Provide the key for each file listed in the control file.

1 files changed, 65 insertions, 33 deletions

diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
index 554cfc4..d12172e 100644
--- a/tests/r_qtl/test_r_qtl2_qc.py
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -18,27 +18,44 @@ from quality_control.errors import InvalidValue
      ("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")),
+      (("geno", "geno.csv"), ("founder_geno", "fgeno.csv"),
+       ("pheno", "pheno.csv"), ("covar", "covar.csv"),
+       ("phenocovar", "phenocovar.csv"), ("gmap", "gmap.csv"),
+       ("pmap", "pmap.csv"), ("phenose", "phenose.csv"),
+       ("sex.file", "sex.csv"), ("cross_info.file", "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")),
+      (("geno", "geno01.csv"), ("geno", "geno02.csv"),
+       ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"),
+       ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"),
+       ("pheno", "pheno02.csv"), ("covar", "covar01.csv"),
+       ("covar", "covar02.csv"), ("phenocovar", "phenocovar01.csv"),
+       ("phenocovar", "phenocovar02.csv"), ("phenocovar", "phenocovar03.csv"),
+       ("phenocovar", "phenocovar04.csv"), ("gmap", "gmap01.csv"),
+       ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"),
+       ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"),
+       ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"),
+       ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo01.csv"),
+       ("cross_info.file", "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")),
+      (("geno", "geno01.csv"), ("geno", "geno02.csv"),
+       ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"),
+       ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"),
+       ("pheno", "pheno02.csv"), ("covar", "covar.csv"),
+       ("phenocovar", "phenocovar.csv"), ("gmap", "gmap01.csv"),
+       ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"),
+       ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"),
+       ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"),
+       ("sex.file", "sex03.csv"), ("cross_info.file", "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"))))
+      (("geno", "geno01.csv"), ("geno", "geno02.csv"),
+       ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"),
+       ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"),
+       ("pheno", "pheno02.csv"), ("covar", "covar.csv"),
+       ("phenocovar", "phenocovar.csv"), ("gmap", "gmap01.csv"),
+       ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"),
+       ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"),
+       ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"),
+       ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo.csv")))))
 def test_bundle_files_list(filepath, expected):
     """
     GIVEN: R/qtl2 bundle with a control file listing files
@@ -56,24 +73,39 @@ def test_bundle_files_list(filepath, expected):
      ("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")),
+      (("geno", "geno.csv"), ("founder_geno", "fgeno.csv"),
+       ("pheno", "pheno.csv"), ("covar", "covar.csv"),
+       ("phenocovar", "phenocovar.csv"), ("gmap", "gmap.csv"),
+       ("pmap", "pmap.csv"), ("phenose", "phenose.csv"),
+       ("sex.file", "sex.csv"), ("cross_info.file", "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")),
+      (("geno", "geno01.csv"), ("geno", "geno02.csv"),
+       ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"),
+       ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"),
+       ("pheno", "pheno02.csv"), ("covar", "covar01.csv"),
+       ("covar", "covar02.csv"), ("phenocovar", "phenocovar01.csv"),
+       ("phenocovar", "phenocovar02.csv"), ("phenocovar", "phenocovar03.csv"),
+       ("phenocovar", "phenocovar04.csv"), ("gmap", "gmap01.csv"),
+       ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"),
+       ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"),
+       ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"),
+       ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo01.csv"),
+       ("cross_info.file", "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")),
+      (("geno", "geno01.csv"), ("geno", "geno02.csv"),
+       ("founder_geno", "fgeno01.csv"), ("founder_geno", "fgeno02.csv"),
+       ("founder_geno", "fgeno03.csv"), ("pheno", "pheno01.csv"),
+       ("pheno", "pheno02.csv"), ("covar", "covar.csv"),
+       ("phenocovar", "phenocovar.csv"), ("gmap", "gmap01.csv"),
+       ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"), ("pmap", "pmap02.csv"),
+       ("phenose", "phenose01.csv"), ("phenose", "phenose02.csv"),
+       ("sex.file", "sex01.csv"), ("sex.file", "sex02.csv"),
+       ("sex.file", "sex03.csv"), ("cross_info.file", "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"))))
+      (("founder_geno", "fgeno01.csv"), ("covar", "covar.csv"),
+       ("gmap", "gmap01.csv"), ("gmap", "gmap02.csv"), ("pmap", "pmap01.csv"),
+       ("pmap", "pmap02.csv"), ("phenose", "phenose02.csv"),
+       ("sex.file", "sex03.csv"), ("cross_info.file", "crossinfo.csv")))))
 def test_missing_files(filepath, expected):
     """
     GIVEN: R/qtl2 bundle with a control file listing files