Merge pull request #89 from ssi-dk/feat/types

feat: added support for multiple tree methods, added type annotations
ssi-dk · Aug 26, 2024 · 360d7a4 · 360d7a4
2 parents aca1aa9 + 12985f2
commit 360d7a4
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Showing 60 changed files with 4,288 additions and 7,585 deletions.
diff --git a/Makefile b/Makefile
@@ -117,7 +117,7 @@ ${mkfile_dir}/web/src/services/bio_api/openapi : ${mkfile_dir}/openapi_specs/bio
 	rm -rf ${mkfile_dir}/web/src/services/bio_api/openapi
 	docker run --rm -v "${mkfile_dir}:/local" \
 		--user ${mkfile_user} \
-		"openapitools/openapi-generator:cli-v5.2.0" \
+		"openapitools/openapi-generator-cli:v7.7.0" \
 		generate \
 		-i /local/openapi_specs/bio_api.yaml \
 		-g python \

diff --git a/app/src/app/analysis/nearest-neighbor/nearest-neighbor-modal.tsx b/app/src/app/analysis/nearest-neighbor/nearest-neighbor-modal.tsx
@@ -40,7 +40,14 @@ export const NearestNeighborModal = (props: Props) => {
   const { selection, onClose } = props;
   const [isSearching, setIsSearching] = useState<boolean>(false);
   const [cutoff, setCutoff] = React.useState(15);
-  const onChangeCutoff = (value: string) => setCutoff(parseInt(value));
+  const onChangeCutoff = (value: string) => {
+    const n = parseInt(value);
+    if (isNaN(n)) {
+      setCutoff(0);
+      return;
+    }
+    setCutoff(n);
+  };
   const [unknownsAreDiffs, setUnknownsAreDiffs] = useState<boolean>(false);
   const toast = useToast();
   const dispatch = useDispatch();

diff --git a/app/src/app/workspaces/send-to-microreact-modal.tsx b/app/src/app/workspaces/send-to-microreact-modal.tsx
@@ -16,7 +16,7 @@ import { sendToMicroreact as sendToMicroreactQuery } from "./microreact-query-co
 import { RootState } from "app/root-reducer";
 import { useSelector } from "react-redux";
 import { TreeMethod, UserInfo, WorkspaceInfo } from "sap-client";
-import { TreeMethodSelect } from "./tree-method-select";
+import { TreeMethodCheckboxGroup } from "./tree-method-checkbox-group";
 
 type Props = {
   workspace: string;
@@ -34,7 +34,9 @@ export const SendToMicroreactModal = (props: Props) => {
     localStorage.getItem(localStorageKey) ?? ""
   );
   const [isSending, setIsSending] = useState<boolean>(false);
-  const [treeMethod, setTreeMethod] = useState<string>(TreeMethod.single);
+  const [treeMethods, setTreeMethods] = useState<Array<string>>([
+    TreeMethod.single,
+  ]);
 
   const workspaceInfo = useSelector<RootState>(
     (s) => s.entities.workspace ?? {}
@@ -45,7 +47,7 @@ export const SendToMicroreactModal = (props: Props) => {
     return sendToMicroreactQuery({
       workspace: workspace,
       mr_access_token: token,
-      tree_method: TreeMethod[treeMethod],
+      tree_methods: treeMethods.map((tm) => TreeMethod[tm]),
     });
   });
 
@@ -89,8 +91,11 @@ export const SendToMicroreactModal = (props: Props) => {
                 />
               </div>
               <div>
-                {t("Tree method")}:
-                <TreeMethodSelect value={treeMethod} onChange={setTreeMethod} />
+                {t("Tree methods")}:
+                <TreeMethodCheckboxGroup
+                  value={treeMethods}
+                  onChange={setTreeMethods}
+                />
               </div>
             </div>
           ) : null}
@@ -104,7 +109,9 @@ export const SendToMicroreactModal = (props: Props) => {
             colorScheme="blue"
             mr={3}
             onClick={onSend}
-            disabled={isSending || !token || !treeMethod}
+            disabled={
+              isSending || !token || !treeMethods || treeMethods.length === 0
+            }
           >
             {t("Send")}
           </Button>

