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CohortEncoder

encapsulate information about a citation that we add to the metadata for display

Source code in pyphetools/creation/citation.py 
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class Citation:
    """encapsulate information about a citation that we add to the metadata for display
    """

    def __init__(self, pmid:str, title:str) -> None:
        """
        :param pmid: PubMed identifier for the publication in which this individual was described (e.g. PMID:321..).
        :type pmid: str
        :param title: Title of the publication in which this individual was described.
        :type title: str
        """
        if pmid is None or isinstance(pmid, float) or not pmid.startswith("PMID"):
            raise ValueError(f"Could not find PubMed identifier")
        if title is None or isinstance(title, float) or len(title) < 5:
            raise ValueError(f"Could not find valid title")
        self._pmid = pmid
        self._title = title

    @property
    def pmid(self) -> str:
        return self._pmid

    @property
    def title(self) -> str:
        return self._title

    def to_external_reference(self) -> ExternalReference202:
        """
        :returns: an ExternalReference object representing this PubMed citation
        :rtype: ExternalReference202
        """
        pm_number = self._pmid.replace("PMID:", "")
        pm_url = f"https://pubmed.ncbi.nlm.nih.gov/{pm_number}" 
        return ExternalReference202(id=self._pmid,
                                    reference=pm_url,
                                    description=self._title)

__init__(pmid, title)

Parameters:

Name Type Description Default
pmid str

PubMed identifier for the publication in which this individual was described (e.g. PMID:321..).

 required
title str

Title of the publication in which this individual was described.

 required
Source code in pyphetools/creation/citation.py 
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def __init__(self, pmid:str, title:str) -> None:
    """
    :param pmid: PubMed identifier for the publication in which this individual was described (e.g. PMID:321..).
    :type pmid: str
    :param title: Title of the publication in which this individual was described.
    :type title: str
    """
    if pmid is None or isinstance(pmid, float) or not pmid.startswith("PMID"):
        raise ValueError(f"Could not find PubMed identifier")
    if title is None or isinstance(title, float) or len(title) < 5:
        raise ValueError(f"Could not find valid title")
    self._pmid = pmid
    self._title = title

to_external_reference()

Returns:

Type Description
ExternalReference202

an ExternalReference object representing this PubMed citation
Source code in pyphetools/creation/citation.py 
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def to_external_reference(self) -> ExternalReference202:
    """
    :returns: an ExternalReference object representing this PubMed citation
    :rtype: ExternalReference202
    """
    pm_number = self._pmid.replace("PMID:", "")
    pm_url = f"https://pubmed.ncbi.nlm.nih.gov/{pm_number}" 
    return ExternalReference202(id=self._pmid,
                                reference=pm_url,
                                description=self._title)