def __init__(self, settings, session, path, uri_set=None):
SourceFile.__init__(self, settings, session, path, uri_set=uri_set)
self.type = 'gff'
self.abstraction_dict = {}
self.domain_knowledge_dict = {}
self.pos_attr_list = [
'position_taxon', 'position_ref', 'position_start', 'position_end',
'position_strand'
]
self.categories_list = ['position_taxon', 'position_ref', 'position_strand']
self.taxon = ''
self.entities = []
self.timestamp = datetime.datetime.now().isoformat()
self.getLabelFromUri = {}
if uri_set and len(uri_set)>0:
self.prefix = self.uri[0]
else:
self.prefix=None
def __init__(self, settings, session, path, uri_set=None):
SourceFile.__init__(self, settings, session, path, uri_set=uri_set)
self.type = 'gff'
self.abstraction_dict = {}
self.domain_knowledge_dict = {}
self.pos_attr_list = [
'position_taxon', 'position_ref', 'position_start', 'position_end',
'position_strand'
]
self.categories_list = [
'position_taxon', 'position_ref', 'position_strand'
]
self.taxon = ''
self.entities = []
self.timestamp = datetime.datetime.now().isoformat()
self.getLabelFromUri = {}
def __init__(self, settings, session, path, file_type='ttl'):
newfile = path
if not file_type == 'ttl':
newfile = self.convert_to_ttl(path,file_type)
SourceFile.__init__(self, settings, session, newfile)
self.type = 'ttl'
self.origine_type = file_type
#overload name
self.name = os.path.basename(path)
def __init__(self, settings, session, path, preview_limit, uri_set=None):
SourceFile.__init__(self, settings, session, path, uri_set=uri_set)
self.type = 'tsv'
self.preview_limit = preview_limit
self.forced_column_types = ['entity']
self.disabled_columns = []
self.key_columns = []
self.headers = self.get_headers_by_file
self.category_values = defaultdict(set)
self.type_dict = {
'numeric' : 'xsd:decimal',
'text' : 'xsd:string',
'category': ':',
'taxon': ':',
'ref': ':',
'strand': ':',
'start': 'xsd:decimal',
'end': 'xsd:decimal',
'entity' : ':',
'entitySym' : ':',
'entity_start' : ':',
'goterm': '',
'date': 'xsd:dateTime'
}
self.delims = {
'numeric' : ('', ''),
'text' : ('', '^^xsd:string'),
'category': ('', ''),
'taxon': ('', ''),
'ref': ('', ''),
'strand': ('', ''),
'start' : ('', ''),
'end' : ('', ''),
'entity' : ('', ''),
'entitySym' : ('', ''),
'entity_start' : ('', ''),
'goterm': ('<http://purl.obolibrary.org/obo/GO_', '>'),
'date': ('', '^^xsd:dateTime')
}
def __init__(self, settings, session, path, preview_limit, uri_set=None):
SourceFile.__init__(self, settings, session, path, uri_set=uri_set)
self.type = 'tsv'
self.preview_limit = preview_limit
self.forced_column_types = ['entity']
self.disabled_columns = []
self.key_columns = []
self.headers = self.get_headers_by_file
self.category_values = defaultdict(set)
self.type_dict = {
'numeric': 'xsd:decimal',
'text': 'xsd:string',
'category': ':',
'taxon': ':',
'ref': ':',
'strand': ':',
'start': 'xsd:decimal',
'end': 'xsd:decimal',
'entity': ':',
'entitySym': ':',
'entity_start': ':',
'goterm': '',
'date': 'xsd:dateTime'
}
self.delims = {
'numeric': ('', ''),
'text': ('', '^^xsd:string'),
'category': ('', ''),
'taxon': ('', ''),
'ref': ('', ''),
'strand': ('', ''),
'start': ('', ''),
'end': ('', ''),
'entity': ('', ''),
'entitySym': ('', ''),
'entity_start': ('', ''),
'goterm': ('<http://purl.obolibrary.org/obo/GO_', '>'),
'date': ('', '^^xsd:dateTime')
}
def __init__(self, settings, session, path, tax, ent):
SourceFile.__init__(self, settings, session, path)
self.type = 'gff'
self.abstraction_dict = {}
self.domain_knowledge_dict = {}
self.pos_attr_list = [
'position_taxon', 'position_ref', 'position_start', 'position_end',
'position_strand'
]
self.categories_list = ['position_taxon', 'position_ref', 'position_strand']
self.taxon = tax
self.entities = ent
def __init__(self, settings, session, path, preview_limit):
SourceFile.__init__(self, settings, session, path)
self.type = 'tsv'
self.preview_limit = preview_limit
self.forced_column_types = ['entity']
self.category_values = defaultdict(set)
self.type_dict = {
'numeric' : 'xsd:decimal',
'text' : 'xsd:string',
'category': ':',
'taxon': ':',
'ref': ':',
'strand': ':',
'start': 'xsd:decimal',
'end': 'xsd:decimal',
'entity' : ':',
'entitySym' : ':',
'entity_start' : ':',
'entityGoterm' : ''}
self.delims = {
'numeric' : ('', ''),
'text' : ('"', '"'),
'category': (':', ''),
'taxon': (':', ''),
'ref': (':', ''),
'strand': (':', ''),
'start' : ('', ''),
'end' : ('', ''),
'entity' : (':', ''),
'entitySym' : (':', ''),
'entity_start' : (':', ''),
'entityGoterm' : ('"', '"')}
def __init__(self, settings, session, path, uri_set=None):
SourceFile.__init__(self, settings, session, path, uri_set=uri_set)
self.type = 'bed'
self.abstraction_dict = {}
self.domain_knowledge_dict = {}
self.pos_attr_list = [
'position_taxon', 'position_ref', 'position_start', 'position_end',
'position_strand'
]
self.categories_list = ['position_taxon', 'position_ref', 'position_strand']
self.taxon = ''
self.timestamp = datetime.datetime.now().isoformat()
self.get_label_from_uri = {}
self.entity = ''
def __init__(self, settings, session, path):
SourceFile.__init__(self, settings, session, path)
self.type = 'ttl'
def __init__(self, settings, session, url):
SourceFile.__init__(self, settings, session, url)
def __init__(self, settings, session, url):
SourceFile.__init__(self, settings, session, url)