Merge branch 'master' into dependabot/npm_and_yarn/client/browserify-…

…sign-4.2.2

.github/workflows/PR-validation.yml

@@ -0,0 +1,53 @@
+name: PR validation
+on:
+  pull_request:
+    types: [synchronize, opened, reopened, edited]
+    branches:
+      - master
+jobs:
+  test-api:
+    permissions:
+      id-token: write # Required for authentication through OIDC to AWS
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Report workflow details
+        run: |
+          echo "Repository ${{ github.repository }}."
+          echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Report files updated in PR
+        run: |
+          git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
+          git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
+        with:
+          java-version: '8'
+          distribution: 'temurin'
+      - name: Install clojure and clojure cli (clj)
+        uses: DeLaGuardo/[email protected]
+        with:
+          cli: 1.10.1.536
+      - name: Report runtime details
+        run: |
+          echo "Github runner OS: ${{ runner.os }}"
+      - name: AWS credentials configuration
+        uses: aws-actions/configure-aws-credentials@v2
+        with:
+          role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
+          role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-test-api
+          aws-region: us-east-1
+      - name: Download and install Datomic Pro
+        run: |
+          aws s3 cp s3://wormbase/datomic-pro/distro/datomic-pro-1.0.6165.zip ./
+          unzip datomic-pro-1.0.6165.zip
+          cd datomic-pro-1.0.6165/
+          bin/maven-install
+      - name: Generate pom file
+        run: |
+          clojure -Spom
+      - name: Run Integration tests
+        run: |
+          make run-tests GOOGLE_APP_PROFILE=dev
+  #TODO: add UI and API build and container packaging test

Makefile

@@ -1,7 +1,7 @@
 ECR_REPO_NAME := wormbase/names
 EB_APP_ENV_FILE := app-env.config
-PROJ_NAME ?= wormbase-names
-LOCAL_GOOGLE_REDIRECT_URI = "http://lvh.me:3000"
+PROJ_NAME ?= wormbase-names-dev
+LOCAL_GOOGLE_REDIRECT_URI := "http://lvh.me:3000"
 ifeq ($(PROJ_NAME), wormbase-names)
 	WB_DB_URI ?= "datomic:ddb://us-east-1/WSNames/wormbase"
 	GOOGLE_REDIRECT_URI ?= "https://names.wormbase.org"
@@ -11,7 +11,7 @@ else ifeq ($(PROJ_NAME), wormbase-names-test)
 	GOOGLE_REDIRECT_URI ?= "https://test-names.wormbase.org"
 	GOOGLE_APP_PROFILE ?= "prod"
 else
-	WB_DB_URI ?= "datomic:ddb://us-east-1/WSNames-test-14/wormbase"
+	WB_DB_URI ?= "datomic:ddb-local://localhost:8000/WBNames_local/wormbase"
 #   Ensure GOOGLE_REDIRECT_URI is defined appropriately as an env variable or CLI argument
 #   if intended for AWS deployment (default is set for local execution)
 	GOOGLE_REDIRECT_URI ?= ${LOCAL_GOOGLE_REDIRECT_URI}
@@ -235,14 +235,17 @@ run-tests: google-oauth2-secrets \
 	@ export API_GOOGLE_OAUTH_CLIENT_ID=${GOOGLE_OAUTH_CLIENT_ID} && \
 	  export API_GOOGLE_OAUTH_CLIENT_SECRET=${GOOGLE_OAUTH_CLIENT_SECRET} && \
 	  export GOOGLE_REDIRECT_URI=${LOCAL_GOOGLE_REDIRECT_URI} && \
-	  clj -A:datomic-pro:webassets:dev:test:run-tests
+	  clojure -A:datomic-pro:logging:webassets:dev:test:run-tests
 
 .PHONY: run-dev-server
+run-dev-webserver: PORT := 4010
 run-dev-webserver: google-oauth2-secrets \
                    $(call print-help,run-dev-webserver PORT=<port> WB_DB_URI=<datomic-uri> \
 				   GOOGLE_REDIRECT_URI=<google-redirect-uri>,\
                    Run a local development webserver.)
-	@ export API_GOOGLE_OAUTH_CLIENT_ID=${GOOGLE_OAUTH_CLIENT_ID} && \
+	@ export WB_DB_URI=${WB_DB_URI} && export PORT=${PORT} && \
+	 export GOOGLE_REDIRECT_URI=${GOOGLE_REDIRECT_URI} && \
+	 export API_GOOGLE_OAUTH_CLIENT_ID=${GOOGLE_OAUTH_CLIENT_ID} && \
 	 export API_GOOGLE_OAUTH_CLIENT_SECRET=${GOOGLE_OAUTH_CLIENT_SECRET} && \
 	 clj -A:logging:datomic-pro:webassets:dev -m wormbase.names.service
 
@@ -259,7 +262,7 @@ run-dev-ui: google-oauth2-secrets\
 .PHONY: google-oauth2-secrets
 google-oauth2-secrets: \
                        $(call print-help,google-oauth2-secrets,\
-                       Store the Google oauth2 client details in a secrets file.)
+                       Store the Google oauth2 client details as env variables.)
 	$(eval GOOGLE_OAUTH_CLIENT_ID = $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-id" --query "Parameter.Value" --output text --with-decryption))
 	$(call check_defined, GOOGLE_OAUTH_CLIENT_ID)
 	$(eval GOOGLE_OAUTH_CLIENT_SECRET = $(shell aws ssm get-parameter --name "/name-service/${GOOGLE_APP_PROFILE}/google-oauth2-app-config/client-secret" --query "Parameter.Value" --output text --with-decryption))

README.md

@@ -11,6 +11,7 @@
     * [REST API](#rest-api)
        - [Tools](#tools)
           * [Running a Clojure REPL](#running-a-clojure-repl)
+          * [Debug printing](#debug-printing)
     * [Client app (web interface)](#client-app-web-interface)
  - [Testing](#testing)
  - [Release & deployment](#release--deployment)
@@ -152,6 +153,28 @@ This can be done via the following command:
 clj -A:outdated
 ```
 
+#### Debug printing
+Standard logging is done using `ch.qos.logback/logback` (`-classic` and `-core`), but this is not flexible
+for limited-scale (local) debug printing during coding and debugging. To enable more flexible debug printing:
+
+ 1. In the file you want to enable temporary debug printing, replace the loading of the `clojure.tools.logging` library
+    with the `taoensso.timbre` library instead (using the same `:log` alias).
+
+ 2. Add the following line below the library loading section
+    ```clojure
+    (log/merge-config! {:level :debug})
+    ```
+    This will enable all log printing up to debug level within that file,
+    but leave the application-default logging outside of it, enabling a
+    more focused log inspection.
+
+ 3. Add any additional debug logging with the standard `(log/debug "string" object)`
+
+`taoensso.timbre` will by default print logs to the following format:
+```
+<date> <timestamp> <device-name> <LOGLEVEL> [<namespace>] - <log message>
+```
+
 ### Client app (web interface)
 Correct functionality of the client app can be tested in two ways:
 - Running a client development server (during development), to test individual functionality. See [instructions below](#local-rest).
@@ -276,7 +299,7 @@ To deploy an update for the main application, change your working dir
 to the repository root dir and execute the following commands (bash):
 ```bash
 # Build the client application to ensure no errors occur.
-make ui-build
+make ui-build GOOGLE_APP_PROFILE=prod
 
 # Generate the pom.xml file (not version-controlled)
 # to ensure no errors occur (in API code)
@@ -309,12 +332,12 @@ sudo service docker start
 # NOTE: To deploy a tagged or branched codeversion that does not equal your (potentially dirty) working-dir content,
 #       use the additional argument REF_NAME=<ref-name>
 #       E.g. make release AWS_PROFILE=wormbase REF_NAME=wormbase-names-1.4.7
-make release [AWS_PROFILE=<profile_name>]
+make release [AWS_PROFILE=<profile_name>] GOOGLE_APP_PROFILE=prod
 
 # Deploy the application to an EB environmnent.
 # Before execution:
-# * Ensure to specify the correct EB environment name, in order to prevent
-#   accidental deployments to the production environment!
+# * Ensure to specify the correct EB environment name,
+#   (otherwise deployment to non-existing dev environment will be attempted)
 # * Check if the hard-coded WB_DB_URI default (see MakeFile) applies.
 #   If not, define WB_DB_URI to point to the appropriate datomic DB.
 # * Ensure to define the correct GOOGLE_REDIRECT_URI for google authentication (http://lvh.me:3000 when developing locally)

client/package.json

@@ -15,7 +15,7 @@
   "dependencies": {
     "@material-ui/core": "3.9.2",
     "@material-ui/icons": "3.0.2",
-    "@react-oauth/google": "^0.8.0",
+    "@react-oauth/google": "0.12.x",
     "classnames": "2.2.6",
     "copy-to-clipboard": "3.2.0",
     "react-copy-to-clipboard": "5.1.0",

client/src/App.js

@@ -7,8 +7,10 @@ import Main from './containers/Main';
 import { theme, MuiThemeProvider } from './components/elements';
 
 export default () => (
-  <GoogleOAuthProvider clientId={process.env.REACT_APP_GOOGLE_OAUTH_CLIENT_ID}>
-    <React.StrictMode>
+  <React.StrictMode>
+    <GoogleOAuthProvider
+      clientId={process.env.REACT_APP_GOOGLE_OAUTH_CLIENT_ID}
+    >
       <BrowserRouter>
         <Authenticate>
           <EntityTypesContextProvider>
@@ -18,6 +20,6 @@ export default () => (
           </EntityTypesContextProvider>
         </Authenticate>
       </BrowserRouter>
-    </React.StrictMode>
-  </GoogleOAuthProvider>
+    </GoogleOAuthProvider>
+  </React.StrictMode>
 );

client/src/components/elements/SpeciesSelect.js

@@ -7,7 +7,7 @@ import { useDataFetch } from '../../containers/Authenticate';
 
 const SpeciesSelect = (props) => {
   const memoizedFetchFunc = useCallback(
-    (authorizedFetch) =>
+    (fetchFn) =>
       mockFetchOrNot(
         (mockFetch) => {
           return mockFetch.get('*', [
@@ -27,7 +27,7 @@ const SpeciesSelect = (props) => {
           ]);
         },
         () =>
-          authorizedFetch(`/api/species`, {
+          fetchFn(`/api/species`, {
             method: 'GET',
           })
       ),

client/src/containers/Authenticate/Login.js

@@ -13,7 +13,7 @@ class Login extends Component {
             <div className={classes.errorMessage}>{errorMessage}</div>
           </div>
         ) : null}
-        <Button onClick={onSignIn} variant="raised">
+        <Button onClick={onSignIn} variant="contained">
           Login with Google
         </Button>
       </div>

client/src/containers/Authenticate/Logout.js

@@ -6,7 +6,7 @@ import { Button } from '../../components/elements';
 const Logout = (props) => {
   return (
     <Button
-      variant="raised"
+      variant="contained"
       onClick={() => {
         props.onLogout();
         props.history.push('/');

client/src/containers/Authenticate/Profile.js

@@ -1,5 +1,4 @@
 import React from 'react';
-import { CopyToClipboard } from 'react-copy-to-clipboard';
 import PropTypes from 'prop-types';
 import { withStyles } from '../../components/elements';
 
@@ -10,19 +9,7 @@ const Profile = (props) => {
       <span>ID: {props.id}</span>
       <br />
       <span>Email: {props.email}</span>
-      <span>
-        ID-token:{' '}
-        <div>
-          <textarea>{props.id_token}</textarea>
-          <br />
-          <CopyToClipboard text={props.id_token}>
-            <div>
-              <button>Copy to clipboard</button>
-            </div>
-          </CopyToClipboard>
-        </div>
-      </span>
-      <div className={props.classes.logout}>{props.children}</div>
+      <div className={props.classes.actions}>{props.children}</div>
     </div>
   );
 };
@@ -32,7 +19,6 @@ Profile.propTypes = {
   name: PropTypes.string.isRequired,
   email: PropTypes.string.isRequired,
   id: PropTypes.string.isRequired,
-  onLogout: PropTypes.func.isRequired,
   children: PropTypes.element,
 };
 
@@ -44,8 +30,8 @@ const styles = (theme) => ({
     justifyContent: 'center',
     alignItems: 'center',
   },
-  logout: {
-    margin: theme.spacing.unit * 6,
+  actions: {
+    margin: theme.spacing.unit * 4,
   },
 });