasureStore } from "../types/backend";
 import { measureStore } from "./measures";
-import type { LensOptions } from "../types/options";
+import type {
+    LensOptions,
+    NegotiateOptions,
+    NegotiateOptionsSiteMapping,
+} from "../types/options";
 
 export const negotiateStore = writable<string[]>([]);
 
-let currentQuery: QueryItem[][] = [[]];
-
-let currentMeasures: MeasureStore = [];
-
 queryStore.subscribe((query) => {
     currentQuery = query;
 });
@@ -104,22 +100,17 @@ export const getHumanReadableQuery = (): string => {
     return humanReadableQuery;
 };
 
-/**
- * sets all options needed for the negotiator
- */
-type NegotiateOptions = {
-    negotiateApp: "negotiator" | "project-manager";
-    siteMapping: { site: string; collection: string }[];
-    newProjectUrl: string;
-    editProjectUrl: string;
+type NegotiatorResponse = Response & {
+    url?: string;
+    redirect_uri?: string;
+    id?: string;
+    status: number;
 };
 
-type NegotiatorResponse = Response & { url?: string; redirect_uri?: string };
-
 let negotiateOptions: NegotiateOptions;
-const siteCollectionMap: Map<string, string> = new Map();
-const urlParams: URLSearchParams = new URLSearchParams(window.location.search);
-const collectionParams: string | null = urlParams.get("collections");
+const siteCollectionMap: Map<string, NegotiateOptionsSiteMapping> = new Map();
+// const urlParams: URLSearchParams = new URLSearchParams(window.location.search);
+// const collectionParams: string | null = urlParams.get("collections");
 
 lensOptions.subscribe((options: LensOptions) => {
     if (!options) return;
@@ -130,48 +121,32 @@ lensOptions.subscribe((options: LensOptions) => {
      */
 
     negotiateOptions = options.negotiateOptions as NegotiateOptions;
-    negotiateOptions?.siteMapping?.forEach(
-        ({ site, collection }: { site: string; collection: string }) => {
-            siteCollectionMap.set(site, collection);
-            if (
-                collectionParams !== null &&
-                collectionParams.split(",").includes(collection)
-            ) {
-                negotiateStore.update((value) => {
-                    return [...value, site];
-                });
-            }
-        },
-    );
+    negotiateOptions?.siteMappings?.forEach((site) => {
+        siteCollectionMap.set(site.site, site);
+        // if (
+        //     collectionParams !== null &&
+        //     collectionParams.split(",").includes(collection)
+        // ) {
+        //     negotiateStore.update((value) => {
+        //         return [...value, site];
+        //     });
+        // }
+    });
 });
 
 /**
  * @param sitesToNegotiate the sites to negotiate with
  * @returns an array of Collection objects
  */
-export const getCollections = (sitesToNegotiate: string[]): Collection[] => {
-    const siteCollections: Collection[] = [];
+export const getCollections = (
+    sitesToNegotiate: string[],
+): NegotiateOptionsSiteMapping[] => {
+    const siteCollections: NegotiateOptionsSiteMapping[] = [];
 
     sitesToNegotiate.forEach((site: string) => {
-        let collectionId: string = "";
-
         // TODO: Why is site id mapped to Uppercase?
         if (siteCollectionMap.has(site) && siteCollectionMap.get(site) !== "") {
-            collectionId = siteCollectionMap.get(site) || "";
-        }
-
-        const siteId: string = site.split(":collection:")[0];
-
-        if (collectionId !== "") {
-            siteCollections.push({
-                siteId,
-                site,
-                collectionId,
-                /**
-                 * TODO: add the local redirect uri here
-                 */
-                localRedirectUri: "some uri",
-            });
+            siteCollections.push(siteCollectionMap.get(site));
         }
     });
 
@@ -185,9 +160,6 @@ export const getCollections = (sitesToNegotiate: string[]): Collection[] => {
  * @param sitesToNegotiate the sites to negotiate with
  */
 export const negotiate = async (sitesToNegotiate: string[]): Promise<void> => {
-    console.log("enter negotiate");
-    console.log("currentMeasures", currentMeasures);
-
     let sendableQuery!: SendableQuery;
     queryStore.subscribe((value: QueryItem[][]) => {
         const uuid = uuidv4();
@@ -197,81 +169,107 @@ export const negotiate = async (sitesToNegotiate: string[]): Promise<void> => {
         };
     });
 
-    const queryBase64String: string = btoa(JSON.stringify(sendableQuery.query));
     const humanReadable: string = getHumanReadableQuery();
-    const collections: Collection[] = getCollections(sitesToNegotiate);
+    const collections: NegotiateOptionsSiteMapping[] =
+        getCollections(sitesToNegotiate);
     // TODO: Implement proper configuration option for the switch between negotiator and project manager
-    const negotiatorResponse = true
-        ? await sendRequestToNegotiator(
-              sendableQuery,
-              humanReadable,
-              collections,
-              queryBase64String,
-          )
-        : await sendRequestToProjectManager(
-              sendableQuery,
-              humanReadable,
-              collections,
-              queryBase64String,
-          );
-
-    console.log(negotiatorResponse);
+    const negotiatorResponse = await sendRequestToNegotiator(
+        sendableQuery,
+        humanReadable,
+        collections,
+    );
+    // : await sendRequestToProjectManager(
+    //       sendableQuery,
+    //       humanReadable,
+    //       collections,
+    //       queryBase64String,
+    //   );
 
     /**
      * handle redirect to project manager url
      */
-    if (negotiateOptions.negotiateApp === "project-manager") {
-        // project manager
-
-        if (!negotiatorResponse.redirect_uri) {
-            console.error("Negotiator response does not contain redirect uri");
-            return;
-        }
-
-        const indexOfQuestionMark: number = negotiatorResponse.redirect_uri
-            .toString()
-            .indexOf("?");
-
-        const subpage = "/project-view";
-        const negotiationURI =
-            negotiatorResponse.redirect_uri
-                .toString()
-                .slice(0, indexOfQuestionMark) +
-            `${subpage}` +
-            negotiatorResponse.redirect_uri
-                .toString()
-                .slice(indexOfQuestionMark);
-
-        window.location.href = negotiationURI;
-    }
+    // if (negotiateOptions.negotiateApp === "project-manager") {
+    //     // project manager
+
+    //     if (!negotiatorResponse.redirect_uri) {
+    //         console.error("Negotiator response does not contain redirect uri");
+    //         return;
+    //     }
+
+    //     const indexOfQuestionMark: number = negotiatorResponse.redirect_uri
+    //         .toString()
+    //         .indexOf("?");
+
+    //     const subpage = "/project-view";
+    //     const negotiationURI =
+    //         negotiatorResponse.redirect_uri
+    //             .toString()
+    //             .slice(0, indexOfQuestionMark) +
+    //         `${subpage}` +
+    //         negotiatorResponse.redirect_uri
+    //             .toString()
+    //             .slice(indexOfQuestionMark);
+
+    //     window.location.href = negotiationURI;
+    // }
 
