def write(syn: Synapse, center_mapping_df: pd.DataFrame,
error_tracker_synid: str):
"""Write center errors to a file
Args:
syn: Synapse connection
center_mapping_df: Center mapping dataframe
error_tracker_synid: Error tracking synapse id
"""
center_errors = get_center_invalid_errors(syn, error_tracker_synid)
for center in center_mapping_df["center"]:
logger.info(center)
staging_synid = center_mapping_df["stagingSynId"][
center_mapping_df["center"] == center][0]
with open(center + "_errors.txt", "w") as errorfile:
if center not in center_errors:
errorfile.write("No errors!")
else:
errorfile.write(center_errors[center])
ent = synapseclient.File(center + "_errors.txt",
parentId=staging_synid)
syn.store(ent)
os.remove(center + "_errors.txt")
def test_teams(syn, project, schedule_for_cleanup):
name = "My Uniquely Named Team " + str(uuid.uuid4())
team = syn.store(Team(name=name, description="A fake team for testing..."))
schedule_for_cleanup(team)
# not logged in, teams are public
anonymous_syn = Synapse()
found_team = anonymous_syn.getTeam(team.id)
assert team == found_team
p = syn.getUserProfile()
found = None
for m in anonymous_syn.getTeamMembers(team):
if m.member.ownerId == p.ownerId:
found = m
break
assert found is not None, "Couldn't find user {} in team".format(
p.userName)
# needs to be retried 'cause appending to the search index is asynchronous
tries = 8
sleep_time = 1
found_team = None
while tries > 0:
try:
found_team = anonymous_syn.getTeam(name)
break
except ValueError:
tries -= 1
if tries > 0:
time.sleep(sleep_time)
sleep_time *= 2
assert team == found_team
def syn():
"""
Create a Synapse instance that can be shared by all tests in the session.
"""
syn = Synapse(debug=False, skip_checks=True)
syn.logger = logging.getLogger(SILENT_LOGGER_NAME)
return syn
def set_evaluation_quota(syn: Synapse, evalid: int, **kwargs):
"""Sets evaluation submission limit quota. This WILL erase any old quota
you had previously set. Note - round_start must be specified with either
round_end or round_duration and number_of_rounds must be defined for the
time limits to work. submission_limit will work without number_of_rounds.
Args:
syn: Synapse object
evalid: Evaluation id
**kwargs:
round_start: Start of round (local time) in YEAR-MM-DDTHH:MM:SS
format (ie. 2020-02-21T17:00:00)
round_end: End of round (local time) in YEAR-MM-DDTHH:MM:SS format
(ie. 2020-02-21T19:00:00)
number_of_rounds: Number of rounds
round_duration: Round duration in milliseconds
submission_limit: Number of submissions allowed per team
Returns:
A synapseclient.Evaluation
Examples:
>>> set_evaluation_quota(syn, 12345,
round_start="2020-02-21T17:00:00",
round_end="2020-02-23T17:00:00",
number_of_rounds=1,
submission_limit=3)
"""
quota = _create_quota(**kwargs)
evaluation = syn.getEvaluation(evalid)
evaluation.quota = vars(quota)
evaluation = syn.store(evaluation)
return evaluation
def create_new_fileformat_table(
syn: Synapse,
file_format: str,
newdb_name: str,
projectid: str,
archive_projectid: str,
) -> dict:
"""Creates new database table based on old database table and archives
old database table
Args:
syn: Synapse object
file_format: File format to update
newdb_name: Name of new database table
projectid: Project id where new database should live
archive_projectid: Project id where old database should be moved
Returns:
{"newdb_ent": New database synapseclient.Table,
"newdb_mappingdf": new databse pd.DataFrame,
"moved_ent": old database synpaseclient.Table}
"""
db_info = get_dbmapping(syn, projectid)
database_mappingdf = db_info["df"]
dbmapping_synid = db_info["synid"]
olddb_synid = getDatabaseSynId(syn,
file_format,
databaseToSynIdMappingDf=database_mappingdf)
olddb_ent = syn.get(olddb_synid)
olddb_columns = list(syn.getTableColumns(olddb_synid))
newdb_ent = _create_schema(
syn,
table_name=newdb_name,
columns=olddb_columns,
parentid=projectid,
annotations=olddb_ent.annotations,
)
newdb_mappingdf = _update_database_mapping(syn, database_mappingdf,
dbmapping_synid, file_format,
newdb_ent.id)
# Automatically rename the archived entity with ARCHIVED
# This will attempt to resolve any issues if the table already exists at
# location
new_table_name = f"ARCHIVED {time.time()}-{olddb_ent.name}"
moved_ent = _move_entity(syn,
olddb_ent,
archive_projectid,
name=new_table_name)
return {
"newdb_ent": newdb_ent,
"newdb_mappingdf": newdb_mappingdf,
"moved_ent": moved_ent,
}
def store_full_maf(syn: Synapse, filepath: str, parentid: str):
"""Stores full maf file
Args:
syn: Synapse connection
filepath: Path to file
parentid: Synapse container id
"""
syn.store(synapseclient.File(filepath, parentId=parentid))
def push_wiki(syn: Synapse,
projectid: str,
workdir: str = "./") -> typing.List[dict]:
"""Pushes Wiki from configuration
Args:
syn: Synapse connection
project: synapseclient.Project or its id
workdir: Location to download markdown files and wiki_config.json.
Defaults to location of where code is being
executed.
Returns:
Wiki Configuration::
[
{
"id": "111",
"title": "title",
"parentId": "33333",
"markdown_path": "home.md"
},
{...}
]
"""
wiki_config = validate_config(workdir)
for wiki_header in wiki_config:
# no markdown path, nothing to update
markdown_path = wiki_header.get('markdown_path')
if not wiki_header.get('markdown_path'):
print(f"Markdown not specified: {wiki_header['title']}")
continue
markdown_path = os.path.join(workdir, markdown_path)
with open(markdown_path, 'r') as md_f:
markdown = md_f.read()
# Create new wiki page if id isn't specified
if wiki_header.get('id') is not None:
wiki = syn.getWiki(projectid, subpageId=wiki_header['id'])
# Don't store if the wiki pages are the same
if wiki.markdown == markdown:
print(f"no updates: {wiki_header['title']}")
continue
print(f"Wiki updated: {wiki_header['title']}")
else:
wiki = synapseclient.Wiki(owner=projectid,
title=wiki_header['title'],
parentWikiId=wiki_header['parentId'])
print(f"Wiki added: {wiki_header['title']}")
wiki.markdown = markdown
wiki = syn.store(wiki)
# If new wiki page is added, must add to wiki_config.json
wiki_header['id'] = wiki['id']
return wiki_config
def _download_from_synapse(self, synid, target_dir):
try:
from synapseclient import Synapse
except ImportError:
raise ImportError("Please install synapseclient using 'pip install synapseclient'")
try:
self._synapse.get(synid, downloadLocation=target_dir)
except:
self._synapse = Synapse()
self._synapse.login()
self._synapse.get(synid, downloadLocation=target_dir)
def testCustomConfigFile(syn, schedule_for_cleanup):
if os.path.isfile(client.CONFIG_FILE):
configPath = './CONFIGFILE'
shutil.copyfile(client.CONFIG_FILE, configPath)
schedule_for_cleanup(configPath)
syn2 = Synapse(configPath=configPath)
syn2.login()
else:
raise ValueError(
"Please supply a username and password in the configuration file.")
def create_site_bundle(syn: Synapse, question: int, site: str):
"""Creates workflow and entity bundles for the internal site submissions
Args:
syn: Synapse connection
question: Question number
site: Site
"""
shutil.copyfile(
os.path.join(SCRIPT_DIR, "../infrastructure/internal_workflow.cwl"),
os.path.join(SCRIPT_DIR,
f"../infrastructure/{question}_internal_workflow.cwl"))
internal = create_evaluation_queue(
syn, f"COVID-19 DREAM {site} - Question {question}")
syn.setPermissions(internal,
accessType=[
'DELETE_SUBMISSION', 'DELETE', 'SUBMIT', 'UPDATE',
'CREATE', 'READ', 'UPDATE_SUBMISSION',
'READ_PRIVATE_SUBMISSION', 'CHANGE_PERMISSIONS'
],
principalId=3407544)
internal_test = create_evaluation_queue(
syn, f"COVID-19 DREAM {site} - Question {question} TEST")
syn.setPermissions(internal_test,
accessType=[
'DELETE_SUBMISSION', 'DELETE', 'SUBMIT', 'UPDATE',
'CREATE', 'READ', 'UPDATE_SUBMISSION',
'READ_PRIVATE_SUBMISSION', 'CHANGE_PERMISSIONS'
],
principalId=3407544)
prod_wf = os.path.join("covid19-challenge-master/infrastructure",
f"{question}_internal_workflow.cwl")
test_wf = os.path.join("covid19-challenge-develop/infrastructure",
f"{question}_internal_workflow.cwl")
ent = create_entity(syn,
name=f"COVID-19 {site} Q{question}",
link=MASTER,
annotations={'ROOT_TEMPLATE': prod_wf})
test_ent = create_entity(syn,
name=f"COVID-19 {site} Q{question} TEST",
link=DEV,
annotations={'ROOT_TEMPLATE': test_wf})
print(f"Add to {site}'s docker-compose .env")
print({internal.id: ent.id, internal_test.id: test_ent.id})
return {
"internal_queueid": internal.id,
"internal_queue_testid": internal_test.id
}
def _set_acl(syn: Synapse, entity: Union[File, Folder, Project],
acl_config: dict):
"""Sets ACLs to Synapse entity
Args:
syn: Synapse connection
entity: Synapse Folder or Project
acl_config: ACL template json configuration
"""
for acl in acl_config:
syn.setPermissions(entity=entity,
principalId=acl['principal_id'],
accessType=acl['access_type'])
def test_create_Link_to_entity_with_the_same_parent():
parent = "syn123"
file = File("new file", parent=parent, id="syn456")
file_bundle = {
'accessControlList': '/repo/v1/entity/syn456/acl',
'entityType': 'org.sagebionetworks.repo.model.FileEntity',
'annotations': '/repo/v1/entity/syn456/annotations',
'uri': '/repo/v1/entity/syn456',
'createdOn': '2018-08-27T20:48:43.562Z',
'parentId': 'syn123',
'versionNumber': 1,
'dataFileHandleId': '3594',
'modifiedOn': '2018-08-27T20:48:44.938Z',
'versionLabel': '1',
'createdBy': '1',
'versions': '/repo/v1/entity/syn456/version',
'name': 'new file',
'concreteType': 'org.sagebionetworks.repo.model.FileEntity',
'etag': '62fd1a76-ed9c-425a-b4a8-1c4e6aad7fc6',
'modifiedBy': '1',
'id': 'syn456',
'versionUrl': '/repo/v1/entity/syn456/version/1'
}
link = Link(targetId=file, parent=parent)
syn = Synapse(skip_checks=True)
with patch.object(syn, "_getEntity", return_value=file_bundle):
pytest.raises(ValueError, syn.store, link)
def syn():
"""
Create a logged in Synapse instance that can be shared by all tests in the session.
"""
print("Python version:", sys.version)
syn = Synapse(debug=False, skip_checks=True)
print("Testing against endpoints:")
print(" " + syn.repoEndpoint)
print(" " + syn.authEndpoint)
print(" " + syn.fileHandleEndpoint)
print(" " + syn.portalEndpoint + "\n")
syn.logger = logging.getLogger(SILENT_LOGGER_NAME)
syn.login()
return syn
def get_dbmapping(syn: Synapse, projectid: str) -> dict:
"""Gets database mapping information
Args:
syn: Synapse connection
projectid: Project id where new data lives
Returns:
{'synid': database mapping syn id,
'df': database mapping pd.DataFrame}
"""
project_ent = syn.get(projectid)
dbmapping_synid = project_ent.annotations.get("dbMapping", "")[0]
database_mapping = syn.tableQuery(f"select * from {dbmapping_synid}")
database_mappingdf = database_mapping.asDataFrame()
return {"synid": dbmapping_synid, "df": database_mappingdf}
def pull_wiki(syn: Synapse,
project: str,
workdir: str = "./") -> typing.List[dict]:
"""Downloads each wikipage's content into a markdown file and
stores a configuration file
Args:
syn: Synapse connection
project: synapseclient.Project or its id
workdir: Location to download markdown files and wiki_config.json
into. Defaults to location of where code is being
executed.
