Merge pull request #123 from samply/feature/merge-develop-and-project…

…-manager-connection Feature/merge develop and project manager connection
samply · Sep 6, 2024 · bd931f2 · bd931f2
2 parents f0a68d2 + 56de19f
commit bd931f2
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Showing 15 changed files with 20,991 additions and 126 deletions.
diff --git a/.gitignore b/.gitignore
@@ -29,3 +29,5 @@ TODO
 docker-compose.override.yml
 *.priv.pem
 traefik.yaml
+
+project-manager.env
diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -47,6 +47,28 @@ services:
     profiles:
       - "beam"
 
+  project-manager:
+    image: samply/project-manager:develop
+    ports:
+      - 8097:8097
+    env_file:
+      - env/project-manager.env
+    volumes:
+      - "./templates:/templates"
+      - "./documents:/documents"
+      - "./public-documents:/public-documents"
+    profiles:
+      - "project-manager"
+
+  project-manager-db:
+    image: postgres:alpine
+    environment:
+      POSTGRES_DB: dev
+      POSTGRES_USER: dev
+      POSTGRES_PASSWORD: dev
+    profiles:
+      - "project-manager"
+
 secrets:
   proxy.pem:
     file: /etc/lens/pki/${LOCAL_BEAM_ID}.priv.pem

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -27,6 +27,8 @@ services:
       - OAUTH2_PROXY_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
       - OAUTH2_PROXY_COOKIE_SECRET=${AUTHENTICATION_SECRET}
       - OAUTH2_PROXY_COOKIE_DOMAINS=.${GUI_HOST}
+      - OAUTH2_PROXY_COOKIE_REFRESH=4m
+      - OAUTH2_PROXY_COOKIE_EXPIRE=24h
       - OAUTH2_PROXY_HTTP_ADDRESS=:4180
       - OAUTH2_PROXY_REVERSE_PROXY=true
       - OAUTH2_PROXY_WHITELIST_DOMAINS=.${GUI_HOST}

diff --git a/packages/demo/public/catalogues/catalogue-dktk-staging.json b/packages/demo/public/catalogues/catalogue-dktk-staging.json
diff --git a/packages/demo/public/catalogues/catalogue-dktk.json b/packages/demo/public/catalogues/catalogue-dktk.json
@@ -20354,56 +20354,5 @@
                 ]
             }
         ]
-    },
-    {
-        "key": "project",
-        "name": "Forschungsprojekte",
-        "infoButtonText": ["Projekt-Übersicht"],
-        "childCategories": [
-            {
-                "key": "pseudo_projects",
-                "name": "Projektname",
-                "fieldType": "single-select",
-                "type": "EQUALS",
-                "system": "",
-                "criteria": [
-                    {
-                        "key": "DKTK000002089",
-                        "name": "EXLIQUID",
-                        "description": ""
-                    },
-                    {
-                        "key": "DKTK000001985",
-                        "name": "RiskY-AML",
-                        "description": ""
-                    },
-                    {
-                        "key": "DKTK000001986",
-                        "name": "MASTER-Programm",
-                        "description": ""
-                    },
-                    {
-                        "key": "DKTK000001950",
-                        "name": "IRCC",
-                        "description": ""
-                    },
-                    {
-                        "key": "DKTK000001951",
-                        "name": "ARMANI",
-                        "description": ""
-                    },
-                    {
-                        "key": "DKTK999999999",
-                        "name": "Testprojekt",
-                        "description": ""
-                    },
-                    {
-                        "key": "DKTK000000791",
-                        "name": "ReKo",
-                        "description": ""
-                    }
-                ]
-            }
-        ]
     }
 ]
diff --git a/packages/demo/public/options-dev.json b/packages/demo/public/options-dev.json
@@ -279,5 +279,93 @@
                 "url": "http://localhost:8080"
             }
         ]
+    },
+    "negotiateOptions": {
+        "negotiateApp": "project-manager",
+        "newProjectUrl": "http://localhost:8097/create-query-and-design-project",
+        "editProjectUrl": "http://localhost:8097/edit-project",
+        "siteMapping": [
+            {
+                "site": "Dresden",
+                "collection": "dresden"
+            },
+            {
+                "site": "Frankfurt",
+                "collection": "bbmri-eric:ID:DE_iBDF:collection:UCT"
+            },
+            {
+                "site": "Berlin",
+                "collection": "bbmri-eric:ID:DE_ZeBanC:collection:Onoloy"
+            },
+            {
+                "site": "Würzburg",
+                "collection": "bbmri-eric:ID:DE_ibdw:collection:bc"
+            },
+            {
+                "site": "Brno",
+                "collection": "bbmri-eric:ID:CZ_MMCI:collection:LTS"
+            },
+            {
+                "site": "Aachen",
+                "collection": "bbmri-eric:ID:DE_RWTHCBMB:collection:RWTHCBMB_BC"
+            },
+            {
+                "site": "Leipzig",
+                "collection": "bbmri-eric:ID:DE_LMB:collection:LIFE_ADULT"
+            },
+            {
+                "site": "München (HMGU)",
+                "collection": "bbmri-eric:ID:DE_Helmholtz-MuenchenBiobank:collection:DE_KORA"
+            },
+            {
+                "site": "Pilsen",
+                "collection": "bbmri-eric:ID:CZ_CUNI_PILS:collection:serum_plasma"
+            },
+            {
+                "site": "Regensburg",
+                "collection": "bbmri-eric:ID:DE_ZBR:collection:Tissue"
+            },
+            {
+                "site": "Heidelberg",
+                "collection": "bbmri-eric:ID:DE_BMBH:collection:Lungenbiobank"
+            },
+            {
+                "site": "Lübeck",
+                "collection": "bbmri-eric:ID:DE_ICBL:collection:ICBL"
+            },
+            {
+                "site": "Augsburg",
+                "collection": "bbmri-eric:ID:DE_ACBB:collection:TISSUE"
+            },
+            {
+                "site": "Mannheim",
+                "collection": "bbmri-eric:ID:DE_BioPsy:collection:Main_collecion"
+            },
+            {
+                "site": "Marburg",
+                "collection": "bbmri-eric:ID:DE_CBBMR:collection:main"
+            },
+            {
+                "site": "Göttingen",
+                "collection": "bbmri-eric:ID:DE_UMGB:collection:UMG-startegy"
+            },
+            {
+                "site": "Hanover",
+                "collection": "bbmri-eric:ID:DE_HUB:collection:ProBase"
+            },
+            {
+                "site": "Olomouc",
+                "collection": "bbmri-eric:ID:CZ_UPOL_LF:collection:all_samples"
+            },
+            {
+                "site": "Prague (FFM)",
+                "collection": "bbmri-eric:ID:CZ_CUNI_PILS:collection:serum_plasma"
+            },
+            {
+                "site": "Prague (IOR)",
+                "collection": "bbmri-eric:ID:CZ_CUNI_LF1:collection"
+            }
+
+        ]
     }
 }
diff --git a/packages/demo/src/AppCCP.svelte b/packages/demo/src/AppCCP.svelte
@@ -13,24 +13,35 @@
         dktkHistologyMeasure,
     } from "./measures";
 
