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Début de correction du RDF #84

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Début de correction du RDF #84

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158 changes: 91 additions & 67 deletions backend/rdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,17 @@ def __init__(self):
def save(self, store_uri, format_="turtle"):
self.graph.serialize(store_uri, format_)

def _create_element_if_defined(self, property, type, value, as_litteral=True):
# Test if value is defined and not in black list
if not value:
return
if value in ("aucun", "Inconnu", "Ne Sait Pas", "None"):
return

if as_litteral:
value = Literal(value)
self.graph.add((property, type, value))

def build_agent(self, who=None):
agent = BNode()
self.graph.add((agent, RDF.type, FOAF["Agent"]))
Expand All @@ -34,7 +45,7 @@ def build_agent(self, who=None):
return agent

def build_recordlevel(self, record):
recordlevel = BNode()
recordlevel = URIRef(Literal(record["jddId"]))
self.graph.add((recordlevel, RDF.type, DCMTERMS.Event))
self.graph.add((recordlevel, DCMTERMS["language"], Literal("fr")))
self.graph.add((recordlevel, DWC["datasetID"], Literal(record["jddId"])))
Expand All @@ -49,53 +60,54 @@ def build_recordlevel(self, record):
return recordlevel

def build_event(self, recordlevel, record):
event = BNode()
self.graph.add((event, RDF.type, DWC["Event"]))
if "permIdGrp" in record.keys():
self.graph.add((event, DWC["eventID"], Literal(record["permIdGrp"])))
event = URIRef(Literal(record["permIdGrp"]))
else:
event = BNode()
self.graph.add((event, RDF.type, DWC["Event"]))

# cas période d'observation
# Date séparée par un / cf https://dwc.tdwg.org/terms/#dwc:eventDate
event_dates = [
dt.isoformat(dt.strptime(record["dateDebut"], "%Y-%m-%d %H:%M:%S"))
]
if not record["dateDebut"] == record["dateFin"]:
event_dates.append(
dt.isoformat(dt.strptime(record["dateFin"], "%Y-%m-%d %H:%M:%S"))
)
self.graph.add(
(
event,
DWC["eventDate"],
Literal(
"/".join(
[
dt.isoformat(
dt.strptime(record["dateDebut"], "%Y-%m-%d %H:%M:%S")
),
dt.isoformat(
dt.strptime(record["dateFin"], "%Y-%m-%d %H:%M:%S")
),
]
)
),
Literal("/".join(event_dates)),
)
)
# self.graph.add(
# (event, DWC['samplingProtocol'], Literal(record['obsMeth']))) # noqa: E501
self.graph.add(
(event, DWC["eventRemarks"], Literal(record["obsCtx"]))
) # noqa: E501
self._create_element_if_defined(event, DWC["eventRemarks"], record["obsCtx"])

self.graph.add((recordlevel, DSW["basisOfRecord"], event))
return event

def build_location(self, event, record):
# Si la localisation de l'événement est déjà défini
if (event, DSW["locatedAt"], None) in self.graph:
return

location = BNode()
self.graph.add((location, RDF.type, DCMTERMS["Location"]))
self.graph.add(
(location, DWC["maximumElevationInMeters"], Literal(record["altMax"]))
) # noqa: E501
self.graph.add(
(location, DWC["minimumElevationInMeters"], Literal(record["altMin"]))
) # noqa: E501

self._create_element_if_defined(
location, DWC["maximumElevationInMeters"], record["altMax"]
)
self._create_element_if_defined(
location, DWC["minimumElevationInMeters"], record["altMin"]
)
self.graph.add((location, DWC["footprintWKT"], Literal(record["geom"])))
self.graph.add((location, DWC["geodeticDatum"], Literal("EPSG:4326")))
self.graph.add(
(
location,
DWC["coordinateUncertaintyInMeters"],
Literal(record["difNivPrec"]),
)

self._create_element_if_defined(
location, DWC["coordinateUncertaintyInMeters"], record["difNivPrec"]
)
self.graph.add(
(
Expand All @@ -121,33 +133,41 @@ def build_occurrence(self, event, record):
occurrence = BNode()
self.graph.add((occurrence, RDF.type, DWC["Occurrence"]))
self.graph.add((occurrence, DWC["occurrenceID"], Literal(record["permId"])))
self.graph.add(
(occurrence, DWC["occurrenceStatus"], Literal(record["statObs"]))

