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"""Helper functions to access wiki entries"""
from typing import List
class MissingDBDataException(Exception):
"""Error due to DB missing some data"""
def get_species_id(cursor, species_name: str) -> int:
"""Find species id given species `Name`"""
cursor.execute("SELECT SpeciesID from Species WHERE Name = %s", (species_name,))
species_ids = cursor.fetchall()
if len(species_ids) != 1:
raise MissingDBDataException(
f"expected 1 species with Name={species_name} but found {len(species_ids)}!"
)
return species_ids[0][0]
def get_next_comment_version(cursor, comment_id: int) -> int:
"""Find the version to add, usually latest_version + 1"""
cursor.execute(
"SELECT MAX(versionId) as version_id from GeneRIF WHERE Id = %s", (comment_id,)
)
latest_version = cursor.fetchone()[0]
if latest_version is None:
raise MissingDBDataException(f"No comment found with comment_id={comment_id}")
return latest_version + 1
def get_categories_ids(cursor, categories: List[str]) -> List[int]:
"""Get the categories_ids from a list of category strings"""
cursor.execute("SELECT Name, Id from GeneCategory")
raw_categories = cursor.fetchall()
dict_cats = dict(raw_categories)
category_ids = []
for category in set(categories):
cat_id = dict_cats.get(category.strip())
if cat_id is None:
raise MissingDBDataException(f"Category with Name={category} not found")
category_ids.append(cat_id)
return category_ids
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