def _create_folder(vault, full_path, tags=None):
"""Create a folder if not exists"""
full_path, path_dict = \
Object.validate_full_path(full_path)
folder_name = path_dict['filename']
try:
new_obj = Object.get_by_full_path(full_path)
if not new_obj.is_folder:
raise SolveError('Object type {} already exists at location: {}'
.format(new_obj.object_type, full_path))
except NotFoundError:
# Create the folder
if path_dict['parent_path'] == '/':
parent_object_id = None
else:
parent = Object.get_by_full_path(path_dict['parent_full_path'],
assert_type='folder')
parent_object_id = parent.id
# Make the API call
new_obj = Object.create(
vault_id=vault.id,
parent_object_id=parent_object_id,
object_type='folder',
filename=folder_name,
tags=tags or []
)
print('Notice: Folder created for {0} at {1}'
.format(folder_name, new_obj.path))
return new_obj
def upload(args):
"""
Given a folder or file, upload all the folders and files contained
within it, skipping ones that already exist on the remote.
"""
base_remote_path, path_dict = Object.validate_full_path(
args.full_path, vault=args.vault, path=args.path)
# Assert the vault exists and is accessible
vault = Vault.get_by_full_path(path_dict['vault_full_path'])
# If not the vault root, validate remote path exists and is a folder
if path_dict['path'] != '/':
Object.get_by_full_path(base_remote_path, assert_type='folder')
for local_path in args.local_path:
local_path = local_path.rstrip('/')
local_start = os.path.basename(local_path)
if os.path.isdir(local_path):
_upload_folder(path_dict['domain'], vault,
base_remote_path, local_path, local_start)
else:
Object.upload_file(local_path, path_dict['path'],
vault.full_path)
def upload(args):
"""
Given a folder or file, upload all the folders and files contained
within it, skipping ones that already exist on the remote.
"""
base_remote_path, path_dict = Object.validate_full_path(args.full_path,
vault=args.vault,
path=args.path)
# Assert the vault exists and is accessible
vault = Vault.get_by_full_path(path_dict['vault_full_path'])
# If not the vault root, validate remote path exists and is a folder
if path_dict['path'] != '/':
Object.get_by_full_path(base_remote_path, assert_type='folder')
for local_path in args.local_path:
local_path = local_path.rstrip('/')
local_start = os.path.basename(local_path)
if os.path.isdir(local_path):
_upload_folder(path_dict['domain'], vault, base_remote_path,
local_path, local_start)
else:
Object.upload_file(local_path, path_dict['path'], vault.full_path)
def get_by_full_path(cls, full_path, **kwargs):
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
obj = Object.get_by_full_path(full_path, assert_type='dataset',
client=_client)
return Dataset.retrieve(obj['dataset_id'], client=_client, **kwargs)
def _get_parent_folder(self, path):
from solvebio import Object
return Object.get_by_full_path(
':'.join([self.full_path, path]),
assert_type='folder',
client=self._client
)
def _download(full_path, local_folder_path, dry_run=False):
"""
Given a folder or file, download all the files contained
within it (not recursive).
"""
if dry_run:
print('Running in dry run mode. Not downloading any files.')
local_folder_path = os.path.expanduser(local_folder_path)
if not os.path.exists(local_folder_path):
print("Creating local download folder {}".format(local_folder_path))
if not dry_run:
if not os.path.exists(local_folder_path):
os.makedirs(local_folder_path)
# API will determine depth based on number of "/" in the glob
# Add */** to match in any vault (recursive)
files = Object.all(glob=full_path, limit=1000, object_type='file')
if not files:
print("No file(s) found at --full-path {}\nIf attempting to download "
"multiple files, try using a glob 'vault:/path/folder/*'"
.format(full_path))
for file_ in files:
if not dry_run:
file_.download(local_folder_path)
print('Downloaded: {} to {}/{}'.format(
file_.full_path, local_folder_path, file_.filename))
def get_by_full_path(cls, full_path, **kwargs):
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
obj = Object.get_by_full_path(full_path,
assert_type='dataset',
client=_client)
return Dataset.retrieve(obj['dataset_id'], client=_client, **kwargs)
def _object_list_helper(self, **params):
from solvebio import Object
params.update({
'vault_id': self.id,
})
items = Object.all(client=self._client, **params)
return items
def _object_list_helper(self, **params):
from solvebio import Object
params.update({
'vault_id': self.id,
})
items = Object.all(client=self._client, **params)
return items
def tag(args):
"""Tags a list of paths with provided tags"""
objects = []
for full_path in args.full_path:
# API will determine depth based on number of "/" in the glob
# Add */** to match in any vault (recursive)
objects.extend(list(Object.all(
glob=full_path, permission='write', limit=1000)))
seen_vaults = {}
taggable_objects = []
exclusions = args.exclude or []
# Runs through all objects to get tagging candidates
# taking exclusions and object_type filters into account.
for object_ in objects:
if should_exclude(object_.full_path, exclusions,
dry_run=args.dry_run):
continue
if should_tag_by_object_type(args, object_):
taggable_objects.append(object_)
seen_vaults[object_.vault_id] = 1
if not taggable_objects:
print('No taggable objects found at provided locations.')
return
# If args.no_input, changes will be applied immediately.
# Otherwise, prints the objects and if tags will be applied or not
for object_ in taggable_objects:
object_.tag(
args.tag, remove=args.remove,
dry_run=args.dry_run, apply_save=args.no_input)
# Prompts for confirmation and then runs with apply_save=True
if not args.no_input:
print('')
res = raw_input(
'Are you sure you want to apply the above changes to '
'{} object(s) in {} vault(s)? [y/N] '
.format(len(taggable_objects), len(seen_vaults.keys()))
)
print('')
if res.strip().lower() != 'y':
print('Not applying changes.')
