diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 66ec16d..0bef4f6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,28 +1,49 @@ -name: ci +name: Deploy Jupyter Book to GitHub Pages on: push: - branches: - - main + branches: [main] +env: + BASE_URL: /${{ github.event.repository.name }} + permissions: - contents: write + contents: read + pages: write + id-token: write + +concurrency: + group: 'pages' + cancel-in-progress: false + jobs: deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - name: Configure Git Credentials - run: | - git config user.name github-actions[bot] - git config user.email 41898282+github-actions[bot]@users.noreply.github.com - - uses: actions/setup-python@v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd + + - name: Setup Pages + uses: actions/configure-pages@45bfe0192ca1faeb007ade9deae92b16b8254a0d + + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 with: - python-version: 3.x - - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV - - uses: actions/cache@v4 + python-version: '3.11' + + - name: Install uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b + + - name: Install dependencies + run: uv sync + + - name: Build HTML Assets + run: uv run jupyter-book build --html --execute + + - name: Upload artifact + uses: actions/upload-pages-artifact@fc324d3547104276b827a68afc52ff2a11cc49c9 with: - key: mkdocs-material-${{ env.cache_id }} - path: ~/.cache - restore-keys: | - mkdocs-material- - - run: pip install mkdocs-material - - run: mkdocs gh-deploy --force \ No newline at end of file + path: './_build/html' + + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@cd2ce8fcbc39b97be8ca5fce6e763baed58fa128 \ No newline at end of file diff --git a/.gitignore b/.gitignore index e686b50..eed1a7f 100644 --- a/.gitignore +++ b/.gitignore @@ -28,3 +28,6 @@ var/ .installed.cfg *.egg .DS_Store + +# MyST build outputs +_build diff --git a/docs/api/quickstart.md b/docs/api/quickstart.md index 3ca6aba..ef03208 100644 --- a/docs/api/quickstart.md +++ b/docs/api/quickstart.md @@ -1,9 +1,11 @@ # Quick start -!!! tip "Time estimate: 5 minutes" - This tutorial walks you through your first requests to the OpenCitations API. You'll start by counting citations for a paper, then retrieve the full citation data, and finally look up bibliographic metadata. +:::{admonition} Time estimate: 5 minutes +:class: tip +This tutorial walks you through your first requests to the OpenCitations API. You'll start by counting citations for a paper, then retrieve the full citation data, and finally look up bibliographic metadata. - No account, no API key, no setup required. +No account, no API key, no setup required. +::: ## What is the OpenCitations API? @@ -56,56 +58,72 @@ You just made your first API call. You opened a URL, and OpenCitations responded Now let's do the same thing from the command line and from Python, which is how you'll use the API in practice: -=== "curl" +::::{tab-set} +:sync-group: code - ```bash - curl 'https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023' - ``` - -=== "Python" - - ```python - import requests +:::{tab-item} curl +:sync: curl +```bash +curl 'https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023' +``` +::: + +:::{tab-item} Python +:sync: python +```python +import requests + +response = requests.get( + "https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023" +) +result = response.json() +print(result) +``` +::: - response = requests.get( - "https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023" - ) - result = response.json() - print(result) - ``` +:::: | Field | Meaning | |-------|---------| | `count` | Number of works that cite the queried paper | -!!! note "Try it yourself" - Replace the DOI in the URL with any DOI you care about. The pattern is always `/index/v2/citation-count/doi:`. +:::{admonition} Try it yourself +:class: note +Replace the DOI in the URL with any DOI you care about. The pattern is always `/index/v2/citation-count/doi:`. - The endpoint also accepts `pmid:` and `omid:` prefixes. +The endpoint also accepts `pmid:` and `omid:` prefixes. +::: ## Step 2: Get the full list of citations A count is useful, but