From 635cf832f4717da6e8e7ef273a675a4ceea42ed0 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 5 Feb 2024 06:08:19 +0300
Subject: Retrieve list of all files, and list of missing files

Add QC a function to list all files listed in the control file, and
another to list only the files missing from the bundle.
---
 .../test_files/allfilesmissing_listmembers.zip     | Bin 0 -> 429 bytes
 .../test_files/allfilesmissing_mixedmembers.zip    | Bin 0 -> 413 bytes
 .../test_files/allfilesmissing_stringmembers.zip   | Bin 0 -> 370 bytes
 .../test_files/somefilesmissing_mixedmembers.zip   | Bin 0 -> 1913 bytes
 tests/r_qtl/test_r_qtl2_qc.py                      |  87 +++++++++++++++++++++
 5 files changed, 87 insertions(+)
 create mode 100644 tests/r_qtl/test_files/allfilesmissing_listmembers.zip
 create mode 100644 tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip
 create mode 100644 tests/r_qtl/test_files/allfilesmissing_stringmembers.zip
 create mode 100644 tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip
 create mode 100644 tests/r_qtl/test_r_qtl2_qc.py

(limited to 'tests')

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
Binary files /dev/null and b/tests/r_qtl/test_files/allfilesmissing_listmembers.zip differ
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
Binary files /dev/null and b/tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip differ
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
Binary files /dev/null and b/tests/r_qtl/test_files/allfilesmissing_stringmembers.zip differ
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
Binary files /dev/null and b/tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip differ
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
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