From e5bcdbc83031c10092f1405b847695ecefbada44 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Tue, 24 Jan 2023 18:17:57 +0000
Subject: search: Abstract out parsing of position spec into separate function.

* gn3/api/search.py (parse_position): New function.
(parse_location_field): Use parse_position.
* tests/unit/test_search.py: Import parse_position from gn3.api.search.
(test_parse_position_close_to_zero_location): New test.
---
 gn3/api/search.py | 27 ++++++++++++++++-----------
 1 file changed, 16 insertions(+), 11 deletions(-)

(limited to 'gn3/api')

diff --git a/gn3/api/search.py b/gn3/api/search.py
index 0d3f9ba..e497743 100644
--- a/gn3/api/search.py
+++ b/gn3/api/search.py
@@ -135,6 +135,19 @@ def apply_si_suffix(location: str) -> int:
         return int(location)
 
 
+def parse_position(spec: str) -> tuple[Maybe[int], Maybe[int]]:
+    """Parse position specifiation converting point locations to ranges."""
+    # Range
+    if ".." in spec:
+        return tuple(limit.map(apply_si_suffix) # type: ignore
+                     for limit in parse_range(spec))
+    # If point location, assume +/- 50 kbases on either side.
+    else:
+        width = 50*10**3
+        point = apply_si_suffix(spec)
+        return Just(max(0, point - width)), Just(point + width)
+
+
 def parse_location_field(species_query: xapian.Query,
                          chromosome_prefix: str, location_slot: int,
                          liftover_function: IntervalLiftoverFunction,
@@ -146,19 +159,11 @@ def parse_location_field(species_query: xapian.Query,
     """
     def split_query(query: str) -> ChromosomalInterval:
         """Split query into chromosome and location tuple."""
-        chromosome, location_str = query.lower().split(":")
+        chromosome, position_spec = query.lower().split(":")
         if not chromosome.startswith("chr"):
             raise ValueError
-        location: tuple[Maybe[int], Maybe[int]]
-        if ".." in location_str:
-            location = tuple(limit.map(apply_si_suffix) # type: ignore
-                             for limit in parse_range(location_str))
-        # If point location, assume +/- 50 kbases on either side.
-        else:
-            width = 50*10**3
-            point = apply_si_suffix(location_str)
-            location = Just(max(0, point - width)), Just(point + width)
-        return ChromosomalInterval(chromosome.removeprefix("chr"), *location)
+        return ChromosomalInterval(chromosome.removeprefix("chr"),
+                                   *parse_position(position_spec))
 
     def make_query(interval: ChromosomalInterval) -> xapian.Query:
         # TODO: Convert the xapian index to use bases instead of megabases.
-- 
cgit v1.2.3