linny-r 1.8.2 → 1.9.1

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

@@ -41,6 +41,7 @@ class ModelAutoSaver {
     this.timeout_id = 0;
     this.interval = 10; // auto-save every 10 minutes
     this.period = 24; // delete models older than 24 hours
+    this.not_implemented = false;
     this.model_list = [];
     // Overwite defaults if settings still in local storage of browser.
     this.getSettings();
@@ -65,6 +66,7 @@ class ModelAutoSaver {
   
   getSettings() {
     // Reads custom auto-save settings from local storage.
+    if(this.not_implemented) return;
     try {
       const item = window.localStorage.getItem('Linny-R-autosave');
       if(item) {
@@ -86,6 +88,7 @@ class ModelAutoSaver {
   
   setSettings() {
     // Writes custom auto-save settings to local storage.
+    if(this.not_implemented) return;
     try {
       window.localStorage.setItem('Linny-R-autosave',
           this.interval + '|' + this.period);
@@ -199,7 +202,7 @@ class ModelAutoSaver {
     // Close the restore auto-save model dialog.
     document.getElementById('confirm-remove-models').style.display = 'none';
     // NOTE: Cancel button or ESC will pass `cancel` as FALSE => do not save.
-    if(!save) {
+    if(!save || this.not_implemented) {
       document.getElementById('restore-modal').style.display = 'none';
       return;
     }

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

@@ -326,6 +326,7 @@ class GUIMonitor {
           } else if(jsr.server) {
             VM.solver_token = jsr.token;
             VM.selectSolver(jsr.solver);
+            VM.solver_list = jsr.solver_list;
             // Remote solver may indicate user-specific solver time limit.
             let utl = '';
             if(jsr.time_limit) {

package/static/scripts/linny-r-gui-repository-browser.js

@@ -368,7 +368,7 @@ class GUIRepositoryBrowser extends RepositoryBrowser {
   }
   
   addRepository(name) {
-    // Adds repository if name is unique and valid
+    // Adds repository if name is unique and valid.
     let r = null,
         can_store = false;
     if(name.endsWith('+')) {
@@ -389,8 +389,8 @@ class GUIRepositoryBrowser extends RepositoryBrowser {
   }
   
   removeRepository() {
-    // Removes selected repository from list
-    // NOTE: do not remove the first item (local host)
+    // Removes selected repository from list.
+    // NOTE: Do not remove the first item (local host).
     if(this.repository_index < 1) return;
     fetch('repo/', postData({
           action: 'remove',
@@ -415,7 +415,8 @@ class GUIRepositoryBrowser extends RepositoryBrowser {
   }
   
   promptForRepository() {
-    // Opens "Add repository" dialog
+    // Open "Add repository" dialog (only on local host).
+    if(!this.isLocalHost) return;
     this.add_modal.element('name').value = '';
     this.add_modal.element('url').value = '';
     this.add_modal.element('token').value = '';
@@ -423,7 +424,7 @@ class GUIRepositoryBrowser extends RepositoryBrowser {
   }
 
   registerRepository() {
-    // Checks whether URL defines a Linny-R repository, and if so, adds it
+    // Check whether URL defines a Linny-R repository, and if so, add it.
     fetch('repo/', postData({
           action: 'add',
           repo: this.add_modal.element('name').value,

