def connect(self):
'''
Prompts for csv file with info we need to upload.
Checks if files to upload exist.
Connects to Blackfynn API and activates top level dataset destination.
Returns csv file name, destination dataset.
'''
try:
b_fynn = Blackfynn(self.working_profile)
except Exception as ex:
sys.exit('Error Connecting to ' + 'Blackfynn. ' + str(ex))
try:
print("Trying to connect to dataset.", flush=True)
dataset = b_fynn.get_dataset(self.dataset_name)
except Exception as ex:
sys.exit('Unable to connect to the dataset.' + str(ex))
print()
print('Dataset: {}\nProfile: {}'.format(data_set,
self.working_profile))
prompt = input('Continue with upload (y/n)? ')
if prompt != 'y':
sys.exit('Aborting upload.')
return dataset
def lambda_handler(event, context):
DATASET = os.environ['DASHBOARD_DATASET_NAME']
bf = Blackfynn()
ds = bf.get_dataset(DATASET)
update(bf, ds)
return {
'statusCode': 200,
'body': json.dumps('Successfully updated the SPARC dashboard')
}
def blackfynn_get(dataset='Timeseries Dataset',collection=0,channels='sine 50 Hz'):
#establish connection with the API
bf = Blackfynn(api_token='**********************************',api_secret='**********************************',)
ds = bf.get_dataset(dataset)
print(ds)
# get all timeseries collections
ts = []
for ds_temp in ds:
ts.append(ds_temp)
# NOTE: THIS NEEDS TO BE MADE MODULAR
data = ts[collection].get_data(length='1s')
# take the data from the channel and process it to be read by javascript
#process y values
temp = np.asarray(data[channels])
java_y = []
for el in temp:
java_y.append(float(str(el)))
#generate x values
#NOTE: CURRENTLY NOT MODULAR
temp2 = np.linspace(0,1,len(temp))
java_x =[]
for el in temp2:
java_x.append(el)
#write to file
f = open('data.js', 'w')
f.write('arbData = ')
f.write(str(java_y))
f.write('\ndate = ')
f.write(repr(java_x))
f.close()
#update gitub
g = git_hub()
g.update()
print('update ran successfully')
def blackfynn_get():
# make a blackfynn API call according to threeWrapper parameters
fpipe = FilePipe()
params = fpipe.receive()
api_key = params['api_key']
api_secret = params['api_secret']
dataset = params['dataset']
collection = params['collection']
channels = params['channels']
window_from_start = params['window_from_start']
start = params['start']
end = params['end']
error = 0
# Process function input:
if start == -1 or end == -1:
has_time_window = False
else:
has_time_window = True
#establish connection with the API
try:
bf = Blackfynn(api_token=api_key, api_secret=api_secret)
except:
fpipe.send({
'error':
'Could not connect to the Blackfynn API. Check your API key and internet connection'
})
return
# get all timeseries collections
try:
ds = bf.get_dataset(dataset)
tstemp = ds.get_items_by_name(collection)
time_series = tstemp[0]
except:
fpipe.send({
'error':
'Could not find the requested Dataset and Collection. Please check your names if you have not already'
})
return
# Get data for all channels according to the length set by parameters
if has_time_window == False:
data = time_series.get_data(length=(str(window_from_start) + 's'))
else:
data = time_series.get_data(start=start, end=end)
# take the data from the channel and process it to be passed into binary (in filePipe)
# process y values
list_y = data[channels].values.tolist()
# generate x values
if has_time_window:
time = np.linspace(start, end, len(list_y))
else:
time = np.linspace(0, window_from_start, len(list_y))
list_x = time.tolist()
cache_dict = create_file_cache(data)
output = {'x': list_x, 'y': list_y, 'cache': cache_dict, 'error': False}
fpipe.send(output)
print('update ran successfully')
class DatcoreClient(object):
def __init__(self,
api_token=None,
api_secret=None,
host=None,
streaming_host=None):
# WARNING: contruction raise exception if service is not available.
# Use datacore_wrapper for safe calls
# TODO: can use https://developer.blackfynn.io/python/latest/configuration.html#environment-variables
self._bf = Blackfynn(
profile=None,
api_token=api_token,
api_secret=api_secret,
host=host,
streaming_host=streaming_host,
)
def profile(self):
"""
Returns profile of current User
"""
return self._bf.profile
def _collection_from_destination(self, destination: str):
destination_path = Path(destination)
parts = destination_path.parts
dataset_name = parts[0]
dataset = self.get_dataset(dataset_name)
if dataset is None:
return None, None
collection_id = dataset.id
collection = dataset
collections = []
if len(parts) > 1:
object_path = Path(*parts[1:])
collections = list(object_path.parts)
collection_id = ""
collection_id = _get_collection_id(dataset, collections,
collection_id)
collection = self._bf.get(collection_id)
return collection, collection_id
def _destination_from_id(self, destination_id: str):
# NOTE: .get(*) logs
# INFO:blackfynn.client.Blackfynn:Unable to retrieve object
# if destination_id refers to a Dataset
destination: Union[DataPackage,
Collection] = self._bf.get(destination_id)
if destination is None:
destination: Dataset = self._bf.get_dataset(destination_id)
return destination
def list_files_recursively(self, dataset_filter: str = ""):
files = []
for dataset in self._bf.datasets():
if not dataset_filter or dataset_filter in dataset.name:
self.list_dataset_files_recursively(files, dataset,
Path(dataset.name))
return files
def list_files_raw_dataset(self, dataset_id: str) -> List[FileMetaDataEx]:
files = [] # raw packages
_files = [] # fmds
data = {} # map to keep track of parents-child
cursor = ""
page_size = 1000
api = self._bf._api.datasets
dataset = self._bf.get_dataset(dataset_id)
if dataset is not None:
while True:
resp = api._get(
api._uri(
"/{id}/packages?cursor={cursor}&pageSize={pageSize}&includeSourceFiles={includeSourceFiles}",
id=dataset_id,
cursor=cursor,
pageSize=page_size,
includeSourceFiles=False,
))
for package in resp.get("packages", list()):
id = package["content"]["id"]
data[id] = package
files.append(package)
cursor = resp.get("cursor")
if cursor is None:
break
for f in files:
if f["content"]["packageType"] != "Collection":
filename = f["content"]["name"]
file_path = ""
file_id = f["content"]["nodeId"]
_f = f
while "parentId" in _f["content"].keys():
parentid = _f["content"]["parentId"]
_f = data[parentid]
file_path = _f["content"]["name"] + "/" + file_path
bucket_name = dataset.name
file_name = filename
file_size = 0
object_name = str(Path(file_path) / file_name)
file_uuid = str(Path(bucket_name) / object_name)
created_at = f["content"]["createdAt"]
last_modified = f["content"]["updatedAt"]
parent_id = dataset_id
if "parentId" in f["content"]:
parentId = f["content"]["parentId"]
parent_id = data[parentId]["content"]["nodeId"]
fmd = FileMetaData(
bucket_name=bucket_name,
file_name=file_name,
object_name=object_name,
location=DATCORE_STR,
location_id=DATCORE_ID,
file_uuid=file_uuid,
file_id=file_id,
raw_file_path=file_uuid,
display_file_path=file_uuid,
created_at=created_at,
last_modified=last_modified,
file_size=file_size,
)
fmdx = FileMetaDataEx(fmd=fmd, parent_id=parent_id)
_files.append(fmdx)
return _files
def list_files_raw(self, dataset_filter: str = "") -> List[FileMetaDataEx]:
_files = []
for dataset in self._bf.datasets():
_files = _files + self.list_files_raw_dataset(dataset.id)
return _files
def list_dataset_files_recursively(self, files: List[FileMetaData],
base: BaseCollection,
current_root: Path):
for item in base:
if isinstance(item, Collection):
_current_root = current_root / Path(item.name)
self.list_dataset_files_recursively(files, item, _current_root)
else:
parts = current_root.parts
bucket_name = parts[0]
file_name = item.name
file_size = 0
# lets assume we have only one file
if item.files:
file_name = Path(
item.files[0].as_dict()["content"]["s3key"]).name
file_size = item.files[0].as_dict()["content"]["size"]
# if this is in the root directory, the object_name is the filename only
if len(parts) > 1:
object_name = str(Path(*list(parts)[1:]) / Path(file_name))
else:
object_name = str(Path(file_name))
file_uuid = str(Path(bucket_name) / Path(object_name))
file_id = item.id
created_at = item.created_at
last_modified = item.updated_at
fmd = FileMetaData(
bucket_name=bucket_name,
file_name=file_name,
object_name=object_name,
location=DATCORE_STR,
location_id=DATCORE_ID,
file_uuid=file_uuid,
file_id=file_id,
raw_file_path=file_uuid,
display_file_path=file_uuid,
created_at=created_at,
last_modified=last_modified,
file_size=file_size,
)
files.append(fmd)
def create_dataset(self, ds_name, *, force_delete=False):
"""
Creates a new dataset for the current user and returns it. Returns existing one
if there is already a dataset with the given name.
