Merge pull request #907 from NFDI4BIOIMAGE/git-bob-mod-bSXx0xjUNQ

Add script to fetch Zenodo authors and ORCIDs and update YAML.

Author: haesleinhuepf

.github/workflows/auto-add-orcids.yml

@@ -0,0 +1,30 @@
+name: Run Weekly Auto-Add ORCIDs
+
+on:
+  schedule:
+    - cron: '0 11 * * 0'  # This runs the job every Sunday at 11 AM
+
+jobs:
+  run-weekly-auto-add-orcids:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+
+    - name: Run Python
+      env:
+        GITHUB_API_KEY: "${{ secrets.GITHUB_TOKEN }}"
+        GITHUB_RUN_ID: "${{ github.run_id }}"
+      run: |
+        python scripts/add_author_orcids.py nfdi4bioimage/training

scripts/add_author_orcids.py

@@ -0,0 +1,95 @@
+import yaml
+from _github_utilities import get_github_repository, create_branch, write_file, send_pull_request
+import requests
+
+def fetch_authors_from_zenodo(record_url):
+    """Fetch author names and ORCIDs from Zenodo REST API.
+
+    Parameters
+    ----------
+    record_url : str
+        A Zenodo record URL.
+
+    Returns
+    -------
+    list of str
+        Authors with or without ORCIDs.
+    """
+    zenodo_api_url = "https://zenodo.org/api/records/" + record_url.split("/")[-1].split(".")[-1]
+    response = requests.get(zenodo_api_url)
+    response.raise_for_status()
+    data = response.json()
+
+    authors = data.get("metadata", {}).get("creators", [])
+
+    author_with_orcid = []
+    for author in authors:
+        name = author.get("name", "")
+        if "," in name:
+            name = name.split(",")[1].strip() + " " + name.split(",")[0].strip()
+
+        if "orcid" in author:
+            author_with_orcid.append(f"{name} https://orcid.org/{author['orcid']}")
+        else:
+            author_with_orcid.append(name)
+    return author_with_orcid
+
+def update_authors_with_orcid(content, repository, file_path):
+    """Update YAML content by adding author_with_orcid field.
+
+    Parameters
+    ----------
+    content : dict
+        Loaded YAML content.
+    repository : str
+        GitHub repository string (e.g., "org/repo").
+    file_path : str
+        Path to the YAML file in the repository.
+    """
+    modified = False
+    do_exit = False
+    for resource in content.get("resources", []):
+        if "author_with_orcid" not in resource:
+            urls = resource.get("url", [])
+            if isinstance(urls, str):
+                urls = [urls]
+            for url in urls:
+                if url.startswith("https://zenodo.org/record") or url.startswith("https://zenodo.org/doi"):
+                    try:
+                        resource["author_with_orcid"] = fetch_authors_from_zenodo(url)
+                        modified = True
+                        break
+                    except Exception as e:
+                        print(f"Error fetching authors for URL {url}: {e}")
+                        if "TOO MANY REQUESTS" in str(e):
+                            print("Too many requests, skipping this URL")
+                            do_exit = True
+                            break
+            if do_exit:
+                break
+    if modified:
+        main_branch = "main"
+        new_branch = create_branch(repository, parent_branch=main_branch)
+        new_content = yaml.dump(content, sort_keys=False, allow_unicode=True)
+        write_file(repository, new_branch, file_path, new_content, "Add authors with ORCIDs to resources")
+        pr_url = send_pull_request(
+            repository,
+            new_branch,
+            "Add authors with ORCIDs",
+            f"This PR adds authors with ORCIDs to resources YAML file."
+        )
+        print(pr_url)
+
+if __name__ == "__main__":
+    import sys
+    repository = sys.argv[1]
+    file_path = "resources/nfdi4bioimage.yml"
+
+    # Authenticate and fetch file content
+    repo = get_github_repository(repository)
+    main_branch = "main"
+    file_content = repo.get_contents(file_path, ref=main_branch)
+    content = yaml.safe_load(file_content.decoded_content.decode())
+
+    # Update YAML content
+    update_authors_with_orcid(content, repository, file_path)