diff options
Diffstat (limited to 'python/fatcat_tools/importers/pubmed.py')
| -rw-r--r-- | python/fatcat_tools/importers/pubmed.py | 27 |
1 files changed, 17 insertions, 10 deletions
diff --git a/python/fatcat_tools/importers/pubmed.py b/python/fatcat_tools/importers/pubmed.py index 97433445..41268925 100644 --- a/python/fatcat_tools/importers/pubmed.py +++ b/python/fatcat_tools/importers/pubmed.py @@ -2,9 +2,11 @@ import datetime import json import sys import warnings +from typing import Any, Dict, List, Optional, Sequence import fatcat_openapi_client from bs4 import BeautifulSoup +from fatcat_openapi_client import ApiClient, ReleaseEntity from fatcat_tools.normal import clean_doi, clean_issn, clean_pmcid, clean_pmid @@ -328,7 +330,9 @@ class PubmedImporter(EntityImporter): TODO: MEDLINE doesn't include PMC/OA license; could include in importer? """ - def __init__(self, api, issn_map_file, lookup_refs=True, **kwargs): + def __init__( + self, api: ApiClient, issn_map_file: Sequence, lookup_refs: bool = True, **kwargs + ): eg_desc = kwargs.get( "editgroup_description", "Automated import of PubMed/MEDLINE XML metadata" @@ -347,10 +351,13 @@ class PubmedImporter(EntityImporter): self.create_containers = kwargs.get("create_containers", True) self.read_issn_map_file(issn_map_file) - def want(self, obj): + def want(self, raw_record: BeautifulSoup) -> bool: return True - def parse_record(self, a): + # TODO: mypy annotations partially skipped on this function ('Any' instead of + # 'BeautifulSoup') for now because XML parsing annotations are large and + # complex + def parse_record(self, a: Any) -> ReleaseEntity: medline = a.MedlineCitation # PubmedData isn't required by DTD, but seems to always be present @@ -482,8 +489,8 @@ class PubmedImporter(EntityImporter): pub_date = journal.PubDate if not pub_date: pub_date = journal.JournalIssue.PubDate - release_date = None - release_year = None + release_date: Optional[str] = None + release_year: Optional[int] = None if pub_date.Year: release_year = int(pub_date.Year.string) if pub_date.find("Day") and pub_date.find("Month"): @@ -578,7 +585,7 @@ class PubmedImporter(EntityImporter): abstracts.append(abst) other_abstracts = medline.find_all("OtherAbstract") for other in other_abstracts: - lang = "en" + lang: Optional[str] = "en" if other.get("Language"): lang = LANG_MAP_MARC.get(other["Language"]) abst = fatcat_openapi_client.ReleaseAbstract( @@ -666,7 +673,7 @@ class PubmedImporter(EntityImporter): # that there may be multiple ReferenceList (eg, sometimes one per # Reference) for ref in pubmed.find_all("Reference"): - ref_extra = dict() + ref_extra: Dict[str, Any] = dict() ref_doi = ref.find("ArticleId", IdType="doi") if ref_doi: ref_doi = clean_doi(ref_doi.string) @@ -740,7 +747,7 @@ class PubmedImporter(EntityImporter): ) return re - def try_update(self, re): + def try_update(self, re: ReleaseEntity) -> bool: # first, lookup existing by PMID (which must be defined) existing = None @@ -831,7 +838,7 @@ class PubmedImporter(EntityImporter): return True - def insert_batch(self, batch): + def insert_batch(self, batch: List[ReleaseEntity]) -> None: self.api.create_release_auto_batch( fatcat_openapi_client.ReleaseAutoBatch( editgroup=fatcat_openapi_client.Editgroup( @@ -841,7 +848,7 @@ class PubmedImporter(EntityImporter): ) ) - def parse_file(self, handle): + def parse_file(self, handle: Any) -> None: # 1. open with beautiful soup soup = BeautifulSoup(handle, "xml") |