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from typing import Iterable, Optional
import csv
from chocula.util import clean_str
from chocula.common import DirectoryLoader
from chocula.database import DirectoryInfo
class EntrezLoader(DirectoryLoader):
"""
CSV Columns:
- JrId
- JournalTitle
- MedAbbr
- "ISSN (Print)"
- "ISSN (Online)"
- IsoAbbr
- NlmId
"""
source_slug = "entrez"
def open_file(self) -> Iterable:
return csv.DictReader(open(self.config.entrez_simple.filepath))
def parse_record(self, record) -> Optional[DirectoryInfo]:
if not (record.get("ISSN (Online)") or record.get("ISSN (Print)")):
return None
return DirectoryInfo(
directory_slug=self.source_slug,
issne=record.get("ISSN (Online)"),
issnp=record.get("ISSN (Print)"),
custom_id=record.get("NlmId").strip() or None,
name=clean_str(record.get("JournalTitle")),
abbrev=clean_str(record["IsoAbbr"]),
)
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