return
for object_ in taggable_objects:
object_.tag(
args.tag, remove=args.remove,
dry_run=args.dry_run, apply_save=True)
def get_or_create_uploads_path(cls, **kwargs):
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
v = cls.get_personal_vault(client=_client)
default_path = 'Uploads'
full_path = '{0}:/{1}'.format(v.full_path, default_path)
try:
upload_dir = Object.get_by_full_path(full_path,
assert_type='folder',
client=_client)
except NotFoundError:
print(
"Uploads directory not found. Creating {0}".format(full_path))
upload_dir = Object.create(vault_id=v.id,
object_type='folder',
filename=default_path,
client=_client)
return upload_dir.path
def get_or_create_uploads_path(cls, **kwargs):
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
v = cls.get_personal_vault(client=_client)
default_path = 'Uploads'
full_path = '{0}:/{1}'.format(v.full_path, default_path)
try:
upload_dir = Object.get_by_full_path(
full_path, assert_type='folder', client=_client)
except NotFoundError:
print("Uploads directory not found. Creating {0}"
.format(full_path))
upload_dir = Object.create(
vault_id=v.id,
object_type='folder',
filename=default_path,
client=_client
)
return upload_dir.path
def import_file(args):
"""
Given a dataset and a local path, upload and import the file(s).
Command arguments (args):
* create_dataset
* template_id
* full_path
* vault (optional, overrides the vault in full_path)
* path (optional, overrides the path in full_path)
* commit_mode
* capacity
* file (list)
* follow (default: False)
"""
full_path, path_dict = Object.validate_full_path(
args.full_path, vault=args.vault, path=args.path)
# Ensure the dataset exists. Create if necessary.
if args.create_dataset:
dataset = create_dataset(args)
else:
try:
dataset = solvebio.Dataset.get_by_full_path(full_path)
except solvebio.SolveError as e:
if e.status_code != 404:
raise e
print("Dataset not found: {0}".format(full_path))
print("Tip: use the --create-dataset flag "
"to create one from a template")
sys.exit(1)
# Generate a manifest from the local files
manifest = solvebio.Manifest()
manifest.add(*args.file)
# Create the manifest-based import
imp = solvebio.DatasetImport.create(
dataset_id=dataset.id,
manifest=manifest.manifest,
commit_mode=args.commit_mode
)
if args.follow:
imp.follow()
else:
mesh_url = 'https://my.solvebio.com/activity/'
print("Your import has been submitted, view details at: {0}"
.format(mesh_url))
def import_file(args):
"""
Given a dataset and a local path, upload and import the file(s).
Command arguments (args):
* create_dataset
* template_id
* full_path
* vault (optional, overrides the vault in full_path)
* path (optional, overrides the path in full_path)
* commit_mode
* capacity
* file (list)
* follow (default: False)
"""
full_path, path_dict = Object.validate_full_path(args.full_path,
vault=args.vault,
path=args.path)
# Ensure the dataset exists. Create if necessary.
if args.create_dataset:
dataset = create_dataset(args)
else:
try:
dataset = solvebio.Dataset.get_by_full_path(full_path)
except solvebio.SolveError as e:
if e.status_code != 404:
raise e
print("Dataset not found: {0}".format(full_path))
print("Tip: use the --create-dataset flag "
"to create one from a template")
sys.exit(1)
# Generate a manifest from the local files
manifest = solvebio.Manifest()
manifest.add(*args.file)
# Create the manifest-based import
imp = solvebio.DatasetImport.create(dataset_id=dataset.id,
manifest=manifest.manifest,
commit_mode=args.commit_mode)
if args.follow:
imp.follow()
else:
mesh_url = 'https://my.solvebio.com/activity/'
print("Your import has been submitted, view details at: {0}".format(
mesh_url))
def create_folder(self, filename, **params):
from solvebio import Object
path = params.pop('path', None)
if path and path != '/':
parent_object = self._get_parent_folder(path)
params['parent_object_id'] = parent_object.id
params.update({
'filename': filename,
'vault_id': self.id,
'object_type': 'folder'
})
return Object.create(client=self._client, **params)
def get_or_create_by_full_path(cls, full_path, **kwargs):
from solvebio import Object
# Assert this is a dataset (for the "get" in get_or_create)
kwargs['assert_type'] = 'dataset'
# Create this is a dataset (for the "create" in get_or_create)
kwargs['object_type'] = 'dataset'
_client = kwargs.pop('client', None) or cls._client or client
obj = Object.get_or_create_by_full_path(full_path,
client=_client,
**kwargs)
return cls.retrieve(obj.dataset_id)
def create_folder(self, filename, **params):
from solvebio import Object
path = params.pop('path', None)
if path and path != '/':
parent_object = self._get_parent_folder(path)
params['parent_object_id'] = parent_object.id
params.update({
'filename': filename,
'vault_id': self.id,
'object_type': 'folder'
})
return Object.create(client=self._client, **params)
def create_dataset(self, name, **params):
from solvebio import Object
params['vault_id'] = self.id
params['object_type'] = 'dataset'
path = params.pop('path', None)
if path == '/' or path is None:
params['parent_object_id'] = None
else:
parent_object = self._get_parent_folder(path)
params['parent_object_id'] = parent_object.id
params['filename'] = name
return Object.create(**params)
def upload_file(cls, local_path, remote_path, vault_full_path, **kwargs):
from solvebio import Vault
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
local_path = os.path.expanduser(local_path)
if os.stat(local_path).st_size == 0:
print('Notice: Cannot upload empty file {0}'.format(local_path))
return
# Get vault
vault = Vault.get_by_full_path(vault_full_path, client=_client)
# Get MD5, mimetype, and file size for the object
md5, _ = md5sum(local_path, multipart_threshold=None)
_, mimetype = mimetypes.guess_type(local_path)
size = os.path.getsize(local_path)
# Lookup parent object
if remote_path == '/':
parent_object_id = None
else:
parent_obj = Object.get_by_full_path(
':'.join([vault.full_path, remote_path]),
assert_type='folder', client=_client)
parent_object_id = parent_obj.id
description = kwargs.get(
'description',
'File uploaded via python client'
)
# Create the file, and upload it to the Upload URL
obj = Object.create(
vault_id=vault.id,
parent_object_id=parent_object_id,
object_type='file',
filename=os.path.basename(local_path),
md5=md5,
mimetype=mimetype,
size=size,
description=description,
client=_client
)
print('Notice: File created for {0} at {1}'.format(local_path,
obj.path))
print('Notice: Upload initialized')
