LIMS field sort adjustment

template/canada_covid19/data.js

@@ -61,9 +61,6 @@ var DATA = [
           "NML_LIMS": [
             {
               "field": "TEXT_ID"
-            },
-            {
-              "field": "VD_LAB_NUMBER"
             }
           ]
         }

template/canada_covid19/data.tsv

@@ -2,7 +2,7 @@ Ontology ID	parent class	label	datatype	source	data status	requirement	min value
 ID	SC %															
 		Database Identifiers														
 	Database Identifiers	specimen collector sample ID	xs:token		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				The user-defined name for the sample.	Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab.	prov_rona_99	Sample ID given by the sample provider	Primary Specimen ID	VD_LAB_NUMBER	sample_name
-	Database Identifiers	NML submitted specimen primary ID	xs:token							The primary ID of the specimen submitted thorough LaSER.	Store the identifier for the specimen submitted through the NML LaSER system.	SR20-12345			TEXT_ID;VD_LAB_NUMBER	
+	Database Identifiers	NML submitted specimen primary ID	xs:token							The primary ID of the specimen submitted thorough LaSER.	Store the identifier for the specimen submitted through the NML LaSER system.	SR20-12345			TEXT_ID	
 	Database Identifiers	NML related specimen primary ID	xs:token		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access					The primary ID of the related specimen previously submitted thorough LaSER	Store the primary ID of the related specimen previously submitted thorough LaSER	SR20-12345		Related Specimen ID|Related Specimen Relationship Type		
 	Database Identifiers	IRIDA sample name	xs:token							The identifier assigned to a sequenced isolate in IRIDA.	Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). 	prov_rona_99				
 	Database Identifiers	umbrella bioproject accession	select						UPPER	The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort.	Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject.	PRJNA623807				

template/canada_covid19/export.js

@@ -410,6 +410,7 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => {
 
   const ExportHeaders = new Map([
     ['VD_LAB_NUMBER',           []],
+    ['TEXT_ID',                 []],
     ['PH_BIOPROJECT_ACCESSION', []],
     ['PH_BIOSAMPLE_ACCESSION',  []],
     ['PH_SRA_ACCESSION',        []],
@@ -444,12 +445,13 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => {
     ['PH_TRAVEL',               []],
     ['PH_EXPOSURE',             []],
     ['PH_TESTING_PROTOCOL',     []],
-    ['RESULT - CANCOGEN_SUBMITTED_RESLT_1',   []], 
-    ['RESULT - CANCOGEN_SUBMITTED_RESLT_1CT', []],
-    ['RESULT - CANCOGEN_SUBMITTED_RESLT_2',   []],
-    ['RESULT - CANCOGEN_SUBMITTED_RESLT_2CT', []],
-    ['RESULT - CANCOGEN_SUBMITTED_RESLT_3',   []],
-    ['RESULT - CANCOGEN_SUBMITTED_RESLT_3CT', []],
+    ['SUBMITTED_RESLT - Gene Target #1',   []], 
+    ['SUBMITTED_RESLT - Gene Target #1 CT Value', []],
+    ['SUBMITTED_RESLT - Gene Target #2',   []],
+    ['SUBMITTED_RESLT - Gene Target #2 CT Value', []],
+    ['SUBMITTED_RESLT - Gene Target #3',   []],
+    ['SUBMITTED_RESLT - Gene Target #3 CT Value', []],
+    ['PH_CANCOGEN_AUTHORS',     []],
     ['HC_COMMENTS', []]
   ]);