def main():
res = {}
with open(DATA_FILE, encoding='utf8') as fp:
for line in fp.read().split('\n'):
if line:
cols = line.split(',')
res[cols[0]] = cols[1:]
ecoregions = [(er['properties']['eco_code'], shape(er['geometry']))
for er in jsonload(data_file('ecoregions.json'))['features']
if er['geometry']
and er['properties']['eco_code'] not in INVALID_ECO_CODES]
for fname in os.listdir(data_file('external', 'gbif')):
sid = fname.split('.')[0]
v = res.get(sid, ['', ''])
if len(v) == 1:
v.append('')
if not v[0] or not v[1]:
occurrences = jsonload(data_file('external', 'gbif',
fname)).get('results', [])
if not v[0]:
v[0] = format_ids(match(occurrences, ecoregions))
if not v[1]:
v[1] = format_ids(r.get('countryCode') for r in occurrences)
res[sid] = v
with open(DATA_FILE, 'w', encoding='utf8') as fp:
for key in sorted(res.keys()):
fp.write('%s,%s\r\n' % (key, ','.join(res[key])))
def check(p):
count = 0
existing = [i['id'] for i in csv_items('cn/' + p) if 'edmond' in i['source_url']]
for id, fname in [(n.split('.')[0], n) for n in os.listdir(data_file('cn/images'))]:
if id in existing:
count += 1
os.remove(data_file('cn', 'images', fname))
print(count)
def check(p):
count = 0
existing = [
i['id'] for i in csv_items('cn/' + p) if 'edmond' in i['source_url']
]
for id, fname in [(n.split('.')[0], n)
for n in os.listdir(data_file('cn/images'))]:
if id in existing:
count += 1
os.remove(data_file('cn', 'images', fname))
print(count)
def test():
data = {n: read_csv(n) for n in CSV}
ids = {n: {r[1]['id'] for r in rows} for n, rows in data.items()}
ids['ecoregions'] = set()
for ecoregion in jsonload(data_file('ecoregions.json'))['features']:
ids['ecoregions'].add(ecoregion['properties']['eco_code'])
ids['sources'] = set()
with io.open(data_file('sources.bib'), encoding='utf8') as fp:
for line in fp:
match = BIB_ID_PATTERN.match(line.strip())
if match:
ids['sources'].add(match.group('id'))
ids['countries'] = set([country.alpha2 for country in countries])
def check_ref(name, line, item):
for ref in item['refs__ids'].split(';'):
if ref:
if '[' in ref:
source_id, pages = ref.split('[', 1)
if not pages.endswith(']'):
error('invalid reference %s' % (ref, ), name, line)
else:
source_id = ref
if source_id not in ids['sources']:
error('invalid sources id referenced: %s' % (source_id, ),
name, line)
for name in ['names', 'taxa']:
for line, item in data[name]:
check_ref(name, line, item)
for name, items in data.items():
for line, item in items:
for col in item.keys():
if '__' in col:
ref, card = col.split('__', 1)
if ref not in ids:
continue
for v in split_ids(item[col]):
if v not in ids[ref]:
error('invalid %s id referenced: %s' % (ref, v),
name, line)
if not SUCCESS:
raise ValueError('integrity checks failed!')
def update_taxa():
parser = argparse.ArgumentParser(
description="""\
Update the supplemental data for taxa from external sources.
We go through the taxa listed in taxa.csv and look for additional information at
GBIF, EOL and Catalogue Of Life.""")
parser.add_argument("--distribution-only", action="store_true")
args = parser.parse_args()
if not args.distribution_only:
fname = data_file('taxa.json')
taxa = jsonload(fname, default=[], object_pairs_hook=OrderedDict)
ids = set(spec['id'] for spec in taxa)
# add stubs for new entries in taxa.csv:
for i, item in enumerate(csv_items('taxa.csv')):
if item['id'] not in ids:
taxa.insert(i, item2spec(item))
for cls in [CatalogueOfLife, GBIF, EOL]:
with cls() as provider:
for i, spec in enumerate(taxa):
if i % 500 == 0:
print(i)
provider.update_taxon(spec)
jsondump(taxa, fname, indent=4)
main()
def update_taxa():
parser = argparse.ArgumentParser(description="""\
Update the supplemental data for taxa from external sources.