     /**
      * handle redirect to negotiator url
      */
     if (negotiateOptions.negotiateApp === "negotiator") {
-        // negotiator
-        if (!negotiatorResponse.url) {
-            console.error("Negotiator response does not contain redirect uri");
-            return;
+        switch (negotiatorResponse.status) {
+            case 201: {
+                if (!negotiatorResponse.url) {
+                    console.error(
+                        "Negotiator response does not contain redirect uri",
+                    );
+                    return;
+                } else {
+                    const data = await negotiatorResponse.json();
+                    window.location.href = data.redirectUrl;
+                }
+                break;
+            }
+            case 401: {
+                alert(
+                    "An unexpected error has occurred. Please contact support if the issue persists.",
+                );
+                break;
+            }
+            case 400:
+            case 500: {
+                alert(
+                    "The service is temporarily unavailable. Please try again in a few minutes.",
+                );
+                break;
+            }
         }
 
-        window.location.href = `https://negotiator.bbmri-eric.eu/requests/${sendableQuery.id}`;
+        // negotiator
     }
 };
 
+interface BbmriCollectionResource {
+    id: string;
+    name: string;
+    organization: {
+        id: number;
+        externalId: string;
+        name: string;
+    };
+}
+
 /**
  *
  * @param sendableQuery the query to be sent to the negotiator
  * @param humanReadable a human readable query string to view in the negotiator project
  * @param collections the collections to negotiate with
- * @param queryBase64String the query in base64 string format
  * @returns the redirect uri from the negotiator
  */
 async function sendRequestToNegotiator(
     sendableQuery: SendableQuery,
     humanReadable: string,
-    collections: Collection[],
-    queryBase64String: string,
+    collections: NegotiateOptionsSiteMapping[],
 ): Promise<NegotiatorResponse> {
     const base64Query: string = btoa(JSON.stringify(sendableQuery.query));
 
@@ -279,29 +277,39 @@ async function sendRequestToNegotiator(
 
     let response!: Response;
 
+    const BBMRI_collection_resource: BbmriCollectionResource[] = [];
+
+    collections.forEach(function (collection) {
+        BBMRI_collection_resource.push({
+            id: collection.collection,
+            name: collection.collection,
+            organization: {
+                id: 0,
+                externalId: collection.site_id,
+                name: collection.site,
+            },
+        });
+    });
+
     try {
-        response = await fetch(
-            `${negotiateOptions.newProjectUrl}?nToken=${sendableQuery.id}`,
-            {
-                method: "POST",
-                headers: {
-                    Accept: "application/json; charset=utf-8",
-                    "Content-Type": "application/json",
-                    Authorization: "TODO: insert auth here",
-                },
-                body: JSON.stringify({
-                    humanReadable: humanReadable,
-                    URL: returnURL,
-                    collections: collections,
-                    nToken: sendableQuery.id,
-                    query: queryBase64String,
-                }),
+        response = await fetch(`${negotiateOptions.newProjectUrl}`, {
+            method: "POST",
+            headers: {
+                Accept: "application/json; charset=utf-8",
+                "Content-Type": "application/json",
+                Authorization:
+                    "Basic YmJtcmktZGlyZWN0b3J5Omw5RFJLVUROcTBTbDAySXhaUGQ2",
             },
-        );
+            body: JSON.stringify({
+                humanReadable: humanReadable,
+                url: returnURL,
+                resources: BBMRI_collection_resource,
+            }),
+        });
 
         return response as NegotiatorResponse;
     } catch (error) {
-        console.log("error", error);
+        console.error(error);
         return new Response() as NegotiatorResponse;
     }
 }
@@ -314,114 +322,114 @@ async function sendRequestToNegotiator(
  * @param queryBase64String the query in base64 string format
  * @returns a promise containing the response from the project manager. The response contains the redirect uri
  */
-async function sendRequestToProjectManager(
-    sendableQuery: SendableQuery,
-    humanReadable: string,
-    collections: Collection[],
-    queryBase64String: string,
-): Promise<NegotiatorResponse> {
-    /**
-     * get temporary token from oauth2
-     */
-    let temporaryToken: string | null = "";
-
-    try {
-        const res = await fetch(`/oauth2/auth`, {
-            method: "GET",
-            credentials: "include",
-        });
-
-        temporaryToken = res.headers.get("Authorization");
-    } catch (error) {
-        console.log("error", error);
-        return new Response() as Response & { redirect_uri: string };
-    }
-
-    /**
-     * build query params
-     */
-    const queryParam: string =
-        queryBase64String != "" ? `&query=${queryBase64String}` : "";
-
-    const negotiationPartners = collections
-        .map((collection) => collection.collectionId.toLocaleLowerCase())
-        .join(",");
-    const returnURL: string = `${window.location.protocol}//${window.location.host}/?collections=${negotiationPartners}${queryParam}`;
-    const urlParams: URLSearchParams = new URLSearchParams(
-        window.location.search,
-    );
-    const projectCode: string | null = urlParams.get("project-code");
-    const projectCodeParam: string = projectCode
-        ? `&project-code=${projectCode}`
-        : "";
-    const negotiateUrl = projectCode
-        ? negotiateOptions.editProjectUrl
-        : negotiateOptions.newProjectUrl;
-
-    let response!: NegotiatorResponse;
-
-    /**
-     * send request to project manager
-     */
-    try {
-        response = await fetch(
-            `${negotiateUrl}?explorer-ids=${negotiationPartners}&query-format=CQL_DATA&human-readable=${humanReadable}&explorer-url=${encodeURIComponent(returnURL)}${projectCodeParam}`,
-            {
-                method: "POST",
-                headers: {
-                    returnAccept: "application/json; charset=utf-8",
-                    "Content-Type": "application/json",
-                    Authorization: temporaryToken ? temporaryToken : "",
-                },
-                body: getCql(),
-            },
-        ).then((response) => response.json());
-
-        /**
-         * replace query-code with project-code
-         * TODO: remove when backend bug is fixed
-         */
-        if (response?.redirect_uri) {
-            response.redirect_uri = response.redirect_uri.replace(
-                "query-code",
-                "project-code",
-            );
-        }
-
-        return response;
-    } catch (error) {
-        console.log("error", error);
-        return new Response() as NegotiatorResponse;
-    }
-}
+// async function sendRequestToProjectManager(
+//     sendableQuery: SendableQuery,
+//     humanReadable: string,
+//     collections: NegotiateOptionsSiteMapping[],
+//     queryBase64String: string,
+// ): Promise<NegotiatorResponse> {
+//     /**
+//      * get temporary token from oauth2
+//      */
+//     let temporaryToken: string | null = "";
+
+//     try {
+//         const res = await fetch(`/oauth2/auth`, {
+//             method: "GET",
+//             credentials: "include",
+//         });
+
+//         temporaryToken = res.headers.get("Authorization");
+//     } catch (error) {
+//         console.log("error", error);
+//         return new Response() as Response & { redirect_uri: string };
+//     }
+
+//     /**
+//      * build query params
+//      */
+//     const queryParam: string =
+//         queryBase64String != "" ? `&query=${queryBase64String}` : "";
+
+//     const negotiationPartners = collections
+//         .map((collection) => collection.collection_id.toLocaleLowerCase())
+//         .join(",");
+//     const returnURL: string = `${window.location.protocol}//${window.location.host}/?collections=${negotiationPartners}${queryParam}`;
+//     const urlParams: URLSearchParams = new URLSearchParams(
+//         window.location.search,
+//     );
+//     const projectCode: string | null = urlParams.get("project-code");
+//     const projectCodeParam: string = projectCode
+//         ? `&project-code=${projectCode}`
+//         : "";
+//     const negotiateUrl = projectCode
+//         ? negotiateOptions.editProjectUrl
+//         : negotiateOptions.newProjectUrl;
+
+//     let response!: NegotiatorResponse;
+
+//     /**
+//      * send request to project manager
+//      */
+//     try {
+//         response = await fetch(
+//             `${negotiateUrl}?explorer-ids=${negotiationPartners}&query-format=CQL_DATA&human-readable=${humanReadable}&explorer-url=${encodeURIComponent(returnURL)}${projectCodeParam}`,
+//             {
+//                 method: "POST",
+//                 headers: {
+//                     returnAccept: "application/json; charset=utf-8",
+//                     "Content-Type": "application/json",
+//                     Authorization: temporaryToken ? temporaryToken : "",
+//                 },
+//                 body: getCql(),
+//             },
+//         ).then((response) => response.json());
+
+//         /**
+//          * replace query-code with project-code
+//          * TODO: remove when backend bug is fixed
+//          */
+//         if (response?.redirect_uri) {
+//             response.redirect_uri = response.redirect_uri.replace(
+//                 "query-code",
+//                 "project-code",
+//             );
+//         }
+
+//         return response;
+//     } catch (error) {
+//         console.log("error", error);
+//         return new Response() as NegotiatorResponse;
+//     }
+// }
 
