linny-r 1.6.0 → 1.6.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "linny-r",
-  "version": "1.6.0",
+  "version": "1.6.1",
   "description": "Executable graphical language with WYSIWYG editor for MILP models",
   "main": "server.js",
   "scripts": {

package/static/scripts/linny-r-gui-controller.js

@@ -2935,8 +2935,8 @@ class GUIController extends Controller {
       }
       const err = MODEL.cloneSelection(prefix, actor_name, renumber);
       if(err) {
-        // Something went wrong, so do not hide the modal, but focus on the
-        // DOM element returned by the model's cloning method
+        // Something went wrong, so do not hide the modal, but focus on
+        // the DOM element returned by the model's cloning method.
         const el = md.element(err);
         if(el) {
           el.focus();
@@ -2956,7 +2956,7 @@ class GUIController extends Controller {
   }
   
   copySelection() {
-    // Save selection as XML in local storage of the browser
+    // Save selection as XML in local storage of the browser.
     const xml = MODEL.selectionAsXML;
     if(xml) {
       window.localStorage.setItem('Linny-R-selection-XML', xml);
@@ -2967,20 +2967,22 @@ class GUIController extends Controller {
   }
   
   get canPaste() {
+    // Return TRUE if the browser has a recent selection-as-XML object
+    // in its local storage.
     const xml = window.localStorage.getItem('Linny-R-selection-XML');
     if(xml) {
       const timestamp = xml.match(/<copy timestamp="(\d+)"/);
       if(timestamp) { 
         if(Date.now() - parseInt(timestamp[1]) < 8*3600000) return true;
       }
-      // Remove XML from local storage if older than 8 hours
+      // Remove XML from local storage if older than 8 hours.
       window.localStorage.removeItem('Linny-R-selection-XML');
     }
     return false;
   }
   
   promptForMapping(mapping) {
-    // Prompt user to specify name conflict resolution strategy
+    // Prompt user to specify name conflict resolution strategy.
     const md = this.paste_modal;
     md.mapping = mapping;
     md.element('from-prefix').innerText = mapping.from_prefix || '';
@@ -3000,7 +3002,8 @@ class GUIController extends Controller {
     if(tc.length) {
       sl.push('<div style="font-weight: bold; margin:4px 2px 2px 2px">',
         'Names for top-level clusters:</div>');
-      // Add text inputs for selected cluster nodes
+      const sll = sl.length;
+      // Add text inputs for selected cluster nodes.
       for(let i = 0; i < tc.length; i++) {
         const
             ti = mapping.top_clusters[tc[i]],
@@ -3012,11 +3015,14 @@ class GUIController extends Controller {
             '" type="text" style="', state, 'font-size: 12px" value="',
             ti, '"></div></div>');
       }
+      // Remove header when no items were added.
+      if(sl.length === sll) sl.pop();
     }
     if(ft.length) {
       sl.push('<div style="font-weight: bold; margin:4px 2px 2px 2px">',
         'Mapping of nodes to link from/to:</div>');
-      // Add selectors for unresolved FROM/TO nodes
+      const sll = sl.length;
+      // Add selectors for unresolved FROM/TO nodes.
       for(let i = 0; i < ft.length; i++) {
         const ti = mapping.from_to[ft[i]];
         if(ft[i] === ti) {
@@ -3036,15 +3042,17 @@ class GUIController extends Controller {
           sl.push('</div>');
         }
       }
+      // Remove header when no items were added.
+      if(sl.length === sll) sl.pop();
     }
     md.element('scroll-area').innerHTML = sl.join('');
-    // Open dialog, which will call pasteSelection(...) on OK
+    // Open dialog, which will call pasteSelection(...) on OK.
     this.paste_modal.show();
   }
   
   setPasteMapping() {
-    // Updates the paste mapping as specified by the modeler and then
-    // proceeds to paste
+    // Update the paste mapping as specified by the modeler and then
+    // proceed to paste.
     const
         md = this.paste_modal,
         mapping = Object.assign(md.mapping, {}),
@@ -3071,7 +3079,7 @@ class GUIController extends Controller {
   pasteSelection(mapping={}) {
     // If selection has been saved as XML in local storage, test to
     // see whether PASTE would result in name conflicts, and if so,
-    // open the name conflict resolution window
+    // open the name conflict resolution window.
     let xml = window.localStorage.getItem('Linny-R-selection-XML');
     try {
       xml = parseXML(xml);
@@ -3095,7 +3103,7 @@ class GUIController extends Controller {
     // AUXILIARY FUNCTIONS
     
     function fullName(node) {
-      // Returns full entity name inferred from XML node data
+      // Return full entity name inferred from XML node data.
       if(node.nodeName === 'from-to' || node.nodeName === 'selc') {
         const
             n = xmlDecoded(nodeParameterValue(node, 'name')),
@@ -3134,12 +3142,12 @@ class GUIController extends Controller {
     }
     
     function nameAndActor(name) {
-      // Returns tuple [entity name, actor name] if `name` ends with
-      // a parenthesized string that identifies an actor in the selection
+      // Return tuple [entity name, actor name] if `name` ends with a
+      // parenthesized string that identifies an actor in the selection.
       const ai = name.lastIndexOf(' (');
       if(ai < 0) return [name, ''];
       let actor = name.slice(ai + 2, -1);
-      // Test whether parenthesized string denotes an actor
+      // Test whether parenthesized string denotes an actor.
       if(actor_names.indexOf(actor) >= 0 || actor === mapping.actor ||
           actor === mapping.from_actor || actor === mapping.to_actor) {
         name = name.substring(0, ai);
@@ -3150,8 +3158,8 @@ class GUIController extends Controller {
     }
 
