feat: ✨ Prepare v12.2.1 release

.github/workflows/Build-and-deploy-linux.yml

@@ -4,6 +4,7 @@ run-name: ${{ github.actor }} is building a linux release for SODA
 on:
   push:
     branches:
+      - staging
       - main
 
 jobs:
@@ -23,10 +24,13 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
+          miniconda-version: "latest"
           activate-environment: env-electron-python
           environment-file: tools/anaconda-env/environment-Linux.yml
+          auto-update-conda: true
           auto-activate-base: false
       - run: |
+          conda activate env-electron-python
           conda info
           conda list
 
@@ -37,10 +41,12 @@ jobs:
       - name: Install package.json modules and their dependencies
         run: npm install --ignore-scripts
 
-      - name: Build and deploy on Linux
+      - name: Build the python server executable
+        run: |
+          npm run python-onefile-build-unix
+
+      - name: Deploy the app to GitHub
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          conda activate env-electron-python
-          npm run python-onefile-build
           npm run deploy-linux

.github/workflows/Build-and-deploy-mac.yml

@@ -4,6 +4,7 @@ run-name: ${{ github.actor }} is building a MAC release for SODA
 on:
   push:
     branches:
+      - staging
       - main
 
 jobs:
@@ -23,10 +24,13 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
+          miniconda-version: "latest"
           activate-environment: env-electron-python
           environment-file: tools/anaconda-env/environment-MAC.yml
+          auto-update-conda: true
           auto-activate-base: false
       - run: |
+          conda activate env-electron-python
           conda info
           conda list
 
@@ -42,12 +46,14 @@ jobs:
           p12-file-base64: ${{ secrets.MACOS_CERTIFICATE }}
           p12-password: ${{ secrets.MACOS_CERTIFICATE_PWD }}
 
-      - name: Build and deploy on MAC
+      - name: Build the python server executable
+        run: |
+          npm run python-onefile-build-unix
+
+      - name: Deploy the app to GitHub
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           appleId: ${{ secrets.APPLE_ID }}
           appleIdPassword: ${{ secrets.APPLE_PASSWORD }}
         run: |
-          conda activate env-electron-python
-          npm run python-onefile-build
           npm run deploy-mac

.github/workflows/Build-and-deploy-win.yml

@@ -5,6 +5,7 @@ on:
   push:
     branches:
       - staging
+      - main
 
 jobs:
   deploy-on-windows:
@@ -17,16 +18,19 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.9
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
+          miniconda-version: "latest"
           activate-environment: env-electron-python
           environment-file: tools/anaconda-env/environment-Windows.yml
+          auto-update-conda: true
           auto-activate-base: false
       - run: |
+          conda activate env-electron-python
           conda info
           conda list
 
@@ -37,9 +41,12 @@ jobs:
       - name: Install package.json modules and their dependencies
         run: npm install --ignore-scripts
 
-      - name: Build and deploy on Windows
+      - name: Build the python server executable
+        run: |
+          npm run python-onefile-build-win
+
+      - name: Deploy the app to GitHub
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          npm run python-onefile-build
           npm run deploy-win

CHANGELOG.md

@@ -5,6 +5,13 @@ All notable changes to SODA will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## v.12.2.1 - 2023-08-18
+
+## Bug fixes:
+
+- Free Form Mode's Standalone Validator feature no longer shows a validation results table when validation fails due to a user missing required metadata files.
+- Linking your ORCID ID with Pennsieve through SODA for SPARC no longer fails to authenticate when given a valid user profile.
+
 ## v.12.2.0 - 2023-08-01
 
 ## Feature Additions:

assets/css/guided.css

@@ -705,20 +705,35 @@
   opacity: 0.75;
 }
 
-/* Styling for tile buttons when selected/not-selected */
 .guided--radio-button.tile-button.selected {
   border: 1px solid var(--color-light-green);
   box-shadow: 0px 0px 3px 0px var(--color-light-green);
   transition: all 0.25s linear;
   -webkit-transition: all 0.25s linear;
 }
 
-/*.guided--radio-button.selected {
-  opacity: 1 !important;
+.guided--simple-radio-button {
+  width: 100%;
+  display: flex;
+  flex-direction: row;
+  align-items: flex-start;
+  padding: 10px;
+  border: 1px solid transparent; /* Set a transparent border by default to prevent layout shift */
+  border-radius: 5px;
+  box-shadow: 0px 0px 10px #d5d5d5;
+  margin: 5px 0px;
+  background-color: #fff;
+}
+
+.guided--simple-radio-button:hover {
+  outline: none;
+  box-shadow: 0px 0px 3px 0px var(--color-light-green);
+  cursor: pointer;
+}
+.guided--simple-radio-button.selected {
+  border: 1px solid var(--color-light-green);
+  box-shadow: 0px 0px 3px 0px var(--color-light-green);
 }
-.guided--radio-button.not-selected {
-  opacity: 0.4 !important;
-}*/
 
