module

info

info(module_name, local=False, outer=None, **kwargs)

info.

PARAMETER	DESCRIPTION
`module_name`	Module name TYPE: `str`
`local`	`True` will search the module in local installation. `False` will fetch the module's information from the OakVar store. TYPE: `bool` DEFAULT: `False`
`outer`	If set, tabulated output will be sent to it. For example, `sys.stdout`. DEFAULT: `None`
`kwargs`	DEFAULT: `{}`

RETURNS	DESCRIPTION
`Optional[Dict[str, Any]]`	`None` if the module is not found. The module's information as a dict if found.

Examples:

Print clinvar module's information to the terminal and get the same information as a dict.

>>> clinvar_info = oakvar.api.module.info("clinvar", outer=sys.stdout)

install

install(
    module_names=[],
    urls=None,
    modules_dir=None,
    overwrite=False,
    clean=False,
    force_data=False,
    yes=False,
    skip_dependencies=False,
    skip_data=False,
    no_fetch=False,
    outer=None,
    stage_handler=None,
    system_worker_state=None,
)

Install modules.

PARAMETER	DESCRIPTION
`module_names`	Module names TYPE: `List[str]` DEFAULT: `[]`
`urls`	URLs of module zip files. If given, `module_names` also should be given to specify the module name of each URL. TYPE: `Optional[str]` DEFAULT: `None`
`yes`	`True` will skip a confirmation prompt. TYPE: `bool` DEFAULT: `False`
`no_fetch`	`True` will skip fetching the latest the OakVar store cache. TYPE: `bool` DEFAULT: `False`
`overwrite`	`True` will overwrite the module even if the same version. TYPE: `bool` DEFAULT: `False`
`force_data`	`True` will re-install module data. TYPE: `bool` DEFAULT: `False`
`skip_data`	`True` will skip installing module data. TYPE: `bool` DEFAULT: `False`
`modules_dir`	custom OakVar modules directory TYPE: `Optional[Path]` DEFAULT: `None`
`skip_dependencies`	`True` will bypass installing dependencies. TYPE: `bool` DEFAULT: `False`
`clean`	clean TYPE: `bool` DEFAULT: `False`
`stage_handler`	DEFAULT: `None`
`system_worker_state`	DEFAULT: `None`
`outer`	DEFAULT: `None`

RETURNS	DESCRIPTION
`Optional[bool]`	`None` if no problem. `False` if there was a problem.

installbase

installbase(
    no_fetch=False,
    conf=None,
    overwrite=False,
    modules_dir=None,
    system_worker_state=None,
    outer=None,
)

Installs OakVar system/default modules.

PARAMETER	DESCRIPTION
`no_fetch`	`True` will skip fetching the latest the OakVar store cache. TYPE: `bool` DEFAULT: `False`
`overwrite`	`True` will overwrite the module even if the same version. TYPE: `bool` DEFAULT: `False`
`modules_dir`	custom OakVar modules directory TYPE: `Optional[Path]` DEFAULT: `None`
`conf`	Custom system configuration as a dict TYPE: `Optional[dict]` DEFAULT: `None`
`outer`	DEFAULT: `None`
`system_worker_state`	DEFAULT: `None`

RETURNS	DESCRIPTION
`Optional[bool]`	`None` if successful. `False` if not.

ls

ls(
    module_names=[".*"],
    module_types=[],
    search_store=False,
    tags=[],
    nameonly=False,
    humanized_size=False,
    outer=None,
    **kwargs
)

List installed and available OakVar modules.

PARAMETER	DESCRIPTION
`module_names`	Module names TYPE: `List[str]` DEFAULT: `['.*']`
`module_types`	Module types TYPE: `List[str]` DEFAULT: `[]`
`search_store`	`True` will search not yet installed modules on the OakVar store. `False` for only locally installed modules. TYPE: `bool` DEFAULT: `False`
`humanized_size`	`True` will show humanized module size. TYPE: `bool` DEFAULT: `False`
`tags`	Module tags to search. Regular expression can be used. TYPE: `List[str]` DEFAULT: `[]`
`nameonly`	`True` will return module names only. TYPE: `bool` DEFAULT: `False`
`outer`	DEFAULT: `None`

RETURNS	DESCRIPTION
`List[Dict[str, Any]]`	List of Dict, each element of which has an installed module's information.

Examples:

Get the information on the installed ClinVar module.

>>> oakvar.api.module.ls(module_names=["clinvar"])

Search for all reporter modules in the OakVar store.

>>> oakvar.api.module.ls(module_types=["reporter"], search_store=True)

Search the OakVar store for modules with "allele" in their tags.

>>> oakvar.api.module.ls(tags=[".*allele.*"], search_store=True)

pack

pack(
    module_name,
    outdir=None,
    code_only=False,
    split=False,
    outer=None,
)

Packs a module's code and optionally data to register it with OakVar store. This will produce zip files. They are supposed to be uploaded to somewhere on the web, and oakvar.api.store.register is used to register the module in the OakVar store. After this, the module will be available to all OakVar users worldwide.

PARAMETER	DESCRIPTION
`module_name`	Module name TYPE: `str`
`outdir`	Directory to store the module pack zip files. Default is the current working directory. TYPE: `Optional[Path]` DEFAULT: `None`
`code_only`	`True` will pack only the code. Useful if only updated code will be registered. TYPE: `bool` DEFAULT: `False`
`split`	`True` will split the code and data zip files by 100MB. TYPE: `bool` DEFAULT: `False`
`outer`	DEFAULT: `None`

RETURNS	DESCRIPTION
`Optional[Dict[str, Optional[Path]]]`	`None` if the module does not exist. A dict of { "code": [Path], "data": [Path] } if successful.}

uninstall

uninstall(module_names=None, yes=False, outer=None)

Uninstall modules.

PARAMETER	DESCRIPTION
`module_names`	Modules names TYPE: `Optional[List[str]]` DEFAULT: `None`
`yes`	`True` to skip a confirmation prompt. TYPE: `bool` DEFAULT: `False`
`outer`	DEFAULT: `None`

RETURNS	DESCRIPTION
`bool`	`True` if successful. `False` if not.

update

update(
    module_name_patterns=[],
    yes=False,
    no_fetch=False,
    force_data=False,
    modules_dir=None,
    outer=None,
    system_worker_state=None,
)

Update installed modules.

PARAMETER	DESCRIPTION
`module_name_patterns`	Module name patterns. For example, `["clin."]` will check `clinvar`, `clingen`, etc. TYPE:* `List[str]` DEFAULT: `[]`
`yes`	`True` to skip a confirmation prompt. TYPE: `bool` DEFAULT: `False`
`no_fetch`	`True` will skip fetching the latest the OakVar store cache. TYPE: `bool` DEFAULT: `False`
`force_data`	`True` will re-install module data. TYPE: `bool` DEFAULT: `False`
`modules_dir`	custom OakVar modules directory TYPE: `Optional[Path]` DEFAULT: `None`
`system_worker_state`	DEFAULT: `None`
`outer`	DEFAULT: `None`

RETURNS	DESCRIPTION
`bool`	`True` if update was successful. `False` if not.