check units for ODE

cases/25-units-check/.gitattributes

@@ -0,0 +1,34 @@
+### Basic .gitattributes for a Heta repo.
+# Note that binary is a macro for -text -diff.
+
+* text=auto
+
+# main files
+# to have heta files in linux style line endings
+*.heta text eol=lf
+*.xlsx binary
+
+# auxilary files
+*.bash text eol=lf
+*.sh text eol=lf
+*.xlsm binary
+*.xls binary
+*.pptx binary
+*.ppt binary
+
+# code
+*.md text
+*.m text
+# -diff
+*.slv text eol=crlf diff=slv
+*.dat text eol=crlf diff=dat
+*.cpp text
+*.svg text diff=xml
+*.xml text diff=xml
+*.sbml text diff=xml
+
+# LFS (large files)
+large/* filter=lfs diff=lfs merge=lfs -text
+literature/* filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text

cases/25-units-check/.gitignore

@@ -0,0 +1,11 @@
+### Heta specific files and dirs
+/dist
+/draft
+/drafts
+/meta
+
+### temporal files
+*.tmp
+~$*.*
+*.log
+.Rhistory

cases/25-units-check/platform.json

@@ -0,0 +1,14 @@
+{
+  "builderVersion": "*",
+  "id": "template",
+  "notes": "platform notes",
+  "version": "v0.1.0",
+  "license": "UNLICENSED",
+  "options": {
+    "unitsCheck": true
+  },
+  "importModule": {
+    "type": "heta",
+    "source": "src/index.heta"
+  }
+}

cases/25-units-check/src/index.heta

@@ -0,0 +1,35 @@
+/*
+  template file for creating platform
+*/
+// add qsp units
+include ./qsp-units.heta;
+t {units: h};
+
+p1 @Record .= 1 {units: uM};
+c1 @Compartment .= 3 {units: L};
+c2 @Compartment .= 4 {units: mL};
+c3 @Compartment .= 5 {units: m};
+
+s1 @Species {compartment: c1, units: mM} .= 10;
+s2 @Species {compartment: c2, units: mM} .= 10;
+s3 @Species {compartment: c3, units: mmole/m} .= 10;
+
+r1 @Reaction {actors: s1=>s2, units: mmole/h} := k1 * s1 * c1;
+/*
+d(s1*c1)/dt = - r1; left: mMole*L/minute, right: 1/h*mMole*h !!!
+d(s2*c2)/dt = r1;   left: mMole*mL/minute, right: 1/h*mMole*h !!!
+*/
+
+k1 @Const = 1e-3 {units: 1/h};
+
+// exports
+#export { format: JSON, filepath: output };
+//#export { format: YAML };
+//#export { format: XLSX, omitRows: 3, splitByClass: true };
+//#export { format: SBML, version: L2V4 };
+//#export { format: SLV, eventsOff: false };
+//#export { format: DBSolve };
+//#export { format: Simbio };
+//#export { format: Mrgsolve };
+//#export { format: Matlab };
+//#export { format: Julia };

