diff --git a/doc/example_odMLs/THGTTG.odml b/doc/example_odMLs/THGTTG.odml index bbed197b..baf2ba0d 100644 --- a/doc/example_odMLs/THGTTG.odml +++ b/doc/example_odMLs/THGTTG.odml @@ -3,244 +3,309 @@ 42 - D. N. Adams - 1979-10-12
+ TheCrew + + person + NameCrewMembers + [Arthur Philip Dent,Zaphod Beeblebrox,Tricia Marie McMillan,Ford Prefect] + 77cdad5c-5d74-4e9f-9d74-c1ce8e79e951 + List of crew members names + + + int + 1 + NoCrewMembers + The Hitchhiker's guide to the Galaxy (novel) + [4] + 05e14adf-1ca2-4b2d-984d-6c84814a84de + Number of crew members +
+ Arthur Philip Dent - [Human] - Species to which subject belongs to string Species + [Human] + f64e9d6a-e38d-499e-a03f-fe59b91ad6ba + Species to which subject belongs to - [The sandwich-maker] - Nickname(s) of the subject string Nickname + [The sandwich-maker] + c9dd7ae6-66a1-49f0-9853-80f2cdf6b574 + Nickname(s) of the subject - [-] - Occupation of the subject string Occupation + [] + 76941971-132a-4b3a-94db-e3cf356ea429 + Occupation of the subject - [male] - Sex of the subject string Gender + [male] + 5f1a5e56-d893-47bd-989a-9d3a596bc29e + Sex of the subject - [Earth] - Home planet of the subject string HomePlanet + [Earth] + 6470acca-5457-4a43-a61c-6744372dff3b + Home planet of the subject Information on Arthur Dent + e547c987-4beb-4250-bcb3-1991c535e7e8 crew/person - Arthur Philip Dent
+ Zaphod Beeblebrox - [Betelgeusian] - Species to which subject belongs to string Species + [Betelgeusian] + 861a8469-708e-4950-be71-12c640d7e7d6 + Species to which subject belongs to - [-] - Nickname(s) of the subject string Nickname + [] + ba06784b-d323-45c8-bb52-918b727f2ef1 + Nickname(s) of the subject - [Ex-Galactic President] - Occupation of the subject string Occupation + [Ex-Galactic President] + 09b96b49-7bf3-4449-9e43-62d87bb23f16 + Occupation of the subject - [male] - Sex of the subject string Gender + [male] + 41f4ab65-afda-43c9-aa08-a384c9fba585 + Sex of the subject - [A planet in the vicinity of Betelgeuse] - Home planet of the subject string HomePlanet + [A planet in the vicinity of Betelgeuse] + c81063a1-4727-4d51-bdfd-574923f387ab + Home planet of the subject Information on Zaphod Beeblebrox + 5d22732f-ebfd-494d-9fb0-0e938fc83291 crew/person - Zaphod Beeblebrox
+ Tricia Marie McMillan - [Betelgeusian] - Species to which subject belongs to string Species + [Human] + 087d4862-50a5-4764-a2b5-01dded29ccab + Species to which subject belongs to - [Trillian Astra] - Nickname(s) of the subject string Nickname + [Trillian Astra] + 15fef4d3-a9ed-4fc2-95db-7f7c90d85a8c + Nickname(s) of the subject - [-] - Occupation of the subject string Occupation + [] + 4ab85d8a-f884-4ef7-bf33-0d42044d95bb + Occupation of the subject - [female] - Sex of the subject string Gender + [female] + dd553e39-b3b1-4ef2-9b21-6145a3222d15 + Sex of the subject - [Earth] - Home planet of the subject string HomePlanet + [Earth] + fe2abddf-f2e7-43f3-b3db-0932f94e17e9 + Home planet of the subject Information on Trillian Astra + b85c4c2d-4722-48fa-a118-5c2f553d7282 crew/person - Tricia Marie McMillan