Returns:
Wiki Configuration::
[
{
"id": "111",
"title": "homepage",
"markdown_path": "111-homepage.md"
},
{...}
]
"""
projectid = synapseclient.core.utils.id_of(project)
wiki_headers = syn.getWikiHeaders(projectid)
for wiki_header in wiki_headers:
wiki = syn.getWiki(projectid, subpageId=wiki_header['id'])
# Convert all special characters to underscore
# This way markdown paths don't have special characters
# and json file can be written without encoding
clean_title = ''.join(letter for letter in wiki['title']
if letter.isalnum())
# Home page title is always blank
if clean_title == '':
clean_title = 'homepage'
wiki_header['title'] = clean_title
# The wiki id is added to the markdown path because wiki ids are
# unique, but wiki titles don't have to be
markdown_path = os.path.join(workdir, f"{wiki.id}-{clean_title}.md")
with open(markdown_path, 'w') as md_file:
md_file.write(wiki['markdown'])
wiki_header['markdown_path'] = f"{wiki.id}-{clean_title}.md"
return wiki_headers
def create_evaluation_queue(syn: Synapse, name: str) -> Evaluation:
"""Creates evaluation queue
Args:
name: Name of queue
Returns:
a synapseclient.Evaluation
"""
queue = Evaluation(name=name, contentSource="syn21849255")
try:
queue = syn.store(queue)
except Exception:
url_name = quote(name)
queue = syn.restGET(f"/evaluation/name/{url_name}")
queue = Evaluation(**queue)
return queue
def create_main_bundle(syn: Synapse, question: int):
"""Creates workflow and entity bundles for the main submission
Args:
syn: Synapse connection
question: Question number
"""
shutil.copyfile(
os.path.join(SCRIPT_DIR, "../infrastructure/main_workflow.cwl"),
os.path.join(SCRIPT_DIR, f"../infrastructure/{question}_workflow.cwl"))
main_queue = create_evaluation_queue(
syn, f"COVID-19 DREAM Challenge - Question {question}")
# Global view
syn.setPermissions(main_queue, accessType=['READ'])
# Participant team
syn.setPermissions(main_queue, accessType=['READ'], principalId=3407543)
# Admin team
syn.setPermissions(main_queue,
accessType=[
'DELETE_SUBMISSION', 'DELETE', 'SUBMIT', 'UPDATE',
'CREATE', 'READ', 'UPDATE_SUBMISSION',
'READ_PRIVATE_SUBMISSION', 'CHANGE_PERMISSIONS'
],
principalId=3407544)
main_queue_test = create_evaluation_queue(
syn, f"COVID-19 DREAM Challenge - Question {question} TEST")
syn.setPermissions(main_queue_test,
accessType=[
'DELETE_SUBMISSION', 'DELETE', 'SUBMIT', 'UPDATE',
'CREATE', 'READ', 'UPDATE_SUBMISSION',
'READ_PRIVATE_SUBMISSION', 'CHANGE_PERMISSIONS'
],
principalId=3407544)
prof_wf = os.path.join("covid19-challenge-master/infrastructure",
f"{question}_workflow.cwl")
test_wf = os.path.join("covid19-challenge-develop/infrastructure",
f"{question}_workflow.cwl")
main_ent = create_entity(syn,
name=f"COVID-19 Q{question}",
link=MASTER,
annotations={'ROOT_TEMPLATE': prof_wf})
main_test_ent = create_entity(syn,
name=f"COVID-19 Q{question} TEST",
link=DEV,
annotations={'ROOT_TEMPLATE': test_wf})
print("Add to NCAT's docker-compose .env")
print({main_queue.id: main_ent.id, main_queue_test.id: main_test_ent.id})
return {
"main_queueid": main_queue.id,
"main_queue_testid": main_queue_test.id
}
def _get_wikipages_and_mapping(
syn: Synapse, entity: Union[File, Folder, Project],
destination: Union[File, Folder, Project]) -> dict:
"""Get entity/destination pages and mapping of wiki pages
Args:
syn: Synapse connection
entity: Synapse File, Project, Folder Entity or Id with
Wiki you want to copy