upload_url = obj.upload_url
headers = {
'Content-MD5': base64.b64encode(binascii.unhexlify(md5)),
'Content-Type': mimetype,
'Content-Length': str(size),
}
# Use a session with a retry policy to handle connection errors.
session = requests.Session()
session.mount('https://', requests.adapters.HTTPAdapter(max_retries=5))
upload_resp = session.put(upload_url,
data=open(local_path, 'rb'),
headers=headers)
if upload_resp.status_code != 200:
print('Notice: Upload status code for {0} was {1}'.format(
local_path, upload_resp.status_code
))
print('See error message below:')
print(upload_resp.content)
# Clean up the failed upload
obj.delete(force=True)
else:
print('Notice: Successfully uploaded {0} to {1}'.format(local_path,
obj.path))
return obj
def _get_parent_folder(self, path):
from solvebio import Object
return Object.get_by_full_path(':'.join([self.full_path, path]),
assert_type='folder',
client=self._client)
def import_file(args):
"""
Given a dataset and a local path, upload and import the file(s).
Command arguments (args):
* create_dataset and it's args
* capacity
* template_id
* template_file
* capacity
* tag
* metadata
* metadata_json_file
* create_vault
* full_path
* commit_mode
* remote_source
* dry_run
* follow
* file (list)
"""
if args.dry_run:
print("NOTE: Running import command in dry run mode")
full_path, path_dict = Object.validate_full_path(args.full_path)
files_list = []
if args.remote_source:
# Validate files
for file_fp in args.file:
files_ = list(Object.all(glob=file_fp, limit=1000))
if not files_:
print("Did not find any {}files at path {}".format(
'remote ' if args.remote_source else '', file_fp))
else:
for file_ in files_:
print("Found file: {}".format(file_.full_path))
files_list.append(file_)
else:
# Local files
# Note: if these are globs or folders, then this will
# create a multi-file manifest which is deprecated
# and should be updated to one file per import.
files_list = [fp for fp in args.file]
if not files_list:
print("Exiting. No files were found at the following {}paths: {}"
.format('remote ' if args.remote_source else '',
', '.join(args.file)))
sys.exit(1)
if args.template_id:
try:
template = DatasetTemplate.retrieve(args.template_id)
except SolveError as e:
if e.status_code != 404:
raise e
print("No template with ID {0} found!".format(args.template_id))
sys.exit(1)
elif args.template_file:
template = _create_template_from_file(args.template_file, args.dry_run)
else:
template = None
# Ensure the dataset exists. Create if necessary.
if args.create_dataset:
dataset = create_dataset(args, template=template)
else:
try:
dataset = Object.get_by_full_path(full_path, assert_type='dataset')
except solvebio.errors.NotFoundError:
print("Dataset not found: {0}".format(full_path))
print("Tip: use the --create-dataset flag "
"to create one from a template")
sys.exit(1)
if args.dry_run:
print("Importing the following files/paths into dataset: {}"
.format(full_path))
for file_ in files_list:
if args.remote_source:
print(file_.full_path)
else:
print(file_)
return
# Generate a manifest from the local files
imports = []
for file_ in files_list:
if args.remote_source:
kwargs = dict(object_id=file_.id)
else:
manifest = solvebio.Manifest()
manifest.add(file_)
kwargs = dict(manifest=manifest.manifest)
# Add template params
if template:
kwargs.update(template.import_params)
# Create the import
import_ = DatasetImport.create(
dataset_id=dataset.id,
commit_mode=args.commit_mode,
**kwargs
)
imports.append(import_)
if args.follow:
dataset.activity(follow=True)
else:
mesh_url = 'https://my.solvebio.com/activity/'
print("Your import has been submitted, view details at: {0}"
.format(mesh_url))
return imports, dataset
def upload(args):
"""
Given a folder or file, upload all the folders and files contained
within it, skipping ones that already exist on the remote.
"""
base_remote_path, path_dict = Object.validate_full_path(args.full_path)
# Assert the vault exists and is accessible
vault = Vault.get_by_full_path(path_dict['vault_full_path'])
# If not the vault root, validate remote path exists and is a folder
if path_dict['path'] != '/':
try:
Object.get_by_full_path(base_remote_path, assert_type='folder')
except:
if not args.create_full_path:
raise
if args.dry_run:
print('[Dry Run] Creating {}'.format(base_remote_path))
else:
# Create the destination path (including subfolders)
# if not found
parent_folder_path = vault.full_path + ':'
folders = path_dict['path'].lstrip('/').split('/')
for folder in folders:
folder_full_path = os.path.join(parent_folder_path, folder)
parent_folder = _create_folder(vault, folder_full_path)
parent_folder_path = parent_folder.full_path
# Exit if there are multiple local paths and the
# exclude paths are not absolute
base_exclude_paths = args.exclude or []
if base_exclude_paths and len(args.local_path) > 1:
rel_exclude_paths = [p for p in base_exclude_paths
if not os.path.isabs(p)]
local_path_parents = set([os.path.dirname(os.path.abspath(p))
for p in args.local_path])
if rel_exclude_paths and len(local_path_parents) > 1:
sys.exit('Exiting. Cannot apply the --exclude relative paths when '
'multiple upload paths with different parent directories '
'are specified. Make --exclude paths absolute or run '
'upload paths one at a time.')
for local_path in args.local_path:
# Expand local path and strip trailing slash
local_path = os.path.abspath(local_path).rstrip('/')
local_name = os.path.basename(local_path)
# add basepath to excludes
exclude_paths = [
os.path.join(local_path, os.path.normpath(exclude_path))
for exclude_path in base_exclude_paths
]
if os.path.isdir(local_path):
_upload_folder(path_dict['domain'], vault,
base_remote_path, local_path,
local_name, exclude_paths=exclude_paths,
dry_run=args.dry_run)
else:
if args.dry_run:
print('[Dry Run] Uploading {} to {}'
.format(local_path, path_dict['path']))
else:
Object.upload_file(local_path, path_dict['path'],
vault.full_path)
def create_dataset(args, template=None):
"""
Attempt to create a new dataset given the following params:
* template_id
* template_file
* capacity
* tag
* metadata
* metadata_json_file
* create_vault
* full_path
* dry_run
"""
if args.dry_run:
print("NOTE: Running create-dataset command in dry run mode")
full_path, path_dict = Object.validate_full_path(args.full_path)
try:
# Fail if a dataset already exists.
Object.get_by_full_path(full_path, assert_type='dataset')
print('A dataset already exists at path: {0}'.format(full_path))
sys.exit(1)
except NotFoundError:
pass
# Accept a template_id or a template_file
if template:
# Template has already been validated/created
# in the import command that called this
pass
elif args.template_id:
try:
template = DatasetTemplate.retrieve(args.template_id)
except SolveError as e:
if e.status_code != 404:
raise e
print("No template with ID {0} found!".format(args.template_id))
sys.exit(1)
elif args.template_file:
template = _create_template_from_file(args.template_file, args.dry_run)
else:
template = None
if template:
print("Creating new dataset {0} using the template '{1}'."
.format(full_path, template.name))
fields = template.fields
description = 'Created with dataset template: {0}' \
.format(str(template.id))
else:
fields = []
description = None
# Create dataset metadata
# Looks at --metadata_json_file first and will update
# that with any other key/value pairs passed in to --metadata
metadata = {}
if args.metadata and args.metadata_json_file:
print('WARNING: Received --metadata and --metadata-json-file. '
'Will update the JSON file values with the --metadata values')
if args.metadata_json_file:
with open(args.metadata_json_file, 'r') as fp:
try:
metadata = json.load(fp)
except:
print('Metadata JSON file {0} could not be loaded. Please '
'pass valid JSON'.format(args.metadata_json_file))
sys.exit(1)
if args.metadata:
metadata.update(args.metadata)
if args.dry_run:
print("Creating new '{}' capacity dataset at {}"
.format(args.capacity, full_path))
if description:
print("Description: {}".format(description))
if fields:
print("Fields: {}".format(fields))
if args.tag:
print("Tags: {}".format(args.tag))
if metadata:
print("Metadata: {}".format(metadata))
return
return Dataset.get_or_create_by_full_path(
full_path,
capacity=args.capacity,
fields=fields,
description=description,
tags=args.tag or [],
metadata=metadata,
create_vault=args.create_vault,
)
def upload_file(self, local_path, remote_path, **kwargs):
from solvebio import Object
return Object.upload_file(local_path, remote_path, self.full_path,
**kwargs)
def create_dataset(args):
"""
Attempt to create a new dataset given the following params:
* template_id
* template_file
* capacity
* create_vault
* [argument] dataset name or full path
NOTE: genome_build has been deprecated and is no longer used.
"""
# For backwards compatibility, the "full_path" argument
# can be a dataset filename, but only if vault and path
# are set. If vault/path are both provided and there
# are no forward-slashes in the "full_path", assume
# the user has provided a dataset filename.
if '/' not in args.full_path and args.vault and args.path:
full_path, path_dict = Object.validate_full_path(
'{0}:/{1}/{2}'.format(args.vault, args.path, args.full_path))
else:
full_path, path_dict = Object.validate_full_path(
args.full_path, vault=args.vault, path=args.path)
# Accept a template_id or a template_file
if args.template_id:
# Validate the template ID
try:
tpl = solvebio.DatasetTemplate.retrieve(args.template_id)
except solvebio.SolveError as e:
if e.status_code != 404:
raise e
print("No template with ID {0} found!"
.format(args.template_id))
sys.exit(1)
elif args.template_file:
mode = 'r'
fopen = open
if check_gzip_path(args.template_file):
mode = 'rb'
fopen = gzip.open
# Validate the template file
with fopen(args.template_file, mode) as fp:
try:
tpl_json = json.load(fp)
except:
print('Template file {0} could not be loaded. Please '
'pass valid JSON'.format(args.template_file))
sys.exit(1)
tpl = solvebio.DatasetTemplate.create(**tpl_json)
print("A new dataset template was created with id: {0}".format(tpl.id))
else:
print("Creating a new dataset {0} without a template."
