Merge pull request #339 from cidgoh/monkeypox-v2.1.1

WIP Monkeypox v2.1.1
cidgoh · Jul 21, 2022 · e2a0a49 · e2a0a49
2 parents 1826760 + b4c04ce
commit e2a0a49
Show file tree

Hide file tree

Showing 10 changed files with 8,220 additions and 1,600 deletions.
diff --git a/script/data-harmonizer/index.js b/script/data-harmonizer/index.js
@@ -22,7 +22,7 @@
  *
  */
 
-const VERSION = '1.3.2';
+const VERSION = '1.3.3';
 
 const VERSION_TEXT = 'DataHarmonizer provenance: v' + VERSION;
 

diff --git a/script/data-harmonizer/validation.js b/script/data-harmonizer/validation.js
@@ -117,6 +117,12 @@ Object.assign(DataHarmonizer, {
 							// Default: any token is valid.
 							valid = true;
 							break;	
+
+						case 'Provenance':
+							// Any provenance string is valid.
+							valid = true;
+							break;	
+
 					} // End switch
 
 

diff --git a/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx b/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx
diff --git a/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx b/template/monkeypox/exampleInput/DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx
diff --git a/template/monkeypox/exampleInput/README.md b/template/monkeypox/exampleInput/README.md
@@ -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:
 
-- `DH_Canadian_MPX_validTestDataset_1-1-0_Jul13_2022.xlsx` is _valid_ for version `1-3-2` of the DataHarmonizer.
+- `DH_Canadian_MPX_validTestDataset_2-1-1_July202022.xlsx` is _valid_ for version `1-3-3` of the DataHarmonizer.
 
 ## Valid Test Data
 

diff --git a/template/monkeypox/export.js b/template/monkeypox/export.js
@@ -242,7 +242,7 @@ var EXPORT_FORMATS = {
 				['TEXT_ID',                 []],
 				//['HC_TEXT5',                []],
 				//['PH_ID_NUMBER_PRIMARY',    []],
-				//['PH_CASE_ID',              []],
+		['PH_CASE_ID',              []],
 				['PH_RELATED_PRIMARY_ID',   []],
 
 				['CUSTOMER',                []],  
@@ -279,28 +279,28 @@ var EXPORT_FORMATS = {
 				['PH_SPECIMEN_TYPE_ORIG',   []],           
 				['COLLECTION_METHOD',       []],
 
-				//['PH_ANIMAL_TYPE',          []],
-				//['PH_HOST_HEALTH',          []],
-				//['PH_HOST_HEALTH_DETAILS',  []],
-				//['PH_HOST_HEALTH_OUTCOME',  []],
+		['PH_ANIMAL_TYPE',          []],
+		['PH_HOST_HEALTH',          []],
+		['PH_HOST_HEALTH_DETAILS',  []],
+		['PH_HOST_HEALTH_OUTCOME',  []],
 				['PH_HOST_DISEASE',         []],
-				//['PH_AGE',                  []],
-				//['PH_AGE_UNIT',             []],
-				//['PH_AGE_GROUP',            []],
-				//['VD_SEX',                  []],
-				//['PH_HOST_COUNTRY',         []],
-				//['PH_HOST_PROVINCE',        []], 
-				//['HC_ONSET_DATE',           []],
-				//['HC_SYMPTOMS',             []],
-				//['PH_VACCINATION_HISTORY',  []],
-				//['VE_SYMP_AVAIL',           []], // Calculated field (not in import)
-				//['PH_EXPOSURE_COUNTRY',     []], 
+		['PH_AGE',                  []],
+		['PH_AGE_UNIT',             []],
+		['PH_AGE_GROUP',            []],
+		['VD_SEX',                  []],
+		['PH_HOST_COUNTRY',         []],
+		['PH_HOST_PROVINCE',        []], 
+		['HC_ONSET_DATE',           []],
+		['HC_SYMPTOMS',             []],
+		['PH_VACCINATION_HISTORY',  []],
+				['VE_SYMP_AVAIL',           []], // Calculated field (not in import)
+		['PH_EXPOSURE_COUNTRY',     []], 
 				['PH_TRAVEL',               []],
 				//['PH_POINT_OF_ENTRY',       []],
 				//['PH_DAY',                  []],
-				//['PH_EXPOSURE',             []],
-				//['PH_EXPOSURE_DETAILS',     []], 
-				//['PH_HOST_ROLE',            []], 
+		['PH_EXPOSURE',             []],
+		['PH_EXPOSURE_DETAILS',     []], 
+		['PH_HOST_ROLE',            []], 
 				['PH_REASON_FOR_SEQUENCING',[]], 
 
 				['PH_REASON_FOR_SEQUENCING_DETAILS', []],