     function mappedName(n) {
-      // Returns full name `n` modified according to the mapping
-      // NOTE: links and constraints require two mappings (recursion!)
+      // Returns full name `n` modified according to the mapping.
+      // NOTE: Links and constraints require two mappings (recursion!).
       if(n.indexOf(UI.LINK_ARROW) > 0) {
         const ft = n.split(UI.LINK_ARROW);
         return mappedName(ft[0]) + UI.LINK_ARROW + mappedName(ft[1]);
@@ -3174,7 +3182,7 @@ class GUIController extends Controller {
         const ai = n.lastIndexOf(mapping.from_actor);
         if(ai > 0) return n.substring(0, ai) + mapping.to_actor;
       }
-      // NOTE: specified actor cannot override existing actor
+      // NOTE: specified actor cannot override existing actor.
       if(mapping.actor && !nameAndActor(n)[1]) {
         return `${n} (${mapping.actor})`;
       }
@@ -3191,23 +3199,27 @@ class GUIController extends Controller {
       if(mapping.from_to && mapping.from_to[n]) {
         return mapping.from_to[n];
       }
-      // No mapping => return original name
+      // No mapping => return original name.
       return n;
     }
 
     function nameConflicts(node) {
       // Maps names of entities defined by the child nodes of `node`
-      // while detecting name conflicts
+      // while detecting name conflicts.
       for(let i = 0; i < node.childNodes.length; i++) {
         const c = node.childNodes[i];
         if(c.nodeName !== 'link' && c.nodeName !== 'constraint') {
           const
               fn = fullName(c),
-              mn = mappedName(fn);
+              mn = mappedName(fn),
+              obj = MODEL.objectByName(mn),
+              // Assume that existing products can be added as product
+              // positions if they are not prefixed.
+              add_pp = (obj instanceof Product && mn.indexOf(UI.PREFIXER) < 0);
           // Name conflict occurs when the mapped name is already in use
           // in the target model, or when the original name is mapped onto
-          // different names (this might occur due to modeler input)
-          if(MODEL.objectByName(mn) || (name_map[fn] && name_map[fn] !== mn)) {
+          // different names (this might occur due to modeler input).
+          if((obj && !add_pp) || (name_map[fn] && name_map[fn] !== mn)) {
             addDistinct(fn, name_conflicts);
           } else {
             name_map[fn] = mn;
@@ -3217,10 +3229,10 @@ class GUIController extends Controller {
     }
     
     function addEntityFromNode(node) {
-      // Adds entity to model based on XML node data and mapping
-      // NOTE: do not add if an entity having this type and mapped name
+      // Adds entity to model based on XML node data and mapping.
+      // NOTE: Do not add if an entity having this type and mapped name
       // already exists; name conflicts accross entity types may occur
-      // and result in error messages
+      // and result in error messages.
       const
           et = node.nodeName,
           fn = fullName(node),
@@ -3282,17 +3294,17 @@ class GUIController extends Controller {
         sp = this.sharedPrefix(cn, fcn),
         fpn = (cn === UI.TOP_CLUSTER_NAME ? '' : cn.replace(sp, '')),
         tpn = (fcn === UI.TOP_CLUSTER_NAME ? '' : fcn.replace(sp, ''));
-    // Infer mapping from XML data and focal cluster name & actor name 
+    // Infer mapping from XML data and focal cluster name & actor name.
     mapping.shared_prefix = sp;
     mapping.from_prefix = (fpn ? sp + fpn + UI.PREFIXER : sp);
     mapping.to_prefix = (tpn ? sp + tpn + UI.PREFIXER : sp);
     mapping.from_actor = (ca === UI.NO_ACTOR ? '' : ca);
     mapping.to_actor = (fca === UI.NO_ACTOR ? '' : fca);
-    // Prompt for mapping when pasting to the same model and cluster
+    // Prompt for mapping when pasting to the same model and cluster.
     if(parseInt(mts) === MODEL.time_created.getTime() &&
         ca === fca && mapping.from_prefix === mapping.to_prefix &&
         !(mapping.prefix || mapping.actor || mapping.increment)) {
-      // Prompt for names of selected cluster nodes
+      // Prompt for names of selected cluster nodes.
       if(selc_node.childNodes.length && !mapping.prefix) {
         mapping.top_clusters = {};
         for(let i = 0; i < selc_node.childNodes.length; i++) {
@@ -3307,7 +3319,7 @@ class GUIController extends Controller {
       return;
     }
     // Also prompt if FROM and/or TO nodes are not selected, and map to
-    // existing entities
+    // existing entities.
     if(from_tos_node.childNodes.length && !mapping.from_to) {
       const
           ft_map = {},
@@ -3323,7 +3335,7 @@ class GUIController extends Controller {
               'Data' : nodeParameterValue(c, 'type'));
         }
       }
-      // Prompt only for FROM/TO nodes that map to existing nodes
+      // Prompt only for FROM/TO nodes that map to existing nodes.
       if(Object.keys(ft_map).length) {
         mapping.from_to = ft_map;
         mapping.from_to_type = ft_type;
@@ -3334,7 +3346,7 @@ class GUIController extends Controller {
 
     // Only check for selected entities; from-to's and extra's should be
     // used if they exist, or should be created when copying to a different
-    // model
+    // model.
     name_map.length = 0;
     nameConflicts(entities_node);
     if(name_conflicts.length) {
@@ -3353,20 +3365,20 @@ console.log('HERE name conflicts', name_conflicts, mapping);
     for(let i = 0; i < entities_node.childNodes.length; i++) {
       addEntityFromNode(entities_node.childNodes[i]);
     }
-    // Update diagram, showing newly added nodes as selection
+    // Update diagram, showing newly added nodes as selection.
     MODEL.clearSelection();
     for(let i = 0; i < selection_node.childNodes.length; i++) {
       const
           n = xmlDecoded(nodeContent(selection_node.childNodes[i])),
           obj = MODEL.objectByName(mappedName(n));
       if(obj) {
-        // NOTE: selected products must be positioned
+        // NOTE: Selected products must be positioned.
         if(obj instanceof Product) MODEL.focal_cluster.addProductPosition(obj);
         MODEL.select(obj);
       }
     }
     // Force redrawing the selection to ensure that links to positioned
-    // products are displayed as arrows instead of block arrows
+    // products are displayed as arrows instead of block arrows.
     fc.clearAllProcesses();
     UI.drawDiagram(MODEL);
     this.paste_modal.hide();