.format(full_path))
tpl = None
fields = []
entity_type = None
description = None
if tpl:
print("Creating new dataset {0} using the template '{1}'."
.format(full_path, tpl.name))
fields = tpl.fields
entity_type = tpl.entity_type
# include template used to create
description = 'Created with dataset template: {0}'.format(str(tpl.id))
return solvebio.Dataset.get_or_create_by_full_path(
full_path,
capacity=args.capacity,
entity_type=entity_type,
fields=fields,
description=description,
create_vault=args.create_vault,
)
def _upload_folder(domain, vault, base_remote_path,
base_local_path, local_start):
# Create the upload root folder if it does not exist on the remote
try:
upload_root_path, _ = Object.validate_full_path(
os.path.join(base_remote_path, local_start)
)
obj = Object.get_by_full_path(upload_root_path, assert_type='folder')
except NotFoundError:
base_remote_path, path_dict = \
Object.validate_full_path(base_remote_path)
if path_dict['path'] == '/':
parent_object_id = None
else:
obj = Object.get_by_full_path(base_remote_path,
assert_type='folder')
parent_object_id = obj.id
# Create base folder
new_folder = Object.create(
vault_id=vault.id,
parent_object_id=parent_object_id,
object_type='folder',
filename=local_start
)
print('Notice: Folder created for {0} at {1}'.format(
base_local_path,
new_folder.path,
))
for root, dirs, files in os.walk(base_local_path):
# Create the sub-folders that do not exist on the remote
for d in dirs:
dirpath = os.path.join(
base_remote_path,
re.sub('^' + os.path.dirname(base_local_path), '', root).lstrip('/'), # noqa
d
)
try:
Object.get_by_full_path(dirpath, object_type='folder')
except NotFoundError:
# Create the folder
if os.path.dirname(dirpath.split(':')[-1]) == '/':
parent_object_id = None
else:
parent_full_path = os.path.dirname(dirpath)
parent = Object.get_by_full_path(
parent_full_path, assert_type='folder')
parent_object_id = parent.id
# Make the API call
new_obj = Object.create(
vault_id=vault.id,
parent_object_id=parent_object_id,
object_type='folder',
filename=d,
)
print('Notice: Folder created for {0} at {1}'
.format(os.path.join(root, d), new_obj.path))
# Upload the files that do not yet exist on the remote
for f in files:
file_full_path = os.path.join(
base_remote_path,
re.sub('^' + os.path.dirname(base_local_path),
'',
root).lstrip('/'),
f,
)
try:
Object.get_by_full_path(file_full_path)
except NotFoundError:
parent_full_path = os.path.dirname(
os.path.join(
base_remote_path,
re.sub('^' + os.path.dirname(base_local_path),
'',
root).lstrip('/'),
f,
)
)
parent = Object.get_by_full_path(
parent_full_path, assert_type='folder')
Object.upload_file(os.path.join(root, f),
parent.path, vault.full_path)
def upload_file(cls, local_path, remote_path, vault_full_path, **kwargs):
from solvebio import Vault
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
local_path = os.path.expanduser(local_path)
if os.stat(local_path).st_size == 0:
print('Notice: Cannot upload empty file {0}'.format(local_path))
return
# Get vault
vault = Vault.get_by_full_path(vault_full_path, client=_client)
# Get MD5, mimetype, and file size for the object
md5, _ = md5sum(local_path, multipart_threshold=None)
_, mimetype = mimetypes.guess_type(local_path)
size = os.path.getsize(local_path)
# Lookup parent object
if remote_path == '/':
parent_object_id = None
else:
parent_obj = Object.get_by_full_path(':'.join(
[vault.full_path, remote_path]),
assert_type='folder',
client=_client)
parent_object_id = parent_obj.id
description = kwargs.get('description',
'File uploaded via python client')
# Create the file, and upload it to the Upload URL
obj = Object.create(vault_id=vault.id,
parent_object_id=parent_object_id,
object_type='file',
filename=os.path.basename(local_path),
md5=md5,
mimetype=mimetype,
size=size,
description=description,
client=_client)
print('Notice: File created for {0} at {1}'.format(
local_path, obj.path))
print('Notice: Upload initialized')
upload_url = obj.upload_url
headers = {
'Content-MD5': base64.b64encode(binascii.unhexlify(md5)),
'Content-Type': mimetype,
'Content-Length': str(size),
}
upload_resp = requests.put(upload_url,
data=open(local_path, 'rb'),
headers=headers)
if upload_resp.status_code != 200:
print('Notice: Upload status code for {0} was {1}'.format(
local_path, upload_resp.status_code))
print('See error message below:')
print(upload_resp.content)
# Clean up the failed upload
obj.delete(force=True)
else:
print('Notice: Successfully uploaded {0} to {1}'.format(
local_path, obj.path))
return obj
def upload_file(self, local_path, remote_path, **kwargs):
from solvebio import Object
return Object.upload_file(
local_path, remote_path, self.full_path, **kwargs)
def _upload_folder(domain, vault, base_remote_path, base_local_path,
local_start):
# Create the upload root folder if it does not exist on the remote
try:
upload_root_path, _ = Object.validate_full_path(
os.path.join(base_remote_path, local_start))
obj = Object.get_by_full_path(upload_root_path, assert_type='folder')
except NotFoundError:
base_remote_path, path_dict = \
Object.validate_full_path(base_remote_path)
if path_dict['path'] == '/':
parent_object_id = None
else:
obj = Object.get_by_full_path(base_remote_path,
assert_type='folder')
parent_object_id = obj.id
# Create base folder
new_folder = Object.create(vault_id=vault.id,
parent_object_id=parent_object_id,
object_type='folder',
