New flag --no-observations to avoid querying Artdatabanken.

1 files changed, 137 insertions, 131 deletions

diff --git a/gis-observation-map b/gis-observation-map
index 8153c9f..fbd9146 100755
--- a/gis-observation-map
+++ b/gis-observation-map
@@ -96,7 +96,9 @@ parser_geom.add_argument('--point', nargs='*', metavar='Y,X', default=[],
     help=f'Coordinates of interest (in {target_srs.GetName()})')
 parser_geom.add_argument('--margin', metavar='N', type=int,
     help='Margin (in meters) around geometry envelopes')
-parser_obs = parser.add_argument_group('Observation file')
+parser_obs = parser.add_argument_group('Observations')
+parser_obs.add_argument('--no-observations', action='store_true',
+    help='Do not fetch observations within the area(s) of interest')
 parser_obs.add_argument('--observation-file', type=Path, metavar='NAME',
     help='Observation file name relative to --project-home')
 parser_obs.add_argument('--observation-format', metavar='FORMAT',
@@ -113,6 +115,9 @@ parser_filter.add_argument('--until', metavar='YYYY-MM-DD',
 
 args = parser.parse_args()
 
+if args.no_observations and (args.observation_file is not None or args.observation_format is not None):
+    parser.error('--no-observations is mutually exclusive with --observation-*')
+
 if args.project_home is not None and args.project_name is not None:
     QgsApplication.setPrefixPath('/usr/bin/qgis', True)
     qgs = QgsApplication([], False)
@@ -671,142 +676,143 @@ def getTaxonRedlistCategories(taxonLists, i):
             taxonRedlistCategories[j] = c
     return taxonRedlistCategories
 
-geographicsFilter = {
-    'geometries': geometricFilter(geometries),
-    'maxAccuracy': 2500,
-    'considerObservationAccuracy': True,
-    'considerDisturbanceRadius': False
-}
-taxonLists, taxonRedlistCategories, taxonListIds = getTaxonLists()
-
-# https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md
-searchFilter = {
-    'geographics': geographicsFilter,
-    'determinationFilter': 'NoFilter',
-    'notRecoveredFilter': 'DontIncludeNotRecovered',
-    'occurrenceStatus': 'Present',
-    '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',
-        ]
+if not args.no_observations:
+    geographicsFilter = {
+        'geometries': geometricFilter(geometries),
+        'maxAccuracy': 2500,
+        'considerObservationAccuracy': True,
+        'considerDisturbanceRadius': False
+    }
+    taxonLists, taxonRedlistCategories, taxonListIds = getTaxonLists()
+
+    # https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md
+    searchFilter = {
+        'geographics': geographicsFilter,
+        'determinationFilter': 'NoFilter',
+        'notRecoveredFilter': 'DontIncludeNotRecovered',
+        'occurrenceStatus': 'Present',
+        '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',
+            ]
+        }
     }
-}
-
-# https://artfakta.se/artinformation/taxa/biota-0/detaljer
-kingdomIds = {
-    'Animalia': 5000001,
-    'Archaea': 5000082,
-    'Bacteria': 5000052,
-    'Chromista': 5000055,
-    'Fungi': 5000039,
-    'Plantae': 5000045,
-    'Protozoa': 5000060,
-    'Viruses': 5000083,
-    'Algae': 6001047,
-}
-
-searchFilter['taxon'] = {
-    'ids': list(map(lambda k: kingdomIds[k], ['Fungi', 'Plantae'])),
-    'includeUnderlyingTaxa': True,
-    # https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md#taxon-lists
-    'taxonListIds': taxonListIds,
-    'taxonListOperator': 'Filter'
-}
 
-if args.data_provider is not None:
-    searchFilter['dataProvider'] = {
-        'ids': mapDataProviders(args.data_provider)
+    # https://artfakta.se/artinformation/taxa/biota-0/detaljer
+    kingdomIds = {
+        'Animalia': 5000001,
+        'Archaea': 5000082,
+        'Bacteria': 5000052,
+        'Chromista': 5000055,
+        'Fungi': 5000039,
+        'Plantae': 5000045,
+        'Protozoa': 5000060,
+        'Viruses': 5000083,
+        'Algae': 6001047,
     }
 
-if args.since is not None or args.until is not None:
-    searchFilter['date'] = {
-        # https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md#date-filter
-        'startDate': args.since,
-        'endDate': args.until,
-        'dateFilterType': 'OverlappingStartDateAndEndDate'
+    searchFilter['taxon'] = {
+        'ids': list(map(lambda k: kingdomIds[k], ['Fungi', 'Plantae'])),
+        'includeUnderlyingTaxa': True,
+        # https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md#taxon-lists
+        'taxonListIds': taxonListIds,
+        'taxonListOperator': 'Filter'
     }
 
-getObservations(taxonLists, taxonRedlistCategories, searchFilter)
+    if args.data_provider is not None:
+        searchFilter['dataProvider'] = {
+            'ids': mapDataProviders(args.data_provider)
+        }
+
+    if args.since is not None or args.until is not None:
+        searchFilter['date'] = {
+            # https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md#date-filter
+            'startDate': args.since,
+            'endDate': args.until,
+            'dateFilterType': 'OverlappingStartDateAndEndDate'
+        }
+
+    getObservations(taxonLists, taxonRedlistCategories, searchFilter)
 
 topo_maps = ['Topografi 10', 'Topografi 50', 'Topografi 100']
 if args.topo_basedir is not None and projectInstance is not None: