Merge branch 'mpox-rename' of https://github.com/cidgoh/DataHarmonizer …

…into mpox-rename
cidgoh · Nov 9, 2023 · a59b629 · a59b629
2 parents fdddbe6 + 1008cad
commit a59b629
Show file tree

Hide file tree

Showing 12 changed files with 528 additions and 504 deletions.
diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js
@@ -489,7 +489,11 @@ class DataHarmonizer {
         rowHeaders: true,
         copyPaste: true,
         manualColumnResize: true,
+
         //colWidths: [100], //Just fixes first column width
+        beforePaste: (data, coords) => {
+          //data is a 2d array of rows and columns
+        },
         afterCopy: function (changes) {
           self.clipboardCache = self.sheetclip.stringify(changes);
         },
@@ -507,18 +511,48 @@ class DataHarmonizer {
             key: 'paste',
             name: 'Paste',
             disabled: function () {
-              return self.clipboardCache.length === 0;
+              // For now always on, since we can't query whether something is
+              // in system cut/paste buffer without prompting user for ok.
+              return false; 
             },
             callback: function () {
               var plugin = this.getPlugin('copyPaste');
-
               this.listen();
-              // BUG: It seems like extra lf is added by sheetclip, causing
-              // empty last row to be added and pasted. Exception is pasting
-              // of single empty cell
-              if (self.clipboardCache.length > 0)
+
+              // Due to asynchronous clipboard calls, this has to be in an 
+              // immediate setTimeout()
+              setTimeout(async () => {
+                const text = await navigator.clipboard.readText();
+                if (text && text.length) {
+
+                  // An odd issue that with handsontable Paste menu item,
+                  // targeted paste area gets extended a row on each 
+                  // subsequent Paste request.  This doesn't happen if one
+                  // uses CTRL-V instead (but that doesn't work on
+                  // FlatpickrEditor fields unless they are later in
+                  // multi-column paste). 
+                  // See https://github.com/handsontable/handsontable/issues/1930
+                  // Solution is to test for and clear out trailing newline.
+
+                  if (text.substr(-1, 1) == '\n')
+                    text = text.slice(0, -1);
+                  //self.clipboardCache = text;
+                  plugin.paste(text);  
+                }
+
+              });
+
+              /*
+              if (
+                self.clipboardCache &&
+                self.clipboardCache.length &&
+                self.clipboardCache.substr(-1, 1) == '\n'
+              ) {
                 self.clipboardCache = self.clipboardCache.slice(0, -1);
+              }
+
               plugin.paste(self.clipboardCache);
+              */
             },
           },
           'remove_row',

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "data-harmonizer",
-  "version": "1.6.0",
+  "version": "1.6.1",
   "description": "A standardized spreadsheet editor and validator that can be run offline and locally",
   "repository": "[email protected]:cidgoh/DataHarmonizer.git",
   "license": "MIT",

diff --git a/web/templates/canada_covid19/schema.json b/web/templates/canada_covid19/schema.json
@@ -2,7 +2,7 @@
   "name": "CanCOGeN_Covid-19",
   "description": "",
   "id": "https://example.com/CanCOGeN_Covid-19",
-  "version": "2.1.3",
+  "version": "2.2.3",
   "prefixes": {
     "linkml": {
       "prefix_prefix": "linkml",
@@ -4128,6 +4128,9 @@
         "Newfoundland and Labrador - Eastern Health": {
           "text": "Newfoundland and Labrador - Eastern Health"
         },
+        "Newfoundland and Labrador - Newfoundland and Labrador Health Services": {
+          "text": "Newfoundland and Labrador - Newfoundland and Labrador Health Services"
+        },
         "Nova Scotia Health Authority": {
           "text": "Nova Scotia Health Authority"
         },
@@ -4220,6 +4223,9 @@
         "Newfoundland and Labrador - Eastern Health": {
           "text": "Newfoundland and Labrador - Eastern Health"
         },
+        "Newfoundland and Labrador - Newfoundland and Labrador Health Services": {
+          "text": "Newfoundland and Labrador - Newfoundland and Labrador Health Services"
+        },
         "Nova Scotia Health Authority": {
           "text": "Nova Scotia Health Authority"
         },