cases/25-units-check/src/qsp-units.heta

@@ -0,0 +1,153 @@
+fmole #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-15 } ]
+};
+pmole #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-12 } ]
+};
+nmole #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-9 } ]
+};
+umole #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-6 } ]
+};
+mmole #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-3 } ]
+};
+fM #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-15 }, { kind: litre, exponent: -1} ]
+};
+
+pM #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-12 }, { kind: litre, exponent: -1} ]
+};
+nM #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-9 }, { kind: litre, exponent: -1} ]
+};
+uM #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-6 }, { kind: litre, exponent: -1} ]
+};
+mM #defineUnit {
+    units: [ { kind: mole, multiplier: 1e-3 }, { kind: litre, exponent: -1} ]
+};
+M #defineUnit {
+    units: [ { kind: mole }, { kind: litre, exponent: -1} ]
+};
+kM #defineUnit {
+    units: [ { kind: mole, multiplier: 1e3 }, { kind: litre, exponent: -1 } ]
+};
+
+fL #defineUnit {
+    units: [ { kind: litre, multiplier: 1e-15 } ]
+};
+pL #defineUnit {
+    units: [ { kind: litre, multiplier: 1e-12 } ]
+};
+nL #defineUnit {
+    units: [ { kind: litre, multiplier: 1e-9 } ]
+};
+uL #defineUnit {
+    units: [ { kind: litre, multiplier: 1e-6 } ]
+};
+mL #defineUnit {
+    units: [ { kind: litre, multiplier: 1e-3 } ]
+};
+dL #defineUnit {
+    units: [ { kind: litre, multiplier: 1e-1 } ]
+};
+L #defineUnit {
+    units: [ { kind: litre } ]
+};
+
+fs #defineUnit {
+    units: [ { kind: second, multiplier: 1e-15 } ]
+};
+ps #defineUnit {
+    units: [ { kind: second, multiplier: 1e-12 } ]
+};
+ns #defineUnit {
+    units: [ { kind: second, multiplier: 1e-9 } ]
+};
+us #defineUnit {
+    units: [ { kind: second, multiplier: 1e-6 } ]
+};
+ms #defineUnit {
+    units: [ { kind: second, multiplier: 1e-3 } ]
+};
+s #defineUnit {
+    units: [ { kind: second } ]
+};
+h #defineUnit {
+    units: [ { kind: hour, multiplier: 1 } ]
+};
+week #defineUnit {
+    units: [ { kind: day, multiplier: 7 } ]
+};
+
+fg #defineUnit {
+    units: [ { kind: kilogram, multiplier: 1e-18 } ]
+};
+pg #defineUnit {
+    units: [ { kind: kilogram, multiplier: 1e-15 } ]
+};
+ng #defineUnit {
+    units: [ { kind: kilogram, multiplier: 1e-12 } ]
+};
+ug #defineUnit {
+    units: [ { kind: kilogram, multiplier: 1e-9 } ]
+};
+mg #defineUnit {
+    units: [ { kind: kilogram, multiplier: 1e-6 } ]
+};
+g #defineUnit {
+    units: [ { kind: kilogram, multiplier: 1e-3 } ]
+};
+kg #defineUnit {
+    units: [ { kind: kilogram } ]
+};
+
+kat #defineUnit {
+    units: [ { kind: katal } ]
+};
+
+cell #defineUnit {
+    units: [ { kind: item } ]
+};
+kcell #defineUnit {
+    units: [ { kind: item, multiplier: 1e3 } ]
+};
+
+cal #defineUnit {
+    units: [ { kind: joule, multiplier: 4.1868 } ]
+};
+kcal #defineUnit {
+    units: [ { kind: joule, multiplier: 4.1868e3 } ]
+};
+
+fm #defineUnit {
+    units: [ { kind: metre, multiplier: 1e-15 } ]
+};
+pm #defineUnit {
+    units: [ { kind: metre, multiplier: 1e-12 } ]
+};
+nm #defineUnit {
+    units: [ { kind: metre, multiplier: 1e-9 } ]
+};
+um #defineUnit {
+    units: [ { kind: metre, multiplier: 1e-6 } ]
+};
+mm #defineUnit {
+    units: [ { kind: metre, multiplier: 1e-13 } ]
+};
+cm #defineUnit {
+    units: [ { kind: metre, multiplier: 1e-2 } ]
+};
+m #defineUnit {
+    units: [ { kind: metre } ]
+};
+
+UL #defineUnit {
+    units: [ { kind: dimensionless } ]
+};
+percent #defineUnit {
+    units: [ { kind: dimensionless, multiplier: 1e-2 } ]
+};

src/builder/index.js

@@ -83,7 +83,7 @@ class Builder {
    * 3. Loading integrated structures into `Platform`.
    * 4. Setting cross-references in platform's elements.
    * 5. Checking circular references in mathematical expressions.
-   * 6. Checking circular unitDef references.
+   * 6. Checking circular unitDef references. Checking circular functionDef rferences.
    * 7. Checking left and right side units compatibility for mathematical expressions.
    * 8. Checking unit\'s terms.
    * 9. Export of a platform to series of formats. 
@@ -116,7 +116,6 @@ class Builder {
 