often you need to know *which* works cited the paper. The `citations` endpoint returns the complete list with details about each citation. -=== "curl" +::::{tab-set} +:sync-group: code - ```bash - curl 'https://api.opencitations.net/index/v2/citations/doi:10.1162/qss_a_00023' - ``` - -=== "Python" - - ```python - response = requests.get( - "https://api.opencitations.net/index/v2/citations/doi:10.1162/qss_a_00023" - ) - citations = response.json() +:::{tab-item} curl +:sync: curl +```bash +curl 'https://api.opencitations.net/index/v2/citations/doi:10.1162/qss_a_00023' +``` +::: + +:::{tab-item} Python +:sync: python +```python +response = requests.get( + "https://api.opencitations.net/index/v2/citations/doi:10.1162/qss_a_00023" +) +citations = response.json() + +for cit in citations[:3]: + print(f"Cited by: {cit['citing']}") + print(f" Date: {cit['creation']}") + print() +``` +::: - for cit in citations[:3]: - print(f"Cited by: {cit['citing']}") - print(f" Date: {cit['creation']}") - print() - ``` +:::: The response is a JSON array. Each element is one citation: @@ -133,32 +151,41 @@ The response is a JSON array. Each element is one citation: The `citing` and `cited` fields contain multiple identifiers separated by spaces. OpenCitations stores all the known IDs for a given work: its internal OMID, the DOI, the OpenAlex ID, etc. -!!! info "What is an OCI?" - The **Open Citation Identifier** (OCI) is a persistent identifier that OpenCitations assigns to each citation. It is composed of two numbers separated by a dash: the first refers to the citing work, the second to the cited work. More details in [What are OCIs](concepts/oci.md). +:::{admonition} What is an OCI? +:class: info +The **Open Citation Identifier** (OCI) is a persistent identifier that OpenCitations assigns to each citation. It is composed of two numbers separated by a dash: the first refers to the citing work, the second to the cited work. More details in [What are OCIs](concepts/oci.md). +::: ## Step 3: Retrieve bibliographic metadata The Index API tells you *who cites whom*, but not the titles or authors. That information lives in the **Meta API**. -=== "curl" +::::{tab-set} +:sync-group: code - ```bash - curl 'https://api.opencitations.net/meta/v1/metadata/doi:10.1162/qss_a_00023' - ``` - -=== "Python" - - ```python - response = requests.get( - "https://api.opencitations.net/meta/v1/metadata/doi:10.1162/qss_a_00023" - ) - metadata = response.json()[0] +:::{tab-item} curl +:sync: curl +```bash +curl 'https://api.opencitations.net/meta/v1/metadata/doi:10.1162/qss_a_00023' +``` +::: + +:::{tab-item} Python +:sync: python +```python +response = requests.get( + "https://api.opencitations.net/meta/v1/metadata/doi:10.1162/qss_a_00023" +) +metadata = response.json()[0] + +print(f"Title: {metadata['title']}") +print(f"Authors: {metadata['author']}") +print(f"Published: {metadata['pub_date']}") +print(f"Venue: {metadata['venue']}") +``` +::: - print(f"Title: {metadata['title']}") - print(f"Authors: {metadata['author']}") - print(f"Published: {metadata['pub_date']}") - print(f"Venue: {metadata['venue']}") - ``` +:::: Response: @@ -216,27 +243,36 @@ To get started: 2. Get your token 3. Include it in your requests: -=== "curl" +::::{tab-set} +:sync-group: code - ```bash - curl -H 'Authorization: YOUR-OPENCITATIONS-ACCESS-TOKEN' \ - 'https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023' - ``` - -=== "Python" - - ```python - session = requests.Session() - session.headers["Authorization"] = "YOUR-OPENCITATIONS-ACCESS-TOKEN" +:::{tab-item} curl +:sync: curl +```bash +curl -H 'Authorization: YOUR-OPENCITATIONS-ACCESS-TOKEN' \ + 'https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023' +``` +::: + +:::{tab-item} Python +:sync: python +```python +session = requests.Session() +session.headers["Authorization"] = "YOUR-OPENCITATIONS-ACCESS-TOKEN" + +# Use session instead of requests for all your calls +result = session.get( + "https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023" +).json() +``` +::: - # Use session instead of requests for all your calls - result = session.get( - "https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023" - ).json() - ``` +:::: -!!! warning "Rate limits" - API calls are rate-limited to **180 requests per minute** per IP address. This limit exists to guarantee fair access to the service for everyone, regardless of who they are or where they come from. For large-scale data retrieval, use the [database dumps](https://download.opencitations.net/) instead. +:::{admonition} Rate limits +:class: warning +API calls are rate-limited to **180 requests per minute** per IP address. This limit exists to guarantee fair access to the service for everyone, regardless of who they are or where they come from. For large-scale data retrieval, use the [database dumps](https://download.opencitations.net/) instead. +::: ## What you've learned @@ -251,4 +287,4 @@ At this point you know how to: ## Next steps - [**Index API v2 full documentation**](https://api.opencitations.net/index/v2): all available operations, parameters, and examples -- [**Meta API v1 full documentation**](https://api.opencitations.net/meta/v1): all metadata operations, including search by author and editor +- [**Meta API v1 full documentation**](https://api.opencitations.net/meta/v1): all metadata operations, including search by author and editor \ No newline at end of file diff --git a/docs/api/use-cases.md b/docs/api/use-cases.md index 36b58fe..11a7ce4 100644 --- a/docs/api/use-cases.md +++ b/docs/api/use-cases.md @@ -1,3 +1,8 @@ +--- +kernelspec: + name: python3 + display_name: Python 3 +--- # Use cases Two practical examples of what you can build with the OpenCitations API. @@ -15,7 +20,8 @@ INPUT_FILE = "list_of_papers.txt" # one DOI per line OUTPUT_FILE = "citation_counts.csv" API_BASE = "https://api.opencitations.net/index/v2/citation-count/doi:" -# Optional: use an access token for better tracking +# Optional: include your access token to help OpenCitations +# monitor anonymous usage of its services # https://opencitations.net/accesstoken TOKEN = None @@ -78,8 +84,10 @@ doi,citation_count ... ``` -!!! warning "Rate limits and large datasets" - At 180 requests per minute, processing 5000 DOIs takes about 28 minutes. If you need citation data for tens of thousands of papers, consider using the [database dumps](https://download.opencitations.net/) instead. +:::{admonition} Rate limits and large datasets +:class: warning +At 180 requests per minute, processing 5000 DOIs takes about 28 minutes. If you need citation data for tens of thousands of papers, consider using the [database dumps](https://download.opencitations.net/) instead. +::: ## 2. Live citation counts on your website @@ -101,6 +109,14 @@ Add this snippet wherever you want the count to appear, and replace the DOI with ``` -The visitor will see: +Here is the same call executed with Python to show the real result: -> **101** citations +```{code-cell} python +import requests + +response = requests.get( + "https://api.opencitations.net/index/v2/citation-count/doi:10.1162/qss_a_00023" +) +data = response.json() +print(f'Results: {data[0]["count"]} citations') +``` \ No newline at end of file diff --git a/docs/assets/oc_logo_small.png b/docs/assets/oc_logo_small.png new file mode 100644 index 0000000..dc4ced7 Binary files /dev/null and b/docs/assets/oc_logo_small.png differ diff --git a/docs/index.md b/docs/index.md index 5842964..34200c6 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,14 +4,14 @@ OpenCitations is an open infrastructure that collects, stores, and publishes bibliographic and citation data from scholarly literature. It is managed by the [Research Centre for Open Scholarly Metadata](https://openscholarlymetadata.org/) at the University of Bologna. -The two datasets are: +The two main datasets are: - **OpenCitations Index**: over 2.4 billion citation links between scholarly works. A citation link connects a citing work to a cited work, with metadata about the citation itself (date, timespan, self-citation flags). - **OpenCitations Meta**: bibliographic metadata for over 129 million publications, including titles, authors, venues, publication dates, and identifiers. -The data comes from multiple sources e.g.: Crossref, DataCite, NIH-OCC (PubMed), OpenAIRE, and JALC. +The