Module manubot.cite.pubmed
View Source
import functools
import json
import logging
import os
from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
from xml.etree import ElementTree
import requests
from manubot.util import get_manubot_user_agent
from .citekey import CiteKey
from .handlers import Handler
class Handler_PubMed(Handler):
standard_prefix = "pubmed"
prefixes = [
"pubmed",
"pmid",
]
accession_pattern = r"[1-9][0-9]{0,7}"
def inspect(self, citekey: CiteKey) -> Optional[str]:
identifier = citekey.accession
# https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
if identifier.startswith("PMC"):
return (
"PubMed Identifiers should start with digits rather than PMC. "
f"Should {citekey.dealiased_id!r} switch the citation source to 'pmc'?"
)
elif not self._get_pattern().fullmatch(identifier):
return "PubMed Identifiers should be 1-8 digits with no leading zeros."
def get_csl_item(self, citekey: CiteKey) -> Dict[str, Any]:
return get_pubmed_csl_item(citekey.standard_accession)
class Handler_PMC(Handler):
standard_prefix = "pmc"
prefixes = [
"pmc",
"pmcid",
]
accession_pattern = r"PMC[0-9]+"
def inspect(self, citekey: CiteKey) -> Optional[str]:
identifier = citekey.accession
# https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
if not identifier.startswith("PMC"):
return "PubMed Central Identifiers must start with 'PMC'."
elif not self._get_pattern().fullmatch(identifier):
return (
"Identifier does not conform to the PMCID regex. "
"Double check the PMCID."
)
def get_csl_item(self, citekey: CiteKey):
return get_pmc_csl_item(citekey.standard_accession)
def get_pmc_csl_item(pmcid: str) -> Dict[str, Any]:
"""
Get the CSL Item for a PubMed Central record by its PMID, PMCID, or
DOI, using the NCBI Citation Exporter API.
https://api.ncbi.nlm.nih.gov/lit/ctxp
https://github.com/manubot/manubot/issues/21
https://twitter.com/dhimmel/status/1061787168820092929
"""
assert pmcid.startswith("PMC")
csl_item = _get_literature_citation_exporter_csl_item("pmc", pmcid[3:])
if "URL" not in csl_item:
csl_item["URL"] = (
f"https://www.ncbi.nlm.nih.gov/pmc/articles/{csl_item.get('PMCID', pmcid)}/"
)
return csl_item
def _get_literature_citation_exporter_csl_item(
database: str, identifier: str
) -> Dict[str, Any]:
"""
https://api.ncbi.nlm.nih.gov/lit/ctxp
"""
if database not in {"pubmed", "pmc"}:
logging.error(
f"Error calling _get_literature_citation_exporter_csl_item.\n"
f'database must be either "pubmed" or "pmc", not {database}'
)
raise AssertionError()
if not identifier:
logging.error(
"Error calling _get_literature_citation_exporter_csl_item.\n"
"identifier cannot be blank"
)
raise AssertionError()
params = {"format": "csl", "id": identifier}
headers = {"User-Agent": get_manubot_user_agent()}
url = f"https://api.ncbi.nlm.nih.gov/lit/ctxp/v1/{database}/"
response = requests.get(url, params, headers=headers)
try:
csl_item = response.json()
except Exception as error:
logging.error(
f"Error fetching {database} metadata for {identifier}.\n"
f"Invalid JSON response from {response.url}:\n{response.text}"
)
raise error
assert isinstance(csl_item, dict)
if csl_item.get("status", "okay") == "error":
logging.error(
f"Error fetching {database} metadata for {identifier}.\n"
f"Literature Citation Exporter returned JSON indicating an error for {response.url}\n"
f"{json.dumps(csl_item, indent=2)}"
)
raise AssertionError()
return csl_item
def get_pubmed_csl_item(pmid: Union[str, int]) -> Dict[str, Any]:
"""
Query NCBI E-Utilities to create CSL Items for PubMed IDs.
