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-rwxr-xr-xgis-observation-map268
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: