Use correct files for basic phenotypes data. Add notes to self.

The basic phenotype data will be in files under the key
"gn-metadata" -> "pheno". We support the possibility of having some
descriptions in the "phenocovar" files, since that can happen also.

1 files changed, 11 insertions, 5 deletions

diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py
index d31ade6..533b0e3 100644
--- a/scripts/load_phenotypes_to_db.py
+++ b/scripts/load_phenotypes_to_db.py
@@ -49,21 +49,27 @@ def save_phenotypes(
     """Read `phenofiles` and save the phenotypes therein."""
     logger.info("Saving new phenotypes.")
     logger.debug("Processing %s 'pheno' files.", len(phenofiles))
-    phenofiles = control_data["pheno"]
+    ## TODO: Replace with something like this: ##
+    # phenofiles = control_data["phenocovar"] + control_data.get(
+    #     "gn-metadata", {}).get("pheno", [])
+    #
+    # This is meant to load (and merge) data from the "phenocovar" and
+    # "gn-metadata -> pheno" files into a single collection of phenotypes.
+    phenofiles = control_data["phenocovar"]
     if len(phenofiles) <= 0:
         return tuple()
 
-    if control_data["pheno_transposed"]:
+    if control_data["phenocovar_transposed"]:
         logger.info("Undoing transposition of the files rows and columns.")
         phenofiles = (
             transpose_csv_with_rename(
                 _file
                 build_line_splitter(control_data)
                 build_line_joiner(control_data))
-            for _file in control_data["pheno"])
+            for _file in control_data["phenocovar"])
 
-    _headers = rqtl2.read_csv_file_headers(control_data["pheno"][0],
-                                           control_data["pheno_transposed"],
+    _headers = rqtl2.read_csv_file_headers(control_data["phenocovar"][0],
+                                           control_data["phenocovar_transposed"],
                                            control_data["sep"],
                                            control_data["comment.char"])
     return create_new_phenotypes(