def _get_data_sources(params, headers):
"""
Returns a list of all Taxonomy Sources
"""
schema = _SCHEMAS['get_data_sources']
# parameters for get_data_sources are not actually required, as omitting
# the parameters (which filter the sources) implies returning all.
if params is not None:
jsonschema.validate(instance=params, schema=schema)
re_params = {
'type': 'taxonomy',
}
# Be nice. Filtering by ns can be skipped by either setting 'ns' to null, or
# omitting it from the params object.
if params is not None and params.get('ns') is not None:
re_params['ns'] = params.get('ns')
response = re_api.query("data_sources_get_data_sources", re_params,
headers.get('Authorization'))
else:
response = re_api.query("data_sources_get_all_data_sources", re_params,
headers.get('Authorization'))
sources = []
for source in response['results']:
del source['_id']
del source['_key']
del source['_rev']
sources.append(source)
return {'sources': sources}
def _get_associated_ws_objects(params, headers):
"""
Get any versioned workspace objects associated with a taxon.
"""
schema = _SCHEMAS['get_associated_ws_objects']
jsonschema.validate(instance=params, schema=schema)
(ns, ns_config) = transform_params(params, ('@taxon_coll', ),
{'id': 'taxon_id'})
results = re_api.query("taxonomy_get_associated_ws_objects", params,
headers.get('Authorization'))
res = results['results'][0]
transform_taxon_results(results['results'], ns, ns_config)
for res in results['results']:
# Write some extra metadata about the workspace for each object
for elem in res['results']:
obj = elem['ws_obj']
obj['workspace'] = {
'refdata_source':
obj['ws_info'].get('metadata', {}).get('refdata_source'),
'narr_name':
obj['ws_info'].get('metadata', {}).get('narrative_nice_Name'),
}
del obj['ws_info']
return {
'stats': results['stats'],
'total_count': res['total_count'],
'results': res['results']
}
def _search_species(params, headers):
"""
Search for a species or strain. Similar to search_taxa, but a stripped down, faster query
Returns (result, err), one of which will be None.
"""
schema = _SCHEMAS['search_species']
jsonschema.validate(instance=params, schema=schema)
params['ts'] = params.get('ts', int(time.time() * 1000))
(ns, ns_config) = transform_params(params,
('@taxon_coll', 'sciname_field'))
resp = re_api.query("taxonomy_search_species", params)
results = resp['results']
transform_taxon_results(results, ns, ns_config)
return {'stats': resp['stats'], 'results': results, 'ts': params['ts']}
def _get_taxon(params, headers):
"""
Fetch a taxon by ID.
Returns (result, err), one of which will be None.
"""
schema = _SCHEMAS['get_taxon']
jsonschema.validate(instance=params, schema=schema)
(ns, ns_config) = transform_params(params, ('@taxon_coll', ))
results = re_api.query("taxonomy_fetch_taxon", params)
transform_taxon_results(results['results'], ns, ns_config)
return {
'stats': results['stats'],
'results': results['results'],
'ts': params['ts']
}
def _get_taxon_from_ws_obj(params, headers):
"""
Fetch the taxon document from a workspace object reference.
"""
schema = _SCHEMAS['get_taxon_from_ws_obj']
jsonschema.validate(instance=params, schema=schema)
(ns, ns_config) = transform_params(params, ('@taxon_coll', ))
params['obj_ref'] = params['obj_ref'].replace('/', ':')
results = re_api.query("taxonomy_get_taxon_from_ws_obj", params)
transform_taxon_results(results['results'], ns, ns_config)
return {
'stats': results['stats'],
'results': results['results'],
'ts': params['ts']
}
def _get_lineage(params, headers):
"""
Fetch ancestor lineage for a taxon by ID.
Returns (result, err), one of which will be None.
"""
schema = _SCHEMAS['get_lineage']
jsonschema.validate(instance=params, schema=schema)
params['ts'] = params.get('ts', int(time.time() * 1000))
(ns, ns_config) = transform_params(params,
('@taxon_coll', '@taxon_child_of'))
results = re_api.query("taxonomy_get_lineage", params)
transform_taxon_results(results['results'], ns, ns_config)
return {
'stats': results['stats'],
'results': results['results'],
'ts': params['ts']
}
def _search_taxa(params, headers):
"""
Search for a taxon vertex by scientific name.
Returns (result, err), one of which will be None.
"""
schema = _SCHEMAS['search_taxa']
jsonschema.validate(instance=params, schema=schema)
(ns, ns_config) = transform_params(params,
('@taxon_coll', 'sciname_field'))
results = re_api.query("taxonomy_search_sci_name", params)
res = results['results'][0]
transform_taxon_results(res['results'], ns, ns_config)
return {
'stats': results['stats'],
'total_count': res.get('total_count'),
'results': res['results'],
'ts': params['ts']
}
def _get_siblings(params, headers):
"""
Fetch the siblings for a taxon by ID.
Returns (result, err), one of which will be None.
"""
schema = _SCHEMAS['get_siblings']
jsonschema.validate(instance=params, schema=schema)
(ns, ns_config) = transform_params(
params, ('@taxon_coll', '@taxon_child_of', 'sciname_field'))
results = re_api.query("taxonomy_get_siblings", params)
res = results['results'][0]
transform_taxon_results(res['results'], ns, ns_config)
return {
'stats': results['stats'],
'total_count': res['total_count'],
'results': res['results'],
'ts': params['ts']
}