def __init__(
self,
hostname: str,
auth: Gen3Auth,
download_list: List[Downloadable],
):
"""
Initialize the DownloadManager so that is ready to start downloading.
Note the downloadable objects are required so that all tokens are available
to support the download.
Args:
hostname (str): Gen3 commons home commons
auth (Gen3Auth) : Gen3 authentication
download_list (List[Downloadable]): list of objects to download
"""
self.hostname = hostname
self.access_token = auth.get_access_token()
self.metadata = Gen3Metadata(auth)
self.wts_endpoints = wts_external_oidc(hostname)
self.resolved_compact_drs = {}
# add COMMONS host as a DRSEndpoint as it does not use the WTS
self.known_hosts = {
self.hostname:
KnownDRSEndpoint(
hostname=self.hostname,
access_token=self.access_token,
use_wts=False,
expire=datetime.fromtimestamp(
decode_token(self.access_token)["exp"]),
)
}
self.download_list = download_list
self.resolve_objects(self.download_list)
def test_batch_create(requests_mock):
"""
Test batch creation
"""
metadata = Gen3Metadata("https://example.com")
metadata_list = [
{"guid": "3c42c819-1dfe-4c3e-8d46-c3ec7eb99bf4", "data": {"foo": "bar"}},
{"guid": "dfa1a1dc-98f4-46be-ba8f-ae9b42b0ee50", "data": {"foo": "bar"}},
]
expected_response = {
"created": [
"3c42c819-1dfe-4c3e-8d46-c3ec7eb99bf4",
"dfa1a1dc-98f4-46be-ba8f-ae9b42b0ee50",
],
"updated": [],
"conflict": [],
}
def _mock_request(url, **kwargs):
assert f"/metadata" in url
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 200
mocked_response.json.return_value = expected_response
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.batch_create(metadata_list)
assert response == expected_response
def test_query_full_metadata(requests_mock):
"""
Test querying for guids with full data
"""
metadata = Gen3Metadata("https://example.com")
expected_response = {
"1cfd6767-7775-4e0d-a4a7-d0fc9db02e1d": {
"dbgap": {
"sex": "male",
"body_site": "Blood",
"repository": "TOPMed_WGS_Amish",
"sample_use": [],
"analyte_type": "DNA",
"biosample_id": "SAMN04109653",
"consent_code": 2,
"dbgap_status": "Loaded",
"sra_sample_id": "SRS1305029",
"dbgap_sample_id": 1784123,
"study_accession": "phs000956.v3.p1",
"dbgap_subject_id": 1360617,
"sra_data_details": {
"runs": "1",
"bases": "145891962638",
"center": "UM-TOPMed",
"status": "public",
"size_Gb": "24",
"platform": "ILLUMINA",
"experiments": "1",
"experiment_type": "WGS",
},
"study_subject_id": "phs000956.v3_DBG00256",
"consent_short_name": "HMB-IRB-MDS",
"study_with_consent": "phs000956.c2",
"submitted_sample_id": "NWD299344",
"submitted_subject_id": "DBG00256",
"study_accession_with_consent": "phs000956.v3.p1.c2",
},
"_guid_type": "indexed_file_object",
}
}
def _mock_request(url, **kwargs):
assert f"/metadata" in url
assert f"foo.bar=fizzbuzz" in url
assert f"data=True" in url
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 200
mocked_response.json.return_value = expected_response
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.query("foo.bar=fizzbuzz", return_full_metadata=True)
assert response == expected_response
def try_delete_discovery_guid(auth, guid):
"""
Deletes all discovery metadata under [guid] if it exists
"""
mds = Gen3Metadata(auth_provider=auth)
try:
metadata = mds.get(guid)
if metadata["_guid_type"] == "discovery_metadata":
mds.delete(guid)
else:
logging.warning(f"{guid} is not discovery metadata. Skipping.")
