oneibl.onelight

ONE light.

Functions

add_default_handler
add_repo	Interactive prompt to add a repository.
config_dir	Path to the config directory.
config_file	Path to the config file.
default_config	Return an empty configuration dictionary.
default_download_dir	Default download directory on the client computer, with {…} placeholders fields.
download_dir	Return the download directory.
download_file	Download a file from HTTP and save it to a file.
figshare_request	Perform a REST request against the figshare API.
find_session_dirs	Iterate over all session directories found in a root directory.
find_session_files	Iterate over all files within session directories found within a root directory.
format_download_dir	Replace the placeholder fields in the download directory by the appropriate values for a given session.
get_config	Return the config file dictionary.
get_one	Get the singleton One instance, loading it from the config file, or using the singleton instance if it has already been instantiated.
get_repo	Get a repository by its name.
is_documented_by
is_file_in_session_dir	Return whether a file path is within a session directory.
is_session_dir	Return whether a path is a session directory.
load_array	Load a single file.
make_http_root_file	Make a root TSV file for an HTTP server.
read_root_file
repo_dir	Path to the local directory of the repository.
repository	Get the current repository.
set_config	Set the config file.
set_figshare_url	Get or create a figshare repo with a given figshare URL.
set_repo	Set the current repository.
update_repo	Update a repository.
walk	Iterate over all files found within a root directory.
write_root_file

Classes

Bunch	A subclass of dictionary with an additional dot syntax.
FigshareOne
FigshareUploader
FtpUploader
HttpOne
LocalOne
ONE

add_default_handler(level='INFO', logger=<Logger oneibl.onelight (DEBUG)>)

class Bunch(*args, **kwargs)

Bases: dict

A subclass of dictionary with an additional dot syntax.

copy()

Return a new Bunch instance which is a copy of the current Bunch instance.

is_documented_by(original)

config_dir()

Path to the config directory.

repo_dir()

Path to the local directory of the repository.

config_file()

Path to the config file.

default_config()

Return an empty configuration dictionary.

get_config()

Return the config file dictionary.

set_config(config)

Set the config file.

get_repo(name=None, config=None)

Get a repository by its name.

update_repo(name=None, **kwargs)

Update a repository.

add_repo(name=None)

Interactive prompt to add a repository.

set_figshare_url(url)

Get or create a figshare repo with a given figshare URL.

read_root_file(path)

write_root_file(path, iterator)

walk(root)

Iterate over all files found within a root directory.

is_session_dir(path)

Return whether a path is a session directory.

Example of a session dir: /path/to/root/mainenlab/Subjects/ZM_1150/2019-05-07/001/

is_file_in_session_dir(path)

Return whether a file path is within a session directory.

find_session_dirs(root)

Iterate over all session directories found in a root directory.

find_session_files(root)

Iterate over all files within session directories found within a root directory.

make_http_root_file(root, base_url, output)

Make a root TSV file for an HTTP server.

Note: the session root directory needs to be the directory that contains the <lab> subdirectories, so that the relative file paths are correctly obtained.

download_file(url, save_to, auth=None, log_level=10)

Download a file from HTTP and save it to a file. If Basic HTTP authentication is needed, pass auth=(username, password).

default_download_dir()

Default download directory on the client computer, with {…} placeholders fields.

download_dir()

Return the download directory.

format_download_dir(session, download_dir)

Replace the placeholder fields in the download directory by the appropriate values for a given session.

load_array(path)

Load a single file.

class FtpUploader(host, login=None, password=None, port=21, remote_root=None)

Bases: object

connect()

upload(root_dir, base_dir=None)

class HttpOne(root_file=None, download_dir=None, auth=None)

Bases: object

list(session)

List all dataset types found in a session.

search(dataset_types=(), **kwargs)

Search all sessions that have all requested dataset types.

load_dataset(session, dataset_type, download_only=False)

Download and load a single dataset in a given session and with a given dataset type.

load_object(session, obj, download_only=False, dry_run=False)

Load all attributes of a given object.

class LocalOne(root_dir)

Bases: oneibl.onelight.HttpOne

figshare_request(endpoint=None, data=None, method='GET', url=None, binary=False, error_level=40)

Perform a REST request against the figshare API.

class FigshareUploader(article_id)

Bases: object

iter_files(private=True)

Iterate over all ALF files of a given figshare article.

upload_dir(root_dir, dry_run=False, limit=None)

Upload to figshare all session files found in a root directory.

clean_publish()

Clean up and publish the figshare article.

class FigshareOne(article_id=None, download_dir=None, private=False)

Bases: oneibl.onelight.HttpOne

set_repo(name=None)

Set the current repository.

repository()

Get the current repository.

get_one(private=False)

Get the singleton One instance, loading it from the config file, or using the singleton instance if it has already been instantiated.

class ONE

Bases: object

set_local_dir(name=None, **kwargs)

set_figshare_url(url)

search_terms()

set_download_dir(path)

Set the download directory. May contain fields like {lab}, {subject}, etc.

search(dataset_types, private=False, **kwargs)

Search all sessions that have all requested dataset types.

list(session)

List all dataset types found in a session.

load_object(session, obj=None, **kwargs)

Load all attributes of a given object.

load_dataset(session, dataset_type, **kwargs)

Download and load a single dataset in a given session and with a given dataset type.