Develop

.gitignore

@@ -75,6 +75,8 @@ typings/
 
 # dotenv environment variables file
 .env
+.env.*
+!.env-template
 
 # Adding the swagger project files:
 api_project.sublime-project

.yarnrc.yml

@@ -1,3 +1 @@
-nodeLinker: node-modules
-
-yarnPath: .yarn/releases/yarn-4.12.0.cjs
+nodeLinker: node-modules

Dockerfile

@@ -1,7 +1,8 @@
 FROM node:22-alpine
 WORKDIR /app
-COPY package*.json ./
-RUN yarn install
+RUN corepack enable
+COPY package.json yarn.lock .yarnrc.yml ./
+RUN yarn install --immutable
 COPY . .
 EXPOSE 3001
-CMD ["npm", "start"]
+CMD ["npm", "start"]

app.js

@@ -15,7 +15,11 @@ const dbtest = require('./database/pgp_db').dbheader;
 const rateLimiter = require('express-rate-limit');
 const dotenv = require('dotenv');
 
-dotenv.config();
+const env = process.env.NODE_ENV || 'development';
+dotenv.config({ path: `.env.${env}` });
+console.log(`Loaded environment from .env.${env}`);
+
+const apiPort = parseInt(process.env.APIPORT, 10) || 3001;
 
 const app = express();
 const cache = apicache.middleware;
@@ -33,18 +37,47 @@ const limiter = rateLimiter({
 
 app.engine('html', require('ejs').renderFile);
 
-// app.use(helmet());
-app.use(cors());
+const {optionalAuth} = require('./v2.0/helpers/validation/sessionauth');
+const corsOptions = {
+  origin: function(origin, callback) {
+    // Allow requests with no Origin header (server-to-server, R package, curl, etc.)
+    if (!origin) return callback(null, true);
+
+    const allowed = [
+      'http://localhost:5173',
+      'http://127.0.0.1:5173',
+      'https://data.neotomadb.org',
+      // add other frontends as needed
+    ];
+
+    if (allowed.includes(origin)) {
+      return callback(null, true);
+    }
+    // For now, log and allow — Neotoma data is public.
+    // Tighten this later if you ever return user-specific data based on Origin.
+    console.warn('CORS: unrecognized origin allowed:', origin);
+    return callback(null, true);
+  },
+  credentials: true,
+  allowedHeaders: ['Content-Type', 'Authorization'],
+};
+
+app.use(cors(corsOptions));
 app.use(limiter);
 app.use(express.json());
-// app.use(cache('5 minutes'));
-app.use(express.static('mochawesome-report'));
+app.use(express.urlencoded({ extended: false }));
+app.use(cookieParser());
 app.use(compression());
+app.use(express.static('public'));
+app.use(express.static('mochawesome-report'));
+app.use(express.static(path.join(__dirname, 'public')));
+// Attach req.user (or null) on every request.
+// Routes that need to *require* auth use requireAuth instead.
+app.use(optionalAuth);
 
 app.locals.db = dbtest();
 
 // test trigger watch restart - 09/12/20
-//
 // create a write stream (in append mode)
 
 const pad = (num) => (num > 9 ? '' : '0') + num;
@@ -72,7 +105,7 @@ app.use(morgan(':date[iso]\t:remote-addr\t:method\t:url\t:status\t:res[content-l
 }));
 
 const options = {
-  swaggerUrl: 'http://localhost:3005/api-docs',
+  swaggerUrl: `http://localhost:${apiPort}/api-docs`,
   customCssUrl: '/custom.css',
 };
 
@@ -99,17 +132,6 @@ const healthwatch = require('./v2.0/routes/healthwatch');
 app.set('views', path.join(__dirname, 'views'));
 app.set('view engine', 'jade');
 
-// uncomment after placing your favicon in /public
-// app.use(favicon(path.join(__dirname, 'public', 'favicon.ico')));
-
-app.use(express.static('public'));
-app.use(express.urlencoded({
-  extended: false,
-}));
-app.use(express.json());
-app.use(cookieParser());
-
-app.use(express.static(path.join(__dirname, 'public')));
 
