def make_all_type_rel(rdf_graph: Graph,
COMMON_PREFIX: str = config.COMMON_PREFIX):
"""
生成subject和object的所有类型关系的SPO三元组
:return: 迭代生成所有三元关系的字符串
Examples
--------
>>> for rel in make_all_type_rel(graph)
>>> print(rel)
"""
global_nm = GlobalNamespaceManager.get()
rdf_type_rel = RDF.term('type')
def extract_type_rel_from_identifier(identifier: Union[BNode, URIRef]):
"""
在一个identifier中提取出 rdf:type 的三元组关系，并将其转化成字符串表示
:return: 转化后的字符串
"""
typename = global_nm.compute_qname_strict(identifier)[0]
return f'{identifier.n3()} {rdf_type_rel.n3()} {URIRef(COMMON_PREFIX + typename).n3()} .'
for s, o in rdf_graph.subject_objects():
try:
yield extract_type_rel_from_identifier(s)
except ValueError:
pass
try:
yield extract_type_rel_from_identifier(o)
except ValueError:
pass
def citation_enhancer_view_core(enhancer_id = None, enhancer_setup = None,
parent_id = None, form_id=None, parent_field=None):
content = stanbol_contenthub_retrieve(parent_id, media_type="rdf", subresource="raw")
additional_constraints = [{
"type": "reference",
"field": str(RDF.term("type")),
"value": "http://purl.uniprot.org/core/Journal_Citation"
}]
formtable = define_table_query_form(form_id,parent_field)
formtable.query.default = remove_first_line(content)
formtable.type.default = "similarity"
formtable.site.default = "uniprot"
formtable.field.requires = None
formtable.field.default = str(RDFS.term("comment"))
formtable.result_limit.default = 500
formtable.additional_constraints.default = json.dumps(additional_constraints)
form = SQLFORM(formtable, submit_button='Search')
form.element(_id="%s_query"%form_id).attributes["_rows"]="5"
form.element(_id="%s_query"%form_id).attributes["_cols"]="120"
form_hide_row(form,form_id,"additional_constraints")
form_hide_row(form,form_id,"site")
form_hide_row(form,form_id,"field")
form_hide_row(form,form_id,"type")
form_hide_row(form,form_id,"result_limit")
form_hide_row(form,form_id,"mode")
return form
def uniprot_reference_controller():
response.view = 'tree/provide_enhancements.html'
jsonquery={
#"selected" :selectedFields.values(),
"limit": 500,
"constraints": [{
"value": request.vars.url,
"type": "reference",
"field": stanbolmod.STANBOL_REFS,
"mode" : "any",
}]
}
#imidlog.log("ref search "+str(request.vars.searched_type))
if request.vars.searched_type is not None and request.vars.searched_type != '':
jsonquery["constraints"].append({
"value": request.vars.searched_type,
"type" : "reference",
"field": str(RDF.term("type")),
"mode": "any",
})
site = "uniprot"
enh = get_formated_enhancements_jsonquery(jsonquery,site)
return dict(parent_id=request.vars.parent_id,
enhancements=enh,
format_enhancement_short=format_enhancement_short)
def gene_enhancer_controller():
response.view = 'tree/provide_enhancements.html'
genes_names=request.vars.genes_names if isinstance(request.vars.genes_names,list) else [request.vars.genes_names];
genelistUP=tuple(gn.strip().upper() for gn in genes_names if len(gn.strip())>0)
genelist_low=tuple(gn.strip().lower() for gn in genes_names if len(gn.strip())>0)
#imidlog.log("Gene Enhancer: "+str(genelistUP))
geneids=db.executesql(db(db.hgnc.approved_symbol.belongs(genelistUP))._select(db.hgnc.gene_id))
geneids=geneids+db.executesql(db(db.hgnc.ucsc_id.belongs(genelist_low))._select(db.hgnc.gene_id))
imidlog.log("Gene Enhancer: "+str(geneids))
genevalues=["http://purl.uniprot.org/geneid/%s"%str(gid[0]) for gid in geneids if gid[0]!='']
jsonquery={
#"selected" :selectedFields.values(),
"limit": 500,
"constraints": [{
"value": genevalues,
"type": "reference",
"field": stanbolmod.STANBOL_REFS,
"mode" : "any",
}],
}
if request.vars.searched_type != '':
jsonquery["constraints"].append({
"value": request.vars.searched_type,
"type" : "reference",
"field": str(RDF.term("type")),
"mode": "any",
})
imidlog.log("Gene Enhancer: "+str(jsonquery))
site = "uniprot"
enh = get_formated_enhancements_jsonquery(jsonquery,site) if len(genevalues)>0 else []