package/static/scripts/linny-r-gui-documentation-manager.js

@@ -338,7 +338,7 @@ class DocumentationManager {
         this.viewer.innerHTML = this.markdown;
         this.edit_btn.classList.remove('disab');
         this.edit_btn.classList.add('enab');
-        // NOTE: permit documentation of the model by raising the dialog
+        // NOTE: Permit documentation of the model by raising the dialog.
         if(this.entity === MODEL) this.dialog.style.zIndex = 101;
       } else if(e instanceof DatasetModifier) {
         this.title.innerHTML = e.selector;
@@ -347,17 +347,17 @@ class DocumentationManager {
         if(e.expression.eligible_prefixes) {
           const el = Object.keys(e.expression.eligible_prefixes)
               .sort(compareSelectors);
-          if(el.length > 0) this.viewer.innerHTML = 'Method <tt>' +
-              e.selector + '</tt> applies to ' +
-              pluralS(el.length, 'prefixed entity group').toLowerCase() +
-              ':<ul><li>' + el.join('</li><li>') + '</li></ul>';
+          if(el.length > 0) this.viewer.innerHTML = [
+              'Method <tt>', e.selector, '</tt> applies to ',
+              pluralS(el.length, 'prefixed entity group'),
+              ':<ul><li>', el.join('</li><li>'), '</li></ul>'].join('');
         }
       }
     }
   }
   
   rewrite(str) {
-    // Apply all the rewriting rules to `str`
+    // Apply all the rewriting rules to `str`.
     str = '\n' + str + '\n';
     this.rules.forEach(
         (rule) => { str = str.replace(rule.pattern, rule.rewrite); });
@@ -365,28 +365,29 @@ class DocumentationManager {
   }
   
   makeList(par, isp, type) {
-    // Split on the *global multi-line* item separator pattern
+    // Split on the *global multi-line* item separator pattern.
     const splitter = new RegExp(isp, 'gm'),
           list = par.split(splitter);
     if(list.length < 2) return false;
-    // Now we know that the paragraph contains at least one list item line
+    // Now we know that the paragraph contains at least one list item line.
     let start = 0;
-    // Paragraph may start with plain text, so check using the original pattern
+    // Paragraph may start with plain text, so check using the original
+    // pattern.
     if(!par.match(isp)) {
       // If so, retain this first part as a separate paragraph...
       start = 1;
-      // NOTE: add it only if it contains text
+      // NOTE: Add it only if it contains text.
       par = (list[0].trim() ? `<p>${this.rewrite(list[0])}</p>` : '');
-      // ... and clear it as list item
+      // ... and clear it as list item.
       list[0] = '';
     } else {
       par = '';
     }
-    // Rewrite each list item fragment that contains text 
+    // Rewrite each list item fragment that contains text.
     for(let j = start; j < list.length; j++) {
       list[j] = (list[j].trim() ? `<li>${this.rewrite(list[j])}</li>` : '');
     }
-    // Return assembled parts
+    // Return assembled parts.
     return [par, '<', type, 'l>', list.join(''), '</', type, 'l>'].join('');
   }
   
@@ -395,16 +396,16 @@ class DocumentationManager {
     const html = this.markup.split(/\n{2,}/);
     let list;
     for(let i = 0; i < html.length; i++) {
-      // Paragraph with only dashes and spaces becomes a horizontal rule 
+      // Paragraph with only dashes and spaces becomes a horizontal rule.
       if(html[i].match(/^( *-)+$/)) {
         html[i] = '<hr>';
-      // Paragraph may contain a bulleted list 
+      // Paragraph may contain a bulleted list.
       } else if ((list = this.makeList(html[i], /^ *- +/, 'u')) !== false) {
         html[i] = list;
-      // Paragraph may contain a numbered list 
+      // Paragraph may contain a numbered list.
       } else if ((list = this.makeList(html[i], /^ *\d+. +/, 'o')) !== false) {
         html[i] = list;
-      // Otherwise: default HTML paragraph
+      // Otherwise: default HTML paragraph.
       } else {
         html[i] = `<p>${this.rewrite(html[i])}</p>`;
       }
@@ -431,7 +432,7 @@ class DocumentationManager {
   }
   
   insertSymbol(sym) {
-    // Insert symbol (clicked item in list below text area) into text area 
+    // Insert symbol (clicked item in list below text area) into text area.
     this.editor.focus();
     let p = this.editor.selectionStart;
     const
@@ -454,7 +455,7 @@ class DocumentationManager {
       } else if(this.entity instanceof Constraint) {
         UI.paper.drawConstraint(this.entity);
       } else if (typeof this.entity.draw === 'function') {
-        // Only draw if the entity responds to that method
+        // Only draw if the entity responds to that method.
         this.entity.draw();
       }
     }
@@ -501,14 +502,14 @@ class DocumentationManager {
   }
 
   addMessage(msg) {
-    // Append message to the info messages list
+    // Append message to the info messages list.
     if(msg) this.info_messages.push(msg);
-    // Update dialog only when it is showing
+    // Update dialog only when it is showing.
     if(!UI.hidden(this.dialog.id)) this.showInfoMessages(true);
   }
   
   showInfoMessages(shift) {
-    // Show all messages that have appeared on the status line
+    // Show all messages that have appeared on the status line.
     const 
         n = this.info_messages.length,
         title = pluralS(n, 'message') + ' since the current model was loaded';
@@ -524,21 +525,21 @@ class DocumentationManager {
             '<div class="', m.status, first, '-msg">', m.text, '</div></div>');
       }
       this.viewer.innerHTML = divs.join('');
-      // Set the dialog title
+      // Set the dialog title.
       this.title.innerHTML = title;
     }
   }
 
   showArrowLinks(arrow) {
-    // Show list of links represented by a composite arrow
+    // Show list of links represented by a composite arrow.
     const
         n = arrow.links.length,
         msg = 'Arrow represents ' + pluralS(n, 'link');
     UI.setMessage(msg);
     if(this.visible && !this.editing) {
-      // Set the dialog title
+      // Set the dialog title.
       this.title.innerHTML = msg;
-      // Show list
+      // Show list.
       const lis = [];
       let l, dn, c, af;
       for(let i = 0; i < n; i++) {
@@ -570,7 +571,8 @@ class DocumentationManager {
   }
 
   showHiddenIO(node, arrow) {
-    // Show list of products or processes linked to node by an invisible arrow
+    // Show list of products or processes linked to node by an invisible
+    // arrow (i.e., links represented by a block arrow).
     let msg, iol;
     if(arrow === UI.BLOCK_IN) {
       iol = node.hidden_inputs;
@@ -586,9 +588,9 @@ class DocumentationManager {
     UI.on_block_arrow = true;
     UI.setMessage(msg);
     if(this.visible && !this.editing) {
-      // Set the dialog title
+      // Set the dialog title.
       this.title.innerHTML = msg;
-      // Show list
+      // Show list.
       const lis = [];
       for(let i = 0; i < iol.length; i++) {
         lis.push(`<li>${iol[i].displayName}</li>`);
@@ -599,17 +601,19 @@ class DocumentationManager {
   }
 
   showAllDocumentation() {
+    // Show (as HTML) all model entities (categorized by type) with their
+    // associated comments (if added by the modeler).
     const
         html = [],
         sl = MODEL.listOfAllComments;
     for(let i = 0; i < sl.length; i++) {
       if(sl[i].startsWith('_____')) {
-        // 5-underscore leader indicates: start of new category
+        // 5-underscore leader indicates: start of new category.
         html.push('<h2>', sl[i].substring(5), '</h2>');
       } else {
         // Expect model element name...
         html.push('<p><tt>', sl[i], '</tt><br><small>');
-        // ... immediately followed by its associated marked-up comments
+        // ... immediately followed by its associated marked-up comments.
         i++;
         this.markup = sl[i];
         html.push(this.markdown, '</small></p>');
@@ -617,7 +621,7 @@ class DocumentationManager {
     }
     this.title.innerHTML = 'Complete model documentation';
     this.viewer.innerHTML = html.join('');
-    // Deselect entity and disable editing
+    // Deselect entity and disable editing.
     this.entity = null;
     this.edit_btn.classList.remove('enab');
     this.edit_btn.classList.add('disab');

package/static/scripts/linny-r-gui-equation-manager.js

@@ -151,7 +151,7 @@ class EquationManager {
           (m === sm ? ' sel-set' : ''),
           '"><td class="equation-selector',
           (method ? ' method' : ''),
-          // Display in gray when method cannot be applied
+          // Display in gray when method cannot be applied.
           (m.expression.noMethodObject ? ' no-object' : ''),
           (m.expression.isStatic ? '' : ' it'), issue,
           (wild ? ' wildcard' : ''), clk, ', false);"', mover, '>',
@@ -268,20 +268,23 @@ class EquationManager {
     if(!this.selected_modifier) return;
     const
         sel = this.rename_modal.element('name').value,
-        // Keep track of old name
+        // Keep track of old name.
         oldm = this.selected_modifier,
         olds = oldm.selector,
-        // NOTE: addModifier returns existing one if selector not changed
+        // NOTE: addModifier returns existing one if selector not changed.
         m = MODEL.equations_dataset.addModifier(sel);
-    // NULL indicates invalid name
+    // NULL indicates invalid name.
     if(!m) return;
-    // If only case has changed, update the selector
-    // NOTE: equation names may contain spaces; if so, reduce to single space
+    // If only case has changed, update the selector.
+    // NOTE: Equation names may contain spaces; if so, reduce to single space.
     if(m === oldm) {
       m.selector = sel.trim().replace(/\s+/g, ' ');
     } else {
-      // When a new modifier has been added, more actions are needed
+      // When a new modifier has been added, more actions are needed.
       m.expression = oldm.expression;
+      // NOTE: The `attribute` property of the expression must be updated
+      // because it identifies the "owner" of the expression.
+      m.expression.attribute = m.selector;
       this.deleteEquation();
       this.selected_modifier = m;
     }

package/static/scripts/linny-r-gui-finder.js

@@ -441,6 +441,7 @@ class Finder {
       }
     }
     document.getElementById('finder-item-header').innerHTML = hdr;
+    occ.sort(compareSelectors);
     for(let i = 0; i < occ.length; i++) {
       const e = MODEL.objectByID(occ[i]);
       el.push(['<tr id="eotr', i, '" class="dataset" onclick="FINDER.reveal(\'',

package/static/scripts/linny-r-milp.js

@@ -51,8 +51,8 @@ module.exports = class MILPSolver {
     // Each external MILP solver application has its own interface
     // NOTE: the list may be extended to accommodate more MILP solvers
     if(this.id === 'gurobi') {
-      this.ext = '.mps';
-      this.user_model = path.join(workspace.solver_output, 'usr_model.mps');
+      this.ext = '.lp';
+      this.user_model = path.join(workspace.solver_output, 'usr_model.lp');
       this.solver_model = path.join(workspace.solver_output, 'solver_model.lp');
       this.solution = path.join(workspace.solver_output, 'model.json');
       this.log = path.join(workspace.solver_output, 'model.log');
@@ -283,17 +283,17 @@ module.exports = class MILPSolver {
         x_dict = {},
         getValuesFromDict = () => {
           // Returns a result vector for as many real numbers (as strings!)
-          // as there are columns (0 if not reported by the solver)
-          // (1) Sort on variable name
+          // as there are columns (0 if not reported by the solver).
+          // First sort on variable name
           const vlist = Object.keys(x_dict).sort();
-          // Start with column 1
+          // Start with column 1.
           let col = 1;
           for(let i = 0; i < vlist.length; i++) {
             const
                 v = vlist[i],
-                // Variable names have zero-padded column numbers, e.g. "X001"
+                // Variable names have zero-padded column numbers, e.g. "X001".
                 vnr = parseInt(v.substring(1));
-            // Add zeros for unreported variables until column number matches
+            // Add zeros for unreported variables until column number matches.
             while(col < vnr) {
               x_values.push('0');
               col++;
@@ -301,23 +301,23 @@ module.exports = class MILPSolver {
             x_values.push(x_dict[v]);
             col++;
           }
-          // Add zeros to vector for remaining columns
+          // Add zeros to vector for remaining columns.
           while(col <= result.columns) {
             x_values.push('0');
             col++;
           }
-          // No return value; function operates on x_values
+          // No return value; function operates on x_values.
         };
 
     if(this.id === 'gurobi') {
-      // `messages` must be an array of strings
+      // `messages` must be an array of strings.
       result.messages = fs.readFileSync(this.log, 'utf8').split(os.EOL);
       if(result.status !== 0) {
-        // Non-zero solver exit code may indicate expired license
+        // Non-zero solver exit code may indicate expired license.
         result.error = 'Your Gurobi license may have expired';
       } else {
         try {
-          // Read JSON string from solution file
+          // Read JSON string from solution file.
           const
               json = fs.readFileSync(this.solution, 'utf8').trim(),
               sol = JSON.parse(json);
@@ -329,13 +329,16 @@ module.exports = class MILPSolver {
             if(!result.error) result.error = 'Unknown solver error';
             console.log(`Solver status: ${result.status} - ${result.error}`);
           }
-          // Objective value
+          // Objective value.
           result.obj = sol.SolutionInfo.ObjVal;
-          // Values of solution vector
+          // Values of solution vector.
           if(sol.Vars) {
+            // Fill dictionary with variable name: value entries.
             for(let i = 0; i < sol.Vars.length; i++) {
-              x_values.push(sol.Vars[i].X);
+              x_dict[sol.Vars[i].VarName] = sol.Vars[i].X;
             }
+            // Fill the solution vector, adding 0 for missing columns.
+            getValuesFromDict();
           }
         } catch(err) {
           console.log('WARNING: Could not read solution file');

package/static/scripts/linny-r-model.js

@@ -1561,13 +1561,21 @@ class LinnyRModel {
   //
 
   alignToGrid() {
-    // Move all positioned model elements to the nearest grid point
+    // Move all positioned model elements to the nearest grid point.
     if(!this.align_to_grid) return;
     let move = false;
     const fc = this.focal_cluster;
     // NOTE: Do not align notes to the grid. This will permit more
     // precise positioning, while aligning will not improve the layout
     // of the diagram because notes are not connected to arrows.
+    // However, when notes relate to nearby nodes, preserve their relative
+    // position to this node.
+    for(let i = 0; i < fc.notes.length; i++) {
+      const
+          note = fc.notes[i],
+          nbn = note.nearbyNode;
+      note.nearby_pos = (nbn ? {node: nbn, oldx: x, oldy: y} : null);
+    }
     for(let i = 0; i < fc.processes.length; i++) {
       move = fc.processes[i].alignToGrid() || move;
     }
@@ -1577,11 +1585,25 @@ class LinnyRModel {
     for(let i = 0; i < fc.sub_clusters.length; i++) {
       move = fc.sub_clusters[i].alignToGrid() || move;
     }
-    if(move) UI.drawDiagram(this);
+    if(move) {
+      // Reposition "associated" notes.
+      for(let i = 0; i < fc.notes.length; i++) {
+        const
+            note = fc.notes[i],
+            nbp = note.nearby_pos;
+        if(nbp) {
+          // Adjust (x, y) so as to retain the relative position.
+          note.x += nbp.node.x - npb.oldx;
+          note.y += nbp.node.y - npb.oldy;
+          note.nearby_pos = null;
+        }
+      }
+      UI.drawDiagram(this);
+    }
   }
   
   translateGraph(dx, dy) {
-    // Move all entities in the focal cluster by (dx, dy) pixels
+    // Move all entities in the focal cluster by (dx, dy) pixels.
     if(!dx && !dy) return;
     const fc = this.focal_cluster;
     for(let i = 0; i < fc.processes.length; i++) {
@@ -1600,9 +1622,9 @@ class LinnyRModel {
       fc.notes[i].x += dx;
       fc.notes[i].y += dy;
     }
-    // NOTE: force drawing, because SVG must immediately be downloadable
+    // NOTE: force drawing, because SVG must immediately be downloadable.
     UI.drawDiagram(this);
-    // If dragging, add (dx, dy) to the properties of the top "move" UndoEdit
+    // If dragging, add (dx, dy) to the properties of the top "move" UndoEdit.
     if(UI.dragged_node) UNDO_STACK.addOffset(dx, dy);
   }
 
@@ -1748,8 +1770,8 @@ class LinnyRModel {
         miny = Math.min(miny, obj.y - obj.height / 2);
       }
     }
-    // Translate entire graph if some elements are above and/or left of the
-    // paper edge
+    // Translate entire graph if some elements are above and/or left of
+    // the paper edge.
     if(minx < 0 || miny < 0) {
       // NOTE: limit translation to 5 pixels to prevent "run-away effect"
       this.translateGraph(Math.min(5, -minx), Math.min(5, -miny));
@@ -2186,8 +2208,8 @@ class LinnyRModel {
   }
   
   deleteSelection() {
-    // Removes all selected nodes (with their associated links and constraints)
-    // and selected links
+    // Remove all selected nodes (with their associated links and constraints)
+    // and selected links.
     // NOTE: This method implements the DELETE action, and hence should be
     // undoable. The UndoEdit is created by the calling routine; the methods
     // that actually delete model elements append their XML to the XML attribute
@@ -2195,7 +2217,7 @@ class LinnyRModel {
     let obj,
         fc = this.focal_cluster;
     // Update the documentation manager (GUI only) if selection contains the
-    // current entity
+    // current entity.
     if(DOCUMENTATION_MANAGER) DOCUMENTATION_MANAGER.clearEntity(this.selection);
     // First delete links and constraints.
     for(let i = this.selection.length - 1; i >= 0; i--) {
@@ -3222,6 +3244,29 @@ class LinnyRModel {
         sl.push(this.datasets[obj].displayName, this.datasets[obj].comments);
       }
     }
+    const keys = Object.keys(this.equations_dataset.modifiers); 
+    sl.push('_____Equations');
+    for(let i = 0; i < keys.length; i++) {
+      const m = this.equations_dataset.modifiers[keys[i]];
+      if(!m.selector.startsWith(':')) {
+        sl.push(m.displayName, '`' + m.expression.text + '`\n');
+      }
+    }
+    sl.push('_____Methods');
+    for(let i = 0; i < keys.length; i++) {
+      const m = this.equations_dataset.modifiers[keys[i]];
+      if(m.selector.startsWith(':')) {
+        let markup = '\n\nDoes not apply to any entity.';
+        if(m.expression.eligible_prefixes) {
+          const el = Object.keys(m.expression.eligible_prefixes)
+              .sort(compareSelectors);
+          if(el.length > 0) markup = '\n\nApplies to ' +
+              pluralS(el.length, 'prefixed entity group') +
+              ':\n- ' + el.join('\n- ');
+        }
+        sl.push(m.displayName, '`' + m.expression.text + '`' + markup);
+      }
+    }
     sl.push('_____Charts');
     for(let i = 0; i < this.charts.length; i++) {
       sl.push(this.charts[i].title, this.charts[i].comments);
@@ -4817,7 +4862,7 @@ class ObjectWithXYWH {
 
   alignToGrid() {
     // Align this object to the grid, and return TRUE if this involved
-    // a move
+    // a move.
     const
         ox = this.x,
         oy = this.y,
@@ -6139,8 +6184,8 @@ class Cluster extends NodeBox {
   }
 
   addProductPosition(p, x=null, y=null) {
-    // Add a product position for product `p` to this cluster unless such pp
-    // already exists; then return this (new) product position
+    // Add a product position for product `p` to this cluster unless such
+    // "pp" already exists, and then return this (new) product position.
     let pp = this.indexOfProduct(p);
     if(pp >= 0) {
       pp = this.product_positions[pp];
@@ -6158,7 +6203,8 @@ class Cluster extends NodeBox {
   }
 
   containsProduct(p) {
-    // Return the subcluster of this cluster that contains product `p`, or null
+    // Return the subcluster of this cluster that contains product `p`,
+    // or NULL if `p` does not occur in this cluster.
     if(this.indexOfProduct(p) >= 0) return this;
     for(let i = 0; i < this.sub_clusters.length; i++) {
       if(this.sub_clusters[i].containsProduct(p)) {
@@ -8712,8 +8758,8 @@ class Dataset {
     return d.join(';');
   }
   
-  // Returns a string denoting the properties of this dataset.
   get propertiesString() {
+    // Return a string denoting the properties of this dataset.
     if(this.data.length === 0) return '';
     let time_prop;
     if(this.array) {
@@ -8724,12 +8770,12 @@ class Dataset {
         DATASET_MANAGER.method_symbols[
             DATASET_MANAGER.methods.indexOf(this.method)]].join('');
     }
-    // Circular arrow symbolizes "repeating"
+    // Circular arrow symbolizes "repeating".
     return '&nbsp;(' + time_prop + (this.periodic ? '&nbsp;\u21BB' : '') + ')'; 
   }
   
   unpackDataString(str) {
-    // Converts semicolon-separated data to a numeric array.
+    // Convert semicolon-separated data to a numeric array.
     this.data.length = 0;
     if(str) {
       const numbers = str.split(';');
@@ -8742,12 +8788,12 @@ class Dataset {
   }
 
   computeVector() {
-    // Converts data to a vector on the model's time scale, i.e., 1 time step
-    // lasting one unit on the model time scale
+    // Convert data to a vector on the time scale of the model, i.e.,
+    // 1 time step lasting one unit on the model time scale.
     
-    // NOTE: since 9 October 2021, a dataset can also be defined as an "array",
-    // which differs from a time series in that the vector is filled with the
-    // data values "as is" to permit accessing a specific value at index # 
+    // NOTE: A dataset can also be defined as an "array", which differs
+    // from a time series in that the vector is filled with the data values
+    // "as is" to permit accessing a specific value at index #. 
     if(this.array) {
       this.vector = this.data.slice();
       return;
@@ -8755,16 +8801,16 @@ class Dataset {
     // Like all vectors, vector[0] corresponds to initial value, and vector[1]
     // to the model setting "Optimize from step t=..."
     // NOTES:
-    // (1) the first number of a datasets time series is ALWAYS assumed to
+    // (1) The first number of a datasets time series is ALWAYS assumed to
     //     correspond to t=1, whereas the simulation may be set to start later!
-    // (2) model run length includes 1 look-ahead period
+    // (2) Model run length includes 1 look-ahead period.
     VM.scaleDataToVector(this.data, this.vector, this.timeStepDuration,
         MODEL.timeStepDuration, MODEL.runLength, MODEL.start_period,
         this.defaultValue, this.periodic, this.method);
   }
 
   computeStatistics() {
-    // Computes descriptive statistics for data (NOT vector!).
+    // Compute descriptive statistics for data (NOT vector!).
     if(this.data.length === 0) {
       this.min = VM.UNDEFINED;
       this.max = VM.UNDEFINED;
@@ -8789,18 +8835,18 @@ class Dataset {
   }
   
   get statisticsAsString() {
-    // Returns descriptive statistics in human-readable form
+    // Return descriptive statistics in human-readable form.
     let s = 'N = ' + this.data.length;
     if(N > 0) {
-      s += ', range = [' + VM.sig4Dig(this.min) + ', ' + VM.sig4Dig(this.max) +
-          ', mean = ' + VM.sig4Dig(this.mean) + ', s.d. = ' +
-          VM.sig4Dig(this.standard_deviation);
+      s += [', range = [', VM.sig4Dig(this.min), ', ', VM.sig4Dig(this.max),
+          '], mean = ', VM.sig4Dig(this.mean), ', s.d. = ',
+          VM.sig4Dig(this.standard_deviation)].join('');
     }
     return s;
   }
   
   attributeValue(a) {
-    // Returns the computed result for attribute `a`.
+    // Return the computed result for attribute `a`.
     // NOTE: Datasets have ONE attribute (their vector) denoted by the empty
     // string; all other "attributes" should be modifier selectors, and
     // their value should be obtained using attributeExpression (see below).
@@ -8809,9 +8855,9 @@ class Dataset {
   }
 
   attributeExpression(a) {
-    // Returns expression for selector `a` (also considering wildcard
+    // Return the expression for selector `a` (also considering wildcard
     // modifiers), or NULL if no such selector exists.
-    // NOTE: selectors no longer are case-sensitive.
+    // NOTE: Selectors no longer are case-sensitive.
     if(a) {
       const mm = this.matchingModifiers([a]);
       if(mm.length > 0) return mm[0].expression;
@@ -8822,29 +8868,29 @@ class Dataset {
   get activeModifierExpression() { 
     if(MODEL.running_experiment) {
       // If an experiment is running, check if dataset modifiers match the
-      // combination of selectors for the active run
+      // combination of selectors for the active run.
       const mm = this.matchingModifiers(MODEL.running_experiment.activeCombination);
-      // If so, use the first match
+      // If so, use the first match.
       if(mm.length > 0) return mm[0].expression;
     }
     if(this.default_selector) {
-      // If no experiment (so "normal" run), use default selector if specified
+      // If no experiment (so "normal" run), use default selector if specified.
       const dm = this.modifiers[UI.nameToID(this.default_selector)];
       if(dm) return dm.expression;
-      // Exception should never occur, but check anyway and log it 
+      // Exception should never occur, but check anyway and log it.
       console.log('WARNING: Dataset "' + this.name +
           `" has no default selector "${this.default_selector}"`, this.modifiers);
     }
-    // Fall-through: return vector instead of expression
+    // Fall-through: return vector instead of expression.
     return this.vector;
   }
   
