Merge pull request #11 from SIMEXP/iss10

Iss10: publications

.github/workflows/deploy-book.yml

@@ -4,8 +4,8 @@ name: deploy-book
 on:
   push:
     branches:
-    - main 
-    
+    - main
+
 # This job installs dependencies, build the book, and pushes it to `gh-pages`
 jobs:
   deploy-book:
@@ -23,6 +23,11 @@ jobs:
       run: |
         pip install -r content/requirements.txt
 
+    # Fetch ORCID records
+    - name: Fetch ORCID records
+      run: |
+        cd content; python orcid_to_bib.py
+
     # Build the page
     - name: Build the book
       run: |

content/.gitignore

@@ -1 +1,2 @@
 _build
+orcid_works_*.bib

content/_config.yml

@@ -4,6 +4,11 @@
 title: SIMEXP lab
 author: SIMEXP lab team
 logo: images/simexp.png
+bibtex_bibfiles:
+  - orcid_works_article.bib
+  - orcid_works_inproceedings.bib
+  - orcid_works_unpublished.bib
+  - orcid_works_misc.bib
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html

content/_toc.yml

@@ -8,3 +8,4 @@ chapters:
 - file: coc
 - file: members
 - file: CONTRIBUTING
+- file: publications

content/orcid_to_bib.py

@@ -0,0 +1,195 @@
+import hashlib
+import requests
+from tqdm import tqdm
+
+# Hardcoded ORCID ID
+ORCID_ID = '0000-0002-9111-0699'
+
+def infer_preprint_server(doi_url):
+    if 'doi.org/10.31234' in doi_url:
+        return 'OSF'
+    if 'doi.org/10.1101' in doi_url:
+        return 'bioRxiv'
+    if 'doi.org/10.31730' in doi_url:
+        return 'PsyArXiv'
+    if 'doi.org/10.55458' in doi_url:
+        return 'Neurolibre'
+    # Add more DOI prefixes as needed
+    return 'Unknown'
+
+def infer_proceedings_venue(doi_url):
+    if 'doi.org/10.1145' in doi_url:
+        return 'ACM Digital Library'
+    # Add more DOI prefixes as needed
+    return ''
+
+def extract_first_author(detailed_work):
+    if detailed_work and 'contributors' in detailed_work:
+        contributors = detailed_work['contributors'].get('contributor', [])
+        for contributor in contributors:
+            if 'contributor-attributes' in contributor and contributor['contributor-attributes'] and contributor['contributor-attributes'].get('contributor-sequence') == 'first':
+                if 'credit-name' in contributor and contributor['credit-name']:
+                    return contributor['credit-name']['value'].split()[-1]
+        if contributors:
+            first_contributor = contributors[0]
+            if 'credit-name' in first_contributor and first_contributor['credit-name']:
+                return first_contributor['credit-name']['value'].split()[-1]
+    return 'unknown'
+
+def sanitize_key(key):
+    return key.replace(' ', '_').replace(',', '').replace(':', '').replace('.', '').replace('-', '_')
+
+def generate_unique_id(work, detailed_work, entry_type):
+    try:
+        title = work['title']['title']['value']
+        year = work.get('publication-date', {}).get('year', {}).get('value', '')
+        first_author = extract_first_author(detailed_work)
+
+        if entry_type == 'unpublished':
+            venue = 'preprint'
+        else:
+            venue = work.get('journal-title', {}).get('value', 'misc') if work.get('journal-title') else 'misc'
+
+        title_hash = hashlib.md5(title.encode('utf-8')).hexdigest()[:8]
+        raw_key = f"{first_author}-{venue}-{year}-{title_hash}"
+        return sanitize_key(raw_key)
+    except Exception as e:
+        print(f"Error generating unique ID: {e}")
+        return 'unknown_id'
+
+def construct_bibtex_entry(work, detailed_work):
+    try:
+        entry_type_map = {
+            'journal-article': 'article',
+            'book-chapter': 'incollection',
+            'conference-paper': 'inproceedings',
+            'preprint': 'unpublished',
+            # Add more mappings as needed
+        }
+
+        entry_type = entry_type_map.get(work.get('type', 'misc'), 'misc')
+        unique_id = generate_unique_id(work, detailed_work, entry_type)
+        title = work['title']['title']['value']
+        journal = work.get('journal-title', {}).get('value', '') if work.get('journal-title') else ''
+        year = work.get('publication-date', {}).get('year', {}).get('value', '') if work.get('publication-date') else ''
+        url = work.get('url', {}).get('value', '') if work.get('url') else ''
+        authors = []
+        if detailed_work and 'contributors' in detailed_work:
+            for contributor in detailed_work['contributors'].get('contributor', []):
+                if 'credit-name' in contributor and contributor['credit-name']:
+                    authors.append(contributor['credit-name']['value'])
+                elif 'contributor-orcid' in contributor and contributor['contributor-orcid']:
+                    authors.append(contributor['contributor-orcid']['path'])
+
+        # Retrieve preprint server or proceedings venue
+        note = ''
+        booktitle = ''
+        if entry_type == 'unpublished' and url:
+            preprint_server = infer_preprint_server(url)
+            note = f"{preprint_server} preprint"
