def upload_zipped_flat_media_files(
gc: GirderClient,
manager: JobManager,
folderId: str,
working_directory: Path,
create_subfolder=False,
):
"""Takes a flat folder of media files and/or annotation and generates a dataset from it"""
listOfFileNames = os.listdir(working_directory)
validation = gc.sendRestRequest('POST',
'/dive_dataset/validate_files',
json=listOfFileNames)
root_folderId = folderId
default_fps = gc.getFolder(root_folderId).get(
f"meta.{constants.FPSMarker}", -1)
if validation.get('ok', False):
manager.write(f"Annotations: {validation['annotations']}\n")
manager.write(f"Media: {validation['media']}\n")
dataset_type = validation['type']
manager.write(f"Type: {dataset_type}\n")
if create_subfolder != '':
sub_folder = gc.createFolder(
folderId,
create_subfolder,
reuseExisting=True,
)
root_folderId = str(sub_folder["_id"])
# Upload all resulting items back into the root folder
manager.updateStatus(JobStatus.PUSHING_OUTPUT)
# create a source folder to place the zipFile inside of
gc.upload(f'{working_directory}/*', root_folderId)
if dataset_type == constants.ImageSequenceType and default_fps == -1:
default_fps = 1
gc.addMetadataToFolder(
str(root_folderId),
{
constants.TypeMarker: dataset_type,
constants.FPSMarker: default_fps
},
)
# After uploading the default files we do a the postprocess for video conversion now
gc.sendRestRequest("POST",
f"/dive_rpc/postprocess/{str(root_folderId)}")
else:
manager.write(f"Message: {validation['message']}\n")
raise Exception("Could not Validate media Files")
def import_calc(config):
try:
target_port = None
if config.port:
target_port = config.port
target_scheme = None
if config.scheme:
target_scheme = config.scheme
target_apiroot = None
if config.apiroot:
target_apiroot = config.apiroot
client = GirderClient(host=config.host, port=target_port,
scheme=target_scheme, apiRoot=target_apiroot)
client.authenticate(apiKey=config.apiKey)
me = client.get('/user/me')
if not me:
print('Error: Girder token invalid, please verify')
return
folderParams = {
'parentId': me['_id'],
'parentType': 'user',
'name': 'Private'
}
# Get the private folder id first
folder = next(client.listResource('folder', folderParams))
folder = next(client.listFolder(me['_id'], 'user', 'Private'))
for file_name in config.datafile:
print ('\nUploading ' + file_name)
file_id = {}
with open(file_name, 'r') as fp:
fileNameBase = os.path.basename(file_name)
size = os.path.getsize(file_name)
file_id = client.uploadFile(folder['_id'], fp, fileNameBase,
size, 'folder')
body = {
'fileId': file_id['_id']
}
if config.public:
body['public'] = True
mol = client.sendRestRequest('POST', 'molecules', data=json.dumps(body))
if mol and '_id' in mol:
config.moleculeId = mol['_id']
print('Molecule ID: ' + mol['_id'])
else:
print(mol)
except HttpError as error:
print(error.responseText, file=sys.stderr)
from girder_client import GirderClient
c = GirderClient(host='localhost', port=9000)
# Create an admin user if there isn't one
try:
c.authenticate('girder', 'girder')
except:
c.sendRestRequest(
'POST', 'user', {
"login": "******",
"password": "******",
"email": "*****@*****.**",
"firstName": "Girder",
"lastName": "Admin"
})
c.authenticate('girder', 'girder')
# Create a tangelo hub collection if there isn't one
coll_search = c.get('resource/search',
parameters={
'q': 'Default',
'types': '["collection"]'
})
if len(coll_search["collection"]) == 0:
collection = c.post('collection',
parameters={
'name': 'Default',
'description': 'Default workspace',
'public': 'true'
})
from girder_client import GirderClient
c = GirderClient(host="localhost", port=9000)
# Create an admin user if there isn't one
try:
c.authenticate("girder", "girder")
except:
c.sendRestRequest(
"POST",
"user",
{
"login": "******",
"password": "******",
"email": "*****@*****.**",
"firstName": "Girder",
"lastName": "Admin",
},
)
c.authenticate("girder", "girder")
# Create a tangelo hub collection if there isn't one
coll_search = c.get("resource/search", parameters={"q": "Default", "types": '["collection"]'})
if len(coll_search["collection"]) == 0:
collection = c.post(
"collection", parameters={"name": "Default", "description": "Default workspace", "public": "true"}
)
c.post(
"folder",
parameters={
"parentType": "collection",
