Get Observations from ArtDataBanken.

1 files changed, 167 insertions, 1 deletions

diff --git a/gis-observation-map b/gis-observation-map
index 4fe06cf..551a8af 100755
--- a/gis-observation-map
+++ b/gis-observation-map
@@ -322,6 +322,78 @@ artDataBankenHeaders = {
     # https://github.com/biodiversitydata-se/SOS/blob/master/Docs/Authentication.md
     'Ocp-Apim-Subscription-Key': config['ArtDataBanken']['Subscription-Key']
 }
+
+def getObservations(taxonLists, taxonRedlistCategories, data):
+    # https://api-portal.artdatabanken.se/docs/services/sos-api-v1/operations/Exports_DownloadGeoJson
+    headers = artDataBankenHeaders.copy()
+    headers['Content-Type'] = 'application/json'
+    headers['Authorization'] = config['ArtDataBanken']['Authorization']
+    params = {
+        'cultureCode': 'sv-SE',
+        'flat': 'true',
+        'excludeNullValues': 'true',
+        'gzip': 'false',
+        #'sensitiveObservations': 'true',
+        'validateSearchFilter': 'true',
+    }
+    resp = requests.post(
+        artDataBankenURL + '/species-observation-system/v1/Exports/Download/GeoJson',
+        headers=headers,
+        params=params,
+        data=json.dumps(data)
+    )
+
+    resp.raise_for_status()
+    obs = resp.json()
+
+    # https://www.rfc-editor.org/rfc/rfc7946
+    if obs is None or type(obs) != dict or 'type' not in obs.keys():
+        raise Exception('invalid GeoJSON output')
+    if 'crs' not in obs.keys():
+        print('WARN: GeoJSON output lacks CRS', file=sys.stderr)
+
+    if obs['type'] == 'FeatureCollection' and 'features' in obs.keys() and type(obs['features']) == list:
+        for feat in obs['features']:
+            if (type(feat) != dict or 'type' not in feat.keys() or feat['type'] != 'Feature'
+                    or 'properties' not in feat.keys() or type(feat['properties']) != dict):
+                print('WARN: Invalid feature in GeoJSON output', file=sys.stderr)
+                continue
+            properties = feat['properties']
+            if 'DyntaxaTaxonId' not in properties.keys() or properties['DyntaxaTaxonId'] is None:
+                print('WARN: Feature lacks taxon ID', file=sys.stderr)
+                continue
+
+            tid = properties['DyntaxaTaxonId']
+            for k, taxonList in taxonLists.items():
+                v = (tid in taxonList)
+                if k in properties.keys() and properties[k] != v:
+                    print(f'WARN: #{tid} {k}: {properties[k]} → {v}', file=sys.stderr)
+                properties[k] = v
+
+            if tid in taxonRedlistCategories.keys():
+                k = 'RedlistCategory'
+                v = taxonRedlistCategories[tid]
+                if k in properties.keys() and properties[k] != v:
+                    print(f'WARN: #{tid} {k}: {properties[k]} → {v}', file=sys.stderr)
+                properties[k] = v
+
+    # TODO generate GPKG instead and reproject to EPSG:3006
+    path = projectHome.joinpath('fynd.geojson')
+    with path.open(mode='w') as fp:
+        json.dump(obs, fp, indent=2, ensure_ascii=False)
+
+    if projectInstance is not None:
+        layer = QgsVectorLayer(path.as_posix() + '''|subset="Kingdom" IN ('Fungi', 'Plantae') AND "IsPositiveObservation" AND "IsNaturalOccurrence" AND "CoordinateUncertaintyInMeters" <= 250''', path.stem, 'ogr')
+        if not layer.isValid():
+            raise Exception(f'ERROR: {path}: failed to load in QGIS')
+        if 'QGIS' in config.keys() and 'style' in config['QGIS']:
+            style = Path(config['QGIS']['style']).expanduser()
+            layer.loadNamedStyle(style.as_posix())
+        layer.setReadOnly(True)
+        layer.setFlags(QgsMapLayer.Identifiable | QgsMapLayer.Searchable)
+        projectInstance.addMapLayer(layer)
