Merge pull request #19 from harmonydata/staging

Releasing Staging version

.env

@@ -2,4 +2,5 @@ REACT_APP_API_URL=https://api.harmonydata.ac.uk
 REACT_APP_API_EXAMPLES=$REACT_APP_API_URL/text/examples
 REACT_APP_API_PARSE=$REACT_APP_API_URL/text/parse
 REACT_APP_API_MATCH=$REACT_APP_API_URL/text/match
+REACT_APP_API_VERSION=$REACT_APP_API_URL/info/version
 REACT_APP_ABSOLUTE_URL_PREFIX=https://harmonydata.github.io

TEST .env.development → .env.development

@@ -2,4 +2,5 @@ REACT_APP_API_URL=https://harmonystagingtmp.azurewebsites.net/
 REACT_APP_API_EXAMPLES=$REACT_APP_API_URL/text/examples
 REACT_APP_API_PARSE=$REACT_APP_API_URL/text/parse
 REACT_APP_API_MATCH=$REACT_APP_API_URL/text/match
+REACT_APP_API_VERSION=$REACT_APP_API_URL/info/version
 REACT_APP_ABSOLUTE_URL_PREFIX=https://harmonydata.github.io

.firebaserc

@@ -0,0 +1,5 @@
+{
+  "projects": {
+    "default": "harmony-6bd51"
+  }
+}

.github/workflows/build_and_deploy.yml

@@ -1,24 +1,27 @@
-# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs
+# build and deploy release branch to GH pages
 
-name: Build and Deploy to GH pages
+name: Build and Deploy Release branch to GH pages
 
+
+# after the next release this should be updated to true
 env:
   CI: false
 
 on:
   push:
-    branches: ["master"]
+    branches: ["release"]
   pull_request:
     types: closed
-    branches: ["master"]
+    branches: ["release"]
   workflow_dispatch:
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+        with:
+          ref: "release"
       - name: Use Node.js 18.x
         uses: actions/setup-node@v3
         with:

.gitignore

@@ -4,3 +4,5 @@
 package-lock.json
 /wireframes
 package-lock.json
+functions/venv
+functions/__pycache__

README.md

@@ -63,11 +63,15 @@ You can contact Harmony team at https://harmonydata.ac.uk/, Thomas Wood at http:
 
 ## Deployment
 
-This app is deployed using Github actions when there is a push to `main` branch. The script to do this is under folder `.github`.
+Commits / pull requests to the master or staging branches will trigger an automatic build on netlifiy - temporay build URLS will be displayed in pull requests and please manually confirm your commits are working as intended.
+
+The staging branch is always available at https://harmony-staging.netlify.app/
+
+This app is deployed to the main website using Github actions when there is a push to `releases` branch - this is a protected branch. The script to do this is under folder `.github`.
 
 Ulster University is managing the domain `harmonydata.ac.uk` which is configured to point to the IPs of the Github Pages deployment.
 
-For the staging app we are using a Netlify build with build hooks - please contact Thomas Wood/John Rogers for details.
+
 
 # How to contribute
 

firebase.json

@@ -0,0 +1,18 @@
+{
+  "firestore": {
+    "rules": "firestore.rules",
+    "indexes": "firestore.indexes.json"
+  },
+  "functions": [
+    {
+      "source": "functions",
+      "codebase": "default",
+      "ignore": [
+        "venv",
+        ".git",
+        "firebase-debug.log",
+        "firebase-debug.*.log"
+      ]
+    }
+  ]
+}

firestore.indexes.json

@@ -0,0 +1,4 @@
+{
+  "indexes": [],
+  "fieldOverrides": []
+}

firestore.rules

@@ -0,0 +1,22 @@
+rules_version = '2';
+
+service cloud.firestore {
+  match /databases/{database}/documents {
+    match /harmonisations/{document} {
+      // allow read access to own or public 
+      allow read: if resource.data.public == true || resource.data.uid == request.auth.uid; 
+      // write access to own
+      allow write: if resource.data.uid == request.auth.uid; 
+      // create access to any logged in
+      allow create: if request.auth != null; 
+  	}
+    match /mismatches/{document} {
+      // allow create access to public 
+      allow create, write: if true ; 
+  	}
+     match /ratings/{document} {
+      // allow create access to public 
+      allow create, write: if true ; 
+  	}
+  }
+}

