Update to Spezi 1.0 and Add NCI Trials Search API OpenAPI Swift Packa…

…ge (#17)

# Update to Spezi 1.0 and Add NCI Trials Search API OpenAPI Swift
Package

## ⚙️ Release Notes 
- Updates the application to Spezi 1.0
- Adds an OpenAPI-based Swift Package for the NIC trials API

### Code of Conduct & Contributing Guidelines 

By submitting creating this pull request, you agree to follow our [Code
of
Conduct](https://github.com/StanfordBDHG/.github/blob/main/CODE_OF_CONDUCT.md)
and [Contributing
Guidelines](https://github.com/StanfordBDHG/.github/blob/main/CONTRIBUTING.md):
- [x] I agree to follow the [Code of
Conduct](https://github.com/StanfordBDHG/.github/blob/main/CODE_OF_CONDUCT.md)
and [Contributing
Guidelines](https://github.com/StanfordBDHG/.github/blob/main/CONTRIBUTING.md).

.firebaserc

@@ -1,5 +1,5 @@
 {
   "projects": {
-    "default": "ownyourdata-7edaf"
+    "default": "ownyourdata-291ff"
   }
 }

.firebaserc.license

@@ -1,4 +1,4 @@
-This source file is part of the Stanford OwnYourData Application project
+This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
 
 SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md)
 

.github/workflows/beta-deployment.yml

@@ -1,5 +1,5 @@
 #
-# This source file is part of the Stanford OwnYourData Application project
+# This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
 #
 # SPDX-FileCopyrightText: 2023 Stanford University
 #
@@ -18,14 +18,27 @@ jobs:
   buildandtest:
     name: Build and Test
     uses: ./.github/workflows/build-and-test.yml
+    permissions:
+      contents: read
     secrets: inherit
   iosapptestflightdeployment:
     name: iOS App TestFlight Deployment
     needs: buildandtest
     uses: StanfordBDHG/.github/.github/workflows/xcodebuild-or-fastlane.yml@v2
-    secrets: inherit
+    permissions:
+      contents: read
     with:
-      artifactname: OwnYourData.xcresult
-      runsonlabels: '["macos-13"]'
-      fastlanelane: beta
+      googleserviceinfoplistpath: 'OwnYourData/Supporting Files/GoogleService-Info.plist'
       setupsigning: true
+      fastlanelane: beta
+    secrets: inherit
+  deployfirebase:
+    name: Deploy Firebase Project
+    needs: iosapptestflightdeployment
+    uses: StanfordBDHG/.github/.github/workflows/firebase-deploy.yml@v2
+    permissions:
+      contents: read
+    with:
+      arguments: '--debug'
+    secrets:
+      GOOGLE_APPLICATION_CREDENTIALS_BASE64: ${{ secrets.GOOGLE_APPLICATION_CREDENTIALS_BASE64 }}

.github/workflows/build-and-test.yml

@@ -1,5 +1,5 @@
 #
-# This source file is part of the Stanford OwnYourData Application project
+# This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
 #
 # SPDX-FileCopyrightText: 2023 Stanford University
 #
@@ -17,20 +17,36 @@ jobs:
   reuse_action:
     name: REUSE Compliance Check
     uses: StanfordBDHG/.github/.github/workflows/reuse.yml@v2
+    permissions:
+      contents: read
   swiftlint:
     name: SwiftLint
     uses: StanfordBDHG/.github/.github/workflows/swiftlint.yml@v2
+    permissions:
+      contents: read
+  markdownlinkcheck:
+    name: Markdown Link Check
+    uses: StanfordBDHG/.github/.github/workflows/markdown-link-check.yml@v2
+    permissions:
+      contents: read
   buildandtest:
     name: Build and Test
     uses: StanfordBDHG/.github/.github/workflows/xcodebuild-or-fastlane.yml@v2
+    permissions:
+      contents: read
     with:
       artifactname: OwnYourData.xcresult
       runsonlabels: '["macOS", "self-hosted"]'
+      setupSimulators: true
       setupfirebaseemulator: true
       customcommand: "firebase emulators:exec 'fastlane test'"
   uploadcoveragereport:
     name: Upload Coverage Report
     needs: buildandtest
     uses: StanfordBDHG/.github/.github/workflows/create-and-upload-coverage-report.yml@v2
+    permissions:
+      contents: read
     with:
       coveragereports: OwnYourData.xcresult
+    secrets:
+      token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/monthly-markdown-link-check.yml.yml

