From 945241acc1def22043b1bfba33da2599688ccbea Mon Sep 17 00:00:00 2001
From: Travis Thompson <ptth222@uky.edu>
Date: Wed, 20 Mar 2024 01:04:24 -0400
Subject: [PATCH] Deleted previously commented out code

---
 isatools/isatab/utils.py  | 26 --------------------------
 isatools/model/process.py | 12 ------------
 2 files changed, 38 deletions(-)

diff --git a/isatools/isatab/utils.py b/isatools/isatab/utils.py
index e769925b..ed06f6af 100644
--- a/isatools/isatab/utils.py
+++ b/isatools/isatab/utils.py
@@ -515,32 +515,6 @@ def get_object_column_map(isatab_header, df_columns):
     return object_column_map
 
 
-# def get_column_header(protocol_type_term, protocol_types_dict):
-#     column_header = None
-#     if protocol_type_term.lower() in \
-#             protocol_types_dict["nucleic acid sequencing"][SYNONYMS] \
-#             + protocol_types_dict["phenotyping"][SYNONYMS] \
-#             + protocol_types_dict["data acquisition"][SYNONYMS]:
-#         column_header = "Assay Name"
-#     elif protocol_type_term.lower() in protocol_types_dict["data collection"][SYNONYMS]:
-#         column_header = "Scan Name"
-#     elif protocol_type_term.lower() in protocol_types_dict["mass spectrometry"][SYNONYMS]:
-#         column_header = "MS Assay Name"
-#     elif protocol_type_term.lower() in protocol_types_dict["nmr spectroscopy"][SYNONYMS]:
-#         column_header = "NMR Assay Name"
-#     elif protocol_type_term.lower() in \
-#             protocol_types_dict["data transformation"][SYNONYMS] \
-#             + protocol_types_dict["sequence analysis data transformation"][SYNONYMS] \
-#             + protocol_types_dict["metabolite identification"][SYNONYMS] \
-#             + protocol_types_dict["protein identification"][SYNONYMS]:
-#         column_header = "Data Transformation Name"
-#     elif protocol_type_term.lower() in protocol_types_dict["normalization"][SYNONYMS]:
-#         column_header = "Normalization Name"
-#     if protocol_type_term.lower() == "unknown protocol":
-#         column_header = "Unknown Protocol Name"
-#     return column_header
-
-
 def get_value_columns(label, x):
     """ Generates the appropriate columns based on the value of the object.
     For example, if the object's .value value is an OntologyAnnotation,
diff --git a/isatools/model/process.py b/isatools/model/process.py
index cc779dfd..1f6bff1f 100644
--- a/isatools/model/process.py
+++ b/isatools/model/process.py
@@ -307,18 +307,6 @@ def from_assay_dict(self, process, technology_type):
         self.name = process.get('name', '')
         self.executes_protocol = indexes.get_protocol(process['executesProtocol']['@id'])
         self.load_comments(process.get('comments', []))
-        # allowed_protocol_type_terms = [
-        #     "nucleic acid sequencing",
-        #     "nmr spectroscopy",
-        #     "mass spectrometry",
-        #     "nucleic acid hybridization",
-        #     "data transformation",
-        #     "data normalization"
-        # ]
-        # if self.executes_protocol.protocol_type.term in allowed_protocol_type_terms or (
-        #         self.executes_protocol.protocol_type.term == 'data collection'
-        #         and technology_type.term == 'DNA microarray'):
-        #     self.name = process['name']
 
         # Inputs / Outputs
         for io_data_target in ['inputs', 'outputs']: