Updating About section

.gitignore

@@ -12,4 +12,7 @@ gha-creds-*.json
 site
 docs/Data-Model
 
+### Script ignores
+scripts/scholarly_*.json
+
 .DS_Store

README.md

@@ -1,18 +1,17 @@
 # Monarch App
 
-
+[![documentation](https://img.shields.io/badge/-Documentation-purple?logo=read-the-docs&logoColor=white&style=for-the-badge)](https://monarch-initiative.github.io/monarch-app/docs)  
 ![](https://github.com/monarch-initiative/monarch-app/actions/workflows/test-backend.yaml/badge.svg)
 ![](https://github.com/monarch-initiative/monarch-app/actions/workflows/test-frontend.yaml/badge.svg)
 ![](https://github.com/monarch-initiative/monarch-app/actions/workflows/deploy-documentation.yaml/badge.svg)
 ![](https://github.com/monarch-initiative/monarch-app/actions/workflows/build-image.yaml/badge.svg)
 
+[The New Website](https://monarch-app.monarchinitiative.org)
+
 This repository contains the source code for the Monarch Initiative website (a Vue TS frontend),  
 as well as `monarch-py`, a Python library for interacting with the Monarch Initiative knowledge graph,  
 which includes an optional FastAPI module that serves as the website's backend.  
 
-[The New Website](https://monarch-app.monarchinitiative.org)
-
-[Documentation](https://monarch-app.monarchinitiative.org/docs)
 
 ### For developers
 

backend/README.md

@@ -1,9 +1,10 @@
 # Monarch-Py
 
+[![documentation](https://img.shields.io/badge/-Documentation-purple?logo=read-the-docs&logoColor=white&style=for-the-badge)](https://monarch-initiative.github.io/monarch-app/docs)
+
 Monarch-Py is a Python library for interfacing with the Monarch Initiative Knowledge graph.  
 It can be used from CLI, as a module, or as a FastAPI app
 
-[Documentation](https://monarch-app.monarchinitiative.org/docs)
 
 
 ## For Developers

backend/pyproject.toml

@@ -40,11 +40,11 @@ mkdocs-material = ">=9.1.16"
 mkdocstrings = {extras = ["python"], version = ">=0.22.0"}
 black = "^22.10.0"
 ruff = "*"
-# isort = "^5.10.1"
-# flake8 = "^5.0.4"
-# autoflake = "^1.7.7"
 uvicorn = {extras = ["standard"], version = "^0.20.0"}
 httpx = "^0.24.1"
+scholarly = "*"
+habanero = "*"
+manubot = "*"
 
 
 [tool.poetry.extras]

frontend/e2e/axe.test.ts

@@ -8,7 +8,6 @@ const paths = [
   "/about",
   "/help",
   "/overview",
-  "/sources",
   "/cite",
   "/team",
   "/publications",

frontend/e2e/node.test.ts

@@ -1,7 +1,7 @@
 import { expect, test } from "@playwright/test";
 
 test("Table of contents works", async ({ page }) => {
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
   await page.setViewportSize({ width: 800, height: 1000 });
 
   /** toggle button exists */
@@ -78,16 +78,16 @@ test("Table of contents works", async ({ page }) => {
 });
 
 test("Title info shows", async ({ page }) => {
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /** text info in top section */
-  await expect(page.getByText(/Marfan syndrome/i).first()).toBeVisible();
+  await expect(page.getByText(/Ehlers-Danlos/i).first()).toBeVisible();
   await expect(page.getByText(/Disease/i).first()).toBeVisible();
-  await expect(page.getByText(/MONDO:0007947/i).first()).toBeVisible();
+  await expect(page.getByText(/MONDO:0007523/i).first()).toBeVisible();
 });
 
 test("Overview items show", async ({ page }) => {
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /** check for description */
   await expect(
@@ -98,10 +98,10 @@ test("Overview items show", async ({ page }) => {
 test("Details items show", async ({ page }) => {
   test.skip(true, "No fixture data yet");
 
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /** check inheritance, xref, etc. */
-  await expect(page.getByText(/MONDO_0007947/i).first()).toBeVisible();
+  await expect(page.getByText(/MONDO_0007523/i).first()).toBeVisible();
   await expect(
     page.getByText(/Autosomal dominant inheritance/i).first(),
   ).toBeVisible();
@@ -110,7 +110,7 @@ test("Details items show", async ({ page }) => {
 });
 
 test("Hierarchy items show", async ({ page }) => {
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /** check super/equiv/sub classes */
   await expect(page.getByText(/myopathy/i).first()).toBeVisible();
@@ -141,7 +141,7 @@ test("Publication specific info shows", async ({ page }) => {
 test("Summary association info shows", async ({ page }) => {
   test.skip(true, "Fixture data not stable yet");
 