-    let catalogueData = "";
-    let libraryOptions = "";
+    let catalogueData: string = "";
+    let libraryOptions: string = "";
+    let catalogueUrl: string = "";
+    let optionsFilePath: string = "";
 
-    fetch("catalogues/catalogue-dktk.json")
+    if (import.meta.env.VITE_TARGET_ENVIRONMENT === "production") {
+        catalogueUrl = "catalogues/catalogue-dktk.json";
+        optionsFilePath = "options.json";
+    } else {
+        catalogueUrl = "catalogues/catalogue-dktk-staging.json";
+        optionsFilePath = "options-ccp-demo.json";
+    }
+
+    /**
+     * VITE_TARGET_ENVIRONMENT is set by the ci pipeline
+     */
+
+    /**
+     * get catalogue file
+     */
+    fetch(catalogueUrl)
         .then((response) => response.text())
         .then((data) => {
             catalogueData = data;
         });
 
-    // VITE_TARGET_ENVIRONMENT should be set by the ci pipeline
-    let optionsFilePath: string = "options-dev.json";
-
-    if (import.meta.env.VITE_TARGET_ENVIRONMENT === "production") {
-        optionsFilePath = "options-ccp-prod.json";
-    } else if (import.meta.env.VITE_TARGET_ENVIRONMENT === "staging") {
-        optionsFilePath = "options-ccp-demo.json";
-    }
-
+    /**
+     * get options file
+     */
     fetch(optionsFilePath)
         .then((response) => response.json())
         .then((data) => {
@@ -52,7 +63,7 @@
     ];
 
     /**
-     * move to config file
+     * TODO: move to config file
      */
     const catalogueText = {
         group: "Group",
@@ -138,6 +149,8 @@
                 <lens-search-modified-display
                     >Diagramme repräsentieren nicht mehr die aktuelle Suche!</lens-search-modified-display
                 >
+                <!-- TODO: comment in when backend is ready -->
+                <!-- <lens-negotiate-button /> -->
             </div>
             <div class="chart-wrapper">
                 <lens-chart

diff --git a/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte b/packages/lib/src/components/buttons/NegotiateButtonComponent.wc.svelte
@@ -1,19 +1,21 @@
+<svelte:options
+    customElement={{
+        tag: "lens-negotiate-button",
+    }}
+/>
+
 <script lang="ts">
-    import { negotiate } from "../../stores/negotiate";
+    import { negotiate, negotiateStore } from "../../stores/negotiate";
 
     export let title: string = "Negotiate with biobanks";
     let disabled: boolean = false;
-
-    /**
-     * TODO: implement negotiator connection
-     */
 </script>
 
 <button
     part={`lens-negotiate-button lens-negotiate-button-${
         disabled ? "disabled" : "active"
     }`}
-    on:click={() => negotiate([])}
+    on:click={() => negotiate($negotiateStore)}
     {disabled}
 >
     <div part="lens-negotiate-button-title">

diff --git a/packages/lib/src/stores/catalogue.ts b/packages/lib/src/stores/catalogue.ts
@@ -22,7 +22,7 @@ export const activeNumberInputs = writable<QueryItem[]>([]);
  * @returns array of strings containing the bottom level items' keys
  */
 export const getCriteria = (category: string): string[] => {
-    let bottomLevelItems = [] as string[];
+    let bottomLevelItems: string[] = [];
 
     catalogue.subscribe((catalogue) => {
         bottomLevelItems = getBottomLevelItems(catalogue, category);