 // optionally, re-factor route paths here to strip version string and
 // identify version from header; still requires version directory paths in
@@ -173,12 +195,8 @@ app.all('*', function(req, res) {
 // in production, port is 3001 and server started in script 'www'
 // The variable is stored in the gitignored `.env` file.
 // This is managed in the www folder.
-if (process.env.NODE_ENV === 'development') {
-  app.listen(3005);
-}
-
-if (process.env.NODE_ENV === 'production') {
-  app.listen(3001);
-}
+app.listen(apiPort, () => {
+  console.log(`Neotoma API listening on port ${apiPort} (NODE_ENV=${process.env.NODE_ENV})`);
+});
 
 module.exports = app;

genoatt.sh

@@ -12,11 +12,12 @@ This bash script also performs some text replacement to account for issues in th
  * We ensure that all altmin values are lower than altmax values.
 
 Options:
-    [none]      build the mocha tests and exit
+    [none]      build the mocha tests and exit (targets localhost:3001 — local production mode)
     -h          display this help and exit
     -t          build the tests and run "npm test"
-    -d          build the tests for the remove development server at api-dev.
-    -p          build the tests for the remove production server at api.neotomadb.org
+    -l          build the tests for the LOCAL DEV server at localhost:3005 (NODE_ENV=development)
+    -d          build the tests for the remote development server at api-dev.
+    -p          build the tests for the remote production server at api.neotomadb.org
 
