6 files changed, 134 insertions, 0 deletions
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
new file mode 100644
index 0000000..f666f40
--- /dev/null
+++ b/r_qtl/r_qtl2_qc.py
@@ -0,0 +1,47 @@
+"""Quality control checks for R/qtl2 data bundles."""
+from zipfile import ZipFile
+from functools import reduce
+from typing import Union, Sequence
+
+from r_qtl import r_qtl2 as rqtl2
+from r_qtl.r_qtl2 import __FILE_TYPES__
+
+def bundle_files_list(zfile, cdata: dict) -> tuple[str]:
+    """Retrieve files listed in control file."""
+    def __merge__(alist: tuple[str, ...], member: Union[str, Sequence[str]]) -> tuple[str, ...]:
+        if isinstance(cdata[member], str):
+            return alist + (cdata[member],)
+        return alist + tuple(cdata[member])
+
+    fileslist = tuple()
+    fileslist = reduce(__merge__,
+                       (key for key in cdata.keys() if key in __FILE_TYPES__),
+                       tuple())
+
+    if "file" in cdata.get("sex", {}):
+        sexfile = cdata["sex"]["file"]
+        fileslist = fileslist + (
+            (sexfile,) if isinstance(sexfile, str) else tuple(sexfile))
+        
+    if "file" in cdata.get("cross_info", {}):
+        crossinfofile = cdata["cross_info"]["file"]
+        fileslist = fileslist + (
+            (crossinfofile,) if isinstance(crossinfofile, str)
+            else tuple(crossinfofile))
+
+    return fileslist
+
+def missing_files(zfile: ZipFile) -> tuple[str]:
+    """
+    Retrieve a list of files listed in the control file that do not exist in the
+    bundle.
+    """
+    def __missing_p__(thefile):
+        try:
+            zfile.getinfo(thefile)
+            return False
+        except KeyError:
+            return True
+
+    return tuple(filter(__missing_p__,
+                        bundle_files_list(zfile, rqtl2.control_data(zfile))))
diff --git a/tests/r_qtl/test_files/allfilesmissing_listmembers.zip b/tests/r_qtl/test_files/allfilesmissing_listmembers.zip
new file mode 100644
index 0000000..8cdbe07
--- /dev/null
+++ b/tests/r_qtl/test_files/allfilesmissing_listmembers.zip
diff --git a/tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip b/tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip
new file mode 100644
index 0000000..9278440
--- /dev/null
+++ b/tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip
diff --git a/tests/r_qtl/test_files/allfilesmissing_stringmembers.zip b/tests/r_qtl/test_files/allfilesmissing_stringmembers.zip
new file mode 100644
index 0000000..2b356ec
--- /dev/null
+++ b/tests/r_qtl/test_files/allfilesmissing_stringmembers.zip
diff --git a/tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip b/tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip
new file mode 100644
index 0000000..b9320fc
--- /dev/null
+++ b/tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
new file mode 100644
index 0000000..5fcccf5
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -0,0 +1,87 @@
+"""Test that the QC functions work as expected"""
+from pathlib import Path
+
+import pytest
+from zipfile import ZipFile
+
+from r_qtl import r_qtl2 as rqtl2
+from r_qtl import r_qtl2_qc as qc
+
+###### DO NOT COMMIT THIS ######
+from quality_control.debug import __pk__
+###### END: DO NOT COMMIT THIS ######
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,expected",
+    (("tests/r_qtl/test_files/empty_control_file_yaml.zip",
+      tuple()),
+     ("tests/r_qtl/test_files/empty_control_file_json.zip",
+      tuple()),
+     ("tests/r_qtl/test_files/allfilesmissing_stringmembers.zip",
+      ("geno.csv", "fgeno.csv", "pheno.csv", "covar.csv", "phenocovar.csv",
+       "gmap.csv", "pmap.csv", "phenose.csv", "sex.csv", "crossinfo.csv")),
+     ("tests/r_qtl/test_files/allfilesmissing_listmembers.zip",
+      ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
+       "pheno01.csv", "pheno02.csv", "covar01.csv", "covar02.csv",
+       "phenocovar01.csv", "phenocovar02.csv", "phenocovar03.csv",
+       "phenocovar04.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv",
+       "phenose01.csv", "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
+       "crossinfo01.csv", "crossinfo02.csv")),
+     ("tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip",
+      ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
+       "pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv",
+       "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv",
+       "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
+       "crossinfo.csv")),
+     ("tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip",
+      ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
+       "pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv",
+       "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv",
+       "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
+       "crossinfo.csv"))))
+def test_bundle_files_list(filepath, expected):
+    """
+    GIVEN: R/qtl2 bundle with a control file listing files
+    WHEN: `bundle_files_list` is called on the bundle
+    THEN: verify that ALL files listed in the control file are returned.
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        assert qc.bundle_files_list(
+            zfile, rqtl2.control_data(zfile)) == expected
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,expected",
+    (("tests/r_qtl/test_files/empty_control_file_yaml.zip",
+      tuple()),
+     ("tests/r_qtl/test_files/empty_control_file_json.zip",
+      tuple()),
+     ("tests/r_qtl/test_files/allfilesmissing_stringmembers.zip",
+      ("geno.csv", "fgeno.csv", "pheno.csv", "covar.csv", "phenocovar.csv",
+       "gmap.csv", "pmap.csv", "phenose.csv", "sex.csv", "crossinfo.csv")),
+     ("tests/r_qtl/test_files/allfilesmissing_listmembers.zip",
+      ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
+       "pheno01.csv", "pheno02.csv", "covar01.csv", "covar02.csv",
+       "phenocovar01.csv", "phenocovar02.csv", "phenocovar03.csv",
+       "phenocovar04.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv",
+       "phenose01.csv", "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
+       "crossinfo01.csv", "crossinfo02.csv")),
+     ("tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip",
+      ("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
+       "pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv",
+       "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv",
+       "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
+       "crossinfo.csv")),
+     ("tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip",
+      ("fgeno01.csv", "covar.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv",
+       "pmap02.csv", "phenose02.csv", "sex03.csv", "crossinfo.csv"))))
+def test_missing_files(filepath, expected):
+    """
+    GIVEN: R/qtl2 bundle with a control file listing files
+    WHEN: `missing_files` is called on the bundle
+    THEN: verify that ALL files listed in the control file, that do not actually
+        exist in the bundle are returned.
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        assert qc.missing_files(zfile) == expected