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|
#!/usr/bin/python3
#----------------------------------------------------------------------
# Create a QGIS project with observations from Artdatabanken
# Copyright © 2023 Guilhem Moulin <guilhem@fripost.org>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#----------------------------------------------------------------------
import argparse
import sys
import json
import re
import requests
import configparser
import tempfile
from datetime import datetime
from requests.exceptions import HTTPError
from xdg import xdg_config_home
from pathlib import Path
from osgeo import gdal, ogr, osr
gdal.UseExceptions()
from qgis.core import (
QgsApplication,
QgsCoordinateReferenceSystem,
QgsLayerDefinition,
QgsLayerTreeModel,
QgsMapLayer,
QgsPointXY,
QgsProject,
QgsRectangle,
QgsUnitTypes,
QgsVectorLayer,
QgsWkbTypes
)
from qgis.gui import QgsLayerTreeView, QgsMapCanvas
from PyQt5.QtGui import QColor
from PyQt5.QtCore import Qt
target_srs = osr.SpatialReference()
target_srs.ImportFromEPSG(3006)
target_srs.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER)
gpkg_drv = ogr.GetDriverByName('GPKG')
geojson_drv = ogr.GetDriverByName('GeoJSON')
programName = 'gis-observation-map'
config = configparser.ConfigParser()
config.read(Path(xdg_config_home()).joinpath(programName).joinpath('config'))
if 'QGIS' not in config.keys() or config['QGIS'] is None:
config['QGIS'] = {}
def ePath(v):
return Path(v).expanduser()
class geometryAction(argparse.Action):
def __init__(self, option_strings, dest, nargs=None, **kwargs):
super().__init__(option_strings, dest, **kwargs)
def __call__(self, parser, namespace, values, option_string=None):
items = getattr(namespace, self.dest, None)
items = items.copy()
style = getattr(namespace, 'geometry_style', None) # get current style
items.append({'path': values, 'style': style})
setattr(namespace, self.dest, items)
parser = argparse.ArgumentParser(
description='Create a QGIS project with observations from Artdatabanken.',
prog = programName,
usage='''%(prog)s --project-home=DIR --project-name=NAME {--geometry=FILE|--point=Y,X} ...
%(prog)s --observation-file=NAME {--geometry=FILE|--point=Y,X} ...'''
)
parser.add_argument('--project-home', type=ePath, metavar='DIRECTORY',
help='Project home directory')
parser.add_argument('--project-name', metavar='NAME',
help='Project filename (and title) relative to --project-home')
parser.add_argument('--topo-basedir', default=config['QGIS']['topo-basedir'], type=ePath, metavar='DIRECTORY',
help='Base directory for "Topografi 10", "Topografi 50", etc.')
parser_geom = parser.add_argument_group('Geographic area of interest')
parser_geom.add_argument('--geometry-style', type=ePath, dest='geometry_style', metavar='STYLE_FILE',
help='QGIS Layer Style File (*.qml) to apply to subsequent geometry files')
parser_geom.add_argument('--geometry', nargs='*', default=[], type=ePath, metavar='GEOMETRY_FILE', action=geometryAction,
help='Geometry file of interest')
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('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',
help='Format for the observation file')
parser_obs.add_argument('--observation-style', default=config['QGIS']['observation-style'], metavar='STYLE_FILE', type=ePath,
help='QGIS Layer Style File (*.qml) to apply to the observation layer (default: %(default)s)')
parser_filter = parser.add_argument_group('Search filter')
