Hi Lewis I escaped the characters using the CGI::escapeHTML function from the CGI perl module.
The differences between the two versions (mine escaped vs yours escaped) is in the encoding of the single quote "'" character, if I am not mistaken. I want to clarify this because your email come as simple ASCII (not HTML) I did try your command and it worked !!! Now the question is how to do this encoding (your version) ☺ Thanks K > -----Original Message----- > From: Lewis John Mcgibbney [mailto:lewis.mcgibb...@gmail.com] > Sent: Wednesday, October 08, 2014 1:43 PM > To: dev@oodt.apache.org > Subject: Re: How to ingest files when metadata contain non standard > characters? > > Hi Kos, > I take you up on your challenge ;) However I don't know if this will > fix it. > > On Tue, Oct 7, 2014 at 11:31 PM, Konstantinos Mavrommatis < > kmavromma...@celgene.com<mailto:kmavromma...@celgene.com>> wrote: > > > > > <val>sailfish quant --index > > /reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex --libtype > > 'T=PE:O=><:S=AS' -1 <(gunzip -c > > /gpfs/archive/RED/DA0000072/RNA- > Seq/RawData/FastqFiles/HP1_3_R1.fastq. > > gz) > > -2 <(gunzip -c > > /gpfs/archive/RED/DA0000072/RNA- > Seq/RawData/FastqFiles/HP1_3_R2.fastq. > > gz) > > -o > > /gpfs/archive/RED/DA0000072/RNA-Seq/Processed/Sailfish- > transcriptCount > > s/HP1_3.Sailfish.txt > > -p 8 --no_bias_correct </val> > > > > OK, the code above is what you intially pasted... > > > > > > > <val>sailfish quant --index > > /reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex --libtype > > *'T=PE:O=><:S=AS'* -1 <(gunzip -c > > /gpfs/archive/RED/DA0000072/RNA- > Seq/RawData/FastqFiles/HP1_3_R1.fastq. > > gz) > > -2 <(gunzip -c > > /gpfs/archive/RED/DA0000072/RNA- > Seq/RawData/FastqFiles/HP1_3_R2.fastq. > > gz) > > -o > > /gpfs/archive/RED/DA0000072/RNA-Seq/Processed/Sailfish- > transcriptCount > > s/HP1_3.Sailfish.txt > > -p 8 --no_bias_correct </val> > > > > > The code above is what you pasted once you had escaped everything. Did > you do this manually? I get a different output which I've pased below > > > 1sailfish quant --index /reference/v1/Homo- > sapiens/GRCh37.p12/SailFishIndex > --libtype *'T=PE:O=><:S=AS'* -1 <(gunzip -c > /gpfs/archive/RED/DA0000072/RNA- > Seq/RawData/FastqFiles/HP1_3_R1.fastq.gz) > -2 <(gunzip -c > /gpfs/archive/RED/DA0000072/RNA- > Seq/RawData/FastqFiles/HP1_3_R2.fastq.gz) > -o > /gpfs/archive/RED/DA0000072/RNA-Seq/Processed/Sailfish- > transcriptCounts/HP1_3.Sailfish.txt > -p 8 --no_bias_correct > Please notice the difference in the part which I have boldened. Can you > try reingesting and see if your come up donald trumps? > > > > > > > org.apache.oodt.cas.filemgr.structs.exceptions.IngestException: > > exception ingesting product: [A1_1.Sailfish.sfish]: Message: Failed > to > > ingest product [org.apache.oodt.cas.filemgr.structs.Product@7c1ba98b] > : > > java.lang.Exception: > > org.apache.oodt.cas.filemgr.structs.exceptions.CatalogException: > Error > > ingesting product > > [org.apache.oodt.cas.filemgr.structs.Product@5d3f1d87] > > : HTTP method failed: HTTP/1.1 400 Bad Request > > > > BTW, you also have AGAIN highlighted the horrible opaque Product > objects we get as Exception output. I logged an issue for this last > week. > https://issues.apache.org/jira/browse/OODT-755 > We need to fix this and I will try my damdest to hack it at the > weekend. > Thanks > Lewis ********************************************************* THIS ELECTRONIC MAIL MESSAGE AND ANY ATTACHMENT IS CONFIDENTIAL AND MAY CONTAIN LEGALLY PRIVILEGED INFORMATION INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR INDIVIDUALS NAMED ABOVE. If the reader is not the intended recipient, or the employee or agent responsible to deliver it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please reply to the sender to notify us of the error and delete the original message. Thank You.