destination: Synapse File, Project, Folder Entity or Id
with Wiki that matches entity
Returns:
{'entity_wiki_pages': {'title': synapseclient.Wiki}
'destination_wiki_pages': {'title': synapseclient.Wiki}
'wiki_mapping': {'wiki_id': 'dest_wiki_id'}}
"""
entity_wiki = _get_headers(syn, entity)
destination_wiki = _get_headers(syn, destination)
entity_wiki_pages = {}
for wiki in entity_wiki:
entity_wiki = syn.getWiki(entity, wiki['id'])
entity_wiki_pages[wiki['title']] = entity_wiki
# Mapping dictionary containing wiki page mapping between
# entity and destination
wiki_mapping = {}
destination_wiki_pages = {}
for wiki in destination_wiki:
destination_wiki = syn.getWiki(destination, wiki['id'])
destination_wiki_pages[wiki['title']] = destination_wiki
# Only map wiki pages that exist in `entity` (source)
if entity_wiki_pages.get(wiki['title']) is not None:
wiki_mapping[entity_wiki_pages[wiki['title']].id] = wiki['id']
else:
logger.info("Title exists at destination but not in "
f"entity: {wiki['title']}")
return {
'entity_wiki_pages': entity_wiki_pages,
'destination_wiki_pages': destination_wiki_pages,
'wiki_mapping': wiki_mapping
}
def test_synapse_client__discrete_sts_token_stores(self, mock_fetch_token):
"""Verify that two Synapse objects will not share the same cached tokens"""
syn1 = Synapse(skip_checks=True)
syn2 = Synapse(skip_checks=True)
expected_token = {
'awsAccessKeyId':
'ABC',
'awsSecretAccessKey':
'456',
'expiration':
datetime_to_iso(datetime.datetime.utcnow() +
datetime.timedelta(hours=12))
}
mock_fetch_token.return_value = expected_token
synapse_id = 'syn_123'
permission = 'read_write'
token = syn1.get_sts_storage_token(synapse_id, permission)
assert expected_token == token
assert mock_fetch_token.call_count == 1
token = syn1.get_sts_storage_token(synapse_id, permission)
assert expected_token == token
# should have been satisfied from cache, not fetched again
assert mock_fetch_token.call_count == 1
# but now fetching from a separate synapse object should not be satisfied from a common cache
token = syn2.get_sts_storage_token(synapse_id, permission)
assert expected_token == token
assert mock_fetch_token.call_count == 2
def _get_team_count(syn: Synapse, teamid: int) -> dict:
"""Rest call wrapper for getting team member count
Args:
syn: Synapse object
teamid: Synapse team id
"""
count = syn.restGET(f"/teamMembers/count/{teamid}")
return count
def get_team_count(syn: Synapse, team: Union[int, str, Team]) -> int:
"""Get number of team members
Args:
syn: Synapse object
team: synaspeclient.Team, its id, or name.
"""
team_obj = syn.getTeam(team)
count = _get_team_count(syn, team_obj.id)
return count['count']
def _download_from_synapse(self, synid, target_dir):
try:
from synapseclient import Synapse
except ImportError:
raise ImportError("Please install synapseclient using 'pip install synapseclient'")
try:
self._synapse.get(synid, downloadLocation=target_dir)
except:
self._synapse = Synapse()
self._synapse.login()
self._synapse.get(synid, downloadLocation=target_dir)
def store_narrow_maf(syn: Synapse, filepath: str, maf_tableid: str):
"""
Stores the narrow maf in Synapse Table
Args:
syn: Synapse connection
filepath: Path to maf file
maf_tableid: database synid
"""
logger.info(f"STORING {filepath}")
# database = syn.get(maf_tableid)
try:
update_table = synapseclient.Table(maf_tableid,
filepath,
separator="\t")
syn.store(update_table)
except SynapseTimeoutError:
# This error occurs because of waiting for table to index.
# Don't worry about this.
pass
def syn_connect(args):
"connect and log in based on options"
syn_conf = LrgaspSynConfig.factory(args)
syn = Synapse()
syn.logger.setLevel(getLrgaspLogger().level) # cut down on noise
# None user/password uses cache or prompts. Command line overrides conf
user = args.synapseUser if args.synapseUser is not None else syn_conf.user
password = args.synapsePassword if args.synapsePassword is not None else syn_conf.password
login_with_prompt(syn, user, password, rememberMe=args.rememberMe)
getLrgaspLogger().debug(f"logged in as synpase user '{syn.username}'")
return syn
def annotate_submission(syn: Synapse,
submissionid: str,
annotation_dict: dict = None,
status: str = None,
is_private: bool = True,
force: bool = False) -> MockResponse:
"""Annotate submission with annotation values from a dict
Args:
syn: Synapse object
submissionid: Submission id
annotation_dict: Annotation dict
status: Submission Status
is_private: Set annotations acl to private (default is True)
force: Force change the annotation from
private to public and vice versa.
Returns:
MockResponse
"""
sub_status = syn.getSubmissionStatus(submissionid)
# Update the status as well
if status is not None:
sub_status.status = status
if annotation_dict is None:
annotation_dict = {}
# Don't add any annotations that are None
annotation_dict = {
key: annotation_dict[key]
for key in annotation_dict if annotation_dict[key] is not None
}
sub_status = update_single_submission_status(sub_status,
annotation_dict,
is_private=is_private,
force=force)
sub_status = update_submission_status(sub_status, annotation_dict)
syn.store(sub_status)
return MockResponse
def mirror(syn: Synapse,
entity: Union[File, Folder, Project],
destination: Union[File, Folder, Project],
force: bool = False,
dryrun: bool = False):
"""Mirrors (sync) wiki pages by using the wikipage titles between two
Synapse Entities. This function only works if `entity` and `destination`
are the same type and both must have wiki pages. Only wiki pages with the
same titles will be copied from `entity` to `destination` - if there is
a wiki page that you want to add, you will have to create a wiki page
first in the `destination` with the same name.
Args:
entity: Synapse File, Project, Folder Entity or Id with
Wiki you want to copy
destination: Synapse File, Project, Folder Entity or Id
with Wiki that matches entity
force: Update a page even if its the same. Default to False.
dryrun: Show the pages that have changed but don't update. Default
is False.
"""
entity = syn.get(entity, downloadFile=False)
destination = syn.get(destination, downloadFile=False)
if type(entity) is not type(destination):
raise ValueError("Can only mirror wiki pages between similar "
"entity types")
# Get entity/destination pages and mapping of wiki pages
pages_and_mappings = _get_wikipages_and_mapping(syn, entity, destination)
if dryrun:
logger.info("Your wiki pages will not be mirrored. `dryrun` is True")
_update_wiki(syn,
**pages_and_mappings,
force=force,
dryrun=dryrun,
entity=entity,
destination=destination)
def get_dbmapping(syn: Synapse, project_id: str) -> dict:
"""Gets database mapping information
Args:
syn: Synapse connection
project_id: Project id where new data lives
Returns:
{'synid': database mapping syn id,
'df': database mapping pd.DataFrame}
"""
project_ent = syn.get(project_id)
dbmapping_synid = project_ent.annotations.get("dbMapping", "")[0]
database_mappingdf = get_syntabledf(syn,
f'select * from {dbmapping_synid}')
return {'synid': dbmapping_synid, 'df': database_mappingdf}
def test_EntityViewSchema__before_synapse_store(syn):
syn = Synapse(debug=True, skip_checks=True)
with patch.object(syn, '_get_default_view_columns') as mocked_get_default,\
patch.object(syn, '_get_annotation_view_columns') as mocked_get_annotations,\
patch.object(SchemaBase, "_before_synapse_store"):
submission_view = EntityViewSchema(scopes=['syn123'], parent="idk")
submission_view._before_synapse_store(syn)
mocked_get_default.assert_called_once_with("entityview",
view_type_mask=1)
mocked_get_annotations.assert_called_once_with(['syn123'],
"entityview",
view_type_mask=1)
def test_EntityViewSchema__repeated_columnName_same_type(syn):
syn = Synapse(debug=True, skip_checks=True)
entity_view = EntityViewSchema("someName", parent="syn123")
columns = [Column(name='annoName', columnType='INTEGER'),
Column(name='annoName', columnType='INTEGER')]
with patch.object(syn, 'getColumns') as mocked_get_columns:
filtered_results = entity_view._filter_duplicate_columns(syn, columns)
mocked_get_columns.assert_called_once_with([])
assert 1 == len(filtered_results)
assert Column(name='annoName', columnType='INTEGER') == filtered_results[0]
def get_registered_challenges(syn: Synapse,
userid: str = None) -> Iterator[Project]:
"""Get the Synapse Challenge Projects a user is registered to.
