Merge branch 'master' into feat/types

app/src/app/analysis/analysis-page.tsx

@@ -49,6 +49,7 @@ import { Judgement } from "./judgement/judgement";
 import { Health } from "./health/health";
 import { Debug } from "./debug";
 import { AnalysisSelectionMenu } from "./analysis-selection-menu";
+import { CellConfirmModal } from "./data-table/cell-confirm-modal";
 
 // When the fields in this array are 'approved', a given sequence is rendered
 // as 'approved' also.
@@ -59,6 +60,13 @@ export default function AnalysisPage() {
   const dispatch = useDispatch();
   const toast = useToast();
 
+  const [isModalOpen, setModalOpen] = useState(false);
+  const [modalInfo, setModalInfo] = useState({
+    rowId: "",
+    columnId: "",
+    value: "",
+  });
+
   const [detailsIsolate, setDetailsIsolate] = useState<
     React.ComponentProps<typeof AnalysisDetailsModal>["isolate"]
   >();
@@ -393,9 +401,24 @@ export default function AnalysisPage() {
     [submitChange]
   );
 
+  const handleConfirm = () => {
+    submitChange({
+      [modalInfo.rowId]: { [modalInfo.columnId]: modalInfo.value },
+    });
+    setModalOpen(false);
+  };
+
+  const handleClose = () => {
+    setModalOpen(false);
+  };
+
   const onFreeTextEdit = React.useCallback(
     (rowId: string, field: string) => (val: string) => {
-      if (columnConfigs[field].editable_format === "date") {
+      // May need a more dynamic check if other fields should use same dialog.
+      if (field === "cluster_id") {
+        setModalInfo({ rowId, columnId: field, value: val });
+        setModalOpen(true);
+      } else if (columnConfigs[field].editable_format === "date") {
         if (val.match(/\d{4}-\d{1,2}-\d{1,2}/) != null) {
           submitChange({ [rowId]: { [field]: val } });
         }
@@ -670,6 +693,14 @@ export default function AnalysisPage() {
             `${t("Staging")} ${Object.keys(selection).length} ${t("records")}.`}
         </Box>
       </Box>
+      <CellConfirmModal
+        rowId={modalInfo.rowId}
+        field={modalInfo.columnId}
+        value={modalInfo.value}
+        isOpen={isModalOpen}
+        onClose={handleClose}
+        onConfirm={handleConfirm}
+      />
       <Debug>
         <p>redux selection:</p>
         <pre>{JSON.stringify(selection, undefined, "  ")}</pre>

app/src/app/analysis/data-table/cell-confirm-modal.tsx

@@ -0,0 +1,47 @@
+import React from "react";
+import {
+  Button,
+  Modal,
+  ModalBody,
+  ModalCloseButton,
+  ModalContent,
+  ModalFooter,
+  ModalHeader,
+  ModalOverlay,
+} from "@chakra-ui/react";
+import { useTranslation } from "react-i18next";
+
+type Props = {
+  rowId: string;
+  field: string;
+  value: string;
+  isOpen: boolean;
+  onClose: () => void;
+  onConfirm: () => void;
+};
+
+export const CellConfirmModal = (props: Props) => {
+  const { rowId, field, value, isOpen, onClose, onConfirm } = props;
+  const { t } = useTranslation();
+
+  return (
+    <Modal isOpen={isOpen} onClose={onClose}>
+      <ModalOverlay />
+      <ModalContent>
+        <ModalHeader>{`${t("Confirm editing")} ${field}?`}</ModalHeader>
+        <ModalCloseButton />
+        <ModalBody>{`${t(
+          "Are you sure you want to change the value on sequence"
+        )} ${rowId} ${t("to")} ${value}`}</ModalBody>
+        <ModalFooter>
+          <Button variant="ghost" mr={3} onClick={onClose}>
+            {t("Close")}
+          </Button>
+          <Button colorScheme="blue" onClick={onConfirm}>
+            {t("Confirm")}
+          </Button>
+        </ModalFooter>
+      </ModalContent>
+    </Modal>
+  );
+};

app/src/app/workspaces/create-workspace.tsx

@@ -12,7 +12,7 @@ export function CreateWorkspace() {
   const [
     createWorkspaceQueryState,
     createWorkspaceMutation,
-  ] = useMutation((name: string) => createWorkspace({ name }));
+  ] = useMutation((name: string) => createWorkspace({ name, samples: [] }));
 
   const [needsNotify, setNeedsNotify] = useState(true);
 

docker-compose.yml

@@ -42,7 +42,7 @@ services:
     command: ["/bin/sh", "-c", "/app/start.sh"]
     depends_on:
       - "keycloak"
-      - "bio_api"
+      - "bioapi"
     restart: on-failure
 
     environment:
@@ -160,7 +160,7 @@ services:
       - ./auth/pg/pg-init:/docker-entrypoint-initdb.d
       - ${PG_DATA_DIR}:/var/lib/postgresql/data/
 