   addModifier(selector, node=null, ioc=null) {
     let s = selector;
-    // Firstly, sanitize the selector
+    // First sanitize the selector.
     if(this === MODEL.equations_dataset) {
       // Equation identifiers cannot contain characters that have special
-      // meaning in a variable identifier
+      // meaning in a variable identifier.
       s = s.replace(/[\*\|\[\]\{\}\@\#]/g, '');
       if(s !== selector) {
         UI.warn('Equation name cannot contain [, ], {, }, |, @, # or *');
@@ -8868,26 +8914,26 @@ class Dataset {
           return null;
         }
       } else {
-        // Prefix it when the IO context argument is defined 
+        // Prefix it when the IO context argument is defined.
         if(ioc) s = ioc.actualName(s);
       }
-      // If equation already exists, return its modifier
+      // If equation already exists, return its modifier.
       const id = UI.nameToID(s);
       if(this.modifiers.hasOwnProperty(id)) return this.modifiers[id];
-      // New equation identifier must not equal some entity ID
+      // New equation identifier must not equal some entity ID.
       const obj = MODEL.objectByName(s);
       if(obj) {
-        // NOTE: also pass selector, or warning will display dataset name
+        // NOTE: Also pass selector, or warning will display dataset name.
         UI.warningEntityExists(obj);
         return null;
       }
     } else {
       // Standard dataset modifier selectors are much more restricted, but
-      // to be user-friendly, special chars are removed automatically
+      // to be user-friendly, special chars are removed automatically.
       s = s.replace(/[^a-zA-Z0-9\+\-\%\_\*\?]/g, '');
       let msg = '';
       if(s !== selector) msg = UI.WARNING.SELECTOR_SYNTAX;
-      // A selector can only contain 1 star
+      // A selector can only contain 1 star.
       if(s.indexOf('*') !== s.lastIndexOf('*')) msg = UI.WARNING.SINGLE_WILDCARD;
       if(msg) {
         UI.warn(msg);
@@ -8898,12 +8944,12 @@ class Dataset {
       UI.warn(UI.WARNING.INVALID_SELECTOR);
       return null;
     }
-    // Then add a dataset modifier to this dataset
+    // Then add a dataset modifier to this dataset.
     const id = UI.nameToID(s);
     if(!this.modifiers.hasOwnProperty(id)) {
       this.modifiers[id] = new DatasetModifier(this, s);
     }
-    // Finally, initialize it when the XML node argument is defined
+    // Finally, initialize it when the XML node argument is defined.
     if(node) this.modifiers[id].initFromXML(node);
     return this.modifiers[id];
   }
@@ -8927,7 +8973,7 @@ class Dataset {
     for(let i = 0; i < sl.length; i++) {
       ml.push(this.modifiers[sl[i]].asXML);
     }
-    // NOTE: "black-boxed" datasets are stored anonymously without comments
+    // NOTE: "black-boxed" datasets are stored anonymously without comments.
     const id = UI.nameToID(n);
     if(MODEL.black_box_entities.hasOwnProperty(id)) {
       n = MODEL.black_box_entities[id];
@@ -8959,7 +9005,7 @@ class Dataset {
     this.periodic = nodeParameterValue(node, 'periodic') === '1';
     this.array = nodeParameterValue(node, 'array') === '1';
     this.black_box = nodeParameterValue(node, 'black-box') === '1';
-    // NOTE: array-type datasets are by definition input => not an outcome
+    // NOTE: Array-type datasets are by definition input => not an outcome.
     if(!this.array) this.outcome = nodeParameterValue(node, 'outcome') === '1';
     this.url = xmlDecoded(nodeContentByTag(node, 'url'));
     if(this.url) {
@@ -8985,10 +9031,10 @@ class Dataset {
   }
   
   rename(name, notify=true) {
-    // Change the name of this dataset
+    // Change the name of this dataset.
     // When `notify` is FALSE, notifications are suppressed while the
-    // number of affected datasets and expressions are counted
-    // NOTE: prevent renaming the equations dataset (just in case...)
+    // number of affected datasets and expressions are counted.
+    // NOTE: Prevent renaming the equations dataset (just in case).
     if(this === MODEL.equations_dataset) return;
     name = UI.cleanName(name);
     if(!UI.validName(name)) {
@@ -9012,31 +9058,31 @@ class Dataset {
   }
   
   resetExpressions() {
-    // Recalculate vector to adjust to model time scale and run length
+    // Recalculate vector to adjust to model time scale and run length.
     this.computeVector();
-    // Reset all modifier expressions
+    // Reset all modifier expressions.
     for(let m in this.modifiers) if(this.modifiers.hasOwnProperty(m)) {
-      // NOTE: "empty" expressions for modifiers default to dataset default
+      // NOTE: "empty" expressions for modifiers default to dataset default.
       this.modifiers[m].expression.reset(this.defaultValue);
       this.modifiers[m].expression_cache = {};
     }
   }
 
   compileExpressions() {
-    // Recompile all modifier expressions
+    // Recompile all modifier expressions.
     for(let m in this.modifiers) if(this.modifiers.hasOwnProperty(m)) {
       this.modifiers[m].expression.compile();
     }
   }
 
   differences(ds) {
-    // Return "dictionary" of differences, or NULL if none
+    // Return "dictionary" of differences, or NULL if none.
     const d = differences(this, ds, UI.MC.DATASET_PROPS);
-    // Check for differences in data
+    // Check for differences in data.
     if(this.dataString !== ds.dataString) {
       d.data = {A: this.statisticsAsString, B: ds.statisticsAsString};
     }
-    // Check for differences in modifiers
+    // Check for differences in modifiers.
     const mdiff = {};
     for(let m in this.modifiers) if(this.modifiers.hasOwnProperty(m)) {
       const
@@ -9055,7 +9101,7 @@ class Dataset {
         mdiff[m] = [UI.MC.DELETED, dsm.selector, dsm.expression.text];
       }
     }
-    // Only add modifiers property if differences were detected
+    // Only add modifiers property if differences were detected.
     if(Object.keys(mdiff).length > 0) d.modifiers = mdiff; 
     if(Object.keys(d).length > 0) return d;
     return null;
@@ -9064,7 +9110,7 @@ class Dataset {
 } // END of class Dataset
 
