def get_merged_namespace_names(
locations: Iterable[str],
check_keywords: bool = True,
) -> Mapping[str, str]:
"""Load many namespaces and combines their names.
:param locations: An iterable of URLs or file paths pointing to BEL namespaces.
:param check_keywords: Should all the keywords be the same? Defaults to ``True``
:return: A dictionary of {names: labels}
Example Usage
>>> from pybel.resources import write_namespace
>>> from pybel_tools.definition_utils import export_namespace, get_merged_namespace_names
>>> graph = ...
>>> original_ns_url = ...
>>> export_namespace(graph, 'MBS') # Outputs in current directory to MBS.belns
>>> value_dict = get_merged_namespace_names([original_ns_url, 'MBS.belns'])
>>> with open('merged_namespace.belns', 'w') as f:
>>> ... write_namespace('MyBrokenNamespace', 'MBS', 'Other', 'Charles Hoyt', 'PyBEL Citation', value_dict, file=f)
"""
resources = {location: get_bel_resource(location) for location in locations}
if check_keywords:
resource_keywords = set(config['Namespace']['Keyword'] for config in resources.values())
if 1 != len(resource_keywords):
raise ValueError('Tried merging namespaces with different keywords: {}'.format(resource_keywords))
result = {}
for resource in resources:
result.update(resource['Values'])
return result
def get_or_create_annotation(self, url: str) -> Namespace:
"""Insert the namespace file at the given location to the cache.
:raises: pybel.resources.exc.ResourceError
"""
result = self.get_namespace_by_url(url)
if result is not None:
return result
t = time.time()
bel_resource = get_bel_resource(url)
result = Namespace(
url=url,
is_annotation=True,
**_get_annotation_insert_values(bel_resource),
)
result.entries = [
NamespaceEntry(name=name, identifier=label)
for name, label in bel_resource['Values'].items() if name
]
self.session.add(result)
self.session.commit()
logger.info(
'inserted annotation: %s (%d terms in %.2f seconds)',
url,
len(bel_resource['Values']),
time.time() - t,
)
return result
def __init__(self, annotation_urls):
self.resources = {}
for key, url in annotation_urls.items():
res = get_bel_resource(url)
self.resources[key] = res
self.failures = defaultdict(set)
def get_or_create_namespace(self, url: str) -> Namespace:
"""Insert the namespace file at the given location to the cache.
If not cachable, returns the dict of the values of this namespace.
:raises: pybel.resources.exc.ResourceError
"""
result = self.get_namespace_by_url(url)
if result is not None:
return result
t = time.time()
bel_resource = get_bel_resource(url)
_clean_bel_namespace_values(bel_resource)
values = bel_resource['Values']
namespace_insert_values = _get_namespace_insert_values(bel_resource)
name_to_id = {}
if url.endswith('-names.belns'):
mapping_url = url[:-len('-names.belns')] + '.belns.mapping'
try:
res = requests.get(mapping_url)
res.raise_for_status()
except requests.exceptions.HTTPError:
logger.warning('No mappings found for %s', url)
else:
mappings = res.json()
logger.debug('got %d mappings', len(mappings))
name_to_id.update({v: k for k, v in res.json().items()})
namespace = Namespace(
url=url,
**namespace_insert_values,
)
logger.debug('building NamespaceEntry instances')
namespace.entries = [
NamespaceEntry(name=name,
encoding=encoding,
identifier=name_to_id.get(name))
for name, encoding in values.items()
]
self.session.add(namespace)
logger.debug('committing namespace')
self.session.commit()
logger.info('inserted namespace: %s (%d terms in %.2f seconds)', url,
len(values),
time.time() - t)
return namespace
def _ensure_namespace_urls(
self,
urls: Iterable[str],
use_tqdm: bool = True,
is_annotation: bool = False,
) -> List[Namespace]:
ext = 'belanno' if is_annotation else 'belns'
rv = []
url_to_namespace = {}
url_to_values = {}
url_to_name_to_id = {}
tag = 'annotations' if is_annotation else 'namespaces'
if use_tqdm:
urls = tqdm(urls, desc=f'downloading {tag}')
for url in urls:
result = self.get_namespace_by_url(url)
if result:
rv.append(result)
continue
bel_resource = get_bel_resource(url)
_clean_bel_namespace_values(bel_resource)
url_to_values[url] = bel_resource['Values']
if is_annotation:
namespace_kwargs = _get_annotation_insert_values(bel_resource)
else:
namespace_kwargs = _get_namespace_insert_values(bel_resource)
result = url_to_namespace[url] = Namespace(url=url,
**namespace_kwargs)
rv.append(result)
if url.endswith(f'-names.{ext}'):
mapping_url = url[:-len(f'-names.{ext}')] + f'.{ext}.mapping'
try:
res = requests.get(mapping_url)
res.raise_for_status()
except requests.exceptions.HTTPError:
logger.warning('No mappings found for %s', url)
else:
mappings = res.json()
logger.debug('got %d mappings', len(mappings))
url_to_name_to_id[url] = {
v: k
for k, v in res.json().items()
}
self.session.add_all(url_to_namespace.values())
self.session.commit()
url_to_id = {
url: namespace.id
for url, namespace in url_to_namespace.items()
}
if not url_to_values:
return rv
rows = []
it = url_to_values.items()
if use_tqdm:
it = tqdm(it, desc=f'making {tag} entry table')
if is_annotation:
for url, values in it:
for name, identifier in values.items():
if not name:
continue
rows.append(
(url_to_id[url], name, None,
identifier)) # TODO is this a fair assumption?
else:
for url, values in it:
name_to_id = url_to_name_to_id.get(url, {})
for name, encoding in values.items():
if not name:
continue
rows.append(
(url_to_id[url], name, encoding, name_to_id.get(name)))
df = pd.DataFrame(
rows, columns=['namespace_id', 'name', 'encoding', 'identifier'])
logger.info('preparing sql objects for %s', tag)
df.to_sql(NamespaceEntry.__tablename__,
con=self.engine,
if_exists='append',
index=False)
logger.info('committing %s', tag)
start_commit_time = time.time()
self.session.commit()
logger.info('done committing %s after %.2f seconds', tag,
time.time() - start_commit_time)
return rv
def get_nift_labels() -> Set[str]:
"""Map NIFT names that have been normalized to the original names."""
bel_resource = get_bel_resource(NIFT_URL)
return set(bel_resource['Values'])
def get_nift_values() -> Mapping[str, str]:
"""Map NIFT names that have been normalized to the original names."""
r = get_bel_resource(
'https://arty.scai.fraunhofer.de/artifactory/bel/namespace/nift/NIFT.belns'
)
return {name.lower(): name for name in r['Values']}
def _disease_ontology_dict(ontology: str) -> Mapping[str, str]:
"""Create a dictionary from the disease ontologies used for mapping HMDB disease names to those ontologies."""
doid_path = ONTOLOGY_NAMESPACES[ontology]
doid_ns = get_bel_resource(doid_path)
return {value.lower(): value for value in doid_ns['Values']}
def test_get_from_url(self):
"""Test downloading a resource by URL."""
with mock_bel_resources:
res = get_bel_resource('https://example.com/test_an_1.belanno')
self._help_test_annotation(res)
def test_get_from_path(self):
"""Test downloading a resource from a file path."""
res = get_bel_resource(TEST_ANNOTATION_PATH)
self._help_test_annotation(res)
def test_raises_on_empty(self):
"""Test that an error is thrown if an empty resource is downloaded."""
with self.assertRaises(EmptyResourceError):
get_bel_resource(TEST_NAMESPACE_EMPTY_PATH)