 HELP
 }
@@ -29,8 +30,8 @@ run_oatt() {
 
     # oatts is a bit silly in picking its variables.  We need to make sure that we're
     # getting the proper polygons, and making sure altmin/altmax are appropriate.
-    find ./test/*.js -type f -exec sed -i.old -E 's/"loc":\ "\{.*?\}"/"loc": "{\"type\":\"Polygon\",\"coordinates\":[[[-104.053249,41.001406],[-104.675999,41.000957],[-104.855273,40.998048],[-105.277138,40.998173],[-105.730421,40.996886],[-106.217573,40.997734],[-106.453859,41.002057],[-106.857773,41.002663],[-107.625624,41.002124],[-108.250649,41.000114],[-108.884138,41.000094],[-109.050076,41.000659],[-109.048044,40.619231],[-109.050946,40.444368],[-109.050615,39.87497],[-109.051363,39.497674],[-109.051512,39.126095],[-109.054189,38.874984],[-109.059541,38.719888],[-109.060062,38.275489],[-109.041762,38.16469],[-109.041058,37.907236],[-109.041865,37.530726],[-109.04581,37.374993],[-109.045223,36.999084],[-108.620309,36.999287],[-108.249358,36.999015],[-108.000623,37.000001],[-107.420913,37.000005],[-106.877292,37.000139],[-106.869796,36.992426],[-106.201469,36.994122],[-105.62747,36.995679],[-105.1208,36.995428],[-105.000554,36.993264],[-104.338833,36.993535],[-103.733247,36.998016],[-103.002199,37.000104],[-102.814616,37.000783],[-102.698142,36.995149],[-102.04224,36.993083],[-102.041974,37.352613],[-102.041574,37.680436],[-102.044644,38.045532],[-102.045324,38.453647],[-102.045388,38.813392],[-102.048449,39.303138],[-102.050422,39.646048],[-102.051744,40.003078],[-102.051725,40.537839],[-102.051614,41.002377],[-102.556789,41.002219],[-102.865784,41.001988],[-103.497447,41.001635],[-104.053249,41.001406]]]}"/g' {} \;
-    find ./test/*.js -type f -exec sed -i.old -E 's/"loc":\ \"\{.*?\}\"/"loc": "{\"type\":\"Polygon\",\"coordinates\":[[[-104.053249,41.001406],[-104.675999,41.000957],[-104.855273,40.998048],[-105.277138,40.998173],[-105.730421,40.996886],[-106.217573,40.997734],[-106.453859,41.002057],[-106.857773,41.002663],[-107.625624,41.002124],[-108.250649,41.000114],[-108.884138,41.000094],[-109.050076,41.000659],[-109.048044,40.619231],[-109.050946,40.444368],[-109.050615,39.87497],[-109.051363,39.497674],[-109.051512,39.126095],[-109.054189,38.874984],[-109.059541,38.719888],[-109.060062,38.275489],[-109.041762,38.16469],[-109.041058,37.907236],[-109.041865,37.530726],[-109.04581,37.374993],[-109.045223,36.999084],[-108.620309,36.999287],[-108.249358,36.999015],[-108.000623,37.000001],[-107.420913,37.000005],[-106.877292,37.000139],[-106.869796,36.992426],[-106.201469,36.994122],[-105.62747,36.995679],[-105.1208,36.995428],[-105.000554,36.993264],[-104.338833,36.993535],[-103.733247,36.998016],[-103.002199,37.000104],[-102.814616,37.000783],[-102.698142,36.995149],[-102.04224,36.993083],[-102.041974,37.352613],[-102.041574,37.680436],[-102.044644,38.045532],[-102.045324,38.453647],[-102.045388,38.813392],[-102.048449,39.303138],[-102.050422,39.646048],[-102.051744,40.003078],[-102.051725,40.537839],[-102.051614,41.002377],[-102.556789,41.002219],[-102.865784,41.001988],[-103.497447,41.001635],[-104.053249,41.001406]]]}"/g' {} \;
+    find ./test/*.js -type f -exec sed -i.old -E 's/"loc":\ "\{[^}]*\}"/"loc": "{\"type\":\"Polygon\",\"coordinates\":[[[-104.053249,41.001406],[-104.675999,41.000957],[-104.855273,40.998048],[-105.277138,40.998173],[-105.730421,40.996886],[-106.217573,40.997734],[-106.453859,41.002057],[-106.857773,41.002663],[-107.625624,41.002124],[-108.250649,41.000114],[-108.884138,41.000094],[-109.050076,41.000659],[-109.048044,40.619231],[-109.050946,40.444368],[-109.050615,39.87497],[-109.051363,39.497674],[-109.051512,39.126095],[-109.054189,38.874984],[-109.059541,38.719888],[-109.060062,38.275489],[-109.041762,38.16469],[-109.041058,37.907236],[-109.041865,37.530726],[-109.04581,37.374993],[-109.045223,36.999084],[-108.620309,36.999287],[-108.249358,36.999015],[-108.000623,37.000001],[-107.420913,37.000005],[-106.877292,37.000139],[-106.869796,36.992426],[-106.201469,36.994122],[-105.62747,36.995679],[-105.1208,36.995428],[-105.000554,36.993264],[-104.338833,36.993535],[-103.733247,36.998016],[-103.002199,37.000104],[-102.814616,37.000783],[-102.698142,36.995149],[-102.04224,36.993083],[-102.041974,37.352613],[-102.041574,37.680436],[-102.044644,38.045532],[-102.045324,38.453647],[-102.045388,38.813392],[-102.048449,39.303138],[-102.050422,39.646048],[-102.051744,40.003078],[-102.051725,40.537839],[-102.051614,41.002377],[-102.556789,41.002219],[-102.865784,41.001988],[-103.497447,41.001635],[-104.053249,41.001406]]]}"/g' {} \;
+    find ./test/*.js -type f -exec sed -i.old -E 's/"loc":\ \"\{[^}]*\}\"/"loc": "{\"type\":\"Polygon\",\"coordinates\":[[[-104.053249,41.001406],[-104.675999,41.000957],[-104.855273,40.998048],[-105.277138,40.998173],[-105.730421,40.996886],[-106.217573,40.997734],[-106.453859,41.002057],[-106.857773,41.002663],[-107.625624,41.002124],[-108.250649,41.000114],[-108.884138,41.000094],[-109.050076,41.000659],[-109.048044,40.619231],[-109.050946,40.444368],[-109.050615,39.87497],[-109.051363,39.497674],[-109.051512,39.126095],[-109.054189,38.874984],[-109.059541,38.719888],[-109.060062,38.275489],[-109.041762,38.16469],[-109.041058,37.907236],[-109.041865,37.530726],[-109.04581,37.374993],[-109.045223,36.999084],[-108.620309,36.999287],[-108.249358,36.999015],[-108.000623,37.000001],[-107.420913,37.000005],[-106.877292,37.000139],[-106.869796,36.992426],[-106.201469,36.994122],[-105.62747,36.995679],[-105.1208,36.995428],[-105.000554,36.993264],[-104.338833,36.993535],[-103.733247,36.998016],[-103.002199,37.000104],[-102.814616,37.000783],[-102.698142,36.995149],[-102.04224,36.993083],[-102.041974,37.352613],[-102.041574,37.680436],[-102.044644,38.045532],[-102.045324,38.453647],[-102.045388,38.813392],[-102.048449,39.303138],[-102.050422,39.646048],[-102.051744,40.003078],[-102.051725,40.537839],[-102.051614,41.002377],[-102.556789,41.002219],[-102.865784,41.001988],[-103.497447,41.001635],[-104.053249,41.001406]]]}"/g' {} \;
     find ./test/*.js -type f -exec sed -i.old -E 's/"altmin":(\ )*-*[0-9]+/"altmin":\ 10/g' {} \;
     find ./test/*.js -type f -exec sed -i.old -E 's/"altmax":(\ )*-*[0-9]+/"altmax":\ 100/g' {} \;
     find ./test/*.js -type f -exec sed -i.old -E 's/"ageold":(\ )*-*[0-9]+/"ageold":\ 10000/g' {} \;
@@ -41,8 +42,8 @@ run_oatt() {
     find ./test/*.js -type f -exec sed -i.old -E 's/"limit":(\ )*-*[0-9]+/"limit":\ 10/g' {} \;
     find ./test/*.js -type f -exec sed -i.old -E 's/"offset":(\ )*-*[0-9]+/"offset":\ 0/g' {} \;
     find ./test/*.js -type f -exec sed -i.old 's/\/[0-9]\{5,\}/\/500/g' {} \;
-    find ./test/*.js -type f -exec sed -i.old -E 's/"prec":(\ )*[0-9\.]*?/"prec": 1000/g' {} \;
-    find ./test/*.js -type f -exec sed -i.old -E 's/"proj":(\ )*[0-9\.]*?/"proj": 4326/g' {} \;
+    find ./test/*.js -type f -exec sed -i.old -E 's/"prec":(\ )*[0-9.]*/"prec": 1000/g' {} \;
+    find ./test/*.js -type f -exec sed -i.old -E 's/"proj":(\ )*[0-9.]*/"proj": 4326/g' {} \;
     rm -f ./test/*.old
 }
 