 /**
  * @returns a base64 encoded CQL query
  */
-function getCql(): string {
-    const ast = buildAstFromQuery(currentQuery);
-
-    /**
-     * TODO:
-     * For now backenMeasures is hardcoded because
-     * this function only needed for dktk project manager so far.
-     * Change if needed for negotiator.
-     *
-     * should be configurable via options other than spot/blaze, so custom backends can be used
-     */
-    const cql = translateAstToCql(
-        ast,
-        false,
-        "DKTK_STRAT_DEF_IN_INITIAL_POPULATION",
-        currentMeasures[0].measures,
-    );
-
-    const library = buildLibrary(`${cql}`);
-    const measure = buildMeasure(
-        library.url,
-        currentMeasures[0].measures.map((measureItem) => measureItem.measure),
-    );
-    const query = { lang: "cql", lib: library, measure: measure };
-
-    return btoa(decodeURI(JSON.stringify(query)));
-}
+// function getCql(): string {
+//     const ast = buildAstFromQuery(currentQuery);
+
+//     /**
+//      * TODO:
+//      * For now backenMeasures is hardcoded because
+//      * this function only needed for dktk project manager so far.
+//      * Change if needed for negotiator.
+//      *
+//      * should be configurable via options other than spot/blaze, so custom backends can be used
+//      */
+//     const cql = translateAstToCql(
+//         ast,
+//         false,
+//         "DKTK_STRAT_DEF_IN_INITIAL_POPULATION",
+//         currentMeasures[0].measures,
+//     );
+
+//     const library = buildLibrary(`${cql}`);
+//     const measure = buildMeasure(
+//         library.url,
+//         currentMeasures[0].measures.map((measureItem) => measureItem.measure),
+//     );
+//     const query = { lang: "cql", lib: library, measure: measure };
+
+//     return btoa(decodeURI(JSON.stringify(query)));
+// }
diff --git a/packages/lib/src/types/options.ts b/packages/lib/src/types/options.ts
index 493f005..8d9c54e 100644
--- a/packages/lib/src/types/options.ts
+++ b/packages/lib/src/types/options.ts
@@ -4,6 +4,20 @@ export type LensOptions = {
     catalogueKeyToResponseKeyMap?: string[][];
 };
 
+export type NegotiateOptionsSiteMapping = {
+    site: string;
+    site_id: string;
+    collection_id: string;
+    collection: string;
+};
+
+export type NegotiateOptions = {
+    negotiateApp: string;
+    newProjectUrl: string;
+    editProjectUrl: string;
+    siteMappings: NegotiateOptionsSiteMapping[];
+};
+
 export type ChartOptions = {
     [key: string]: ChartOption;
 };

From 070a2c4fb54578d597f8f73b305a37a8302be89d Mon Sep 17 00:00:00 2001
From: Patrick Skowronek <patrick.skowronek@dkfz-heidelberg.de>
Date: Wed, 30 Oct 2024 10:12:51 +0100
Subject: [PATCH 2/5] feat: seperate bbmri and ccp data requests

---
 packages/lib/src/services/bbmriNegotiate.ts   | 176 ++++++++++++++++++
 .../lib/src/services/ccpProjectManager.ts     | 175 +++++++++++++++++
 packages/lib/src/stores/datarequests.ts       |  83 +++++++++
 3 files changed, 434 insertions(+)
 create mode 100644 packages/lib/src/services/bbmriNegotiate.ts
 create mode 100644 packages/lib/src/services/ccpProjectManager.ts
 create mode 100644 packages/lib/src/stores/datarequests.ts

