Get taxon lists.

1 files changed, 99 insertions, 0 deletions

diff --git a/gis-observation-map b/gis-observation-map
index 7e97fb9..9c478c7 100755
--- a/gis-observation-map
+++ b/gis-observation-map
@@ -21,6 +21,10 @@
 import argparse
 import sys
 import json
+import requests
+import configparser
+from requests.exceptions import HTTPError
+from xdg import xdg_config_home
 from pathlib import Path
 from osgeo import gdal, ogr, osr
 gdal.UseExceptions()
@@ -46,8 +50,10 @@ target_srs.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER)
 gpkg_drv = ogr.GetDriverByName('GPKG')
 geojson_drv = ogr.GetDriverByName('GeoJSON')
 
+programName = 'gis-observation-map'
 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=X,Y} ...
        %(prog)s {--geometry=FILE|--point=X,Y} ...'''
 )
@@ -60,6 +66,9 @@ parser.add_argument('--point', nargs='*', default=[], help=f'Coordinates of inte
 
 args = parser.parse_args()
 
+config = configparser.ConfigParser()
+config.read(Path(xdg_config_home()).joinpath(programName).joinpath('config'))
+
 if args.project_home is not None and args.project_name is not None:
     QgsApplication.setPrefixPath('/usr/bin/qgis', True)
     qgs = QgsApplication([], False)
@@ -305,6 +314,96 @@ def geometricFilter(geometries):
 
     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 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))
+    taxonLists2 = {}
+
+    # https://github.com/biodiversitydata-se/SOS/blob/master/Src/SOS.lib/Resources/TaxonLists.json
+    # https://artfakta.se/artinformation/taxa
+    getTaxonList(taxonLists, taxonLists2, 'ProtectedByLaw', 'Protected by law species')
+    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')
+
+    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 not i in taxonLists2[d0]:
+                raise Exception(f'missing taxon #{i} (in {d}) from {d0}')
+    for i in taxonLists2['Natura2000HabitatsDirectiveArticle2PrioritySpecie']:
+        if not i in taxonLists2['Natura2000HabitatsDirectiveArticle2']:
+            raise Exception(f'missing taxon #{i} (in Natura2000HabitatsDirectiveArticle2PrioritySpecie) from Natura2000HabitatsDirectiveArticle2')
+
+    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 not i in taxonLists2[d0]:
+                raise Exception(f'missing taxon #{i} (in {d}) from {d0}')
+
+    return taxonLists2
+
+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 found for taxon list "{name}"')
+
+    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}
+
+taxonLists = getTaxonLists()
+
 geograficsFilter = {
     'geometries': geometricFilter(geometries),
     #'maxAccuracy': 5000,