-  bio_api:
+  bioapi:
     image: ghcr.io/ssi-dk/bio_api:latest
     user: ${CURRENT_UID}
     ports:

web/src/SAP/src/controllers/MicroreactController.py

@@ -34,7 +34,7 @@ def send_to_microreact(user, token_info, body: NewMicroreactProjectRequestData):
     tree_calcs=[]
     samples = list(map(lambda s: s["id"], workspace["samples"]))
 
-    with ApiClient(Configuration(host="http://bio_api:8000")) as api_client:
+    with ApiClient(Configuration(host="http://bioapi:8000")) as api_client:
         # Distance
         api_instance = DistancesApi(api_client)
         request = DistanceMatrixRequest(seq_collection="samples",

web/src/SAP/src/controllers/NearestNeighborsController.py

@@ -16,11 +16,10 @@
 
 def post(user, token, body: NearestNeighborsRequest):
     assert_user_has("search", token)
-
     if body.id is None:
         return abort(400)
-
-    with ApiClient(Configuration(host="http://bio_api:8000")) as api_client:
+    
+    with ApiClient(Configuration(host="http://bioapi:8000")) as api_client:
         sample = get_single_sample(body.id)
         detected_species = sample["categories"]["species_detection"]["summary"]["detected_species"]
 

web/src/SAP/src/controllers/UserController.py

@@ -6,12 +6,16 @@
 
 
 def who_am_i(user, token_info):
+    groups=[]
+    if "security-groups" in token_info:
+        groups=[item.lstrip('/') for item in token_info["security-groups"]]
+
     return jsonify(
         UserInfo(
             user_id=token_info["email"],
             data_clearance=token_info["sofi-data-clearance"],
             institution=token_info["institution"],
-            groups=[item.lstrip('/') for item in token_info["security-groups"]],
+            groups=groups,
             permissions=list_permissions(token_info),
         )
     )

web/src/SAP/src/repositories/workspaces.py

@@ -54,6 +54,10 @@ def delete_workspace_sample(user: str, workspace_id: str, sample_id: str):
 
 def create_workspace(user: str, workspace: CreateWorkspace):
     workspaces = get_collection(WORKSPACES_COL_NAME)
+
+    if workspace.samples is None:
+        workspace.samples = []
+
     record = {**workspace.to_dict(), "created_by": user}
     return workspaces.update_one({'created_by': user, 'name': workspace.name}, {"$set": record}, upsert=True)
 

web/src/SAP/src/security/permission_check.py

@@ -14,16 +14,21 @@ def list_permissions(token_info: Dict[str, str]) -> List[str]:
     if PERMISSION_CONFIG is None:
         return permissions
 
+    if not "security-groups" in token_info:
+        return permissions
+
     for group in [item.lstrip('/') for item in token_info["security-groups"]]:
         for perm in PERMISSION_CONFIG[group]:
             permissions.append(perm)
     return permissions
 
-
 def user_has(permission: str, token_info: Dict[str, str]) -> bool:
     if PERMISSION_CONFIG is None:
         return False
 
+    if not "security-groups" in token_info:
+        return False
+
     for group in [item.lstrip('/') for item in token_info["security-groups"]]:
         for perm in PERMISSION_CONFIG[group]:
             if perm == permission:
@@ -40,6 +45,9 @@ def authorized_to_edit(token_info: Dict[str, str], metadata: Dict[str, Any]):
     # User must have the approve claim to do modifications
     if not user_has("approve", token_info):
         return False
+    # I no institution, allow
+    if not "institution" in metadata:
+        return True
     # When user's not from the same institution as the sample, they can't modify it
     if token_info["institution"] == metadata["institution"]:
         return True