feat: remove samples from workspace

app/src/app/analysis/data-table/data-table.tsx

@@ -69,7 +69,9 @@ type DataTableProps<T extends NotEmpty> = {
   renderCellControl: (
     rowId: string,
     columnId: string,
-    value: string
+    value: string,
+    columnIndex: number,
+    original: T
   ) => JSX.Element;
 };
 
@@ -494,7 +496,9 @@ function DataTable<T extends NotEmpty>(props: DataTableProps<T>) {
             {renderCellControl(
               rowId,
               columnId,
-              rows[rowIndex - 1].original[columnId]
+              rows[rowIndex - 1].original[columnId],
+              columnIndex,
+              rows[rowIndex - 1].original
             )}
           </Flex>
         </div>

app/src/app/workspaces/workspace.tsx

@@ -1,9 +1,12 @@
-import React from "react";
-import { Box, Heading, Spinner } from "@chakra-ui/react";
+import React, { useCallback } from "react";
+import { Box, Heading, IconButton, Spinner } from "@chakra-ui/react";
 import { useTranslation } from "react-i18next";
 import HalfHolyGrailLayout from "layouts/half-holy-grail";
-import { useRequest } from "redux-query-react";
-import { getWorkspace } from "./workspaces-query-configs";
+import { useMutation, useRequest } from "redux-query-react";
+import {
+  getWorkspace,
+  removeWorkspaceSample,
+} from "./workspaces-query-configs";
 import { useSelector } from "react-redux";
 import { RootState } from "app/root-reducer";
 import {
@@ -20,6 +23,7 @@ import { Column } from "react-table";
 import { UserDefinedViewInternal } from "models/user-defined-view-internal";
 import { Loading } from "loading";
 import { AnalysisViewSelector } from "app/analysis/view-selector/analysis-view-selector";
+import { DeleteIcon } from "@chakra-ui/icons";
 
 type Props = {
   id: string;
@@ -64,22 +68,40 @@ export function Workspace(props: Props) {
     [columnConfigs, t]
   );
 
+  const deleteWorkspaceSampleCallback = useMutation((sampleId: string) =>
+    removeWorkspaceSample({ sampleId, workspaceId: id })
+  )[1];
+
+  const onRemoveSample = useCallback(
+    (sampleId) => {
+      const ok = confirm(
+        t("Are you sure you want to remove the sequence from the workspace?")
+      );
+      if (ok) {
+        deleteWorkspaceSampleCallback(sampleId);
+      }
+    },
+    [deleteWorkspaceSampleCallback, t]
+  );
+
   const renderCellControl = React.useCallback(
-    (rowId: string, columnId: string, value) => {
+    (
+      rowId: string,
+      columnId: string,
+      value,
+      columnIndex: number,
+      original: AnalysisResult
+    ) => {
       if (
-        value !== 0 &&
-        value !== false &&
-        !value &&
-        !columnConfigs[columnId].editable
+        value === undefined ||
+        value === null ||
+        String(value) === "Invalid Date"
       ) {
-        return <div />;
+        value = "";
       }
       let v = `${value}`;
-      if (v === "Invalid Date") {
-        return <div />;
-      }
-      // any other dates
-      else if (value instanceof Date) {
+
+      if (value instanceof Date) {
         // Fancy libraries could be used, but this will do the trick just fine
         v = value.toISOString().split("T")[0];
       } else if (
@@ -119,9 +141,23 @@ export function Workspace(props: Props) {
         }
       }
 
-      return <div style={{ backgroundColor: "white" }}>{`${v}`}</div>;
+      return (
+        <div style={{ backgroundColor: "white" }}>
+          {columnIndex === 0 ? (
+            <IconButton
+              size="1em"
+              variant="unstyled"
+              onClick={() => onRemoveSample(original.id)}
+              aria-label="Remove"
+              icon={<DeleteIcon marginTop="-0.5em" />}
+              ml="1"
+            />
+          ) : null}
+          {`${v}`}
+        </div>
+      );
     },
-    [columnConfigs]
+    [onRemoveSample]
   );
 
   if (!columnLoadState.isFinished) {

app/src/app/workspaces/workspaces-query-configs.ts

@@ -5,8 +5,10 @@ import {
   createWorkspace as createWorkspaceApi,
   getWorkspace as getWorkspaceApi,
   postWorkspace as postWorkspaceApi,
+  deleteWorkspaceSample as deleteWorkspaceSampleApi,
   DeleteWorkspaceRequest,
   PostWorkspaceRequest,
+  DeleteWorkspaceSampleRequest,
 } from "sap-client";
 import { CreateWorkspace, WorkspaceInfo } from "sap-client/models";
 import { getUrl } from "service";
@@ -66,6 +68,21 @@ export const deleteWorkspace = (params: DeleteWorkspaceRequest) => {
   return base;
 };
 
+export const removeWorkspaceSample = (params: DeleteWorkspaceSampleRequest) => {
+  const base = deleteWorkspaceSampleApi(params);
+  base.url = getUrl(base.url);
+  base.update = {
+    workspace: (oldValue) => {
+      return {
+        ...oldValue,
+        samples: oldValue.samples.filter((s) => s.id !== params.sampleId),
+      };
+    },
+  };
+  base.force = true;
+  return base;
+};
+
 export const createWorkspace = (params: CreateWorkspace) => {
   const base = createWorkspaceApi({ createWorkspace: params });
   base.url = getUrl(base.url);

app/src/sap-client/apis/WorkspacesApi.ts

@@ -37,6 +37,11 @@ export interface DeleteWorkspaceRequest {
     workspaceId: string;
 }
 
+export interface DeleteWorkspaceSampleRequest {
+    workspaceId: string;
+    sampleId: string;
+}
+
 export interface GetWorkspaceRequest {
     workspaceId: string;
 }
@@ -135,6 +140,56 @@ export function deleteWorkspace<T>(requestParameters: DeleteWorkspaceRequest, re
     return deleteWorkspaceRaw(requestParameters, requestConfig);
 }
 
+/**
+ * Delete sample from workspace
+ */
+function deleteWorkspaceSampleRaw<T>(requestParameters: DeleteWorkspaceSampleRequest, requestConfig: runtime.TypedQueryConfig<T, void> = {}): QueryConfig<T> {
+    if (requestParameters.workspaceId === null || requestParameters.workspaceId === undefined) {
+        throw new runtime.RequiredError('workspaceId','Required parameter requestParameters.workspaceId was null or undefined when calling deleteWorkspaceSample.');
+    }
+
+    if (requestParameters.sampleId === null || requestParameters.sampleId === undefined) {
+        throw new runtime.RequiredError('sampleId','Required parameter requestParameters.sampleId was null or undefined when calling deleteWorkspaceSample.');
+    }
+
+    let queryParameters = null;
+
+
+    const headerParameters : runtime.HttpHeaders = {};
+
+
+    const { meta = {} } = requestConfig;
+
+    meta.authType = ['bearer'];
+    const config: QueryConfig<T> = {
+        url: `${runtime.Configuration.basePath}/workspace/{workspace_id}/{sample_id}`.replace(`{${"workspace_id"}}`, encodeURIComponent(String(requestParameters.workspaceId))).replace(`{${"sample_id"}}`, encodeURIComponent(String(requestParameters.sampleId))),
+        meta,
+        update: requestConfig.update,
+        queryKey: requestConfig.queryKey,
+        optimisticUpdate: requestConfig.optimisticUpdate,
+        force: requestConfig.force,
+        rollback: requestConfig.rollback,
+        options: {
+            method: 'DELETE',
+            headers: headerParameters,
+        },
+        body: queryParameters,
+    };
+
+    const { transform: requestTransform } = requestConfig;
+    if (requestTransform) {
+    }
+
+    return config;
+}
+
+/**
+* Delete sample from workspace
+*/
+export function deleteWorkspaceSample<T>(requestParameters: DeleteWorkspaceSampleRequest, requestConfig?: runtime.TypedQueryConfig<T, void>): QueryConfig<T> {
+    return deleteWorkspaceSampleRaw(requestParameters, requestConfig);
+}
+
 /**
  * Get an existing workspace
  */

openapi_specs/SOFI/SOFI.yaml

@@ -43,6 +43,30 @@ paths:
       tags:
         - workspaces
       x-openapi-router-controller: web.src.SAP.generated.controllers.workspaces_controller
+  /workspace/{workspace_id}/{sample_id}:
+    delete:
+      description: Delete sample from workspace
+      operationId: delete_workspace_sample
+      tags:
+        - workspaces
+      x-openapi-router-controller: web.src.SAP.generated.controllers.workspaces_controller
+      parameters:
+        - name: workspace_id
+          in: path
+          required: true
+          schema:
+            type: string
+          description: Id of workspace to modify
+        - name: sample_id
+          in: path
+          required: true
+          schema:
+            type: string
+          description: Id of the sample to remove
+      responses:
+        '204':
+          description: Sample removed from workspace successfully.
+
   /workspaces/{workspace_id}:
     get:
       description: Get an existing workspace

web/openapi_specs/SOFI/SOFI.yaml

@@ -43,6 +43,30 @@ paths:
       tags:
         - workspaces
       x-openapi-router-controller: web.src.SAP.generated.controllers.workspaces_controller
+  /workspace/{workspace_id}/{sample_id}:
+    delete:
+      description: Delete sample from workspace
+      operationId: delete_workspace_sample
+      tags:
+        - workspaces
+      x-openapi-router-controller: web.src.SAP.generated.controllers.workspaces_controller
+      parameters:
+        - name: workspace_id
+          in: path
+          required: true
+          schema:
+            type: string
+          description: Id of workspace to modify
+        - name: sample_id
+          in: path
+          required: true
+          schema:
+            type: string
+          description: Id of the sample to remove
+      responses:
+        '204':
+          description: Sample removed from workspace successfully.
+
   /workspaces/{workspace_id}:
     get:
       description: Get an existing workspace

web/src/SAP/generated/controllers/workspaces_controller.py

@@ -31,6 +31,20 @@ def delete_workspace(user, token_info, workspace_id):  # noqa: E501
     """
     return WorkspacesController.delete_workspace(user, token_info, workspace_id)
 
+def delete_workspace_sample(user, token_info, workspace_id, sample_id):  # noqa: E501
+    """delete_workspace_sample
+
+    Delete sample from workspace # noqa: E501
+
+    :param workspace_id: Id of workspace to modify
+    :type workspace_id: str
+    :param sample_id: Id of the sample to remove
+    :type sample_id: str
+
+    :rtype: None
+    """
+    return WorkspacesController.delete_workspace_sample(user, token_info, workspace_id, sample_id)
+
 def get_workspace(user, token_info, workspace_id):  # noqa: E501
     """get_workspace
 

web/src/SAP/generated/openapi/openapi.yaml

@@ -531,6 +531,33 @@ paths:
       tags:
       - user
       x-openapi-router-controller: web.src.SAP.generated.controllers.user_controller
+  /workspace/{workspace_id}/{sample_id}:
+    delete:
+      description: Delete sample from workspace
+      operationId: delete_workspace_sample
+      parameters:
+      - description: Id of workspace to modify
+        explode: false
+        in: path
+        name: workspace_id
+        required: true
+        schema:
+          type: string
+        style: simple
+      - description: Id of the sample to remove
+        explode: false
+        in: path
+        name: sample_id
+        required: true
+        schema:
+          type: string
+        style: simple
+      responses:
+        "204":
+          description: Sample removed from workspace successfully.
+      tags:
+      - workspaces
+      x-openapi-router-controller: web.src.SAP.generated.controllers.workspaces_controller
   /workspaces:
     get:
       description: Gets workspaces

web/src/SAP/generated/test/test_workspaces_controller.py

@@ -51,6 +51,21 @@ def test_delete_workspace(self):
         self.assert200(response,
                        'Response body is : ' + response.data.decode('utf-8'))
 
+    def test_delete_workspace_sample(self):
+        """Test case for delete_workspace_sample
+
+        
+        """
+        headers = { 
+            'Authorization': 'Bearer special-key',
+        }
+        response = self.client.open(
+            '/api/workspace/{workspace_id}/{sample_id}'.format(workspace_id='workspace_id_example')sample_id='sample_id_example'),
+            method='DELETE',
+            headers=headers)
+        self.assert200(response,
+                       'Response body is : ' + response.data.decode('utf-8'))
+
     def test_get_workspace(self):
         """Test case for get_workspace
 

web/src/SAP/src/controllers/WorkspacesController.py

@@ -3,6 +3,7 @@
 from flask.json import jsonify
 from ..repositories.workspaces import get_workspaces as get_workspaces_db
 from ..repositories.workspaces import delete_workspace as delete_workspace_db
+from ..repositories.workspaces import delete_workspace_sample as delete_workspace_sample_db
 from ..repositories.workspaces import create_workspace as create_workspace_db
 from ..repositories.workspaces import update_workspace as update_workspace_db
 from ..repositories.workspaces import get_workspace as get_workspace_db
@@ -29,3 +30,7 @@ def post_workspace(user, token_info, workspace_id: str, body):
 
 def get_workspace(user, token_info, workspace_id: str):
     return jsonify(get_workspace_db(user, workspace_id))
+
+def delete_workspace_sample(user, token_info, workspace_id, sample_id):
+    res = delete_workspace_sample_db(user, workspace_id, sample_id)
+    return None if res.modified_count > 0 else abort(404)

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

@@ -41,6 +41,16 @@ def delete_workspace(user: str, workspace_id: str):
         {"_id": ObjectId(workspace_id), "created_by": user}
     )
 
+def delete_workspace_sample(user: str, workspace_id: str, sample_id: str):
+    conn = get_connection()
+    mydb = conn[DB_NAME]
+    workspaces = mydb[WORKSPACES_COL_NAME]
+
+    filter = {'created_by': user, '_id': ObjectId(workspace_id)}
+    update = {"$pull": {"samples": sample_id}}
+    return workspaces.update_one(filter, update, upsert=True)
+
+
 def create_workspace(user: str, workspace: CreateWorkspace):
     conn = get_connection()
     db = conn[DB_NAME]