 
-// CLASS ChartVariable defines properties of chart time series
+// CLASS ChartVariable defines properties of chart time series.
 class ChartVariable {
   constructor(c) {
     this.chart = c;

package/static/scripts/linny-r-utils.js

@@ -743,17 +743,28 @@ function xmlDecoded(str) {
 }
 
 function customizeXML(str) {
-  // NOTE: this function can be customized to pre-process a model file,
+  // NOTE: This function can be customized to pre-process a model file,
   // for example to rename entities in one go -- USE WITH CARE!
-  // First modify `str` -- by default, do nothing
-  
+  // To prevent unintended customization, check whether the model name
+  // ends with "!!CUSTOMIZE". This check ensures that the modeler must
+  // first save the model with this text as the (end of the) model name
+  // and then load it again for the customization to be performed.
+  if(str.indexOf('!!CUSTOMIZE</name><author>') >= 0) {
+    // Modify `str` -- by default, do nothing, but typical modifications
+    // will replace RexEx patterns by other strings.
+    
 /*
-  if(str.indexOf('<version>1.4.') >= 0) {
-    str = str.replace(/<url>NL\/(\w+)\.csv<\/url>/g, '<url></url>');
-  }
+    const
+        re = /xyz/gi,
+        r = 'abc';
 */
 
-  // Finally, return the modified string
+    // Trace the changes to the console.
+    console.log('Customizing:', re, r);
+    console.log('Matches:', str.match(re));
+    str = str.replace(re, r);
+  }
+  // Finally, return the modified string.
   return str;
 }
 

package/static/scripts/linny-r-vm.js

@@ -4319,7 +4319,7 @@ class VirtualMachine {
     // `cbl` is the cropped block length (applies only to last block).
     let bb = (block - 1) * MODEL.block_length + 1,
         abl = this.chunk_length,
-        cbl = this.actualBlockLength;
+        cbl = this.actualBlockLength(block);
     // For the last block, crop the actual block length so it does not
     // extend beyond the simulation period (these results should be ignored).
     // If no results computed, preserve those already computed for the
@@ -4761,7 +4761,7 @@ class VirtualMachine {
   
   setupBlock() {
     if(DEBUGGING) this.logCode();
-    const abl = this.actualBlockLength;
+    const abl = this.actualBlockLength(this.block_count);
     // NOTE: Tableau segment length is the number of time steps between
     // updates of the progress needle. The default progress needle interval
     // is calibrated for 1000 VMI instructions.
@@ -4955,12 +4955,12 @@ class VirtualMachine {
     setTimeout(() => VM.solveBlock(), 0);
   }
   
-  get actualBlockLength() {
+  actualBlockLength(block) {
     // The actual block length is the number of time steps to be considered
     // by the solver; the abl of the last block is likely to be shorter
     // than the standard, as it should not go beyond the end time plus
     // look-ahead.
-    if(this.block_count < this.nr_of_blocks) return this.chunk_length;
+    if(block < this.nr_of_blocks) return this.chunk_length;
     // Last block length equals remainder of simulation period divided
     // by block length.
     let rem = (MODEL.runLength - MODEL.look_ahead) % MODEL.block_length;
@@ -5005,7 +5005,7 @@ class VirtualMachine {
     // behavior can still be generated by limiting time series length to
     // the simulation period.
     const
-        abl = this.actualBlockLength,
+        abl = this.actualBlockLength(this.block_count),
         // Get the number digits for variable names
         z = this.columnsInBlock.toString().length,
         // LP_solve uses semicolon as separator between equations
@@ -5240,7 +5240,7 @@ class VirtualMachine {
     // instead of row-based, hence for each column a separate string list.
     // NOTE: Columns are numbered from 1 to N, hence a dummy list for c=0.
     const
-        abl = this.actualBlockLength,
+        abl = this.actualBlockLength(this.block_count),
         cols = [[]],
         rhs = [];
     let nrow = this.matrix.length,
@@ -5248,7 +5248,7 @@ class VirtualMachine {
         c,
         p,
         r;
-    this.numeric_issue = '';
+   this.numeric_issue = '';
     this.lines = '';
     for(c = 1; c <= ncol; c++) cols.push([]);
     this.decimals = Math.max(nrow, ncol).toString().length;
@@ -5422,7 +5422,7 @@ class VirtualMachine {
     // Add the SOS section.
     if(this.sos_var_indices.length > 0) {
       this.lines += 'SOS\n';
-      const abl = this.actualBlockLength;
+      const abl = this.actualBlockLength(this.block_count);
       let sos = 1;
       for(let j = 0; j < abl; j++) {
         for(let i = 0; i < this.sos_var_indices.length; i++) {
@@ -5594,7 +5594,7 @@ Solver status = ${json.status}`);
     const
         bwr = this.blockWithRound,
         fromt = (this.block_count - 1) * MODEL.block_length + 1,
-        abl = this.actualBlockLength;
+        abl = this.actualBlockLength(this.block_count);
     MONITOR.updateBlockNumber(bwr);
     // NOTE: Add blank line to message to visually separate rounds.
     this.logMessage(this.block_count, ['\nSetting up block #', bwr,
@@ -5626,7 +5626,8 @@ Solver status = ${json.status}`);
     }
     // Generate lines of code in format that should be accepted by solver.
     if(this.solver_name === 'gurobi') {
-      this.writeMPSFormat();
+      //this.writeMPSFormat();
+      this.writeLpFormat(true);
     } else if(this.solver_name === 'scip' || this.solver_name === 'cplex') {
       // NOTE: The CPLEX LP format that is also used by SCIP differs from
       // the LP_solve format that was used by the first versions of Linny-R.