Update for version 4.12.0

common.py

@@ -1,3 +1,3 @@
 
 # The path to the freezeman sample submission template used by the convertor.
-FMS_SUBMISSION_TEMPLATE_PATH = "config/fms_sample_submission_template_4.9.xlsx"
+FMS_SUBMISSION_TEMPLATE_PATH = "config/fms_sample_submission_template_4.12.xlsx"

convertor/freezeman/freezeman_config_data.py

@@ -7,7 +7,7 @@
         "PROJECT": "Project",
         "COHORT": "Cohort",
         "EXPERIMENTAL_GROUP": "Experimental Group",
-        "TAXON": "NCBI Taxon ID #",
+        "TAXON": "Taxon",
         "SAMPLE_COORD": "Sample Coord",
         "CONTAINER_KIND": "Container Kind",
         "CONTAINER_NAME": "Container Name",
@@ -17,9 +17,6 @@
         "INDIVIDUAL_NAME": "Individual Name",
         "INDIVIDUAL_ALIAS": "Individual Alias",
         "SEX": "Sex",
-        "PEDIGREE": "Pedigree",
-        "MOTHER_NAME": "Mother Name",
-        "FATHER_NAME": "Father Name",
         "VOLUME": "Volume (uL)",
         "CONCENTRATION": "Conc. (ng/uL)",
         "COLLECTION_SITE": "Collection Site",

convertor/freezeman/sample.py

@@ -14,9 +14,6 @@ def __init__(self):
         self.containerCoord = ""
         self.individualName = ""
         self.sex = ""
-        self.pedigree = ""
-        self.motherName = ""
-        self.fatherName = ""
         self.volume = ""
         self.concentration = ""
         self.collectionSite = ""

convertor/freezeman/sample_headers.py

@@ -13,9 +13,6 @@ class SampleHeaders:
     CONTAINER_COORD = "Container Coord"
     INDIVIDUAL_NAME = "Individual Name"
     SEX = "Sex"
-    PEDIGREE = "Pedigree"
-    MOTHER_NAME = "Mother Name"
-    FATHER_NAME = "Father Name"
     VOLUME = "Volume (uL)"
     CONCENTRATION = "Conc. (ng/uL)"
     COLLECTION_SITE = "Collection Site"
@@ -39,9 +36,6 @@ class SampleHeaders:
         CONTAINER_COORD,
         INDIVIDUAL_NAME,
         SEX,
-        PEDIGREE,
-        MOTHER_NAME,
-        FATHER_NAME,
         VOLUME,
         CONCENTRATION,
         COLLECTION_SITE,

convertor/moh/moh_config_data.py

@@ -74,9 +74,9 @@
         "TUBE": "Tube"
     },
     "taxonTypeMap": {
-        "Eukaryota:Homo sapiens (Taxon ID:9606)": 9606,
-        "Eukaryota:Mus musculus (Taxon ID:10090)": 10090,
-        "Viruses:Severe acute respiratory syndrome coronavirus 2 (Taxon ID:2697049)": 2697049,
+        "Eukaryota:Homo sapiens (Taxon ID:9606)": "Homo sapiens",
+        "Eukaryota:Mus musculus (Taxon ID:10090)": "Mus musculus",
+        "Viruses:Severe acute respiratory syndrome coronavirus 2 (Taxon ID:2697049)": "Sars-Cov-2",
         "NOT_IN_MOH": "Ixodes Scapularis"
     },
     "concentration_units": {

version.py

@@ -1,4 +1,4 @@
-CONVERTOR_VERSION = '4.9'
+CONVERTOR_VERSION = '4.12'
 
 # 3.12.1: 	Updated streamlit and Pillow because of security warnings
 # 3.13.0: 	Updated for freezeman 3.13.0 submission template
@@ -11,4 +11,5 @@
 # 4.4:		Updated version number only - no template changes
 # 4.5:		Updated version number - Template replaced individuals ID by Name
 # 4.6:		Updated version number - no template changes
-# 4.9:		Updated version number - no template changes
+# 4.9:		Updated version number - no template changes
+# 4.12:   Updated version number - Template removed header fields and changed Taxon ID to Taxon name