@lhncbc/ucum-lhc 4.2.0 → 5.0.2

package/source-cjs/ucumXmlDocument.js

@@ -4,7 +4,6 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.UcumXmlDocument = void 0;
-
 /**
  * This class handles opening, reading and parsing the XML file of ucum
  * definitions (prefixes, base units, and unit atoms).
@@ -13,31 +12,21 @@ exports.UcumXmlDocument = void 0;
  *
  */
 var Prefix = require("./prefix.js").Prefix;
-
 var PrefixTables = require("./prefixTables.js").PrefixTables;
-
 var Unit = require("./unit.js").Unit;
-
 var UnitString = require("./unitString.js").UnitString;
-
 var UnitTables = require('./unitTables.js').UnitTables;
-
 var packArray = require('./jsonArrayPack.js').packArray;
-
 var jsonfile = require('jsonfile');
-
 var xmldoc = require('xmldoc');
-
 var fs = require('fs');
-
 var essenceFile_ = '../data/ucum-essence.xml';
+
 /**
  * The full xml document
  * @type XmlDocument
  */
-
 var xmlInput_ = null;
-
 class UcumXmlDocument {
   /**
    * Constructor.  This reads the XML document (essenceFile_) into the
@@ -49,29 +38,30 @@ class UcumXmlDocument {
   constructor() {
     // read the XML file and create an xmlDocument object from it.
     let data = fs.readFileSync(essenceFile_);
-    xmlInput_ = new xmldoc.XmlDocument(data); // Array of unit codes in the ucum-essence.xml file that indicate a
+    xmlInput_ = new xmldoc.XmlDocument(data);
+
+    // Array of unit codes in the ucum-essence.xml file that indicate a
     // mole based unit.  The moleExp_ attribute for these units needs to be
     // set, but there doesn't seem to be an algorithmic way to find these.
     // Creation of unit objects after this file is processed will pick up
     // the moleExp_ value from the base mole unit, but the ones defined in
     // this file will not necessarily do that.
+    this.moleCodes_ = ['mol', 'eq', 'osm', 'kat', 'U'];
 
-    this.moleCodes_ = ['mol', 'eq', 'osm', 'kat', 'U']; // Make this a singleton.  See UnitTables constructor for details.
+    // Make this a singleton.  See UnitTables constructor for details.
 
     let holdThis = UcumXmlDocument.prototype;
-
     exports.UcumXmlDocument = UcumXmlDocument = function () {
       throw new Error('UcumXmlDocument is a Singleton.  ' + 'Use UcumXmlDocument.getInstance() instead.');
     };
-
     if (exports) exports.UcumXmlDocument = UcumXmlDocument;
     UcumXmlDocument.prototype = holdThis;
     let self = this;
-
     UcumXmlDocument.getInstance = function () {
       return self;
     };
   }
+
   /**
    * This method controls parsing of the XML into objects used by this
    * program.  It uses separate methods to parse the prefixes, the
@@ -79,16 +69,16 @@ class UcumXmlDocument {
    *
    * @returns nothing
    */
-
-
   parseXml() {
     this.parsePrefixes(xmlInput_.childrenNamed("prefix"));
     this.parseBaseUnits(xmlInput_.childrenNamed("base-unit"));
-    this.parseUnitStrings(xmlInput_.childrenNamed("unit")); // Create or replace the json file of the prefix and unit definitions
+    this.parseUnitStrings(xmlInput_.childrenNamed("unit"));
 