Args:
ds_name (str): Name for the dataset (_,-,' ' and capitalization are ignored)
force_delete (bool, optional): Delete first if dataset already exists
"""
ds = None
with suppress(Exception):
ds = self._bf.get_dataset(ds_name)
if force_delete:
ds.delete()
ds = None
if ds is None:
ds = self._bf.create_dataset(ds_name)
return ds
def get_dataset(self, ds_name, create_if_not_exists=False):
"""
Returns dataset with the given name. Creates it if required.
Args:
ds_name (str): Name for the dataset
create_if_not_exists (bool, optional): Create first if dataset already exists
"""
ds = None
with suppress(Exception):
ds = self._bf.get_dataset(ds_name)
if ds is None and create_if_not_exists:
ds = self._bf.create_dataset(ds_name)
return ds
def delete_dataset(self, ds_name):
"""
Deletes dataset with the given name.
Args:
ds_name (str): Name for the dataset
"""
# this is not supported
ds = self.get_dataset(ds_name)
if ds is not None:
self._bf.delete(ds.id)
def exists_dataset(self, ds_name):
"""
Returns True if dataset with the given name exists.
Args:
ds_name (str): Name for the dataset
"""
ds = self.get_dataset(ds_name)
return ds is not None
def upload_file(self,
destination: str,
filepath: str,
meta_data=None) -> bool:
"""
Uploads a file to a given dataset/collection given its filepath on the host. Optionally
adds some meta data
Args:
dataset (dataset): The dataset into whioch the file shall be uploaded
filepath (path): Full path to the file
meta_data (dict, optional): Dictionary of meta data
Note:
Blackfynn postprocesses data based on filendings. If it can do that
the filenames on the server change.
"""
# parse the destination and try to find the package_id to upload to
collection, collection_id = self._collection_from_destination(
destination)
if collection is None:
return False
files = [
filepath,
]
self._bf._api.io.upload_files(collection,
files,
display_progress=True,
use_agent=False)
collection.update()
if meta_data is not None:
for f in files:
filename = os.path.basename(f)
package = self.get_package(collection, filename)
if package is not None:
self._update_meta_data(package, meta_data)
return True
def _update_meta_data(self, package, meta_data):
"""
Updates or replaces metadata for a package
Args:
package (package): The package for which the meta data needs update
meta_data (dict): Dictionary of meta data
"""
for key in meta_data.keys():
package.set_property(key, meta_data[key], category="simcore")
package.update()
def download_file(self, source, filename, destination_path):
"""
Downloads a frile from a source dataset/collection given its filename. Stores
it under destination_path
Args:
source (dataset/collection): The dataset or collection to donwload from
filename (str): Name of the file
destination__apth (str): Path on host for storing file
"""
url = self.download_link(source, filename)
if url:
_file = urllib.URLopener() # nosec
_file.retrieve(url, destination_path)
return True
return False
def download_link(self, destination, filename):
"""
returns presigned url for download, destination is a dataset or collection
"""
collection, collection_id = self._collection_from_destination(
destination)
for item in collection:
if isinstance(item, DataPackage):
if Path(item.files[0].as_dict()["content"]
["s3key"]).name == filename:
file_desc = self._bf._api.packages.get_sources(item.id)[0]
url = self._bf._api.packages.get_presigned_url_for_file(
item.id, file_desc.id)
return url
return ""
def download_link_by_id(self, file_id):
"""
returns presigned url for download of a file given its file_id
"""
url = ""
filename = ""
package = self._bf.get(file_id)
if package is not None:
filename = Path(
package.files[0].as_dict()["content"]["s3key"]).name
file_desc = self._bf._api.packages.get_sources(file_id)[0]
url = self._bf._api.packages.get_presigned_url_for_file(
file_id, file_desc.id)
return url, filename
def get_package(self, source, filename):
"""
Returns package from source by name if exists
Args:
source (dataset/collection): The dataset or collection to donwload from
filename (str): Name of the file
"""
source.update()
for item in source:
if item.name == filename:
return item
return None
def delete_file(self, destination, filename):
"""
Deletes file by name from destination by name
Args:
destination (dataset/collection): The dataset or collection to delete from
filename (str): Name of the file
"""
collection, collection_id = self._collection_from_destination(
destination)
if collection is None:
return False
collection.update()
for item in collection:
if isinstance(item, DataPackage):
if Path(item.files[0].as_dict()["content"]
["s3key"]).name == filename:
self._bf.delete(item)
return True
return False
def delete_file_by_id(self, id: str) -> bool:
"""
Deletes file by id
Args:
datcore id for the file
"""
package: DataPackage = self._bf.get(id)
package.delete()
return not package.exists
def delete_files(self, destination):
"""
Deletes all files in destination
Args:
destination (dataset/collection): The dataset or collection to delete
"""
collection, collection_id = self._collection_from_destination(
destination)
if collection is None:
return False
collection.update()
for item in collection:
self._bf.delete(item)
def update_meta_data(self, dataset, filename, meta_data):
"""
Updates metadata for a file
Args:
dataset (package): Which dataset
filename (str): Which file
meta_data (dict): Dictionary of meta data
"""
filename = os.path.basename(filename)
package = self.get_package(dataset, filename)
if package is not None:
self._update_meta_data(package, meta_data)
def get_meta_data(self, dataset, filename):
"""
Returns metadata for a file
Args:
dataset (package): Which dataset
filename (str): Which file
"""
meta_data = {}
filename = os.path.basename(filename)
package = self.get_package(dataset, filename)
if package is not None:
meta_list = package.properties
for m in meta_list:
meta_data[m.key] = m.value
return meta_data
def delete_meta_data(self, dataset, filename, keys=None):
"""
Deletes specified keys in meta data for source/filename.