+ Ford Prefect - [Betelgeusian] - Species to which subject belongs to string Species + [Betelgeusian] + 1493fb9b-6fb2-479e-923c-61242567ffd7 + Species to which subject belongs to - [Ix] - Nickname(s) of the subject string Nickname + [Ix] + 4b6eb605-dbfb-40e0-83c4-acca43e4fdbb + Nickname(s) of the subject - [Researcher for the Hitchhiker's Guide to the Galaxy] - Occupation of the subject string Occupation + [Researcher/Reporter] + 3a69dba5-c780-447a-b9d9-e8da3cbbd4f4 + Occupation of the subject - [male] - Sex of the subject string Gender + [male] + 01b8b16c-c80b-4432-93a9-0fab8de74e22 + Sex of the subject - [A planet in the vicinity of Betelgeuse] - Home planet of the subject string HomePlanet + [A planet in the vicinity of Betelgeuse] + f47c0d5e-e2b8-425b-83f3-57bcbe44164d + Home planet of the subject Information on Ford Prefect + 97cbf33c-5aa8-41af-b158-13247e7481dd crew/person - Ford Prefect
- - [Arthur Philip Dent,Zaphod Beeblebrox,Tricia Marie McMillan,Ford Prefect] - List of crew members names - person - NameCrewMembers - - - [4] - Number of crew members - int - NoCrewMembers - Information on the crew + 6df940b5-b502-4749-8ad9-33d7432064f3 crew - TheCrew
-
-
- Information on Marvin - starship/cybernetics - Marvin -
-
- Information on Eddie - starship/cybernetics - Eddie -
- - [Genuine People Personalities] - Type of robots - string - RobotType - - - [Sirius Cybernetics Corporation] - Manufacturer of robots - string - Manufacturer - - - [2] - Number of cybernetic robots on the ship - int - NoOfCybernetics - - Information on cybernetics present on the ship - starship/cybernetics - Cybernetics -
+ TheStarship - [Heart of Gold] - Name of person/device string Name + [Heart of Gold] + b0f80f23-e976-4a06-b146-b81e5f565d6b + Name of person/device - [stolen] - Owner status of device string OwnerStatus + [stolen] + 43b26234-6023-4e7f-8bc4-401b0fd0504a + Owner status of device - [Infinite Propability Drive] - Type of drive string DriveType + [Infinite Propability Drive] + 828d51ea-f5c8-4525-b2ff-757555449190 + Type of drive - [secret] - Technology used to built device string Technology + [secret] + 0117aaa2-fa5d-4623-a63c-4342733205ec + Technology used to built device + float + Length m [150.0] + 7e2a3940-833c-407b-9047-918d317af204 Length of device - float - Length - [various] - Shape of device string Shape + [various] + f34bfcbb-1a57-4905-bc8b-ef953c0e736e + Shape of device - [Damogran] - Planet where device was constructed string FactoryPlanet + [Damogran] + c39386b4-2023-4dd3-bf03-57bd3c65d5c0 + Planet where device was constructed - Information on the crew - crew - TheStarship +
+ Cybernetics + + int + NoOfCybernetics + [2] + 534155a2-8d6a-471d-a7cb-8a950ff5e157 + Number of cybernetic robots on the ship + + + string + NamesOfCybernetics + [Marvin,Eddie] + 7c00d7e3-2822-42b5-b5b3-b5c7dc51f67e + Names of cybernetic robots on the ship + +
+ Marvin + + string + Type + [Genuine People Personality] + 7f74bd80-4d08-43b3-aedc-7e3668b48d34 + Type of robot + + + string + Manufacturer + [Sirius Cybernetics Corporation] + 45cb21b1-b0e6-4eb0-a153-2059dd3d3444 + Manufacturer of robots + + Information on Marvin + 2d66ac3e-5d25-45cc-89c1-1cc5890daa7b + starship/cybernetics +
+
+ Eddie + + string + Type + [Genuine People Personality] + 2899d6df-7f15-48f5-aa11-aa368ba75eeb + Type of robot + + + string + Manufacturer + [Sirius Cybernetics Corporation] + dda738bb-47e4-462b-821c-ea900633dbee + Manufacturer of robots + + Information on Eddie + 953852d6-bbca-44d5-bad1-fb9bbca08655 + starship/cybernetics +
