Repository: Sage-Bionetworks/Genie

Issue:
Modify error message for maf.py check
for _check_tsa1_tsa2 in maf.py, modify error message.

https://github.com/Sage-Bionetworks/Genie/blob/develop/genie_registry/maf.py#L25

Instead of

> The values in TUMOR_SEQ_ALLELE1 must be the same as all the values in REFERENCE_ALLELE OR TUMOR_SEQ_ALLELE2

maybe

> All values  in TUMOR_SEQ_ALLELE1 must match all values in REFERENCE_ALLELE or all values in TUMOR_SEQ_ALLELE2

Discussion:

Patch:
diff --git a/genie_registry/maf.py b/genie_registry/maf.py
index f4dae91..714233a 100644
--- a/genie_registry/maf.py
+++ b/genie_registry/maf.py
@@ -25,8 +25,8 @@ def _check_tsa1_tsa2(df):
             error = (
                 "maf: Contains both "
                 "TUMOR_SEQ_ALLELE1 and TUMOR_SEQ_ALLELE2 columns. "
-                "The values in TUMOR_SEQ_ALLELE1 must be the same as "
-                "all the values in REFERENCE_ALELLE OR TUMOR_SEQ_ALLELE2."
+                "All values in TUMOR_SEQ_ALLELE1 must match all values in "
+                "REFERENCE_ALLELE or all values in TUMOR_SEQ_ALLELE2.\n"
             )
     return error
 


Test patch:
diff --git a/tests/test_maf.py b/tests/test_maf.py
index edc9105..75bcecd 100644
--- a/tests/test_maf.py
+++ b/tests/test_maf.py
@@ -211,8 +211,8 @@ def test_invalid__check_tsa1_tsa2():
     assert error == (
         "maf: Contains both "
         "TUMOR_SEQ_ALLELE1 and TUMOR_SEQ_ALLELE2 columns. "
-        "The values in TUMOR_SEQ_ALLELE1 must be the same as "
-        "all the values in REFERENCE_ALELLE OR TUMOR_SEQ_ALLELE2."
+        "All values in TUMOR_SEQ_ALLELE1 must match all values in "
+        "REFERENCE_ALLELE or all values in TUMOR_SEQ_ALLELE2.\n"
     )