def pull_occurrences_from_ala(params, dest_url, context, import_multspecies_params):
# 1. set progress
set_progress('RUNNING', 'Download occurrence dataset from ala', None, context)
# 2. Download all the occurrence dataset in the params list
results = []
try:
item, results = download_occurrence_from_ala(params, context)
# This is the zip file path of the occurrence dataset
ala_csv = item.get('file').get('url').split('file://')[1]
# Add the number of occurrence records to the metadata
# TODO: This is a hack. Any better solution.
occurrence_csv_filename = os.path.join('data', 'ala_occurrence.csv')
if occurrence_csv_filename in item['filemetadata']:
# FIXME: copy all occurrence metadata to zip level, for backwards
# compatibility... this should go away after we fully support 'layered'
# occurrence zips.
for key in ('rows', 'headers', 'bounds'): # what about 'species' ?
if key in item['filemetadata'][occurrence_csv_filename]['metadata']:
item['filemetadata'][key] = item['filemetadata'][occurrence_csv_filename]['metadata'][key]
# move data file to destination and build data_url
src = build_source('file://{}'.format(ala_csv))
dst = build_destination(os.path.join(dest_url, os.path.basename(ala_csv)), app.conf.get('bccvl', {}))
item['file']['url'] = dst['url']
movelib.move(src, dst)
# tell importer about new dataset (import it)
set_progress("RUNNING", u"Import dataset '{0}' from ALA".format(item['title']), None, context)
cleanup_job = import_cleanup_job(dest_url, context)
import_job = import_ala_job([item], dest_url, context)
import_job.link_error(set_progress_job(
"FAILED", u"Import of dataset '{0}' from ALA failed".format(item['title']), None, context))
import_job.link_error(cleanup_job)
finish_job = set_progress_job("COMPLETED", u"ALA import '{}' complete".format(item['title']), None, context)
# Split multi-species dataset
if import_multspecies_params:
import_multispecies_job = import_multi_species_csv_job(item.get('file').get('url'),
import_multspecies_params['results_dir'],
import_multspecies_params['import_context'],
context)
import_multispecies_job.link_error(set_progress_job(
"FAILED", u"Split multi-species dataset '{0}' from ALA failed".format(item['title']), None, context))
import_multispecies_job.link_error(cleanup_job)
(import_job | import_multispecies_job | cleanup_job | finish_job).delay()
else:
(import_job | cleanup_job | finish_job).delay()
except Exception as e:
set_progress('FAILED', 'Download occurrence dataset from ALA: {}'.format(e), None, context)
import_cleanup(dest_url, context)
LOG.error('Download from %s to %s failed: %s', params, dest_url, e, exc_info=True)
finally:
for tmpdir in results:
if tmpdir and os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
def pull_occurrences_from_gbif(lsid, dest_url, context):
# 1. set progress
set_progress('RUNNING', 'Download {0} from gbif'.format(lsid), None, context)
# 2. do move
src = None
dst = None
try:
tmpdir = tempfile.mkdtemp(prefix='gbif_download_')
src = build_source('gbif://gbif?lsid={}'.format(lsid))
dst = build_destination('file://{}'.format(tmpdir))
movelib.move(src, dst)
# extract metadata and do other stuff....
set_progress('RUNNING', 'Extract metadata {0} from gbif'.format(lsid), None, context)
# open gbif_dateset.json
gbif_ds = json.load(open(os.path.join(tmpdir, 'gbif_dataset.json'), 'r'))
# collect files inside ds per datatype
files = dict(((f['dataset_type'], f) for f in gbif_ds['files']))
# read gbif metadata from attribution file
gbif_md = json.load(open(files['attribution']['url'], 'r'))
gbif_csv = files['occurrence']['url']
# build bccvl metadata:
bccvlmd = {
'genre': 'DataGenreSpeciesOccurrence',
'categories': ['occurrence'],
'species': {
'scientificName': gbif_md.get('scientificName', None),
'vernacularName': gbif_md.get('vernacularName', None),
'taxonID': gbif_md.get('key', None),
'rank': gbif_md.get('rank', None),
'genus': gbif_md.get('genus', None),
'genusGuid': gbif_md.get('genusKey', None),
'family': gbif_md.get('family', None),
'familyGuid': gbif_md.get('familyKey', None),
'order': gbif_md.get('order', None),
'orderGuid': gbif_md.get('orderKey', None),
'clazz': gbif_md.get('class', None),
'clazzGuid': gbif_md.get('classKey', None),
'phylum': gbif_md.get('phylum', None),
'phylumGuid': gbif_md.get('phylumKey', None),
'kingdom': gbif_md.get('kingdom', None),
'kingdomGuid': gbif_md.get('kingdomKey', None)
},
}
# build item to import
item = {
'title': gbif_ds['title'],
'description': gbif_ds['description'],
'file': {
'url': 'file://{}'.format(gbif_csv), # local file url
'contenttype': 'application/zip',
'filename': os.path.basename(gbif_csv)
},
'bccvlmetadata': bccvlmd,
'filemetadata': extract_metadata(gbif_csv, 'application/zip'),
}
# Add the number of occurrence records to the metadata
# TODO: This is a hack. Any better solution.
occurrence_csv_filename = os.path.join('data', 'gbif_occurrence.csv')
if occurrence_csv_filename in item['filemetadata']:
# FIXME: copy all occurrence metadata to zip level, for backwards
# compatibility... this should go away after we fully support 'layered'
# occurrence zips.
for key in ('rows', 'headers', 'bounds'): # what about 'species' ?
if key in item['filemetadata'][occurrence_csv_filename]['metadata']:
item['filemetadata'][key] = item['filemetadata'][occurrence_csv_filename]['metadata'][key]
# move data file to destination and build data_url
src = build_source('file://{}'.format(gbif_csv))
dst = build_destination(os.path.join(dest_url, os.path.basename(gbif_csv)), app.conf.get('bccvl', {}))
item['file']['url'] = dst['url']
movelib.move(src, dst)
# tell importer about new dataset (import it)
set_progress('RUNNING', 'Import gbif data {0}'.format(lsid), None, context)
cleanup_job = import_cleanup_job(dest_url, context)
import_job = import_ala_job([item], dest_url, context)
import_job.link_error(set_progress_job("FAILED", "Import of gbif data failed {0}".format(lsid), None, context))
import_job.link_error(cleanup_job)
finish_job = set_progress_job("COMPLETED", 'GBIF import {} complete'.format(lsid), None, context)
(import_job | cleanup_job | finish_job).delay()
except Exception as e:
set_progress('FAILED', 'Download {0} from gbif: {1}'.format(lsid, e), None, context)
import_cleanup(dest_url, context)
LOG.error('Download from %s to %s failed: %s', src, dest_url, e, exc_info=True)
finally:
if tmpdir and os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