diff --git a/app/src/app/workspaces/tree-method-checkbox-group.tsx b/app/src/app/workspaces/tree-method-checkbox-group.tsx
@@ -0,0 +1,38 @@
+import { Checkbox, CheckboxGroup, Stack } from "@chakra-ui/react";
+import React, { useCallback, useMemo } from "react";
+import { TreeMethod } from "sap-client";
+import { StringOrNumber } from "utils";
+
+type Props = {
+  onChange: (id: Array<string>) => void;
+  value: Array<string>;
+};
+
+export const TreeMethodCheckboxGroup = (props: Props) => {
+  const { onChange, value } = props;
+
+  const treeMethods = useMemo(() => {
+    const methods = new Array<string>();
+    for (const tm in TreeMethod) {
+      methods.push(tm);
+    }
+    return methods;
+  }, []);
+
+  const onChangeCallback = useCallback(
+    (checkboxValue: StringOrNumber[]) => {
+      onChange(checkboxValue.map((v) => String(v)));
+    },
+    [onChange]
+  );
+
+  return (
+    <CheckboxGroup defaultValue={value} onChange={onChangeCallback}>
+      <Stack spacing={2}>
+        {treeMethods?.map((treeMethod) => {
+          return <Checkbox value={treeMethod}>{treeMethod}</Checkbox>;
+        })}
+      </Stack>
+    </CheckboxGroup>
+  );
+};
diff --git a/app/src/sap-client/models/NewMicroreactProjectRequest.ts b/app/src/sap-client/models/NewMicroreactProjectRequest.ts
@@ -38,17 +38,17 @@ export interface NewMicroreactProjectRequest  {
     mr_access_token: string;
     /**
      * 
-     * @type {TreeMethod}
+     * @type {Array<TreeMethod>}
      * @memberof NewMicroreactProjectRequest
      */
-    tree_method: TreeMethod;
+    tree_methods: Array<TreeMethod>;
 }
 
 export function NewMicroreactProjectRequestFromJSON(json: any): NewMicroreactProjectRequest {
     return {
         'workspace': json['workspace'],
         'mr_access_token': json['mr_access_token'],
-        'tree_method': TreeMethodFromJSON(json['tree_method']),
+        'tree_methods': (json['tree_methods'] as Array<any>).map(TreeMethodFromJSON),
     };
 }
 
@@ -59,7 +59,7 @@ export function NewMicroreactProjectRequestToJSON(value?: NewMicroreactProjectRe
     return {
         'workspace': value.workspace,
         'mr_access_token': value.mr_access_token,
-        'tree_method': TreeMethodToJSON(value.tree_method),
+        'tree_methods': (value.tree_methods as Array<any>).map(TreeMethodToJSON),
     };
 }
 

diff --git a/bifrost/bifrost_queue_broker/common/database.py b/bifrost/bifrost_queue_broker/common/database.py
@@ -2,7 +2,7 @@
 import binascii
 import logging
 
-from typing import Dict
+from typing import Dict, Literal, Tuple, overload
 
 from dateutil import parser
 from pymongo import MongoClient, mongo_client
@@ -37,6 +37,15 @@
 ) = SOFI_BIFROST_ENCRYPTION_NAMESPACE.split(".", 1)
 
 # The MongoClient is thread safe and pooled, so no problem sharing it :)
+@overload
+def get_connection() -> MongoClient: ...
+
+@overload
+def get_connection(with_enc: Literal[False]) -> MongoClient: ...
+
+@overload
+def get_connection(with_enc: Literal[True]) -> Tuple[MongoClient, ClientEncryption]: ...
+
 def get_connection(with_enc=False):
     """
     Returns instance of global pooled connection.
@@ -119,6 +128,10 @@ def get_connection(with_enc=False):
         else:
             return CONNECTION
 
+def get_collection(collection: str):
+    conn = get_connection()
+    db = conn[DB_NAME]
+    return db[collection]
 
 def recursive_replace(data, replacement_fn, filter_list=None, filtered_parent=False):
     # If no filter_list is provided, then assume all leaf nodes in tree must be replaced

diff --git a/openapi_specs/SOFI/SOFI.yaml b/openapi_specs/SOFI/SOFI.yaml
@@ -1589,12 +1589,14 @@ components:
           type: string
         mr_access_token:
           type: string
-        tree_method:
-          $ref: "#/components/schemas/TreeMethod"
+        tree_methods:
+          type: array
+          items:
+            $ref: "#/components/schemas/TreeMethod"
       required:
         - workspace
         - mr_access_token
-        - tree_method
+        - tree_methods
 
     NewMicroreactProjectResponse:
       properties:

diff --git a/web/openapi_specs/SOFI/SOFI.yaml b/web/openapi_specs/SOFI/SOFI.yaml
@@ -1589,12 +1589,14 @@ components:
           type: string
         mr_access_token:
           type: string
-        tree_method:
-          $ref: "#/components/schemas/TreeMethod"
+        tree_methods:
+          type: array
+          items:
+            $ref: "#/components/schemas/TreeMethod"
       required:
         - workspace
         - mr_access_token
-        - tree_method
+        - tree_methods
 
     NewMicroreactProjectResponse:
       properties:

diff --git a/web/requirements.txt b/web/requirements.txt
@@ -20,4 +20,5 @@ python-jose[cryptography]
 six>=1.9
 jwcrypto >= 0.8
 Flask-JWT-Extended >= 3.25.1
-openapi-spec-validator==0.2.9
+openapi-spec-validator==0.2.9
+pydantic==2.8.2
diff --git a/web/src/SAP/common/database.py b/web/src/SAP/common/database.py
@@ -2,7 +2,7 @@
 import binascii
 import logging
 
-from typing import Dict
+from typing import Dict, Literal, Tuple, overload
 
 from dateutil import parser
 from pymongo import MongoClient, mongo_client
@@ -37,6 +37,15 @@
 ) = SOFI_BIFROST_ENCRYPTION_NAMESPACE.split(".", 1)
 
