ctd, release3 branch, error during import about bio2rdf-scripts HOT 8 CLOSED

i can't replicate this from the codebase. can you tell me exactly how you got this file?

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I used the ctd script with download=true and process=true. I did run this script early last week, so my checkout might have not have fixes that have since been committed over the last week. I'm running the loader now and will keep you posted. Cheers!

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I'm no longer encountering the error. Just wondering though, how long does it usually take to load the entire curated ctd dataset? I'm running virtuoso-7 with storage on network drive (NFS). PharmGKB and ClinicalTrials were smaller datasets, and both didn't take more than half a day.

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sorry, I haven't loaded the data in virtuoso 7 yet. has it finished? have you maximized the available buffers?

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So far, no errors, but the script is still just working on

ctd_chem_gene_ixn_types.nq.gz

I've configured the buffers to 120+ GB

NumberOfBuffers          = 14500000
MaxDirtyBuffers          = 10000000

The script has been running since

Thu Oct 03 13:00:46

from bio2rdf-scripts.

Paul, i don't think it should take a week to load the file! something is
wrong... but it's not obvious what the problem is from this end. have a
look and see if there are t1.txt or t2.txt files in the load directory -
these are generated by the loader when there are syntax problems in the
file and it tries to advance by a row. normally it only tries this 10
times before stopping (and generates an error). if nothing, i suggest you
kill the script and try to load the files that have not been loaded.

On Thu, Oct 10, 2013 at 5:38 AM, Paul Rigor [email protected]:

So far, no errors, but the script is still just working on

ctd_chem_gene_ixn_types.nq.gz

I've configured the buffers to 120+ GB

NumberOfBuffers = 14500000
MaxDirtyBuffers = 10000000

The script has been running since

Thu Oct 03 13:00:46

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/333#issuecomment-26026980
.

Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford
University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

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Hi,I'm encountering the error. How do you solve this problem? @theoryno3
XML parser detected an error:
ERROR: syntax error in the attribute list(no whitespace)

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Give me exactly what you run in the command line

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