functions/.gitignore

@@ -0,0 +1,2 @@
+venv
+__pycache__

functions/main.py

@@ -0,0 +1,44 @@
+# Welcome to Cloud Functions for Firebase for Python!
+# To get started, simply uncomment the below code or create your own.
+# Deploy with `firebase deploy`
+
+from firebase_functions import https_fn
+from firebase_admin import initialize_app
+from firebase_admin import firestore
+import json
+import datetime
+
+app = initialize_app()
+db = firestore.client()
+
+# Define a custom function to serialize datetime objects 
+def serialize_datetime(obj): 
+    if isinstance(obj, datetime.datetime): 
+        return obj.isoformat() 
+    raise TypeError("Type not serializable") 
+
+@https_fn.on_request(region="europe-west1")
+def api(req: https_fn.Request) -> https_fn.Response:
+    data = []
+    match req.path:
+        case "/mismatches":
+            docs = db.collection("mismatches").stream()
+            for doc in docs:
+                d = doc.to_dict()
+                d["fbid"] = doc.id
+                data.append(d)
+        case "/harmonisations":
+            docs = db.collection("harmonisations").stream()
+            for doc in docs:
+                d = doc.to_dict()
+                d["fbid"] = doc.id
+                data.append(d)
+        case "/ratings":
+            docs = db.collection("ratings").stream()
+            for doc in docs:
+                d = doc.to_dict()
+                d["fbid"] = doc.id
+                data.append(d)
+        case _ :
+            data.append("No such end point " + req.path )
+    return https_fn.Response(json.dumps(data, default=serialize_datetime), mimetype="application/json")

functions/requirements.txt

@@ -0,0 +1 @@
+firebase_functions~=0.1.0

src/components/App.js

@@ -25,7 +25,6 @@ import logoWithText from "../img/Logo-04-min.svg";
 import ResultsOptions from "./ResultsOptions";
 import { deepmerge } from "@mui/utils";
 import { ColorModeContext } from "../contexts/ColorModeContext";
-import postData from "../utilities/postData";
 import { useData } from "../contexts/DataContext";
 import { utils as XLSXutils, writeFile as XLSXwriteFile } from "xlsx";
 import ReactGA from "react-ga4";
@@ -47,7 +46,7 @@ function App() {
   });
   const prefersDarkMode = useMediaQuery("(prefers-color-scheme: dark)");
   const [mode, setMode] = useState();
-  const { storeHarmonisation, reportRating } = useData();
+  const { storeHarmonisation, reportRating, exampleInstruments } = useData();
   const [ratingValue, setRatingValue] = useState();
   const [computedMatches, setComputedMatches] = useState();
   const [fileInfos, setFileInfos] = useState();
@@ -88,15 +87,15 @@ function App() {
       ReactGA.initialize("G-S79J6E39ZP");
       console.log("GA enabled");
     }
-    postData(process.env.REACT_APP_API_EXAMPLES)
+    exampleInstruments()
       .then((data) => {
         setExistingInstruments(data);
         console.log(data);
       })
       .catch((e) => {
         console.log(e);
       });
-  }, []);
+  }, [exampleInstruments]);
 
   const colorMode = useMemo(
     () => ({
@@ -202,11 +201,14 @@ function App() {
           instrument1: q.instrument.name,
           question1_no: q.question_no,
           question1_text: q.question_text,
-          question1_topics: q.topics_auto.toString(),
+          question1_topics:
+            Array.isArray(q.topics_strengths) && q.topics_strengths.join(", "),
           instrument2: mq.instrument.name,
           question2_no: mq.question_no,
           question2_text: mq.question_text,
-          question2_topics: mq.topics_auto.toString(),
+          question2_topics:
+            Array.isArray(mq.topics_strengths) &&
+            mq.topics_strengths.join(", "),
           match: cm.match,
         });
         return a;
@@ -328,16 +330,33 @@ function App() {
                       Harmonise questionnaire items
                     </h1>
                     <p>
-                      Harmony is an AI tool which can read questionnaires and find questions with similar meanings, such as{" "}
+                      Harmony is an AI tool which can read questionnaires and
+                      find questions with similar meanings, such as{" "}
                       <i>anxiety</i> vs <i>I feel anxious</i>.
                     </p>
                     <p>
-                      Psychologists sometimes need to combine survey results, especially when surveys
-                      have been run by different organisations or in different
-                      countries.
+                      Psychologists sometimes need to combine survey results,
+                      especially when surveys have been run by different
+                      organisations or in different countries.
                     </p>
                     <p>
-                      Try two example PDFs: <a target="gad7-pdf" style={{ color: "white" }} href="https://adaa.org/sites/default/files/GAD-7_Anxiety-updated_0.pdf">GAD-7 PDF</a> vs <a target="phq-pdf" style={{ color: "white" }} href="https://www.apa.org/depression-guideline/patient-health-questionnaire.pdf">PHQ-9 PDF</a>.
+                      Try two example PDFs:{" "}
+                      <a
+                        target="gad7-pdf"
+                        style={{ color: "white" }}
+                        href="https://adaa.org/sites/default/files/GAD-7_Anxiety-updated_0.pdf"
+                      >
+                        GAD-7 PDF
+                      </a>{" "}
+                      vs{" "}
+                      <a
+                        target="phq-pdf"
+                        style={{ color: "white" }}
+                        href="https://www.apa.org/depression-guideline/patient-health-questionnaire.pdf"
+                      >
+                        PHQ-9 PDF
+                      </a>
+                      .
                     </p>
                     <p>
                       <a
@@ -406,7 +425,8 @@ function App() {
                       setResultsOptions={setResultsOptions}
                       resultsOptions={resultsOptions}
                       toaster={toast}
-                      reportComputedMatches={setComputedMatches}
+                      computedMatches={computedMatches}
+                      setComputedMatches={setComputedMatches}
                       ReactGA={ReactGA}
                     />
                   </Route>