Args:
dataset (package): Which dataset
filename (str): Which file
keys (list of str, optional): Deletes specified keys, deletes
all meta data if None
"""
filename = os.path.basename(filename)
package = self.get_package(dataset, filename)
if package is not None:
if keys is None:
for p in package.properties:
package.remove_property(p.key, category="simcore")
else:
for k in keys:
package.remove_property(k, category="simcore")
def search(self, what, max_count):
"""
Seraches a thing in the database. Returns max_count results
Args:
what (str): query
max_count (int): Max number of results to return
"""
return self._bf.search(what, max_count)
def upload_file_to_id(self, destination_id: str, filepath: str):
"""
Uploads file to a given dataset/collection by id given its filepath on the host
adds some meta data.
Returns the id for the newly created resource
Note: filepath could be an array
Args:
destination_id : The dataset/collection id into which the file shall be uploaded
filepath (path): Full path to the file
"""
_id = ""
destination = self._destination_from_id(destination_id)
if destination is None:
return _id
files = [
filepath,
]
try:
# TODO: PC->MAG: should protected API
# TODO: add new agent SEE https://developer.blackfynn.io/python/latest/CHANGELOG.html#id31
result = self._bf._api.io.upload_files(destination,
files,
display_progress=True,
use_agent=False)
if result and result[0] and "package" in result[0][0]:
_id = result[0][0]["package"]["content"]["id"]
except Exception:
logger.exception("Error uploading file to datcore")
return _id
def create_collection(self, destination_id: str, collection_name: str):
"""
Create a empty collection within destination
Args:
destination_id : The dataset/collection id into which the file shall be uploaded
filepath (path): Full path to the file
"""
destination = self._destination_from_id(destination_id)
_id = ""
if destination is None:
return _id
new_collection = Collection(collection_name)
destination.add(new_collection)
new_collection.update()
destination.update()
_id = new_collection.id
return _id
def list_datasets(self) -> DatasetMetaDataVec:
data = []
for dataset in self._bf.datasets():
dmd = DatasetMetaData(dataset_id=dataset.id,
display_name=dataset.name)
data.append(dmd)
return data
sys.exit()
elif opt in '-l':
for ds in dsets:
printf("%s\n", ds[0])
sys.exit()
elif opt in "-f":
filename = arg
FILE = True
if not file_exists(filename):
printf("file, %s, does not exist.\n", filename)
sys.exit()
elif opt in '-d':
DATASET = True
dsetname = arg
try:
dset = bf.get_dataset(dsdict[arg])
except:
printf("Dataset, %s, does NOT exist.\n", arg)
sys.exit()
# Using single Dataset
if not ALL and SOURCE and DESTINATION and DATASET:
destination = locate_path(dset, dest)
source = locate_path(dset, src)
bf.move(destination, source)
printf("%s: %s moved to %s\n", dsetname, src, dest)
# Using a file containing Dataset names
elif not ALL and not DATASET and FILE:
with open(filename) as f:
fdsets = f.read().splitlines()
except getopt.GetoptError:
printf("%s\n", syntax())
sys.exit()
dsets, dsdict = get_datasets()
for opt, arg in opts:
if opt == '-h':
printf("%s\n", syntax())
sys.exit()
elif opt in '-l':
for ds in dsets:
printf("%s\n", ds[0])
sys.exit()
elif opt in '-d':
dset = bf.get_dataset(dsdict[arg])
elif opt in '-n':
if db_exists(arg, dsets):
printf("Dataset %s already exists. Can not continue.\n", arg)
EXISTS = True
sys.exit()
else:
printf("Creating new dataset: %s\n", arg)
bf.create_dataset(arg)
newdset = bf.get_dataset(arg)
create_duplicate(dset, newdset)
class BlackfynnDataModel(object):
def __init__(self):
self._settings = {'active-profile': ''}
self._cache = {}
self._bf = None
def addProfile(self, profile):
self._settings[profile['name']] = {'api_token': profile['token'], 'api_secret': profile['secret']}
def setActiveProfile(self, profile_name):