diff --git a/packages/lib/src/services/bbmriNegotiate.ts b/packages/lib/src/services/bbmriNegotiate.ts
new file mode 100644
index 0000000..8f6204f
--- /dev/null
+++ b/packages/lib/src/services/bbmriNegotiate.ts
@@ -0,0 +1,176 @@
+import { queryStore } from "../stores/query";
+
+import { lensOptions } from "../stores/options";
+import { v4 as uuidv4 } from "uuid";
+import type { QueryItem, SendableQuery } from "../types/queryData";
+import type {
+    LensOptions,
+    NegotiateOptions,
+    NegotiateOptionsSiteMapping,
+} from "../types/options";
+import { getHumanReadableQuery } from "../stores/datarequests";
+
+type NegotiatorResponse = Response & {
+    url?: string;
+    redirect_uri?: string;
+    id?: string;
+    status: number;
+};
+
+let negotiateOptions: NegotiateOptions;
+const siteCollectionMap: Map<string, NegotiateOptionsSiteMapping> = new Map();
+
+lensOptions.subscribe((options: LensOptions) => {
+    if (!options) return;
+
+    /**
+     * TODO: implement multiple collections per site
+     * need to know how multiple collections are returned from the backend
+     */
+
+    negotiateOptions = options.negotiateOptions as NegotiateOptions;
+    negotiateOptions?.siteMappings?.forEach((site) => {
+        siteCollectionMap.set(site.site, site);
+    });
+});
+
+/**
+ * @param sitesToNegotiate the sites to negotiate with
+ * @returns an array of Collection objects
+ */
+export const getCollections = (
+    sitesToNegotiate: string[],
+): NegotiateOptionsSiteMapping[] => {
+    const siteCollections: NegotiateOptionsSiteMapping[] = [];
+
+    sitesToNegotiate.forEach((site: string) => {
+        // TODO: Why is site id mapped to Uppercase?
+        if (siteCollectionMap.has(site) && siteCollectionMap.get(site) !== "") {
+            siteCollections.push(siteCollectionMap.get(site));
+        }
+    });
+
+    return siteCollections;
+};
+
+/**
+ * builds a sendable query object from the current query
+ * sends query to negotiator
+ * redirects to negotiator
+ * @param sitesToNegotiate the sites to negotiate with
+ */
+export const negotiate = async (sitesToNegotiate: string[]): Promise<void> => {
+    let sendableQuery!: SendableQuery;
+    queryStore.subscribe((value: QueryItem[][]) => {
+        const uuid = uuidv4();
+        sendableQuery = {
+            query: value,
+            id: `${uuid}__search__${uuid}`,
+        };
+    });
+
+    const humanReadable: string = getHumanReadableQuery();
+    const collections: NegotiateOptionsSiteMapping[] =
+        getCollections(sitesToNegotiate);
+    const negotiatorResponse = await sendRequestToNegotiator(
+        sendableQuery,
+        humanReadable,
+        collections,
+    );
+
+    switch (negotiatorResponse.status) {
+        case 201: {
+            if (!negotiatorResponse.url) {
+                console.error(
+                    "Negotiator response does not contain redirect uri",
+                );
+                return;
+            } else {
+                const data = await negotiatorResponse.json();
+                window.location.href = data.redirectUrl;
+            }
+            break;
+        }
+        case 401: {
+            alert(
+                "An unexpected error has occurred. Please contact support if the issue persists.",
+            );
+            break;
+        }
+        case 400:
+        case 500: {
+            alert(
+                "The service is temporarily unavailable. Please try again in a few minutes.",
+            );
+            break;
+        }
+    }
+};
+
+interface BbmriCollectionResource {
+    id: string;
+    name: string;
+    organization: {
+        id: number;
+        externalId: string;
+        name: string;
+    };
+}
+
+/**
+ *
+ * @param sendableQuery the query to be sent to the negotiator
+ * @param humanReadable a human readable query string to view in the negotiator project
+ * @param collections the collections to negotiate with
+ * @returns the redirect uri from the negotiator
+ */
+async function sendRequestToNegotiator(
+    sendableQuery: SendableQuery,
+    humanReadable: string,
+    collections: NegotiateOptionsSiteMapping[],
+): Promise<NegotiatorResponse> {
+    const base64Query: string = btoa(JSON.stringify(sendableQuery.query));
+
+    /**
+     * handle redirect to negotiator url
+     */
+    const returnURL: string = `${window.location.protocol}//${window.location.host}/?nToken=${sendableQuery.id}&query=${base64Query}`;
+
+    let response!: Response;
+
+    const BBMRI_collection_resource: BbmriCollectionResource[] = [];
+
+    collections.forEach(function (collection) {
+        BBMRI_collection_resource.push({
+            id: collection.collection,
+            name: collection.collection,
+            organization: {
+                id: 0,
+                externalId: collection.site_id,
+                name: collection.site,
+            },
+        });
+    });
+
+    try {
+        response = await fetch(`${negotiateOptions.newProjectUrl}`, {
+            method: "POST",
+            headers: {
+                Accept: "application/json; charset=utf-8",
+                "Content-Type": "application/json",
+                Authorization:
+                    "Basic YmJtcmktZGlyZWN0b3J5Omw5RFJLVUROcTBTbDAySXhaUGQ2",
+            },
+            body: JSON.stringify({
+                humanReadable: humanReadable,
+                url: returnURL,
+                resources: BBMRI_collection_resource,
+            }),
+        });
+
+        return response as NegotiatorResponse;
+    } catch (error) {
+        console.error(error);
+        return new Response() as NegotiatorResponse;
+    }
+}
diff --git a/packages/lib/src/services/ccpProjectManager.ts b/packages/lib/src/services/ccpProjectManager.ts
new file mode 100644
index 0000000..bf99185
--- /dev/null
+++ b/packages/lib/src/services/ccpProjectManager.ts
@@ -0,0 +1,175 @@
+// const urlParams: URLSearchParams = new URLSearchParams(window.location.search);
+// const collectionParams: string | null = urlParams.get("collections");
+
+// if (
+//     collectionParams !== null &&
+//     collectionParams.split(",").includes(collection)
+// ) {
+//     negotiateStore.update((value) => {
+//         return [...value, site];
+//     });
+// }
+
+// let sendableQuery!: SendableQuery;
+// queryStore.subscribe((value: QueryItem[][]) => {
+//     const uuid = uuidv4();
+//     sendableQuery = {
+//         query: value,
+//         id: `${uuid}__search__${uuid}`,
+//     };
+// });
+
+// : await sendRequestToProjectManager(
+//       sendableQuery,
+//       humanReadable,
+//       collections,
+//       queryBase64String,
+//   );
+
+/**
+ * handle redirect to project manager url
+ */
+// if (negotiateOptions.negotiateApp === "project-manager") {
+//     // project manager
+
+//     if (!negotiatorResponse.redirect_uri) {
+//         console.error("Negotiator response does not contain redirect uri");
+//         return;
+//     }
+
+//     const indexOfQuestionMark: number = negotiatorResponse.redirect_uri
+//         .toString()
+//         .indexOf("?");
+
+//     const subpage = "/project-view";
+//     const negotiationURI =
+//         negotiatorResponse.redirect_uri
+//             .toString()
+//             .slice(0, indexOfQuestionMark) +
+//         `${subpage}` +
+//         negotiatorResponse.redirect_uri
+//             .toString()
+//             .slice(indexOfQuestionMark);
+
+//     window.location.href = negotiationURI;
+// },
+
+/**
+ *
+ * @param sendableQuery the query to be sent to the negotiator
+ * @param humanReadable a human readable query string to view in the negotiator project
+ * @param collections the collections to negotiate with
+ * @param queryBase64String the query in base64 string format
+ * @returns a promise containing the response from the project manager. The response contains the redirect uri
+ */
+// async function sendRequestToProjectManager(
+//     sendableQuery: SendableQuery,
+//     humanReadable: string,
+//     collections: NegotiateOptionsSiteMapping[],
+//     queryBase64String: string,
+// ): Promise<NegotiatorResponse> {
+//     /**
+//      * get temporary token from oauth2
+//      */
+//     let temporaryToken: string | null = "";
+
+//     try {
+//         const res = await fetch(`/oauth2/auth`, {
+//             method: "GET",
+//             credentials: "include",
+//         });
+
+//         temporaryToken = res.headers.get("Authorization");
+//     } catch (error) {
+//         console.log("error", error);
+//         return new Response() as Response & { redirect_uri: string };
+//     }
+
+//     /**
+//      * build query params
+//      */
+//     const queryParam: string =
+//         queryBase64String != "" ? `&query=${queryBase64String}` : "";
+
+//     const negotiationPartners = collections
+//         .map((collection) => collection.collection_id.toLocaleLowerCase())
+//         .join(",");
+//     const returnURL: string = `${window.location.protocol}//${window.location.host}/?collections=${negotiationPartners}${queryParam}`;
+//     const urlParams: URLSearchParams = new URLSearchParams(
+//         window.location.search,
+//     );
+//     const projectCode: string | null = urlParams.get("project-code");
+//     const projectCodeParam: string = projectCode
+//         ? `&project-code=${projectCode}`
+//         : "";
+//     const negotiateUrl = projectCode
+//         ? negotiateOptions.editProjectUrl
+//         : negotiateOptions.newProjectUrl;
+
+//     let response!: NegotiatorResponse;
+
+//     /**
+//      * send request to project manager
+//      */
+//     try {
+//         response = await fetch(
+//             `${negotiateUrl}?explorer-ids=${negotiationPartners}&query-format=CQL_DATA&human-readable=${humanReadable}&explorer-url=${encodeURIComponent(returnURL)}${projectCodeParam}`,
+//             {
+//                 method: "POST",
+//                 headers: {
+//                     returnAccept: "application/json; charset=utf-8",
+//                     "Content-Type": "application/json",
+//                     Authorization: temporaryToken ? temporaryToken : "",
+//                 },
+//                 body: getCql(),
+//             },
+//         ).then((response) => response.json());
+
+//         /**
+//          * replace query-code with project-code
+//          * TODO: remove when backend bug is fixed
+//          */
+//         if (response?.redirect_uri) {
+//             response.redirect_uri = response.redirect_uri.replace(
+//                 "query-code",
+//                 "project-code",
+//             );
+//         }
+
+//         return response;
+//     } catch (error) {
+//         console.log("error", error);
+//         return new Response() as NegotiatorResponse;
+//     }
+// }
+
+/**
+ * @returns a base64 encoded CQL query
+ */
+// function getCql(): string {
+//     const ast = buildAstFromQuery(currentQuery);
+
+//     /**
+//      * TODO:
+//      * For now backenMeasures is hardcoded because
+//      * this function only needed for dktk project manager so far.
+//      * Change if needed for negotiator.
+//      *
+//      * should be configurable via options other than spot/blaze, so custom backends can be used
+//      */
+//     const cql = translateAstToCql(
+//         ast,
+//         false,
+//         "DKTK_STRAT_DEF_IN_INITIAL_POPULATION",
+//         currentMeasures[0].measures,
+//     );
+
+//     const library = buildLibrary(`${cql}`);
+//     const measure = buildMeasure(
+//         library.url,
+//         currentMeasures[0].measures.map((measureItem) => measureItem.measure),
+//     );
+//     const query = { lang: "cql", lib: library, measure: measure };
+
+//     return btoa(decodeURI(JSON.stringify(query)));
+// }
diff --git a/packages/lib/src/stores/datarequests.ts b/packages/lib/src/stores/datarequests.ts
new file mode 100644
index 0000000..864806c
--- /dev/null
+++ b/packages/lib/src/stores/datarequests.ts
@@ -0,0 +1,83 @@
+import { writable } from "svelte/store";
+
+import { buildAstFromQuery } from "../helpers/ast-transformer";
+import type { AstElement, AstTopLayer } from "../types/ast";
+import type { QueryItem } from "../types/queryData";
+import { queryStore } from "./query";
+
+export const datarequestsStore = writable<string[]>([]);
+
+/**
+ * Recursively builds a human readable query string from the AST
+ * @param queryLayer the current layer of the query
+ * @param humanReadableQuery string to append to
+ * @returns a human readable query string
+ */
+export const buildHumanReadableRecursively = (
+    queryLayer: AstElement,
+    humanReadableQuery: string,
+): string => {
+    if (
+        queryLayer === null ||
+        !("children" in queryLayer) ||
+        ("children" in queryLayer &&
+            (queryLayer.children === null ||
+                queryLayer.children.length === 0 ||
+                queryLayer.children[0] === null))
+    ) {
+        return humanReadableQuery;
+    }
+
+    if (queryLayer.children.length > 1) {
+        humanReadableQuery += "(";
+    }
+
+    queryLayer.children.forEach((child: AstElement, index: number): void => {
+        if ("type" in child && "value" in child && "key" in child) {
+            if (typeof child.value === "string") {
+                humanReadableQuery += `(${child.key} ${child.type} ${child.value})`;
+            }
+            if (
+                typeof child.value === "object" &&
+                "min" in child.value &&
+                "max" in child.value
+            ) {
+                humanReadableQuery += `(${child.key} ${child.type} ${child.value.min} and ${child.value.max})`;
+            }
+        }
+
+        humanReadableQuery = buildHumanReadableRecursively(
+            child,
+            humanReadableQuery,
+        );
+
+        if (index === queryLayer.children.length - 1) {
+        }
+        if (index < queryLayer.children.length - 1) {
+            humanReadableQuery += ` ${queryLayer.operand} `;
+        }
+    });
+
+    if (queryLayer.children.length > 1) {
+        humanReadableQuery += ")";
+    }
+
+    return humanReadableQuery;
+};
+
+/**
+ * @returns a human readable query string built from the current query
+ */
+export const getHumanReadableQuery = (): string => {
+    let humanReadableQuery: string = "";
+
+    queryStore.subscribe((value: QueryItem[][]) => {
+        const query: AstTopLayer = buildAstFromQuery(value);
+        humanReadableQuery = buildHumanReadableRecursively(
+            query,
+            humanReadableQuery,
+        );
+    });
+
+    return humanReadableQuery;
+};

From 3f7e83059e47a9d72cdcf41b68fd61d7cf3099f8 Mon Sep 17 00:00:00 2001
From: Patrick Skowronek <patrick.skowronek@dkfz-heidelberg.de>
Date: Wed, 30 Oct 2024 10:32:36 +0100
Subject: [PATCH 3/5] fix: changed to datarequestsstore

---
 .../buttons/InfoButtonComponent.wc.svelte     |   2 +-
 .../NegotiateButtonComponent.wc.svelte        |   9 +-
 .../results/ResultTableComponent.wc.svelte    |  10 +-
 .../results/TableItemComponent.svelte         |   8 +-
 packages/lib/src/stores/datarequests.ts       |   2 +
 packages/lib/src/stores/negotiate.ts          | 435 ------------------
 6 files changed, 17 insertions(+), 449 deletions(-)
 delete mode 100644 packages/lib/src/stores/negotiate.ts

diff --git a/packages/lib/src/components/buttons/InfoButtonComponent.wc.svelte b/packages/lib/src/components/buttons/InfoButtonComponent.wc.svelte
index 2719705..fd07aeb 100644
--- a/packages/lib/src/components/buttons/InfoButtonComponent.wc.svelte
+++ b/packages/lib/src/components/buttons/InfoButtonComponent.wc.svelte
@@ -8,7 +8,7 @@
     import {
         getHumanReadableQuery,
         buildHumanReadableRecursively,
-    } from "../../stores/negotiate";
+    } from "../../stores/datarequests";
     import { returnNestedValues } from "../../helpers/ast-transformer";
     import type { AstElement } from "../../types/ast";
     import type { QueryItem } from "../../types/queryData";
diff --git a/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte b/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte
index d1c20e6..3761a9f 100644
--- a/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte
+++ b/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte
@@ -5,17 +5,18 @@
 />
 
