incorrect mitab samples

[GoogleCodeExporter]

In 
http://code.google.com/p/psimi/source/browse/trunk/psimitab-parser/src/?r=369#sr
c%2Ftest%2Fresources%2Fmitab-samples, the first line in each sample file should 
probably begin with '#'.

Original issue reported on code.google.com by [email protected] on 5 Feb 2014 at 9:50

[GoogleCodeExporter]

It looks like, at least formally, there should be no header line at all as it 
is not
mentioned in the specification. 
In practice, adding header/comment/footer line(s) marked by '#' is not unheard 
off. 

lukasz

Original comment by [email protected] on 5 Feb 2014 at 11:12

[GoogleCodeExporter]

Hi Lucasz,

I just found that without '#' in the first line, PsimiTabReader
read(inputStream) throws exception (blaming that line)... I uses psimitab
1.8.4.

PsimiTabReader reader = new PsimiTabReader();
InputStream is =
getClass().getClassLoader().getResourceAsStream("12167173.txt");
Collection<BinaryInteraction> its = reader.read(is); //exception

psidev.psi.mi.tab.PsimiTabException: Exception parsing line 0: [ID
interactor A, ID interactor B, Alt. ID interactor A, Alt. ID interactor B,
Alias(es) interactor A, Alias(es) interactor B, Interaction detection
method(s), Publication 1st author(s), Publication Identifier(s), Taxid
interactor A, Taxid interactor B, Interaction type(s), Source database(s),
Interaction identifier(s), Confidence value(s)]
 at psidev.psi.mi.tab.PsimiTabReader.handleError(PsimiTabReader.java:265)
at psidev.psi.mi.tab.PsimiTabReader.read(PsimiTabReader.java:48)
 at psidev.psi.mi.tab.PsimiTabReader.read(PsimiTabReader.java:133)
at
org.mskcc.psibiopax.converter.TestMappingL3.testMitabToMi(TestMappingL3.java:268
)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
 at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:43)
at java.lang.reflect.Method.invoke(Method.java:606)
 at
org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java
:45)
at
org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:
15)
 at
org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:4
2)
at
org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20
)
 at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:263)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:68
)
 at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:47
)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:231)
 at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:60)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:229)
 at org.junit.runners.ParentRunner.access$000(ParentRunner.java:50)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:222)
 at org.junit.runners.ParentRunner.run(ParentRunner.java:300)
at
org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:236)
 at
org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.ja
va:134)
at
org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:113)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
 at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.jav
a:43)
at java.lang.reflect.Method.invoke(Method.java:606)
 at
org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionU
tils.java:189)
at
org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFa
ctory.java:165)
 at
org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.
java:85)
at
org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.ja
va:103)
 at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:74)
Caused by: psidev.psi.mi.tab.model.builder.IllegalFormatException: String
cannot be parsed to create a cross reference (check the syntax): {ID
interactor A}
 at
psidev.psi.mi.tab.model.builder.MitabParserUtils.splitCrossReferences(MitabParse
rUtils.java:353)
at
psidev.psi.mi.tab.model.builder.MitabParserUtils.buildBinaryInteraction(MitabPar
serUtils.java:169)
 at psidev.psi.mi.tab.PsimiTabReader.read(PsimiTabReader.java:45)
... 31 more


Igor.

Original comment by [email protected] on 5 Feb 2014 at 11:36