Merge pull request #386 from cidgoh/PGP-issue-9etc

Pgp issue 9etc
cidgoh · Apr 5, 2023 · 94616d1 · 94616d1
2 parents a9ca9d2 + 479f619
commit 94616d1
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Showing 9 changed files with 25 additions and 30 deletions.
diff --git a/web/templates/canada_covid19/export.js b/web/templates/canada_covid19/export.js
@@ -529,6 +529,9 @@ export default {
         ['SUBMITTED_RESLT - Gene Target #3 CT Value', []],
         ['PH_CANCOGEN_AUTHORS', []],
         ['HC_COMMENTS', []],
+
+        ['host (scientific name)', []] // Special rule below
+
       ]);
 
       const sourceFields = dh.getFields(dh.table);
@@ -558,6 +561,7 @@ export default {
 
       for (const inputRow of dh.getTrimmedData(dh.hot)) {
         const outputRow = [];
+
         for (const [headerName, sources] of ExportHeaders) {
           if (headerName === 'HC_CURRENT_ID') {
             // Assign constant value.
@@ -587,6 +591,8 @@ export default {
           }
 
           // A complicated rule about what is stored in 'Specimen Source'
+          // Note that common name field will override scientific name in
+          // export to PH_SPECIMEN_SOURCE
           if (headerName === 'PH_SPECIMEN_SOURCE') {
             let cellValue = '';
             for (const fieldName of [
@@ -595,19 +601,21 @@ export default {
               'environmental material',
               'environmental site',
             ]) {
-              const value = inputRow[sourceFieldNameMap[fieldName]];
+              let value = inputRow[sourceFieldNameMap[fieldName]];
 
               // Ignore all null value types
               if (!value || null_values.has(value)) {
                 continue;
               }
+              value = value.toLowerCase();
               if (
-                fieldName === 'host (scientific name)' ||
+                fieldName === 'host (scientific name)' ||  
                 fieldName === 'host (common name)'
               ) {
-                if (value === 'Homo sapiens' || value === 'Human')
+                if (value === 'homo sapiens' || value === 'human')
                   cellValue = 'Human';
-                else cellValue = 'ANIMAL';
+                else 
+                  cellValue = 'ANIMAL';
                 break;
               }
               if (

diff --git a/web/templates/canada_covid19/schema.json b/web/templates/canada_covid19/schema.json
@@ -2306,10 +2306,7 @@
       "permissible_values": {
         "Homo sapiens": {
           "text": "Homo sapiens",
-          "meaning": "NCBITaxon:9606",
-          "exact_mappings": [
-            "NML_LIMS:Human"
-          ]
+          "meaning": "NCBITaxon:9606"
         },
         "Bos taurus": {
           "text": "Bos taurus",

diff --git a/web/templates/canada_covid19/schema.yaml b/web/templates/canada_covid19/schema.yaml
@@ -4408,8 +4408,6 @@ enums:
       Homo sapiens:
         text: Homo sapiens
         meaning: NCBITaxon:9606
-        exact_mappings:
-        - NML_LIMS:Human
       Bos taurus:
         text: Bos taurus
         meaning: NCBITaxon:9913

diff --git a/web/templates/canada_covid19/schema_enums.tsv b/web/templates/canada_covid19/schema_enums.tsv
@@ -496,7 +496,7 @@ collection device menu	ENVO:00003968	Air filter
 	OBI:0002866	Virus Transport Medium										
 
 
-host (scientific name) menu	NCBITaxon:9606	Homo sapiens								Human		
+host (scientific name) menu	NCBITaxon:9606	Homo sapiens										
 	NCBITaxon:9913	Bos taurus										
 	NCBITaxon:9615	Canis lupus familiaris										
 	NCBITaxon:9397	Chiroptera										

diff --git a/web/templates/monkeypox/export.js b/web/templates/monkeypox/export.js
@@ -320,7 +320,7 @@ export default {
         ['PH_REASON_FOR_SEQUENCING_DETAILS', []],
         ['PH_SEQUENCING_DATE', []],
         ['PH_LIBRARY_PREP_KIT', []],
-
+        ['PH_SEQUENCING_INSTRUMENT', []],
         ['PH_TESTING_PROTOCOL', []],
         //['PH_SEQ_PROTOCOL_NAME',     []],
         ['PH_RAW_SEQUENCE_METHOD', []],
@@ -347,7 +347,7 @@ export default {
 				['SUBMITTED_RESLT - Gene Target #5',   []],
 				['SUBMITTED_RESLT - Gene Target #5 CT Value', []],
 