except requests.exceptions.HTTPError as e:
logging.warning(e)
def test_get_index_key_paths_error(requests_mock):
"""
Test getting key paths error
"""
metadata = Gen3Metadata("https://example.com")
def _mock_request(url, **kwargs):
assert url.endswith("/metadata_index")
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 500
mocked_response.json.return_value = {"error": "blah"}
mocked_response.raise_for_status.side_effect = HTTPError("uh oh")
return mocked_response
requests_mock.side_effect = _mock_request
with pytest.raises(Exception):
response = metadata.get_index_key_paths()
async def _update_metadata(guid, metadata, auth, commons_url, lock):
"""
Gets a semaphore then updates metadata for guid
Args:
guid (str): indexd record globally unique id
metadata (str): the metadata to add
auth (Gen3Auth): Gen3 auth or tuple with basic auth name and password
commons_url (str): root domain for commons where metadata service lives
lock (asyncio.Semaphore): semaphones used to limit ammount of concurrent http
connections
"""
mds = Gen3Metadata(commons_url, auth_provider=auth)
async with lock:
# default ssl handling unless it's explicitly http://
ssl = None
if "https" not in commons_url:
ssl = False
response = await mds.async_update(guid, metadata, _ssl=ssl)
return response
async def _get_record_from_mds(guid, commons_url, lock):
"""
Gets a semaphore then requests a record for the given guid
Args:
guid (str): mds record globally unique id
commons_url (str): root domain for commons where mds lives
lock (asyncio.Semaphore): semaphones used to limit ammount of concurrent http
connections
"""
mds = Gen3Metadata(commons_url)
async with lock:
# default ssl handling unless it's explicitly http://
ssl = None
if "https" not in commons_url:
ssl = False
try:
return await mds.async_get(guid, _ssl=ssl)
except aiohttp.client_exceptions.ClientResponseError:
return None
def test_create_index_key_paths_error(requests_mock):
"""
Test create index key paths error
"""
metadata = Gen3Metadata("https://example.com")
path = "/blah"
def _mock_request(url, **kwargs):
assert f"/metadata_index/{path}" in url
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 500
mocked_response.json.return_value = {"error": "blah"}
mocked_response.raise_for_status.side_effect = HTTPError("uh oh")
return mocked_response
requests_mock.side_effect = _mock_request
with pytest.raises(Exception):
response = metadata.create_index_key_path(path)
def test_get_index_key_paths(requests_mock):
"""
Test getting index key paths
"""
metadata = Gen3Metadata("https://example.com")
expected_response = ["abc"]
def _mock_request(url, **kwargs):
assert url.endswith("/metadata_index")
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 200
mocked_response.json.return_value = expected_response
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.get_index_key_paths()
assert response == expected_response
def test_get_version(requests_mock):
"""
Test getting version
"""
metadata = Gen3Metadata("https://example.com")
def _mock_request(url, **kwargs):
assert url.endswith("/version")
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 200
mocked_response.text = "1.2.0"
mocked_response.json.return_value = {}
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.get_version()
assert response
def test_is_not_healthy(requests_mock):
"""
Test is not healthy response
"""
metadata = Gen3Metadata("https://example.com")
def _mock_request(url, **kwargs):
assert url.endswith("/_status")
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 500
mocked_response.text = "Not Healthy"
mocked_response.json.return_value = {}
mocked_response.raise_for_status.side_effect = HTTPError("uh oh")
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.is_healthy()
assert not response
def test_delete_index_key_path(requests_mock):
"""
Test deleting the index key path
"""
metadata = Gen3Metadata("https://example.com")
path = "/blah"
expected_response = {}
def _mock_request(url, **kwargs):
assert f"/metadata_index/{path}" in url
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 204
mocked_response.json.return_value = expected_response
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.delete_index_key_path(path)
assert response.status_code == 204
def test_delete(requests_mock):
"""
Test deleting guids
"""
metadata = Gen3Metadata("https://example.com")
guid = "95a41871-244c-48ae-8004-63f4ed1f0291"
expected_response = {}
def _mock_request(url, **kwargs):
assert f"/metadata/{guid}" in url
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 200
mocked_response.json.return_value = expected_response
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.delete(guid=guid)
assert response == expected_response
def test_query(requests_mock):
"""
Test querying for guids
"""
metadata = Gen3Metadata("https://example.com")
expected_response = ["1cfd6767-7775-4e0d-a4a7-d0fc9db02e1d"]
def _mock_request(url, **kwargs):
assert f"/metadata" in url
assert f"foo.bar=fizzbuzz" in url
assert f"data=False" in url
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 200
mocked_response.json.return_value = expected_response
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.query("foo.bar=fizzbuzz")
assert response == expected_response
def test_update(requests_mock):
"""
Test updating for guids
"""
metadata = Gen3Metadata("https://example.com")
guid = "95a41871-244c-48ae-8004-63f4ed1f0291"
data = {"foo": "bar", "fizz": "buzz", "nested_details": {"key1": "value1"}}
expected_response = data
def _mock_request(url, **kwargs):
assert f"/metadata/{guid}" in url
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 200
mocked_response.json.return_value = expected_response
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.update(guid=guid, metadata=data)
assert response == expected_response
def test_is_healthy(requests_mock):
"""
Test is healthy response
"""
metadata = Gen3Metadata("https://example.com")
def _mock_request(url, **kwargs):
assert url.endswith("/_status")
mocked_response = MagicMock(requests.Response)
mocked_response.status_code = 200
mocked_response.json.return_value = {
"status": "OK",
"timestamp": "2020-03-13T15:23:53.765568+00:00",
}
mocked_response.raise_for_status.side_effect = lambda *args: None
return mocked_response
requests_mock.side_effect = _mock_request
response = metadata.is_healthy()
assert response
async def output_expanded_discovery_metadata(auth,
endpoint=None,
limit=500,
use_agg_mds=False):
"""
fetch discovery metadata from a commons and output to {commons}-discovery-metadata.tsv
"""
if endpoint:
mds = Gen3Metadata(
auth_provider=auth,
endpoint=endpoint,
service_location="mds/aggregate" if use_agg_mds else "mds",
)
else:
mds = Gen3Metadata(
auth_provider=auth,
service_location="mds/aggregate" if use_agg_mds else "mds",
)
count = 0
with tempfile.TemporaryDirectory() as metadata_cache_dir:
all_fields = set()
num_tags = 0
for offset in range(0, limit, MAX_GUIDS_PER_REQUEST):
partial_metadata = mds.query(
"_guid_type=discovery_metadata",
return_full_metadata=True,
limit=min(limit, MAX_GUIDS_PER_REQUEST),
offset=offset,
use_agg_mds=use_agg_mds,
)
# if agg MDS we will flatten the results as they are in "common" : dict format
# However this can result in duplicates as the aggregate mds is namespaced to
# handle this, therefore prefix the commons in front of the guid
if use_agg_mds:
partial_metadata = {
f"{c}__{i}": d
for c, y in partial_metadata.items() for x in y
for i, d in x.items()
}
if len(partial_metadata):
for guid, guid_metadata in partial_metadata.items():
with open(f"{metadata_cache_dir}/{guid.replace('/', '_')}",
"w+") as cached_guid_file:
guid_discovery_metadata = guid_metadata[
"gen3_discovery"]
json.dump(guid_discovery_metadata, cached_guid_file)
all_fields |= set(guid_discovery_metadata.keys())
num_tags = max(
num_tags,
len(guid_discovery_metadata.get("tags", [])))
else:
break
output_columns = (["guid"]
# "tags" is flattened to _tag_0 through _tag_n
+ sorted(list(all_fields - set(["tags"]))) +
[f"_tag_{n}" for n in range(num_tags)])
base_schema = {column: "" for column in output_columns}
output_filename = _metadata_file_from_auth(auth)
with open(
output_filename,
"w+",
) as output_file:
writer = csv.DictWriter(
output_file,
**{
**BASE_CSV_PARSER_SETTINGS, "fieldnames": output_columns
},
)
writer.writeheader()
for guid in sorted(os.listdir(metadata_cache_dir)):
with open(f"{metadata_cache_dir}/{guid}") as f:
fetched_metadata = json.load(f)
flattened_tags = {
f"_tag_{tag_num}": f"{tag['category']}: {tag['name']}"
for tag_num, tag in enumerate(
fetched_metadata.pop("tags", []))
}
true_guid = guid
if use_agg_mds:
true_guid = guid.split("__")[1]
output_metadata = _sanitize_tsv_row({
**base_schema,
**fetched_metadata,
**flattened_tags,
"guid":
true_guid,
})
writer.writerow(output_metadata)
return output_filename
async def publish_discovery_metadata(auth,
metadata_filename,
endpoint=None,
omit_empty_values=False):
"""
Publish discovery metadata from a tsv file
"""
if endpoint:
mds = Gen3Metadata(auth_provider=auth, endpoint=endpoint)
else:
mds = Gen3Metadata(auth_provider=auth)
if not metadata_filename:
metadata_filename = _metadata_file_from_auth(auth)
delimiter = "," if metadata_filename.endswith(".csv") else "\t"
with open(metadata_filename) as metadata_file:
metadata_reader = csv.DictReader(
metadata_file, **{
**BASE_CSV_PARSER_SETTINGS, "delimiter": delimiter
})
tag_columns = [
column for column in metadata_reader.fieldnames
if "_tag_" in column
]
pending_requests = []
for metadata_line in metadata_reader:
discovery_metadata = {
key: _try_parse(value)
for key, value in metadata_line.items()
}
if len(tag_columns):
# all columns _tag_0 -> _tag_n are pushed to a "tags" column
coalesced_tags = [{
"name": tag_name.strip(),
"category": tag_category.strip()
} for tag_category, tag_name in [
tag.split(":")
for tag in map(discovery_metadata.pop, tag_columns)
if tag != ""
]]
discovery_metadata["tags"] = coalesced_tags
guid = discovery_metadata.pop("guid")
if omit_empty_values:
discovery_metadata = {
key: value
for key, value in discovery_metadata.items()
if value not in ["", [], {}]
}
metadata = {
"_guid_type": "discovery_metadata",
"gen3_discovery": discovery_metadata,
}
pending_requests += [
mds.async_create(guid, metadata, overwrite=True)
]
if len(pending_requests) == MAX_CONCURRENT_REQUESTS:
await asyncio.gather(*pending_requests)
pending_requests = []
await asyncio.gather(*pending_requests)