use file handlers

package.json

@@ -4,7 +4,7 @@
   "description": "Programming platform for Quantitative Systems Pharmacology modeling in NodeJS",
   "main": "src/index.js",
   "scripts": {
-    "test:dev": "mocha test/cases/0 --config=./test/.mocharc.json",
+    "test:dev": "mocha test/cases/14 --config=./test/.mocharc.json",
     "test": "mocha test --config=./test/.mocharc.json",
     "jsdoc": "jsdoc -r -c .jsdoc.json --readme api-references.md -d docs/dev src",
     "test:cov": "nyc --reporter=lcov npm run test",

src/builder/index.js

@@ -38,8 +38,12 @@ const { StdoutTransport } = require('../logger');
  * @property {object[]} exportArray Storage for `_Export` instances.
  */
 class Builder {
-  constructor(declaration = {}, coreDirname = '.') {
-
+  constructor(
+    declaration = {},
+    coreDirname = '.',
+    fileReadHandler = (fn) => fs.readFileSync(fn), // return text
+    fileWriteHandler = (fn, text) => fs.outputFileSync(fn, text) // return undefined
+  ) {
     // create container
     this.container = new Container();
     this.container._builder = this; // back reference to parent builder
@@ -49,6 +53,10 @@ class Builder {
     let minLogLevel = declaration?.options?.logLevel || 'info'; // use logLevel before declaration check
     logger.addTransport(new StdoutTransport(minLogLevel));
 
+    // file handlers
+    this.fileReadHandler = fileReadHandler;
+    this.fileWriteHandler = fileWriteHandler;
+
     // check based on schema, use default values from schema
     let validate = ajv.compile(declarationSchema);
     let valid = validate(declaration);
@@ -115,12 +123,11 @@ class Builder {
    * @method Builder#run
    * 
    */
-  run(){
+  run() {
     this.logger.info(`Compilation of module "${this.importModule.source}" of type "${this.importModule.type}"...`);
 
     // 1. Parsing
-    let fileHandler = (filename) => fs.readFileSync(filename);
-    let ms = new ModuleSystem(this.container.logger, fileHandler);
+    let ms = new ModuleSystem(this.logger, this.fileReadHandler);
     let absFilename = path.join(this._coreDirname, this.importModule.source);
     ms.addModuleDeep(absFilename, this.importModule.type, this.importModule);
 
@@ -130,7 +137,7 @@ class Builder {
         let relPath = path.relative(this._coreDirname, name + '.json');
         let absPath = path.join(this._metaDirname, relPath);
         let str = JSON.stringify(ms.moduleCollection[name], null, 2);
-        fs.outputFileSync(absPath, str);
+        this.fileWriteHandler(absPath, str);
         this.logger.info(`Meta file was saved to ${absPath}`);
       });
     }
@@ -187,7 +194,7 @@ class Builder {
           .join('\n');  
       }
 
-      fs.outputFileSync(this._logPath, logs);
+      this.fileWriteHandler(this._logPath, logs);
       this.logger.info(`All logs was saved to file: "${this._logPath}"`);
     }
     return;
@@ -206,15 +213,15 @@ class Builder {
 }
 
 function _makeAndSave(exportItem, pathPrefix) {
-  let { logger } = exportItem._builder;
+  let { logger, fileWriteHandler } = exportItem._builder;
   let absPath = path.resolve(pathPrefix, exportItem.filepath);
   let msg = `Exporting to "${absPath}" of format "${exportItem.format}"...`;
   logger.info(msg);
 
   exportItem.make().forEach((out) => {
     let filePath = [absPath, out.pathSuffix].join('');
     try {
-      fs.outputFileSync(filePath, out.content);
+      fileWriteHandler(filePath, out.content);
     } catch (err) {
       let msg =`Heta compiler cannot export to file: "${err.path}": ${err.message}`;
       logger.error(msg, {type: 'ExportError'});

src/container/main.js

@@ -117,7 +117,7 @@ class Container {
   load(q, isCore = false){
     // estimate action, default is upsert
     let actionName = q.action || 'upsert';
-    if (typeof this[actionName] !== 'function') {
+    if (!this[actionName] || typeof this[actionName] !== 'function') {
       this.logger.error(
         `Action #${actionName} is unknown and will be skipped.`,
         {type: 'QError', action: actionName}
@@ -147,11 +147,10 @@ class Container {
    * @returns {number} Total number of components + `UnitDef` + `Functiondef` + `Scenario`.
    */
   get length(){
-    return [...this.namespaceStorage]
-      .reduce((acc, x) => acc + x[1].size, 0)
-        + this.unitDefStorage.size // global elements
-        + this.functionDefStorage.size
-        + this.scenarioStorage.size;
+    return [...this.namespaceStorage].reduce((acc, x) => acc + x[1].size, 0) // number of components in all namespaces
+        + this.unitDefStorage.size // number of UnitDef
+        + this.functionDefStorage.size // number of FunctionDef
+        + this.scenarioStorage.size; // number of Scenario
   }
 
   /**
@@ -166,10 +165,7 @@ class Container {
     // knit functionDef
     this.functionDefStorage.forEach((fd) => fd.bind());
     // knit components, only for concrete namespace
-    this.namespaceStorage.forEach((ns) => {
-      // knit only concrete namespace
-      if (!ns.isAbstract) ns.knit();
-    });
+    this.namespaceStorage.forEach((ns) => !ns.isAbstract && ns.knit());
     // knit scenario
     this.scenarioStorage.forEach((sc) => sc.bind());
 

src/module-system/index.js

@@ -32,13 +32,13 @@ class ModuleSystem {
    * @property {Logger} logger Object to analyze log events.
    * @property {_Module} _top Top-level module. Usually created from `index.heta` file.
    */
-  constructor(logger, fileHandler){
+  constructor(logger, fileReadHandler){
     // stores modules in format
     // { filepath : module, ...}
     this.moduleCollection = {};
     this.graph = new TopoSort();
     this.logger = logger;
-    this.fileHandler = fileHandler;
+    this.fileReadHandler = fileReadHandler;
   }
 
   /**
@@ -137,7 +137,7 @@ class ModuleSystem {
     }
 
     try {
-      let fileContent = this.fileHandler(filename);
+      let fileContent = this.fileReadHandler(filename);
       var parsed = loader(fileContent, options);
     } catch (e) {
       if (e.name === 'HetaLevelError') {

test/cases/14.js

@@ -1,6 +1,6 @@
 /* global describe, it */
 
-const { Builder } = require('../../src/builder');
+const { Builder } = require('../../src');
 const { expect, use } = require('chai');
 
 const json_correct = require('../../cases/14-sbml-module/master/output.json');