heuristic for checking if SBML file is Cellesigner or not

CHANGELOG

@@ -29,6 +29,8 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
   * Small improvement: Info tab provides information about model annotations
     and submap tabs provide information about submaps annotations if applicable
     (#591)
+  * Small improvement: uploading sbml file should automatically discover a file
+    type (#784)
   * Bug fix: progress bar of gene genome mapping upload is refreshing properly
     (#728)
   * Bug fix: when editing project Disease and Organism could not be removed

frontend-js/package-lock.json

@@ -4958,6 +4958,15 @@
         }
       }
     },
+    "stream-to-blob": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/stream-to-blob/-/stream-to-blob-1.0.1.tgz",
+      "integrity": "sha512-aRy4neA4rf+qMtLT9fCRLPGWdrsIKtCx4kUdNTIPgPQ2hkHkdxbViVAvABMx9oRM6yCWfngHx6pwXfbYkVuPuw==",
+      "dev": true,
+      "requires": {
+        "once": "1.4.0"
+      }
+    },
     "string-width": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/string-width/-/string-width-1.0.2.tgz",

frontend-js/package.json

@@ -37,6 +37,7 @@
     "mocha": "^3.5.3",
     "mock-local-storage": "^1.1.8",
     "molart": "1.3.1",
+    "stream-to-blob": "^1.0.1",
     "uglifyjs": "^2.4.10"
   },
   "dependencies": {

frontend-js/src/main/js/gui/admin/AddProjectDialog.js

@@ -171,7 +171,24 @@ AddProjectDialog.prototype.createGeneralTabContent = function () {
   });
   self.addListener("onFileUpload", function (e) {
     var file = e.arg;
-    return self.setFileParserForFilename(file.name);
+    return new Promise(function (resolve, reject) {
+      var reader = new FileReader();
+      reader.readAsText(file);
+
+      reader.onload = function (e) {
+        try {
+          resolve(e.target.result);
+        } catch (error) {
+          reject(error);
+        }
+      };
+      reader.onerror = function () {
+        reject(new Error("Problem reading file"));
+      };
+
+    }).then(function (content) {
+      return self.setFileParserForFilename(file.name, content);
+    })
   });
 
   var manualUrl = self.getConfiguration().getOption(ConfigurationType.USER_MANUAL_FILE).getValue();
@@ -1083,25 +1100,46 @@ AddProjectDialog.prototype.isSemanticZoomingContainsMultipleOverlays = function
 /**
  *
  * @param {string} filename
+ * @param {string} content
  */
-AddProjectDialog.prototype.setFileParserForFilename = function (filename) {
+AddProjectDialog.prototype.setFileParserForFilename = function (filename, content) {
   var self = this;
   self._filename = filename;
   var select = $("[name='project-format']", self.getElement)[0];
   var options = select.options;
   var optionId = 0;
+
+  var isCellDesigner = self.isCellDesignerContent(content);
+
   for (var i = 0; i < options.length; i++) {
     var option = options[i];
     if (option.value !== undefined) {
       var extension = option.data;
       if (filename.endsWith(extension) && optionId <= 0) {
-        optionId = i;
+        if (extension === "xml") { //for xml we need to check if it's CellDesigner option
+          if (isCellDesigner) {
+            optionId = i;
+          } else if (option.innerHTML.indexOf("CellDesigner") === -1) {
+            optionId = i;
+          }
+        } else {
+          optionId = i;
+        }
       }
     }
   }
   options[optionId].selected = true;
 };
 
+/**
+ *
+ * @param {string} content
+ * @return {boolean}
+ */
+AddProjectDialog.prototype.isCellDesignerContent = function (content) {
+  return content.indexOf("xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\"") >= 0;
+};
+
 /**
  *
  * @returns {*}
@@ -1336,19 +1374,20 @@ AddProjectDialog.prototype.createZipEntry = function (jsZipEntry, zipObject) {
   }
   if (type === "MAP") {
     var name = jsZipEntry.name.toLowerCase();
-    this.setFileParserForFilename(name);
-    if (name.indexOf(".") > 0) {
-      name = name.substr(0, name.indexOf("."));
-    }
-    if (name.lastIndexOf("\\") >= 0) {
-      name = name.substr(name.lastIndexOf("\\") + 1);
-    }
-    if (name.lastIndexOf("/") >= 0) {
-      name = name.substr(name.lastIndexOf("/") + 1);
-    }
-    data.name = name;
 