 <script lang="ts">
-    import { negotiate, negotiateStore } from "../../stores/negotiate";
+    import { datarequestsStore } from "../../stores/datarequests";
+    import { negotiate } from "../../services/bbmriNegotiate.ts";
 
     export let title: string = "Negotiate with biobanks";
 </script>
 
 <button
     part={`lens-negotiate-button lens-negotiate-button-${
-        $negotiateStore.length === 0 ? "disabled" : "active"
+        $datarequestsStore.length === 0 ? "disabled" : "active"
     }`}
-    on:click={() => negotiate($negotiateStore)}
-    disabled={$negotiateStore.length === 0}
+    on:click={() => negotiate($datarequestsStore)}
+    disabled={$datarequestsStore.length === 0}
 >
     <div part="lens-negotiate-button-title">
         {title}
diff --git a/packages/lib/src/components/results/ResultTableComponent.wc.svelte b/packages/lib/src/components/results/ResultTableComponent.wc.svelte
index 0facb44..1726292 100644
--- a/packages/lib/src/components/results/ResultTableComponent.wc.svelte
+++ b/packages/lib/src/components/results/ResultTableComponent.wc.svelte
@@ -6,7 +6,7 @@
 
 <script lang="ts">
     import { uiSiteMappingsStore } from "../../stores/mappings";
-    import { negotiateStore } from "../../stores/negotiate";
+    import { datarequestsStore } from "../../stores/datarequests.ts";
     import {
         getSitePopulationForCode,
         getSitePopulationForStratumCode,
@@ -134,11 +134,11 @@
     );
 
     /**
-     * watches the negotiateStore for changes to check or uncheck the checkbox
+     * watches the datarequestsStore for changes to check or uncheck the checkbox
      */
     let allChecked: boolean = false;
     $: allChecked =
-        $negotiateStore.length === tableRowData.length &&
+        $datarequestsStore.length === tableRowData.length &&
         tableRowData.length !== 0;
 
     /**
@@ -146,9 +146,9 @@
      */
     const checkAllBiobanks = (): void => {
         if (allChecked) {
-            $negotiateStore = [];
+            $datarequestsStore = [];
         } else {
-            $negotiateStore = tableRowData.map(
+            $datarequestsStore = tableRowData.map(
                 (tableRow: (string | number)[]) => tableRow[0] as string,
             );
         }
diff --git a/packages/lib/src/components/results/TableItemComponent.svelte b/packages/lib/src/components/results/TableItemComponent.svelte
index 0d99023..e7c752b 100644
--- a/packages/lib/src/components/results/TableItemComponent.svelte
+++ b/packages/lib/src/components/results/TableItemComponent.svelte
@@ -1,22 +1,22 @@
 <script lang="ts">
-    import { negotiateStore } from "../../stores/negotiate";
+    import { datarequestsStore } from "../../stores/datarequests";
 
     export let tableRow: (string | number)[];
 
     let checked: boolean = false;
-    $: checked = $negotiateStore.includes(tableRow[0] as string);
+    $: checked = $datarequestsStore.includes(tableRow[0] as string);
 
     /**
      * adds and removes tableRows from the negotiateStore whenever the checkbox is checked or unchecked
      */
     const updateStoreOnCheck = (): void => {
         if (!checked) {
-            negotiateStore.update((store: string[]) => {
+            datarequestsStore.update((store: string[]) => {
                 return [...store, tableRow[0] as string];
             });
         }
         if (checked) {
-            negotiateStore.update((store: string[]) => {
+            datarequestsStore.update((store: string[]) => {
                 return store.filter((site: string) => site !== tableRow[0]);
             });
         }
diff --git a/packages/lib/src/stores/datarequests.ts b/packages/lib/src/stores/datarequests.ts
index 864806c..7f144bc 100644
--- a/packages/lib/src/stores/datarequests.ts
+++ b/packages/lib/src/stores/datarequests.ts
@@ -33,6 +33,7 @@ export const buildHumanReadableRecursively = (
     }
 
     queryLayer.children.forEach((child: AstElement, index: number): void => {
+        if (child !== null) {
         if ("type" in child && "value" in child && "key" in child) {
             if (typeof child.value === "string") {
                 humanReadableQuery += `(${child.key} ${child.type} ${child.value})`;
@@ -56,6 +57,7 @@ export const buildHumanReadableRecursively = (
         if (index < queryLayer.children.length - 1) {
             humanReadableQuery += ` ${queryLayer.operand} `;
         }
+    }
     });
 
