Merge pull request #100 from Clinical-Genomics-Lund/99-prp-crashed-if…

…-mlst-type-was-not-called

Fixed that MLST results without called alleles crashed PRP

CHANGELOG.md

@@ -4,6 +4,12 @@
 
 ### Fixed
 
+- Fixed issue where mlst results with no calls crashed PRP.
+
+### Changed
+
+- Added mypy as test dependency
+
 ### Changed
 
 ## [0.11.1]

prp/parse/typing.py

@@ -43,14 +43,17 @@ def parse_mlst_results(mlst_fpath: str) -> TypingResultMlst:
     LOG.info("Parsing mlst results")
     with open(mlst_fpath, "r", encoding="utf-8") as jsonfile:
         result = json.load(jsonfile)[0]
+        # get raw allele info
+        alleles = {} if result.get("alleles") is None else result["alleles"]
+        # create typing result object
         result_obj = TypingResultMlst(
             scheme=result["scheme"],
             sequence_type=(
                 None if result["sequence_type"] == "-" else result["sequence_type"]
             ),
             alleles={
                 gene: _process_allele_call(allele)
-                for gene, allele in result["alleles"].items()
+                for gene, allele in alleles.items()
             },
         )
     return MethodIndex(

pyproject.toml

@@ -46,6 +46,7 @@ dev = [
 ]
 test = [
     "pytest-cov ~=4.1.0",
+    "mypy == 1.13.0"
 ]
 
 [build-system]

tests/fixtures/__init__.py

@@ -5,3 +5,8 @@
 from .saureus import *
 from .shigella import *
 from .streptococcus import *
+
+@pytest.fixture()
+def mlst_result_path_no_call(data_path):
+    """Get path for mlst file where alleles was not called."""
+    return str(data_path.joinpath("mlst.nocall.json"))

tests/fixtures/mlst.nocall.json

@@ -0,0 +1,9 @@
+[
+   {
+      "sequence_type" : "-",
+      "scheme" : "-",
+      "alleles" : null,
+      "id" : "unique_file_id",
+      "filename" : "assembly_file_name.fasta"
+   }
+]

tests/parse/test_typing.py

@@ -2,7 +2,7 @@
 
 import pytest
 import logging
-from prp.parse.typing import replace_cgmlst_errors
+from prp.parse.typing import replace_cgmlst_errors, parse_mlst_results
 from prp.models.typing import ChewbbacaErrors
 
 # build test cases for handeling chewbacca allele caller errors and annotations
@@ -84,4 +84,28 @@ def test_replace_cgmlst_errors_warnings(caplog):
     # run test that a warning was triggered if input is unknown string
     allele = "A_STRANGE_STRING"
     replace_cgmlst_errors(allele, include_novel_alleles=True, correct_alleles=True)
-    assert allele in caplog.text
+    assert allele in caplog.text
+
+
+def test_parse_mlst_result(ecoli_mlst_path):
+    """Test parsing of MLST result file."""
+    # FIRST run result parser
+    res_obj = parse_mlst_results(ecoli_mlst_path)
+
+    # THEN verify result type
+    assert res_obj.type == 'mlst'
+    # THEN verify software
+    assert res_obj.software == 'mlst'
+    # THEN verify sequence type and allele assignment
+    assert res_obj.result.sequence_type == 58
+    assert len(res_obj.result.alleles) == 8
+
+
+def test_parse_mlst_result_w_no_call(mlst_result_path_no_call):
+    """Test parsing of MLST results file where the alleles was not called."""
+    # FIRST run result parser
+    res_obj = parse_mlst_results(mlst_result_path_no_call)
+
+    # THEN verify that sequence type is None
+    assert res_obj.result.sequence_type is None
+    assert len(res_obj.result.alleles) == 0