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incorrect mitab samples #7

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
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 rod...@gmail.com on 5 Feb 2014 at 9:50

GoogleCodeExporter commented 9 years ago 
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 lukas...@gmail.com on 5 Feb 2014 at 11:12

GoogleCodeExporter commented 9 years ago 
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 rod...@gmail.com on 5 Feb 2014 at 11:36