+ Information on cybernetics present on the ship + 4f6f4994-cc0f-4d10-a643-4cdda5aa8248 + starship/cybernetics +
+ Information on the starship + 38a36e78-ceca-4045-87a5-53a4dac29f10 + starship
+ D. N. Adams + 1979-10-12 + cf6d24de-c780-4ad2-91ce-45dd5157d6b8 diff --git a/doc/example_odMLs/ex_1.odml b/doc/example_odMLs/ex_1.odml new file mode 100644 index 00000000..e95622b9 --- /dev/null +++ b/doc/example_odMLs/ex_1.odml @@ -0,0 +1,52 @@ + + + + + D. N. Adams + http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml +
+ + person + [Arthur Philip Dent,Zaphod Beeblebrox,Tricia Marie McMillan,Ford Prefect] + 7b0572c1-fcfc-4010-aebf-730397ac29af + NameCrewMembers + List of crew members names + + + int + 1 + [4] + The Hitchhiker's guide to the Galaxy (novel) + 298938a6-0996-4a92-982b-837a08a1a220 + NoCrewMembers + Number of crew members + + crew + Information on the crew + 0f96a050-2d9b-498f-a532-fbfcc6aae55e + TheCrew +
+ + string + [Human] + 635035cc-1c05-4e44-a4b7-0fb3d6295abf + Species + Species to which subject belongs to + + + string + [] + 0cec018b-20e3-4b13-bb95-b41de12db97f + Nickname + Nickname(s) of the subject + + crew/person + Information on Arthur Dent + 1d6469b5-5322-408b-916e-3224b7a22008 + Arthur Philip Dent +
+
+ 1979-10-12 + 79b613eb-a256-46bf-84f6-207df465b8f7 + 42 + diff --git a/doc/example_odMLs/ex_1.rdf b/doc/example_odMLs/ex_1.rdf new file mode 100644 index 00000000..cb7a1e2a --- /dev/null +++ b/doc/example_odMLs/ex_1.rdf @@ -0,0 +1,142 @@ + + + + + + + + + + + + 1979-10-12 + + + + D. N. Adams + 1979-10-12 + + 42 + + + + + 42 + + + D. N. Adams + + 1979-10-12 + 1979-10-12 + + + + + + crew + s11 + Information on the crew + + + + + + + + Human + + + + Species + string + Species to which subject belongs to + + + crew/person + + + + Nickname(s) of the subject + string + Nickname + + + Arthur Philip Dent + Information on Arthur Dent + + + Number of crew members + int + 1 + NoCrewMembers + + + + 4 + + + + + Information on the crew + + crew + s21 + + + + s1 + + crew + + + + crew + Information on the crew + s12 + + + + Information on the crew + + + + crew + + + List of crew members names + person + + + + Zaphod Beeblebrox + Ford Prefect + Arthur Philip Dent + Tricia Marie McMillan + + + NameCrewMembers + + + + Information on the crew + TheCrew + + + + crew + + s21 + s121 + Information on the crew + + + s2 + + Information on the crew + + crew + + diff --git a/doc/example_odMLs/ex_2.odml b/doc/example_odMLs/ex_2.odml new file mode 100644 index 00000000..136e9b77 --- /dev/null +++ b/doc/example_odMLs/ex_2.odml @@ -0,0 +1,47 @@ + + + + + http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml +
+ Information on the crew +
+ Information on the crew + da908cda-19e1-4df8-b873-d1f6cd1b164d + crew + s11 +
+
+ Information on the crew +
+ Information on the crew + 18bb5a7e-2097-43f2-a782-e6f612107e93 + crew + s21 + s121 +
+ 8d68e6fe-8dda-4dfe-a1d8-edaa0f410255 + crew + s12 +
+ d1e70848-5318-4466-82d0-1c3e99a8ba85 + crew + s1 +
+
+ Information on the crew +
+ Information on the crew + 4b2d0e9d-6352-4676-97d7-fc0a795e83a9 + crew + s21 +
+ bc6cc466-5769-4da1-b90e-8e5595903a4a + crew + s2 +
+ 1979-10-12 + 9b862019-643a-403f-b5a9-3b46db012961 + 42 + D. N. Adams + diff --git a/doc/example_odMLs/odml_ex_1_generator.py b/doc/example_odMLs/odml_ex_1_generator.py new file mode 100644 index 00000000..028de1c8 --- /dev/null +++ b/doc/example_odMLs/odml_ex_1_generator.py @@ -0,0 +1,63 @@ +import datetime +import os + +import odml + +odml_pythonpath = "./g-node/python-odml" +odmlrepo = 'http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml' + +# CREATE A DOCUMENT +doc = odml.Document(author="D. N. Adams", + date=datetime.date(1979, 10, 12), + version=42, + repository=odmlrepo) + +# CREATE AND APPEND THE MAIN SECTIONs +doc.append(odml.Section(name="TheCrew", + definition="Information on the crew", + type="crew")) + +# SET NEW PARENT NODE +parent = doc['TheCrew'] + +# APPEND SUBSECTIONS +parent.append(odml.Section(name="Arthur Philip Dent", + type="crew/person", + definition="Information on Arthur Dent")) + + +# APPEND PROPERTIES WITH VALUES +parent.append(odml.Property(name="NameCrewMembers", + value=["Arthur Philip Dent", + "Zaphod Beeblebrox", + "Tricia Marie McMillan", + "Ford Prefect"], + dtype=odml.DType.person, + definition="List of crew members names")) + +parent.append(odml.Property(name="NoCrewMembers", + value=4, + dtype=odml.DType.int, + definition="Number of crew members", + uncertainty=1, + reference="The Hitchhiker's guide to the Galaxy (novel)")) + +# SET NEW PARENT NODE +parent = doc['TheCrew']['Arthur Philip Dent'] + +# APPEND SUBSECTIONS + +# APPEND PROPERTIES WITH VALUES +parent.append(odml.Property(name="Species", + value="Human", + dtype=odml.DType.string, + definition="Species to which subject belongs to")) + +parent.append(odml.Property(name="Nickname", + value=None, + dtype=odml.DType.string, + definition="Nickname(s) of the subject")) + +save_to = os.path.join(odml_pythonpath, "doc", "example_odMLs", "ex_1.odml") + +odml.save(doc, save_to) diff --git a/odml/tools/__init__.py b/odml/tools/__init__.py index 4e7194dd..826c03b0 100644 --- a/odml/tools/__init__.py +++ b/odml/tools/__init__.py @@ -1,4 +1,5 @@ - from odml.tools import dumper -from odml.tools import xmlparser from odml.tools import jsonparser +from odml.tools import rdf_converter +from odml.tools import xmlparser + diff --git a/odml/tools/rdf_converter.py b/odml/tools/rdf_converter.py new file mode 100644 index 00000000..af8ec26f --- /dev/null +++ b/odml/tools/rdf_converter.py @@ -0,0 +1,134 @@ +import sys +import uuid + +from rdflib import Graph, Literal, URIRef +from rdflib.namespace import XSD, RDF + +import odml +import odml.format + +try: + unicode = unicode +except NameError: + unicode = str + +odmlns = odml.format.Format.namespace() + + +class RDFWriter(object): + """ + Creates the RDF graph storing information about the odML document + """ + + def __init__(self, odml_documents, hub_id=None): + self.docs = odml_documents + self.hub_id = hub_id + self.hub_root = None + self.g = Graph() + self.g.bind("odml", odmlns) + + def create_hub_root(self): + if self.hub_root is None: + if self.hub_id is None: + self.hub_root = URIRef(odmlns + str(uuid.uuid4())) + else: + self.hub_root = URIRef(odmlns + self.hub_id) + + def