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|
#cython: language_level=3
from urllib.parse import urlparse, urlunparse, parse_qs, ParseResultBytes
from os.path import isdir, isfile, basename, join
import sys
from obitools3.dms.dms import DMS
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.genbank import genbankIterator
from obitools3.parsers.universal import entryIteratorFactory
from obitools3.writers.fasta import FastaNucWriter
from obitools3.writers.fastq import FastqWriter
from obitools3.writers.tab import TabWriter
from obitools3.format.fasta import FastaFormat
from obitools3.format.fastq import FastqFormat
from obitools3.format.tab import TabFormat
from obitools3.dms.obiseq import Nuc_Seq
from obitools3.apps.config import getConfiguration,logger
from obitools3.apps.temp import get_temp_dms
from obitools3.utils cimport tobytes, count_entries # TODO tobytes because can't read options as bytes
from obitools3.files.universalopener cimport uopen
from obitools3.dms.capi.obierrno cimport obi_errno, \
OBIVIEW_ALREADY_EXISTS_ERROR
class MalformedURIException(RuntimeError):
pass
cdef open_dms(bytes path, bint create=False):
"""
Opens a DMS from the path part of an URI
"""
cdef int pos=1
cdef bytes dmspath
cdef bytes dmsdirname
cdef bytes dmsname
while(pos>0):
pos = path.find(b"/",pos)
if pos>0:
dmspath=path[0:pos]
else:
dmspath=path
if not isdir(dmspath):
dmsdirname=dmspath+b".obidms"
if isdir(dmsdirname):
dmsname=basename(dmspath)
if isfile(join(dmsdirname,dmsname+b"_infos")):
dms = DMS.open(dmspath)
if pos > 0:
return(dms,path[pos+1:])
else:
return(dms,b'')
elif create:
dms=DMS.new(dmspath)
if pos > 0:
return(dms,path[pos+1:])
else:
return(dms,b'')
pos=pos+1
return None
def open_dms_element(DMS dms,
bytes path,
bint create=False,
type newviewtype=View):
"""
"""
cdef list path_parts = path.split(b'/')
# The URI is only composed of a DMS
if not path:
return (dms,dms)
# The URI targets a taxonomy
# dms:dmspath/taxonomy/taxoname[/taxid]
if path_parts[0]==b"taxonomy":
if len(path_parts) > 1:
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]]]
if create:
view = newviewtype.new(dms,path_parts[0])
else:
view = newviewtype.open(dms,path_parts[0])
if len(path_parts) > 1:
if path_parts[1]==b'*':
if len(path_parts) == 2:
return (dms,view)
else:
column = view[path_parts[2]]
if len(path_parts) == 3:
return (dms,column)
elif len(path_parts) == 4:
raise NotImplementedError()
else:
raise MalformedURIException('Malformed View * URI')
try:
part = int(path_parts[1])
except ValueError:
part = path_parts[1]
part = view[part]
else:
return (dms,view)
if len(path_parts) > 2:
if isinstance(part, Column):
if path_parts[2]==b"*":
if len(path_parts) == 4:
raise NotImplementedError()
elif len(path_parts) == 3:
return (dms,part)
else:
raise MalformedURIException('Malformed View * URI')
else:
subpart = part[int(path_parts[2])]
else:
subpart = part[path_parts[2]]
else:
return (dms,part)
if len(path_parts) > 3:
try:
subsubpart = int(path_parts[3])
except ValueError:
subsubpart = path_parts[3]
subsubpart = subpart[subsubpart]
else:
return (dms,subpart)
# URI with too many sub-parts
if len(path_parts) > 4:
raise MalformedURIException('Malformed View URI')
return (dms, subsubpart)
'''
#TODO discuss returned object. Return a dict? or some class instance?
