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ISA-tools / MAGEtoISAconverter

Converter which can pull from ArrayExpress (by an accession number) or read local files and convert them to ISAtab. Lead by Philippe Rocca-Serra & Eamonn Maguire, University of Oxford
http://isa-tools.org
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SDRF File Not Found Error #7

Closed psm3426 closed 12 years ago

psm3426 commented 12 years ago

Hello. I've been using the JAR file on my local machine, and I noticed every so often when I converted files from ArrayExpress, that I would get an error that looked like this:

log4j:WARN No appenders could be found for logger (org.isatools.magetoisatab.io.DownloadUtils). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-26565/E-GEOD-26565.idf.txt Alternative Design Tag found at: Comment[AEExperimentType] ChIP-seq transcription profiling by array transcription profiling DNA microarray transcription profiling DNA microarray http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-26565/E-GEOD-26565.sdrf.txt ERROR: file not found!

When looking at experiments that threw a similar error, it seems that the problem is that for these studies, the SDRF.TXT file is broken up into two files: xxx.HYB.SDRF.TXT and xxx.SEQ.SDRF.TXT.

It looks like line 56 of MAGETabObtain.java currently only allows the converter to find the SDRF file if there is a single file: sdrfUrl = "http://www.ebi.ac.uk/arrayexpress/files/" + accessionNumber + "/" + accessionNumber + ".sdrf.txt";

Could this be fixed please?

SusannaSansone commented 12 years ago

Current version 1.0 beta works with 'valid' MAGE-Tab where one SDRF exists; this beta version does not support a MAGE-Tab file where there are 2 SDRF files, as this case is NOT valid formatting according to the current MAGE-Tab specification.

eamonnmag commented 12 years ago

This is now fixed.