+    // Create or replace the json file of the prefix and unit definitions
     this.writeJsonFile();
     this.writeVersionText();
   }
+
   /**
    * Creates prefix objects from the xml prefix nodes passed in and gets
    * them added to the prefix tables.
@@ -98,39 +88,38 @@ class UcumXmlDocument {
    *
    * @returns nothing
    */
-
-
   parsePrefixes(prefixes) {
     let plen = prefixes.length;
-
     for (let p = 0; p < plen; p++) {
       let curPfx = prefixes[p];
       let attrs = {};
       attrs["code_"] = curPfx.attr.Code;
       attrs["ciCode_"] = curPfx.attr.CODE;
       attrs["name_"] = curPfx.childNamed('name').val;
-      attrs["printSymbol_"] = curPfx.childNamed('printSymbol').val; // Set the prefix value.  If there is a <sup> element in the
+      attrs["printSymbol_"] = curPfx.childNamed('printSymbol').val;
+
+      // Set the prefix value.  If there is a <sup> element in the
       // value node, then this is a base 10 based prefix (10 to the x power).
       // Set the value to 10 taken to the indicated power.
       // Otherwise this is not 10 based and the value contains the
       // actual value for the prefix.
-
       let pValNode = curPfx.childNamed('value');
       attrs["value_"] = null;
       attrs["exp_"] = pValNode.childNamed('sup');
-
       if (attrs["exp_"] != null) {
         attrs["exp_"] = attrs["exp_"].val;
-        attrs["value_"] = Math.pow(10, attrs["exp_"]);
+        // Use parseFloat('1eSOMETHING') instead of Math.pow() to avoid
+        // small number changes like 1.0000000000000001e-21. See LF-2830.
+        // attrs["value_"] = Math.pow(10, attrs["exp_"]);
+        attrs["value_"] = parseFloat(`1e${attrs["exp_"]}`);
       } else {
         attrs["value_"] = pValNode.val;
         attrs["exp_"] = null;
-      } // Make sure the prefix has not already been created.  If it hasn't,
-      // create the prefix object and then add it to the prefix tables.
-
+      }
 
+      // Make sure the prefix has not already been created.  If it hasn't,
+      // create the prefix object and then add it to the prefix tables.
       let ptab = PrefixTables.getInstance();
-
       if (ptab.isDefined(attrs["code_"])) {
         throw new Error('Prefix constructor called for prefix already ' + `defined; code = ${attrs["code_"]}`);
       } else {
@@ -150,12 +139,9 @@ class UcumXmlDocument {
    *
    * @returns nothing
    */
-
-
   parseBaseUnits(unitNodes) {
     let blen = unitNodes.length;
     let utab = UnitTables.getInstance();
-
     for (let b = 0; b < blen; b++) {
       let curBUnit = unitNodes[b];
       let attrs = {};
@@ -183,14 +169,11 @@ class UcumXmlDocument {
    *
    * @returns nothing
    */
-
-
   parseUnitStrings(unitStrings) {
     let utab = UnitTables.getInstance();
     let uStrParser = UnitString.getInstance();
     let stopNow = false;
     let alen = unitStrings.length;
-
     for (let a = 0; a < alen && !stopNow; a++) {
       let haveUnit = true;
       let curUA = unitStrings[a];
@@ -201,14 +184,14 @@ class UcumXmlDocument {
       attrs['csCode_'] = curUA.attr.Code;
       if (curUA.attr.CODE) attrs['ciCode_'] = curUA.attr.CODE;else attrs['ciCode_'] = curUA.attr.Code.toUpperCase();
       attrs['property_'] = curUA.childNamed('property').val;
-
       if (curUA.childNamed('printSymbol')) {
         let sym = curUA.childNamed('printSymbol');
         let symVal = sym.val;
         symVal = symVal.replace(/\n/g, "");
         symVal = symVal.trim();
         let symI = sym.childNamed('i');
-        if (symI) //symVal = '<i>' + symI.val + '</>';
+        if (symI)
+          //symVal = '<i>' + symI.val + '</>';
           symVal = symI.toString({
             compressed: true
           });
@@ -222,68 +205,69 @@ class UcumXmlDocument {
         });
         attrs['printSymbol_'] = symVal;
       }
-
       if (curUA.attr.isMetric === "yes") attrs['isMetric_'] = true;else attrs['isMetric_'] = false;
       if (curUA.attr.isArbitrary) attrs['isArbitrary_'] = true;else attrs['isArbitrary_'] = false;
-
       if (curUA.attr.class) {
         attrs['class_'] = curUA.attr.class;
       }
-
       let valNode = curUA.childNamed('value');
-      if (this.moleCodes_.indexOf(curUA.attr.Code) !== -1) attrs['moleExp_'] = 1;else attrs['moleExp_'] = 0; // Process special units
+      if (this.moleCodes_.indexOf(curUA.attr.Code) !== -1) attrs['moleExp_'] = 1;else attrs['moleExp_'] = 0;
 