parser_filter.add_argument('--data-provider', nargs='*', metavar='IDENTIFIER', default=[],
help='Data provider identifier(s), for instance "Artportalen,MVM"')
parser_filter.add_argument('--since', metavar='YYYY-MM-DD',
help='Start date for observations in ISO 8601 format')
parser_filter.add_argument('--until', metavar='YYYY-MM-DD',
help='End date for observations in ISO 8601 format')
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)
qgs.initQgis()
args.project_home.mkdir(mode=0o755, exist_ok=True)
projectPath = args.project_home.joinpath(args.project_name)
if projectPath.suffix not in ['.qgs', '.qgz']:
projectPath = projectPath.with_suffix('.qgz')
if projectPath.exists():
raise Exception(f'{projectPath}: file exists')
projectInstance = QgsProject.instance()
projectInstance.setFileName(projectPath.as_posix())
projectInstance.setDistanceUnits(QgsUnitTypes.DistanceMeters)
projectInstance.setAreaUnits(QgsUnitTypes.AreaSquareMeters)
projectInstance.setTitle(Path(args.project_name).stem)
layerTreeRoot = projectInstance.layerTreeRoot()
qgis_crs = QgsCoordinateReferenceSystem(target_srs.ExportToWkt())
if qgis_crs.isValid():
projectInstance.setCrs(qgis_crs)
else:
raise Exception('Invalid CRS')
if args.observation_file is None:
args.observation_file = Path('fynd')
elif args.observation_file is not None:
projectInstance = None
elif args.project_home is None or args.project_name is None:
parser.print_usage()
exit(1)
if len(args.geometry) == 0 and len(args.point) == 0:
parser.print_usage()
exit(1)
if len(args.point) > 0 and (args.margin is None or args.margin <= 0):
parser.error('--point requires positive --margin')
for k in ['since', 'until']:
v = getattr(args, k, None)
if v is not None:
d = datetime.fromisoformat(v)
setattr(args, k, d.isoformat())
if projectInstance is not None:
if len(args.geometry) > 1:
sourceGroup = layerTreeRoot.addGroup('Source geometry')
sourceGroup.setItemVisibilityChecked(False)
for i, geom in enumerate(args.geometry):
path = geom['path']
ds = ogr.Open(geom['path'].as_posix(), update=0)
layername = ds.GetLayer().GetName()
ds = None
layer = QgsVectorLayer(path.as_posix(), layername, 'ogr')
if not layer.isValid():
raise Exception(f'ERROR: {path}: failed to load in QGIS')
layer.setReadOnly(True)
layer.setFlags(QgsMapLayer.Identifiable | QgsMapLayer.Searchable)
if geom['style'] is not None:
layer.loadNamedStyle(geom['style'].as_posix())
elif layer.geometryType() == QgsWkbTypes.PointGeometry:
symbol = layer.renderer().symbol().symbolLayers()[0]
symbol.setSize(2.0)
symbol.setFillColor(QColor('#db1e2a'))
symbol.setStrokeColor(QColor('#801119'))
symbol.setStrokeStyle(Qt.SolidLine)
symbol.setStrokeWidth(0)
elif layer.geometryType() == QgsWkbTypes.LineGeometry:
symbol = layer.renderer().symbol().symbolLayers()[0]
symbol.setColor(QColor('black'))
symbol.setPenStyle(Qt.DashLine)
symbol.setWidth(0.39)
elif layer.geometryType() == QgsWkbTypes.PolygonGeometry:
symbol = layer.renderer().symbol().symbolLayers()[0]
symbol.setBrushStyle(Qt.NoBrush)
symbol.setStrokeColor(QColor('black'))
symbol.setStrokeStyle(Qt.DashLine)
symbol.setStrokeWidth(0.39)
if len(args.geometry) == 1:
projectInstance.addMapLayer(layer)
layerTreeRoot.findLayer(layer.id()).setItemVisibilityChecked(False)
else:
projectInstance.addMapLayer(layer, False)
sourceGroup.addLayer(layer)
if i == 0:
#layerTreeModel = QgsLayerTreeModel(layerTreeRoot)
#layerTreeView = QgsLayerTreeView()
