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Cython API: URI decoding now returns the character string with the

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object path if it could not be opened
This commit is contained in:
Celine Mercier
2018-07-28 17:00:42 +02:00
parent 3e8c187f0b
commit c02c15b93f
1 changed files with 38 additions and 33 deletions
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71
python/obitools3/uri/decode.pyx
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@ -9,6 +9,7 @@ from obitools3.parsers.fasta import fastaNucIterator
from obitools3.parsers.fastq import fastqIterator
from obitools3.parsers.tab import tabIterator
from obitools3.parsers.ngsfilter import ngsfilterIterator
from obitools3.parsers.embl import emblIterator
from obitools3.parsers.universal import entryIteratorFactory
from obitools3.dms.obiseq import Nuc_Seq
@ -66,18 +67,20 @@ def open_dms_element(DMS dms, bytes path,
if not path:
return (dms,dms)
# TODO SHOULD READ AND RETURN PREFIX TO NEW TAXO WITHOUT CREATING ANYTHING
# The URI targets a taxonomy
# dms:dmspath/taxonomy/taxoname[/taxid]
if path_parts[0]==b"taxonomy":
if len(path_parts) > 1:
taxo = Taxonomy.open(dms,path_parts[1])
if len(path_parts) == 3:
taxon=taxo[int(path_parts[2])]
return (dms,taxon)
elif len(path_parts) > 3:
raise MalformedURIException('Malformed Taxonomy URI')
return (dms,taxo)
if Taxonomy.exists(dms, path_parts[1]):
taxo = Taxonomy.open(dms, path_parts[1])
if len(path_parts) == 3:
taxon=taxo[int(path_parts[2])]
return (dms, taxon)
elif len(path_parts) > 3:
raise MalformedURIException('Malformed Taxonomy URI')
else:
return (dms, path_parts[1]) # return prefix for creation eventually
return (dms, taxo)
# The URI targets a view
# dms:dmspath/viewname[/columnname|#line|*[/#line|columnname|*[/subcolumn]]]
@ -165,7 +168,7 @@ def open_uri(uri,
create=not input
scheme = urip.scheme
error = None
if scheme==b"" or scheme==b"dms" :
@ -199,18 +202,19 @@ def open_uri(uri,
error=e
if scheme==b"dms" :
logger('error','cannot open DMS: %s', uri)
logger('Error','cannot open DMS: %s', uri)
raise FileNotFoundError('uri')
if not urip.scheme:
urib=b"file:"+urib
#if not urip.scheme: # TODO not sure what it was supposed to do but not working as intended
# urib=b"file:"+urib
try:
file = uopen(tostr(urib))
logger('info','Opened file : %s', tostr(urib))
except Exception as e:
file = None
error=e
file = uopen(urib)
logger('info','Opened file: %s', tostr(urib))
except Exception as e: # TODO discuss: if can't open file, return the character string itself
file = urib
iseq = urib
objclass = bytes
if file is not None:
qualifiers=parse_qs(urip.query)
@ -384,6 +388,10 @@ def open_uri(uri,
only=only,
offset=offset,
noquality=noquality)
elif format==b"embl":
iseq = emblIterator(file,
skip=skip,
only=only)
else:
raise NotImplementedError('Sequence file format not implemented')
elif seqtype==b"prot":
@ -410,25 +418,22 @@ def open_uri(uri,
skip = skip,
only = only)
else:
iseq,objclass = entryIteratorFactory(file,
skip, only,
seqtype,
offset,
noquality,
skiperror,
header,
sep,
dec,
nastring,
stripwhite,
blanklineskip,
commentchar)
iseq, objclass = entryIteratorFactory(file,
skip, only,
seqtype,
offset,
noquality,
skiperror,
header,
sep,
dec,
nastring,
stripwhite,
blanklineskip,
commentchar)
#tmpdms = get_temp_dms()
return (file, iseq, objclass, urib)