-    processingPromise = processingPromise.then(function () {
+    processingPromise = zipObject.file(jsZipEntry.name).async("string").then(function (content) {
+      self.setFileParserForFilename(name, content);
+      if (name.indexOf(".") > 0) {
+        name = name.substr(0, name.indexOf("."));
+      }
+      if (name.lastIndexOf("\\") >= 0) {
+        name = name.substr(name.lastIndexOf("\\") + 1);
+      }
+      if (name.lastIndexOf("/") >= 0) {
+        name = name.substr(name.lastIndexOf("/") + 1);
+      }
+      data.name = name;
+    }).then(function () {
       var configuration = self.getConfiguration();
       var mapTypes = configuration.getMapTypes();
       for (var i = 0; i < mapTypes.length; i++) {

frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js

@@ -6,13 +6,13 @@ var AddProjectDialog = require('../../../../main/js/gui/admin/AddProjectDialog')
 var ServerConnector = require('../../ServerConnector-mock');
 var ValidationError = require('../../../../main/js/ValidationError');
 
-var Promise = require('bluebird');
-
 var logger = require('../../logger');
 
 var fs = require("fs");
 var chai = require('chai');
 var assert = chai.assert;
+var toBlob = require('stream-to-blob');
+
 
 describe('AddProjectDialog', function () {
   /**
@@ -75,6 +75,49 @@ describe('AddProjectDialog', function () {
         return dialog.destroy();
       });
     });
+
+    it('sbml file', function () {
+      var dialog = createDialog();
+      var file;
+
+      return new Promise(function (resolve, reject) {
+        toBlob(fs.createReadStream('testFiles/map/sbml.xml'), function (err, blob) {
+          if (err) return reject(err.message);
+          file = blob;
+          file.name = "sbml.xml";
+          resolve(blob);
+        })
+      }).then(function () {
+        return dialog.init();
+      }).then(function () {
+        return dialog.callListeners("onFileUpload", file);
+      }).then(function () {
+        var converter = dialog.getConverter();
+        assert.equal("sbml", converter.name.toLowerCase());
+        return dialog.destroy();
+      });
+    });
+    it('CellDesigner file', function () {
+      var dialog = createDialog();
+      var file;
+
+      return new Promise(function (resolve, reject) {
+        toBlob(fs.createReadStream('testFiles/map/cell_designer.xml'), function (err, blob) {
+          if (err) return reject(err.message);
+          file = blob;
+          file.name = "sbml.xml";
+          resolve(blob);
+        })
+      }).then(function () {
+        return dialog.init();
+      }).then(function () {
+        return dialog.callListeners("onFileUpload", file);
+      }).then(function () {
+        var converter = dialog.getConverter();
+        assert.notEqual("sbml", converter.name.toLowerCase());
+        return dialog.destroy();
+      });
+    });
   });
 
   describe('setZipFileContent', function () {

frontend-js/testFiles/map/cell_designer.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases/>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+</model>
+</sbml>

frontend-js/testFiles/map/sbml.xml

+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<!-- Created by minerva version 12.2.1 on 2019-04-04 at 12:55:58 CEST with JSBML version 1.4. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" layout:required="false" level="3" multi:required="true" render:required="false" version="2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1" xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
+  <model areaUnits="area" extentUnits="mole" id="untitled" lengthUnits="metre" name="NEW DISEASE MAP" substanceUnits="mole" timeUnits="second" volumeUnits="litre">
+    <notes>
+      <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+    </notes>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="minerva_layout">
+        <layout:dimensions layout:height="400" layout:width="600"/>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="default" layout:id="default_compartment">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="400" layout:width="600"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance" name="substance">
+        <listOfUnits>
+          <unit exponent="1" kind="mole" multiplier="1" scale="0"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area" name="area">
+        <listOfUnits>
+          <unit exponent="2" kind="metre" multiplier="1" scale="0"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time" name="time">
+        <listOfUnits>
+          <unit exponent="1" kind="second" multiplier="1" scale="0"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="length" name="length">
+        <listOfUnits>
+          <unit exponent="1" kind="metre" multiplier="1" scale="0"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume" name="volume">
+        <listOfUnits>
+          <unit exponent="1" kind="litre" multiplier="1" scale="0"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment constant="false" id="default" multi:isType="false" size="1" spatialDimensions="3">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+        </notes>
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#">
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+            </compartment>
+    </listOfCompartments>
+  </model>
+</sbml>
\ No newline at end of file