+        layerTreeRoot.findLayer(layer.id()).setItemVisibilityChecked(True)
+
 def getTaxonLists():
     resp = requests.get(
         artDataBankenURL + '/species-observation-system/v1/TaxonLists?cultureCode=en-US',
@@ -442,7 +514,101 @@ geograficsFilter = {
     'considerDisturbanceRadius': True
 }
 taxonLists, taxonRedlistCategories = getTaxonLists()
-exit()
+
+# https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md
+searchFilter = {
+    'geographics': geograficsFilter,
+    'determinationFilter': 'NoFilter',
+    'notRecoveredFilter': 'NoFilter',
+    'occurrenceStatus': 'BothPresentAndAbsent',
+    'verificationStatus': 'BothVerifiedAndNotVerified',
+    'output': {
+        'fields': [
+            # https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md#fields
+            # https://github.com/biodiversitydata-se/SOS/blob/master/Docs/Observation.md
+            'dataProviderId',
+            'datasetName',
+            #'basisOfRecord',
+            'rightsHolder',
+
+            'modified',
+            'sensitive',
+            'measurementOrFacts',
+            'projects',
+
+            'occurrence.occurrenceId',
+            'occurrence.occurrenceRemarks',
+            'occurrence.recordedBy',
+            'occurrence.reportedBy',
+            'occurrence.reportedDate',
+            'occurrence.occurrenceStatus',
+            'occurrence.activity',
+            'occurrence.behavior',
+            'occurrence.biotope',
+            'occurrence.biotopeDescription',
+            'occurrence.lifeStage',
+            'occurrence.reproductiveCondition',
+            'occurrence.sex',
+            'occurrence.associatedMedia',
+            'occurrence.associatedReferences',
+            'occurrence.individualCount',
+            'occurrence.organismQuantityInt',
+            'occurrence.organismQuantityUnit',
+            'occurrence.sensitivityCategory',
+            'occurrence.isNaturalOccurrence',
+            'occurrence.isNeverFoundObservation',
+            'occurrence.isNotRediscoveredObservation',
+            'occurrence.isPositiveObservation',
+            'occurrence.substrate.description',
+            'occurrence.substrate.name',
+            'occurrence.length',
+            'occurrence.weight',
+            'occurrence.url',
+
+            'event.startDate',
+            'event.endDate',
+            'event.habitat',
+            'event.eventRemarks',
+            'event.discoveryMethod',
+            'event.measurementOrFacts',
+            'event.fieldNotes',
+
+            'identification.verified',
+            'identification.uncertainIdentification',
+            'identification.verificationStatus',
+            'identification.confirmedBy',
+            'identification.confirmedDate',
+            'identification.identifiedBy',
+            'identification.dateIdentified',
+            'identification.verifiedBy',
+            'identification.determinationMethod',
+            'identification.identificationRemarks',
+
+            'location.locality',
+            'location.county',
+            'location.municipality',
+            'location.coordinateUncertaintyInMeters',
+
+            'taxon.id',
+            'taxon.scientificName',
+            'taxon.scientificNameAuthorship',
+            'taxon.vernacularName',
+            'taxon.genus',
+            'taxon.family',
+            'taxon.order',
+            'taxon.class',
+            'taxon.phylum',
+            'taxon.kingdom',
+
+            'taxon.attributes.taxonCategory',
+            'taxon.attributes.organismGroup',
+
+            'taxon.attributes.redlistCategory',
+        ]
+    }
+}
+
+getObservations(taxonLists, taxonRedlistCategories, searchFilter)
 
 topo_maps = ['Topografi 10', 'Topografi 50', 'Topografi 100']
 if projectInstance is not None: