[ENH] Removed NB_IS_FEDERATION_API environment variable (#245)

* Removed code related to `NB_IS_FEDERATION` env var * Update workflow config files * Updated README.md * Fixed formatting
neurobagel · Aug 9, 2024 · 34e083b · 34e083b
1 parent 93d0176
commit 34e083b
Show file tree

Hide file tree

Showing 7 changed files with 53 additions and 84 deletions.
diff --git a/.github/workflows/component-test.yaml b/.github/workflows/component-test.yaml
@@ -16,7 +16,7 @@ jobs:
 
       - name: Create .env file
         run: |
-          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/\nNB_IS_FEDERATION_API=true" > .env
+          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/" > .env
 
       - name: build
         run: npm install && npm run build

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -33,7 +33,7 @@ jobs:
           cache: 'npm'
       - name: Create .env file
         run: |
-          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/\nNB_IS_FEDERATION_API=true" > .env
+          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/" > .env
       - name: Install dependencies
         run: npm ci
       - name: Build

diff --git a/.github/workflows/e2e-test.yaml b/.github/workflows/e2e-test.yaml
@@ -21,7 +21,7 @@ jobs:
 
       - name: Create .env file
         run: |
-          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/\nNB_IS_FEDERATION_API=true\nNB_ENABLE_AUTH=true\nNB_QUERY_CLIENT_ID=mockclientid" > .env
+          echo -e "NB_API_QUERY_URL=https://federate.neurobagel.org/\nNB_ENABLE_AUTH=true\nNB_QUERY_CLIENT_ID=mockclientid" > .env
 
       - name: build
         run: npm install && npm run build

diff --git a/README.md b/README.md
@@ -50,7 +50,6 @@ but before proceeding with either you need to set the environment variables.
 | Environment variable     | Type    | Required                                 | Default value if not set | Example                                                   |
 | ------------------------ | ------- | ---------------------------------------- | ------------------------ | --------------------------------------------------------- |
 | `NB_API_QUERY_URL`       | string  | Yes                                      | -                        | `https://federate.neurobagel.org/`                        |
-| `NB_IS_FEDERATION_API`   | boolean | No                                       | `true`                   | `true`                                                    |
 | `NB_QUERY_APP_BASE_PATH` | string  | No                                       | `/`                      | `/query/`                                                 |
 | `NB_ENABLE_AUTH`         | boolean | No                                       | `false`                  | `false`                                                   |
 | `NB_QUERY_CLIENT_ID`     | string  | Yes (if `NB_ENABLE_AUTH` is set to true) | -                        | `46923719231972-dhsahgasl3123.apps.googleusercontent.com` |
@@ -59,10 +58,6 @@ but before proceeding with either you need to set the environment variables.
 
 You'll need to set the `NB_API_QUERY_URL` environment variable required to run the query tool. `NB_API_QUERY_URL` is the [Neurobagel API](https://github.com/neurobagel/api) URL that the query tool uses to send requests to for results.
 
-#### `NB_IS_FEDERATION_API`
-
-If the API you'd like to send queries to is not a [federation api](https://neurobagel.org/federate/), you need to set the `NB_IS_FEDERATION_API` to `false` as it is `true` by default.
-
 #### `NB_QUERY_APP_BASE_PATH`
 
 If you are using a custom configuration where the query tool is accessible via a path other than the root (`/`), you need to set the `NB_QUERY_APP_BASE_PATH` to your custom path. This ensures that the query tool is correctly rendered and accessible at the specified URL
@@ -82,16 +77,15 @@ To set environment variables, create a `.env` file in the root directory and add
 
 ```bash
 NB_API_QUERY_URL=http://localhost:8000/
-NB_IS_FEDERATION_API=false # For node API
 ```
 
-if you're using the remote (in this example federation) api, your `.env` file would look something like this:
+if you're using the remote api, your `.env` file would look something like this:
 
 ```bash
 NB_API_QUERY_URL=https://federate.neurobagel.org/
 ```
 
-if you're using a federation api with authentication, your `.env` file would look something like this:
+if you're using a remote api with authentication, your `.env` file would look something like this:
 
 ```bash
 NB_API_QUERY_URL=https://federate.neurobagel.org/

diff --git a/src/App.tsx b/src/App.tsx
@@ -6,7 +6,7 @@ import CloseIcon from '@mui/icons-material/Close';
 import { SnackbarKey, SnackbarProvider, closeSnackbar, enqueueSnackbar } from 'notistack';
 import { jwtDecode } from 'jwt-decode';
 import { googleLogout } from '@react-oauth/google';
-import { queryURL, attributesURL, isFederationAPI, nodesURL, enableAuth } from './utils/constants';
+import { queryURL, attributesURL, nodesURL, enableAuth } from './utils/constants';
 import {
   RetrievedAttributeOption,
   AttributeOption,
@@ -136,17 +136,15 @@ function App() {
       }
     }
 
-    if (isFederationAPI) {
-      getNodeOptions(nodesURL).then((nodeResponse) => {
-        if (nodeResponse === null) {
-          enqueueSnackbar('Failed to retrieve Node options', { variant: 'error', action });
-        } else if (nodeResponse.length === 0) {
-          enqueueSnackbar('No options found for Node', { variant: 'info', action });
-        } else {
-          setAvailableNodes([...nodeResponse, { NodeName: 'All', ApiURL: 'allNodes' }]);
-        }
-      });
-    }
+    getNodeOptions(nodesURL).then((nodeResponse) => {
+      if (nodeResponse === null) {
+        enqueueSnackbar('Failed to retrieve Node options', { variant: 'error', action });
+      } else if (nodeResponse.length === 0) {
+        enqueueSnackbar('No options found for Node', { variant: 'info', action });
+      } else {
+        setAvailableNodes([...nodeResponse, { NodeName: 'All', ApiURL: 'allNodes' }]);
+      }
+    });
   }, []);
 
   useEffect(() => {
@@ -309,34 +307,24 @@ function App() {
           'Content-Type': 'application/json',
         },
       });
-      // TODO: remove this branch once there is no more non-federation option
-      if (isFederationAPI) {
-        setResult(response.data);
-        switch (response.data.nodes_response_status) {
-          case 'partial success': {
-            response.data.errors.forEach((error: NodeError) => {
-              enqueueSnackbar(`${error.node_name} failed to respond`, {
-                variant: 'warning',
-                action,
-              });
+      setResult(response.data);
+      switch (response.data.nodes_response_status) {
+        case 'partial success': {
+          response.data.errors.forEach((error: NodeError) => {
+            enqueueSnackbar(`${error.node_name} failed to respond`, {
+              variant: 'warning',
+              action,
             });
-            break;
-          }
-          case 'fail': {
-            enqueueSnackbar('Error: All nodes failed to respond', { variant: 'error', action });
-            break;
-          }
-          default: {
-            break;
-          }
+          });
+          break;
+        }
+        case 'fail': {
+          enqueueSnackbar('Error: All nodes failed to respond', { variant: 'error', action });
+          break;
+        }
+        default: {
+          break;
         }
-      } else {
-        const myResponse = {
-          responses: response.data,
-          nodes_response_status: 'success',
-          errors: [],
-        };
-        setResult(myResponse);
       }
     } catch (error) {
       enqueueSnackbar('Failed to retrieve results', { variant: 'error', action });

diff --git a/src/components/QueryForm.tsx b/src/components/QueryForm.tsx
@@ -6,7 +6,7 @@ import {
   FormHelperText,
 } from '@mui/material';
 import SendIcon from '@mui/icons-material/Send';
-import { isFederationAPI, sexes, modalities } from '../utils/constants';
+import { sexes, modalities } from '../utils/constants';
 import { NodeOption, AttributeOption, FieldInput } from '../utils/types';
 import CategoricalField from './CategoricalField';
 import ContinuousField from './ContinuousField';
@@ -78,35 +78,27 @@ function QueryForm({
     minNumImagingSessionsHelperText !== '';
 
   return (
-    <div
-      className={
-        isFederationAPI
-          ? 'grid grid-cols-2 grid-rows-9 gap-2'
-          : 'grid grid-cols-2 grid-rows-10 gap-2'
-      }
-    >
-      {isFederationAPI && (
-        <div className="col-span-2">
-          <CategoricalField
-            label="Neurobagel graph"
-            options={availableNodes.map((n) => ({
-              label: n.NodeName,
-              id: n.ApiURL,
-            }))}
-            onFieldChange={(label, value) => updateCategoricalQueryParams(label, value)}
-            multiple
-            inputValue={selectedNode}
-          />
-        </div>
-      )}
-      <div className={isFederationAPI ? 'row-start-2' : ''}>
+    <div className="grid grid-cols-2 grid-rows-10 gap-2">
+      <div className="col-span-2">
+        <CategoricalField
+          label="Neurobagel graph"
+          options={availableNodes.map((n) => ({
+            label: n.NodeName,
+            id: n.ApiURL,
+          }))}
+          onFieldChange={(label, value) => updateCategoricalQueryParams(label, value)}
+          multiple
+          inputValue={selectedNode}
+        />
+      </div>
+      <div className="row-start-2">
         <ContinuousField
           helperText={minAgeExceedsMaxAge ? '' : minAgeHelperText}
           label="Minimum age"
           onFieldChange={updateContinuousQueryParams}
         />
       </div>
-      <div className={isFederationAPI ? 'row-start-2' : ''}>
+      <div className="row-start-2">
         <ContinuousField
           helperText={minAgeExceedsMaxAge ? '' : maxAgeHelperText}
           label="Maximum age"
@@ -131,7 +123,7 @@ function QueryForm({
           inputValue={sex}
         />
       </div>
-      <div className={isFederationAPI ? 'col-span-2 row-start-5' : 'col-span-2 row-start-4'}>
+      <div className="col-span-2 row-start-5">
         <div className="grid grid-cols-12 items-center gap-4">
           <div className="col-span-9">
             <CategoricalField
@@ -155,29 +147,29 @@ function QueryForm({
           </div>
         </div>
       </div>
-      <div className={isFederationAPI ? 'col-span-2 row-start-6' : 'col-span-2 row-start-5'}>
+      <div className="col-span-2 row-start-6">
         <ContinuousField
           helperText={minNumImagingSessionsHelperText}
           label="Minimum number of imaging sessions"
           onFieldChange={updateContinuousQueryParams}
         />
       </div>
-      <div className={isFederationAPI ? 'col-span-2 row-start-7' : 'col-span-2 row-start-6'}>
+      <div className="col-span-2 row-start-7">
         <ContinuousField
           helperText={minNumPhenotypicSessionsHelperText}
           label="Minimum number of phenotypic sessions"
           onFieldChange={updateContinuousQueryParams}
         />
       </div>
-      <div className={isFederationAPI ? 'col-span-2 row-start-8' : 'col-span-2 row-start-7'}>
+      <div className="col-span-2 row-start-8">
         <CategoricalField
           label="Assessment tool"
           options={assessmentOptions.map((a) => ({ label: a.Label, id: a.TermURL }))}
           onFieldChange={(label, value) => updateCategoricalQueryParams(label, value)}
           inputValue={assessmentTool}
         />
       </div>
-      <div className={isFederationAPI ? 'col-span-2 row-start-9' : 'col-span-2 row-start-8'}>
+      <div className="col-span-2 row-start-9">
         <CategoricalField
           label="Imaging modality"
           options={Object.entries(modalities).map(([, value]) => ({
@@ -188,7 +180,7 @@ function QueryForm({
           inputValue={imagingModality}
         />
       </div>
-      <div className={isFederationAPI ? 'row-start-10' : 'row-start-9'}>
+      <div className="row-start-10">
         <Button
           data-cy="submit-query-button"
           disabled={disableSubmit}

diff --git a/src/utils/constants.ts b/src/utils/constants.ts
@@ -9,11 +9,6 @@ export const nodesURL: string = baseAPIURL.endsWith('/')
   ? `${baseAPIURL}nodes`
   : `${baseAPIURL}/nodes`;
 
-export const isFederationAPI: boolean =
-  import.meta.env.NB_IS_FEDERATION_API === undefined
-    ? true
-    : import.meta.env.NB_IS_FEDERATION_API.toLowerCase() === 'true';
-
 export const appBasePath: string = import.meta.env.NB_QUERY_APP_BASE_PATH ?? '/';
 
 export const enableAuth: boolean =