self._settings['active-profile'] = profile_name
def getActiveProfile(self):
return self._settings['active-profile']
def getExistingProfileNames(self):
profile_names = [*self._settings]
profile_names.remove('active-profile')
return profile_names
def _getBlackfynn(self, profile_name):
api_key = self._settings[profile_name]['api_token']
api_secret = self._settings[profile_name]['api_secret']
print('[{0}]:[{1}]'.format(api_key, api_secret))
self._bf = Blackfynn(api_token=api_key, api_secret=api_secret)
return self._bf
def getDatasets(self, profile_name, refresh=False):
if profile_name in self._cache and not refresh:
datasets = self._cache[profile_name]['datasets']
elif refresh:
bf = self._getBlackfynn(profile_name)
datasets = bf.datasets()
if profile_name in self._cache:
self._cache[profile_name]['datasets'] = datasets
else:
self._cache[profile_name] = {'datasets': datasets}
else:
datasets = []
return datasets
def getDataset(self, profile_name, dataset_name, refresh=False):
if profile_name in self._cache and dataset_name in self._cache[profile_name] and not refresh:
dataset = self._cache[profile_name][dataset_name]
elif refresh:
bf = self._getBlackfynn(profile_name)
dataset = bf.get_dataset(dataset_name)
self._cache[profile_name][dataset_name] = dataset
else:
dataset = []
return dataset
def getTimeseriesData(self, profile_name, dataset_name, timeseries_name):
for stored_dataset in self._cache[profile_name][dataset_name]:
if stored_dataset.name == timeseries_name:
timeseries_dframe = stored_dataset.get_data(length='16s')
cache_output = self._create_file_cache(timeseries_dframe)
absolute_timeseries_values = timeseries_dframe.axes[0]
relative_times = []
for time in absolute_timeseries_values:
relative_times.append( round( time.timestamp() - absolute_timeseries_values[0].timestamp(), 6) )
return [cache_output, relative_times]
def _create_file_cache(self, data_frame):
cache_dictionary = {}
keys = natsorted(data_frame.keys()) # Sort the keys in 'natural' order
for key in keys:
cache_dictionary[key] = data_frame[key].values.tolist()
return cache_dictionary
def uploadRender(self, filePath):
# uploadRender: Takes a given file path and uploads it to blackfynn in a folder called 'Zinc Exports' for the
# user currently logged in.
try:
ds = self._bf.get_dataset('Zinc Exports')
except:
self._bf.create_dataset('Zinc Exports')
ds = self._bf.get_dataset('Zinc Exports')
ds.upload(filePath)
def getSettings(self):
return self._settings
def setSettings(self, settings):
print('set settings {0}',format(settings))
self._settings.update(settings)
except getopt.GetoptError:
printf("%s\n", syntax())
sys.exit()
dsets, dsdict = get_datasets()
for opt, arg in opts:
if opt == '-h':
printf("%s\n", syntax())
sys.exit()
elif opt == '-i':
CASE=False
printf("Note: case-insensitive compares\n")
elif opt in ('-d'):
try:
dset = bf.get_dataset(dsdict[arg])
except:
printf("Dataset, %s, does NOT exist.\n", arg)
sys.exit()
elif opt == '--all':
ALL = True
dsets = []
for ds in bf.datasets():
if 'HPAP-' in ds.name: dsets.append(ds)
dsets.sort(key = lambda x: x.name)
elif opt in ('-l'):
for ds in dsets: printf("%s\n", ds[0])
sys.exit()
elif opt in ('--data'):
FILE = True
elif opt in ('-p'):
def convert_ncs2bfts(dataFolder,
resultFolder=None,
bfFileName=None,
dsName=None,
fs=None):
"""
param dataFolder: folder containing ncs files
param resultFolder: folder to contain results
param bfFileName: name to save generated bfts file
param dsName: name (or id) of dataset
param fs: sampling rate
return: _____
"""
dataFolder = os.path.abspath(dataFolder)
if not bfFileName:
bfFileName = os.path.basename(dataFolder) + '.bfts'
if resultFolder:
resultFolder = os.path.abspath(resultFolder)
resultFile = os.path.join(resultFolder, bfFileName)
else:
resultFile = bfFileName
#
if os.path.isfile(resultFile):
print(bfFileName, 'exists')
else:
print('Converting to', bfFileName, '...')
