Merge pull request #391 from WormBase/object-creation-caltech-replay

Object creation caltech replay

.gitignore

@@ -25,6 +25,8 @@ pm_to_blib
 release-archives/
 target/
 .cpcache/
+.classpath
+.factorypath
 
 # Elastic Beanstalk Files
 .ebextensions/app-env.config
@@ -53,5 +55,11 @@ data/
 # Source code linter cache
 /.clj-kondo/.cache/
 
+# IDE project/module settings
+.vscode
+.project
+.settings
+
 # VS Code calva extension configs
 .calva
+.lsp

Makefile

@@ -10,7 +10,7 @@ ifeq ($(PROJ_NAME), wormbase-names)
 else ifeq ($(PROJ_NAME), wormbase-names-test)
 	WB_DB_URI ?= "datomic:ddb://${AWS_DEFAULT_REGION}/WSNames-test-14/wormbase"
 	GOOGLE_REDIRECT_URI ?= "https://test-names.wormbase.org"
-	APP_PROFILE ?= "prod"
+	APP_PROFILE ?= "test"
 else
 	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
@@ -170,7 +170,7 @@ docker-tag: ENV.VERSION_TAG \
 	@docker tag ${ECR_REPO_NAME}:${VERSION_TAG} ${ECR_REPO_URI}
 
 .PHONY: eb-def-app-env
-eb-def-app-env: google-oauth2-secrets ENV.VERSION_TAG \
+eb-def-app-env: google-oauth2-secrets caltech-api-secrets ENV.VERSION_TAG \
                 $(call print-help,eb-def-app-env \
 				[WB_DB_URI=<datomic-db-uri>] [GOOGLE_REDIRECT_URI=<google-redirect-uri>],\
                 Define the ElasticBeanStalk app-environment config file.)
@@ -185,6 +185,9 @@ endif
 	sed -i -r 's~(API_GOOGLE_OAUTH_CLIENT_ID:\s+)".*"~\1"'"${GOOGLE_OAUTH_CLIENT_ID}"'"~' .ebextensions/${EB_APP_ENV_FILE}
 	sed -i -r 's~(API_GOOGLE_OAUTH_CLIENT_SECRET:\s+)".*"~\1"'"${GOOGLE_OAUTH_CLIENT_SECRET}"'"~' .ebextensions/${EB_APP_ENV_FILE}
 	sed -i -r 's~(GOOGLE_REDIRECT_URI:\s+)".*"~\1"'"${GOOGLE_REDIRECT_URI}"'"~' .ebextensions/${EB_APP_ENV_FILE}
+	sed -i -r 's~(CALTECH_API_URL:\s+)".*"~\1"'"${CALTECH_API_URL}"'"~' .ebextensions/${EB_APP_ENV_FILE}
+	sed -i -r 's~(CALTECH_API_USER:\s+)".*"~\1"'"${CALTECH_API_USER}"'"~' .ebextensions/${EB_APP_ENV_FILE}
+	sed -i -r 's~(CALTECH_API_PASSWORD:\s+)".*"~\1"'"${CALTECH_API_PASSWORD}"'"~' .ebextensions/${EB_APP_ENV_FILE}
 	sed  -i -r 's~(WB_NAMES_RELEASE: ).+~\1'${VERSION_TAG}'~' .ebextensions/${EB_APP_ENV_FILE}
 
 .PHONY: eb-create
@@ -306,24 +309,30 @@ release: ENV.VERSION_TAG deploy-ecr \
          Release the applicaton.)
 