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

@@ -341,7 +341,7 @@ module.exports = class MILPSolver {
           'write problem', s.solver_model,
           'set limit time %T%',
           'set numerics feastol %I%',
-          // NOTE: MIP gap setting for SCIP is unclear, hence ignored.
+          'set limit gap %M%',
           'optimize',
           'write solution', s.solution,
           'quit'
@@ -392,6 +392,7 @@ module.exports = class MILPSolver {
       s.args = [
           '-timeout %T%',
           '-v4',
+          '-ac 5e-6',
           '-e %I%',
           '-gr %M%',
           '-epsel 1e-7',
@@ -838,14 +839,13 @@ module.exports = class MILPSolver {
         }
       }
       if(solved) {
-        // Look for line with first variable.
-        let i = 0;
-        while(i < output.length && !output[i].startsWith('X')) i++;
+        // Line 0 holds solution status, line 1 the objective value,
+        // and lines 2+ the variables.
+        result.obj = parseFloat(output[1].split(':')[1]);
         // Fill dictionary with variable name: value entries .
-        while(i < output.length) {
+        for(let i = 2; i < output.length; i++) {
           const v = output[i].split(/\s+/);
           x_dict[v[0]] = parseFloat(v[1]);
-          i++;
         }
         // Fill the solution vector, adding 0 for missing columns.
         getValuesFromDict();
@@ -873,6 +873,8 @@ module.exports = class MILPSolver {
       }
       result.messages = msgs;
       if(solved) {
+        // Get value of objective function
+        result.obj = parseFloat(output[i].split(':')[1]);
         // Look for line with first variable.
         while(i < output.length && !output[i].startsWith('X')) i++;
         // Fill dictionary with variable name: value entries.

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

@@ -70,6 +70,8 @@ class LinnyRModel {
     this.charts = [];
     this.experiments = [];
     this.dimensions = [];
+    this.selector_order_string = '';
+    this.selector_order_list = [];
     this.next_process_number = 0;
     this.next_product_number = 0;
     this.focal_cluster = null;
@@ -104,7 +106,8 @@ class LinnyRModel {
     this.preferred_solver = ''; // empty string denotes "use default"
     this.integer_tolerance = 5e-7; // integer feasibility tolerance
     this.MIP_gap = 1e-4; // relative MIP gap
-    this.always_diagnose = false;
+    this.always_diagnose = true;
+    this.show_notices = true;
 
     // Sensitivity-related properties
     this.base_case_selectors = '';
@@ -2668,6 +2671,7 @@ class LinnyRModel {
       this.report_results = nodeParameterValue(node, 'report-results') === '1';
       this.show_block_arrows = nodeParameterValue(node, 'block-arrows') === '1';
       this.always_diagnose = nodeParameterValue(node, 'diagnose') === '1';
+      this.show_notices = nodeParameterValue(node, 'show-notices') === '1';
       this.name = xmlDecoded(nodeContentByTag(node, 'name'));
       this.author = xmlDecoded(nodeContentByTag(node, 'author'));
       this.comments = xmlDecoded(nodeContentByTag(node, 'notes'));
@@ -2905,6 +2909,10 @@ class LinnyRModel {
         }
       }
     }
+    // Infer selector order list by splitting text on any white space.
+    this.selector_order_string = xmlDecoded(nodeContentByTag(node,
+        'selector-order'));
+    this.selector_order_list = this.selector_order_string.trim().split(/\s+/);
     // Infer dimensions of experimental design space
     this.inferDimensions();
     // NOTE: when including a model, IGNORE sensitivity analysis, experiments
@@ -3017,6 +3025,7 @@ class LinnyRModel {
     if(this.report_results) p += ' report-results="1"';
     if(this.show_block_arrows) p += ' block-arrows="1"';
     if(this.always_diagnose) p += ' diagnose="1"';
+    if(this.show_notices) p += ' show-notices="1"';
     let xml = this.xml_header + ['<model', p, '><name>',  xmlEncoded(this.name),
         '</name><author>', xmlEncoded(this.author),
         '</author><notes>', xmlEncoded(this.comments),
@@ -3074,8 +3083,11 @@ class LinnyRModel {
       if(this.datasets.hasOwnProperty(obj)) xml += this.datasets[obj].asXML;
     }
     xml += '</datasets><charts>';
-      for(let i = 0; i < this.charts.length; i++) xml += this.charts[i].asXML;
-      xml += '</charts>';
+    for(let i = 0; i < this.charts.length; i++) {
+      xml += this.charts[i].asXML;
+    }
+    xml += '</charts><selector-order>' +
+        xmlEncoded(this.selector_order_string) + '</selector-order>';
     // NOTE: when "black-boxing", SA and experiments are not stored 
     if(!this.black_box) {
       xml += '<base-case-selectors>' +
@@ -7943,54 +7955,59 @@ class Product extends Node {
   }
 
