Raise exception on reading non-existing file

The validation checks ensure that whatever files are listed in the
control file exist in the zip file bundle. It is still possible,
however, that the code tries to read a file that does not exist in the
file and is not listed in the control file. In those cases, raise the
appropriate exception.

3 files changed, 48 insertions, 16 deletions

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index a8958a0..d3a3805 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -189,23 +189,26 @@ def file_data(zfile: ZipFile,
                   [str, tuple[str, ...], tuple[str, ...]],
                   tuple[dict, ...]] = __default_process_value_transposed__) -> Iterator[dict]:
     """Load data from files in R/qtl2 zip bundle."""
-    if isinstance(cdata[member_key], list):
-        for row in (line for lines in
-                    (file_data(
-                        zfile, member_key, {**cdata, member_key: innerfile},
-                        process_value, process_transposed_value)
-                     for innerfile in cdata[member_key])
-                    for line in lines):
-            yield row
-        return
-    if not cdata.get(f"{member_key}_transposed", False):
-        for row in with_non_transposed(zfile, member_key, cdata, process_value):
-            yield row
-        return
+    try:
+        if isinstance(cdata[member_key], list):
+            for row in (line for lines in
+                        (file_data(
+                            zfile, member_key, {**cdata, member_key: innerfile},
+                            process_value, process_transposed_value)
+                         for innerfile in cdata[member_key])
+                        for line in lines):
+                yield row
+            return
+        if not cdata.get(f"{member_key}_transposed", False):
+            for row in with_non_transposed(zfile, member_key, cdata, process_value):
+                yield row
+            return
 
-    for row in with_transposed(
-            zfile, member_key, cdata, process_transposed_value):
-        yield row
+        for row in with_transposed(
+                zfile, member_key, cdata, process_transposed_value):
+            yield row
+    except KeyError as exc:
+        raise InvalidFormat(*exc.args) from exc
 
 def cross_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
     """Load cross information where present."""
diff --git a/tests/r_qtl/test_files/nonexistent.zip b/tests/r_qtl/test_files/nonexistent.zip
new file mode 100644
index 0000000..4a31bf1
--- /dev/null
+++ b/tests/r_qtl/test_files/nonexistent.zip
diff --git a/tests/r_qtl/test_r_qtl2_nonexistent_file.py b/tests/r_qtl/test_r_qtl2_nonexistent_file.py
new file mode 100644
index 0000000..c783a76
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_nonexistent_file.py
@@ -0,0 +1,29 @@
+"""Test accessing nonexistent member."""
+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,memberkey",
+    (("tests/r_qtl/test_files/nonexistent.zip", "geno"),
+     ("tests/r_qtl/test_files/nonexistent.zip", "founder_geno"),
+     ("tests/r_qtl/test_files/nonexistent.zip", "pheno"),
+     ("tests/r_qtl/test_files/nonexistent.zip", "covar"),
+     ("tests/r_qtl/test_files/nonexistent.zip", "phenocovar"),
+     ("tests/r_qtl/test_files/nonexistent.zip", "gmap"),
+     ("tests/r_qtl/test_files/nonexistent.zip", "pmap")))
+def test_loading_nonexistent_file(filepath, memberkey):
+    """
+    GIVEN: A zipfile with a valid control file, but some files mentioned in the
+        control file do not exist in the zipfile
+    WHEN: access is made to such missing files
+    THEN: raise an exception
+    """
+    with (ZipFile(Path(filepath).absolute(), "r") as zfile,
+          pytest.raises(rqtl2.InvalidFormat)):
+        cdata = rqtl2.control_data(zfile)
+        tuple(rqtl2.file_data(zfile, memberkey, cdata))