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from gn2.base import data_set
from gn2.base.trait import create_trait
from gn2.base.species import TheSpecies
from gn2.utility import hmac
from gn2.utility.tools import get_setting
from gn2.wqflask.database import database_connection
def clean_xapian_query(query: str) -> str:
"""
Clean and optimize a Xapian query string by removing filler words,
and ensuring the query is tailored for optimal results from Fahamu.
Args:
query (str): The original Xapian query string.
Returns:
str: The cleaned and optimized query string.
"""
xapian_prefixes = {
"author",
"species",
"group",
"tissue",
"dataset",
"symbol",
"description",
"rif",
"wiki",
}
xapian_operators = {"AND", "NOT", "OR", "XOR", "NEAR", "ADJ"}
range_prefixes = {"mean", "peak", "position", "peakmb", "additive", "year"}
query_context = ["genes"]
cleaned_query_parts = []
for token in query.split():
if token in xapian_operators:
continue
prefix, _, suffix = token.partition(":")
if ".." in suffix and prefix in range_prefixes:
continue
if prefix in xapian_prefixes:
query_context.insert(0, prefix)
cleaned_query_parts.append(f"{prefix} {suffix}")
else:
cleaned_query_parts.append(prefix)
cleaned_query = " ".join(cleaned_query_parts)
context = ",".join(query_context)
return f"Provide answer on {cleaned_query} context {context}"
def get_species_dataset_trait(self, start_vars):
if "temp_trait" in list(start_vars.keys()):
if start_vars['temp_trait'] == "True":
self.dataset = data_set.create_dataset(
dataset_name="Temp",
dataset_type="Temp",
group_name=start_vars['group'])
else:
self.dataset = data_set.create_dataset(start_vars['dataset'])
else:
self.dataset = data_set.create_dataset(start_vars['dataset'])
self.species = TheSpecies(dataset=self.dataset)
self.this_trait = create_trait(dataset=self.dataset,
name=start_vars['trait_id'],
cellid=None,
get_qtl_info=True)
def get_trait_db_obs(self, trait_db_list):
if isinstance(trait_db_list, str):
trait_db_list = trait_db_list.split(",")
self.trait_list = []
for trait in trait_db_list:
data, _separator, hmac_string = trait.rpartition(':')
data = data.strip()
assert hmac_string == hmac.hmac_creation(data), "Data tampering?"
trait_name, dataset_name = data.split(":")[:2]
if dataset_name == "Temp":
dataset_ob = data_set.create_dataset(
dataset_name=dataset_name, dataset_type="Temp",
group_name=trait_name.split("_")[2])
else:
dataset_ob = data_set.create_dataset(dataset_name)
trait_ob = create_trait(dataset=dataset_ob,
name=trait_name,
cellid=None)
if trait_ob:
self.trait_list.append((trait_ob, dataset_ob))
def get_species_groups():
"""Group each species into a group"""
_menu = {}
species, group_name = None, None
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
cursor.execute(
"SELECT s.MenuName, i.InbredSetName FROM InbredSet i "
"INNER JOIN Species s ON s.SpeciesId = i.SpeciesId "
"ORDER BY i.SpeciesId ASC, i.Name ASC"
)
for species, group_name in cursor.fetchall():
if species in _menu:
if _menu.get(species):
_menu = _menu[species].append(group_name)
else:
_menu[species] = [group_name]
return [{"species": key,
"groups": value} for key, value in
list(_menu.items())]
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