     if (queryLayer.children.length > 1) {
diff --git a/packages/lib/src/stores/negotiate.ts b/packages/lib/src/stores/negotiate.ts
deleted file mode 100644
index 01517e5..0000000
--- a/packages/lib/src/stores/negotiate.ts
+++ /dev/null
@@ -1,435 +0,0 @@
-import { writable } from "svelte/store";
-import { queryStore } from "./query";
-import type { QueryItem } from "../types/queryData";
-import { buildAstFromQuery } from "../helpers/ast-transformer";
-import type { AstElement, AstTopLayer } from "../types/ast";
-import { lensOptions } from "./options";
-import { v4 as uuidv4 } from "uuid";
-import type { SendableQuery } from "../types/queryData";
-import { measureStore } from "./measures";
-import type {
-    LensOptions,
-    NegotiateOptions,
-    NegotiateOptionsSiteMapping,
-} from "../types/options";
-
-export const negotiateStore = writable<string[]>([]);
-
-queryStore.subscribe((query) => {
-    currentQuery = query;
-});
-
-measureStore.subscribe((measures) => {
-    currentMeasures = measures;
-});
-
-/**
- * Recursively builds a human readable query string from the AST
- * @param queryLayer the current layer of the query
- * @param humanReadableQuery string to append to
- * @returns a human readable query string
- */
-export const buildHumanReadableRecursively = (
-    queryLayer: AstElement,
-    humanReadableQuery: string,
-): string => {
-    if (
-        queryLayer === null ||
-        !("children" in queryLayer) ||
-        ("children" in queryLayer &&
-            (queryLayer.children === null ||
-                queryLayer.children.length === 0 ||
-                queryLayer.children[0] === null))
-    ) {
-        return humanReadableQuery;
-    }
-
-    if (queryLayer.children.length > 1) {
-        humanReadableQuery += "(";
-    }
-
-    queryLayer.children.forEach((child: AstElement, index: number): void => {
-        if (child !== null) {
-            if ("type" in child && "value" in child && "key" in child) {
-                if (typeof child.value === "string") {
-                    humanReadableQuery += `(${child.key} ${child.type} ${child.value})`;
-                }
-                if (
-                    typeof child.value === "object" &&
-                    "min" in child.value &&
-                    "max" in child.value
-                ) {
-                    humanReadableQuery += `(${child.key} ${child.type} ${child.value.min} and ${child.value.max})`;
-                }
-            }
-
-            humanReadableQuery = buildHumanReadableRecursively(
-                child,
-                humanReadableQuery,
-            );
-
-            if (index === queryLayer.children.length - 1) {
-            }
-            if (index < queryLayer.children.length - 1) {
-                humanReadableQuery += ` ${queryLayer.operand} `;
-            }
-        }
-    });
-
-    if (queryLayer.children.length > 1) {
-        humanReadableQuery += ")";
-    }
-
-    return humanReadableQuery;
-};
-
-/**
- * @returns a human readable query string built from the current query
- */
-export const getHumanReadableQuery = (): string => {
-    let humanReadableQuery: string = "";
-
-    queryStore.subscribe((value: QueryItem[][]) => {
-        const query: AstTopLayer = buildAstFromQuery(value);
-        humanReadableQuery = buildHumanReadableRecursively(
-            query,
-            humanReadableQuery,
-        );
-    });
-
-    return humanReadableQuery;
-};
-
-type NegotiatorResponse = Response & {
-    url?: string;
-    redirect_uri?: string;
-    id?: string;
-    status: number;
-};
-
-let negotiateOptions: NegotiateOptions;
-const siteCollectionMap: Map<string, NegotiateOptionsSiteMapping> = new Map();
-// const urlParams: URLSearchParams = new URLSearchParams(window.location.search);
-// const collectionParams: string | null = urlParams.get("collections");
-
-lensOptions.subscribe((options: LensOptions) => {
-    if (!options) return;
-
-    /**
-     * TODO: implement multiple collections per site
-     * need to know how multiple collections are returned from the backend
-     */
-
-    negotiateOptions = options.negotiateOptions as NegotiateOptions;
-    negotiateOptions?.siteMappings?.forEach((site) => {
-        siteCollectionMap.set(site.site, site);
-        // if (
-        //     collectionParams !== null &&
-        //     collectionParams.split(",").includes(collection)
-        // ) {
-        //     negotiateStore.update((value) => {
-        //         return [...value, site];
-        //     });
-        // }
-    });
-});
-
-/**
- * @param sitesToNegotiate the sites to negotiate with
- * @returns an array of Collection objects
- */
-export const getCollections = (
-    sitesToNegotiate: string[],
-): NegotiateOptionsSiteMapping[] => {
-    const siteCollections: NegotiateOptionsSiteMapping[] = [];
-
-    sitesToNegotiate.forEach((site: string) => {
-        // TODO: Why is site id mapped to Uppercase?
-        if (siteCollectionMap.has(site) && siteCollectionMap.get(site) !== "") {
-            siteCollections.push(siteCollectionMap.get(site));
-        }
-    });
-
-    return siteCollections;
-};
-
-/**
- * builds a sendable query object from the current query
- * sends query to negotiator
- * redirects to negotiator
- * @param sitesToNegotiate the sites to negotiate with
- */
-export const negotiate = async (sitesToNegotiate: string[]): Promise<void> => {
-    let sendableQuery!: SendableQuery;
-    queryStore.subscribe((value: QueryItem[][]) => {
-        const uuid = uuidv4();
-        sendableQuery = {
-            query: value,
-            id: `${uuid}__search__${uuid}`,
-        };
-    });
-
-    const humanReadable: string = getHumanReadableQuery();
-    const collections: NegotiateOptionsSiteMapping[] =
-        getCollections(sitesToNegotiate);
-    // TODO: Implement proper configuration option for the switch between negotiator and project manager
-    const negotiatorResponse = await sendRequestToNegotiator(
-        sendableQuery,
-        humanReadable,
-        collections,
-    );
-    // : await sendRequestToProjectManager(
-    //       sendableQuery,
-    //       humanReadable,
-    //       collections,
-    //       queryBase64String,
-    //   );
-
-    /**
-     * handle redirect to project manager url
-     */
-    // if (negotiateOptions.negotiateApp === "project-manager") {
-    //     // project manager
-
-    //     if (!negotiatorResponse.redirect_uri) {
-    //         console.error("Negotiator response does not contain redirect uri");
-    //         return;
-    //     }
-
-    //     const indexOfQuestionMark: number = negotiatorResponse.redirect_uri
-    //         .toString()
-    //         .indexOf("?");
-
-    //     const subpage = "/project-view";
-    //     const negotiationURI =
-    //         negotiatorResponse.redirect_uri
-    //             .toString()
-    //             .slice(0, indexOfQuestionMark) +
-    //         `${subpage}` +
-    //         negotiatorResponse.redirect_uri
-    //             .toString()
-    //             .slice(indexOfQuestionMark);
-
-    //     window.location.href = negotiationURI;
-    // }
-
-    /**
-     * handle redirect to negotiator url
-     */
-    if (negotiateOptions.negotiateApp === "negotiator") {
-        switch (negotiatorResponse.status) {
-            case 201: {
-                if (!negotiatorResponse.url) {
-                    console.error(
-                        "Negotiator response does not contain redirect uri",
-                    );
-                    return;
-                } else {
-                    const data = await negotiatorResponse.json();
-                    window.location.href = data.redirectUrl;
-                }
-                break;
-            }
-            case 401: {
-                alert(
-                    "An unexpected error has occurred. Please contact support if the issue persists.",
-                );
-                break;
-            }
-            case 400:
-            case 500: {
-                alert(
-                    "The service is temporarily unavailable. Please try again in a few minutes.",
-                );
-                break;
-            }
-        }
-
-        // negotiator
-    }
-};
-
-interface BbmriCollectionResource {
-    id: string;
-    name: string;
-    organization: {
-        id: number;
-        externalId: string;
-        name: string;
-    };
-}
-
-/**
- *
- * @param sendableQuery the query to be sent to the negotiator
- * @param humanReadable a human readable query string to view in the negotiator project
- * @param collections the collections to negotiate with
- * @returns the redirect uri from the negotiator
- */
-async function sendRequestToNegotiator(
-    sendableQuery: SendableQuery,
-    humanReadable: string,
-    collections: NegotiateOptionsSiteMapping[],
-): Promise<NegotiatorResponse> {
-    const base64Query: string = btoa(JSON.stringify(sendableQuery.query));
-
-    const returnURL: string = `${window.location.protocol}//${window.location.host}/?nToken=${sendableQuery.id}&query=${base64Query}`;
-
-    let response!: Response;
-
-    const BBMRI_collection_resource: BbmriCollectionResource[] = [];
-
-    collections.forEach(function (collection) {
-        BBMRI_collection_resource.push({
-            id: collection.collection,
-            name: collection.collection,
-            organization: {
-                id: 0,
-                externalId: collection.site_id,
-                name: collection.site,
-            },
-        });
-    });
-
-    try {
-        response = await fetch(`${negotiateOptions.newProjectUrl}`, {
-            method: "POST",
-            headers: {
-                Accept: "application/json; charset=utf-8",
-                "Content-Type": "application/json",
-                Authorization:
-                    "Basic YmJtcmktZGlyZWN0b3J5Omw5RFJLVUROcTBTbDAySXhaUGQ2",
-            },
-            body: JSON.stringify({
-                humanReadable: humanReadable,
-                url: returnURL,
-                resources: BBMRI_collection_resource,
-            }),
-        });
-
-        return response as NegotiatorResponse;
-    } catch (error) {
-        console.error(error);
-        return new Response() as NegotiatorResponse;
-    }
-}
-
-/**
- *
- * @param sendableQuery the query to be sent to the negotiator
- * @param humanReadable a human readable query string to view in the negotiator project
- * @param collections the collections to negotiate with
- * @param queryBase64String the query in base64 string format
- * @returns a promise containing the response from the project manager. The response contains the redirect uri
- */
-// async function sendRequestToProjectManager(
-//     sendableQuery: SendableQuery,
-//     humanReadable: string,
-//     collections: NegotiateOptionsSiteMapping[],
-//     queryBase64String: string,
-// ): Promise<NegotiatorResponse> {
-//     /**
-//      * get temporary token from oauth2
-//      */
-//     let temporaryToken: string | null = "";
-
-//     try {
-//         const res = await fetch(`/oauth2/auth`, {
-//             method: "GET",
-//             credentials: "include",
-//         });
-
-//         temporaryToken = res.headers.get("Authorization");
-//     } catch (error) {
-//         console.log("error", error);
-//         return new Response() as Response & { redirect_uri: string };
-//     }
-
-//     /**
-//      * build query params
-//      */
-//     const queryParam: string =
-//         queryBase64String != "" ? `&query=${queryBase64String}` : "";
-
-//     const negotiationPartners = collections
-//         .map((collection) => collection.collection_id.toLocaleLowerCase())
-//         .join(",");
-//     const returnURL: string = `${window.location.protocol}//${window.location.host}/?collections=${negotiationPartners}${queryParam}`;
-//     const urlParams: URLSearchParams = new URLSearchParams(
-//         window.location.search,
-//     );
-//     const projectCode: string | null = urlParams.get("project-code");
-//     const projectCodeParam: string = projectCode
-//         ? `&project-code=${projectCode}`
-//         : "";
-//     const negotiateUrl = projectCode
-//         ? negotiateOptions.editProjectUrl
-//         : negotiateOptions.newProjectUrl;
-
-//     let response!: NegotiatorResponse;
-
-//     /**
-//      * send request to project manager
-//      */
-//     try {
-//         response = await fetch(
-//             `${negotiateUrl}?explorer-ids=${negotiationPartners}&query-format=CQL_DATA&human-readable=${humanReadable}&explorer-url=${encodeURIComponent(returnURL)}${projectCodeParam}`,
-//             {
-//                 method: "POST",
-//                 headers: {
-//                     returnAccept: "application/json; charset=utf-8",
-//                     "Content-Type": "application/json",
-//                     Authorization: temporaryToken ? temporaryToken : "",
-//                 },
-//                 body: getCql(),
-//             },
-//         ).then((response) => response.json());
-
-//         /**
-//          * replace query-code with project-code
-//          * TODO: remove when backend bug is fixed
-//          */
-//         if (response?.redirect_uri) {
-//             response.redirect_uri = response.redirect_uri.replace(
-//                 "query-code",
-//                 "project-code",
-//             );
-//         }
-
-//         return response;
-//     } catch (error) {
-//         console.log("error", error);
-//         return new Response() as NegotiatorResponse;
-//     }
-// }
-
-/**
- * @returns a base64 encoded CQL query
- */
-// function getCql(): string {
-//     const ast = buildAstFromQuery(currentQuery);
-
-//     /**
-//      * TODO:
-//      * For now backenMeasures is hardcoded because
-//      * this function only needed for dktk project manager so far.
-//      * Change if needed for negotiator.
-//      *
-//      * should be configurable via options other than spot/blaze, so custom backends can be used
-//      */
-//     const cql = translateAstToCql(
-//         ast,
-//         false,
-//         "DKTK_STRAT_DEF_IN_INITIAL_POPULATION",
-//         currentMeasures[0].measures,
-//     );
-
-//     const library = buildLibrary(`${cql}`);
-//     const measure = buildMeasure(
-//         library.url,
-//         currentMeasures[0].measures.map((measureItem) => measureItem.measure),
-//     );
-//     const query = { lang: "cql", lib: library, measure: measure };
-
-//     return btoa(decodeURI(JSON.stringify(query)));
-// }