chls = OrderedDict() # dictionary to store channel values
for chFile in os.listdir(dataFolder):
if chFile.endswith('ncs'):
ncs = ncs2py.load_ncs(
os.path.join(dataFolder, chFile)
) # import neuralynx data. NOTE: import stores information as a dictionary
rawData = ncs['data']
rawData = resample_poly(rawData, 1.0,
ncs['sampling_rate'] / fs)
chls.update({'ch' + chFile.split('.')[0][3:]: rawData})
#
TimeCreated = [
line.strip() for line in ncs['raw_header'].split('\r\n')
if line != '' if 'TimeCreated' == line.strip()[1:12]
][0]
TimeCreated = ncs2py.parse_neuralynx_time_string(TimeCreated)
TimeCreated = (TimeCreated -
datetime(1970, 1, 1)).total_seconds() * (1e6)
timeVec = ncs['timestamp'] + TimeCreated
timeVec = arange(timeVec[0],
timeVec[-1], (1.0 / fs) * (1e6),
dtype=int64)
sampleSize = timeVec.shape[0]
#
df = DataFrame(chls)[0:sampleSize]
df.insert(0, 'timeStamp', timeVec)
df.to_csv(resultFile, index=False)
#
if dsName:
bf = Blackfynn()
ds = bf.get_dataset(dsName)
if os.path.basename(resultFile)[:-5] in ds.get_items_names():
print(bfFileName, 'uploaded')
else:
print('uploading', bfFileName, 'to Blackfynn...')
ds.upload(resultFile)
def blackfynn_cli():
args = docopt(__doc__,
version='bf version {}'.format(blackfynn.__version__),
options_first=True)
# Test for these two commands first as they
# do not require a Blackfynn client
if args['<command>'] in ['help', None]:
print((__doc__.strip('\n')))
return
if args['<command>'] == 'profile':
from blackfynn.cli import bf_profile
bf_profile.main()
return
# Display warning message if config.ini is not found
settings = Settings(
) # create a dummy settings object to load environment variables and defaults only
if not os.path.exists(settings.config_file):
print(
"\033[31m* Warning: No config file found, run 'bf profile' to start the setup assistant\033[0m"
)
# Try to use profile specified by --profile, exit if invalid
try:
bf = Blackfynn(args['--profile'])
except Exception as e:
exit(e)
#Try to use dataset specified by --dataset, exit if invalid
try:
if args['--dataset'] is not None:
dataset = bf.get_dataset(args['--dataset'])
set_working_dataset(dataset.id)
except Exception as e:
exit(e)
if args['<command>'] == 'status':
from blackfynn.cli import bf_status
bf_status.main(bf)
elif args['<command>'] == 'use':
from . import bf_use
bf_use.main(bf)
elif args['<command>'] == 'init':
from . import bf_init
bf_init.main(bf)
elif args['<command>'] in ['datasets', 'ds']:
from . import bf_datasets
bf_datasets.main(bf)
elif args['<command>'] in ['organizations', 'orgs']:
from . import bf_organizations
bf_organizations.main(bf)
elif args['<command>'] in ['share', 'unshare', 'collaborators']:
from . import bf_share
bf_share.main(bf)
elif args['<command>'] == 'cache':
from . import bf_cache
bf_cache.main(bf)
elif args['<command>'] == 'create':
from . import bf_create
bf_create.main(bf)
elif args['<command>'] == 'delete':
from . import bf_delete
bf_delete.main(bf)
elif args['<command>'] == 'move':
from . import bf_move
bf_move.main(bf)
elif args['<command>'] == 'rename':
from . import bf_rename
bf_rename.main(bf)
elif args['<command>'] == 'props':
from . import bf_props
bf_props.main(bf)
elif args['<command>'] == 'get':
from . import bf_get
bf_get.main(bf)
elif args['<command>'] == 'where':
from . import bf_where
bf_where.main(bf)
elif args['<command>'] == 'upload':
from . import bf_upload
bf_upload.main(bf)
elif args['<command>'] == 'append':
from . import bf_append
bf_append.main(bf)
elif args['<command>'] == 'search':
from . import bf_search
bf_search.main(bf)
else:
exit("Invalid command: '{}'\nSee 'bf help' for available commands".