 # The MongoClient is thread safe and pooled, so no problem sharing it :)
+@overload
+def get_connection() -> MongoClient: ...
+
+@overload
+def get_connection(with_enc: Literal[False]) -> MongoClient: ...
+
+@overload
+def get_connection(with_enc: Literal[True]) -> Tuple[MongoClient, ClientEncryption]: ...
+
 def get_connection(with_enc=False):
     """
     Returns instance of global pooled connection.
@@ -119,6 +128,10 @@ def get_connection(with_enc=False):
         else:
             return CONNECTION
 
+def get_collection(collection: str):
+    conn = get_connection()
+    db = conn[DB_NAME]
+    return db[collection]
 
 def recursive_replace(data, replacement_fn, filter_list=None, filtered_parent=False):
     # If no filter_list is provided, then assume all leaf nodes in tree must be replaced

diff --git a/web/src/SAP/generated/models/new_microreact_project_request.py b/web/src/SAP/generated/models/new_microreact_project_request.py
@@ -19,31 +19,31 @@ class NewMicroreactProjectRequest(Model):
     Do not edit the class manually.
     """
 
-    def __init__(self, workspace=None, mr_access_token=None, tree_method=None):  # noqa: E501
+    def __init__(self, workspace=None, mr_access_token=None, tree_methods=None):  # noqa: E501
         """NewMicroreactProjectRequest - a model defined in OpenAPI
 
         :param workspace: The workspace of this NewMicroreactProjectRequest.  # noqa: E501
         :type workspace: str
         :param mr_access_token: The mr_access_token of this NewMicroreactProjectRequest.  # noqa: E501
         :type mr_access_token: str
-        :param tree_method: The tree_method of this NewMicroreactProjectRequest.  # noqa: E501
-        :type tree_method: TreeMethod
+        :param tree_methods: The tree_methods of this NewMicroreactProjectRequest.  # noqa: E501
+        :type tree_methods: List[TreeMethod]
         """
         self.openapi_types = {
             'workspace': str,
             'mr_access_token': str,
-            'tree_method': TreeMethod,
+            'tree_methods': List[TreeMethod],
         }
 
         self.attribute_map = {
             'workspace': 'workspace',
             'mr_access_token': 'mr_access_token',
-            'tree_method': 'tree_method',
+            'tree_methods': 'tree_methods',
         }
 
         self._workspace = workspace
         self._mr_access_token = mr_access_token
-        self._tree_method = tree_method
+        self._tree_methods = tree_methods
 
     @classmethod
     def from_dict(cls, dikt):
@@ -103,24 +103,24 @@ def mr_access_token(self, mr_access_token):
         self._mr_access_token = mr_access_token
 
     @property
-    def tree_method(self):
-        """Gets the tree_method of this NewMicroreactProjectRequest.
+    def tree_methods(self):
+        """Gets the tree_methods of this NewMicroreactProjectRequest.
 
 
-        :return: The tree_method of this NewMicroreactProjectRequest.
-        :rtype: TreeMethod
+        :return: The tree_methods of this NewMicroreactProjectRequest.
+        :rtype: List[TreeMethod]
         """
-        return self._tree_method
+        return self._tree_methods
 
-    @tree_method.setter
-    def tree_method(self, tree_method):
-        """Sets the tree_method of this NewMicroreactProjectRequest.
+    @tree_methods.setter
+    def tree_methods(self, tree_methods):
+        """Sets the tree_methods of this NewMicroreactProjectRequest.
 
 
-        :param tree_method: The tree_method of this NewMicroreactProjectRequest.
-        :type tree_method: TreeMethod
+        :param tree_methods: The tree_methods of this NewMicroreactProjectRequest.
+        :type tree_methods: List[TreeMethod]
         """
-        if tree_method is None:
-            raise ValueError("Invalid value for `tree_method`, must not be `None`")  # noqa: E501
+        if tree_methods is None:
+            raise ValueError("Invalid value for `tree_methods`, must not be `None`")  # noqa: E501
 
-        self._tree_method = tree_method
+        self._tree_methods = tree_methods
diff --git a/web/src/SAP/generated/openapi/openapi.yaml b/web/src/SAP/generated/openapi/openapi.yaml
@@ -1600,17 +1600,22 @@ components:
     NewMicroreactProjectRequest:
       example:
         workspace: workspace
+        tree_methods:
+        - null
+        - null
         mr_access_token: mr_access_token
       properties:
         workspace:
           type: string
         mr_access_token:
           type: string
-        tree_method:
-          $ref: '#/components/schemas/TreeMethod'
+        tree_methods:
+          items:
+            $ref: '#/components/schemas/TreeMethod'
+          type: array
       required:
       - mr_access_token
-      - tree_method
+      - tree_methods
       - workspace
       type: object
     NewMicroreactProjectResponse:

diff --git a/web/src/SAP/generated/test/test_microreact_controller.py b/web/src/SAP/generated/test/test_microreact_controller.py
@@ -20,6 +20,7 @@ def test_send_to_microreact(self):
         """
         body = {
   "workspace" : "workspace",
+  "tree_methods" : [ null, null ],
   "mr_access_token" : "mr_access_token"
 }
         headers = {