+        elif entry_type == 'inproceedings':
+            booktitle = work.get('journal-title', {}).get('value', '')
+            if not booktitle:
+                booktitle = infer_proceedings_venue(url)
+                if booktitle == 'ACM Digital Library':
+                    booktitle = 'Proceedings of the ACM Digital Library'
+
+        bibtex_entry = f"@{entry_type}{{{unique_id},\n"
+        bibtex_entry += f"  title = {{{title}}},\n"
+        if journal:
+            bibtex_entry += f"  journal = {{{journal}}},\n"
+        if note:
+            bibtex_entry += f"  note = {{{note}}},\n"
+        if booktitle:
+            bibtex_entry += f"  booktitle = {{{booktitle}}},\n"
+        if year:
+            bibtex_entry += f"  year = {{{year}}},\n"
+        if url:
+            bibtex_entry += f"  url = {{{url}}},\n"
+        if authors:
+            author_list = ' and '.join(authors)
+            bibtex_entry += f"  author = {{{author_list}}},\n"
+        bibtex_entry += "}\n"
+        return bibtex_entry
+    except Exception as e:
+        print(f"Error constructing BibTeX entry: {e}")
+        return ''
+
+def fetch_detailed_work(orcid_id, put_code):
+    try:
+        url = f'https://pub.orcid.org/v3.0/{orcid_id}/work/{put_code}'
+        headers = {
+            'Accept': 'application/json'
+        }
+        response = requests.get(url, headers=headers)
+        if response.status_code == 200:
+            return response.json()
+        else:
+            raise Exception(f"Failed to retrieve detailed work. HTTP Status code: {response.status_code}")
+    except Exception as e:
+        print(f"Error fetching detailed work: {e}")
+        return None
+
+def fetch_orcid_works(orcid_id):
+    url = f'https://pub.orcid.org/v3.0/{orcid_id}/works'
+    headers = {
+        'Accept': 'application/json'
+    }
+    response = requests.get(url, headers=headers)
+    if response.status_code == 200:
+        works = response.json()['group']
+        bib_entries = {
+            'article': [],
+            'unpublished': [],
+            'incollection': [],
+            'inproceedings': [],
+            'misc': []
+        }
+        ignored_entries = []
+        entry_type_map = {
+            'journal-article': 'article',
+            'book-chapter': 'incollection',
+            'conference-paper': 'inproceedings',
+            'preprint': 'unpublished',
+            # Add more mappings as needed
+        }
+        for work_group in tqdm(works, desc="Fetching works", unit="work"):
+            work_summary = work_group['work-summary'][0]
+            try:
+                detailed_work = fetch_detailed_work(orcid_id, work_summary['put-code'])
+                if detailed_work:
+                    bibtex_entry = construct_bibtex_entry(work_summary, detailed_work)
+                    if bibtex_entry:
+                        entry_type = work_summary.get('type', 'misc')
+                        entry_type_key = entry_type_map.get(entry_type, 'misc')
+                        bib_entries[entry_type_key].append(bibtex_entry)
+                    else:
+                        ignored_entries.append((work_summary, 'BibTeX entry construction failed'))
+                else:
+                    ignored_entries.append((work_summary, 'Detailed work fetch failed'))
+            except Exception as e:
+                print(f"Error: {e}")
+                ignored_entries.append((work_summary, str(e)))
+        return bib_entries, ignored_entries
+    else:
+        raise Exception(f"Failed to retrieve works. HTTP Status code: {response.status_code}")
+
+def save_bibtex_files(bib_entries):
+    for entry_type, entries in bib_entries.items():
+        with open(f'orcid_works_{entry_type}.bib', 'w') as bib_file:
+            bib_file.write('\n\n'.join(entries))
+
+def main():
+    orcid_id = ORCID_ID
+    bib_entries, ignored_entries = fetch_orcid_works(orcid_id)
+    save_bibtex_files(bib_entries)
+    print("BibTeX files updated successfully.")
+
+    if ignored_entries:
+        print("\nWarning: Some entries were ignored due to errors.")
+        for entry, error in ignored_entries:
+            print(f"\nEntry: {entry}")
+            print(f"Error: {error}")
+
+if __name__ == "__main__":
+    main()

content/publications.md

@@ -0,0 +1,27 @@
+# Publications
+
+Here is a list of publications from the laboratory, which is automatically generated from the [ORCID record](https://orcid.org/0000-0002-9111-0699) of Dr Bellec:
+
+## Journal articles
+```{bibliography} orcid_works_article.bib
+:filter: (year >= "2010")
+:style: unsrtalpha
+```
+
+## Proceedings
+```{bibliography} orcid_works_inproceedings.bib
+:filter: (year >= "2010")
+:style: unsrtalpha
+```
+
+## Preprints
+```{bibliography} orcid_works_unpublished.bib
+:filter: (year >= "2010")
+:style: unsrtalpha
+```
+
+## Misc
+```{bibliography} orcid_works_misc.bib
+:filter: (year >= "2010")
+:style: unsrtalpha
+```

content/requirements.txt

@@ -2,3 +2,5 @@ jupyter-book
 matplotlib
 numpy
 sphinx_design
+requests
+tqdm