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update dependencies, define port schemas, use GraphParameterType()
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@muddymudskipper
muddymudskipper committed Sep 23, 2024
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2 changes: 1 addition & 1 deletion .idea/cmem-plugin-shapes.iml
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93 changes: 0 additions & 93 deletions cmem_plugin_shapes/parameter_types.py
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18 changes: 12 additions & 6 deletions cmem_plugin_shapes/plugin_shapes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,17 +17,17 @@
from cmem.cmempy.workspace.projects.project import get_prefixes
from cmem_plugin_base.dataintegration.context import ExecutionContext
from cmem_plugin_base.dataintegration.description import Icon, Plugin, PluginParameter
from cmem_plugin_base.dataintegration.parameter.graph import GraphParameterType
from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin
from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType
from cmem_plugin_base.dataintegration.ports import FixedNumberOfInputs
from cmem_plugin_base.dataintegration.types import BoolParameterType
from cmem_plugin_base.dataintegration.utils import setup_cmempy_user_access
from rdflib import RDF, RDFS, SH, XSD, Graph, Literal, Namespace, URIRef
from rdflib.namespace import split_uri
from str2bool import str2bool
from urllib3.exceptions import InsecureRequestWarning
from validators import url

from cmem_plugin_shapes.parameter_types import GraphParameterTypeNew

from . import __path__

environ["SSL_VERIFY"] = "false"
Expand All @@ -48,13 +48,16 @@ def format_namespace(iri: str) -> str:
documentation="",
parameters=[
PluginParameter(
param_type=GraphParameterTypeNew(),
param_type=GraphParameterType(allow_only_autocompleted_values=True),
name="data_graph_iri",
label="Input data graph.",
description="",
),
PluginParameter(
param_type=StringParameterType(),
param_type=GraphParameterType(
classes=["https://vocab.eccenca.com/shui/ShapeCatalog"],
allow_only_autocompleted_values=False,
),
name="shapes_graph_iri",
label="Output SHACL shapes graph.",
description="",
Expand Down Expand Up @@ -105,6 +108,9 @@ def __init__( # noqa: PLR0913
self.import_shapes = import_shapes
self.prefix_cc = prefix_cc

self.input_ports = FixedNumberOfInputs([])
self.output_port = None

def get_prefixes(self) -> dict:
"""Get list of prefixes from prefix.cc or use local copy"""
err = None
Expand Down Expand Up @@ -250,7 +256,7 @@ def import_shapes_graph(self) -> None:
setup_cmempy_user_access(self.context.user)
post(query)

def execute(self, inputs: tuple, context: ExecutionContext) -> None: # noqa: ARG002
def execute(self, inputs: None, context: ExecutionContext) -> None: # noqa: ARG002
"""Execute plugin"""
setup_cmempy_user_access(context.user)
if not self.overwrite and self.shapes_graph_iri in [i["iri"] for i in get_graphs_list()]:
Expand Down
33 changes: 31 additions & 2 deletions cmem_plugin_shapes/prefix.cc.json
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
"afn": "http://jena.apache.org/ARQ/function#",
"afpo": "http://purl.obolibrary.org/obo/AfPO_",
"afr": "http://purl.allotrope.org/ontologies/result#",
"after": "http://rds.posccaesar.org/ontology/plm/ds/",
"agent": "http://eulersharp.sourceforge.net/2003/03swap/agent#",
"agents": "http://eulersharp.sourceforge.net/2003/03swap/agent#",
"agetec": "http://www.agetec.org/",
Expand All @@ -58,7 +59,9 @@
