Error in annotation and modules downloading

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archana bhardwaj

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Jan 18, 2018, 10:07:23 AM1/18/18
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Dear Developer

I  found your tool Very nice and interesting. I have expression and Mutation data of humans. I successfully draw heatmap based on expression data. But I want to perform annotation and do some in depth interpretation of data. I downloaded latest version Gitools-2.3.1 . During annotation downloading, I am getting following errors

Query ERROR: caught BioMart::Exception::Usage: Attribute snp_refsnp_id NOT FOUND
Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed

waiting for suggestions

Thank you in advance 

archana bhardwaj

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Jan 19, 2018, 3:50:07 AM1/19/18
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Hello

I faced this error only when I try to download Annotation -> Biomart Table .. so on But If I try to download via modules -> Biomart Modules .., then it is working properly. 

archana bhardwaj

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Jan 19, 2018, 7:09:09 AM1/19/18
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Hello , 

After downloding GO dataset, Now I am getting error in KEGG PATHWAYS dataset. I want to download the human latest Ensembl based KEGG mapping in order to do enrichment analysis on my dataset via use of gitools. I tried all different parameters and setting, still no output. 

Thank you in advance 

On Thursday, January 18, 2018 at 4:07:23 PM UTC+1, archana bhardwaj wrote:

archana bhardwaj

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Jan 19, 2018, 8:54:44 AM1/19/18
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Please check following error . Every tile I am getting this error 


org.gitools.datasources.idmapper.MappingException: java.io.IOException: Server returned HTTP response code: 400 for URL: http://rest.kegg.jp/link/genes/path:hsa00190
org.gitools.datasources.modules.importer.ModulesImporterException: org.gitools.datasources.idmapper.MappingException: java.io.IOException: Server returned HTTP response code: 400 for URL: http://rest.kegg.jp/link/genes/path:hsa00190
at org.gitools.datasources.kegg.modules.EnsemblKeggModulesImporter.importMap(EnsemblKeggModulesImporter.java:580)
at org.gitools.ui.app.actions.file.AbstractImportModulesAction$1.run(AbstractImportModulesAction.java:79)
at org.gitools.ui.platform.progress.JobThread$5.run(JobThread.java:177)
at org.gitools.ui.platform.progress.JobThread$4.run(JobThread.java:153)
Caused by: org.gitools.datasources.idmapper.MappingException: java.io.IOException: Server returned HTTP response code: 400 for URL: http://rest.kegg.jp/link/genes/path:hsa00190
at org.gitools.datasources.kegg.idmapper.KeggPathwaysMapper.map(KeggPathwaysMapper.java:81)
at org.gitools.datasources.idmapper.MappingEngine.run(MappingEngine.java:225)
at org.gitools.datasources.kegg.modules.EnsemblKeggModulesImporter.importMap(EnsemblKeggModulesImporter.java:558)
... 3 more
Caused by: java.io.IOException: Server returned HTTP response code: 400 for URL: http://rest.kegg.jp/link/genes/path:hsa00190
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at org.gitools.datasources.kegg.service.KeggService.createReader(KeggService.java:148)
at org.gitools.datasources.kegg.service.KeggService.getGenesByPathway(KeggService.java:120)
at org.gitools.datasources.kegg.idmapper.KeggPathwaysMapper.map(KeggPathwaysMapper.java:76)
... 5 more



On Thursday, January 18, 2018 at 4:07:23 PM UTC+1, archana bhardwaj wrote:

Jordi Deu

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Jan 22, 2018, 6:31:40 AM1/22/18
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Hi Archana,

 there is already an open issue reporting this problem [1]. The problem it's that KEGG did a change in their REST API breaking the compatibility with previous versions. We still have to figure out how to do the same now and find someone and some time to fix it. 


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Jordi Deu-Pons, Software Engineer
Barcelona Biomedical Genomics Lab
Institute for research in Biomedicine (IRB)

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