Fix: use first content element if no apply element is present

api/v1/controller/AbstractSyntaxTreeController.js

@@ -18,7 +18,7 @@ module.exports = {
       .then((ast) => {
         res.json(ast);
       })
-      .catch((err) => { next(Boom.badData(err.message, JSON.stringify(err))); });
+      .catch((err) => { next(Boom.badData(err.message, res.locals.mathml.toLocaleString())); });
   },
 
   parseCytoscapedAST: (req, res, next) => {
@@ -71,7 +71,7 @@ module.exports = {
         });
       })
       .catch((err) => {
-        next(Boom.badData(err.message));
+        next(Boom.badData(err.message, res.locals.mathml));
       });
   },
 
@@ -85,7 +85,7 @@ module.exports = {
       }).then((cytoscapedMergedAST) => {
         res.json({ cytoscapedMergedAST });
       })
-        .catch((err) => { next(Boom.badData(err.message, JSON.stringify(err))); });
+        .catch((err) => { next(Boom.badData(err.message)); });
     },
 
   renderMergedAst:
@@ -102,14 +102,14 @@ module.exports = {
             res.sendFile(tmpFilename);
           });
       })
-        .catch((err) => { next(Boom.badData(err.message, JSON.stringify(err))); });
+        .catch((err) => { next(Boom.badData(err.message)); });
     },
 
   renderMML:
     (req, res, next) => {
       MathJaxRenderer.renderMML(req.body.mathml).then((svg) => {
         res.send(svg);
       })
-        .catch((err) => { next(Boom.badData(err.message, JSON.stringify(err))); });
+        .catch((err) => { next(Boom.badData(err.message, req.body.mathml.toLocaleString())); });
     }
 };

data/6-single-element.mml.xml

@@ -0,0 +1,9 @@
+<math xmlns="http://www.w3.org/1998/Math/MathML" id="p1.1.m1.1" class="ltx_Math" alttext="m" display="inline">
+  <semantics id="p1.1.m1.1a">
+    <mi id="p1.1.m1.1.1" xref="p1.1.m1.1.1.cmml">m</mi>
+    <annotation-xml encoding="MathML-Content" id="p1.1.m1.1b">
+      <ci id="p1.1.m1.1.1.cmml" xref="p1.1.m1.1.1">𝑚</ci>
+    </annotation-xml>
+    <annotation encoding="application/x-tex" id="p1.1.m1.1c">m</annotation>
+  </semantics>
+</math>

errorHandler/ErrorHandler.js

@@ -2,6 +2,7 @@
 
 const log = require('lib/logger');
 const Boom = require('boom');
+const CircularJSON = require('circular-json');
 
 module.exports = (app) => {
   // catch 404s
@@ -10,7 +11,7 @@ module.exports = (app) => {
   });
 
   app.use((err, req, res, next) => { // eslint-disable-line no-unused-vars
-    log.error(err);
+    log.error(CircularJSON.stringify(err));
     const BoomError = !err.isBoom ? Boom.wrap(err) : err;
     if (res.headersSent) {
       app.log('Skip error handler.');

lib/ASTParser/ASTParser.js

@@ -4,61 +4,83 @@ const xmldom = require('xmldom');
 const xpath = require('xpath');
 const opMap = require('./operationMap');
 const Serializer = xmldom.XMLSerializer;
+const log = require('lib/logger');
 
 module.exports = class ASTParser {
   constructor(xml, options = {}) {
-    this.doc = xml;
+    this.doc = this.clean(xml);
     this.select = xpath.useNamespaces({ m: 'http://www.w3.org/1998/Math/MathML' });
     this.options = Object.assign({
       collapseSingleOperandNodes: true,
       nodesToBeCollapsed: []
     }, options);
   }
+  // from https://www.sitepoint.com/removing-useless-nodes-from-the-dom/
+  clean(node) {
+    for (let n = 0; n < node.childNodes.length; n++) {
+      const child = node.childNodes[n];
+      if (child.nodeType === 8 || (child.nodeType === 3 && !/\S/.test(child.nodeValue))) {
+        node.removeChild(child);
+        n--;
+      } else if (child.nodeType === 1) {
+        this.clean(child);
+      }
+    }
+    return node;
+  }
 
   parse() {
     return new Promise((resolve, reject) => {
       try {
-        const content = this.select('//m:annotation-xml[@encoding="MathML-Content"]', this.doc)[0];
-        const result = this.parseApply(this.select('m:apply', content)[0]);
-        resolve(result);
+        const mainElement = this.getMainElement();
+        resolve(mainElement);
       } catch (e) {
+        log.error(e);
         reject(e);
       }
     });
   }
 
+  getMainElement() {
+    const content = this.select('//m:annotation-xml[@encoding="MathML-Content"]', this.doc, true);
+    if (!content) {
+      throw new Error("No content MathML present");
+    }
+    return this.parseApply(content.firstChild);
+  }
+
   parseApply(applyElement) {
     const childElements = this.select('*', applyElement);
-    const operationElement = childElements.shift();
+    const operationElement = childElements.shift() || applyElement;
 
