lschuetze / gql4jung Goto Github PK

I (Jens) have added an initial set of three antipatterns/smells described
using the GQL. Find some more - go through the respective papers/books and
see how we can formalise them. This might require some language
redesign/extension. 

What steps will reproduce the problem?
1. accessing abc.graphml file from  server
2. Error displayed as "The method LoadGraphML was removed from calling 
javascript"
3.

What is the expected output? What do you see instead?
The .graphml file included in html to render properly.Outcome is the Error 
message

What version of the product are you using? On what operating system?


Please provide any additional information below.

Attached the html file and the screenshot for the error

Implement nz.ac.massey.cs.gpl4jung.xml.XMLMotifReader, dummy already exists. 
XMLMotifReader can be configured so that validation of streams is supported
(before parsing them). If validation fails, throw a MotifReaderException. 

It is recommended to generate the parser from the schema, use jaxb
(https://jaxb.dev.java.net/, also part of the wsdp
(http://java.sun.com/webservices/downloads/previous/index.jsp). 

unit tests should go into test.nz.ac.massey.cs.gpl4jung.xml

Create package nz.ac.massey.cs.gpl4jung.impl, and add an implementation
class of nz.ac.massey.cs.gpl4jung.GQL to this package. 

Test cases should go into test.nz.ac.massey.cs.gpl4jung (so that the same
test cases can be used for alternative implementations of GQL). 
The JUNG graphs used for testing should be simple graphs build in memory. 

[deleted issue]

Write a class that imports ODEM graphs into JUNG graphs. Note that Barrio
already contains such a module, please talk to Slava about details.
For more info on ODEM, see http://www.dependency-analyzer.org/. 

Background: we can use a tools called CDA to extract the graph from byet
code of programs, the result is an ODEM file that we have to convert into a
JUNG graph for analysis. We need this module to test our approach with real
world data. 

Important: there is a slight difference to the graph used in Barrio, we
also want to represent packages and containers as vertexes, and add new
edge type "contains". 

Develop an XML schema for the XML based query language. 

All sample files (currently in docs/spec/querysamples) should validate
against this schema. 

This should be expressed in JUnit 4 test cases, test cases should be in
package test.nz.ac.massey.cs.gpl4jung.xml.validation

for an example how to validate in Java, see
http://java.sun.com/j2se/1.5.0/docs/api/javax/xml/validation/package-summary.htm
l

there should also be some tests where validation fails on purpose

jung allows only one edge between a pair of vertices. This is a problem
when we have parallel extends/implements and uses relationships like in
composite patterns. 

Solution: change string property type to an integer flags for all boolean
properties in Vertex and Edge. Like in java.lang.reflect.Modifier. This
wold allow "multi labels", and would also be more efficient. 

Add JVM check when application starts. 1.6 is required, but many users may
use an earlier version and may have problems to understand the error message.

Implement nz.ac.massey.cs.gpl4jung.QueryOptimizer , and validate
performance against real world data. 

Real world data can be obtained from Ewen Tempero's collection of open
source programs (Jens has DVD), extract graph with CDA and convert. 

For an example how a query optimizer could work, see WebOfPatterns program. 

What steps will reproduce the problem?

1. Open the attached file in gql4jung

What is the expected output? What do you see instead?
The file should open. Instead, the following stack trace is produced:

39750 [Thread-4] ERROR nz.ac.massey.cs.gql4jung.browser.ResultBrowser  -
Error loading data file
edu.uci.ics.jung.io.GraphIOException: java.lang.NullPointerException
        at
nz.ac.massey.cs.gql4jung.io.GraphMLReader.readGraph(GraphMLReader.jav
a:75)
        at
nz.ac.massey.cs.gql4jung.browser.ResultBrowser$32.run(ResultBrowser.j
ava:1061)
        at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NullPointerException
        at
nz.ac.massey.cs.gql4jung.io.GraphMLReader.readGraph(GraphMLReader.jav
a:56)
        ... 2 more
39750 [Thread-4] ERROR nz.ac.massey.cs.gql4jung.browser.ResultBrowser  -
Error l
oading data file
edu.uci.ics.jung.io.GraphIOException: java.lang.NullPointerException
        at
nz.ac.massey.cs.gql4jung.io.GraphMLReader.readGraph(GraphMLReader.jav
a:75)
        at
nz.ac.massey.cs.gql4jung.browser.ResultBrowser$32.run(ResultBrowser.j
ava:1061)
        at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NullPointerException
        at
nz.ac.massey.cs.gql4jung.io.GraphMLReader.readGraph(GraphMLReader.jav
a:56)
        ... 2 more

What version of the product are you using? On what operating system?
Using version 2.0 (gql4jung-0.4.3.zip from the website.) on windows XP 32bit.

Please provide any additional information below.
Also been having problems with "Content is not allowed in prolog"
exceptions when I try to open some GraphML files I have created, with
encoding utf-8. Changing the encoding is changed to iso-8859-1 generates
the problem described above.

See the following stack trace.

559434 [Thread-8] ERROR nz.ac.massey.cs.gql4jung.browser.ResultBrowser  - Error
loading data file
edu.uci.ics.jung.io.GraphIOException: org.jdom.input.JDOMParseException:
Error o
n line 1: Content is not allowed in prolog.
        at
nz.ac.massey.cs.gql4jung.io.GraphMLReader.readGraph(GraphMLReader.jav
a:75)
        at
nz.ac.massey.cs.gql4jung.browser.ResultBrowser$32.run(ResultBrowser.j
ava:1061)
        at java.lang.Thread.run(Unknown Source)
Caused by: org.jdom.input.JDOMParseException: Error on line 1: Content is
not al
lowed in prolog.
        at org.jdom.input.SAXBuilder.build(SAXBuilder.java:504)
        at org.jdom.input.SAXBuilder.build(SAXBuilder.java:888)
        at
nz.ac.massey.cs.gql4jung.io.GraphMLReader.readGraph(GraphMLReader.jav
a:52)
        ... 2 more
Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
        at
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAX
ParseException(Unknown Source)
        at
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalErro
r(Unknown Source)
        at
com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(
Unknown Source)
        at
com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(U
nknown Source)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$Prolog
Driver.next(Unknown Source)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(U
nknown Source)
        at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next
(Unknown Source)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImp
l.scanDocument(Unknown Source)
        at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(U
nknown Source)
        at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(U
nknown Source)
        at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown So
urce)
        at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Un
known Source)
        at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.p
arse(Unknown Source)
        at org.jdom.input.SAXBuilder.build(SAXBuilder.java:489)
        ... 4 more

[deleted issue]

Uses of annotations are not correctly recorded. This is DepFind issue, and
will be fixed by upgrading DependencyFinder (email conversation with Jean
Tessier). 

Related test case: JarReaderTests#testEdges9

Reorganise project to follow a standard project layout, probably use this one:

http://jakarta.apache.org/site/dirlayout.html