   get isSinkNode() {
-    // Returns TRUE if this product behaves as a sink
+    // Return TRUE if this product behaves as a sink.
     return (this.is_sink || this.allOutputsAreData) &&
       !(this.upper_bound.defined ||
-        // NOTE: UB may be set by equalling it to LB
+        // NOTE: UB may be set by equalling it to LB.
         (this.equal_bounds && this.lower_bound.defined));
   }
   
   highestUpperBound(visited) {
-    // Infers the upper bound for this product from its own UB, or from its
-    // ingoing links (type, rate, and UB of their from nodes)
-    // NOTE: this is used while compiling the VM instructions that compute the
-    // ON/OFF binary variable for this product
-    // NOTE: this method performs a graph traversal. If this product is part
-    // of a cycle in the graph, its highest UB co-depends on its own, which
-    // is not constrained, so return +INF
-    // NOTE: no need to check for sink nodes, as even on those nodes a max. UB
-    // might be inferred from their max. inflows
+    // Infer the upper bound for this product from its own UB, or from
+    // its ingoing links (type, rate, and UB of their from nodes).
+    // This is used while compiling the VM instructions that compute the
+    // ON/OFF binary variable for this product.
+    // This method performs a graph traversal. If this product is part
+    // of a cycle in the graph, its highest UB co-depends on its own UB,
+    // which is not constrained, so then return +INF.
+    // No need to check for sink nodes, as even on those nodes a max. UB
+    // might be inferred from their max. inflows.
     if(visited.indexOf(this) >= 0) return VM.PLUS_INFINITY;
     let ub = (this.equal_bounds ? this.lower_bound : this.upper_bound);
-    // If an expression, return +INF to signal "no lower UB can be inferred"
+    // If dynamic expression, return +INF to signal "no lower UB can be inferred".
     if(ub.defined && !ub.isStatic) return VM.PLUS_INFINITY;
-    // If static, use its value as initial highest value
-    const max_ub = ub.result(0);
-    // See if the sum of its max. inflows will be lower than this value
+    // If static, use its value as initial highest value.
+    const max_ub = (ub.defined ? ub.result(0) : VM.PLUS_INFINITY);
+    // See if the sum of its max. inflows will be lower than this value.
     let sum = 0;
-    // Preclude infinite recursion
+    // Preclude infinite recursion.
     visited.push(this);
     for(let i = 0; i < this.inputs.length; i++) {
       const
           l = this.inputs[i],
           r = l.relative_rate,
           fn = l.from_node;
-      // Dynamic rate => inflows cannot constrain the UB any further
+      // Dynamic rate => inflows cannot constrain the UB any further.
       if(!r.isStatic) return max_ub;
+      let rate = r.result(0);
       if([VM.LM_STARTUP, VM.LM_POSITIVE, VM.LM_ZERO, VM.LM_FIRST_COMMIT,
             VM.LM_SHUTDOWN].indexOf(l.multiplier) >= 0) {
-        // For binary multipliers, the rate is the highest possible flow
-        // NOTE: do not add negative flows, as actual flow may be 0
-        sum += Math.max(0, r.result(0));
+        // For binary multipliers, the rate is the highest possible flow.
+        // NOTE: Do not add negative flows, as actual flow may be 0.
+        sum += Math.max(0, rate);
       } else {
-        // For other multipliers, max flow = rate * UB of the FROM node
-        // (for products, this will recurse; processes return their UB)
+        // For other multipliers, max flow = rate * UB of the FROM node.
+        // For products, this will recurse; processes return their UB.
         let fnub = fn.highestUpperBound(visited);
         // If +INF, no lower UB can be inferred => return initial maximum
         if(fnub >= VM.PLUS_INFINITY) return max_ub;
-        // Otherwise, add rate * UB to the max. total inflow
-        // NOTE: do not add negative flows, as actual flow may be 0
-        sum += Math.max(0, r.result(0) * fnub);
+        // Otherwise, add rate * UB to the max. total inflow.
+        // NOTE: For SUM multipliers, also consider the delay.
+        if(l.multiplier === VM.LM_SUM) {
+          rate *= Math.max(1, l.flow_delay.result(0));
+        }
+        // NOTE: Do not add negative flows, as actual flow may be 0.
+        sum += Math.max(0, rate * fnub);
       }
     }
     // Return the sum of max. inflows as the lowest max. UB, or the initial