@@ -53,7 +54,7 @@ run_oatt() {
 test=0
 remote=localhost:3001
 
- while getopts "htdpa" opt; do
+ while getopts "htldpa" opt; do
      case $opt in
          h)
              show_help
@@ -62,7 +63,10 @@ remote=localhost:3001
          t)
              test=1
              ;;
-         d)            
+         l)
+             remote=localhost:3005
+             ;;
+         d)
              remote=api-dev.neotomadb.org
              ;;
          p)

nodemon.json

@@ -2,6 +2,10 @@
   "ext": "sql js json yaml",
   "ignore": [
     ".git",
-    "node_modules/**/node_modules"
+    "node_modules/**/node_modules",
+    "test/**",
+    "public/**",
+    "openapi.yaml",
+    "*.old"
   ]
 }

package.json

@@ -12,6 +12,7 @@
   "private": true,
   "scripts": {
     "start": "NODE_ENV=production nodemon --legacy-watch app.js",
+    "dev": "NODE_ENV=development nodemon --legacy-watch app.js",
     "test": "node ./node_modules/mocha/bin/mocha --config=test/.mocharc.yml --reporter-options reportDir=public,reportFilename=tests",
     "build:openapi": "(cd ./openapi && node ./scripts/build-openapi.js)",
     "validate:openapi": "yarn build:openapi && bash genoatt.sh && sleep 4 && bash runmochabatch.sh"
@@ -72,5 +73,6 @@
     "nodemon": "^3.1.4",
     "pre-commit": "^1.0.10",
     "supertest": "^7.2.2"
-  }
+  },
+  "packageManager": "yarn@4.12.0+sha512.f45ab632439a67f8bc759bf32ead036a1f413287b9042726b7cc4818b7b49e14e9423ba49b18f9e06ea4941c1ad062385b1d8760a8d5091a1a31e5f6219afca8"
 }