fix: caches must be named differently

backend/src/api/similar.py

@@ -13,13 +13,13 @@
 def get_similar_pdb(protein_name: str):
  query_name = pdb_file_name(protein_name)
  PDB = create_db("PDB", "pdb")
- similar = easy_search(query_name, PDB, out_format=["target", "prob"])
+ similar = easy_search(query_name, PDB, out_format="target,prob")
  return [SimilarProtein(name=s[0].split(".")[0], prob=s[1]) for s in similar]
 
 
 @router.get("/similar-venome/{protein_name:str}", response_model=list[SimilarProtein])
 def get_similar_venome(protein_name: str):
  query_name = pdb_file_name(protein_name)
  target_folder = "src/data/pdbAlphaFold/"
- similar = easy_search(query_name, target_folder, out_format=["target", "prob"])
+ similar = easy_search(query_name, target_folder, out_format="target,prob")
  return [SimilarProtein(name=revert_pdb_filename(s[0]), prob=s[1]) for s in similar]

backend/src/foldseek.py

@@ -1,5 +1,6 @@
 import subprocess
 import logging as log
+from functools import lru_cache
 
 EXTERNAL_DATABASES = [
  "Alphafold/UniProt",
@@ -15,6 +16,22 @@ def bash_cmd(cmd: str | list[str]) -> str:
  return subprocess.check_output(cmd, shell=True).decode()
 
 
+active_caches = 0
+
+
+class GenerateDirName:
+ def __enter__(self):
+ global active_caches
+ active_caches += 1
+ self.temp_dir = ".foldseek_cache_" + str(active_caches)
+ return self.temp_dir
+
+ def __exit__(self, *args):
+ global active_caches
+ active_caches -= 1
+ bash_cmd("rm -rf " + self.temp_dir)
+
+
 def to_columnar_array(arr: list[list]) -> list[list]:
  columnar = []
  for i in range(len(arr[0])):
@@ -42,12 +59,11 @@ def parse_output(filepath: str) -> list[list]:
  return parsed_lines
 
 
+@lru_cache(maxsize=32)
 def easy_search(
  query: str,
  target: str,
- out_format: list[str] = ["query", "target", "prob"],
- out_file=".foldseek_cache/output",
- temp_dir=".foldseek_cache",
+ out_format: str = "query, target, prob",
  print_stdout=False,
  foldseek_executable="./foldseek/bin/foldseek",
  columnar=False,
@@ -58,23 +74,23 @@ def easy_search(
  Returns:
  list[list]: a list of the matches from the search
  """
+ with GenerateDirName() as temp_dir:
+ out_file = temp_dir + "/output"
+
+ # Then call the easy-search
+ flags = f"--format-output {out_format}" if out_format else ""
+ cmd = f"{foldseek_executable} easy-search {query} {target} {out_file} {temp_dir} {flags}"
+ try:
+ stdout = bash_cmd(cmd)
+ except Exception as e:
+ log.warn(e)
+ return []
 
- # Then call the easy-search
- flags = f"--format-output {','.join(out_format)}" if len(out_format) > 0 else ""
- cmd = f"{foldseek_executable} easy-search {query} {target} {out_file} {temp_dir} {flags}"
- try:
- stdout = bash_cmd(cmd)
- except Exception as e:
- log.warn(e)
- return []
-
- if print_stdout:
- log.warn(stdout)
+ if print_stdout:
+ log.warn(stdout)
 
- if columnar:
- return to_columnar_array(parse_output(out_file))
- else:
- return parse_output(out_file)
+ parsed_output = parse_output(out_file)
+ return to_columnar_array(parsed_output) if columnar else parsed_output
 
 
 def create_db(
@@ -112,6 +128,5 @@ def create_db(
  output = easy_search(
  query=test_targets,
  target=test_targets,
- out_format=["query", "target", "prob"],
  )
  print(output)