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From Konstantinos Mavrommatis <kmavromma...@celgene.com>
Subject RE: How to ingest files when metadata contain non standard characters?
Date Thu, 09 Oct 2014 03:55:11 GMT
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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