From 54e35daac643978cf80d914fc0e3bb494447d114 Mon Sep 17 00:00:00 2001
From: Patrick Skowronek <patrick.skowronek@dkfz-heidelberg.de>
Date: Wed, 30 Oct 2024 10:36:01 +0100
Subject: [PATCH 4/5] chore: remove negotiate button

---
 packages/demo/src/AppCCP.svelte | 1 -
 1 file changed, 1 deletion(-)

diff --git a/packages/demo/src/AppCCP.svelte b/packages/demo/src/AppCCP.svelte
index 7793dfa..d5b9985 100644
--- a/packages/demo/src/AppCCP.svelte
+++ b/packages/demo/src/AppCCP.svelte
@@ -160,7 +160,6 @@
                 <lens-search-modified-display
                     >Diagramme repräsentieren nicht mehr die aktuelle Suche!</lens-search-modified-display
                 >
-                <lens-negotiate-button />
             </div>
             <div class="chart-wrapper">
                 <lens-chart

From ef908edc122a4682149a37d77c82d2841f975c97 Mon Sep 17 00:00:00 2001
From: Patrick Skowronek <patrick.skowronek@dkfz-heidelberg.de>
Date: Wed, 30 Oct 2024 10:52:02 +0100
Subject: [PATCH 5/5] chore: formating

---
 packages/lib/src/stores/datarequests.ts | 40 ++++++++++++-------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/packages/lib/src/stores/datarequests.ts b/packages/lib/src/stores/datarequests.ts
index 7f144bc..5259e4d 100644
--- a/packages/lib/src/stores/datarequests.ts
+++ b/packages/lib/src/stores/datarequests.ts
@@ -34,30 +34,30 @@ export const buildHumanReadableRecursively = (
 
     queryLayer.children.forEach((child: AstElement, index: number): void => {
         if (child !== null) {
-        if ("type" in child && "value" in child && "key" in child) {
-            if (typeof child.value === "string") {
-                humanReadableQuery += `(${child.key} ${child.type} ${child.value})`;
+            if ("type" in child && "value" in child && "key" in child) {
+                if (typeof child.value === "string") {
+                    humanReadableQuery += `(${child.key} ${child.type} ${child.value})`;
+                }
+                if (
+                    typeof child.value === "object" &&
+                    "min" in child.value &&
+                    "max" in child.value
+                ) {
+                    humanReadableQuery += `(${child.key} ${child.type} ${child.value.min} and ${child.value.max})`;
+                }
             }
-            if (
-                typeof child.value === "object" &&
-                "min" in child.value &&
-                "max" in child.value
-            ) {
-                humanReadableQuery += `(${child.key} ${child.type} ${child.value.min} and ${child.value.max})`;
-            }
-        }
 
-        humanReadableQuery = buildHumanReadableRecursively(
-            child,
-            humanReadableQuery,
-        );
+            humanReadableQuery = buildHumanReadableRecursively(
+                child,
+                humanReadableQuery,
+            );
 
-        if (index === queryLayer.children.length - 1) {
-        }
-        if (index < queryLayer.children.length - 1) {
-            humanReadableQuery += ` ${queryLayer.operand} `;
+            if (index === queryLayer.children.length - 1) {
+            }
+            if (index < queryLayer.children.length - 1) {
+                humanReadableQuery += ` ${queryLayer.operand} `;
+            }
         }
-    }
     });
 
     if (queryLayer.children.length > 1) {