"aiiso": "http://purl.org/vocab/aiiso/schema#",
"aimaix": "https://w3id.org/aimaix#",
"aims": "http://aims.fao.org/aos/common/",
"aio": "https://paul.ti.rw.fau.de/~jo00defe/SemWoT/aio#",
"air": "http://dig.csail.mit.edu/TAMI/2007/amord/air#",
"airo": "https://w3id.org/airo#",
"airport": "http://www.daml.org/2001/10/html/airport-ont#",
"airs": "https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl#",
"aism": "http://purl.obolibrary.org/obo/AISM_",
Expand All @@ -82,6 +85,7 @@
"ams": "http://data.amadeus.com/",
"amsl": "http://vocab.ub.uni-leipzig.de/amsl/",
"amt": "http://academic-meta-tool.xyz/vocab#",
"amv": "https://w3id.org/amv/",
"anca": "http://users.utcluj.ro/~raluca/rdf_ontologies_ralu/ralu_modified_ontology_pizzas2_0#",
"aneo": "http://akonadi-project.org/ontologies/aneo#",
"ann": "http://www.w3.org/2000/10/annotation-ns#",
Expand Down Expand Up @@ -213,6 +217,7 @@
"biogrid": "http://thebiogrid.org/",
"biol": "http://purl.org/NET/biol/ns#",
"biolink": "https://w3id.org/biolink/vocab/",
"biomodels": "http://purl.obolibrary.org/obo/KISAO_",
"biopax": "http://www.biopax.org/release/biopax-level3.owl#",
"biordf": "http://purl.org/net/biordfmicroarray/ns#",
"bioschemas": "https://bioschemas.org/",
Expand Down Expand Up @@ -374,8 +379,10 @@
"cmd": "https://w3id.org/cmd#",
"cmdi": "http://www.clarin.eu/cmd/",
"cmdm": "http://infra.clarin.eu/cmd/",
"cmf": "http://purl.obolibrary.org/obo/CMF_",
"cmo": "http://purl.org/twc/ontologies/cmo.owl#",
"cmp": "http://www.ontologydesignpatterns.org/cp/owl/componency.owl#",
"cmso": "http://purls.helmholtz-metadaten.de/cmso/",
"cnt": "http://www.w3.org/2011/content#",
"co": "http://purl.org/ontology/co/core#",
"cob": "http://purl.obolibrary.org/obo/COB_",
Expand Down Expand Up @@ -452,9 +459,10 @@
"crm": "http://www.cidoc-crm.org/cidoc-crm/",
"crmdig": "http://www.ics.forth.gr/isl/CRMdig/",
"crmeh": "http://purl.org/crmeh#",
"crmgeo": "http://www.ics.forth.gr/isl/CRMgeo/",
"crminf": "http://www.cidoc-crm.org/cidoc-crm/CRMinf/",
"crml": "http://semweb.mmlab.be/ns/rml/condition#",
"crmsci": "http://cidoc-crm.org/crmsci/",
"crmsci": "http://www.ics.forth.gr/isl/CRMsci/",
"cro": "http://rhizomik.net/ontologies/copyrightonto.owl#",
"crowd": "http://purl.org/crowd/",
"crsw": "http://courseware.rkbexplorer.com/ontologies/courseware#",
Expand Down Expand Up @@ -737,6 +745,7 @@
"ecore": "http://www.eclipse.org/emf/2002/Ecore#",
"ecos": "http://purl.org/ecos#",
"ecowlim": "http://ecowlim.tfri.gov.tw/lode/resource/",
"ecp": "http://www.ebu.ch/metadata/ontologies/ebucoreplus#",
"ecpo": "http://purl.org/ontology/ecpo#",
"ecrm": "http://erlangen-crm.org/current/",
"ecs": "http://rdf.ecs.soton.ac.uk/ontology/ecs#",
Expand All @@ -749,6 +758,7 @@
"edm": "http://www.europeana.eu/schemas/edm/",
"edo": "http://semanticweb.org/edo#",
"edr": "https://w3id.org/laas-iot/edr#",
"edtf": "http://id.loc.gov/datatypes/EDTFScheme/",
"edu": "https://schema.edu.ee/",
"edupro": "http://ns.inria.fr/semed/eduprogression#",
"eem": "http://purl.org/eem#",
Expand Down Expand Up @@ -1039,7 +1049,7 @@
"gg": "http://www.gemeentegeschiedenis.nl/gg-schema#",
"ggbn": "http://data.ggbn.org/schemas/ggbn/terms/",
"ghga": "http://w3id.org/ghga/",
"gist": "http://ontologies.semanticarts.com/gist#",
"gist": "https://ontologies.semanticarts.com/o/gistCore#",
"giving": "http://ontologi.es/giving#",
"gl": "http://schema.geolink.org/",
"gldp": "http://www.w3.org/ns/people#",
Expand Down Expand Up @@ -1324,6 +1334,7 @@
"ksam": "http://kulturarvsdata.se/ksamsok#",
"ksamsok": "http://kulturarvsdata.se/ksamsok#",
"kupkb": "http://www.e-lico.eu/data/kupkb/",
"kvasir": "https://kvasir.discover.ilabt.imec.be/vocab#",
"kw": "http://kwantu.net/kw/",
"kwijibo": "http://kwijibo.talis.com/",
"l2sp": "http://www.linked2safety-project.eu/properties/",
Expand All @@ -1332,6 +1343,7 @@
"la": "https://linked.art/ns/terms/",
"laabs": "http://dbpedia.org/resource/",
"label": "http://purl.org/net/vocab/2004/03/label#",
"labo": "http://purl.obolibrary.org/obo/LABO_",
"lado": "http://archaeology.link/ontology#",
"lang": "http://ontologi.es/lang/core#",
"language": "http://id.loc.gov/vocabulary/iso639-1/",
Expand Down Expand Up @@ -1414,6 +1426,7 @@
"linkml": "https://w3id.org/linkml/",
"linkrel": "https://www.w3.org/ns/iana/link-relations/relation#",
"lio": "http://purl.org/net/lio#",
"liph": "https://gallosiciliani.unict.it/ns/lpont#",
"lipro": "http://purl.obolibrary.org/obo/LIPRO_",
"lis": "http://rds.posccaesar.org/ontology/lis14/rdl/",
"list": "http://www.w3.org/2000/10/swap/list#",
Expand Down Expand Up @@ -1506,6 +1519,7 @@
"mag": "https://makg.org/property/",
"magmardl": "http://www.semanticweb.org/magma-core/rdl#",
"magmauser": "http://www.semanticweb.org/magma-core/user#",
"maid": "https://mutual-aid.app/ns/core#",
"malaka": "http://george.gr/",
"malignneo": "http://www.agfa.com/w3c/2009/malignantNeoplasm#",
"mammal": "http://lod.taxonconcept.org/ontology/p01/Mammalia/index.owl#",
Expand All @@ -1522,6 +1536,7 @@
"marshall": "http://sites.google.com/site/xgmaitc/",
"maso": "http://securitytoolbox.appspot.com/MASO#",
"master1": "http://idl.u-grenoble3.fr/",
"mat": "http://purl.obolibrary.org/obo/MAT_",
"math": "http://www.w3.org/2000/10/swap/math#",
"matmine": "http://materialsmine.org/ns/",
"matrycs": "http://matrycs.com/",
Expand All @@ -1544,6 +1559,7 @@
"meb": "http://rdf.myexperiment.org/ontologies/base/",
"media": "http://search.yahoo.com/searchmonkey/media/",
"medred": "http://w3id.org/medred/medred#",
"mee": "http://www.w3.org/ns/pim/meeting#",
"meeting": "http://www.w3.org/2002/07/meeting#",
"meetup": "http://www.lotico.com/meetup/",
"mei": "http://www.music-encoding.org/ns/mei/",
Expand Down Expand Up @@ -1621,6 +1637,7 @@
"movie": "http://data.linkedmdb.org/resource/movie/",
"movieo": "http://movie.com/ontology/",
"mp": "http://jicamaro.info/mp#",
"mpath": "http://purl.obolibrary.org/obo/MPATH_",
"mpbv": "http://meta-pfarrerbuch.evangelische-archive.de/vocabulary#",
"mpeg7": "http://rhizomik.net/ontologies/2005/03/Mpeg7-2001.owl#",
"mpg123": "https://devuan.net.br/wiki/mpg123/",
Expand Down Expand Up @@ -1747,6 +1764,7 @@
"oad": "http://lod.xdams.org/reload/oad/",
"oae": "http://www.ics.forth.gr/isl/oae/core#",
"oan": "http://data.lirmm.fr/ontologies/oan/",
"oarcs": "http://purl.obolibrary.org/obo/OARCS_",
"oarj": "http://opendepot.org/reference/linked/1.0/",
"oat": "http://openlinksw.com/schemas/oat/",
"oauth": "http://demiblog.org/vocab/oauth#",
Expand Down Expand Up @@ -1829,6 +1847,7 @@
"olac": "http://www.language-archives.org/OLAC/1.0/",
"olac11": "http://www.language-archives.org/OLAC/1.1/",
"olad": "http://openlad.org/vocab#",
"olatdv": "http://purl.obolibrary.org/obo/OlatDv_",
"olca": "http://www.lingvoj.org/olca#",
"olia": "http://purl.org/olia/olia.owl#",
"olias": "http://purl.org/olia/system.owl#",
Expand All @@ -1842,6 +1861,7 @@
"omdoc": "http://omdoc.org/ontology/",
"ome": "http://purl.org/ontomedia/core/expression#",
"omg": "https://w3id.org/omg#",
"omiabis": "http://purl.obolibrary.org/obo/OMIABIS_",
