[DAS2] early dasypus output

Allen Day allenday at ucla.edu
Tue Jun 7 07:53:44 UTC 2005 

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
> 
> _______________________________________________
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> DAS2 at portal.open-bio.org
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