[error] maybe OBO related

[inesboxexa]

Hi Alan,

While using the most recent versus of SA in git and attempting to generate the total spectrum, Rory is getting the following error:

Mar 19, 2021 11:39:58 AM com.alanmrace.jimzmlparser.obo.HTTPOBOLoader getInputStream
SEVERE: Failed to download OBO for use later
javax.net.ssl.SSLException: Received fatal alert: protocol_version
at sun.security.ssl.Alerts.getSSLException(Unknown Source)
at sun.security.ssl.Alerts.getSSLException(Unknown Source)
at sun.security.ssl.SSLSocketImpl.recvAlert(Unknown Source)
at sun.security.ssl.SSLSocketImpl.readRecord(Unknown Source)
at sun.security.ssl.SSLSocketImpl.performInitialHandshake(Unknown Source)
at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source)
at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source)
at java.net.URL.openStream(Unknown Source)
at com.alanmrace.jimzmlparser.obo.OBO.downloadOBO(OBO.java:189)
at com.alanmrace.jimzmlparser.obo.HTTPOBOLoader.getInputStream(HTTPOBOLoader.java:16)
at com.alanmrace.jimzmlparser.obo.OBO.(OBO.java:79)
at com.alanmrace.jimzmlparser.obo.OBO.loadOntologyFromURL(OBO.java:244)
at com.alanmrace.jimzmlparser.obo.OBO.getOBO(OBO.java:173)
at com.alanmrace.jimzmlparser.parser.ImzMLHandler.parseimzML(ImzMLHandler.java:178)
at com.alanmrace.jimzmlparser.parser.ImzMLHandler.parseimzML(ImzMLHandler.java:156)
at com.alanmrace.jimzmlparser.parser.ImzMLHandler.parseimzML(ImzMLHandler.java:140)
Undefined variable "com" or class "com.alanmrace.JSpectralAnalysis.RegionOfInterest.createROIList".
Error in PostProcessing/setUpFastMethods (line 130)
this.javaROIList = com.alanmrace.JSpectralAnalysis.RegionOfInterest.createROIList();
Error in TotalSpectrum/process (line 26)
[canUseFastMethods, workflow] = this.setUpFastMethods(dataRepresentation);

Error in f_saving_spectra_details (line 77)
totalSpectrum = spectrumGeneration.process(data); % computing total spectrum

Do you have any idea of what might be wrong?

Thank you
Teresa

[AlanRace]

Hi Teresa,
This shouldn't be an issue with the OBO - if it fails to download the latest version (as it seems to do here), then it checks the working directory for a file and if that isn't there either it defaults to using the last version that was included with the parser.

The problematic error seems to be this one:

Undefined variable "com" or class "com.alanmrace.JSpectralAnalysis.RegionOfInterest.createROIList".
Error in PostProcessing/setUpFastMethods (line 130)
this.javaROIList = com.alanmrace.JSpectralAnalysis.RegionOfInterest.createROIList();
Error in TotalSpectrum/process (line 26)
[canUseFastMethods, workflow] = this.setUpFastMethods(dataRepresentation);

So it seems that MATLAB isn't recognising the com.alanmrace.JSpectralAnalysis.RegionOfInterest class and/or the createROIList function. You might want to check which version of JSpectralAnalysis.jar is being loaded and whether any function from that .jar is callable. If it's loaded, but you can't call any function then perhaps it's a version mismatch with MATLAB and Java?

Alan