diff --git a/web/templates/canada_covid19/schema.yaml b/web/templates/canada_covid19/schema.yaml
@@ -1,7 +1,7 @@
 id: https://example.com/CanCOGeN_Covid-19
 name: CanCOGeN_Covid-19
 description: ''
-version: 2.1.3
+version: 2.2.3
 imports:
 - linkml:types
 prefixes:
@@ -5762,6 +5762,8 @@ enums:
         text: "New Brunswick - Vitalit\xE9 Health Network"
       Newfoundland and Labrador - Eastern Health:
         text: Newfoundland and Labrador - Eastern Health
+      Newfoundland and Labrador - Newfoundland and Labrador Health Services:
+        text: Newfoundland and Labrador - Newfoundland and Labrador Health Services
       Nova Scotia Health Authority:
         text: Nova Scotia Health Authority
       Ontario Institute for Cancer Research (OICR):
@@ -5823,6 +5825,8 @@ enums:
         text: "New Brunswick - Vitalit\xE9 Health Network"
       Newfoundland and Labrador - Eastern Health:
         text: Newfoundland and Labrador - Eastern Health
+      Newfoundland and Labrador - Newfoundland and Labrador Health Services:
+        text: Newfoundland and Labrador - Newfoundland and Labrador Health Services
       Nova Scotia Health Authority:
         text: Nova Scotia Health Authority
       Nunavut:

diff --git a/web/templates/canada_covid19/schema_core.yaml b/web/templates/canada_covid19/schema_core.yaml
@@ -1,7 +1,7 @@
 id: https://example.com/CanCOGeN_Covid-19
 name: CanCOGeN_Covid-19
 description: ""
-version: 2.1.3
+version: 2.2.3
 imports:
 - 'linkml:types'
 prefixes:

diff --git a/web/templates/canada_covid19/schema_enums.tsv b/web/templates/canada_covid19/schema_enums.tsv
@@ -887,6 +887,7 @@ sequence submitted by menu		Alberta Precision Labs (APL)
 		National Microbiology Laboratory (NML)										
 		New Brunswick - Vitalité Health Network										
 		Newfoundland and Labrador - Eastern Health										
+		Newfoundland and Labrador - Newfoundland and Labrador Health Services										
 		Nova Scotia Health Authority										
 		Ontario Institute for Cancer Research (OICR)										
 		Prince Edward Island - Health PEI										
@@ -917,6 +918,7 @@ sequence submitted by menu		Alberta Precision Labs (APL)
 		National Microbiology Laboratory (NML)										
 		New Brunswick - Vitalité Health Network										
 		Newfoundland and Labrador - Eastern Health										
+		Newfoundland and Labrador - Newfoundland and Labrador Health Services										
 		Nova Scotia Health Authority										
 		Nunavut										
 		Ontario Institute for Cancer Research (OICR)										
@@ -1202,6 +1204,4 @@ geo_loc_name (country) menu	GAZ:00006882	Afghanistan
 	GAZ:00000564	Western Sahara										
 	GAZ:00005284	Yemen										
 	GAZ:00001107	Zambia										
-	GAZ:00001106	Zimbabwe										
-
-
+	GAZ:00001106	Zimbabwe										
diff --git a/web/templates/canada_covid19/schema_slots.tsv b/web/templates/canada_covid19/schema_slots.tsv
@@ -158,5 +158,4 @@ CanCOGeN Covid-19		GENEPIO:0001122	Database Identifiers
 
 		GENEPIO:0001516	Contributor acknowledgement																			
 	Contributor acknowledgement	GENEPIO:0001517	authors		WhitespaceMinimizedString					TRUE					Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.	Include the first and last names of all individuals that should be attributed, separated by a comma.	Tejinder Singh, Fei Hu, Joe Blogs	Authors	Authors	PH_CANCOGEN_AUTHORS		
-	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0	DataHarmonizer provenance	Additional Comments	HC_COMMENTS		
-
+	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0	DataHarmonizer provenance	Additional Comments	HC_COMMENTS