[DAS2] early dasypus output

Tue Jun 7 07:32:14 UTC 2005

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