 .guided--card-large {
   max-width: 180px !important;

main.js

@@ -91,10 +91,13 @@ const getScriptPath = () => {
     return path.join(__dirname, PY_FLASK_FOLDER, PY_FLASK_MODULE + ".py");
   }
   if (process.platform === "win32") {
-    return path.join(__dirname, PY_FLASK_DIST_FOLDER, PY_FLASK_MODULE + ".exe");
+    const winPath = path.join(__dirname, PY_FLASK_DIST_FOLDER, PY_FLASK_MODULE + ".exe");
+    log.info("Path to server executable: " + winPath);
+    return winPath;
   } else {
-    log.info("Since app is packaged returning path: ");
-    return path.join(process.resourcesPath, PY_FLASK_MODULE);
+    const unixPath = path.join(process.resourcesPath, PY_FLASK_MODULE);
+    log.info("Path to server executable: " + unixPath);
+    return unixPath;
   }
 };
 const selectPort = () => {
@@ -108,7 +111,7 @@ const createPyProc = async () => {
   if (require("fs").existsSync(script)) {
     log.info("server exists at specified location");
   } else {
-    log.info("server does not exist at specified location");
+    log.info("server doesn't exist at specified location");
   }
   fp(PORT, PORT + portRange)
     .then(([freePort]) => {

package.json

@@ -1,7 +1,7 @@
 {
   "name": "soda-for-sparc",
   "productName": "SODA for SPARC",
-  "version": "12.2.0",
+  "version": "12.2.1",
   "description": "Keep Calm and Curate ",
   "main": "main.js",
   "scripts": {
@@ -12,7 +12,8 @@
     "deploy-win": "electron-builder build --win --publish always",
     "deploy-mac": "electron-builder build --mac --publish always",
     "deploy-linux": "electron-builder build --linux --publish always",
-    "python-onefile-build": "python -m PyInstaller --onefile --clean ./pyflask/app.py --distpath ./pyflaskdist",
+    "python-onefile-build-unix": "python -m PyInstaller --onefile --clean ./pyflask/app.py --distpath ./pyflaskdist",
+    "python-onefile-build-win": "python -m PyInstaller --onefile --add-data libcrypto-1_1-x64.dll;. --add-data libssl-1_1-x64.dll;. --clean ./pyflask/app.py --distpath ./pyflaskdist",
     "postinstall": "electron-builder install-app-deps",
     "format": "prettier --ignore-path .gitignore --ignore-path .prettierignore \"./**/*.+(html|css|js|md|yml)\" --write",
     "commit": "cz",

pyflask/authentication/authenticate.py

@@ -321,4 +321,4 @@ def get_pennsieve_api_key_secret(email, password, keyname):
             "name": profile_name
         }
     except Exception as e:
-        raise e
+        raise e

pyflask/startup/minimumApiVersion.py

@@ -3,5 +3,5 @@
 def get_api_version():
     """
     Returns the version of the API
-    """ 
-    return {'version': os.getenv('API_VERSION', "12.2.0")}
+    """
+    return {'version': os.getenv('API_VERSION', "12.2.1")}

pyflask/users/user.py

@@ -4,18 +4,16 @@
 from constants import PENNSIEVE_URL
 from utils import (
     create_request_headers,
-    connect_pennsieve_client,
-    authenticate_user_with_client,
 )
 from namespaces import NamespaceEnum, get_namespace_logger
 from flask import abort
-from authentication import get_access_token, get_cognito_userpool_access_token, bf_add_account_username, bf_delete_account, bf_delete_default_profile, delete_duplicate_keys
+from authentication import get_access_token, get_cognito_userpool_access_token, bf_add_account_username, delete_duplicate_keys
 
 logger = get_namespace_logger(NamespaceEnum.USER)
 
 
 
-def integrate_orcid_with_pennsieve(access_code, pennsieve_account):
+def integrate_orcid_with_pennsieve(access_code):
   """
   Given an OAuth access code link a user's ORCID ID to their Pennsieve account.
   This is required in order to publish a dataset for review with the SPARC Consortium.
@@ -24,17 +22,11 @@ def integrate_orcid_with_pennsieve(access_code, pennsieve_account):
   if access_code == "" or access_code is None:
     abort(400, "Cannot integrate your ORCID iD to Pennsieve without an access code.")
 
-  # verify Pennsieve account
-  try:
-    ps = connect_pennsieve_client()
-    authenticate_user_with_client(ps, pennsieve_account)
-  except Exception as e:
-     abort(400, "Error: Please select a valid Pennsieve account")
+  token = get_access_token()
 
-
   try:
     jsonfile = {"authorizationCode": access_code}
-    r = requests.post(f"{PENNSIEVE_URL}/user/orcid", json=jsonfile, headers=create_request_headers(ps))
+    r = requests.post(f"{PENNSIEVE_URL}/user/orcid", json=jsonfile, headers=create_request_headers(token))
     r.raise_for_status()
 
     return r.json()