Port /data/orthology and /data/orthologies to node; 405 and RFD header on every ported endpoint

deploy/nginx/common/routes-core.conf

@@ -107,6 +107,16 @@ location ~ ^/ContentService/data/(entity|event)/[^/]+/in-depth$ {
     proxy_pass http://content_node;
 }
 
+# An event's or entity's counterpart in another species, one id by GET or up
+# to twenty by POST (graph-core's OrthologyService), written by the domain
+# serialiser; the POST's map in the order Java's HashMap writes it. The
+# Pathway Browser asks both when the species is changed. Byte-identical to
+# Java, errors included -- bar '.', which is not found here and Java's 500.
+location ~ ^/ContentService/data/(orthology/[^/]+/species|orthologies/ids/species)/[^/]+$ {
+    include /etc/nginx/common/upstream-proxy.conf;
+    proxy_pass http://content_node;
+}
+
 # A person, by dbId or ORCID, and the publications they authored (by dbId,
 # ORCID or e-mail address), written by the domain serialiser in each of Java's
 # views. Java matches the person by a property no index serves -- 1.1s by dbId;

projects/website-angular/src/scripts/proxy-order.spec.ts

@@ -180,6 +180,17 @@ describe('the dev server proxy', () => {
     });
   }
 
+  for (const url of [
+    '/ContentService/data/orthology/R-HSA-69620/species/48892',
+    '/ContentService/data/orthology/69620/species/0xBEFC?view=nested',
+    // The POST the species selector sends.
+    '/ContentService/data/orthologies/ids/species/48892',
+  ]) {
+    it(`sends ${url} to the content service`, async () => {
+      expect(await targetOf(url)).toBe(contentNode);
+    });
+  }
+
   for (const other of [
     // Other attributes of the same Java endpoint are not ported.
     '/ContentService/data/query/70486/displayName',
@@ -193,9 +204,12 @@ describe('the dev server proxy', () => {
     '/ContentService/data/query/70486/NORMALPATHWAY',
     // Spring also matches a trailing slash; only the plain object is routed.
     '/ContentService/data/query/70486/',
-    // Java's POST /query/ids (a batch of objects); node serves no POST.
+    // Java's POST /query/ids (a batch of objects), which node does not serve.
     '/ContentService/data/query/ids',
     '/ContentService/data/query/abridged/70486',
+    // Spring's own 404s: no species, or more after it.
+    '/ContentService/data/orthology/R-HSA-69620/species/',
+    '/ContentService/data/orthologies/ids/species/48892/x',
     '/ContentService/data/person/68285/authoredPathwaysAndMore',
     // Only the ancestors of an event are ported.
     '/ContentService/data/event/R-HSA-5672965/ancestorsAndMore',

proxy.conf.js

@@ -109,6 +109,10 @@ module.exports = {
   '^/ContentService/data/query/enhanced/[^/?]+(\\?|$)': contentNode,
   // An entity or an event and everything below it, for the object tree.
   '^/ContentService/data/(entity|event)/[^/?]+/in-depth(\\?|$)': contentNode,
+  // An event's or entity's counterpart in another species: one id (GET), or
+  // up to twenty (POST), for the species selector.
+  '^/ContentService/data/(orthology/[^/?]+/species|orthologies/ids/species)/[^/?]+(\\?|$)':
+    contentNode,
   // A person, and the publications they authored. Not the other attributes
   // under /person/{id}/, which Java serves.
   '^/ContentService/data/person/[^/?]+(/publications)?(\\?|$)': contentNode,

tools/content-node/diff.mjs

@@ -27,8 +27,19 @@ function flag(name, fallback = '') {
 
 /** Fetch one path from both, as text plus content type. */
 async function fetchBoth(path) {
+  // A POST endpoint is sent its sample body, or the --ids given, as text.
+  const endpoint = endpointFor(path);
+  const post = endpoint?.method === 'post';
+  const ids = flag('ids');
+  const init = post
+    ? {
+        method: 'POST',
+        headers: { 'Content-Type': 'text/plain' },
+        body: ids || endpoint.sampleBody,
+      }
+    : {};
   const get = async (base) => {
-    const response = await fetch(base + path, { redirect: 'follow' });
+    const response = await fetch(base + path, { redirect: 'follow', ...init });
     return {
       status: response.status,
       type: (response.headers.get('content-type') || '').split(';')[0].trim(),
@@ -196,14 +207,18 @@ function paths() {
 
   const skipped = [];
   const expanded = chosen.flatMap((endpoint) => {
-    if (!endpoint.path.includes('{id}')) return [endpoint.path];
+    // Path variables other than {id} take the endpoint's own sample values.
+    let template = endpoint.path;
+    for (const [name, value] of Object.entries(endpoint.samplePath ?? {}))
+      template = template.replace(`{${name}}`, value);
+    if (!template.includes('{id}')) return [template];
     // An endpoint that takes an id is expanded over the ids given, or over its
     // own sample when none are. Without the sample it expanded to *nothing* and
     // was silently absent from every run: `/data/pathways/top/{id}` was merged
     // for weeks, never once compared, and carried three real differences.
     const use = ids.length ? ids : endpoint.sample ? [endpoint.sample] : [];
     if (!use.length) skipped.push(endpoint.path);
-    return use.map((id) => endpoint.path.replace('{id}', id));
+    return use.map((id) => template.replace('{id}', id));
   });
 
   // Said out loud. A run that tests fewer endpoints than the table holds is the

tools/content-node/domain.mjs

@@ -59,6 +59,18 @@ class Relation {
   }
 }
 
+/**
+ * A Java Map written as a JSON object, its entries in the order given -- the
+ * Map's own iteration order, which the caller decides (see JavaHashMap in
+ * service.mjs). Its values are written in one pass with everything else, so
+ * `@id` numbering runs on across them as Jackson's does.
+ */
+export class JsonMap {
+  constructor(entries) {
+    this.entries = entries;
+  }
+}
+
 /** Has.Util.wrapUniqueElements: a plain relationship as Has.Default, for composedOf. */
 const wrap = (entities, type) =>
   (entities ?? []).map((entity) => new Relation('Default', entity, {}, type));
@@ -429,6 +441,15 @@ export function writeDomain(value, view = VIEW.flatten, { jsog = false } = {}) {
       open(out, work, current, view, jsog ? `"@id":"${seen.size}"` : undefined);
     } else if (current instanceof Relation) {
       open(out, work, current, view);
+    } else if (current instanceof JsonMap) {
+      out.push('{');
+      work.push('}');
+      for (let at = current.entries.length - 1; at >= 0; at -= 1) {
+        const [key, entry] = current.entries[at];
+        work.push({ value: entry, floating });
+        work.push(`${javaString(key)}:`);
+        if (at > 0) work.push(',');
+      }
     } else if (Array.isArray(current)) {
       out.push('[');
       work.push(']');