[DAS2] early dasypus output

Allen Day allenday at ucla.edu
Tue Jun 7 08:06:43 UTC 2005 

Okay, new code is up.  I believe I have fixed the bug from below

> > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing

as well as

> > WARNING: VERSION tag not closed

> > WARNING: Adding X-DAS-Server header 'gmod/0.0'

> > {http://www.biodas.org/ns/das/2.00}SOURCES; should be  

-Allen


On Tue, 7 Jun 2005, Allen Day wrote:

> This is very helpful.  I'm updating the test server tonight, have a look 
> again in a few hours.
> 
> -Allen
> 
> On Tue, 7 Jun 2005, Andrew Dalke wrote:
> 
> > While at this point its mostly readable only by me, here's an example
> > of the current dasypus validation.
> > 
> > As you can see, there are many things to fix in both the current
> > server and the spec.
> > 
> > 				Andrew
> > 
> > 
> > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke% python  
> > dasypus.py
> >   ========> client.sources <===============
> > 
> > 
> > ERROR Unknown content-type 'text/x-das-source+xml' for service 'sources'
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: Fixing DAS namespace  
> > {http://www.biodas.org/ns/das/2.00}SOURCES; should be  
> > {http://www.biodas.org/ns/das/genome/2.00}SOURCES
> > WARNING: Fixing base of http://das.biopackages.net:0/das; should be  
> > http://das.biopackages.net/das/genome/
> > Comparing sources with single source
> >   ========> client.source <===============
> > 
> > 
> > ERROR Unknown content-type 'text/das-source+xml' for service 'source'
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: Fixing DAS namespace  
> > {http://www.biodas.org/ns/das/2.00}SOURCES; should be  
> > {http://www.biodas.org/ns/das/genome/2.00}SOURCES
> > Different:
> >    taxon: 'FIXME' != 'http://www.ncbi.nlm.nih.gov/taxon-browser?id=FIXME'
> >   ========> client.detailed_source <===============
> > 
> > 
> > ERROR Unknown content-type 'text/x-das-source-details+xml' for service  
> > 'detailed_source'
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: VERSION tag not closed
> > WARNING: Fixing DAS namespace  
> > {http://www.biodas.org/ns/das/2.00}SOURCE; should be  
> > {http://www.biodas.org/ns/das/genome/2.00}SOURCE
> > WARNING: Detailed SOURCE description=='blahblahblah'
> > WARNING: Detailed SOURCE VERSION[0] description=='blahblahblah'
> > ERROR Detailed SOURCE VERSION[0] created=='FIXME, a timestamp' not ISO  
> > date
> > ERROR Detailed SOURCE VERSION[0] modified=='FIXME, a timestamp' not ISO  
> > date
> >    different id  
> > 'http://das.biopackages.net/das/genome/chado/chado-Hsa-17' != 'chado'
> > types_url http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing
> > WARNING: TYPES TYPE[1] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[1] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[1] source=="whatever"
> > WARNING: TYPES TYPE[1] uses xml:base; add to the DAS/2 spec
> > ERROR server gives 505 error with '%s'.  Removing.
> > WARNING: TYPES TYPE[2] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[2] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[2] source=="whatever"
> > WARNING: TYPES TYPE[2] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[2] id=="SO:five_prime_UTR" is not a valid relative  
> > URL; fixing
> > WARNING: TYPES TYPE[3] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[3] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[3] source=="whatever"
> > WARNING: TYPES TYPE[3] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[3] id=="SO:gene_part" is not a valid relative URL;  
> > fixing
> > WARNING: TYPES TYPE[4] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[4] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[4] source=="whatever"
> > WARNING: TYPES TYPE[4] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[4] id=="SO:located_sequence_feature" is not a valid  
> > relative URL; fixing
> > WARNING: TYPES TYPE[5] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[5] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[5] source=="whatever"
> > WARNING: TYPES TYPE[5] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[5] id=="SO:mature_peptide" is not a valid relative  
> > URL; fixing
> > WARNING: TYPES TYPE[6] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[6] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[6] source=="whatever"
> > WARNING: TYPES TYPE[6] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[6] id=="SO:mRNA" is not a valid relative URL; fixing
> > WARNING: TYPES TYPE[7] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[7] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[7] source=="whatever"
> > WARNING: TYPES TYPE[7] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[7] id=="SO:PCR_product" is not a valid relative URL;  
> > fixing
> > WARNING: TYPES TYPE[8] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[8] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[8] source=="whatever"
> > WARNING: TYPES TYPE[8] uses xml:base; add to the DAS/2 spec
> > ERROR server gives 505 error with '%s'.  Removing.
> > WARNING: TYPES TYPE[9] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[9] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[9] source=="whatever"
> > WARNING: TYPES TYPE[9] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[9] id=="SO:polypeptide" is not a valid relative URL;  
> > fixing
> > WARNING: TYPES TYPE[10] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[10] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[10] source=="whatever"
> > WARNING: TYPES TYPE[10] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[10] id=="SO:primary_transcript" is not a valid  
> > relative URL; fixing
> > WARNING: TYPES TYPE[11] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[11] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[11] source=="whatever"
> > WARNING: TYPES TYPE[11] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[11] id=="SO:processed_transcript" is not a valid  
