def set_default_values( self ):
# Default values.
if not self.datatypes_by_extension:
self.datatypes_by_extension = {
'ab1' : binary.Ab1(),
'axt' : sequence.Axt(),
'bam' : binary.Bam(),
'bed' : interval.Bed(),
'coverage' : coverage.LastzCoverage(),
'customtrack' : interval.CustomTrack(),
'csfasta' : sequence.csFasta(),
'fasta' : sequence.Fasta(),
'eland' : tabular.Eland(),
'fastq' : sequence.Fastq(),
'fastqsanger' : sequence.FastqSanger(),
'gtf' : interval.Gtf(),
'gff' : interval.Gff(),
'gff3' : interval.Gff3(),
'genetrack' : tracks.GeneTrack(),
'interval' : interval.Interval(),
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
'qual454' : qualityscore.QualityScore454(),
'sam' : tabular.Sam(),
'scf' : binary.Scf(),
'sff' : binary.Sff(),
'tabular' : tabular.Tabular(),
'taxonomy' : tabular.Taxonomy(),
'txt' : data.Text(),
'wig' : interval.Wiggle(),
'xml' : xml.GenericXml(),
}
self.mimetypes_by_extension = {
'ab1' : 'application/octet-stream',
'axt' : 'text/plain',
'bam' : 'application/octet-stream',
'bed' : 'text/plain',
'customtrack' : 'text/plain',
'csfasta' : 'text/plain',
'eland' : 'application/octet-stream',
'fasta' : 'text/plain',
'fastq' : 'text/plain',
'fastqsanger' : 'text/plain',
'gtf' : 'text/plain',
'gff' : 'text/plain',
'gff3' : 'text/plain',
'interval' : 'text/plain',
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
'memexml' : 'application/xml',
'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
'qual454' : 'text/plain',
'sam' : 'text/plain',
'scf' : 'application/octet-stream',
'sff' : 'application/octet-stream',
'tabular' : 'text/plain',
'taxonomy' : 'text/plain',
'txt' : 'text/plain',
'wig' : 'text/plain',
'xml' : 'application/xml',
}
# super supertype fix for input steps in workflows.
if 'data' not in self.datatypes_by_extension:
self.datatypes_by_extension[ 'data' ] = data.Data()
self.mimetypes_by_extension[ 'data' ] = 'application/octet-stream'
# Default values - the order in which we attempt to determine data types is critical
# because some formats are much more flexibly defined than others.
if len( self.sniff_order ) < 1:
self.sniff_order = [
binary.Bam(),
binary.Sff(),
xml.GenericXml(),
sequence.Maf(),
sequence.Lav(),
sequence.csFasta(),
qualityscore.QualityScoreSOLiD(),
qualityscore.QualityScore454(),
sequence.Fasta(),
sequence.Fastq(),
interval.Wiggle(),
images.Html(),
sequence.Axt(),
interval.Bed(),
interval.CustomTrack(),
interval.Gtf(),
interval.Gff(),
interval.Gff3(),
tabular.Pileup(),
interval.Interval(),
tabular.Sam(),
tabular.Eland()
]
else:
self.log.warning( "Error appending sniffer for datatype '%s' to sniff_order: %s" % ( dtype, str( exc ) ) )
self.upload_file_formats.sort()
# Persist the xml form of the registry into a temporary file so that it
# can be loaded from the command line by tools and set_metadata processing.
self.to_xml_file()
# Default values.
if not self.datatypes_by_extension:
self.datatypes_by_extension = {
'ab1' : binary.Ab1(),
'axt' : sequence.Axt(),
'bam' : binary.Bam(),
'bed' : interval.Bed(),
'coverage' : coverage.LastzCoverage(),
'customtrack' : interval.CustomTrack(),
'csfasta' : sequence.csFasta(),
'fasta' : sequence.Fasta(),
'eland' : tabular.Eland(),
'fastq' : sequence.Fastq(),
'fastqsanger' : sequence.FastqSanger(),
'gtf' : interval.Gtf(),
'gff' : interval.Gff(),
'gff3' : interval.Gff3(),
'genetrack' : tracks.GeneTrack(),
'interval' : interval.Interval(),
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
"Error appending sniffer for datatype '%s' to sniff_order: %s" % (dtype, str(exc))
)
self.upload_file_formats.sort()
# Persist the xml form of the registry into a temporary file so that it
# can be loaded from the command line by tools and set_metadata processing.
self.to_xml_file()
# Default values.
if not self.datatypes_by_extension:
self.datatypes_by_extension = {
"ab1": binary.Ab1(),
"axt": sequence.Axt(),
"bam": binary.Bam(),
"bed": interval.Bed(),
"coverage": coverage.LastzCoverage(),
"customtrack": interval.CustomTrack(),
"csfasta": sequence.csFasta(),
"fasta": sequence.Fasta(),
"eland": tabular.Eland(),
"fastq": sequence.Fastq(),
"fastqsanger": sequence.FastqSanger(),
"gtf": interval.Gtf(),
"gff": interval.Gff(),
"gff3": interval.Gff3(),
"genetrack": tracks.GeneTrack(),
"interval": interval.Interval(),
"laj": images.Laj(),
"lav": sequence.Lav(),
"maf": sequence.Maf(),
"pileup": tabular.Pileup(),
"qualsolid": qualityscore.QualityScoreSOLiD(),
"qualsolexa": qualityscore.QualityScoreSolexa(),