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Source code for galaxy.datatypes.triples
"""
Triple format classes
"""
import logging
import re
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.protocols import DatasetProtocol
from galaxy.datatypes.sniff import (
build_sniff_from_prefix,
FilePrefix,
)
from . import (
binary,
data,
text,
xml,
)
log = logging.getLogger(__name__)
TURTLE_PREFIX_PATTERN = re.compile(r"@prefix\s+[^:]*:\s+<[^>]*>\s\.")
TURTLE_BASE_PATTERN = re.compile(r"@base\s+<[^>]*>\s\.")
SBOL_PATTERN = re.compile(r"http[s]?://[w\.]*sbol[s]?.org/v(\d{1})#")
[docs]class Triples(data.Data):
"""
The abstract base class for the file format that can contain triples
"""
edam_data = "data_0582"
edam_format = "format_2376"
file_ext = "triples"
[docs] def sniff(self, filename: str) -> bool:
"""
Returns false and the user must manually set.
"""
return False
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.get_file_name())
dataset.blurb = "Triple data"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]@build_sniff_from_prefix
class NTriples(data.Text, Triples):
"""
The N-Triples triple data format
"""
edam_format = "format_3256"
file_ext = "nt"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
# <http://example.org/dir/relfile> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://example.org/type> .
if re.compile(r"<[^>]*>\s<[^>]*>\s<[^>]*>\s\.").search(file_prefix.contents_header):
return True
return False
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.get_file_name())
dataset.blurb = "N-Triples triple data"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]class N3(data.Text, Triples):
"""
The N3 triple data format
"""
edam_format = "format_3257"
file_ext = "n3"
[docs] def sniff(self, filename: str) -> bool:
"""
Returns false and the user must manually set.
"""
return False
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.get_file_name())
dataset.blurb = "Notation-3 Triple data"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]@build_sniff_from_prefix
class Turtle(data.Text, Triples):
"""
The Turtle triple data format
"""
edam_format = "format_3255"
file_ext = "ttl"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
# @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
if file_prefix.search(TURTLE_PREFIX_PATTERN):
return True
if file_prefix.search(TURTLE_BASE_PATTERN):
return True
return False
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.get_file_name())
dataset.blurb = "Turtle triple data"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
# TODO: we might want to look at rdflib or a similar, larger lib/egg
[docs]@build_sniff_from_prefix
class Rdf(xml.GenericXml, Triples):
"""
Resource Description Framework format (http://www.w3.org/RDF/).
"""
edam_format = "format_3261"
file_ext = "rdf"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
# <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" ...
match = re.compile(r'xmlns:([^=]*)="http://www.w3.org/1999/02/22-rdf-syntax-ns#"').search(
file_prefix.contents_header
)
if match and (f"{match.group(1)}:RDF") in file_prefix.contents_header:
return True
return False
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.get_file_name())
dataset.blurb = "RDF/XML triple data"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]@build_sniff_from_prefix
class Jsonld(text.Json, Triples):
"""
The JSON-LD data format
"""
# format not defined in edam so we use the json format number
edam_format = "format_3464"
file_ext = "jsonld"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
if self._looks_like_json(file_prefix):
if '"@id"' in file_prefix.contents_header or '"@context"' in file_prefix.contents_header:
return True
return False
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.get_file_name())
dataset.blurb = "JSON-LD triple data"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]class HDT(binary.Binary, Triples):
"""
The HDT triple data format
"""
edam_format = "format_2376"
file_ext = "hdt"
[docs] def sniff(self, filename: str) -> bool:
with open(filename, "rb") as f:
if f.read(4) == b"$HDT":
return True
return False
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.get_file_name())
dataset.blurb = "HDT triple data"
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"
[docs]@build_sniff_from_prefix
class Sbol(data.Text, Triples):
"""
The SBOL data format (https://sbolstandard.org).
"""
MetadataElement(name="version", default="", readonly=True, visible=True, optional=True)
edam_format = "format_3725"
file_ext = "sbol"
[docs] def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
file_prefix = FilePrefix(filename=dataset.get_file_name())
match = file_prefix.search(SBOL_PATTERN)
if match and match.group(1):
dataset.metadata.version = match.group(1)
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
# http://sbols.org/v2#
if file_prefix.search(SBOL_PATTERN):
return True
return False
[docs] def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text"""
if not dataset.dataset.purged:
dataset.peek = data.get_file_peek(dataset.get_file_name())
msg = "SBOL data"
if dataset.metadata.version != "":
msg += " v" + dataset.metadata.version
dataset.blurb = msg
else:
dataset.peek = "file does not exist"
dataset.blurb = "file purged from disk"