Source code for galaxy.datatypes.triples

"""
Triple format classes
"""
import logging
import re

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\.')


[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):
        """
        Returns false and the user must manually set.
        """
        return False

[docs]    def set_peek(self, dataset):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek(dataset.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):
        # <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):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek(dataset.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):
        """
        Returns false and the user must manually set.
        """
        return False

[docs]    def set_peek(self, dataset):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek(dataset.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):
        # @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):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek(dataset.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):
        # <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):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek(dataset.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):
        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):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek(dataset.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):
        with open(filename, "rb") as f:
            if f.read(4) == b"$HDT":
                return True

[docs]    def set_peek(self, dataset):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek(dataset.file_name)
            dataset.blurb = 'HDT triple data'
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'