data comes from multiple sources: Crossref, DataCite, NIH-OCC (PubMed), OpenAIRE, and JALC. -All data is released under a [CC0 public domain dedication](https://creativecommons.org/public-domain/cc0/) and can be freely reused for any purpose. +All data is released under a [CC0 public domain dedication](https://creativecommons.org/public-domain/cc0/) and can be freely reused for any purpose, including commercial use. ## What OpenCitations is not @@ -28,13 +28,13 @@ OpenCitations provides the raw citation data and bibliographic metadata. It is t There are several ways to access OpenCitations data, depending on your needs. -**[Search](search/howto.md)**: a web interface at [search.opencitations.net](https://search.opencitations.net) for looking up citations and references of individual works. No technical knowledge required. +**[Search](search/index.md)**: a web interface at [search.opencitations.net](https://search.opencitations.net) for looking up citations and references of individual works. No technical knowledge required. **[REST API](api/quickstart.md)**: programmatic access to citation data (Index API) and bibliographic metadata (Meta API). Useful for building scripts, pipelines, and integrations. The full endpoint documentation is available at [api.opencitations.net](https://api.opencitations.net). **[SPARQL endpoints](https://sparql.opencitations.net)**: for advanced users who want to query the data using SPARQL. -**[Data dumps](https://download.opencitations.net)**: complete database exports available on Zenodo, Figshare, and the Internet Archive. This is the best option for large-scale analysis when the API rate limits are not enough. We provide provenance too. +**[Data dumps](https://download.opencitations.net)**: complete database exports available on Zenodo, Figshare, and the Internet Archive. This is the best option for large-scale analysis when the API rate limits are not enough. ## License diff --git a/docs/search/howto.md b/docs/search/howto.md index f97f02b..cdf3017 100644 --- a/docs/search/howto.md +++ b/docs/search/howto.md @@ -29,5 +29,5 @@ You can search using any of the following. Enter the value directly, without pre | Type | Example | |------|---------| | DOI | `10.1162/qss_a_00023` | -| PubMed ID | `35821898` | +| PubMed ID | `33817056` | | OpenAlex ID | `W3106215946` | \ No newline at end of file diff --git a/myst.yml b/myst.yml new file mode 100644 index 0000000..cd16a26 --- /dev/null +++ b/myst.yml @@ -0,0 +1,38 @@ +# See docs at: https://mystmd.org/guide/frontmatter +version: 1 +project: + id: a985d373-0239-480f-8063-605f68e4705f + title: OpenCitations Documentation + description: Official documentation and tutorials for OpenCitations services + keywords: + - opencitations + - opencitations tutorials + github: https://github.com/opencitations/oc_docs + # To autogenerate a Table of Contents, run "jupyter book init --write-toc" + toc: + - file: docs/index + - title: API + children: + - file: docs/api/quickstart + - file: docs/api/use-cases + - title: Guides + children: + - file: docs/api/guides/filtering + - file: docs/api/guides/pagination + - file: docs/api/guides/output-formats + - file: docs/api/guides/error-handling + - title: Concepts + children: + - file: docs/api/concepts/data-model + - file: docs/api/concepts/oci + - file: docs/api/concepts/index-vs-meta + - title: Search + children: + - file: docs/search/howto + +site: + template: book-theme + options: + favicon: docs/assets/favicon.png + logo_text: Opencitations + #logo: docs/assets/oc_logo_small.png diff --git a/pyproject.toml b/pyproject.toml index 28ecd85..0b38b2d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,5 +5,6 @@ description = "OpenCitations documentations" readme = "README.md" requires-python = ">=3.11" dependencies = [ - "mkdocs-material>=9.7.6", + "jupyter-book>=2.0.0", + "requests>=2.33.1", ] diff --git a/uv.lock b/uv.lock index 80e13c7..6e3ae5a 100644 --- a/uv.lock +++ b/uv.lock @@ -1,37 +1,214 @@ version = 1 revision = 3 requires-python = ">=3.11" +resolution-markers = [ + "python_full_version >= '3.14'", + "python_full_version < '3.14'", +] + 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