format(args['<command>']))
import glob
import os
import time
import sys
if sys.platform == 'win32':
rootPath = 'R:\\'
else:
rootPath = os.path.join('//', 'media', 'rnelshare')
sys.path.append(
os.path.join(rootPath, 'users', 'amn69', 'Projects', 'cat', 'selectivity',
'surface paper', 'v2018'))
import helperFcns as hf
bf = Blackfynn('lumbar_selectivity')
catDS = bf.get_dataset('N:dataset:1cc6b671-0dea-4aab-ad30-ed3884e17028')
db = hf.db
collection = db.blackfynnUpload
for iSub in ['HA04'
]: #['Electro','Freeze','HA02','HA04','Galactus','Hobgoblin']:
print iSub
if collection.find({'subject': iSub}).count() == 0:
subjFolder = catDS.create_collection(iSub)
else:
subjFolder = catDS.get_items_by_name(iSub)[0]
targetSessions = sorted(hf.PWbySession[iSub].keys())
for iSesh in targetSessions:
print iSesh
class DatcoreClient(object):
def __init__(self, api_token=None, api_secret=None, host=None, streaming_host=None):
self.client = Blackfynn(profile=None, api_token=api_token, api_secret=api_secret,
host=host, streaming_host=streaming_host)
def _context(self):
"""
Returns current organizational context
"""
return self.client.context
def profile(self):
"""
Returns profile of current User
"""
return self.client.profile
def organization(self):
"""
Returns organization name
"""
return self.client.context.name
def list_datasets(self):
ds = []
for item in self.client.datasets():
ds.append(item.name)
return ds
def list_files(self):
files = []
for ds in self.client.datasets():
for item in ds:
files.append(os.path.join(ds.name, item.name))
return files
def create_dataset(self, ds_name, force_delete=False):
"""
Creates a new dataset for the current user and returns it. Returns existing one
if there is already a dataset with the given name.
Args:
ds_name (str): Name for the dataset (_,-,' ' and capitalization are ignored)
force_delete (bool, optional): Delete first if dataset already exists
"""
ds = None
try:
ds = self.client.get_dataset(ds_name)
if force_delete:
delete_dataset(ds)
ds = None
except Exception: # pylint: disable=W0703
pass
if ds is None:
ds = self.client.create_dataset(ds_name)
return ds
def get_dataset(self, ds_name, create_if_not_exists=False):
"""
Returns dataset with the given name. Creates it if required.
Args:
ds_name (str): Name for the dataset
create_if_not_exists (bool, optional): Create first if dataset already exists
"""
ds = None
try:
ds = self.client.get_dataset(ds_name)
except Exception: # pylint: disable=W0703
pass
if ds is None and create_if_not_exists:
ds = self.client.create_dataset(ds_name)
return ds
def delete_dataset(self, ds_name):
"""
Deletes dataset with the given name.
Args:
ds_name (str): Name for the dataset
"""
# this is not supported
ds = self.get_dataset(ds_name)
if ds is not None:
self.client.delete(ds.id)
def exists_dataset(self, ds_name):
"""
Returns True if dataset with the given name exists.
Args:
ds_name (str): Name for the dataset
"""
ds = self.get_dataset(ds_name)
return ds is not None
def upload_file(self, dataset, filepaths, meta_data = None):
"""
Uploads a file to a given dataset given its filepath on the host. Optionally
adds some meta data
Args:
dataset (dataset): The dataset into whioch the file shall be uploaded
filepath (path): Full path to the file
meta_data (dict, optional): Dictionary of meta data
Note:
Blackfynn postprocesses data based on filendings. If it can do that
the filenames on the server change. This makes it difficult to retrieve
them back by name (see get_sources below). Also, for now we assume we have
only single file data.