Reads an URI and returns a tuple containing:
(1) The opened file or DMS, or the URI itself if nothing could be opened by the function
(2) The opened view or iterator on the opened file or writer
(3) The class of object returned or handled by (2)
(4) The original URI in bytes
(5) The number of entries (if input URI) or -1 if unavailable
'''
def open_uri(uri,
bint input=True,
type newviewtype=View,
dms_only=False,
force_file=False):
if type(uri) == str and not uri.isascii():
raise Exception("Paths must be ASCII characters only")
cdef bytes urib = tobytes(uri)
cdef bytes scheme
cdef tuple dms
cdef dict qualifiers
cdef DMS default_dms
if urib is None:
urib = b""
# Reformat URI if it was built with autocomplete
urib = urib.replace(b".obidms", b"")
urib = urib.replace(b".obiview", b"")
urib = urib.replace(b".obicol", b"")
urib = urib.replace(b"/VIEWS", b"")
urib = urib.replace(b"TAXONOMY", b"taxonomy")
config = getConfiguration()
urip = urlparse(urib)
if 'obi' not in config:
config['obi']={}
if not force_file and "defaultdms" in config["obi"]:
default_dms=config["obi"]["defaultdms"]
else:
default_dms=None
try:
create=(not input) and (not config["obi"]["nocreatedms"])
except KeyError:
create=not input
scheme = urip.scheme
error = None
if b'/taxonomy/' in urib or \
(urib != b"-" and \
(scheme==b"dms" or \
(scheme==b"" and \
(((not input) and "outputformat" not in config["obi"]) or \
(input and "inputformat" not in config["obi"]))))): # TODO maybe not best way
if default_dms is not None and b"/" not in urip.path: # assuming view to open in default DMS (TODO discuss)
dms=(default_dms, urip.path)
else:
dms = open_dms(urip.path, create)
if dms is None and default_dms is not None:
dms=(default_dms, urip.path)
if dms is not None:
if dms_only:
return (dms[0],
dms[1],
type(dms[1]),
urlunparse(urip),
len(dms[0]))
#if dms[1]:
try:
resource=open_dms_element(dms[0],
dms[1],
create,
newviewtype)
scheme=b"dms"
urip = ParseResultBytes(scheme=b"dms",
netloc=urip.netloc,
path=urip.path,
params=urip.params,
query=urip.query,
fragment=urip.fragment)
if default_dms is None:
config["obi"]["defaultdms"]=resource[0]
return (resource[0],
resource[1],
type(resource[1]),
urlunparse(urip),
len(resource[1]))
except Exception as e:
global obi_errno
if obi_errno == OBIVIEW_ALREADY_EXISTS_ERROR:
raise Exception("View name already exists in this DMS")
error=e
if scheme==b"dms" :
logger('Error','Could not open DMS URI: %s', uri)
raise FileNotFoundError()
if not urip.scheme:
urib=b"file:"+urib
if input:
try:
file = uopen(urip.path, mode='rb')
logger('info','Opened file: %s', tostr(urip.path))
except Exception as e: # TODO discuss: if can't open file, return the character string itself
file = tobytes(uri)
iseq = urib
objclass = bytes
else: # TODO update uopen to be able to write?
if 'outputformat' in config['obi'] and config['obi']['outputformat'] == b'metabaR':
if 'metabarprefix' not in config['obi']:
raise Exception("Prefix needed when exporting for metabaR (--metabaR-prefix option)")
else:
file = open(config['obi']['metabarprefix']+'.tab', 'wb')
elif not urip.path or urip.path == b'-':
file = sys.stdout.buffer
else:
file = open(urip.path, 'wb')
if file is not None:
qualifiers=parse_qs(urip.query)
if input and b'format' in qualifiers:
format = qualifiers[b'format'][0]
else: # TODO discuss priorities
if urip.scheme:
format = urip.scheme
else:
try:
if input:
formatkey = "inputformat"
else:
formatkey = "outputformat"
format=config["obi"][formatkey]
except KeyError:
format=None
if b'seqtype' in qualifiers:
seqtype=qualifiers[b'seqtype'][0]
else:
if format == b"ngsfilter" or format == b"tabular" or format == b"metabaR": # TODO discuss
seqtype=None
else:
try:
seqtype=config["obi"]["seqtype"]
except KeyError:
seqtype=b"nuc"
config["obi"]["seqtype"] = seqtype
if b'skip' in qualifiers:
skip=int(qualifiers[b"skip"][0])
else:
try:
skip=config["obi"]["skip"]
except KeyError:
skip=0
if skip < 0:
raise MalformedURIException('Malformed skip argument in URI')
if b'only' in qualifiers:
only=int(qualifiers[b"only"][0])
else:
try:
only=config["obi"]["only"]
except KeyError:
only=None
if only is not None and only <= 0:
raise MalformedURIException('Malformed only argument in URI')
if b"skiperror" in qualifiers:
try:
skiperror=eval(qualifiers[b"skiperror"][0])
except Exception as e:
raise MalformedURIException('Malformed skiperror argument in URI')
else:
try:
skiperror=config["obi"]["skiperror"]
except KeyError:
skiperror=True
if not isinstance(skiperror, bool):
raise MalformedURIException('Malformed skiperror argument in URI')
if b"noquality" in qualifiers:
try:
noquality=eval(qualifiers[b"noquality"][0])
except Exception as e:
raise MalformedURIException('Malformed noquality argument in URI')
else:
try:
noquality=config["obi"]["noquality"]
except KeyError:
noquality=False
if not isinstance(noquality, bool):
raise MalformedURIException('Malformed noquality argument in URI')
if b"qualityformat" in qualifiers:
if qualifiers[b"qualityformat"][0]==b"sanger":
offset=33
elif qualifiers[b"qualityformat"][0]==b"solexa":
offset=64
else:
try:
if config["obi"]["qualityformat"]==b"sanger":
offset=33
elif config["obi"]["qualityformat"]==b"solexa":
offset=64
#offset=config["obi"]["offset"] # TODO discuss
except KeyError:
offset=33
if b"header" in qualifiers:
try:
header=eval(qualifiers[b"header"][0])
except Exception as e:
raise MalformedURIException('Malformed header argument in URI')
else:
try:
header=config["obi"]["header"]
except KeyError:
header=False
if not isinstance(header, bool):
raise MalformedURIException('Malformed header argument in URI')
if b"sep" in qualifiers:
sep = tobytes(qualifiers[b"sep"][0][0])
else:
try:
sep = tobytes(config["obi"]["sep"])
except KeyError:
sep=None
# if b"quote" in qualifiers:
# pass
if b"dec" in qualifiers:
dec=tobytes(qualifiers[b"dec"][0][0])
else:
try:
dec=tobytes(config["obi"]["dec"])
except KeyError:
dec=b"."
if b"printna" in qualifiers:
try:
printna=eval(qualifiers[b"printna"][0])
except Exception as e:
raise MalformedURIException("Malformed 'print NA' argument in URI")
else:
try:
printna=config["obi"]["printna"]
except KeyError:
printna=False
if b"nastring" in qualifiers:
nastring=tobytes(qualifiers[b"nastring"][0])
else:
try:
if input:
nakey = "inputnastring"
else:
nakey = "outputnastring"
nastring=tobytes(config["obi"][nakey])
except KeyError:
nastring=b'NA'
if b"na_int_to_0" in qualifiers:
try:
na_int_to_0=eval(qualifiers[b"na_int_to_0"][0])
except Exception as e:
raise MalformedURIException("Malformed 'NA_int_to_0' argument in URI")
else:
try:
na_int_to_0=config["obi"]["na_int_to_0"]
except KeyError:
if format==b"tabular" or format==b"metabaR":
na_int_to_0=True
else:
na_int_to_0=False
if b"stripwhite" in qualifiers:
try:
stripwhite=eval(qualifiers[b"stripwhite"][0])
except Exception as e:
raise MalformedURIException('Malformed stripwhite argument in URI')
else:
try:
stripwhite=config["obi"]["stripwhite"]
except KeyError:
stripwhite=True
if not isinstance(stripwhite, bool):
raise MalformedURIException('Malformed stripwhite argument in URI')
if b"blanklineskip" in qualifiers:
try:
blanklineskip=eval(qualifiers[b"blanklineskip"][0])
except Exception as e:
