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From Lewis John Mcgibbney <lewis.mcgibb...@gmail.com>
Subject Re: How to ingest files when metadata contain non standard characters?
Date Thu, 09 Oct 2014 19:09:49 GMT
Thanks Kos,
Please see
https://issues.apache.org/jira/browse/OODT-759
We will track it there from now on and determine what needs to be done.

On Wed, Oct 8, 2014 at 8:55 PM, Konstantinos Mavrommatis <
kmavrommatis@celgene.com> wrote:

> Here is the offending file before escape:
>
>
>
> <cas:metadata xmlns:cas="http://oodt.jpl.nasa.gov/1.0/cas">
>         <keyval>
>                 <key>derived_from</key>
>
> <val>/gpfs/celgene/reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex</val>
>
> <val>/gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HM1_1_R1.fastq.gz</val>
>
> <val>/gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HM1_1_R2.fastq.gz</val>
>         </keyval>
>         <keyval>
>                 <key>FilePath</key>
>
> <val>/gpfs/archive/RED/DA0000072/RNA-Seq/Processed/Sailfish-transcriptCounts/HM1_1.Sailfish.sfish</val>
>         </keyval>
>         <keyval>
>                 <key>start_execution</key>
>                 <val>Tue Oct  7 20:49:12 2014</val>
>         </keyval>
>         <keyval>
>                 <key>ingest_user</key>
>                 <val>kmavrommatis</val>
>         </keyval>
>         <keyval>
>                 <key>end_execution</key>
>                 <val>Tue Oct  7 21:03:47 2014</val>
>         </keyval>
>         <keyval>
>                 <key>run_user</key>
>                 <val>kmavrommatis</val>
>         </keyval>
>         <keyval>
>                 <key>file_host</key>
>                 <val>ussdgsphpccas02</val>
>         </keyval>
>         <keyval>
>                 <key>generator</key>
>                 <val>sailfish</val>
>         </keyval>
>         <keyval>
>                 <key>run_host</key>
>                 <val>ussdgsphpccmp01</val>
>         </keyval>
>         <keyval>
>                 <key>sample_id</key>
>                 <val>2569</val>
>         </keyval>
>         <keyval>
>                 <key>generator_version</key>
>                 <val>sailfish[0.6.3]</val>
>         </keyval>
>         <keyval>
>                 <key>ProductType</key>
>                 <val>GenericFile</val>
>         </keyval>
>         <keyval>
>                 <key>analysis_task</key>
>                 <val>38</val>
>         </keyval>
>         <keyval>
>                 <key>generator_string</key>
>                 <val>"sailfish quant --index
> /gpfs/celgene/reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex --libtype
> 'T=PE:O=><:S=AS' -1 <(gunzip -c
> /gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HM1_1_R1.fastq.gz)
> -2 <(gunzip -c
> /gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HM1_1_R2.fastq.gz)
> -o
> /gpfs/archive/RED/DA0000072/RNA-Seq/Processed/Sailfish-transcriptCounts/HM1_1.Sailfish.txt
> -p 8  --no_bias_correct "</val>
>         </keyval>
> </cas:metadata>
>
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-- 
*Lewis*

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