convert_to_rdf(self, docs): + self.create_hub_root() + if docs: + self.g.add((self.hub_root, odmlns.Hub, URIRef(odmlns.Hub))) + for doc in docs: + self.save_element(doc) + return self.g + + def save_element(self, e, node=None): + """ + Save the current element to the RDF graph + :param e: current element + :param node: A node to pass the earlier created node to inner elements + :return: the RDF graph + """ + fmt = e._format + + if not node: + curr_node = URIRef(odmlns + str(e.id)) + else: + curr_node = node + + self.g.add((curr_node, RDF.type, URIRef(fmt.rdf_type()))) + + # adding doc to the hub + if isinstance(fmt, odml.format.Document.__class__): + self.g.add((self.hub_root, odmlns.hasDocument, curr_node)) + + for k in fmt._rdf_map: + if k == 'id': + continue + elif (isinstance(fmt, odml.format.Document.__class__) or + isinstance(fmt, odml.format.Section.__class__)) and k == "repository": + terminology_url = getattr(e, k) + if terminology_url is None or not terminology_url: + continue + terminology_node = self._get_terminology_by_value(terminology_url) + if terminology_node: + self.g.add((curr_node, fmt.rdf_map(k), terminology_node)) + else: + # adding terminology to the hub and to link with the doc + node = URIRef(odmlns + str(uuid.uuid4())) + self.g.add((node, odmlns.Terminology, URIRef(terminology_url))) + self.g.add((self.hub_root, odmlns.hasTerminology, node)) + self.g.add((curr_node, fmt.rdf_map(k), node)) + # generating nodes for entities: sections, properties and bags of values + elif (isinstance(fmt, odml.format.Document.__class__) or + isinstance(fmt, odml.format.Section.__class__)) and \ + k == 'sections' and len(getattr(e, k)) > 0: + sections = getattr(e, k) + for s in sections: + node = URIRef(odmlns + str(s.id)) + self.g.add((curr_node, fmt.rdf_map(k), node)) + self.save_element(s, node) + elif isinstance(fmt, odml.format.Section.__class__) and \ + k == 'properties' and len(getattr(e, k)) > 0: + properties = getattr(e, k) + for p in properties: + node = URIRef(odmlns + str(p.id)) + self.g.add((curr_node, fmt.rdf_map(k), node)) + self.save_element(p, node) + elif isinstance(fmt, odml.format.Property.__class__) and \ + k == 'value' and len(getattr(e, k)) > 0: + values = getattr(e, k) + bag = URIRef(str(uuid.uuid4())) + self.g.add((bag, RDF.type, RDF.Bag)) + self.g.add((curr_node, fmt.rdf_map(k), bag)) + for v in values: + self.g.add((bag, RDF.li, Literal(v))) + # adding entities' properties + else: + val = getattr(e, k) + if val is None or not val: + continue + elif k == 'date': + self.g.add((curr_node, fmt.rdf_map(k), Literal(val, datatype=XSD.date))) + else: + self.g.add((curr_node, fmt.rdf_map(k), Literal(val))) + return self.g + + def _get_terminology_by_value(self, url): + return self.g.value(predicate=odmlns.Terminology, object=URIRef(url)) + + def __str__(self): + return self.convert_to_rdf(self.docs).serialize(format='turtle').decode("utf-8") + + def __unicode__(self): + return self.convert_to_rdf(self.docs).serialize(format='turtle').decode("utf-8") + + def write_file(self, filename): + if sys.version_info < (3,): + data = unicode(self).encode('utf-8') + else: + data = str(self) + + f = open(filename, "w") + f.write(data) + f.close() \ No newline at end of file