Defaults to the logged in synapse user.
Args:
syn: Synapse connection
userid: Specify userid if you want to know the challenges
another Synapse user is registered to.
Yields:
A synapseclient.Project
"""
challenge_api = ChallengeApi(syn=syn)
# This will return the logged in user profile if None is passed in
profile = syn.getUserProfile(userid)
userid = profile.ownerId
registered = challenge_api.get_registered_challenges(participantId=userid)
for challenge in registered:
challenge_ent = syn.get(challenge.projectId)
print(challenge_ent.name)
yield challenge_ent
def test_login(test_state):
alt_syn = Synapse()
username = "******"
password = "******"
with patch.object(alt_syn, "login") as mock_login, \
patch.object(alt_syn, "getUserProfile", return_value={"userName": "******", "ownerId": "ownerId"})\
as mock_get_user_profile:
run(test_state,
'synapse'
'--skip-checks', 'login',
'-u', username,
'-p', password,
'--rememberMe',
syn=alt_syn)
mock_login.assert_called_once_with(username, password, forced=True, rememberMe=True, silent=False)
mock_get_user_profile.assert_called_once_with()
def submit_to_challenge(filename, challenge, label, retry=True):
try:
client = Synapse()
client.login()
evaluation = client.getEvaluation(CODES[challenge])
filename = filename + '.gct' if challenge == 'sc1' else filename + '.zip'
myfile = File(RESULTS_FOLDER + filename, parent=PROJECT_ID)
myfile = client.store(myfile)
client.submit(evaluation, myfile, name=label, teamName=TEAM)
except:
if retry:
submit_to_challenge(filename, challenge, label, retry=False)
else:
print 'failed to submit', label, 'to', challenge
if (aws_access_key_id is None) or (aws_secret_access_key is None):
break
else:
s3Connections.append(S3Connection(aws_access_key_id, aws_secret_access_key))
iamConnections.append(
IAMConnection(aws_access_key_id=aws_access_key_id, aws_secret_access_key=aws_secret_access_key)
)
i = i + 1
if len(s3Connections) == 0:
raise ("No AWS crdentials provided")
MAXIMUM_USER_NAME_LENGTH = 63
## connect to Synapse
syn = Synapse()
syn.login(synapseUserId, synapseUserPw)
ownUserProfile = syn.getUserProfile()
ownPrincipalId = ownUserProfile["ownerId"]
## get all Participants for Evaluation
participants = syn.restGET("/evaluation/" + evaluationId + "/participant?limit=99999")["results"]
print "total number of results: " + str(len(participants))
## For each participant
participantList = []
anyNewUsers = False
for i, part in enumerate(participants):
## add to a list the user's first name, last name, email address, user name and principal ID
## "user name" is defined as <firstName>.<lastName>.<principalId>.wcpe.sagebase.org
partId = part["userId"]
class KrakenDownload(object):
"""Utility to download Kraken DB and place them in a local directory
::
from sequana import KrakenDownload
kd = KrakenDownload()
kd.download('toydb')
kd.download('minikraken')
A large database (8Gb) is available on synapse and has the following DOI::
doi:10.7303/syn6171000
It can be downloaded manually or if you have a Synapse login
(https://www.synapse.org), you can use::
from sequana import KrakenDownload
kd = KrakenDownload()
kd.downloaded("sequana_db1")
"""
dv = DevTools()
def download(self, name, verbose=True):
if name == "minikraken":
self._download_minikraken(verbose=verbose)
elif name == "toydb":
self._download_kraken_toydb(verbose=verbose)
elif name == "sequana_db1":
self._download_sequana_db1(verbose=verbose)
else:
raise ValueError("name must be toydb or minikraken, or sequana_db1")