 .PHONY: run-tests
-run-tests: google-oauth2-secrets \
+run-tests: google-oauth2-secrets caltech-api-secrets \
            $(call print-help,run-tests,\
            Run all tests.)
-	@ export API_GOOGLE_OAUTH_CLIENT_ID=${GOOGLE_OAUTH_CLIENT_ID} && \
-	  export API_GOOGLE_OAUTH_CLIENT_SECRET=${GOOGLE_OAUTH_CLIENT_SECRET} && \
-	  export GOOGLE_REDIRECT_URI=${LOCAL_GOOGLE_REDIRECT_URI} && \
+	@ export API_GOOGLE_OAUTH_CLIENT_ID="${GOOGLE_OAUTH_CLIENT_ID}" && \
+	  export API_GOOGLE_OAUTH_CLIENT_SECRET="${GOOGLE_OAUTH_CLIENT_SECRET}" && \
+	  export CALTECH_API_URL="${CALTECH_API_URL}" && \
+	  export CALTECH_API_USER="${CALTECH_API_USER}" && \
+	  export CALTECH_API_PASSWORD="${CALTECH_API_PASSWORD}" && \
+	  export GOOGLE_REDIRECT_URI="${LOCAL_GOOGLE_REDIRECT_URI}" && \
 	  clojure -A:datomic-pro:logging:webassets:dev:test:run-tests
 
 .PHONY: run-dev-webserver
 run-dev-webserver: PORT := 4010
-run-dev-webserver: google-oauth2-secrets \
+run-dev-webserver: google-oauth2-secrets caltech-api-secrets \
                    $(call print-help,run-dev-webserver PORT=<port> WB_DB_URI=<datomic-uri> \
 				   GOOGLE_REDIRECT_URI=<google-redirect-uri>,\
                    Run a local development webserver.)
 	@ export WB_DB_URI=${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} && \
+	 export GOOGLE_REDIRECT_URI="${GOOGLE_REDIRECT_URI}" && \
+	 export API_GOOGLE_OAUTH_CLIENT_ID="${GOOGLE_OAUTH_CLIENT_ID}" && \
+	 export API_GOOGLE_OAUTH_CLIENT_SECRET="${GOOGLE_OAUTH_CLIENT_SECRET}" && \
+	 export CALTECH_API_URL="${CALTECH_API_URL}" && \
+	 export CALTECH_API_USER="${CALTECH_API_USER}" && \
+	 export CALTECH_API_PASSWORD="${CALTECH_API_PASSWORD}" && \
 	 clj -A:logging:datomic-pro:webassets:dev -m wormbase.names.service
 
 .PHONY: run-dev-ui
@@ -356,11 +365,46 @@ ENV.GOOGLE_OAUTH_CLIENT_SECRET: source-secrets \
 	$(call check_defined, GOOGLE_OAUTH_CLIENT_SECRET, Check the defined APP_PROFILE value\
 	 and ensure the AWS_PROFILE variable is appropriately defined)
 
