Open GoogleCodeExporter opened 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
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
Original issue reported on code.google.com by
rod...@gmail.com
on 5 Feb 2014 at 9:50