     // 3. Translation
     this.container.loadMany(qArr, false);
-    //console.log([...this.container.unitDefStorage]); // XXX: debugging
 
     // 4. Binding
     this.logger.info('Setting references in elements, total length ' + this.container.length);

src/container/main.js

@@ -254,6 +254,11 @@ class Container {
   checkUnits(){
     this.namespaceStorage.forEach((ns) => {
       if (!ns.isAbstract) {
+        // check units for t
+        let timeUnits = ns.get('t').unitsParsed;
+        if (!timeUnits) {
+          this.logger.warn('No units set for "t", cannot check ODE units.');
+        }
         // check Record.assignments
         ns.selectByInstanceOf('Record')
           .forEach((rec) => rec.checkUnits());

src/core/expression.js

@@ -186,8 +186,8 @@ class Expression {
 
     return isBooleanOperator || isBooleanValue;
   }
-  calcUnit(record){
-    return _calcUnit(this.exprParsed, record);
+  calcUnit(component) { // component here is used for logger and index
+    return _calcUnit(this.exprParsed, component);
   }
 }
 

src/core/math-calc-unit.js

@@ -1,14 +1,14 @@
 /*
 This module calculates units based on expressions
-Records of the expressions must be bound before running this method
+Records of the expressions must be bound before running the method
 */
 const { Unit } = require('./unit');
 
 /*
   _this : Node
   record : Record
 */
-function _calcUnit(_this, record){
+function _calcUnit(_this, record) {
   const logger = record.namespace.container.logger;
 
   if (_this.type === 'ParenthesisNode') {

src/core/species.js

@@ -80,6 +80,56 @@ class Species extends Record {
     return super._references()
       .concat(classSpecificRefs);
   }
+  /*
+  Check units for left and right side of ODE
+  Works only for bound records
+  */
+  checkUnits() {
+    super.checkUnits();
+
+    let logger = this.namespace?.container?.logger;
+
+    // if not in processes do not check
+    let processes = this.backReferences.map(x => x._process_);
+    if (!processes.length) {
+      return; // BRAKE
+    }
+
+    // if no units for t skip check, message in Container.checkUnits()
+    let timeUnits = this.namespace.get('t').unitsParsed;
+    if (!timeUnits) {
+      return; // BRAKE
+    }
+
+    let compartmentUnits = this.compartmentObj?.unitsParsed;
+    if (!compartmentUnits && !this.isAmount) {
+      logger.warn(`No units set for compartment "${this.compartment}", cannot check units for "${this.index}" associated ODE.`);
+      return; // BRAKE
+    }
+
+    let speciesUnits = this.unitsParsed;
+    if (!speciesUnits) {
+      logger.warn(`No units set for "${this.index}", cannot check units for associated ODE.`);
+      return; // BRAKE
+    }
+
+    // d(s*c)/dt
+    let leftSideUnits = speciesUnits
+      .multiply(compartmentUnits)
+      .divide(timeUnits)
+      .simplify();
+    // r1 + r2 + r3
+    processes.forEach((proc) => {
+      let processUnits = proc.unitsParsed;
+      if (!processUnits) {
+        // message was in Process.checkUnits
+        return; // BRAKE
+      }
+      if (!leftSideUnits.equal(processUnits, true)) {
+        logger.warn(`Unit inconsistency for ${this.id} associated ODE. Left: ${leftSideUnits.toString()}. Right: ${processUnits.toString()} (${proc.id})`);
+      }
+    });
+  }
   get legalTerms() {
     let actualCompartmentTerm = this.compartmentObj?.unitsParsed?.toTerm();