> > relative URL; fixing
> > WARNING: TYPES TYPE[12] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[12] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[12] source=="whatever"
> > WARNING: TYPES TYPE[12] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[12] id=="SO:reagent" is not a valid relative URL;  
> > fixing
> > WARNING: TYPES TYPE[13] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[13] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[13] source=="whatever"
> > WARNING: TYPES TYPE[13] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[13] id=="SO:region" is not a valid relative URL; fixing
> > WARNING: TYPES TYPE[14] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[14] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[14] source=="whatever"
> > WARNING: TYPES TYPE[14] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[14] id=="SO:SNP" is not a valid relative URL; fixing
> > WARNING: TYPES TYPE[15] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[15] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[15] source=="whatever"
> > WARNING: TYPES TYPE[15] uses xml:base; add to the DAS/2 spec
> > ERROR server gives 505 error with '%s'.  Removing.
> > WARNING: TYPES TYPE[16] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[16] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[16] source=="whatever"
> > WARNING: TYPES TYPE[16] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[16] id=="SO:three_prime_UTR" is not a valid relative  
> > URL; fixing
> > WARNING: TYPES TYPE[17] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[17] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[17] source=="whatever"
> > WARNING: TYPES TYPE[17] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[17] id=="SO:transcript" is not a valid relative URL;  
> > fixing
> > WARNING: TYPES TYPE[18] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[18] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[18] source=="whatever"
> > WARNING: TYPES TYPE[18] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[18] id=="SO:UTR" is not a valid relative URL; fixing
> > WARNING: TYPES TYPE[19] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[19] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[19] source=="whatever"
> > WARNING: TYPES TYPE[19] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[19] id=="SO:protein" is not a valid relative URL;  
> > fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:CDS
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:CDS" is not a valid relative URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > five_prime_UTR
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:five_prime_UTR" is not a valid relative  
> > URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > gene_part
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:gene_part" is not a valid relative URL;  
> > fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > located_sequence_feature
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:located_sequence_feature" is not a valid  
> > relative URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > mature_peptide
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:mature_peptide" is not a valid relative  
> > URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:mRNA
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:mRNA" is not a valid relative URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > PCR_product
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:PCR_product" is not a valid relative URL;  
> > fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > polypeptide
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:polypeptide" is not a valid relative URL;  
> > fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > primary_transcript
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:primary_transcript" is not a valid relative  
> > URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > processed_transcript
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:processed_transcript" is not a valid  
> > relative URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > reagent
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:reagent" is not a valid relative URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:region
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:region" is not a valid relative URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:SNP
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:SNP" is not a valid relative URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > three_prime_UTR
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:three_prime_UTR" is not a valid relative  
> > URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > transcript
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:transcript" is not a valid relative URL;  
> > fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO:UTR
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:UTR" is not a valid relative URL; fixing
> > Trying  
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/type/SO: 
> > protein
> > WARNING: Adding X-DAS-Server header 'gmod/0.0'
> > WARNING: TYPES TYPE[0] has a 'name' attribute; add to the DAS/2 spec
> > WARNING: TYPES TYPE[0] has a 'definition' attribute; add to the DAS/2  
> > spec
> > WARNING: TYPES TYPE[0] source=="whatever"
> > WARNING: TYPES TYPE[0] uses xml:base; add to the DAS/2 spec
> > ERROR TYPES TYPE[0] id=="SO:protein" is not a valid relative URL; fixing
> > [Andrew-Dalkes-Computer:~/cvses/dasypus/dasypus] dalke%
> > 
> > 					Andrew
> > 					dalke at dalkescientific.com
> > 
> > _______________________________________________
> > DAS2 mailing list
> > DAS2 at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/das2
> > 
> _______________________________________________
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