#layerTreeView.setModel(layerTreeModel)
#layerTreeView.setCurrentLayer(layer)
canvas = QgsMapCanvas()
canvas.setExtent( layer.extent() )
def gpkg_intersects(path, geometries):
ds = gpkg_drv.Open(path, update=0)
for i in range(ds.GetLayerCount()):
layer = ds.GetLayerByIndex(i)
source_srs = layer.GetSpatialRef()
transform_srs = osr.CoordinateTransformation(source_srs, target_srs)
feature = layer.GetNextFeature()
while feature is not None:
geometry = feature.GetGeometryRef()
geometry.Transform(transform_srs)
for source_geometry in geometries:
if geometry.Intersects(source_geometry):
ds = None
return True
feature = layer.GetNextFeature()
return False
def idx_intersects(idx_path, geometries):
ds = geojson_drv.Open(idx_path, update=0)
if ds.GetLayerCount() != 1:
print(f'WARN: {idx_path}: has {ds.GetLayerCount()} != 1 layers', file=sys.stderr)
layer = ds.GetLayer()
source_srs = layer.GetSpatialRef()
transform_srs = osr.CoordinateTransformation(source_srs, target_srs)
locFieldIdx = layer.FindFieldIndex('location', True)
locations = []
union = None
feature = layer.GetNextFeature()
while feature is not None:
geometry = feature.GetGeometryRef()
geometry.Transform(transform_srs)
for source_geometry in geometries:
if geometry.Intersects(source_geometry):
loc = feature.GetField(locFieldIdx)
locations.append(loc)
break
if union is None:
union = geometry.Clone()
else:
union = union.Union(geometry)
feature = layer.GetNextFeature()
contains = True
for source_geometry in geometries:
if not union.Contains(source_geometry):
contains = False
break
ds = None
return locations, contains
def find_qlr(basedir):
if not basedir.is_dir():
return None
qlr = sorted(basedir.glob('*.qlr'))
if len(qlr) == 0 or not qlr[0].is_file():
print(f'WARN: {basedir}: does not contain any layer definition file, skipping', file=sys.stderr)
return None
return qlr[0]
geometries = []
for pt in args.point:
y, x = pt.split(',', 1)
x = int(x)
y = int(y)
minX = x - args.margin
maxX = x + args.margin
minY = y - args.margin
maxY = y + args.margin
ring = ogr.Geometry(ogr.wkbLinearRing)
ring.AddPoint_2D(minX, maxY)
ring.AddPoint_2D(maxX, maxY)
ring.AddPoint_2D(maxX, minY)
ring.AddPoint_2D(minX, minY)
ring.AddPoint_2D(minX, maxY)
bbox = ogr.Geometry(ogr.wkbPolygon)
bbox.AddGeometry(ring)
geometries.append(bbox)
for geom in args.geometry:
ds = ogr.Open(geom['path'].as_posix(), update=0)
for i in range(ds.GetLayerCount()):
layer = ds.GetLayerByIndex(i)
source_srs = layer.GetSpatialRef()
transform_srs = osr.CoordinateTransformation(source_srs, target_srs)
feature = layer.GetNextFeature()
while feature is not None:
geometry = feature.GetGeometryRef()
geometry.Transform(transform_srs)
if args.margin is None:
geometry = geometry.Clone()
geometry.FlattenTo2D()
else:
minX, maxX, minY, maxY = geometry.GetEnvelope()
minX -= args.margin
maxX += args.margin
minY -= args.margin
maxY += args.margin
ring = ogr.Geometry(ogr.wkbLinearRing)
ring.AddPoint_2D(minX, maxY)
ring.AddPoint_2D(maxX, maxY)
ring.AddPoint_2D(maxX, minY)
ring.AddPoint_2D(minX, minY)
ring.AddPoint_2D(minX, maxY)
bbox = ogr.Geometry(ogr.wkbPolygon)
bbox.AddGeometry(ring)
geometry = bbox
geometries.append(geometry)
feature = layer.GetNextFeature()
if len(args.geometry) == 0 and projectInstance is not None:
r = geometries[0].GetGeometryRef(0)
pt0X, pt0Y = r.GetPoint_2D(0)
pt1X, pt1Y = r.GetPoint_2D(2)
canvas = QgsMapCanvas()
extent = QgsRectangle(QgsPointXY(pt0X, pt0Y), QgsPointXY(pt1X, pt1Y))