@@ -0,0 +1,21 @@
+#
+# This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
+#
+# SPDX-FileCopyrightText: 2023 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: Monthly Markdown Link Check
+
+on:
+  # Runs at midnight on the first of every month
+  schedule:
+    - cron: "0 0 1 * *"
+
+jobs:
+  markdown_link_check:
+    name: Markdown Link Check
+    uses: StanfordBDHG/.github/.github/workflows/markdown-link-check.yml@v2
+    permissions:
+      contents: read

.gitignore

@@ -1,5 +1,5 @@
 #
-# This source file is part of the Stanford OwnYourData Application project
+# This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
 #
 # SPDX-FileCopyrightText: 2023 Stanford University
 #
@@ -10,7 +10,8 @@
 *.xcodeproj
 .swiftpm
 .derivedData
-.build/
+.build
+.docs
 !OwnYourData.xcodeproj
 
 # IDE related folders
@@ -42,3 +43,6 @@ firebase-debug.*.log*
 
 # Firebase cache
 .firebase/
+
+# Swift Package List
+OwnYourData/package-list.json

.reuse/dep5

@@ -0,0 +1,12 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+
+Files: OwnYourData/Resources/Assets.xcassets/*
+Copyright: 2024 Stanford University and the project authors (see CONTRIBUTORS.md)
+License: MIT
+Comment: All figures are part of the OwnYourData based on the Stanford Spezi Template Application project
+
+Files: NCIClinicalTrialsSearchAPI/*
+Copyright: 2024 National Cancer InstituteCI
+License: MIT
+Comment: The Swift Package was generated based on the OpenAPI spec retrived from https://clinicaltrialsapi.cancer.gov/doc. For information on NCI's efforts to improve how patients and oncologists find information and learn about cancer clinical trials please visit:
+https://www.cancer.gov/syndication/api.

.swiftlint.yml

@@ -1,12 +1,11 @@
 #
-# This source file is part of the Stanford OwnYourData Application project
+# This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
 #
 # SPDX-FileCopyrightText: 2023 Stanford University
 #
 # SPDX-License-Identifier: MIT
 #
 
-
 # The whitelist_rules configuration also includes rules that are enabled by default to provide a good overview of all rules.
 only_rules:
   # All Images that provide context should have an accessibility label. Purely decorative images can be hidden from accessibility.
@@ -380,7 +379,9 @@ deployment_target: # Availability checks or attributes shouldn’t be using olde
 excluded: # paths to ignore during linting. Takes precedence over `included`.
   - .build
   - .swiftpm
+  - .codeql
   - .derivedData
+  - NCIClinicalTrialsSearchAPI
 
 closure_body_length: # Closure bodies should not span too many lines.
   - 35 # warning - default: 20

CITATION.cff

@@ -1,5 +1,5 @@
 #
-# This source file is part of the Stanford OwnYourData Application project
+# This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
 #
 # SPDX-FileCopyrightText: 2023 Stanford University
 #
@@ -18,6 +18,4 @@ authors:
 - family-names: "Aalami"
   given-names: "Oliver"
   orcid: "https://orcid.org/0000-0002-7799-2429"
-title: "Stanford OwnYourData Applicationn"
-doi: doi.org/10.5281/zenodo.7600783
-url: "https://github.com/StanfordBDHG/OwnYourData"
+title: "OwnYourData"

CONTRIBUTORS.md

@@ -1,14 +1,17 @@
 <!--
 
-This source file is part of the Stanford OwnYourData Application project
+This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
 
 SPDX-FileCopyrightText: 2023 Stanford University
 
 SPDX-License-Identifier: MIT
 
 -->
 
-Template Application Contributors
+OwnYourData Contributors
 =================================
 
 * [Paul Schmiedmayer](https://github.com/PSchmiedmayer)
+* [Andreas Bauer](https://github.com/Supereg)
+* [Philipp Zagar](https://github.com/philippzagar)
+* [Nikolai Madlener](https://github.com/NikolaiMadlener)

Gemfile

@@ -1,5 +1,5 @@
 #
-# This source file is part of the Stanford OwnYourData Application project
+# This source file is part of the OwnYourData based on the Stanford Spezi Template Application project
 #
 # SPDX-FileCopyrightText: 2023 Stanford University
 #