Merge pull request #18 from opencobra/constructor_dev

Constructor dev

Author: Yifang-Guo

curationTool/reactions/static/reactions/js_VMH_workspace/handleAdd2VMH.js

@@ -448,12 +448,24 @@ confirmAddToVMHBtn && confirmAddToVMHBtn.addEventListener('click', addToVMH);
 // Close the alert modal when the user clicks on <span> (x)
 document.querySelector('.close-alert-btn').addEventListener('click', function () {
 	document.getElementById('alertModal').style.display = 'none';
+
+	if (window.pkPendingRemoval !== null) {
+		const li = document.querySelector(`#wsAvailableReactionList li[data-pk="${window.pkPendingRemoval}"]`);
+		if (li) li.remove();
+		window.pkPendingRemoval = null;
+	}
 });
 
 // Also close the modal if the user clicks anywhere outside of the modal
 window.onclick = function (event) {
 	if (event.target == document.getElementById('alertModal')) {
 		document.getElementById('alertModal').style.display = 'none';
+
+		if (window.pkPendingRemoval !== null) {
+			const li = document.querySelector(`#wsAvailableReactionList li[data-pk="${window.pkPendingRemoval}"]`);
+			if (li) li.remove();
+			window.pkPendingRemoval = null;
+		}
 	}
 };
 

curationTool/reactions/static/reactions/js_VMH_workspace/workspace.js

@@ -36,6 +36,7 @@ document.querySelectorAll('.subtabs').forEach((bar) => {
 	// 1 – draw the list of abbreviations
 	const availableListEl = document.getElementById('wsAvailableReactionList');
 	const availableDetailEl = document.getElementById('wsAvailableReactionDetails');
+	window.pkPendingRemoval = null;
 
 	// Load available reactions
 	reactions_active.forEach((r) => {
@@ -80,13 +81,15 @@ document.querySelectorAll('.subtabs').forEach((bar) => {
 				'An error occurred while fetching data from VMH. Check console for error. Please try again later.';
 			document.getElementById('alertModal').style.display = 'block';
 			document.getElementById('loadingIndicator').style.display = 'none';
+			window.pkPendingRemoval = reaction.pk;
 			return '';
 		}
 
 		if (vmhResponse.status === 'error') {
 			document.getElementById('alertMessage').textContent = vmhResponse.message;
 			document.getElementById('alertModal').style.display = 'block';
 			document.getElementById('loadingIndicator').style.display = 'none';
+			window.pkPendingRemoval = reaction.pk;
 			return '';
 		}
 

curationTool/reactions/utils/add_to_vmh_utils.py

@@ -386,10 +386,10 @@ def update_vmh_info(items_info, names_vmh, abbr_vmh, found_info):
 
 def validate_reaction_fields(reactions):
     """
-    Validate that each reaction has non-empty short_name, abbreviation, and confidence_score.
+    Validate that each reaction has non-empty description, abbreviation, and confidence_score.
     Also check for duplicates in the list.
     """
-    missing_names = [reaction['short_name'] == '' for reaction in reactions]
+    missing_names = [reaction['description'] == '' for reaction in reactions]
     if True in missing_names:
         return JsonResponse({'status': 'error',
                              'message': 'Please enter a description for reaction'})
@@ -404,7 +404,7 @@ def validate_reaction_fields(reactions):
         return JsonResponse({'status': 'error',
                              'message': 'Please enter a confidence score for reaction'})
 
-    names_list = [reaction['short_name'] for reaction in reactions]
+    names_list = [reaction['description'] for reaction in reactions]
     for name in names_list:
         if names_list.count(name) > 1:
             return JsonResponse({'status': 'error',
@@ -423,13 +423,13 @@ def validate_reaction_existence(reactions):
     Validate that the reaction names and abbreviations do not already exist in VMH.
     """
     name_in_vmh, abbr_in_vmh = check_names_abbrs_vmh(
-        [(reaction['short_name'], reaction['abbreviation']) for reaction in reactions]
+        [(reaction['description'], reaction['abbreviation']) for reaction in reactions]
     )
     if True in list(name_in_vmh.values()):
         name_in_vmh_reactions = [
             reaction for reaction, in_vmh in zip(reactions, name_in_vmh.values()) if in_vmh
         ]
-        reaction_names = ", ".join([reaction["short_name"] for reaction in name_in_vmh_reactions])
+        reaction_names = ", ".join([reaction["description"] for reaction in name_in_vmh_reactions])
         return JsonResponse({'status': 'error',
                              'message': f'The following reaction descriptions are already in VMH: {reaction_names}'})
 

curationTool/reactions/views/vmh_views.py

@@ -534,7 +534,7 @@ def add_to_vmh(request):
 
     reaction_identifiers, reaction_names = [
         reaction['abbreviation'] for reaction in reactions], [
-        reaction['description'] for reaction in reaction_objs]
+        reaction.description for reaction in reaction_objs]
     matlab_session = None  if all_vmh  else  MatlabSessionManager() 
     if not all_vmh:
         unique_abbrs, unique_mols, unique_types, unique_names = get_nonfound_metabolites(