Python API

module pephubclient.pephubclient

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class PEPHubClient

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property sample

view represents the PHCSample class which contains all samples API

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property view

view represents the PHCView class which contains all views API

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method find_project

find_project(
    namespace: str,
    query_string: str = '',
    limit: int = 100,
    offset: int = 0,
    filter_by: Literal['submission_date', 'last_update_date'] = None,
    start_date: str = None,
    end_date: str = None
) → SearchReturnModel

Find project in specific namespace and return list of PEP annotation

• :param namespace: Namespace where to search for projects
• :param query_string: Search query
• :param limit: Return limit
• :param offset: Return offset
• :param filter_by: Use filter date. Option: [submission_date, last_update_date]
• :param start_date: filter beginning date
• :param end_date: filter end date (if none today's date is used) :return:

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method load_project

load_project(
    project_registry_path: str,
    query_param: Optional[dict] = None
) → Project

Load peppy project from PEPhub in peppy.Project object

• :param project_registry_path: registry path of the project

• :param query_param: query parameters used in get request :return Project: peppy project.

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method load_raw_pep

load_raw_pep(registry_path: str, query_param: Optional[dict] = None) → dict

Request PEPhub and return the requested project as peppy.Project object.

• :param registry_path: Project namespace, eg. "geo/GSE124224:tag"
• :param query_param: Optional variables to be passed to PEPhub :return: Raw project in dict.

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method login

login() → NoReturn

Log in to PEPhub

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method logout

logout() → NoReturn

Log out from PEPhub

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method pull

pull(
    project_registry_path: str,
    force: Optional[bool] = False,
    zip: Optional[bool] = False,
    output: Optional[str] = None
) → None

Download project locally

• :param str project_registry_path: Project registry path in PEPhub (e.g. databio/base:default)
• :param bool force: if project exists, overwrite it.
• :param bool zip: if True, save project as zip file
• :param str output: path where project will be saved :return: None

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method push

push(
    cfg: str,
    namespace: str,
    name: Optional[str] = None,
    tag: Optional[str] = None,
    is_private: Optional[bool] = False,
    force: Optional[bool] = False
) → None

Push (upload/update) project to Pephub using config/csv path

• :param str cfg: Project config file (YAML) or sample table (CSV/TSV) with one row per sample to constitute project
• :param str namespace: namespace
• :param str name: project name
• :param str tag: project tag
• :param bool is_private: Specifies whether project should be private [Default= False]
• :param bool force: Force push to the database. Use it to update, or upload project. [Default= False] :return: None

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method upload

upload(
    project: Project,
    namespace: str,
    name: str = None,
    tag: str = None,
    is_private: bool = False,
    force: bool = True
) → None

Upload peppy project to the PEPhub.

• :param peppy.Project project: Project object that has to be uploaded to the DB
• :param namespace: namespace
• :param name: project name
• :param tag: project tag
• :param force: Force push to the database. Use it to update, or upload project.
• :param is_private: Make project private
• :param force: overwrite project if it exists :return: None

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