F sample name

Summary

For https://gitlab.indiscale.com/caosdb/customers/glaz_awi/management/-/issues/386. Introduce sample names to export and upload. Also does the sorting and renaming in https://gitlab.indiscale.com/caosdb/customers/glaz_awi/management/-/issues/378.

Focus

There is new special treatment for sample names (which is needed since name is not a regular property).

Test Environment

Run the test profile, then play around with exporting and uploading samples with names, e.g.,

• Give a name to a sample entity via the edit mode and verify that it is exported correctly
• register samples and select sample name as additional column. Fill with value and upload. Verify that the names have been updated.
• Export a sample. Change the name, upload again, and verify that the name has been set.

Check List for the Author

Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab comments for the reviewer. They should guide the reviewer through the changes, explain your changes and also point out open questions. For further good practices have a look at our review guidelines

• All automated tests pass
• Reference related issues
• Up-to-date CHANGELOG.md (or not necessary)
• Up-to-date JSON schema (or not necessary)
• Appropriate user and developer documentation (or not necessary)
  • How do I use the software? Assume "stupid" users.
  • How do I develop or debug the software? Assume novice developers.
• Annotations in code (Gitlab comments)
  • Intent of new code
  • Problems with old code
  • Why this implementation?

Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• Up-to-date CHANGELOG.md (or not necessary)
• Appropriate user and developer documentation (or not necessary)
• The test environment setup works and the intended behavior is reproducible in the test environment
• In-code documentation and comments are up-to-date.
• Check: Are there specifications? Are they satisfied?

For further good practices have a look at our review guidelines.

sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js

@@ -19,11 +19,11 @@
 const ext_samplemanagement = function($, navbar, log, form_elements, form_panel, sample_management_reference_resolver) {
     const logger = log.getLogger("samplemanagement_form");
     const tool_box = "Sample Management"
-    const upload_sample_template_title = "Upload sample template"; // title of the form and text in the toolbox
+    const upload_sample_template_title = "Update samples"; // title of the form and text in the toolbox
     const upload_sample_template_panel_id = "upload_sample_template_form_panel";
-    const register_new_samples_title = "Register new samples"; // title of the form and text in the toolbox
+    const register_new_samples_title = "Register samples"; // title of the form and text in the toolbox
     const register_new_samples_panel_id = "register_new_samples_form_panel";
-    const registerNewChildSamplesTitle = "Register new child samples"; // title of the form and text in the toolbox
+    const registerNewChildSamplesTitle = "Register child samples"; // title of the form and text in the toolbox
     const registerNewChildSamplesPanelId = "register_new_children_form_panel";
     const upload_pdf_id = "upload_pdf_form_panel";
     const upload_pdf_title = "Upload PDF file";
@@ -39,36 +39,35 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
     const required_column_names = [
         "LinkAhead ID",
         "Main User",
-        "Latitude start",
-        "Longitude start",
-        "Elevation start",
-        "Start date",
-        "Storage ID",
-        "Device"
     ];
     const requiredColumnNamesChildren = [
         "LinkAhead ID",
         "Main User",
         "Parent LinkAhead ID",
-        "SampleType",
-        "Storage ID",
     ];
     const non_sample_rt_column_names = [
+        "Latitude start",
+        "Storage ID",
         "Biome",
         "Campaign",
-        "Start date",
+        "Device",
+        "Elevation start",
+        "Elevation stop",
         "End date",
+        "Event responsible",
         "IGSN DOI",
+        "Latitude stop",
         "Level",
         "Locality description",
         "Locality name",
-        "Sphere",
-        "Event responsible",
-        "Latitude stop",
+        "Longitude start",
         "Longitude stop",
-        "Elevation stop",
         "PDFReport",
         "Parent LinkAhead ID",
+        "Sample name",
+        "Sphere",
+        "Start date",
+        "Start date",
     ];
     const allColumnNames = non_sample_rt_column_names.concat(requiredColumnNamesChildren).concat(required_column_names);
 
@@ -77,7 +76,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
         "Event",
         "Container",
         'NagoyaCase',
-        "Parent_sample",
+        "Parent_Sample",
     ]
 
     const upload_sample_template_form_config = {
@@ -191,7 +190,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
         // refresh the options of the column names select field once the list
         // is available (The sample RT needs to be retrieved
         var column_name_select = $(form).find("select[name='column_names']");
-        collect_column_names(requiredColumnNames).then(function(names) {
+        collect_column_names(requiredColumnNames, true).then(function(names) {
             for (let option of names) {
                 column_name_select.append(
                     form_elements._make_option(option.value, option.label));
@@ -260,11 +259,14 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
      *
      * @return {Array} Options
      */
-    const collect_column_names = async function(requiredColumnNames) {
+    const collect_column_names = async function(requiredColumnNames, sorted) {
         const a = await query('find recordtype with name=sample');
         const column_names = $(a[0]).find(".caosdb-property-name").toArray().map(e => e.textContent);
         var options = [...new Set(allColumnNames.concat(column_names))];
         options = options.filter(n => !(unused_property_names.includes(n) || requiredColumnNames.includes(n))).sort();
+        if (sorted == true) {
+            options.sort();
+        }
         return options.map(e => ({
             value: e,
             label: e
@@ -305,12 +307,6 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
      */
     const init_show_samplemanagement_panel_button = async function() {
         //var form_wrapper = form_elements.make_form(config);
-        navbar.add_tool(upload_sample_template_title, tool_box, {
-            callback: form_panel.create_show_form_callback(
-                upload_sample_template_panel_id,
-                upload_sample_template_title,
-                upload_sample_template_form_config)
-        });
         navbar.add_tool(register_new_samples_title, tool_box, {
             callback: form_panel.create_show_form_callback(
                 register_new_samples_panel_id,
@@ -325,12 +321,11 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
                 undefined,
                 initRegisterChildSamplesForm)
         });
-        navbar.add_tool("Create sample template", tool_box, {
+        navbar.add_tool(upload_sample_template_title, tool_box, {
             callback: form_panel.create_show_form_callback(
-                "create-sample-template",
-                "Create sample template",
-                undefined,
-                initRegisterTemplateForm)
+                upload_sample_template_panel_id,
+                upload_sample_template_title,
+                upload_sample_template_form_config)
         });
         // Set auto_focus=false because of WebUI bug: https://gitlab.com/linkahead/linkahead-webui/-/issues/258
         navbar.add_tool(upload_pdf_title, tool_box, {
@@ -359,6 +354,14 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
                 input_field.addEventListener("blur", check_pattern);
             }
         });
+
+        navbar.add_tool("Create sample template", tool_box, {
+            callback: form_panel.create_show_form_callback(
+                "create-sample-template",
+                "Create sample template",
+                undefined,
+                initRegisterTemplateForm)
+        });
     };