+      // Process special units
       if (curUA.attr.isSpecial) {
         attrs['isSpecial_'] = curUA.attr.isSpecial === "yes";
         let funcNode = valNode.childNamed('function');
         attrs['cnv_'] = funcNode.attr.name;
         attrs['csUnitString_'] = funcNode.attr.Unit;
-
         if (attrs['csUnitString_'] === '1') {
           attrs['baseFactor_'] = 1;
         } else if (attrs['csCode_'] === '[pH]') {
           attrs['baseFactor_'] = parseFloat(funcNode.attr.value);
         } else {
           let slashPos = attrs['csUnitString_'].indexOf('/');
-          let ar = []; // unit string = K/9 or K/4 or m2/s4/Hz
+          let ar = [];
 
+          // unit string = K/9 or K/4 or m2/s4/Hz
           if (slashPos >= 0) {
             ar = attrs['csUnitString_'].split('/');
-          } // unit string = K/9 or K/4
-
-
+          }
+          // unit string = K/9 or K/4
           if (slashPos >= 0 && ar.length === 2) {
             attrs['csUnitString_'] = ar[0];
             attrs['baseFactor_'] = parseFloat(funcNode.attr.value / ar[1]);
-          } // unit string = 10*-5.Pa
+          }
+          // unit string = 10*-5.Pa
           else if (attrs['csCode_'] === 'B[SPL]') {
-              attrs['baseFactor_'] = Math.pow(10, -5) * 2;
-              attrs['csUnitString_'] = "Pa";
-            } // unit string = m1/s4/Hz, K, deg, V, mV, uV, nV, W, kW
-            else {
-                attrs['baseFactor_'] = parseFloat(funcNode.attr.value);
-              }
+            attrs['baseFactor_'] = Math.pow(10, -5) * 2;
+            attrs['csUnitString_'] = "Pa";
+          }
+          // unit string = m1/s4/Hz, K, deg, V, mV, uV, nV, W, kW
+          else {
+            attrs['baseFactor_'] = parseFloat(funcNode.attr.value);
+          }
         } // end if the unit string is not 1
-
       } // end if the unit is special
       else {
-          // what I'm calling the unit string is the string that defines the
-          // unit based on other units, e.g., rad2 (radian squared) to define
-          // a steradian unit.  It's not necessarily a proper base unit, although
-          // it ultimately builds on base units.
-          attrs['csUnitString_'] = valNode.attr.Unit;
-          attrs['ciUnitString_'] = valNode.attr.UNIT; // what I'm calling the factor here (string and number versions)
-          // is the magnitude used in conjunction with the unit string to define
-          // the new unit, e.g., 3 for a yard that is based in the definition
-          // of feet.
+        // what I'm calling the unit string is the string that defines the
+        // unit based on other units, e.g., rad2 (radian squared) to define
+        // a steradian unit.  It's not necessarily a proper base unit, although
+        // it ultimately builds on base units.
+        attrs['csUnitString_'] = valNode.attr.Unit;
+        attrs['ciUnitString_'] = valNode.attr.UNIT;
+
+        // what I'm calling the factor here (string and number versions)
+        // is the magnitude used in conjunction with the unit string to define
+        // the new unit, e.g., 3 for a yard that is based in the definition
+        // of feet.
+
+        attrs['baseFactorStr_'] = valNode.attr.value;
+        if (attrs['csCode_'] === '[pi]') attrs['baseFactor_'] = parseFloat(attrs['baseFactorStr_']);else if (valNode.childNamed('sup')) {
+          attrs['baseFactor_'] = parseFloat(valNode.attr.value);
+        } else {
+          attrs['baseFactor_'] = parseFloat(valNode.val);
+        }
+      } // end if this is not a special unit
 