self._create_element_if_defined(
occurrence, DWC["occurrenceStatus"], record["statObs"]
)
self.graph.add(
(occurrence, DWC["occurrenceRemarks"], Literal(record["obsDescr"]))

self._create_element_if_defined(
occurrence, DWC["occurrenceRemarks"], record["obsDescr"]
)
self.graph.add(
(occurrence, DWC["organismQuantityType"], Literal(record["objDenbr"]))
) # noqa: E501
self.graph.add(
(occurrence, DWC["occurrenceQuantity"], Literal(record["denbrMin"]))
) # noqa: E501
self.graph.add(
(occurrence, DWC["establishmentMeans"], Literal(record["ocNat"]))

self._create_element_if_defined(
occurrence, DWC["organismQuantityType"], record["objDenbr"]
)
self.graph.add((occurrence, DWC["lifeStage"], Literal(record["ocStade"])))
self.graph.add(
(occurrence, DWC["occurrenceStatus"], Literal(record["statObs"]))

self._create_element_if_defined(
occurrence, DWC["occurrenceQuantity"], record["denbrMin"]
)

self._create_element_if_defined(
occurrence, DWC["establishmentMeans"], record["ocNat"]
)

self._create_element_if_defined(occurrence, DWC["lifeStage"], record["ocStade"])

self._create_element_if_defined(
occurrence, DWC["occurrenceStatus"], record["statObs"]
)

if "observer" in record.keys():
observer = self.build_agent(record["observer"])
self.graph.add((occurrence, DWC["recordedBy"], observer))

self.graph.add(
(occurrence, DWC["occurrenceRemarks"], Literal(record["obsDescr"]))
self._create_element_if_defined(
occurrence, DWC["occurrenceRemarks"], record["obsDescr"]
)

self.graph.add((occurrence, DSW["atEvent"], event))
self.graph.add((event, DSW["eventOf"], occurrence))
return occurrence
Expand All @@ -162,19 +182,11 @@ def build_organism(self, occurrence, record):
def build_identification(self, organism, record):
identification = BNode()
self.graph.add((identification, RDF.type, DWC["Identification"]))
self.graph.add(
(
identification,
DWC["identificationVerificationStatus"],
Literal(record["preuveOui"]),
)
self._create_element_if_defined(
identification, DWC["identificationVerificationStatus"], record["preuveOui"]
) # noqa: E501
self.graph.add(
(
identification,
DWC["identificationRemarks"],
Literal(record["preuvNoNum"]),
)
self._create_element_if_defined(
identification, DWC["identificationRemarks"], record["preuvNoNum"]
) # noqa: E501

if "determiner" in record.keys():
Expand All @@ -186,16 +198,28 @@ def build_identification(self, organism, record):
return identification

def build_taxon(self, identification, record):
taxon = BNode()
self.graph.add((taxon, RDF.type, DWC["Taxon"]))
self.graph.add((taxon, DWC["scientificName"], Literal(record["nom_complet"])))
self.graph.add(
(taxon, DWC["vernacularName"], Literal(record["nomCite"], lang="fr"))
)
self.graph.add((taxon, DWC["taxonID"], Literal(record["cdNom"])))
# Il y a un soucis entre la définition du taxon au sens taxref
# c-a-d basé sur le cd_nom
# et le taxon au sens identification
# qui se base sur cd_nom avec potentiellement un nom cité parataxonomique

# TODO : pour le moment version de taxref fixée à 12
# car la 13 n'est pas implémentée dans le lod
# a suivre
taxon = URIRef(
Literal(
"http://taxref.mnhn.fr/lod/taxon/{}/13.0".format(str(record["cdRef"]))
)
)
self.graph.add((taxon, RDF.type, DWC["Taxon"]))
self.graph.add((taxon, DWC["scientificName"], Literal(record["nom_complet"])))
# Désactivé car le nom cité ne correspond pas forcement au vernacularName
# et qui n'est pas unique pour un taxon
# self.graph.add(
# (taxon, DWC["vernacularName"], Literal(record["nomCite"], lang="fr"))
# )
self.graph.add((taxon, DWC["taxonID"], Literal(record["cdNom"])))

self.graph.add(
(
taxon,
Expand Down
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