aboutsummaryrefslogtreecommitdiff
path: root/gn2/utility/helper_functions.py
diff options
context:
space:
mode:
Diffstat (limited to 'gn2/utility/helper_functions.py')
-rw-r--r--gn2/utility/helper_functions.py45
1 files changed, 45 insertions, 0 deletions
diff --git a/gn2/utility/helper_functions.py b/gn2/utility/helper_functions.py
index fc101959..8c35df5f 100644
--- a/gn2/utility/helper_functions.py
+++ b/gn2/utility/helper_functions.py
@@ -8,6 +8,51 @@ 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":