filename=local_start)
print('Notice: Folder created for {0} at {1}'.format(
base_local_path,
new_folder.path,
))
for root, dirs, files in os.walk(base_local_path):
# Create the sub-folders that do not exist on the remote
for d in dirs:
dirpath = os.path.join(
base_remote_path,
re.sub('^' + os.path.dirname(base_local_path), '',
root).lstrip('/'), # noqa
d)
try:
Object.get_by_full_path(dirpath, object_type='folder')
except NotFoundError:
# Create the folder
if os.path.dirname(dirpath.split(':')[-1]) == '/':
parent_object_id = None
else:
parent_full_path = os.path.dirname(dirpath)
parent = Object.get_by_full_path(parent_full_path,
assert_type='folder')
parent_object_id = parent.id
# Make the API call
new_obj = Object.create(
vault_id=vault.id,
parent_object_id=parent_object_id,
object_type='folder',
filename=d,
)
print('Notice: Folder created for {0} at {1}'.format(
os.path.join(root, d), new_obj.path))
# Upload the files that do not yet exist on the remote
for f in files:
file_full_path = os.path.join(
base_remote_path,
re.sub('^' + os.path.dirname(base_local_path), '',
root).lstrip('/'),
f,
)
try:
Object.get_by_full_path(file_full_path)
except NotFoundError:
parent_full_path = os.path.dirname(
os.path.join(
base_remote_path,
re.sub('^' + os.path.dirname(base_local_path), '',
root).lstrip('/'),
f,
))
parent = Object.get_by_full_path(parent_full_path,
assert_type='folder')
Object.upload_file(os.path.join(root, f), parent.path,
vault.full_path)
def _upload_folder(domain, vault, base_remote_path, base_local_path,
local_start, exclude_paths=None, dry_run=False):
# Create the upload root folder if it does not exist on the remote
try:
upload_root_path, _ = Object.validate_full_path(
os.path.join(base_remote_path, local_start)
)
Object.get_by_full_path(upload_root_path, assert_type='folder')
except NotFoundError:
base_remote_path, path_dict = \
Object.validate_full_path(base_remote_path)
base_folder_path = os.path.join(base_remote_path, local_start)
if dry_run:
print('[Dry Run] Creating folder {}'.format(base_folder_path))
else:
_create_folder(vault, base_folder_path)
# Create folders and upload files
for abs_local_parent_path, folders, files in os.walk(base_local_path):
# Strips off the local path and adds the parent directory at
# each phase of the loop
local_parent_path = re.sub(
'^' + os.path.dirname(base_local_path), '', abs_local_parent_path
).lstrip('/')
if should_exclude(abs_local_parent_path, exclude_paths,
dry_run=dry_run):
continue
remote_folder_full_path = \
os.path.join(base_remote_path, local_parent_path)
# Create folders
for folder in folders:
new_folder_path = os.path.join(abs_local_parent_path, folder)
if should_exclude(new_folder_path, exclude_paths,
dry_run=dry_run):
continue
remote_path = os.path.join(remote_folder_full_path, folder)
if dry_run:
print('[Dry Run] Creating folder {}'.format(remote_path))
else:
_create_folder(vault, remote_path)
# Upload the files that do not yet exist on the remote
for f in files:
local_file_path = os.path.join(abs_local_parent_path, f)
if should_exclude(local_file_path, exclude_paths, dry_run=dry_run):
continue
if dry_run:
print('[Dry Run] Uploading {} to {}'
.format(local_file_path, remote_folder_full_path))
else:
remote_parent = Object.get_by_full_path(
remote_folder_full_path, assert_type='folder')
Object.upload_file(local_file_path, remote_parent.path,
vault.full_path)
def upload_file(cls, local_path, remote_path, vault_full_path, **kwargs):
from solvebio import Vault
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
local_path = os.path.expanduser(local_path)
if os.stat(local_path).st_size == 0:
print('Notice: Cannot upload empty file {0}'.format(local_path))
return
# Get vault
vault = Vault.get_by_full_path(vault_full_path, client=_client)
# Get MD5, mimetype, and file size for the object
local_md5, _ = md5sum(local_path, multipart_threshold=None)
_, mimetype = mimetypes.guess_type(local_path)
size = os.path.getsize(local_path)
# Check if object exists already and compare md5sums
full_path, path_dict = Object.validate_full_path(os.path.join(
'{}:{}'.format(vault.full_path, remote_path),
os.path.basename(local_path)),
client=_client)
try:
obj = cls.get_by_full_path(full_path, client=_client)
if not obj.is_file:
print('WARNING: A {} currently exists at {}'.format(
obj.object_type, full_path))
else:
# Check against md5sum of remote file
if obj.md5 == local_md5:
print('WARNING: File {} (md5sum {}) already exists, '
'not uploading'.format(full_path, local_md5))
return obj
else:
print('WARNING: File {} exists on SolveBio with different '
'md5sum (local: {} vs remote: {}) Uploading anyway, '
'but not overwriting.'.format(
full_path, local_md5, obj.md5))
except NotFoundError:
pass
# Lookup parent object
if path_dict['parent_path'] == '/':
parent_object_id = None
else:
parent_obj = Object.get_by_full_path(path_dict['parent_full_path'],
assert_type='folder',
client=_client)
parent_object_id = parent_obj.id
description = kwargs.get('description')
# Create the file, and upload it to the Upload URL
obj = Object.create(vault_id=vault.id,
parent_object_id=parent_object_id,
object_type='file',
filename=os.path.basename(local_path),
md5=local_md5,
mimetype=mimetype,
size=size,
description=description,
tags=kwargs.get('tags', []) or [],
client=_client)
print('Notice: File created for {0} at {1}'.format(
local_path, obj.path))
print('Notice: Upload initialized')