-          attrs['baseFactorStr_'] = valNode.attr.value;
-          if (attrs['csCode_'] === '[pi]') attrs['baseFactor_'] = parseFloat(attrs['baseFactorStr_']);else if (valNode.childNamed('sup')) {
-            attrs['baseFactor_'] = parseFloat(valNode.attr.value);
-          } else {
-            attrs['baseFactor_'] = parseFloat(valNode.val);
-          }
-        } // end if this is not a special unit
       // Arbitrary units are defined in the UCUM spec as "not of any
       // specific dimension and are not commensurable with any other
       // unit" (3.2.24).  All arbitrary units in the units definition
@@ -292,118 +276,123 @@ class UcumXmlDocument {
       // unit string is the "international unit" with a code of [iU],
       // which is also an arbitrary unit - with a unit string of 1.
       // So I am assuming [IU] is just another code for the same unit.
-
-
       if (attrs['isArbitrary_'] === true) {
         attrs['magnitude_'] = 1;
         attrs['dim_'] = null;
-      } // units with class = "dimless" don't have dimension arrays.
+      }
+
+      // units with class = "dimless" don't have dimension arrays.
       // They're things like the number pi or the number 10 or percent.
       // Haven't figured out how to handle them yet.
       else if (attrs['class_'] === 'dimless' || attrs['csCode_'] === 'mol') {
-          attrs['dim_'] = null; // figure the magnitude based on the unit string
-          // if it's 1, the magnitude is the value specified for
-          // the base factor, e.g., 3.141592653589793238462 ... for pi
-
-          if (attrs['csUnitString_'] === '1') {
-            attrs['magnitude_'] = attrs['baseFactor_'];
-          } // else if the unit string starts with 10*, the magnitude is
-          // 10 to the power specified following 10* e.g., unit = 10*-2
-          // for the "%" unit.  Except for the mole, which is that
-          // multiplied by the base factor, which in this case (only,
-          // I think) is not 1.
-          else if (attrs['csUnitString_'].substr(0, 3) == "10*") {
-              let exp = parseInt(attrs['csUnitString_'].substr(3));
-              attrs['magnitude_'] = Math.pow(10, exp);
-
-              if (attrs['baseFactor_'] !== 1) {
-                attrs['magnitude_'] *= attrs['baseFactor_'];
-              }
-            } // else I don't know what it is.
+        attrs['dim_'] = null;
+        // figure the magnitude based on the unit string
+        // if it's 1, the magnitude is the value specified for
+        // the base factor, e.g., 3.141592653589793238462 ... for pi
+        if (attrs['csUnitString_'] === '1') {
+          attrs['magnitude_'] = attrs['baseFactor_'];
+        }
+        // else if the unit string starts with 10*, the magnitude is
+        // 10 to the power specified following 10* e.g., unit = 10*-2
+        // for the "%" unit.  Except for the mole, which is that
+        // multiplied by the base factor, which in this case (only,
+        // I think) is not 1.
+        else if (attrs['csUnitString_'].substr(0, 3) == "10*") {
+          let exp = parseInt(attrs['csUnitString_'].substr(3));
+          attrs['magnitude_'] = Math.pow(10, exp);
+          if (attrs['baseFactor_'] !== 1) {
+            attrs['magnitude_'] *= attrs['baseFactor_'];
+          }
+        }
+        // else I don't know what it is.
+        else {
+          attrs['defError_'] = true;
+          console.log('unexpected dimless unit definition, unit code ' + 'is ' + attrs['csCode_']);
+        }
+      } // end if this is a unit with class = dimless
+
+      // Handle carat of gold alloys - which doesn't get a dimension
+      //
+      else if (attrs['csCode_'] === "[car_Au]") {
+        attrs['magnitude_'] = 1 / 24;
+        attrs['dim_'] = null;
+      } else {
+        // Make sure there's a unit string to base the new unit on.  There
+        // should be, but I'm just checking here to make sure.  And omit
+        // ones with a unit string of 1.  That won't do us any good.
+        if (attrs['csUnitString_'] && attrs['csUnitString_'] !== '1' && attrs['csUnitString_'] !== 1) {
+          haveUnit = false;
+          // Handle some special cases
+          // 1. the Oersted unit, whose string is /[pi].A/m and whose
+          //    value is 250.  Set the baseFactor to 250/[pi] and
+          //    the unit string to A/m
+          if (attrs['csCode_'] === 'Oe') {
+            attrs['baseFactor_'] = 250 / Math.PI;
+            attrs['csUnitString_'] = "A/m";
+          }
+          // 2.  Strings that start with '/'.  Set the function to
+          //     the inverse function and trim the '/' off the front
+          //     of the string.
+          else if (attrs['csUnitString_'][0] === '/') {
+            attrs['cnv_'] = 'inv';
+            attrs['csUnitString_'] = attrs['csUnitString_'].substr(1);
+          }
+          // 3.  the Svedberg unit, whose string is 10*-13.s.  Set the
+          //     base factor to 10*-13 and the unit string to s.
+          else if (attrs['csCode_'] === '[S]') {
+            attrs['baseFactor_'] = Math.pow(10, -13);
+            attrs['csUnitString_'] = 's';
+          }
+          // 4.  permeability of vaccuum - code [mu_0], unit given is
+          //     4.[pi].10*-7.N/A2
+          else if (attrs['csCode_'] === '[mu_0]') {
+            attrs['baseFactor_'] = 4 * Math.PI * Math.pow(10, -7);
+            attrs['csUnitString_'] = 'N/A2';
+          }
+          // The unit string parser will use the unit(s) named in the