https://github.com/manubot/manubot/issues/21
https://github.com/ncbi/citation-exporter/issues/3#issuecomment-355313143
"""
pmid = str(pmid)
params = {"db": "pubmed", "id": pmid, "retmode": "xml"}
headers = {"User-Agent": get_manubot_user_agent()}
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
with _get_eutils_rate_limiter():
response = requests.get(url, params, headers=headers)
try:
xml_article_set = ElementTree.fromstring(response.text)
assert isinstance(xml_article_set, ElementTree.Element)
assert xml_article_set.tag == "PubmedArticleSet"
(xml_article,) = list(xml_article_set)
assert xml_article.tag in ["PubmedArticle", "PubmedBookArticle"]
except Exception as error:
logging.error(
f"Error fetching PubMed metadata for {pmid}.\n"
f"Unsupported XML response from {response.url}:\n{response.text}"
)
raise error
try:
csl_item = csl_item_from_pubmed_article(xml_article)
except Exception as error:
msg = f"Error parsing the following PubMed metadata for PMID {pmid}:\n{response.text}"
logging.error(msg)
raise error
return csl_item
def csl_item_from_pubmed_article(article: ElementTree.Element) -> Dict[str, Any]:
"""
Extract a CSL Item dictionary from a PubmedArticle XML element.
https://github.com/citation-style-language/schema/blob/master/csl-data.json
"""
if not article.tag == "PubmedArticle":
raise ValueError(
f"Expected article to be an XML element with tag PubmedArticle, received tag {article.tag!r}"
)
csl_item = {}
if not article.find("MedlineCitation/Article"):
raise NotImplementedError("Unsupported PubMed record: no <Article> element")
title = article.findtext("MedlineCitation/Article/ArticleTitle")
if title:
csl_item["title"] = title
volume = article.findtext("MedlineCitation/Article/Journal/JournalIssue/Volume")
if volume:
csl_item["volume"] = volume
issue = article.findtext("MedlineCitation/Article/Journal/JournalIssue/Issue")
if issue:
csl_item["issue"] = issue
page = article.findtext("MedlineCitation/Article/Pagination/MedlinePgn")
if page:
csl_item["page"] = page
journal = article.findtext("MedlineCitation/Article/Journal/Title")
if journal:
csl_item["container-title"] = journal
journal_short = article.findtext("MedlineCitation/Article/Journal/ISOAbbreviation")
if journal_short:
csl_item["container-title-short"] = journal_short
issn = article.findtext("MedlineCitation/Article/Journal/ISSN")
if issn:
csl_item["ISSN"] = issn
date_parts = extract_publication_date_parts(article)
if date_parts:
csl_item["issued"] = {"date-parts": [date_parts]}
authors_csl = []
authors = article.findall("MedlineCitation/Article/AuthorList/Author")
for author in authors:
author_csl = {}
given = author.findtext("ForeName")
if given:
author_csl["given"] = given
family = author.findtext("LastName")
if family:
author_csl["family"] = family
authors_csl.append(author_csl)
if authors_csl:
csl_item["author"] = authors_csl
for id_type, key in ("pubmed", "PMID"), ("pmc", "PMCID"), ("doi", "DOI"):
xpath = f"PubmedData/ArticleIdList/ArticleId[@IdType='{id_type}']"
value = article.findtext(xpath)
if value:
csl_item[key] = value.lower() if key == "DOI" else value
abstract = article.findtext("MedlineCitation/Article/Abstract/AbstractText")
if abstract:
csl_item["abstract"] = abstract
csl_item["URL"] = f"https://www.ncbi.nlm.nih.gov/pubmed/{csl_item['PMID']}"
csl_item["type"] = "article-journal"
return csl_item
month_abbrev_to_int: Dict[str, int] = {
"Jan": 1,
"Feb": 2,
"Mar": 3,
"Apr": 4,
"May": 5,
"Jun": 6,
"Jul": 7,
"Aug": 8,
"Sep": 9,
"Oct": 10,
"Nov": 11,
"Dec": 12,
}
def extract_publication_date_parts(article: ElementTree.Element) -> List[int]:
"""
Extract date published from a PubmedArticle XML element.
"""
date_parts = []
# Electronic articles
date = article.find("MedlineCitation/Article/ArticleDate")
if date:
for part in "Year", "Month", "Day":
part = date.findtext(part)
if not part:
break
date_parts.append(int(part))
return date_parts
# Print articles
date = article.find("MedlineCitation/Article/Journal/JournalIssue/PubDate")
year = date.findtext("Year")
if year:
date_parts.append(int(year))
month = date.findtext("Month")
if month:
try:
date_parts.append(month_abbrev_to_int[month])
except KeyError:
date_parts.append(int(month))
day = date.findtext("Day")
if day:
date_parts.append(int(day))
return date_parts
def get_pmcid_and_pmid_for_doi(doi: str) -> Dict[str, str]:
"""
Query PMC's ID Converter API to retrieve the PMCID and PMID for a DOI.
Does not work for DOIs that are in Pubmed but not PubMed Central.
https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
"""
assert isinstance(doi, str)
assert doi.startswith("10.")
params = {"ids": doi, "tool": "manubot"}
url = "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/"
response = requests.get(url, params)
if not response.ok:
logging.warning(f"Status code {response.status_code} querying {response.url}\n")
return {}
try:
element_tree = ElementTree.fromstring(response.text)
assert element_tree.tag == "pmcids"
except Exception:
logging.warning(
f"Error fetching PMC ID conversion for {doi}.\n"
f"Response from {response.url}:\n{response.text}"
)
return {}
records = element_tree.findall("record")
if len(records) != 1:
logging.warning(
f"Expected PubMed Central ID converter to return a single XML record for {doi}.\n"
f"Response from {response.url}:\n{response.text}"
)
return {}
(record,) = records
if record.findtext("status", default="okay") == "error":
return {}
id_dict = {}
for id_type in "pmcid", "pmid":
id_ = record.get(id_type)
if id_:
id_dict[id_type.upper()] = id_
return id_dict
def get_pmid_for_doi(doi: str) -> Optional[str]:
"""
Query NCBI's E-utilities to retrieve the PMID for a DOI.
"""
assert isinstance(doi, str)
assert doi.startswith("10.")
params = {"db": "pubmed", "term": f"{doi}[DOI]"}
headers = {"User-Agent": get_manubot_user_agent()}
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
with _get_eutils_rate_limiter():
response = requests.get(url, params, headers=headers)
if not response.ok:
logging.warning(f"Status code {response.status_code} querying {response.url}\n")
return None
try:
element_tree = ElementTree.fromstring(response.text)
assert isinstance(element_tree, ElementTree.Element)
assert element_tree.tag == "eSearchResult"
except Exception:
logging.warning(
f"Error in ESearch XML for DOI: {doi}.\n"
f"Response from {response.url}:\n{response.text}"
)
return None
id_elems = element_tree.findall("IdList/Id")
if len(id_elems) != 1:
logging.debug(
f"No PMIDs found for {doi}.\n"
f"Response from {response.url}:\n{response.text}"
)
return None
(id_elem,) = id_elems
return id_elem.text
def get_pubmed_ids_for_doi(doi: str) -> Dict[str, str]:
"""
Return a dictionary with PMCID and PMID, if they exist, for the specified
DOI. See https://github.com/manubot/manubot/issues/45.
"""
pubmed_ids = get_pmcid_and_pmid_for_doi(doi)
if not pubmed_ids:
pmid = get_pmid_for_doi(doi)
if pmid:
pubmed_ids["PMID"] = pmid
return pubmed_ids
if TYPE_CHECKING:
# support PyrateLimiter return type while avoiding unused runtime import
# https://stackoverflow.com/a/39757388/4651668
from pyrate_limiter import Limiter
@functools.lru_cache
def _get_eutils_rate_limiter() -> "Limiter":
"""
Rate limiter to cap NCBI E-utilities queries to <= 3 per second as per
https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
https://pyratelimiter.readthedocs.io/en/latest/
https://github.com/vutran1710/PyrateLimiter
"""
# does not work pyrate_limiter v3
# https://github.com/manubot/manubot/issues/367
from pyrate_limiter import Duration, Limiter, RequestRate
if "CI" in os.environ:
# multiple CI jobs might be running concurrently
rate = RequestRate(limit=1, interval=Duration.SECOND * 2)
else:
rate = RequestRate(limit=2, interval=Duration.SECOND)
return Limiter(rate).ratelimit("ncbi_eutils", delay=True)
Variables
TYPE_CHECKING
month_abbrev_to_int
Functions
csl_item_from_pubmed_article
def csl_item_from_pubmed_article(
article: xml.etree.ElementTree.Element
) -> Dict[str, Any]
Extract a CSL Item dictionary from a PubmedArticle XML element.
https://github.com/citation-style-language/schema/blob/master/csl-data.json
View Source
def csl_item_from_pubmed_article(article: ElementTree.Element) -> Dict[str, Any]:
"""
Extract a CSL Item dictionary from a PubmedArticle XML element.
https://github.com/citation-style-language/schema/blob/master/csl-data.json
"""
if not article.tag == "PubmedArticle":
raise ValueError(
f"Expected article to be an XML element with tag PubmedArticle, received tag {article.tag!r}"
)
csl_item = {}
if not article.find("MedlineCitation/Article"):
raise NotImplementedError("Unsupported PubMed record: no <Article> element")
title = article.findtext("MedlineCitation/Article/ArticleTitle")
if title:
csl_item["title"] = title
volume = article.findtext("MedlineCitation/Article/Journal/JournalIssue/Volume")
if volume:
csl_item["volume"] = volume
issue = article.findtext("MedlineCitation/Article/Journal/JournalIssue/Issue")
if issue:
csl_item["issue"] = issue
page = article.findtext("MedlineCitation/Article/Pagination/MedlinePgn")
if page:
csl_item["page"] = page
journal = article.findtext("MedlineCitation/Article/Journal/Title")
if journal:
csl_item["container-title"] = journal
journal_short = article.findtext("MedlineCitation/Article/Journal/ISOAbbreviation")
if journal_short:
csl_item["container-title-short"] = journal_short
issn = article.findtext("MedlineCitation/Article/Journal/ISSN")
if issn:
csl_item["ISSN"] = issn
date_parts = extract_publication_date_parts(article)
if date_parts:
csl_item["issued"] = {"date-parts": [date_parts]}
authors_csl = []
authors = article.findall("MedlineCitation/Article/AuthorList/Author")
for author in authors:
author_csl = {}
given = author.findtext("ForeName")
if given:
author_csl["given"] = given
family = author.findtext("LastName")
if family:
author_csl["family"] = family
authors_csl.append(author_csl)
if authors_csl:
csl_item["author"] = authors_csl
for id_type, key in ("pubmed", "PMID"), ("pmc", "PMCID"), ("doi", "DOI"):
xpath = f"PubmedData/ArticleIdList/ArticleId[@IdType='{id_type}']"
value = article.findtext(xpath)
if value:
csl_item[key] = value.lower() if key == "DOI" else value
abstract = article.findtext("MedlineCitation/Article/Abstract/AbstractText")
if abstract:
csl_item["abstract"] = abstract
csl_item["URL"] = f"https://www.ncbi.nlm.nih.gov/pubmed/{csl_item['PMID']}"
csl_item["type"] = "article-journal"
return csl_item
extract_publication_date_parts
def extract_publication_date_parts(
article: xml.etree.ElementTree.Element
) -> List[int]
Extract date published from a PubmedArticle XML element.
View Source
def extract_publication_date_parts(article: ElementTree.Element) -> List[int]:
"""
Extract date published from a PubmedArticle XML element.
"""
date_parts = []
# Electronic articles
date = article.find("MedlineCitation/Article/ArticleDate")
if date:
for part in "Year", "Month", "Day":
part = date.findtext(part)
if not part:
break
date_parts.append(int(part))
return date_parts
# Print articles
date = article.find("MedlineCitation/Article/Journal/JournalIssue/PubDate")
year = date.findtext("Year")
if year:
date_parts.append(int(year))
month = date.findtext("Month")
if month:
try:
date_parts.append(month_abbrev_to_int[month])
except KeyError:
date_parts.append(int(month))
day = date.findtext("Day")
if day:
date_parts.append(int(day))
return date_parts
get_pmc_csl_item
def get_pmc_csl_item(
pmcid: str
) -> Dict[str, Any]
Get the CSL Item for a PubMed Central record by its PMID, PMCID, or
DOI, using the NCBI Citation Exporter API.
https://api.ncbi.nlm.nih.gov/lit/ctxp https://github.com/manubot/manubot/issues/21 https://twitter.com/dhimmel/status/1061787168820092929
View Source
def get_pmc_csl_item(pmcid: str) -> Dict[str, Any]:
"""
Get the CSL Item for a PubMed Central record by its PMID, PMCID, or
DOI, using the NCBI Citation Exporter API.
https://api.ncbi.nlm.nih.gov/lit/ctxp
https://github.com/manubot/manubot/issues/21
https://twitter.com/dhimmel/status/1061787168820092929
"""
assert pmcid.startswith("PMC")
csl_item = _get_literature_citation_exporter_csl_item("pmc", pmcid[3:])
if "URL" not in csl_item:
csl_item["URL"] = (
f"https://www.ncbi.nlm.nih.gov/pmc/articles/{csl_item.get('PMCID', pmcid)}/"
)
return csl_item
get_pmcid_and_pmid_for_doi
def get_pmcid_and_pmid_for_doi(
doi: str
) -> Dict[str, str]
Query PMC's ID Converter API to retrieve the PMCID and PMID for a DOI.
Does not work for DOIs that are in Pubmed but not PubMed Central. https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
View Source
def get_pmcid_and_pmid_for_doi(doi: str) -> Dict[str, str]:
"""
Query PMC's ID Converter API to retrieve the PMCID and PMID for a DOI.
Does not work for DOIs that are in Pubmed but not PubMed Central.
https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
"""
assert isinstance(doi, str)
assert doi.startswith("10.")
params = {"ids": doi, "tool": "manubot"}
url = "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/"
response = requests.get(url, params)
if not response.ok:
logging.warning(f"Status code {response.status_code} querying {response.url}\n")
return {}
try:
element_tree = ElementTree.fromstring(response.text)
assert element_tree.tag == "pmcids"
except Exception:
logging.warning(
f"Error fetching PMC ID conversion for {doi}.\n"
f"Response from {response.url}:\n{response.text}"
)
return {}
records = element_tree.findall("record")
if len(records) != 1:
logging.warning(
f"Expected PubMed Central ID converter to return a single XML record for {doi}.\n"
f"Response from {response.url}:\n{response.text}"
)
return {}
(record,) = records
if record.findtext("status", default="okay") == "error":
return {}
id_dict = {}
for id_type in "pmcid", "pmid":
id_ = record.get(id_type)
if id_:
id_dict[id_type.upper()] = id_
return id_dict
get_pmid_for_doi
def get_pmid_for_doi(
doi: str
) -> Optional[str]
Query NCBI's E-utilities to retrieve the PMID for a DOI.
View Source
def get_pmid_for_doi(doi: str) -> Optional[str]:
"""
Query NCBI's E-utilities to retrieve the PMID for a DOI.
"""
assert isinstance(doi, str)
assert doi.startswith("10.")
params = {"db": "pubmed", "term": f"{doi}[DOI]"}
headers = {"User-Agent": get_manubot_user_agent()}
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
with _get_eutils_rate_limiter():
response = requests.get(url, params, headers=headers)
if not response.ok:
logging.warning(f"Status code {response.status_code} querying {response.url}\n")
return None
try:
element_tree = ElementTree.fromstring(response.text)
assert isinstance(element_tree, ElementTree.Element)
assert element_tree.tag == "eSearchResult"
except Exception:
logging.warning(
f"Error in ESearch XML for DOI: {doi}.\n"
f"Response from {response.url}:\n{response.text}"
)
return None
id_elems = element_tree.findall("IdList/Id")
if len(id_elems) != 1:
logging.debug(
f"No PMIDs found for {doi}.\n"
f"Response from {response.url}:\n{response.text}"
)
return None
(id_elem,) = id_elems
return id_elem.text
get_pubmed_csl_item
def get_pubmed_csl_item(
pmid: Union[str, int]
) -> Dict[str, Any]
Query NCBI E-Utilities to create CSL Items for PubMed IDs.