upload_url = obj.upload_url
headers = {
'Content-MD5': base64.b64encode(binascii.unhexlify(local_md5)),
'Content-Type': mimetype,
'Content-Length': str(size),
}
# Use a session with a retry policy to handle connection errors.
session = requests.Session()
max_retries = 5
retry = Retry(
total=max_retries,
read=max_retries,
connect=max_retries,
backoff_factor=0.3,
status_forcelist=(500, 502, 504, 400),
)
session.mount('https://',
requests.adapters.HTTPAdapter(max_retries=retry))
upload_resp = session.put(upload_url,
data=open(local_path, 'rb'),
headers=headers)
if upload_resp.status_code != 200:
print('WARNING: Upload status code for {0} was {1}'.format(
local_path, upload_resp.status_code))
# Clean up the failed upload
obj.delete(force=True)
raise FileUploadError(upload_resp.content)
else:
print('Notice: Successfully uploaded {0} to {1}'.format(
local_path, obj.path))
return obj
def get_or_create_by_full_path(cls, full_path, **kwargs):
from solvebio import Vault
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
create_vault = kwargs.pop('create_vault', False)
create_folders = kwargs.pop('create_folders', True)
# Check for object type assertion, if not explicitly added, see
# if user has passed object_type, as their intent was to get/create
# an object of that type.
assert_type = kwargs.pop('assert_type',
kwargs.get('object_type', None))
try:
return cls.get_by_full_path(full_path,
assert_type=assert_type,
client=_client)
except NotFoundError:
pass
# Object type required when creating Object
object_type = kwargs.get('object_type')
if not object_type:
raise Exception("'object_type' is required when creating a new "
"Object. Pass one of: file, folder, dataset")
# TODO should we require file contents?
# Technically a user could then use this object to the call
# upload_file()
# if object_type == 'file' and not kwargs.get('content'):
# raise Exception('')
# Object not found, create it step-by-step
full_path, parts = Object.validate_full_path(full_path, client=_client)
if create_vault:
vault = Vault.get_or_create_by_full_path('{0}:{1}'.format(
parts['domain'], parts['vault']),
client=_client)
else:
vaults = Vault.all(account_domain=parts['domain'],
name=parts['vault'],
client=_client)
if len(vaults.solve_objects()) == 0:
raise Exception('Vault with name {0}:{1} does not exist. Pass '
'create_vault=True to auto-create'.format(
parts['domain'], parts['vault']))
vault = vaults.solve_objects()[0]
# Create the folders to hold the object if they do not already exist.
object_path = parts['path']
curr_path = os.path.dirname(object_path)
folders_to_create = []
new_folders = []
id_map = {'/': None}
while curr_path != '/':
try:
obj = Object.get_by_path(curr_path,
vault_id=vault.id,
assert_type='folder',
client=_client)
id_map[curr_path] = obj.id
break
except NotFoundError:
if not create_folders:
raise Exception('Folder {} does not exist. Pass '
'create_folders=True to auto-create '
'missing folders')
folders_to_create.append(curr_path)
curr_path = '/'.join(curr_path.split('/')[:-1])
if curr_path == '':
break
for folder in reversed(folders_to_create):
new_folder = Object.create(
object_type='folder',
vault_id=vault.id,
filename=os.path.basename(folder),
parent_object_id=id_map[os.path.dirname(folder)],
client=_client)
new_folders.append(new_folder)
id_map[folder] = new_folder.id
if os.path.dirname(object_path) == '/':
parent_folder_id = None
elif new_folders:
parent_folder_id = new_folders[-1].id
else:
parent_folder_id = id_map[os.path.dirname(object_path)]
return Object.create(filename=os.path.basename(object_path),
vault_id=vault.id,
parent_object_id=parent_folder_id,
client=_client,
**kwargs)
def get_or_create_by_full_path(cls, full_path, **kwargs):
from solvebio import Vault
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
create_vault = kwargs.pop('create_vault', False)
create_folders = kwargs.pop('create_folders', True)
try:
return Dataset.get_by_full_path(full_path,
assert_type='dataset',
client=_client)
except NotFoundError:
pass
# Dataset not found, create it step-by-step
full_path, parts = Object.validate_full_path(full_path, client=_client)
if create_vault:
vault = Vault.get_or_create_by_full_path('{0}:{1}'.format(
parts['domain'], parts['vault']),
client=_client)
else:
vaults = Vault.all(account_domain=parts['domain'],
name=parts['vault'],
client=_client)
if len(vaults.solve_objects()) == 0:
raise Exception(
'Vault does not exist with name {0}:{1}'.format(
parts['domain'], parts['vault']))
vault = vaults.solve_objects()[0]
