Merge pull request #336 from cidgoh/monkeypox-update

Monkeypox update

Author: ddooley

script/data-harmonizer/index.js

@@ -22,7 +22,7 @@
  *
  */
 
-const VERSION = '1.3.1';
+const VERSION = '1.3.2';
 
 const VERSION_TEXT = 'DataHarmonizer provenance: v' + VERSION;
 

template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx

@@ -1,7 +1,7 @@
 # Monkeypox Example Input Data
 This directory contains example input/test data for the Canadian Network for Public Health Intelligence (CNPHI) DataHarmonizer application template: `Monkeypox`. This data is appropriate for testing up to the version appended to the end of the file name, for example:
 
-- `validTestData_1-0-0.csv` is _valid_ for version `1-0-0` of the DataHarmonizer.
+- `DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx` is _valid_ for version `1-3-2` of the DataHarmonizer.
 
 ## Valid Test Data
 

template/monkeypox/exampleInput/DH_MPX_validTestData_0-6-2_Jun122022.xlsx

@@ -244,10 +244,7 @@ var EXPORT_FORMATS = {
 				//['PH_ID_NUMBER_PRIMARY',    []],
 				//['PH_CASE_ID',              []],
 				['PH_RELATED_PRIMARY_ID',   []],
-				//['PH_BIOPROJECT_ACCESSION', []],
-				//['PH_BIOSAMPLE_ACCESSION',  []],
-				//['PH_SRA_ACCESSION',        []],
-				['SUBMISSIONS - GISAID Accession ID', []],
+
 				['CUSTOMER',                []],  
 
 				['PH_SEQUENCING_CENTRE',    []],     
@@ -261,7 +258,14 @@ var EXPORT_FORMATS = {
 				['HC_PROVINCE',             []],
 
 				['HC_CURRENT_ID',           []],
-				['RESULT - CANCOGEN_SUBMISSIONS',   []],
+
+				['SUBMISSIONS - BioProject Accession', []],
+				['SUBMISSIONS - BioSample Accession', []],
+				['SUBMISSIONS - SRA Accession', []],
+				['SUBMISSIONS - GenBank Accession', []],
+				['SUBMISSIONS - GISAID Virus Name', []],
+				['SUBMISSIONS - GISAID Accession', []],
+
 				['HC_SAMPLE_CATEGORY',      []], 
 				['PH_SAMPLING_DETAILS',     []],
 				['PH_SPECIMEN_TYPE',        []],
@@ -356,6 +360,7 @@ var EXPORT_FORMATS = {
 
 			]);
 
+
 			const sourceFields = dh.getFields(dh.table);
 			const sourceFieldNameMap = dh.getFieldNameMap(sourceFields);