"omim": "http://purl.bioontology.org/ontology/OMIM/",
"omit": "http://purl.obolibrary.org/obo/OMIT_",
"oml": "http://def.seegrid.csiro.au/ontology/om/om-lite#",
Expand Down Expand Up @@ -1888,6 +1908,7 @@
"openlinks": "http://www.openlinksw.com/schemas/virtrdf#",
"opensearch": "http://a9.com/-/spec/opensearch/1.1/",
"openskos": "http://openskos.org/xmlns#",
"openwemi": "https://ns.dublincore.org/openwemi/",
"oper": "http://sweet.jpl.nasa.gov/2.0/mathOperation.owl#",
"opl": "http://openlinksw.com/schema/attribution#",
"oplacl": "http://www.openlinksw.com/ontology/acl#",
Expand Down Expand Up @@ -2326,6 +2347,7 @@
"rdfdata": "http://rdf.data-vocabulary.org/rdf.xml#",
"rdfdf": "http://www.openlinksw.com/virtrdf-data-formats#",
"rdfg": "http://www.w3.org/2004/03/trix/rdfg-1/",
"rdfl": "https://w3id.org/rdf-lens/ontology#",
"rdfp": "https://w3id.org/rdfp/",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"rdfsharp": "https://rdfsharp.codeplex.com/",
Expand Down Expand Up @@ -2380,6 +2402,7 @@
"rml": "http://w3id.org/rml/",
"rmlt": "http://semweb.mmlab.be/ns/rml-target#",
"rmo": "http://eatld.et.tu-dresden.de/rmo#",
"rnao": "http://purl.obolibrary.org/obo/RNAO_",
"rnce": "https://data.cultureelerfgoed.nl/id/rnce#",
"rnews": "http://iptc.org/std/rNews/2011-10-07#",
"ro": "http://purl.org/wf4ever/ro#",
Expand Down Expand Up @@ -2580,6 +2603,7 @@
"skosxl": "http://www.w3.org/2008/05/skos-xl#",
"sl": "http://www.semanlink.net/2001/00/semanlink-schema#",
"slm": "http://urn.fi/URN:NBN:fi:au:slm:",
"slso": "http://purl.obolibrary.org/obo/SLSO_",
"sm": "http://topbraid.org/sparqlmotion#",
"smartapi": "http://smart-api.io/ontology/1.0/smartapi#",
"smf": "http://topbraid.org/sparqlmotionfunctions#",
Expand Down Expand Up @@ -2989,6 +3013,7 @@
"toby": "http://tobyinkster.co.uk/#",
"top": "http://w3id.org/topologicpy#",
"topo": "http://data.ign.fr/def/topo#",
"tops": "http://www.topbraid.org/tops#",
"tosh": "http://topbraid.org/tosh#",
"tp": "https://triplydb.com/Triply/tp/def/",
"tr": "http://www.thomsonreuters.com/",
Expand Down Expand Up @@ -3076,6 +3101,7 @@
"vacseen1": "http://www.semanticweb.org/parthasb/ontologies/2014/6/vacseen1/",
"vaem": "http://www.linkedmodel.org/schema/vaem#",
"vag": "http://www.essepuntato.it/2013/10/vagueness/",
"vair": "https://w3id.org/vair#",
"value": "http://gfgfd.vs/",
"valueflows": "https://w3id.org/valueflows/",
"vam": "http://www.metmuseum.org/",
Expand Down Expand Up @@ -3141,6 +3167,7 @@
"vra": "http://purl.org/vra/",
"vrank": "http://purl.org/voc/vrank#",
"vs": "http://www.w3.org/2003/06/sw-vocab-status/ns#",
"vsao": "http://purl.obolibrary.org/obo/VSAO_",
"vsearch": "http://vocab.sti2.at/vsearch#",
"vso": "http://purl.org/vso/ns#",
"vsr": "http://purl.org/twc/vocab/vsr#",
Expand All @@ -3150,6 +3177,7 @@
"vstoi": "http://hadatac.org/ont/vstoi#",
"vsw": "http://verticalsearchworks.com/ontology/",
"vsws": "http://verticalsearchworks.com/ontology/synset#",
"vt": "http://purl.obolibrary.org/obo/VT_",
"vto": "http://purl.obolibrary.org/obo/VTO_",
"vvo": "http://purl.org/vvo/ns#",
"w3": "http://www.w3.org/",
Expand Down Expand Up @@ -3245,6 +3273,7 @@
"wsdl": "http://www.w3.org/ns/wsdl-rdf#",
"wsl": "http://www.wsmo.org/ns/wsmo-lite#",
"wv": "http://vocab.org/waiver/terms/",
"xao": "http://purl.obolibrary.org/obo/XAO_",
"xapi": "https://w3id.org/xapi/ontology#",
"xbrli": "http://www.xbrl.org/2003/instance#",
"xbrll": "https://w3id.org/vocab/xbrll#",
Expand Down
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