+.PHONY: ENV.CALTECH_API_URL
+ENV.CALTECH_API_URL: \
+	$(call print-help,ENV.CALTECH_API_URL,\
+	Retrieve the CALTECH_API_URL env variable for make targets from aws ssm if undefined.)
+	$(eval ACTION_MSG := $(if ${CALTECH_API_URL},"Using predefined CALTECH_API_URL.","Retrieving CALTECH_API_URL from AWS SSM (APP_PROFILE '${APP_PROFILE}')."))
+	@echo ${ACTION_MSG}
+	$(if ${CALTECH_API_URL},,$(eval CALTECH_API_URL := $(shell ${AWS_CLI_BASE} ssm get-parameter --name "/name-service/${APP_PROFILE}/caltech-api-config/url" --query "Parameter.Value" --output text --with-decryption)))
+	$(call check_defined, CALTECH_API_URL, Check the defined APP_PROFILE value\
+	 and ensure the AWS_PROFILE variable is appropriately defined)
+
+.PHONY: ENV.CALTECH_API_USER
+ENV.CALTECH_API_USER: \
+	$(call print-help,ENV.CALTECH_API_USER,\
+	Retrieve the CALTECH_API_USER env variable for make targets from aws ssm if undefined.)
+	$(eval ACTION_MSG := $(if ${CALTECH_API_USER},"Using predefined CALTECH_API_USER.","Retrieving CALTECH_API_USER from AWS SSM (APP_PROFILE '${APP_PROFILE}')."))
+	@echo ${ACTION_MSG}
+	$(if ${CALTECH_API_USER},,$(eval CALTECH_API_USER := $(shell ${AWS_CLI_BASE} ssm get-parameter --name "/name-service/${APP_PROFILE}/caltech-api-config/username" --query "Parameter.Value" --output text --with-decryption)))
+	$(call check_defined, CALTECH_API_USER, Check the defined APP_PROFILE value\
+	 and ensure the AWS_PROFILE variable is appropriately defined)
+
+.PHONY: ENV.CALTECH_API_PASSWORD
+ENV.CALTECH_API_PASSWORD: \
+	$(call print-help,ENV.CALTECH_API_PASSWORD,\
+	Retrieve the CALTECH_API_PASSWORD env variable for make targets from aws ssm if undefined.)
+	$(eval ACTION_MSG := $(if ${CALTECH_API_PASSWORD},"Using predefined CALTECH_API_PASSWORD.","Retrieving CALTECH_API_PASSWORD from AWS SSM (APP_PROFILE '${APP_PROFILE}')."))
+	@echo ${ACTION_MSG}
+	$(if ${CALTECH_API_PASSWORD},,$(eval CALTECH_API_PASSWORD := $(shell ${AWS_CLI_BASE} ssm get-parameter --name "/name-service/${APP_PROFILE}/caltech-api-config/password" --query "Parameter.Value" --output text --with-decryption)))
+	$(call check_defined, CALTECH_API_PASSWORD, Check the defined APP_PROFILE value\
+	 and ensure the AWS_PROFILE variable is appropriately defined)
+
 .PHONY: google-oauth2-secrets
 google-oauth2-secrets: ENV.GOOGLE_OAUTH_CLIENT_ID ENV.GOOGLE_OAUTH_CLIENT_SECRET \
                        $(call print-help,google-oauth2-secrets,\
                        Store the Google oauth2 client details as env variables.)
 
+.PHONY: caltech-api-secrets
+caltech-api-secrets: ENV.CALTECH_API_URL ENV.CALTECH_API_USER ENV.CALTECH_API_PASSWORD \
+                     $(call print-help,caltech-api-secrets,\
+                     Store the Caltech API details as env variables.)
+
 ${STORE_SECRETS_FILE}: google-oauth2-secrets
 	@install -m 600 /dev/null ${STORE_SECRETS_FILE}
 	@echo "GOOGLE_OAUTH_CLIENT_ID:=${GOOGLE_OAUTH_CLIENT_ID}" >> ${STORE_SECRETS_FILE}

client/package.json

@@ -25,7 +25,6 @@
     "prop-types": "15.7.2",
     "query-string": "5",
     "react": "16.8.5",
-    "react-document-title": "2.0.3",
     "react-dom": "16.8.5",
     "react-router-dom": "5.3.4",
     "react-storage-hooks": "3.0.1",

client/src/components/elements/NotFound.js

@@ -1,20 +1,23 @@
-import React, { Component } from 'react';
+import React from 'react';
 import PropTypes from 'prop-types';
 import { Typography, withStyles } from '@material-ui/core';
 
-class NotFound extends Component {
-  render() {
-    const { classes } = this.props;
-    return (
-      <div className={classes.root}>
-        <Typography variant="h3" gutterBottom>
-          Not Found
-        </Typography>
-        {this.props.children}
-      </div>
-    );
-  }
-}
+import { useTitle } from '../../hooks/useTitle';
+
+const NotFound = (props) => {
+  const { classes } = props;
+
+  useTitle('Not found');
+
+  return (
+    <div className={classes.root}>
+      <Typography variant="h3" gutterBottom>
+        Not Found
+      </Typography>
+      {props.children}
+    </div>
+  );
+};
 
 NotFound.propTypes = {
   children: PropTypes.element,

client/src/components/elements/Page/index.js

@@ -2,11 +2,15 @@ import React from 'react';
 import PropTypes from 'prop-types';
 import { withStyles } from '@material-ui/core';
 