     // Lookup operation name from Presentation MathML,
     // fallback on tagName if no xref attribute present
-    const opXrefAttr = this.select('@xref', operationElement)[0];
-    const opXref = opXrefAttr ? opXrefAttr.value : null;
+    const opXrefAttr = operationElement.getAttribute('xref');
+    const opXref = opXrefAttr || null;
     const opName = operationElement.tagName;
 
     // presentation MathML for the operation Element
     const opPresentationElement = opMap.hasOwnProperty(opName) ? opMap[opName] : this.getElementById(opXref);
 
     // presentation mathml for full subtree
     let presentationElement = null;
-    const applyXref = this.select('@xref', applyElement)[0];
-    if (applyXref) { presentationElement = this.getElementById(applyXref.value); }
+    const applyXref = applyElement.getAttribute('xref');
+    if (applyXref) { presentationElement = this.getElementById(applyXref); }
     if (!applyElement.hasAttribute('id')) {
       throw new Error('MathML apply elements don\'t have ids.');
     }
-    const applyId = this.select('@id', applyElement)[0].value;
+    const applyId = applyElement.getAttribute('id');
 
-    const operationCd = this.select('@cd', operationElement);
+    const operationCd = operationElement.getAttribute('cd');
 
     // return whole subtree mathml if element is marked ambiguous
-    if (operationCd.length > 0 && operationCd[0].value === 'ambiguous') {
+    if (operationCd === 'ambiguous') {
       return {
         name: 'ambiguous',
         presentation: this.constructor.serialize(presentationElement),
         nodePresentation: this.constructor.serialize(presentationElement),
         id: applyId,
-        presentation_id: applyXref.value
+        presentation_id: applyXref
       };
     }
 
@@ -69,16 +91,16 @@ module.exports = class ASTParser {
         !this.isNodeToBeCollapsed(element)) {
         return this.parseApply(element);
       }
-      const xref = this.select('@xref', element);
-      const elementId = this.select('@id', element)[0].value;
+      const xref = element.getAttribute('xref');
+      const elementId = element.getAttribute('id');
 
       let name = null;
       let leafPresentation = null;
       if (xref.length > 0) {
-        leafPresentation = this.getElementById(xref[0].value);
-        name = this.getXrefTextContent(xref[0].value);
+        leafPresentation = this.getElementById(xref);
+        name = this.getXrefTextContent(xref);
       } else {
-        name = this.select('text()', element);
+        name = element.textContent;// this.select('text()', element);
       }
       const cd = element.getAttribute('cd');
       let qId = 0;
@@ -92,7 +114,7 @@ module.exports = class ASTParser {
         name,
         id: elementId,
         qId,
-        presentation_id: xref[0].value
+        presentation_id: xref
       };
     });
 
@@ -102,7 +124,7 @@ module.exports = class ASTParser {
       nodePresentation: this.constructor.serialize(opPresentationElement),
       children,
       id: applyId,
-      presentation_id: applyXref.value
+      presentation_id: applyXref
     };
   }
 
@@ -125,15 +147,18 @@ module.exports = class ASTParser {
   }
 
   getXrefTextContent(xref) {
-    const textContent = this.select(`//*[@id="${xref}"]/text()`, this.doc);
-    return textContent.length > 0 ? textContent[0].nodeValue : 'collapsed content';
+    const textElement = this.select(`//*[@id="${xref}"]/text()`, this.doc, true);
+    if (textElement) {
+      return textElement.textContent;
+    }
+    return 'collapsed content';
   }
 
   getElementById(xref) {
-    return this.select(`//*[@id="${xref}"]`, this.doc)[0];
+    return this.select(`//*[@id="${xref}"]`, this.doc, true);
   }
 
   isNodeToBeCollapsed(element) {
-    return this.options.nodesToBeCollapsed.includes(this.select('@id', element)[0].value);
+    return this.options.nodesToBeCollapsed.includes(element.getAttribute('id'));
   }
 };

package.json

@@ -35,9 +35,9 @@
     "base64-stream": "^0.1.3",
     "boom": "^4.1.0",
     "cheerio": "^0.22.0",
+    "circular-json": "^0.5.1",
     "compression": "^1.6.2",
     "cytoscape": "^2.7.13",
-    "cytoscape-qtip": "^2.7.1",
     "cytosnap": "^1.1.2",
     "d3": "^4.3.0",
     "express": "^4.16.2",

test/api/basic.js

@@ -35,6 +35,14 @@ describe('api test', () => {
         .expect(200, done);
     });
   });
+  singleEndpoints.forEach((t) => {
+    it('handle single mathml requests ' + t, function testSlash (done) {
+      request(server)
+        .post(`/api/v1/math/${t}`)
+        .field('mathml', app.locals.mml[6])
+        .expect(200, done);
+    });
+  });
   mergedEndpoints.forEach((t) => {
     it('handle mathml requests ' + t, function testSlash (done) {
       request(server)

vmext.iml

@@ -5,5 +5,7 @@
     <content url="file:///media/physikerwelt/Windows/git/ag-gipp/vmext" />
     <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="jquery" level="application" />
+    <orderEntry type="library" name="jquery.qtip" level="application" />
   </component>
 </module>