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /** check node, relation, target node */
   await expect(
@@ -159,12 +159,12 @@ test("Summary association info shows", async ({ page }) => {
 test("Table association info shows", async ({ page }) => {
   test.skip(true, "Fixture data not stable yet");
 
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /** check node, relation, target node */
   await page.getByText(/Table/i).first().click();
   await expect(
-    page.locator("tr", { hasText: /Marfan syndrome/ }).first(),
+    page.locator("tr", { hasText: /Ehlers-Danlos/ }).first(),
   ).toBeVisible();
   await expect(
     page
@@ -185,7 +185,7 @@ test("Table association info shows", async ({ page }) => {
 test("Association mode switching works", async ({ page }) => {
   test.skip(true, "Fixture data not stable yet");
 
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
   await expect(page).toHaveURL(/associations=phenotype/i);
 
   /** switch to table mode and variant associations */
@@ -210,7 +210,7 @@ test("Association mode switching works", async ({ page }) => {
 test("Association table has extra metadata columns", async ({ page }) => {
   test.skip(true, "No fixture data yet");
 
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /** switch to table mode */
   await page.getByText(/Table/i).first().click();
@@ -276,7 +276,7 @@ test("Association table has extra metadata columns", async ({ page }) => {
 test("Evidence viewer works", async ({ page }) => {
   test.skip(true, "Fixture data not stable yet");
 
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /** get evidence section */
   const evidence = page.locator("#evidence").locator("..");
@@ -319,14 +319,14 @@ test("Breadcrumbs section works", async ({ page, browserName }) => {
     "Clearly a Firefox bug or peculiarity with Playwright, works fine in real Firefox",
   );
 
-  await page.goto("/node/MONDO:0007947");
+  await page.goto("/node/MONDO:0007523");
 
   /**
    * visit chain of nodes. include clicking on both association links and
    * hierarchy item links
    */
   const chain = [
-    "Marfan syndrome",
+    "Ehlers-Danlos syndrome, hypermobility type",
     "Has Phenotype",
     "Dural ectasia",
     "Has Phenotype",

frontend/fixtures/index.ts

@@ -2,7 +2,6 @@ import { rest } from "msw";
 /** url bases */
 import { biolink, monarch } from "@/api";
 import { feedbackEndpoint } from "@/api/feedback";
-import { obo } from "@/api/ontologies";
 import { efetch, esummary } from "@/api/publications";
 import { uptimeRobot } from "@/api/uptime";
 import associations from "./association-table.json";
@@ -13,7 +12,6 @@ import histopheno from "./histopheno.json";
 import nodePublicationAbstract from "./node-publication-abstract.json";
 import nodePublicationSummary from "./node-publication-summary.json";
 import node from "./node.json";
-import ontologies from "./ontologies.json";
 import phenotypeExplorerCompare from "./phenotype-explorer-compare.json";
 import phenotypeExplorerSearch from "./phenotype-explorer-search.json";
 import search from "./search.json";
@@ -30,9 +28,6 @@ export const handlers = [
   rest.get(regex(biolink, "/metadata/datasets"), (req, res, ctx) =>
     res(ctx.status(200), ctx.json(datasets)),
   ),
-  rest.get(regex(obo), (req, res, ctx) =>
-    res(ctx.status(200), ctx.json(ontologies)),
-  ),
 
   /** api status monitoring on /help */
   rest.post(regex(uptimeRobot), (req, res, ctx) =>
@@ -88,8 +83,8 @@ export const handlers = [
     const replace: {
       [key: string]: { name?: string; category?: string };
     } = {
-      "MONDO:0007947": {
-        name: "Marfan syndrome",
+      "MONDO:0007523": {
+        name: "Ehlers-Danlos syndrome, hypermobility",
         category: "biolink:Disease",
       },
       "HP:0100775": {

frontend/src/App.vue

@@ -7,9 +7,9 @@
     This web app is the
     <strong v-if="apiName === 'beta'">BETA VERSION</strong
     ><strong v-if="apiName === 'dev'">DEV VERSION</strong> successor to the
-    <a href="https://monarchinitiative.org/">old web app here</a>. Not all
-    features are implemented yet. Please use the feedback form to tell us what
-    you think!
+    <AppLink to="https://monarchinitiative.org/">old web app here</AppLink>. Not
+    all features are implemented yet. Please use the feedback form to tell us
+    what you think!
   </TheBanner>
 
   <TheHeader />