def _download_kraken_toydb(self, verbose=True):
"""Download the kraken DB toy example from sequana_data into
.config/sequana directory
Checks the md5 checksums. About 32Mb of data
"""
dv = DevTools()
base = sequana_config_path + os.sep + "kraken_toydb"
taxondir = base + os.sep + "taxonomy"
dv.mkdir(base)
dv.mkdir(taxondir)
baseurl = "https://github.com/sequana/data/raw/master/"
# download only if required
logger.info("Downloading the database into %s" % base)
md5sums = [
"28661f8baf0514105b0c6957bec0fc6e",
"97a39d44ed86cadea470352d6f69748d",
"d91a0fcbbc0f4bbac918755b6400dea6",
"c8bae69565af2170ece194925b5fdeb9"]
filenames = [
"database.idx",
"database.kdb",
"taxonomy/names.dmp",
"taxonomy/nodes.dmp"]
for filename, md5sum in zip(filenames, md5sums):
url = baseurl + "kraken_toydb/%s" % filename
filename = base + os.sep + filename
if os.path.exists(filename) and md5(filename) == md5sum:
logger.warning("%s already present" % filename)
else:
logger.info("Downloading %s" % url)
wget(url, filename)
def _download_minikraken(self, verbose=True):
dv = DevTools()
base = sequana_config_path + os.sep + ""
taxondir = base + os.sep + "taxonomy"
dv.mkdir(base)
dv.mkdir(taxondir)
logger.info("Downloading minikraken (4Gb)")
filename = base + os.sep + "minikraken.tgz"
if os.path.exists(filename) and md5(filename) == "30eab12118158d0b31718106785195e2":
logger.warning("%s already present" % filename)
else:
wget("https://ccb.jhu.edu/software/kraken/dl/minikraken.tgz", filename)
# unzipping. requires tar and gzip
def _download_from_synapse(self, synid, target_dir):
try:
from synapseclient import Synapse
except ImportError:
raise ImportError("Please install synapseclient using 'pip install synapseclient'")
try:
self._synapse.get(synid, downloadLocation=target_dir)
except:
self._synapse = Synapse()
self._synapse.login()
self._synapse.get(synid, downloadLocation=target_dir)
def _download_sequana_db1(self, verbose=True):
dbname = "sequana_db1"
from easydev import md5
dir1 = sequana_config_path + os.sep + dbname
dir2 = dir1 + os.sep + "taxonomy"
self.dv.mkdir(dir1)
self.dv.mkdir(dir2)
logger.info("Downloading about 8Gb of data (if not already downloaded) from"
" Synapse into %s" % dir1)
from os.path import exists
filename = dir1 + "ena_list.txt"
if exists(filename) and md5(filename) == "a9cc6268f3338d1632c4712a412593f2":
pass
else:
self._download_from_synapse('syn6171700', dir1)
# database.idx
filename = dir1 + "database.idx"
if exists(filename) and md5(filename) == "2fa4a99a4f52f2f04c5a965adb1534ac":
pass
else:
self._download_from_synapse('syn6171017', dir1)
# database.kdb ; this one is large (8Gb)
filename = dir1 + "database.kdb"
if exists(filename) and md5(filename) == "ff698696bfc88fe83bc201937cd9cbdf":
pass
else:
self._download_from_synapse('syn6171107', dir1)
# Then, the taxonomy directory
filename = dir1 + "names.dmp"
if exists(filename) and md5(filename) == "10bc7a63c579de02112d125a51fd65d0":
pass
else:
self._download_from_synapse('syn6171286', dir2)
filename = dir1 + "nodes.dmp"
if exists(filename) and md5(filename) == "a68af5a60434e2067c4a0a16df873980":
pass
else:
self._download_from_synapse('syn6171289', dir2)
filename = dir1 + "taxons.txt"
if exists(filename) and md5(filename) == "e78fbb43b3b41cbf4511d6af16c0287f":
pass
else:
self._download_from_synapse('syn6171290', dir2)
logger.info('done. You should have a kraken DB in %s' % dir1)
# The annotations
wget("https://github.com/sequana/data/raw/master/sequana_db1/annotations.csv",
dir1 + os.sep + "annotations.csv")