return dict(parent_id=request.vars.parent_id,
enhancements=enh,
format_enhancement_short=format_enhancement_short)
def stanbol_enhancements_view_core(enhancer_id = None, enhancer_setup = None,
parent_id = None, form_id=None, parent_field=None):
meta=stanbol.contenthub_retrieve(parent_id, media_type="rdf", subresource="metadata")
js=stanbolmod.rdf_to_json(meta)
selectedFields = dict(
titlep = "http://purl.uniprot.org/core/title",
title = "http://purl.org/dc/terms/title",
comment = str(RDFS.term("comment")),
label = str(RDFS.term("label")),
mnemonic = "http://purl.uniprot.org/core/mnemonic",
type = str(RDF.term("type")),
)
def __getField(r,fieldList,default="id"):
for f in fieldList:
try:
return r[selectedFields[f]][0]["value"]
except:
pass
return r[default]
enh = []
try:
res = json.loads(qry)
for r in res["results"]:
enh.append( dict(id =r["id"],
title = __getField(r,["title","titlep","label","mnemonic","type"]),
description=__getField(r,["comment","type"]) ) )
except Exception as e:
enh.append( dict(id=qry, title="There was an error:", description=str(e)) )
#[
# for (k,v) in js.iteritems() if not k.startswith("urn:enhancement")]
#fields = [Field("E%d"%i,"string",default=url,writable=False) for (i,url) in enumerate(md)]
#def_tab_args=[form_id]+fields+[parent_field]
#form = SQLFORM(SQLDB(None).define_table(*def_tab_args),
# submit_button='Review&Accept')
return form
def get_formated_enhancements_jsonquery(jsonquery,site=None):
#Useful information for enhancements
selectedFields = dict(
titlep = "http://purl.uniprot.org/core/title",
title = "http://purl.org/dc/terms/title",
comment = str(RDFS.term("comment")),
label = str(RDFS.term("label")),
mnemonic = "http://purl.uniprot.org/core/mnemonic",
type = str(RDF.term("type")),
)
jsonquery["selected"]=selectedFields.values()
try:
qry = stanbol.entityhub_query(jsonquery,site)
except Exception as e:
qry = str(e)
def __getField(r,fieldList,default="id"):
for f in fieldList:
try:
return r[selectedFields[f]][0]["value"]
except:
pass
return r[default]
enh = []
try:
res = json.loads(qry)
for r in res["results"]:
enh.append( dict(id =r["id"],
title = __getField(r,["title","titlep","label","mnemonic","type"]),
description=__getField(r,["comment","type"]) ) )
except Exception as e:
enh.append( dict(id=qry, title="There was an error:", description=str(e)) )
return enh
import inspect
import os
from rdflib import Graph, RDFS, RDF, OWL
from itertools import chain
owl_class = OWL.term('Class')
owl_obj_property = OWL.term('ObjectProperty')
owl_data_property = OWL.term('DatatypeProperty')
rdf_type = RDF.term('type')
rdfs_domain = RDFS.term('domain')
rdfs_range = RDFS.term('range')
rdfs_subClassOf = RDFS.term('subClassOf')
def create_onto_py_URIs(file, form='turtle', add_imports=True):
g = Graph()
root = os.path.dirname(
os.path.abspath(inspect.getfile(inspect.currentframe())))
root += '/OwlFiles/'
g.parse(root + file, format=form)
file_content = ''
if add_imports:
file_content = "# Auto generated file #\n" \
"from rdflib import Graph,URIRef\n" \
"import os\n" \
"import inspect\n\n\n" \
file_content += "graph = Graph()\n" \
"root = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))\n" \
"root += '/OwlFiles/'\n" \
from rdflib import Graph
from rdflib import Literal
from rdflib import OWL
from rdflib import RDF
from rdflib import RDFS
from rdflib import URIRef
from rdflib import XSD
from utils import write_graph
a = RDF.term('type')
rdfs_domain = RDFS.term('domain')
rdfs_range = RDFS.term('range')
rdfs_subClassOf = RDFS.term('subClassOf')
xsd_double = XSD.term('double')
owl_Class = OWL.term('Class')
owl_DatatypeProperty = OWL.term('DatatypeProperty')
owl_FunctionalProperty = OWL.term('FunctionalProperty')
class Iris2RDFConverter(object):
"""
Attribute Information:
1. sepal length in cm
2. sepal width in cm
3. petal length in cm
4. petal width in cm