We go through the taxa listed in taxa.csv and look for additional information at
GBIF, EOL and Catalogue Of Life.""")
parser.add_argument("--distribution-only", action="store_true")
args = parser.parse_args()
if not args.distribution_only:
fname = data_file('taxa.json')
taxa = jsonload(fname, default=[], object_pairs_hook=OrderedDict)
ids = set(spec['id'] for spec in taxa)
# add stubs for new entries in taxa.csv:
for i, item in enumerate(csv_items('taxa.csv')):
if item['id'] not in ids:
taxa.insert(i, item2spec(item))
for cls in [CatalogueOfLife, GBIF, EOL]:
with cls() as provider:
for i, spec in enumerate(taxa):
if i % 500 == 0:
print(i)
provider.update_taxon(spec)
jsondump(taxa, fname, indent=4)
main()
def test():
data = {n: read_csv(n) for n in CSV}
ids = {n: {r[1]['id'] for r in rows} for n, rows in data.items()}
ids['ecoregions'] = set()
for ecoregion in jsonload(data_file('ecoregions.json'))['features']:
ids['ecoregions'].add(ecoregion['properties']['eco_code'])
ids['sources'] = set()
with io.open(data_file('sources.bib'), encoding='utf8') as fp:
for line in fp:
match = BIB_ID_PATTERN.match(line.strip())
if match:
ids['sources'].add(match.group('id'))
ids['countries'] = set([country.alpha2 for country in countries])
def check_ref(name, line, item):
for ref in item['refs__ids'].split(';'):
if ref:
if '[' in ref:
source_id, pages = ref.split('[', 1)
if not pages.endswith(']'):
error('invalid reference %s' % (ref,), name, line)
else:
source_id = ref
if source_id not in ids['sources']:
error('invalid sources id referenced: %s' % (source_id,), name, line)
for name in ['names', 'taxa']:
for line, item in data[name]:
check_ref(name, line, item)
for name, items in data.items():
for line, item in items:
for col in item.keys():
if col and '__' in col:
ref, card = col.split('__', 1)
if ref not in ids:
continue
for v in split_ids(item[col]):
if v not in ids[ref]:
error('invalid %s id referenced: %s' % (ref, v), name, line)
if not SUCCESS:
raise ValueError('integrity checks failed!')
def update(p):
data = jsonload(data_file('cn', 'images.json'), default={})
try:
info = None
for img in csv_items('cn/' + p):
key = '%s-%s' % (img['taxa__id'], img['tags'])
if key in data:
print('+++', img['id'] or img['source'], data[key]['source'])
continue
info = get_image_info(img)
if info:
data[key] = get_image(info, data_file('cn', 'images'))
except:
print('----->')
print(img)
if info:
print(info)
jsondump(data, data_file('cn', 'images.json'), indent=4)
raise
jsondump(data, data_file('cn', 'images.json'), indent=4)
def update(p):
data = jsonload(data_file('cn', 'images.json'), default={})
try:
info = None
for img in csv_items('cn/' + p):
key = '%s-%s' % (img['taxa__id'], img['tags'])
if key in data:
print('+++', img['id'] or img['source'], data[key]['source'])
continue
info = get_image_info(img)
if info:
data[key] = get_image(info, data_file('cn', 'images'))
except:
print('----->')
print(img)
if info:
print(info)
jsondump(data, data_file('cn', 'images.json'), indent=4)
raise
jsondump(data, data_file('cn', 'images.json'), indent=4)
def save_occurrences(sid, sname):
api = GBIF()
out = data_file('external', 'gbif', '%s.json' % sid)
if not os.path.exists(out):
try:
res = api.get_info(api.get_id(sname))
jsondump(res, out)
print('%s: %s occurrences' % (sname, min([res['count'], res['limit']])))
except:
# we'll have to try again next time!
res = None
else:
try:
res = jsonload(out)
except:
os.remove(out)
res = None
return res
def save_occurrences(sid, sname):
api = GBIF()
out = data_file('external', 'gbif', '%s.json' % sid)
if not os.path.exists(out):
try:
res = api.get_info(api.get_id(sname))
jsondump(res, out)
print('%s: %s occurrences' %
(sname, min([res['count'], res['limit']])))
except:
# we'll have to try again next time!
res = None
else:
try:
res = jsonload(out)
except:
os.remove(out)
res = None
return res
def rewrite(p):
visit('cn/' + p, JSON2CSV(data_file('cn', 'images.json')))
def select(p):
shutil.copy(data_file('cn', p), data_file('cn', 'staged_images.csv'))
visit('cn/staged_images.csv', Selector())
print(
len(open(data_file('cn', 'staged_images.csv')).read().split('\n')) - 1)
def __init__(self):
self._data = {i['id']: i for i in jsonload(data_file('taxa.json'))}
def rewrite(p):
visit('cn/' + p, JSON2CSV(data_file('cn', 'images.json')))
def select(p):
shutil.copy(data_file('cn', p), data_file('cn', 'staged_images.csv'))
visit('cn/staged_images.csv', Selector())
print(len(open(data_file('cn', 'staged_images.csv')).read().split('\n')) - 1)
def __init__(self):
self._data = {i['id']: i for i in jsonload(data_file('taxa.json'))}
('order', item['order'].capitalize() or None),
('family', item['family'].capitalize() or None),
('genus', item['genus'].capitalize() or None),
('ecoregions', split_ids(item.get('ecoregions__ids', ''))),
('countries', split_ids(item.get('countries__ids', ''))),
('wikipedia_url', wikipedia_url(item.get('wikipedia_url', ''))),
('eol_id', None),
('gbif_id', None),
('catalogueoflife_id', None),
]:
spec[k] = v
return spec
if __name__ == '__main__':
fname = data_file('taxa.json')
taxa = jsonload(fname, default=[], object_pairs_hook=OrderedDict)
ids = set(spec['id'] for spec in taxa)
# add stubs for new entries in taxa.csv:
for i, item in enumerate(csv_items('taxa.csv')):
if item['id'] not in ids:
taxa.insert(i, item2spec(item))
for cls in [CatalogueOfLife, GBIF, EOL]:
with cls() as provider:
for i, spec in enumerate(taxa):
if i % 500 == 0:
print(i)
provider.update_taxon(spec)
def __init__(self):
self.cols = {}
with open(data_file('images_md.json'), 'rb') as fp:
self.md = json.load(fp)
self.count = 0
from __future__ import print_function, unicode_literals
import os
from io import open
from shapely.geometry import shape, Point
from shapely.geos import PredicateError, TopologicalError
from tsammalexdata.util import data_file, jsonload, unique
INVALID_ECO_CODES = {'AA0803', 'Lake', 'AT1202', 'IM1303', 'AA0803'}
DATA_FILE = data_file('distribution.csv')
def format_ids(iterable):
return ';'.join(unique(iterable))
def main():
res = {}
with open(DATA_FILE, encoding='utf8') as fp:
for line in fp.read().split('\n'):
if line:
cols = line.split(',')
res[cols[0]] = cols[1:]
ecoregions = [(er['properties']['eco_code'], shape(er['geometry']))
for er in jsonload(data_file('ecoregions.json'))['features']
if er['geometry']
and er['properties']['eco_code'] not in INVALID_ECO_CODES]
for fname in os.listdir(data_file('external', 'gbif')):
def __init__(self):
self.edmond_urls = file_urls(data_file('Edmond.xml'))
self.cols = {}
self.count = 0
self.edmond_urls = file_urls(data_file('Edmond.xml'))
self.cols = {}
self.count = 0
def __call__(self, index, row):
if index == 0:
self.cols = {col: i for i, col in enumerate(row)}
return row
_id = row[self.cols['id']]
if _id in self.edmond_urls:
row[self.cols['source_url']] = self.edmond_urls[_id]['full']
self.count += 1
else:
#
# FIXME: check whether source_url is an Edmond image URL, if not, upload the
# image to Edmond, insert the URL here! Depends on the imeji API being
# available on Edmond.
#
print(_id, row)
return row
if __name__ == '__main__':
with open(data_file('Edmond.xml'), 'w', encoding='utf8') as fp:
fp.write(requests.get(URL).text)
v = Visitor()
visit(sys.argv[1] if len(sys.argv) > 1 else 'images.csv', v)
print(v.count)