"""
if isinstance(filepaths, list):
files = filepaths
else:
files = [filepaths]
# pylint: disable = E1101
self.client._api.io.upload_files(dataset, files, display_progress=True)
dataset.update()
if meta_data is not None:
filename = os.path.basename(filepath)
package = self.get_package(dataset, filename)
if package is not None:
self._update_meta_data(package, meta_data)
def _update_meta_data(self, package, meta_data):
"""
Updates or replaces metadata for a package
Args:
package (package): The package for which the meta data needs update
meta_data (dict): Dictionary of meta data
"""
for key in meta_data.keys():
package.set_property(key, meta_data[key], category='simcore')
package.update()
def download_file(self, source, filename, destination_path):
"""
Downloads a frile from a source dataset/collection given its filename. Stores
it under destination_path
Args:
source (dataset/collection): The dataset or collection to donwload from
filename (str): Name of the file
destination__apth (str): Path on host for storing file
"""
# pylint: disable = E1101
url = self.download_link(source, filename)
if url:
_file = urllib.URLopener()
_file.retrieve(url, destination_path)
return True
return False
def download_link(self, source, filename):
"""
returns presigned url for download, source is a dataset
"""
# pylint: disable = E1101
for item in source:
if item.name == filename:
file_desc = self.client._api.packages.get_sources(item.id)[0]
url = self.client._api.packages.get_presigned_url_for_file(item.id, file_desc.id)
return url
return ""
def exists_file(self, source, filename):
"""
Checks if file exists in source
Args:
source (dataset/collection): The dataset or collection to donwload from
filename (str): Name of the file
"""
source.update()
for item in source:
if item.name == filename:
return True
return False
def get_package(self, source, filename):
"""
Returns package from source by name if exists
Args:
source (dataset/collection): The dataset or collection to donwload from
filename (str): Name of the file
"""
source.update()
for item in source:
if item.name == filename:
return item
return None
def delete_file(self, source, filename):
"""
Deletes file by name from source by name
Args:
source (dataset/collection): The dataset or collection to donwload from
filename (str): Name of the file
"""
source.update()
for item in source:
if item.name == filename:
self.client.delete(item)
def delete_files(self, source):
"""
Deletes all files in source
Args:
source (dataset/collection): The dataset or collection to donwload from
"""
source.update()
for item in source:
self.client.delete(item)
def update_meta_data(self, dataset, filename, meta_data):
"""
Updates metadata for a file
Args:
dataset (package): Which dataset
filename (str): Which file
meta_data (dict): Dictionary of meta data
"""
filename = os.path.basename(filename)
package = self.get_package(dataset, filename)
if package is not None:
self._update_meta_data(package, meta_data)
def get_meta_data(self, dataset, filename):
"""
Returns metadata for a file
Args:
dataset (package): Which dataset
filename (str): Which file
"""
meta_data = {}
filename = os.path.basename(filename)
package = self.get_package(dataset, filename)
if package is not None:
meta_list = package.properties
for m in meta_list:
meta_data[m.key] = m.value
return meta_data
def delete_meta_data(self, dataset, filename, keys=None):
"""
Deletes specified keys in meta data for source/filename.
Args:
dataset (package): Which dataset
filename (str): Which file
keys (list of str, optional): Deletes specified keys, deletes
all meta data if None
"""
filename = os.path.basename(filename)
package = self.get_package(dataset, filename)
if package is not None:
if keys is None:
for p in package.properties:
package.remove_property(p.key, category='simcore')
else:
for k in keys:
package.remove_property(k, category='simcore')
def search(self, what, max_count):
"""
Seraches a thing in the database. Returns max_count results
Args:
what (str): query
max_count (int): Max number of results to return
"""
return self.client.search(what, max_count)
if outdir == '.': outdir = os.getcwd()
elif opt in ('-l'):
for ds in dsets: printf("%s\n", ds[0])
sys.exit()
elif opt in ('-c'):
CATEGORY = True
cat = arg
if cat not in categories:
printf("Category, %s, does NOT exist.\n", arg)
sys.exit()
elif opt in ('-d'):
DATASET = True
try:
dsname = arg
if dsname.lower() != "all":
dset = bf.get_dataset(dsdict[dsname])
else:
dset = "all"
except:
printf("Dataset, %s, does NOT exist.\n", arg)
sys.exit()
elif opt == '-q':
QUICKSYNC = True
#################
# start the sync
#################
if DATASET and dsname != "all":
printf("Gathering Collections from %s ...\n",dset.name)
collections = list()
dslist = get_collections(dset,collections)
dspaths,relpaths = create_paths(dsname, outdir, dslist)
import click
import sparc_dash
from blackfynn import Blackfynn
bf = Blackfynn('sparc-consortium')
ds = bf.get_dataset('SPARC Datasets')
@click.group()
def cli():
pass
@click.command()
def clear():
print('Clearing')
out = sparc_dash.clearRecords(ds)
@click.command()
def create_models():
"""Example script."""
out = sparc_dash.create_models(ds)
@click.command()
def update():
"""Example script."""
out = sparc_dash.update(bf, ds)