5. class:
-- Iris Setosa
-- Iris Versicolour
# -*- coding: utf-8 -*-
import rdflib
from rdflib.namespace import Namespace
from rdflib import RDFS, RDF, OWL
SH = Namespace('http://www.w3.org/ns/shacl#')
# Classes
RDF_Property = RDF.term('Property')
RDF_List = RDF.term('List')
RDFS_Resource = RDFS.term('Resource')
RDFS_Class = RDFS.term('Class')
OWL_Ontology = OWL.term("Ontology")
OWL_Class = OWL.term("Class")
OWL_DatatypeProperty = OWL.term("DatatypeProperty")
SH_NodeShape = SH.term('NodeShape')
SH_PropertyShape = SH.term('PropertyShape')
SH_ValidationResult = SH.term('ValidationResult')
SH_ValidationReport = SH.term('ValidationReport')
SH_Violation = SH.term('Violation')
SH_Info = SH.term('Info')
SH_Warning = SH.term('Warning')
SH_IRI = SH.term('IRI')
SH_BlankNode = SH.term('BlankNode')
SH_Literal = SH.term('Literal')
SH_BlankNodeOrIRI = SH.term('BlankNodeOrIRI')
SH_BlankNodeORLiteral = SH.term('BlankNodeOrLiteral')
SH_IRIOrLiteral = SH.term('IRIOrLiteral')
SH_SPARQLFunction = SH.term('SPARQLFunction')
SH_SPARQLRule = SH.term('SPARQLRule')
SH_NodeShape = SH.term('NodeShape')
SH_PropertyShape = SH.term('PropertyShape')
SH_ValidationResult = SH.term('ValidationResult')
SH_ValidationReport = SH.term('ValidationReport')
SH_Violation = SH.term('Violation')
SH_Info = SH.term('Info')
SH_Warning = SH.term('Warning')
SH_IRI = SH.term('IRI')
SH_BlankNode = SH.term('BlankNode')
SH_Literal = SH.term('Literal')
SH_BlankNodeOrIRI = SH.term('BlankNodeOrIRI')
SH_BlankNodeORLiteral = SH.term('BlankNodeOrLiteral')
SH_IRIOrLiteral = SH.term('IRIOrLiteral')
# predicates
RDF_type = RDF.term('type')
RDFS_subClassOf = RDFS.term('subClassOf')
SH_path = SH.term('path')
SH_deactivated = SH.term('deactivated')
SH_message = SH.term('message')
SH_name = SH.term('name')
SH_description = SH.term('description')
SH_property = SH.term('property')
SH_node = SH.term('node')
SH_targetClass = SH.term('targetClass')
SH_targetNode = SH.term('targetNode')
SH_targetObjectsOf = SH.term('targetObjectsOf')
SH_targetSubjectsOf = SH.term('targetSubjectsOf')
SH_focusNode = SH.term('focusNode')
SH_resultSeverity = SH.term('resultSeverity')
SH_resultPath = SH.term('resultPath')
# -*- coding: utf-8 -*-
#
"""A collection of handy utility RDF functions, will one day be split out into its own installable module."""
from rdflib import RDF, RDFS, Namespace
RDFS_Resource = RDFS.term('Resource')
RDF_first = RDF.term('first')
SH = Namespace('http://www.w3.org/ns/shacl#')
from .load import load_from_source, get_rdf_from_web
from .stringify import stringify_blank_node, stringify_graph, stringify_literal, stringify_node
from .clone import clone_blank_node, clone_literal, clone_graph, clone_node, mix_graphs
from .compare import compare_blank_node, order_graph_literal, compare_node, compare_literal
SH_NodeShape = SH.term('NodeShape')
SH_PropertyShape = SH.term('PropertyShape')
SH_ValidationResult = SH.term('ValidationResult')
SH_ValidationReport = SH.term('ValidationReport')
SH_Violation = SH.term('Violation')
SH_Info = SH.term('Info')
SH_Warning = SH.term('Warning')
SH_IRI = SH.term('IRI')
SH_BlankNode = SH.term('BlankNode')
SH_Literal = SH.term('Literal')
SH_BlankNodeOrIRI = SH.term('BlankNodeOrIRI')
SH_BlankNodeORLiteral = SH.term('BlankNodeOrLiteral')
SH_IRIOrLiteral = SH.term('IRIOrLiteral')
# predicates
RDF_type = RDF.term('type')
RDF_first = RDF.term('first')
RDF_rest = RDF.term('rest')
RDFS_subClassOf = RDFS.term('subClassOf')
SH_path = SH.term('path')
SH_deactivated = SH.term('deactivated')
SH_message = SH.term('message')
SH_name = SH.term('name')
SH_description = SH.term('description')
SH_property = SH.term('property')
SH_node = SH.term('node')
SH_targetClass = SH.term('targetClass')
SH_targetNode = SH.term('targetNode')
SH_targetObjectsOf = SH.term('targetObjectsOf')
SH_targetSubjectsOf = SH.term('targetSubjectsOf')
SH_focusNode = SH.term('focusNode')