Test parsing of multiple files for single key

1 files changed, 57 insertions, 0 deletions

diff --git a/tests/r_qtl/test_r_qtl2_parse_multiple.py b/tests/r_qtl/test_r_qtl2_parse_multiple.py
new file mode 100644
index 0000000..c4c8ccb
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_parse_multiple.py
@@ -0,0 +1,57 @@
+"""Test the parsing of the R/qtl2 bundles with multiple values for file keys."""
+from pathlib import Path
+
+import pytest
+from zipfile import ZipFile
+
+from r_qtl import r_qtl2 as rqtl2
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,filekey,expected",
+    (("tests/r_qtl/test_files/test_geno_multiple.zip",
+      "geno",
+      ({
+          "id": "1", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1,
+          "EC.66C": 1
+      }, {
+          "id": "2", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1,
+          "EC.66C": 1
+      }, {
+          "id": "3", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": None,
+          "EC.480C": 1, "EC.66C": 1
+      }, {
+          "id": "4", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1,
+          "EC.66C": 1
+      }, {
+          "id": "5", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2,
+          "EC.66C": 2
+      }, {
+          "id": "6", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2,
+          "EC.66C": 2
+      }, {
+          "id": "7", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1,
+          "EC.66C": 1
+      }, {
+          "id": "8", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 1,
+          "EC.66C": 1
+      }, {
+          "id": "9", "PVV4": None, "AXR-1": 2, "HH.335C-Col/PhyA": 2,
+          "EC.480C": 2, "EC.66C": 2
+      }, {
+          "id": "10", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2,
+          "EC.66C": 2
+      })),))
+def test_parse_multiple_files(filepath, filekey, expected):
+    """Test parsing of files from R/qtl2 bundle where file keys have multiple values.
+
+    GIVEN: Path to a zip file with R/qtl2 data
+    WHEN: we parse the geno file
+    THEN: ensure that the data we get is as expected
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        cdata = rqtl2.control_data(zfile)
+        process_fns = (rqtl2.make_process_data_geno(cdata)
+                       if filekey == "geno" else tuple())
+        assert tuple(rqtl2.file_data(
+            zfile, filekey, cdata, *process_fns)) == expected