https://github.com/manubot/manubot/issues/21 https://github.com/ncbi/citation-exporter/issues/3#issuecomment-355313143
View Source
def get_pubmed_csl_item(pmid: Union[str, int]) -> Dict[str, Any]:
"""
Query NCBI E-Utilities to create CSL Items for PubMed IDs.
https://github.com/manubot/manubot/issues/21
https://github.com/ncbi/citation-exporter/issues/3#issuecomment-355313143
"""
pmid = str(pmid)
params = {"db": "pubmed", "id": pmid, "retmode": "xml"}
headers = {"User-Agent": get_manubot_user_agent()}
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
with _get_eutils_rate_limiter():
response = requests.get(url, params, headers=headers)
try:
xml_article_set = ElementTree.fromstring(response.text)
assert isinstance(xml_article_set, ElementTree.Element)
assert xml_article_set.tag == "PubmedArticleSet"
(xml_article,) = list(xml_article_set)
assert xml_article.tag in ["PubmedArticle", "PubmedBookArticle"]
except Exception as error:
logging.error(
f"Error fetching PubMed metadata for {pmid}.\n"
f"Unsupported XML response from {response.url}:\n{response.text}"
)
raise error
try:
csl_item = csl_item_from_pubmed_article(xml_article)
except Exception as error:
msg = f"Error parsing the following PubMed metadata for PMID {pmid}:\n{response.text}"
logging.error(msg)
raise error
return csl_item
get_pubmed_ids_for_doi
def get_pubmed_ids_for_doi(
doi: str
) -> Dict[str, str]
Return a dictionary with PMCID and PMID, if they exist, for the specified
DOI. See https://github.com/manubot/manubot/issues/45.
View Source
def get_pubmed_ids_for_doi(doi: str) -> Dict[str, str]:
"""
Return a dictionary with PMCID and PMID, if they exist, for the specified
DOI. See https://github.com/manubot/manubot/issues/45.
"""
pubmed_ids = get_pmcid_and_pmid_for_doi(doi)
if not pubmed_ids:
pmid = get_pmid_for_doi(doi)
if pmid:
pubmed_ids["PMID"] = pmid
return pubmed_ids
Classes
Handler_PMC
class Handler_PMC(
prefix_lower: str
)
A Handler is a class that provides support for a certain type of citekey.
For example, a Handler subclass could provide support for DOI citekeys. Subclasses enable custom logic for different citekey prefixes, including how to standardize the citekey and how to retrieve CSL Item metadata.
View Source
class Handler_PMC(Handler):
standard_prefix = "pmc"
prefixes = [
"pmc",
"pmcid",
]
accession_pattern = r"PMC[0-9]+"
def inspect(self, citekey: CiteKey) -> Optional[str]:
identifier = citekey.accession
# https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
if not identifier.startswith("PMC"):
return "PubMed Central Identifiers must start with 'PMC'."
elif not self._get_pattern().fullmatch(identifier):
return (
"Identifier does not conform to the PMCID regex. "
"Double check the PMCID."
)
def get_csl_item(self, citekey: CiteKey):
return get_pmc_csl_item(citekey.standard_accession)
Ancestors (in MRO)
- manubot.cite.handlers.Handler
Class variables
accession_pattern
prefixes
standard_prefix
Methods
get_csl_item
def get_csl_item(
self,
citekey: manubot.cite.citekey.CiteKey
)
Return a CSL_Item with bibliographic details for citekey.
View Source
def get_csl_item(self, citekey: CiteKey):
return get_pmc_csl_item(citekey.standard_accession)
inspect
def inspect(
self,
citekey: manubot.cite.citekey.CiteKey
) -> Optional[str]
Check citekeys adhere to expected formats. If an issue is detected a
string describing the issue is returned. Otherwise returns None.