+          // string to create a new unit with the appropriate dimension
+          // object and magnitude before it's multiplied by the one
+          // specified in the input node.
+          try {
+            let retObj = uStrParser.parseString(attrs['csUnitString_'], 'validate', false);
+            let ret = retObj[0];
+            let retString = retObj[1];
+            let retMsg = retObj[2];
+
+            // Get the dimension object and magnitude (and adjust by
+            // specified magnitude factor) from the unit created and
+            // assign them to the attributes we'll use to create the
+            // unit for this listing.
+            if (ret) {
+              attrs['dim_'] = ret.getProperty('dim_');
+              let newMag = ret.getProperty('magnitude_');
+              newMag *= attrs['baseFactor_'];
+              attrs['magnitude_'] = newMag;
+              haveUnit = true;
+            }
+            // if there's no unit, report an error
             else {
-                attrs['defError_'] = true;
-                console.log('unexpected dimless unit definition, unit code ' + 'is ' + attrs['csCode_']);
-              }
-        } // end if this is a unit with class = dimless
-        // Handle carat of gold alloys - which doesn't get a dimension
-        //
-        else if (attrs['csCode_'] === "[car_Au]") {
-            attrs['magnitude_'] = 1 / 24;
-            attrs['dim_'] = null;
-          } else {
-            // Make sure there's a unit string to base the new unit on.  There
-            // should be, but I'm just checking here to make sure.  And omit
-            // ones with a unit string of 1.  That won't do us any good.
-            if (attrs['csUnitString_'] && attrs['csUnitString_'] !== '1' && attrs['csUnitString_'] !== 1) {
-              haveUnit = false; // Handle some special cases
-              // 1. the Oersted unit, whose string is /[pi].A/m and whose
-              //    value is 250.  Set the baseFactor to 250/[pi] and
-              //    the unit string to A/m
-
-              if (attrs['csCode_'] === 'Oe') {
-                attrs['baseFactor_'] = 250 / Math.PI;
-                attrs['csUnitString_'] = "A/m";
-              } // 2.  Strings that start with '/'.  Set the function to
-              //     the inverse function and trim the '/' off the front
-              //     of the string.
-              else if (attrs['csUnitString_'][0] === '/') {
-                  attrs['cnv_'] = 'inv';
-                  attrs['csUnitString_'] = attrs['csUnitString_'].substr(1);
-                } // 3.  the Svedberg unit, whose string is 10*-13.s.  Set the
-                //     base factor to 10*-13 and the unit string to s.
-                else if (attrs['csCode_'] === '[S]') {
-                    attrs['baseFactor_'] = Math.pow(10, -13);
-                    attrs['csUnitString_'] = 's';
-                  } // 4.  permeability of vaccuum - code [mu_0], unit given is
-                  //     4.[pi].10*-7.N/A2
-                  else if (attrs['csCode_'] === '[mu_0]') {
-                      attrs['baseFactor_'] = 4 * Math.PI * Math.pow(10, -7);
-                      attrs['csUnitString_'] = 'N/A2';
-                    } // The unit string parser will use the unit(s) named in the
-              // string to create a new unit with the appropriate dimension
-              // object and magnitude before it's multiplied by the one
-              // specified in the input node.
-
-
-              try {
-                let retObj = uStrParser.parseString(attrs['csUnitString_'], 'validate', false);
-                let ret = retObj[0];
-                let retString = retObj[1];
-                let retMsg = retObj[2]; // Get the dimension object and magnitude (and adjust by
-                // specified magnitude factor) from the unit created and
-                // assign them to the attributes we'll use to create the
-                // unit for this listing.
-
-                if (ret) {
-                  attrs['dim_'] = ret.getProperty('dim_');
-                  let newMag = ret.getProperty('magnitude_');
-                  newMag *= attrs['baseFactor_'];
-                  attrs['magnitude_'] = newMag;
-                  haveUnit = true;
-                } // if there's no unit, report an error
-                else {
-                    attrs['defError_'] = true;
-                    console.log(`unit definition error; code = ${attrs['csCode_']}; ` + `msg = ${retMsg}`);
-                    attrs['dim_'] = null;
-                    attrs['magnitude_'] = null;
-                  }
-              } catch (err) {
-                console.log('error thrown from unit parsing code for unit name ' + attrs['name_'] + '\n' + err.message);
-                stopNow = true;
-              }
-            } // end if there is a unit string to parse
-
-          } // end if this is not a dimless unit
-
+              attrs['defError_'] = true;
+              console.log(`unit definition error; code = ${attrs['csCode_']}; ` + `msg = ${retMsg}`);
+              attrs['dim_'] = null;
+              attrs['magnitude_'] = null;
+            }
+          } catch (err) {
+            console.log('error thrown from unit parsing code for unit name ' + attrs['name_'] + '\n' + err.message);
+            stopNow = true;
+          }
+        } // end if there is a unit string to parse
+      } // end if this is not a dimless unit
 