# Create the folders to hold the dataset if they do not already exist.
object_path = parts['path']
curr_path = os.path.dirname(object_path)
folders_to_create = []
new_folders = []
id_map = {'/': None}
while curr_path != '/':
try:
obj = Object.get_by_path(curr_path,
vault_id=vault.id,
assert_type='folder',
client=_client)
id_map[curr_path] = obj.id
break
except NotFoundError:
if not create_folders:
raise Exception('Folder {} does not exist. Pass '
'create_folders=True to auto-create '
'missing folders')
folders_to_create.append(curr_path)
curr_path = '/'.join(curr_path.split('/')[:-1])
if curr_path == '':
break
for folder in reversed(folders_to_create):
new_folder = Object.create(
object_type='folder',
vault_id=vault.id,
filename=os.path.basename(folder),
parent_object_id=id_map[os.path.dirname(folder)],
client=_client)
new_folders.append(new_folder)
id_map[folder] = new_folder.id
if os.path.dirname(object_path) == '/':
parent_folder_id = None
elif new_folders:
parent_folder_id = new_folders[-1].id
else:
parent_folder_id = id_map[os.path.dirname(object_path)]
return Dataset.create(name=os.path.basename(object_path),
vault_id=vault.id,
vault_parent_object_id=parent_folder_id,
client=_client,
**kwargs)
def vault_object(self):
from solvebio import Object
return Object.retrieve(self['vault_object_id'], client=self._client)
def vault_object(self):
from solvebio import Object
return Object.retrieve(self['vault_object_id'], client=self._client)
def get_or_create_by_full_path(cls, full_path, **kwargs):
from solvebio import Vault
from solvebio import Object
_client = kwargs.pop('client', None) or cls._client or client
create_vault = kwargs.pop('create_vault', False)
create_folders = kwargs.pop('create_folders', True)
try:
return Dataset.get_by_full_path(full_path, assert_type='dataset',
client=_client)
except NotFoundError:
pass
# Dataset not found, create it step-by-step
full_path, parts = Object.validate_full_path(full_path, client=_client)
if create_vault:
vault = Vault.get_or_create_by_full_path(
'{0}:{1}'.format(parts['domain'], parts['vault']),
client=_client)
else:
vaults = Vault.all(account_domain=parts['domain'],
name=parts['vault'],
client=_client)
if len(vaults.solve_objects()) == 0:
raise Exception(
'Vault does not exist with name {0}:{1}'.format(
parts['domain'], parts['vault'])
)
vault = vaults.solve_objects()[0]
# Create the folders to hold the dataset if they do not already exist.
object_path = parts['path']
curr_path = os.path.dirname(object_path)
folders_to_create = []
new_folders = []
id_map = {'/': None}
while curr_path != '/':
try:
obj = Object.get_by_path(curr_path,
vault_id=vault.id,
assert_type='folder',
client=_client)
id_map[curr_path] = obj.id
break
except NotFoundError:
if not create_folders:
raise Exception('Folder {} does not exist. Pass '
'create_folders=True to auto-create '
'missing folders')
folders_to_create.append(curr_path)
curr_path = '/'.join(curr_path.split('/')[:-1])
if curr_path == '':
break
for folder in reversed(folders_to_create):
new_folder = Object.create(
object_type='folder',
vault_id=vault.id,
filename=os.path.basename(folder),
parent_object_id=id_map[os.path.dirname(folder)],
client=_client
)
new_folders.append(new_folder)
id_map[folder] = new_folder.id
if os.path.dirname(object_path) == '/':
parent_folder_id = None
elif new_folders:
parent_folder_id = new_folders[-1].id
else:
parent_folder_id = id_map[os.path.dirname(object_path)]
return Dataset.create(name=os.path.basename(object_path),
vault_id=vault.id,
vault_parent_object_id=parent_folder_id,
client=_client,
**kwargs)
def create_dataset(args):
"""
Attempt to create a new dataset given the following params:
* template_id
* template_file
* capacity
* create_vault
* [argument] dataset name or full path
NOTE: genome_build has been deprecated and is no longer used.
"""
# For backwards compatibility, the "full_path" argument
# can be a dataset filename, but only if vault and path
# are set. If vault/path are both provided and there
# are no forward-slashes in the "full_path", assume
# the user has provided a dataset filename.
if '/' not in args.full_path and args.vault and args.path:
full_path, path_dict = Object.validate_full_path('{0}:/{1}/{2}'.format(
args.vault, args.path, args.full_path))
else:
full_path, path_dict = Object.validate_full_path(args.full_path,
vault=args.vault,
path=args.path)
# Accept a template_id or a template_file
if args.template_id:
# Validate the template ID
try:
tpl = solvebio.DatasetTemplate.retrieve(args.template_id)
except solvebio.SolveError as e:
if e.status_code != 404:
raise e
print("No template with ID {0} found!".format(args.template_id))
sys.exit(1)
elif args.template_file:
mode = 'r'
fopen = open
if check_gzip_path(args.template_file):
mode = 'rb'
fopen = gzip.open
# Validate the template file
with fopen(args.template_file, mode) as fp:
try:
tpl_json = json.load(fp)
except:
print('Template file {0} could not be loaded. Please '
'pass valid JSON'.format(args.template_file))
sys.exit(1)
tpl = solvebio.DatasetTemplate.create(**tpl_json)
print("A new dataset template was created with id: {0}".format(tpl.id))
else:
print(
"Creating a new dataset {0} without a template.".format(full_path))
tpl = None
fields = []
entity_type = None
description = None
if tpl:
print("Creating new dataset {0} using the template '{1}'.".format(
full_path, tpl.name))
fields = tpl.fields
entity_type = tpl.entity_type
# include template used to create
description = 'Created with dataset template: {0}'.format(str(tpl.id))
return solvebio.Dataset.get_or_create_by_full_path(
full_path,
capacity=args.capacity,
entity_type=entity_type,
fields=fields,
description=description,
create_vault=args.create_vault,
)