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

@@ -492,7 +492,7 @@ function matchingNumber(m, s) {
   // (where asterisks match 0 or more characters, and question marks 1
   // character) and the matching parts jointly denote an integer.
   // NOTE: A "+" must be escaped, "*" and "?" must become groups.
-  let raw = s.replaceAll('+', '\+')
+  let raw = s.replaceAll('+', '\\+')
           .replace(/\*/g, '(.*)').replace(/\?/g, '(.)'),
       match = m.match(new RegExp(`^${raw}$`)),
       n = '';
@@ -534,9 +534,21 @@ function compareSelectors(s1, s2) {
   // Dataset selectors comparison is case-insensitive, and puts wildcards
   // last, where * comes later than ?, and leading colons come AFTER
   // regular selector names.
-  // NOTE: Without wildcards, strings that are identical except for the
-  // digits they *end* on are sorted on this "end number" (so abc12 > abc2).
-  // NOTE: This also applies to percentages ("end number"+ %).
+  // NOTES:
+  // (1) Without wildcards, strings that are identical except for
+  //     the digits they *end* on are sorted on this "end number"
+  //     (so abc12 > abc2).
+  // (2) This also applies to percentages ("end number"+ %).
+  // (3) As of version 1.9.0, the order of selectors can be (partially)
+  //     specified by the modeler.
+  if(MODEL) {
+    const
+        i1 = MODEL.selector_order_list.indexOf(s1),
+        i2 = MODEL.selector_order_list.indexOf(s2);
+    // BOTH selectors must be in the list, or regular sorting order is
+    // applied.
+    if(i1 >= 0 && i2 >= 0) return i1 - i2;
+  }
   if(s1 === s2) return 0;
   if(s1 === '*') return 1;
   if(s2 === '*') return -1;
@@ -580,22 +592,36 @@ function compareSelectors(s1, s2) {
   // by as many spaces (ASCII 32) and add a '!' (ASCII 33). This will then
   // "sorts things out".
   let n = s_1.length,
-      i = n - 1;
+      i = n - 1,
+      plusmin = false;
   while(i >= 0 && s_1[i] === '-') i--;
-  // If trailing minuses, replace by as many spaces and add an exclamation point
+  // If trailing minuses, replace by as many spaces and add an exclamation
+  // point.
   if(i < n - 1) {
-    s_1 = s_1.substring(0, i);
+    s_1 = s_1.substring(0, i + 1);
+    // NOTE: Consider X- as lower than just X.
+    if(s_1 === s_2) return -1;
     while(s_1.length < n) s_1 += ' ';
     s_1 += '!';
+    plusmin = true;
   }
-  // Do the same for the second "normalized" selector
+  // Do the same for the second "normalized" selector.
   n = s_2.length;
   i = n - 1;
   while(i >= 0 && s_2[i] === '-') i--;
   if(i < n - 1) {
-    s_2 = s_2.substring(0, i);
+    s_2 = s_2.substring(0, i + 1);
+    // NOTE: Consider X as higher than X-.
+    if(s_2 === s_1) return 1;
     while(s_2.length < n) s_2 += ' ';
     s_2 += '!';
+    plusmin = true;
+  }
+  if(plusmin) {
+    // As X0 typically denotes "base case", replace a trailing zero by
+    // ")" to ensure that X- < X0 < X+.
+    s_1.replace(/([^0])0$/, '$1)');
+    s_2.replace(/([^0])0$/, '$1)');
   }
   // Now compare the two "normalized" selectors
   if(s_1 < s_2) return -1;