export field separator fix

template/canada_covid19/data.js

@@ -34,7 +34,10 @@ var DATA = [
           ],
           "NML_LIMS": [
             {
-              "field": "VD_LAB_NUMBER|TEXT_ID"
+              "field": "VD_LAB_NUMBER"
+            },
+            {
+              "field": "TEXT_ID"
             }
           ],
           "BIOSAMPLE": [
@@ -80,7 +83,10 @@ var DATA = [
         "exportField": {
           "CNPHI": [
             {
-              "field": "Related Specimen ID|Related Specimen Relationship Type"
+              "field": "Related Specimen ID"
+            },
+            {
+              "field": "Related Specimen Relationship Type"
             }
           ]
         }
@@ -1649,7 +1655,10 @@ var DATA = [
         "exportField": {
           "CNPHI": [
             {
-              "field": "Related Specimen ID|Related Specimen Relationship Type"
+              "field": "Related Specimen ID"
+            },
+            {
+              "field": "Related Specimen Relationship Type"
             }
           ]
         },

template/canada_covid19/data.tsv

@@ -1,9 +1,9 @@
 Ontology ID	parent class	label	datatype	source	data status	requirement	min value	max value	capitalize	description	guidance	examples	EXPORT_GISAID	EXPORT_CNPHI	EXPORT_NML_LIMS	EXPORT_BIOSAMPLE
 ID	SC %															
 		Database Identifiers														
-	Database Identifiers	specimen collector sample ID	xs:unique		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|TEXT_ID	sample_name
+	Database Identifiers	specimen collector sample ID	xs:unique		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;TEXT_ID	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				
-	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	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				
 	Database Identifiers	bioproject accession	xs:token						UPPER	The INSDC accession number of the BioProject(s) to which the BioSample belongs.	Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. 	PRJNA608651		BioProject Accession	PH_BIOPROJECT_ACCESSION	bioproject_accession
@@ -29,7 +29,7 @@ ID	SC %
 	Sample collection and processing	purpose of sampling	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				The reason that the sample was collected.	The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. 	Diagnostic testing		Reason for Sampling	HC_SAMPLE_CATEGORY	purpose_of_sampling
 	Sample collection and processing	purpose of sampling details	xs:token		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				The description of why the sample was collected, providing specific details.	Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value.	The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. 		Details on the Reason for Sampling		description
 	Sample collection and processing	NML submitted specimen type	select		 	required				The type of specimen submitted to the NML for testing.	This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”.	swab		Specimen Type	PH_SPECIMEN_TYPE	
-	Sample collection and processing	NML related specimen relationship type	select							The relationship of the related specimen to the previous submission.	Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system.	Follow-up		Related Specimen ID|Related Specimen Relationship Type		
+	Sample collection and processing	NML related specimen relationship type	select							The relationship of the related specimen to the previous submission.	Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system.	Follow-up		Related Specimen ID;Related Specimen Relationship Type		
 	Sample collection and processing	anatomical material	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				A substance obtained from an anatomical part of an organism e.g. tissue, blood.	Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact [email protected]. If not applicable, do not leave blank. Choose a null value. 	Blood	Specimen source	Anatomical Material	PH_ISOLATION_SITE_DESC	isolation_source;anatomical_material
 	Sample collection and processing	anatomical part	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				An anatomical part of an organism e.g. oropharynx.	Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact [email protected]. If not applicable, do not leave blank. Choose a null value. 	Nasopharynx (NP)	Specimen source	Anatomical Site	PH_ISOLATION_SITE	isolation_source;anatomical_part
 	Sample collection and processing	body product	select		Not Applicable; Missing; Not Collected; Not Provided; Restricted Access	required				A substance excreted/secreted from an organism e.g. feces, urine, sweat.	Provide a descriptor if a body product was sampled. Use the picklist provided in the template.  If a desired term is missing from the picklist, contact [email protected]. If not applicable, do not leave blank. Choose a null value. 	Feces	Specimen source	Body Product	PH_SPECIMEN_SOURCE_DESC	isolation_source;body_product