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BLAST: Fix sniffer for some dataset. Closes #567. Set mimetype to application/xml. Closes #569

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This commit is contained in:
Kanwei Li
2011-06-02 17:36:38 -04:00
parent 08204a78bf
commit f2286c240a
3 changed files with 25 additions and 12 deletions
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datatypes_conf.xml.sample
+2 -2
View File
@@ -117,8 +117,8 @@
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
<datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" display_in_upload="true"/>
<datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/>
<datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
<converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
lib/galaxy/datatypes/registry.py
+2 -1
View File
@@ -187,7 +187,7 @@ class Registry( object ):
'axt' : 'text/plain',
'bam' : 'application/octet-stream',
'bed' : 'text/plain',
'blastxml' : 'text/plain',
'blastxml' : 'application/xml',
'customtrack' : 'text/plain',
'csfasta' : 'text/plain',
'fasta' : 'text/plain',
@@ -200,6 +200,7 @@ class Registry( object ):
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
'memexml' : 'application/xml',
'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
lib/galaxy/datatypes/xml.py
+21 -9
View File
@@ -26,19 +26,31 @@ class BlastXml( data.Text ):
>>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
>>> BlastXml().sniff( fname )
True
>>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' )
>>> BlastXml().sniff( fname )
True
>>> fname = get_test_fname( 'interval.interval' )
>>> BlastXml().sniff( fname )
False
"""
blastxml_header = [ '<?xml version="1.0"?>',
'<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
'<BlastOutput>' ]
for i, line in enumerate( file( filename ) ):
if i >= len( blastxml_header ):
return True
line = line.rstrip( '\n\r' )
if line != blastxml_header[ i ]:
return False
#TODO - Use a context manager on Python 2.5+ to close handle
handle = open(filename)
line = handle.readline()
if line.strip() != '<?xml version="1.0"?>':
handle.close()
return False
line = handle.readline()
if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
'<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
handle.close()
return False
line = handle.readline()
if line.strip() != '<BlastOutput>':
handle.close()
return False
handle.close()
return True
class MEMEXml( data.Text ):
"""MEME XML Output data"""