wbib.wbib

def render_dashboard(
    info,
    mode="basic",
    query_options=DEFAULT_QUERY_OPTIONS,
    sections_to_add=DEFAULT_SESSIONS,
    site_title="Wikidata Bibtex",
    site_subtitle="Demonstration",
    filepath=".",
    pages={},
):
    """
    Renders a plain html string coding for a dashboard with embedded Wikidata SPARQL queries.
    At the same time, it saves the html to the file system via the filepath argument.


    ```
    DEFAULT_SESSIONS = [
        "map of institutions",
        "articles",
        "list of authors",
        "list of topics",
        "list of journals",
        "curation of author items",
        "curation of author affiliations",
    ]
    ```

    ```
    DEFAULT_QUERY_OPTIONS = {
        "map of institutions": {
            "label": "map of institutions",
            "query": wbib.queries.get_query_url_for_locations
        },
        "articles": {
            "label": "articles",
            "query": wbib.queries.get_query_url_for_articles
        },
        "list of authors": {
            "label": "list of authors",
            "query": wbib.queries.get_query_url_for_authors
        },
        "list of topics": {
            "label": "list of co-studied topics",
            "query": wbib.queries.get_topics_as_table
        },
        "list of journals": {
            "label": "list of venues",
            "query": wbib.queries.get_query_url_for_venues
        },
        "curation of author items": {
            "label": "curation: curate author strings that are not yet linked to items",
            "query": wbib.queries.get_query_url_for_missing_author_items
        },
        "curation of author affiliations": {
            "label": "curation: add affiliation/employment for authors lacking it",
            "query": queries.get_query_url_for_author_without_affiliation
        }
    }
    ```
    ```
    EXAMPLE_PAGES = {"home": {"href": "/", "name": "Home"}}
    ```
    Args:
        info (dict): Either a dict containing complex information for the selector or a list of QIDs.
        mode (str): A string representing the mode. If "advanced", then a config is expected for the
            info parameters. If "basic", a list of QIDs is expected. Defaults to "advanced".
        query_options (dict): A set of queries that might be used by the dashboard.
            See default for customizing queries or labels.
        sections_to_add (list): Names of the queries to be included in the dashboard.
            Standard is to include all.
        site_title (str): A title for the dashboard (if in "basic" mode)
        site_subtitle (str): A subtitle for the dashboard (if in "basic" mode)
        filepath (str): The filepath to write the dashboard to.
        pages (dict): The pages that will be part of the final dashboard, as to make a simple navbar.

    Returns:
        str: The html content for a static Wikidata-based dashboard.
            Note: also saves the file to the file system.
    """

    if mode == "advanced":
        if not isinstance(info, dict):
            raise TypeError(
                "In advanced mode, 'info' needs to be a dict obtained from the standard yaml file"
            )
        else:
            license_statement = info["license_statement"]
            scholia_credit_statement = info["scholia_credit"]
            creator_statement = info["creator_credit"]
            site_title = info["title"]
            site_subtitle = info["subtitle"]
            sections_to_add = info["sections"]

    if mode == "basic":

        license_statement = """
            This content is available under a <a target="_blank" href="https://creativecommons.org/publicdomain/zero/1.0/"> 
                Creative Commons CC0</a> license.
        """

        scholia_credit_statement = """
        SPARQL queries adapted from <a target="_blank" href="https://scholia.toolforge.org/">Scholia</a>
        """

        creator_statement = """
        Dashboard  generated via <a target="_blank" href="https://pypi.org/project/wbib/">Wikidata Bib</a>
        """

    sections = render.render_sections(sections_to_add, query_options, info, mode)

    template = env.get_template("template.html.jinja")
    rendered_template = template.render(
        site_title=site_title,
        site_subtitle=site_subtitle,
        sections=sections,
        license_statement=license_statement,
        scholia_credit=scholia_credit_statement,
        creator_statement=creator_statement,
        pages=pages,
    )

    filename = "{}.html".format(site_title.lower().strip().replace(" ", "_"))
    path_to_write = (
        Path(filepath).joinpath(filename) if filepath is "." else Path(filepath)
    )

    with open(path_to_write, "w") as html:
        html.write(rendered_template)

    return rendered_template

def convert_doi_to_qid(list_of_dois):
    """
    Converts a list of DOI ids to Wikidata QIDs.

    Args:
      list_of_dois (list): DOIs without prefix. For example:
        ["10.3897/RIO.2.E9342", "10.3389/fimmu.2019.02736"]

    Returns:
      dict: A dict with two key-value pairs. The "missing" key contains a set
          with the DOIs not found, the "qids" key contain a set with the
          QIDs found on Wikidata.
    """

    formatted_dois = '{ "' + '" "'.join(list_of_dois) + '"}'
    query = f"""SELECT ?id ?item  ?itemLabel
  WHERE {{
      {{
      SELECT ?item ?id WHERE {{
          VALUES ?unformatted_id {formatted_dois}
          BIND(UCASE(?unformatted_id) AS ?id)
          ?item wdt:P356 ?id.
      }}
      }}
      SERVICE wikibase:label 
      {{ bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }}}}
  """

    query_result = wikidata2df(query)

    result = {}

    result["qids"] = list(query_result["item"].values)
    result["missing"] = []

    for doi in list_of_dois:
        if doi.upper() not in list(query_result["id"].values):
            result["missing"].append(doi)

    result["qids"] = set(result["qids"])
    result["missing"] = set(result["missing"])
    return result