View Source
def inspect(self, citekey: CiteKey) -> Optional[str]:
identifier = citekey.accession
# https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
if not identifier.startswith("PMC"):
return "PubMed Central Identifiers must start with 'PMC'."
elif not self._get_pattern().fullmatch(identifier):
return (
"Identifier does not conform to the PMCID regex. "
"Double check the PMCID."
)
standardize_prefix_accession
def standardize_prefix_accession(
self,
accession: str
) -> Tuple[str, str]
Return (prefix, accession) in standardized form.
This method defaults to returning self.standard_prefix
(or self.prefix_lower if standard_prefix is not defined).
Subclasses can override this method with more specific standardization logic.
View Source
def standardize_prefix_accession(self, accession: str) -> Tuple[str, str]:
"""
Return (prefix, accession) in standardized form.
This method defaults to returning `self.standard_prefix`
(or `self.prefix_lower` if standard_prefix is not defined).
Subclasses can override this method with more specific standardization logic.
"""
standard_prefix = getattr(self, "standard_prefix", self.prefix_lower)
standard_accession = accession
return standard_prefix, standard_accession
Handler_PubMed
class Handler_PubMed(
prefix_lower: str
)
A Handler is a class that provides support for a certain type of citekey.
For example, a Handler subclass could provide support for DOI citekeys. Subclasses enable custom logic for different citekey prefixes, including how to standardize the citekey and how to retrieve CSL Item metadata.
View Source
class Handler_PubMed(Handler):
standard_prefix = "pubmed"
prefixes = [
"pubmed",
"pmid",
]
accession_pattern = r"[1-9][0-9]{0,7}"
def inspect(self, citekey: CiteKey) -> Optional[str]:
identifier = citekey.accession
# https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
if identifier.startswith("PMC"):
return (
"PubMed Identifiers should start with digits rather than PMC. "
f"Should {citekey.dealiased_id!r} switch the citation source to 'pmc'?"
)
elif not self._get_pattern().fullmatch(identifier):
return "PubMed Identifiers should be 1-8 digits with no leading zeros."
def get_csl_item(self, citekey: CiteKey) -> Dict[str, Any]:
return get_pubmed_csl_item(citekey.standard_accession)
Ancestors (in MRO)
- manubot.cite.handlers.Handler
Class variables
accession_pattern
prefixes
standard_prefix
Methods
get_csl_item
def get_csl_item(
self,
citekey: manubot.cite.citekey.CiteKey
) -> Dict[str, Any]
Return a CSL_Item with bibliographic details for citekey.
View Source
def get_csl_item(self, citekey: CiteKey) -> Dict[str, Any]:
return get_pubmed_csl_item(citekey.standard_accession)
inspect
def inspect(
self,
citekey: manubot.cite.citekey.CiteKey
) -> Optional[str]
Check citekeys adhere to expected formats. If an issue is detected a
string describing the issue is returned. Otherwise returns None.
View Source
def inspect(self, citekey: CiteKey) -> Optional[str]:
identifier = citekey.accession
# https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
if identifier.startswith("PMC"):
return (
"PubMed Identifiers should start with digits rather than PMC. "
f"Should {citekey.dealiased_id!r} switch the citation source to 'pmc'?"
)
elif not self._get_pattern().fullmatch(identifier):
return "PubMed Identifiers should be 1-8 digits with no leading zeros."
standardize_prefix_accession
def standardize_prefix_accession(
self,
accession: str
) -> Tuple[str, str]
Return (prefix, accession) in standardized form.
This method defaults to returning self.standard_prefix
(or self.prefix_lower if standard_prefix is not defined).
Subclasses can override this method with more specific standardization logic.
View Source
def standardize_prefix_accession(self, accession: str) -> Tuple[str, str]:
"""
Return (prefix, accession) in standardized form.
This method defaults to returning `self.standard_prefix`
(or `self.prefix_lower` if standard_prefix is not defined).
Subclasses can override this method with more specific standardization logic.
"""
standard_prefix = getattr(self, "standard_prefix", self.prefix_lower)
standard_accession = accession
return standard_prefix, standard_accession