canvas.setExtent(extent)
def geometricFilterPolygon(polygon):
polygon2 = []
if polygon.GetGeometryType() != ogr.wkbPolygon:
raise Exception('Not a polygon')
for i in range(polygon.GetGeometryCount()):
ring = polygon.GetGeometryRef(i)
n = ring.GetPointCount()
if ring.GetGeometryType() != ogr.wkbLineString:
raise Exception('Not a linestring')
if n > 0 and ring.GetPoint(0) != ring.GetPoint(n-1):
raise Exception('Not a linear ring')
ring2 = []
for i in range(n):
lon, lat = ring.GetPoint_2D(i)
ring2.append([lon, lat])
polygon2.append(ring2)
return {
'type': 'polygon',
'coordinates': polygon2
}
# https://github.com/biodiversitydata-se/SOS/blob/master/Docs/SearchFilter.md#geographics-filter
def geometricFilter(geometries):
wgs84 = osr.SpatialReference()
wgs84.ImportFromEPSG(4326) # WGS84
wgs84.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER)
towgs84 = osr.CoordinateTransformation(target_srs, wgs84)
myGeometries = []
for geom in geometries:
geom = geom.Clone()
geom.Transform(towgs84)
geometryType = geom.GetGeometryType()
if geometryType == ogr.wkbPoint or geometryType == ogr.wkbMultiPoint:
parser.error('Point geometry requires positive --margin')
elif geometryType == ogr.wkbLineString or geometryType == ogr.wkbMultiLineString:
parser.error('Line geometry requires positive --margin')
elif geometryType == ogr.wkbPolygon:
gfp = geometricFilterPolygon(geom)
myGeometries.append(gfp)
elif geometryType == ogr.wkbMultiPolygon:
for i in range(geom.GetGeometryCount()):
geom2 = geom.GetGeometryRef(i)
gfp = geometricFilterPolygon(geom2)
myGeometries.append(gfp)
else:
raise Exception('Unsuported geometry (try --margin=0)')
return myGeometries
artDataBankenURL = 'https://api.artdatabanken.se'
artDataBankenHeaders = {
'X-Api-Version': '1.5',
'X-Requesting-System': '',
# https://github.com/biodiversitydata-se/SOS/blob/master/Docs/Authentication.md
'Ocp-Apim-Subscription-Key': config['ArtDataBanken']['Subscription-Key']
}
def getObservations(taxonLists, taxonRedlistCategories, searchFilter):
# 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(searchFilter)
)
resp.raise_for_status()
if resp.text == '':
obs = { 'crs': 'EPSG:4326', 'type': 'FeatureCollection', 'features': [] }
else:
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:
print(f'{len(obs["features"])} observations found', file=sys.stderr)
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
if args.observation_file.is_absolute():
path = args.observation_file
elif args.project_home is None:
path = args.observation_file.expanduser()
else:
path = args.project_home.joinpath(args.observation_file)
drv = None
suffix = path.suffix
if suffix is not None and suffix != '' and suffix != '.':
# try to infer format from extension
for i in range(ogr.GetDriverCount()):
drv2 = ogr.GetDriver(i)
if drv2 is None:
continue
v = drv2.GetMetadataItem(gdal.DMD_EXTENSIONS)
if v is None:
continue
if suffix.removeprefix('.') in v.split(' '):
drv = drv2
break
if drv is None:
if args.observation_format is None:
observation_format = 'GPKG'
else:
observation_format = args.observation_format
drv = ogr.GetDriverByName(observation_format)
if drv is None:
raise Exception(f'Invalid format {observation_format}')
suffixes = drv.GetMetadataItem(gdal.DMD_EXTENSIONS).split(' ')
if len(suffixes) < 1 or suffixes[0] == '':
raise Exception(f'Invalid format {observation_format}')
if suffix is not None and suffix != '' and suffix != '.':
