proxy input (#563)

* update

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update

* update

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* remove check yaml

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -6,7 +6,6 @@ repos:
  hooks:
  - id: trailing-whitespace
  - id: end-of-file-fixer
- - id: check-yaml
  - id: check-added-large-files
  - repo: https://github.com/pre-commit/mirrors-prettier
  rev: "v2.7.1" # Use the sha / tag you want to point at

proxy/kube.yml

@@ -3,7 +3,7 @@ kind: Deployment
 metadata:
  name: taxonium-proxy-deployment
 spec:
- replicas: 1  # Number of replicas
+ replicas: 1 # Number of replicas
  selector:
  matchLabels:
  app: taxonium-proxy
@@ -13,10 +13,10 @@ spec:
  app: taxonium-proxy
  spec:
  containers:
- - name: taxonium-proxy
- image: theosanderson/taxonium_proxy:master
- ports:
- - containerPort: 3000
+  - name: taxonium-proxy
+  image: theosanderson/taxonium_proxy:master
+  ports:
+  - containerPort: 3000
 
 ---
 apiVersion: v1
@@ -36,20 +36,20 @@ kind: Ingress
 metadata:
  name: taxonium-proxy-ingress
  annotations:
- kubernetes.io/ingress.class: "nginx"  # assuming you are using nginx ingress controller
+ kubernetes.io/ingress.class: "nginx" # assuming you are using nginx ingress controller
 spec:
  rules:
- - host: proxy.taxonium.org
- http:
- paths:
- - pathType: Prefix
- path: "/"
- backend:
- service:
- name: taxonium-proxy-service
- port:
- number: 80
+  - host: proxy.taxonium.org
+  http:
+  paths:
+  - pathType: Prefix
+  path: "/"
+  backend:
+  service:
+  name: taxonium-proxy-service
+  port:
+  number: 80
  tls:
- - hosts:
- - proxy.taxonium.org
- secretName: tls-proxy2
+  - hosts:
+  - proxy.taxonium.org
+  secretName: tls-proxy2

proxy/server.js

@@ -22,7 +22,6 @@ const corsOptions = {
 
 app.use(cors(corsOptions));
 
-
 // Rate limiting middleware
 const limiter = rateLimit({
  windowMs: 15 * 60 * 1000, // 15 minutes

taxonium_component/src/utils/processNextstrain.js

@@ -419,26 +419,31 @@ async function json_to_tree(json) {
  console.log("META PROV", json.meta.data_provenance);
  config.source = "";
  if (json.meta && json.meta.data_provenance) {
- config.source = config.source +
- json.meta.data_provenance.map((source) => source.name).join(" & ") 
-
+ config.source =
+ config.source +
+ json.meta.data_provenance.map((source) => source.name).join(" & ");
  }
 
  config.overlay = `<p>This is a tree generated from a <a href='//nextstrain.org'>Nextstrain</a> JSON file, being visualised in Taxonium.</p>.`;
 
  if (json.meta && json.meta.updated) {
- config.source = config.source + " on " +
- json.meta.updated ;
+ config.source = config.source + " on " + json.meta.updated;
  }
  if (json.meta && json.meta.maintainers) {
- config.source = config.source + " in a build maintained by " +
+ config.source =
+ config.source +
+ " in a build maintained by " +
  json.meta.maintainers.map((source) => source.name).join(" & ");
-
- const maintainerLinks = json.meta.maintainers.map((source) => `<a class='underline' href='${source.url}'>${source.name}</a>`).join(" & ");
+
+ const maintainerLinks = json.meta.maintainers
+ .map(
+ (source) =>
+ `<a class='underline' href='${source.url}'>${source.name}</a>`
+ )
+ .join(" & ");
  config.overlay += `<p>The Nextstrain build is maintained by ${maintainerLinks}.</p>`;
  }
 
-
  if (json.meta.build_url) {
  config.overlay += `<p>The Nextstrain build is available <a class='underline' href='${json.meta.build_url}'>here</a>.</p>`;
  }

taxonium_website/src/components/InputSupplier.jsx

@@ -30,17 +30,24 @@ export const InputSupplier = ({ inputHelper, className }) => {
  });
 
  const [tempURL, setTempURL] = useState("");
+ const [useProxy, setUseProxy] = useState(true); // New state for proxy usage
 
  const { inputs, setInputs } = inputHelper;
  const [addingText, setAddingText] = useState(false);
  const [text, setText] = useState("");
 
  const addFromTempURL = useCallback(() => {
- if (tempURL) {
- inputHelper.addFromURL(tempURL);
+ let finalURL = tempURL;
+ if (useProxy) {
+ finalURL = `https://proxy.taxonium.org/proxy?url=${encodeURIComponent(
+ tempURL
+ )}`;
+ }
+ if (finalURL) {
+ inputHelper.addFromURL(finalURL);
  setTempURL("");
  }
- }, [tempURL, inputHelper]);
+ }, [tempURL, useProxy, inputHelper]); // Include useProxy in the dependency array
 
  return (
  <div className={className}>
@@ -185,17 +192,25 @@ export const InputSupplier = ({ inputHelper, className }) => {
  value={tempURL}
  className="border p-1 mr-1 text-sm "
  onChange={(e) => {
- setTempURL(
- e.target.value
-
- );
+ setTempURL(e.target.value);
  }}
  onKeyUp={(e) => {
  if (e.key === "Enter") {
  addFromTempURL();
  }
  }}
  />{" "}
+ {tempURL !== "" && (
+ <>
+ <input
+ type="checkbox"
+ checked={useProxy}
+ className="mr-2 text-sm text-gray-600"
+ onChange={(e) => setUseProxy(e.target.checked)}
+ />{" "}
+ Use Proxy
+ </>
+ )}
  <Button onClick={addFromTempURL} className="">
  Add
  </Button>

taxonium_website/src/hooks/useInputHelper.jsx

@@ -160,9 +160,7 @@ export const useInputHelper = ({
 
  function addFromURL(url) {
  const file_obj = { name: url, supplyType: "url" };
- window.alert(
- "Please note: URL based loading will only work if the web server supports CORS. If the tree does not load please download the tree to your own computer and load the file into Taxonium from there."
- );
+
  addInput(file_obj);
  }