RE: How to ingest files when metadata contain non standard characters?

[Konstantinos Mavrommatis]

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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