print(f'WARN: unknown extension "{suffix}", appending ".{suffixes[0]}"', file=sys.stderr)
suffix += '.' + suffixes[0]
path = path.with_suffix(suffix)
if args.observation_format is not None and drv.name.lower() != args.observation_format.lower():
print(f'WARN: overwriting observation file format to {drv.name}', file=sys.stderr)
layername = 'fynd'
obs['name'] = layername
if drv.name == geojson_drv.name:
# for GeoJSON, don't reproject and pretty-print the output; this
# is useful for manual inspection and/or debugging
with path.open(mode='w') as fp:
json.dump(obs, fp, indent=2, ensure_ascii=False)
else:
with tempfile.NamedTemporaryFile(suffix='.geojson', mode='w') as fp:
json.dump(obs, fp)
fp.flush()
gdal.VectorTranslate(
path.as_posix(), fp.name, format=drv.name,
layerName=layername,
geometryType='POINT',
accessMode='overwrite',
reproject=True, dstSRS=target_srs)
obs = None
if projectInstance is not None:
query = '''"IsPositiveObservation" AND "IsNaturalOccurrence" AND "CoordinateUncertaintyInMeters" <= 250'''
layer = QgsVectorLayer(f'{path.as_posix()}|layername={layername}|subset={query}', layername.title(), 'ogr')
if not layer.isValid():
raise Exception(f'ERROR: {path}: failed to load in QGIS')
if args.observation_style is not None:
layer.loadNamedStyle(args.observation_style.as_posix())
layer.setReadOnly(True)
layer.setFlags(QgsMapLayer.Identifiable | QgsMapLayer.Searchable)
projectInstance.addMapLayer(layer)
layerTreeRoot.findLayer(layer.id()).setItemVisibilityChecked(True)
def mapDataProviders(names):
# https://github.com/biodiversitydata-se/SOS/blob/master/Docs/DataProviders.md
params = {
'cultureCode': 'sv-SE',
'includeProvidersWithNoObservations': 'false',
}
resp = requests.get(
artDataBankenURL + '/species-observation-system/v1/DataProviders',
headers=artDataBankenHeaders
)
resp.raise_for_status()
dataProviders = resp.json()
#print(json.dumps(dataProviders, indent=2, ensure_ascii=False))
ids = []
for ns in names:
for name in ns.split(','):
i = None
for p in dataProviders:
if p['identifier'].lower() == name.lower():
if i is not None:
raise Exception(f'multiple results found for provider "{name}"')
i = p['id']
if i is None:
raise Exception(f'Unknown data provider "{name}"\nValid providers are {", ".join([p["identifier"] for p in dataProviders])}')
ids.append(i)
return ids
def getTaxonLists():
resp = requests.get(
artDataBankenURL + '/species-observation-system/v1/TaxonLists?cultureCode=en-US',
headers=artDataBankenHeaders
)
resp.raise_for_status()
taxonLists = resp.json()
#print(json.dumps(taxonLists, indent=2, ensure_ascii=False))
taxonLists2 = {}
# https://github.com/biodiversitydata-se/SOS/blob/master/Src/SOS.lib/Resources/TaxonLists.json
# https://artfakta.se/artinformation/taxa
i1 = getTaxonList(taxonLists, taxonLists2, 'ProtectedByLaw', 'Protected by law species')
i2 = getTaxonList(taxonLists, taxonLists2, 'TaxonIsSignalSpecie', 'Signal species')
#getTaxonList(taxonLists, taxonLists2, 'TaxonIsInvasive', 'Invasive species')
#getTaxonList(taxonLists, taxonLists2, 'TaxonIsInvasiveInSweden', 'Invasive species in Sweden')
#getTaxonList(taxonLists, taxonLists2, 'TaxonIsInvasiveEuRegulation', 'EU regulation 1143/2014')
i8 = getTaxonList(taxonLists, taxonLists2, 'Natura2000HabitatsDirective', 'Habitats directive species')
getTaxonList(taxonLists, taxonLists2, 'Natura2000HabitatsDirectiveArticle2', 'Habitats directive Annex 2')
getTaxonList(taxonLists, taxonLists2, 'Natura2000HabitatsDirectiveArticle2PrioritySpecie', 'Habitats directive Annex 2, priority species')
