From 61a8c244daefcd03010a20b8b9c3a008afe8d3c0 Mon Sep 17 00:00:00 2001
From: schroeder5 <s.schroeder@fz-juelich.de>
Date: Fri, 29 Jan 2021 08:55:44 +0000
Subject: [PATCH] enabled saving onthologies in different formats
---
toardb/utils/TOARII_ontology.py | 104 ++++++++++++++++++++++++++++++--
1 file changed, 98 insertions(+), 6 deletions(-)
diff --git a/toardb/utils/TOARII_ontology.py b/toardb/utils/TOARII_ontology.py
index d2ab10e..58eef45 100644
--- a/toardb/utils/TOARII_ontology.py
+++ b/toardb/utils/TOARII_ontology.py
@@ -33,7 +33,7 @@ class TOAR_Ontology:
get_class(title):
find the onthology class for the given title
- get_class_by_id(self, id):
+ get_class_by_id(id):
find the onthology class for the given id
show_class_definition(ont_class):
@@ -42,7 +42,7 @@ class TOAR_Ontology:
show_entries(ont_class):
show information on given ontology class
- add_entry(self, ont_class, idcount, label, definition):
+ add_entry(ont_class, idcount, label, definition):
add entry to given ontology class
check_entry(entry, ont_class):
@@ -51,14 +51,24 @@ class TOAR_Ontology:
print(format=""):
Prints the onthology in the given format
- save(self, filename):
- save the onthology in json-ld format to the given file
+ save(filename, format):
+ save the onthology in given format to the given file
"""
def __init__(self, filename):
"""
initialize the onthology
+
+ Parameters
+ ----------
+ filename: str
+ filename containing the ontology in json-ld format
+
+ Returns
+ -------
+ TOAR_Ontology
"""
+
self.filename = filename
g = rdflib.Graph()
self.graph = g.parse(self.filename,format='json-ld')
@@ -66,6 +76,15 @@ class TOAR_Ontology:
def get_class(self, title):
"""
find the onthology class for the given title
+
+ Parameters
+ ----------
+ title: str
+ title of class
+
+ Returns
+ -------
+ OWL.Class
"""
for s, p, o in self.graph.triples( (None, RDF.type, OWL.Class) ):
value = self.graph.value(subject=s,predicate=RDFS.label)
@@ -76,6 +95,15 @@ class TOAR_Ontology:
def get_class_by_id(self, id):
"""
find the onthology class for the given id
+
+ Parameters
+ ----------
+ id: str
+ id of class
+
+ Returns
+ -------
+ OWL.Class
"""
for s, p, o in self.graph.triples( (None, RDF.type, OWL.Class) ):
if s.strip() == id.strip():
@@ -85,6 +113,15 @@ class TOAR_Ontology:
def show_class_definition(self, ont_class):
"""
show information on given ontology class
+
+ Parameters
+ ----------
+ ont_class: OWL.class
+ onthology class
+
+ Returns
+ -------
+ None
"""
for s, p, o in self.graph.triples( (ont_class, SKOS.definition, None) ):
print(f"definition of {ont_class}: {o}")
@@ -92,6 +129,15 @@ class TOAR_Ontology:
def show_entries(self, ont_class):
"""
show information on given ontology class
+
+ Parameters
+ ----------
+ ont_class: OWL.class
+ onthology class
+
+ Returns
+ -------
+ None
"""
for s, p, o in self.graph.triples( (None, RDF.type, ont_class ) ):
label=self.graph.value(subject=s,predicate=RDFS.label)
@@ -102,6 +148,21 @@ class TOAR_Ontology:
def add_entry(self, ont_class, idcount, label, definition):
"""
add entry to given ontology class
+
+ Parameters
+ ----------
+ ont_class: OWL.class
+ onthology class
+ id_count: int
+ integer for constructing ID "OWLNamedIndividual_nnnnnn"
+ label: str
+ title of entry to be inserted
+ definition: str
+ definition of entry to be inserted
+
+ Returns
+ -------
+ None
"""
# still to do:
# how to get rid of "http://www.fz-juelich.de/ontologies/2020/ToarOntotology"?!
@@ -134,6 +195,17 @@ class TOAR_Ontology:
def check_entry(self, entry, ont_class):
"""
check whether entry is a valid value of the ontology
+
+ Parameters
+ ----------
+ entry: str
+ title of entry to be checked
+ ont_class: OWL.class
+ onthology class
+
+ Returns
+ -------
+ None
"""
found=False
for s, p, o in self.graph.triples( (None, RDF.type, ont_class ) ):
@@ -144,15 +216,35 @@ class TOAR_Ontology:
def print(self, format='json-ld'):
"""
print the onthology in the given format
+
+ Parameters
+ ----------
+ format: str, optional
+ output format (default: json-ld)
+
+ Returns
+ -------
+ None
"""
print(self.graph.serialize(format=format).decode("utf-8"))
- def save(self, filename):
+ def save(self, filename, format='json-ld'):
"""
save the onthology in json-ld format to the given file
+
+ Parameters
+ ----------
+ filename: str
+ output file name
+ format: str, optional
+ output format (default: json-ld)
+
+ Returns
+ -------
+ None
"""
outfile = open(filename,'w')
- outfile.write(self.graph.serialize(format='json-ld').decode("utf-8"))
+ outfile.write(self.graph.serialize(format=format).decode("utf-8"))
# #check_entry would have been nicer, if something like this worked:
# subj2 = rdflib.URIRef("http://www.fz-juelich.de/ontologies/2020/ToarOntotology#OWLNamedIndividual_000141")
--
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