-        ['PH_CANCOGEN_AUTHORS', []],
+        ['PH_SEQUENCING_AUTHORS', []],
         ['HC_COMMENTS', []],
 
         ['sample collector contact email', []],
@@ -428,6 +428,8 @@ export default {
           }
 
           // A complicated rule about what is stored in 'Specimen Source'
+          // Note that common name field will override scientific name in
+          // export to PH_SPECIMEN_SOURCE
           if (headerName === 'PH_SPECIMEN_SOURCE') {
             let cellValue = '';
             for (const fieldName of [

diff --git a/web/templates/monkeypox/schema.json b/web/templates/monkeypox/schema.json
@@ -1597,10 +1597,7 @@
       "permissible_values": {
         "Homo sapiens": {
           "text": "Homo sapiens",
-          "meaning": "NCBITaxon:9606",
-          "exact_mappings": [
-            "NML_LIMS:Human"
-          ]
+          "meaning": "NCBITaxon:9606"
         }
       }
     },
@@ -1610,10 +1607,7 @@
       "permissible_values": {
         "Homo sapiens [NCBITaxon:9606]": {
           "text": "Homo sapiens [NCBITaxon:9606]",
-          "meaning": "NCBITaxon:9606",
-          "exact_mappings": [
-            "NML_LIMS:Human"
-          ]
+          "meaning": "NCBITaxon:9606"
         }
       }
     },
@@ -12543,7 +12537,7 @@
       "annotations": {
         "version": {
           "tag": "version",
-          "value": "3.3.2"
+          "value": "3.3.3"
         }
       },
       "description": "International specification for Monkeypox clinical virus biosample data gathering",

diff --git a/web/templates/monkeypox/schema.yaml b/web/templates/monkeypox/schema.yaml
@@ -783,7 +783,7 @@ classes:
     is_a: dh_interface
     see_also: templates/monkeypox/SOP_Monkeypox_international.pdf
     annotations:
-      version: 3.3.2
+      version: 3.3.3
     slots:
     - specimen collector sample ID
     - case ID
@@ -4117,16 +4117,12 @@ enums:
       Homo sapiens:
         text: Homo sapiens
         meaning: NCBITaxon:9606
-        exact_mappings:
-        - NML_LIMS:Human
   host (scientific name) international menu:
     name: host (scientific name) international menu
     permissible_values:
       Homo sapiens [NCBITaxon:9606]:
         text: Homo sapiens [NCBITaxon:9606]
         meaning: NCBITaxon:9606
-        exact_mappings:
-        - NML_LIMS:Human
   host health state menu:
     name: host health state menu
     permissible_values:

diff --git a/web/templates/monkeypox/schema_core.yaml b/web/templates/monkeypox/schema_core.yaml
@@ -25,7 +25,7 @@ classes:
     is_a: dh_interface
     see_also: templates/monkeypox/SOP_Monkeypox_international.pdf
     annotations:
-      version: 3.3.2
+      version: 3.3.3
 slots: {}
 enums: {}
 types:

diff --git a/web/templates/monkeypox/schema_enums.tsv b/web/templates/monkeypox/schema_enums.tsv
@@ -325,9 +325,9 @@ host (common name) international menu	NCBITaxon:9606	Human [NCBITaxon:9606]
 	NCBITaxon:10116		Rat									
 	FOODON:03411389		Squirrel									
 
-host (scientific name) menu	NCBITaxon:9606	Homo sapiens								Human		
+host (scientific name) menu	NCBITaxon:9606	Homo sapiens										
 
-host (scientific name) international menu	NCBITaxon:9606	Homo sapiens [NCBITaxon:9606]								Human		
+host (scientific name) international menu	NCBITaxon:9606	Homo sapiens [NCBITaxon:9606]										
 
 host health state menu	NCIT:C3833	Asymptomatic										
 	NCIT:C28554	Deceased