       if (haveUnit) {
         // Now create the unit we want based on the attributes we've
         // accumulated from the xml input and from figuring the dimension
         // and magnitude.  Add it to the unit tables
         let newUnit = new Unit(attrs);
-        utab.addUnit(newUnit); // for now, create a list of the units created and save it to a file
-        // for debugging.  This is a temporary file.
+        utab.addUnit(newUnit);
 
+        // for now, create a list of the units created and save it to a file
+        // for debugging.  This is a temporary file.
         let uList = utab.printUnits();
         fs.writeFileSync('UnitsList.txt', uList, {
           encoding: 'utf8',
@@ -411,9 +400,7 @@ class UcumXmlDocument {
           flag: 'w'
         });
       } // end if have a parsed unit
-
     } // end for a => - to alen
-
   } // end parseUnitStrings
 
   /**
@@ -422,8 +409,6 @@ class UcumXmlDocument {
    *
    * This creates or replace the file "ucumDefs.json" in the data directory.
    */
-
-
   writeJsonFile() {
     let licenseText = "The following data (prefixes and units) was generated " + "by the UCUM LHC code from the UCUM data and selected " + "LOINC combinations of UCUM units.  The license for " + "the UCUM LHC code (demo and library code as well as " + "the combined units) is located at " + "https://github.com/lhncbc/ucum-lhc/blob/LICENSE.md.";
     let pfxTabs = PrefixTables.getInstance();
@@ -457,8 +442,6 @@ class UcumXmlDocument {
    * current Date object value to "ucumDefs" so that this does not run
    * into problems with a previously existing file.
    */
-
-
   writeVersionText() {
     let rootNode = xmlInput_;
     let versionNum = rootNode.attr.version;
@@ -481,8 +464,6 @@ class UcumXmlDocument {
       flag: 'w'
     });
   } // end writeVersionText
-
-
 } // end UcumXmlDocument
 
 /**
@@ -496,15 +477,12 @@ class UcumXmlDocument {
  *
  *  @return the singleton UcumXmlDocument object.
  */
-
-
 exports.UcumXmlDocument = UcumXmlDocument;
-
 UcumXmlDocument.getInstance = function () {
   return new UcumXmlDocument();
-}; // Perform the first request for the document object, to get the
-// getInstance method set.
-
+};
 
+// Perform the first request for the document object, to get the
+// getInstance method set.
 UcumXmlDocument.getInstance();
 //# sourceMappingURL=ucumXmlDocument.js.map