raise MalformedURIException('Malformed blanklineskip argument in URI')
else:
try:
blanklineskip=config["obi"]["blanklineskip"]
except KeyError:
blanklineskip=True
if not isinstance(blanklineskip, bool):
raise MalformedURIException('Malformed blanklineskip argument in URI')
if b"commentchar" in qualifiers:
commentchar=tobytes(qualifiers[b"commentchar"][0][0])
else:
try:
commentchar=tobytes(config["obi"]["commentchar"])
except KeyError:
commentchar=b'#'
if b"only_keys" in qualifiers:
only_keys=qualifiers[b"only_keys"][0] # not sure that works but no one ever uses qualifiers
else:
try:
only_keys_str=config["obi"]["only_keys"]
only_keys=[]
for key in only_keys_str:
only_keys.append(tobytes(key))
except KeyError:
only_keys=[]
if b"metabaR_prefix" in qualifiers:
metabaR_prefix = tobytes(qualifiers[b"metabaR_prefix"][0][0])
else:
try:
metabaR_prefix = tobytes(config["obi"]["metabarprefix"])
except KeyError:
metabaR_prefix=None
if format is not None:
if seqtype==b"nuc":
objclass = Nuc_Seq # Nuc_Seq_Stored? TODO
if format==b"fasta" or format==b"silva" or format==b"rdp" or format == b"unite" or format == b"sintax":
if input:
iseq = fastaNucIterator(file,
skip=skip,
only=only,
nastring=nastring)
else:
iseq = FastaNucWriter(FastaFormat(tags=only_keys, printNAKeys=printna, NAString=nastring),
file,
skip=skip,
only=only)
elif format==b"fastq":
if input:
iseq = fastqIterator(file,
skip=skip,
only=only,
offset=offset,
noquality=noquality,
nastring=nastring)
else:
iseq = FastqWriter(FastqFormat(tags=only_keys, printNAKeys=printna, NAString=nastring),
file,
skip=skip,
only=only)
elif format==b"embl":
if input:
iseq = emblIterator(file,
skip=skip,
only=only)
else:
raise NotImplementedError('Output sequence file format not implemented')
elif format==b"genbank":
if input:
iseq = genbankIterator(file,
skip=skip,
only=only)
else:
raise NotImplementedError('Output sequence file format not implemented')
else:
raise NotImplementedError('Sequence file format not implemented')
elif seqtype==b"prot":
raise NotImplementedError()
elif format==b"tabular":
objclass = dict
if input:
iseq = tabIterator(file,
header = header,
sep = sep,
dec = dec,
stripwhite = stripwhite,
blanklineskip = blanklineskip,
commentchar = commentchar,
nastring=nastring,
skip = skip,
only = only)
else:
iseq = TabWriter(TabFormat(tags=only_keys, header=header, NAString=nastring, sep=sep, NAIntTo0=na_int_to_0),
file,
skip=skip,
only=only,
header=header)
elif format==b"metabaR":
objclass = dict
if input:
raise NotImplementedError('Input data file format not implemented')
else:
iseq = TabWriter(TabFormat(tags=only_keys, header=header, NAString=nastring, sep=sep, NAIntTo0=na_int_to_0, metabaR=True),
file,
skip=skip,
only=only,
header=header)
elif format==b"ngsfilter":
objclass = dict
if input:
iseq = ngsfilterIterator(file,
sep = sep,
dec = dec,
stripwhite = stripwhite,
blanklineskip = blanklineskip,
commentchar = commentchar,
nastring=nastring,
skip = skip,
only = only)
else:
raise NotImplementedError('Output data file format not implemented')
else:
if input:
iseq, objclass, format = entryIteratorFactory(file,
skip, only,
seqtype,
offset,
noquality,
skiperror,
header,
sep,
dec,
nastring,
stripwhite,
blanklineskip,
commentchar)
else: # default export is in fasta? or tab? TODO
objclass = Nuc_Seq # Nuc_Seq_Stored? TODO
iseq = FastaNucWriter(FastaFormat(tags=only_keys, printNAKeys=printna, NAString=nastring),
file,
skip=skip,
only=only)
#tmpdms = get_temp_dms()
entry_count = -1
if input:
entry_count = count_entries(file, format, header)
return (file, iseq, objclass, urib, entry_count)
|
