Cython: updated the URI decoding to handle outputs other than DMS
This commit is contained in:
Celine Mercier
@ -12,6 +12,11 @@ from obitools3.parsers.ngsfilter import ngsfilterIterator
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from obitools3.parsers.embl import emblIterator
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from obitools3.parsers.universal import entryIteratorFactory
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from obitools3.writers.fasta import FastaNucWriter
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from obitools3.writers.fastq import FastqWriter
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from obitools3.format.fasta import FastaFormat
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from obitools3.format.fastq import FastqFormat
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from obitools3.dms.obiseq import Nuc_Seq
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from obitools3.apps.config import getConfiguration,logger
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from obitools3.apps.temp import get_temp_dms
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@ -56,7 +61,9 @@ cdef open_dms(bytes path, bint create=False):
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pos=pos+1
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return None
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def open_dms_element(DMS dms, bytes path,
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def open_dms_element(DMS dms,
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bytes path,
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bint create=False,
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type newviewtype=View):
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"""
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@ -139,12 +146,21 @@ def open_dms_element(DMS dms, bytes path,
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if len(path_parts) > 4:
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raise MalformedURIException('Malformed View URI')
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return (dms,subsubpart)
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return (dms, subsubpart)
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'''
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#TODO discuss returned object. Return a dict? or some class instance?
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Reads an URI and returns a tuple containing:
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(1) The opened file or DMS, or the URI itself if nothing could be opened by the function
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(2) The opened view or iterator on the opened file or writer
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(3) The class of object returned or handled by (2)
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(4) The original URI in bytes
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'''
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def open_uri(uri,
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bint input=True,
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type newviewtype=View):
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cdef bytes urib = tobytes(uri)
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cdef bytes scheme
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cdef tuple dms
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@ -153,7 +169,7 @@ def open_uri(uri,
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config = getConfiguration()
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urip = urlparse(urib)
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if 'obi' not in config:
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config['obi']={}
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@ -166,22 +182,26 @@ def open_uri(uri,
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create=(not input) and (not config["obi"]["nocreatedms"])
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except KeyError:
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create=not input
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scheme = urip.scheme
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error = None
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if scheme==b"" or scheme==b"dms" :
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dms = open_dms(urip.path,create)
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if scheme==b"dms" or \
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(scheme==b"" and \
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(((not input) and "outputformat" not in config["obi"]) or \
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(input and "inputformat" not in config["obi"]))): # TODO maybe not best way
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dms = open_dms(urip.path, create)
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if dms is None and default_dms is not None:
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dms=(default_dms, urip.path)
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if dms is not None:
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try:
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resource=open_dms_element(dms[0],dms[1],
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resource=open_dms_element(dms[0],
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dms[1],
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create,
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newviewtype
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)
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newviewtype)
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scheme=b"dms"
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urip = ParseResultBytes(scheme=b"dms",
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@ -200,32 +220,42 @@ def open_uri(uri,
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urlunparse(urip))
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except Exception as e:
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error=e
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if scheme==b"dms" :
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logger('Error','cannot open DMS: %s', uri)
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raise FileNotFoundError('uri')
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#if not urip.scheme: # TODO not sure what it was supposed to do but not working as intended
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# urib=b"file:"+urib
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if not urip.scheme:
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urib=b"file:"+urib
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try:
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file = uopen(urib)
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logger('info','Opened file: %s', tostr(urib))
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except Exception as e: # TODO discuss: if can't open file, return the character string itself
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file = urib
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iseq = urib
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objclass = bytes
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if input:
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try:
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file = uopen(urip.path, mode='rb')
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logger('info','Opened file: %s', urip.path)
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except Exception as e: # TODO discuss: if can't open file, return the character string itself
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file = tobytes(uri)
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iseq = urib
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objclass = bytes
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else: # TODO update uopen to be able to write?
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file = open(urip.path, 'wb')
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if file is not None:
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qualifiers=parse_qs(urip.query)
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if b'format' in qualifiers:
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if input and b'format' in qualifiers:
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format = qualifiers[b'format'][0]
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else:
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try:
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format=config["obi"]["format"]
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except KeyError:
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format=None
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else: # TODO discuss priorities
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if urip.scheme:
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format = urip.scheme
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else:
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try:
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if input:
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formatkey = "inputformat"
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else:
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formatkey = "outputformat"
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format=config["obi"][formatkey]
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except KeyError:
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format=None
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if b'seqtype' in qualifiers:
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seqtype=qualifiers[b'seqtype'][0]
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@ -248,7 +278,6 @@ def open_uri(uri,
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if skip < 0:
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raise MalformedURIException('Malformed skip argument in URI')
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if b'only' in qualifiers:
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only=int(qualifiers[b"only"][0])
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else:
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@ -259,7 +288,6 @@ def open_uri(uri,
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if only is not None and only <= 0:
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raise MalformedURIException('Malformed only argument in URI')
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if b"skiperror" in qualifiers:
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try:
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skiperror=eval(qualifiers[b"skiperror"][0])
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@ -332,12 +360,27 @@ def open_uri(uri,
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dec=tobytes(config["obi"]["dec"])
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except KeyError:
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dec=b"."
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if b"printna" in qualifiers:
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try:
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printna=eval(qualifiers[b"printna"][0])
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except Exception as e:
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raise MalformedURIException("Malformed 'print NA' argument in URI")
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else:
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try:
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printna=config["obi"]["printna"]
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except KeyError:
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printna=False
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if b"nastring" in qualifiers:
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nastring=tobytes(qualifiers[b"nastring"][0])
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else:
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try:
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nastring=tobytes(config["obi"]["nastring"])
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if input:
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nakey = "inputnastring"
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else:
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nakey = "outputnastring"
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nastring=tobytes(config["obi"][nakey])
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except KeyError:
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nastring=b'NA'
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@ -377,63 +420,91 @@ def open_uri(uri,
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if format is not None:
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if seqtype==b"nuc":
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objclass = Nuc_Seq
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objclass = Nuc_Seq # Nuc_Seq_Stored? TODO
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if format==b"fasta":
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iseq = fastaNucIterator(file,
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if input:
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iseq = fastaNucIterator(file,
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skip=skip,
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only=only)
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else:
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iseq = FastaNucWriter(FastaFormat(printNAKeys=printna, NAString=nastring),
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file,
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skip=skip,
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only=only)
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elif format==b"fastq":
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if input:
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iseq = fastqIterator(file,
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skip=skip,
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only=only,
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offset=offset,
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noquality=noquality)
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else:
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iseq = FastqWriter(FastqFormat(printNAKeys=printna, NAString=nastring),
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file,
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skip=skip,
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only=only)
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elif format==b"embl":
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if input:
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iseq = emblIterator(file,
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skip=skip,
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only=only)
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elif format==b"fastq":
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iseq = fastqIterator(file,
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skip=skip,
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only=only,
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offset=offset,
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noquality=noquality)
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elif format==b"embl":
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iseq = emblIterator(file,
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skip=skip,
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only=only)
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else:
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raise NotImplementedError('Output sequence file format not implemented')
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else:
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raise NotImplementedError('Sequence file format not implemented')
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elif seqtype==b"prot":
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raise NotImplementedError()
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elif format==b"tabular":
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objclass = dict
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iseq = tabIterator(file,
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header = header,
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sep = sep,
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dec = dec,
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stripwhite = stripwhite,
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blanklineskip = blanklineskip,
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commentchar = commentchar,
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skip = skip,
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only = only)
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if input:
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iseq = tabIterator(file,
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header = header,
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sep = sep,
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dec = dec,
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stripwhite = stripwhite,
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blanklineskip = blanklineskip,
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commentchar = commentchar,
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skip = skip,
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only = only)
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else:
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raise NotImplementedError('Output sequence file format not implemented')
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elif format==b"ngsfilter":
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objclass = dict
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iseq = ngsfilterIterator(file,
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sep = sep,
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dec = dec,
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stripwhite = stripwhite,
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blanklineskip = blanklineskip,
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commentchar = commentchar,
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skip = skip,
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only = only)
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if input:
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iseq = ngsfilterIterator(file,
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sep = sep,
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dec = dec,
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stripwhite = stripwhite,
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blanklineskip = blanklineskip,
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commentchar = commentchar,
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skip = skip,
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only = only)
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else:
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raise NotImplementedError('Output sequence file format not implemented')
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else:
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iseq, objclass = entryIteratorFactory(file,
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skip, only,
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seqtype,
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offset,
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noquality,
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skiperror,
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header,
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sep,
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dec,
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nastring,
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stripwhite,
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blanklineskip,
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commentchar)
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if input:
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iseq, objclass = entryIteratorFactory(file,
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skip, only,
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seqtype,
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offset,
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noquality,
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skiperror,
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header,
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sep,
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dec,
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nastring,
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stripwhite,
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blanklineskip,
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commentchar)
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else: # default export is in fasta? or tab? TODO
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objclass = Nuc_Seq # Nuc_Seq_Stored? TODO
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iseq = FastaNucWriter(FastaFormat(printNAKeys=printna, NAString=nastring),
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file,
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skip=skip,
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only=only)
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#tmpdms = get_temp_dms()
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return (file, iseq, objclass, urib)
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