getTaxonList(taxonLists, taxonLists2, 'Natura2000HabitatsDirectiveArticle4', 'Habitats directive Annex 4')
getTaxonList(taxonLists, taxonLists2, 'Natura2000HabitatsDirectiveArticle5', 'Habitats directive Annex 5')
# sanity check
directives = [
'Natura2000HabitatsDirectiveArticle2',
'Natura2000HabitatsDirectiveArticle2PrioritySpecie',
'Natura2000HabitatsDirectiveArticle4',
'Natura2000HabitatsDirectiveArticle5'
]
d0 = 'Natura2000HabitatsDirective'
for i in taxonLists2[d0]:
if not any(map(lambda d: i in taxonLists2[d], directives)):
raise Exception(f'missing taxon #{i} (in {d0}) from directives {",".join(directives)}')
for d in directives:
for i in taxonLists2[d]:
if i not in taxonLists2[d0]:
raise Exception(f'missing taxon #{i} (in {d}) from {d0}')
for i in taxonLists2['Natura2000HabitatsDirectiveArticle2PrioritySpecie']:
if i not in taxonLists2['Natura2000HabitatsDirectiveArticle2']:
raise Exception(f'missing taxon #{i} (in Natura2000HabitatsDirectiveArticle2PrioritySpecie) from Natura2000HabitatsDirectiveArticle2')
#i13 = getTaxonList(taxonLists, taxonLists2, 'BirdDirective', 'Birds Directive')
#getTaxonList(taxonLists, taxonLists2, 'BirdDirectiveArticle1', 'Birds directive - Annex 1')
#getTaxonList(taxonLists, taxonLists2, 'BirdDirectiveArticle2', 'Birds directive - Annex 2')
#getTaxonList(taxonLists, taxonLists2, 'TaxonIsPriorityBird', 'Priority birds')
#
#directives = ['BirdDirectiveArticle1', 'BirdDirectiveArticle2']
#d0 = 'BirdDirective'
##for i in taxonLists2[d0]:
## if not any(map(lambda d: i in taxonLists2[d], directives)):
## raise Exception(f'missing taxon #{i} (in {d0}) from directives {",".join(directives)}')
#for d in directives:
# for i in taxonLists2[d]:
# if i not in taxonLists2[d0]:
# raise Exception(f'missing taxon #{i} (in {d}) from {d0}')
i7 = getTaxonList(taxonLists, taxonLists2, 'TaxonIsRedlisted', 'Redlisted species')
taxonRedlistCategories = getTaxonRedlistCategories(taxonLists, i7)
i18 = getTaxonList(taxonLists, None, None, 'Swedish forest agency nature conservation species')
taxonListIds = [i1, i2, i7, i8, i18]
return taxonLists2, taxonRedlistCategories, taxonListIds
def getTaxonList(taxonLists, taxonLists2, key, name):
i = None
for t in taxonLists:
if t['name'] == name:
if i is not None:
raise Exception(f'multiple results found for taxon list "{name}"')
i = t['id']
if i is None:
raise Exception(f'no result found for taxon list "{name}"')
if taxonLists2 is not None and key is not None:
resp = requests.get(
artDataBankenURL + f'/species-observation-system/v1/TaxonLists/{i}/Taxa',
headers=artDataBankenHeaders
)
resp.raise_for_status()
resp = resp.json()
if type(resp) != list:
raise Exception(f'expected list, got {type(resp)}')
taxonLists2[key] = {r['id'] for r in resp}
return i
def getTaxonRedlistCategories(taxonLists, i):
taxonRedlistCategories = {}
r = re.compile(r'\(([A-Z][A-Z])\)\Z')
for t in taxonLists:
if 'parentId' not in t.keys() or t['parentId'] != i:
continue
name = t['name']
c = r.search(name)
if not c:
raise Exception(f'invalid redlist name "{name}"')
c = c.group(1)
resp = requests.get(
artDataBankenURL + f'/species-observation-system/v1/TaxonLists/{t["id"]}/Taxa',
headers=artDataBankenHeaders
)
resp.raise_for_status()
resp = resp.json()
if type(resp) != list:
raise Exception(f'expected list, got {type(resp)}')
for t in resp:
j = t['id']
if j in taxonRedlistCategories.keys():