-function page({ classes, ...others }) {
-  return <div className={classes.root} {...others} />;
-}
-page.propTypes = {
+import { useTitle } from '../../../hooks/useTitle';
+
+const Page = (props) => {
+  useTitle(props.title);
+  return <div className={props.classes.root} {...props} />;
+};
+Page.propTypes = {
   classes: PropTypes.object.isRequired,
+  title: PropTypes.string,
 };
 
 function pageMain({ classes, ...others }) {
@@ -30,15 +34,15 @@ pageRight.propTypes = {
   classes: PropTypes.object.isRequired,
 };
 
-export const Page = withStyles((theme) => ({
+export default withStyles((theme) => ({
   root: {
     display: 'flex',
     margin: theme.spacing(4),
     [theme.breakpoints.down('sm')]: {
       flexDirection: 'column',
     },
   },
-}))(page);
+}))(Page);
 
 export const PageLeft = withStyles((theme) => ({
   left: {
@@ -70,5 +74,3 @@ export const PageMain = withStyles((theme) => ({
 //     },
 //   },
 // }))(pageRight);
-
-export default Page;

client/src/components/elements/TextArea.js

@@ -2,5 +2,5 @@ import React from 'react';
 import TextField from './TextField';
 
 export default function TextArea(props) {
-  return <TextField multiline fullWidth rows={4} {...props} />;
+  return <TextField multiline fullWidth minRows={4} {...props} />;
 }

client/src/components/elements/index.js

@@ -6,7 +6,7 @@ import {
 
 import {
   MuiThemeProvider,
-  createMuiTheme,
+  createTheme,
   withStyles,
   Dialog as MuiDialog,
   withMobileDialog,
@@ -44,13 +44,12 @@ export { default as AutocompleteSuggestion } from './AutocompleteSuggestion';
 export { default as BaseForm } from './BaseForm';
 export { default as BiotypeSelect } from './BiotypeSelect';
 export { default as Button } from './Button';
-export { default as DocumentTitle } from './DocumentTitle';
 export { default as EntityTypeSelect } from './EntityTypeSelect';
 export { default as ErrorBoundary } from './ErrorBoundary';
 export { default as SimpleAjax } from './SimpleAjax';
 export { default as NoData } from './NoData';
 export { default as NotFound } from './NotFound';
-export { Page, PageLeft, PageMain } from './Page';
+export { default as Page, PageLeft, PageMain } from './Page';
 export * from './ProgressButton';
 export { default as ProgressButton } from './ProgressButton';
 export { default as SimpleListPagination } from './SimpleListPagination';
@@ -85,7 +84,7 @@ export const Dialog = withMobileDialog()(
 // };
 // All the following keys are optional.
 // We try our best to provide a great default value.
-export const theme = createMuiTheme({
+export const theme = createTheme({
   palette: {
     primary: {
       main: primaryColor[700],
@@ -104,4 +103,4 @@ export const theme = createMuiTheme({
   },
 });
 
-export { MuiThemeProvider, createMuiTheme, withStyles };
+export { MuiThemeProvider, createTheme, withStyles };

client/src/containers/Authenticate/Profile.js

@@ -2,7 +2,10 @@ import React from 'react';
 import PropTypes from 'prop-types';
 import { withStyles } from '../../components/elements';
 
+import { useTitle } from '../../hooks/useTitle';
+
 const Profile = (props) => {
+  useTitle('Your profile');
   return (
     <div className={props.classes.root}>
       <h2>{props.name}</h2>

client/src/containers/Authenticate/ProfileButton.js

@@ -4,12 +4,13 @@ import { Button, withStyles } from '../../components/elements';
 import { Link } from 'react-router-dom';
 import PersonIcon from '@material-ui/icons/Person';
 
+const my_profile_link = React.forwardRef(function(props, ref) {
+  return <Link to="/me" {...props} ref={ref} />;
+});
+
 const ProfileButton = (props) => {
   return props.name ? (
-    <Button
-      component={({ ...props }) => <Link to="/me" {...props} />}
-      className={props.classes.button}
-    >
+    <Button component={my_profile_link} className={props.classes.button}>
       <PersonIcon className={props.classes.icon} />
       Hi, {props.name.split(/\s+/)[0]}
     </Button>