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module pephubclient.pephubclient

class PEPHubClient

property sample

view represents the PHCSample class which contains all samples API

property view

view represents the PHCView class which contains all views API

method 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:

method 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.

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.

method login

login()  NoReturn

Log in to PEPhub

method logout

logout()  NoReturn

Log out from PEPhub

method 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

method 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

method 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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