raise Exception(f'duplicate redlist classification for taxon #{j}')
taxonRedlistCategories[j] = c
return taxonRedlistCategories
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)
}
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:
idxContains = {}
for topo in topo_maps:
qlr_paths = []
qlr_merged = None
d = args.topo_basedir.joinpath(topo)
if not d.is_dir():
continue
idx = d.joinpath('index.geojson')
if idx.is_file():
tiles, idxContains[topo] = idx_intersects(idx.as_posix(), geometries)
if len(tiles) == 0:
continue
if args.project_home is None:
for tile in tiles:
t = d.joinpath(tile)
qlr_path = find_qlr(t)
if qlr_path is None:
continue
qlr_paths.append(qlr_path)
else:
t0 = d.joinpath(tiles[0])
qlr_path = find_qlr(d)
if qlr_path is None:
continue
d2 = args.project_home.joinpath(topo)
d2.mkdir(mode=0o755, exist_ok=True)
d2.joinpath(qlr_path.name).symlink_to(qlr_path, target_is_directory=False)
qlr_merged = d2.joinpath(qlr_path.name)
gpkgs = set()
for tile in tiles:
for gpkg in d.joinpath(tile).glob('*.gpkg'):
gpkgs.add(gpkg.name)
for gpkg in gpkgs:
dst = d2.joinpath(gpkg)
if dst.exists():
raise Exception(f'{dst}: file exists')
for tile in tiles:
src = d.joinpath(tile).joinpath(gpkg)
if src.is_file():
gdal.VectorTranslate(dst.as_posix(), src.as_posix(), format='GPKG', accessMode='upsert')
else:
if args.project_home is not None:
l = args.project_home.joinpath(topo)
l.symlink_to(d, target_is_directory=True)
d = l
for t in sorted(d.glob('*')):
qlr_path = find_qlr(t)
if qlr_path is None:
continue
gpkg_name = 'mark.gpkg'
gpkg_path = t.joinpath(gpkg_name)
if not gpkg_path.is_file():
print(f'WARN: {t}: lacks {gpkg_name}, skipping', file=sys.stderr)
continue
if not gpkg_intersects(gpkg_path.as_posix(), geometries):
continue
qlr_paths.append(qlr_path)
if projectInstance is not None:
if qlr_merged is not None:
QgsLayerDefinition.loadLayerDefinition(qlr_merged.as_posix(), projectInstance, layerTreeRoot)
lt = layerTreeRoot.children()[-1]
lt.setName(topo)
lyrSubTree = [lt]
elif len(qlr_paths) > 0:
rootGroup = layerTreeRoot.addGroup(topo)
for qlr_path in qlr_paths:
QgsLayerDefinition.loadLayerDefinition(qlr_path.as_posix(), projectInstance, rootGroup)
lyrSubTree = rootGroup.children()
rootGroup.setExpanded(False)
if len(lyrSubTree) == len(qlr_paths):
for i, lt in enumerate(lyrSubTree):
name = qlr_paths[i].parent.stem
lt.setName(name)
for lt in lyrSubTree:
lt.setExpanded(False)
lt.setItemVisibilityChecked(True)
for lyr in lt.findLayers():
lyr.setItemVisibilityChecked(True)
lyr = lyr.layer()
lyr.setReadOnly(True)
lyr.setFlags(QgsMapLayer.Removable)
if projectInstance is not None:
maxScale = 1
for topo in topo_maps:
minScale = None
rootGroup = QgsProject.instance().layerTreeRoot().findGroup(topo)
if rootGroup is None:
continue
if topo in idxContains.keys() and not idxContains[topo]:
# if the tileset doesn't entirely covers the area of interest,
# then uncheck the layer group and disable scale-based visibility
rootGroup.setItemVisibilityChecked(False)
elif topo == 'Topografi 10':
minScale = 50000
elif topo == 'Topografi 50':
minScale = 100000
elif topo == 'Topografi 100':
minScale = 10000000
if minScale is not None:
for lt in rootGroup.findLayers():
lyr = lt.layer()
lyr.setScaleBasedVisibility(True)
lyr.setMinimumScale(minScale)
lyr.setMaximumScale(maxScale)
maxScale = minScale
if projectInstance is not None:
projectInstance.write()
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