chemicalchecker.database.datasource.Datasource

class Datasource(**kwargs)[source]

Bases: Base

Datasource table class.

Parameters:

name (str) – primary key, simple unique name for the Datasource.
url (str) – the download link.
user (str) – few downloads require credentials.
password (str) – few downloads require credentials.
description (str) – free text description of the resource.
filename (str) – optional, a molrepo name. NB this name is the value of Molrepo.molrepo_name also is defininf the Parser that will be used.
calcdata (bool) – the datasource is actually from one of the calculated data.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

Methods

`add`	Add a new row to the table.
`download`	Download the Datasource.
`download_hpc`	Run HPC jobs downloading the resources.
`from_csv`	Add entries from CSV file.
`get`	Get Datasources associated to the given dataset.
`test_all_downloaded`	Check if all Datasources have been downloaded.
`test_all_valid_url`	Check if all Datasources urls are valid.

Attributes

`available`	Check if Datasource is available.
`calcdata`
`data_path`	Check if Datasource is available.
`datasets`
`datasource_name`
`description`
`filename`
`is_db`
`metadata`
`molrepos`
`password`
`registry`
`url`
`username`
`valid_url`	Check if Datasource url is valid.

static add(kwargs)[source]

Add a new row to the table.

download(force=False)[source]

Download the Datasource.

force(bool): Force download overwriting previous download.

static download_hpc(job_path, only_essential=False, **kwargs)[source]

Run HPC jobs downloading the resources.

Parameters:

job_path (str) – Path (usually in scratch) where the script files are generated.
only_essential (bool) – Download only the essential datasources (default: False).

static from_csv(filename)[source]

Add entries from CSV file.

static get(name=None)[source]

Get Datasources associated to the given dataset.

static test_all_downloaded(only_essential=False)[source]

Check if all Datasources have been downloaded.

Parameters:: only_essential (bool) – Check only datasources that are essential

static test_all_valid_url()[source]: Check if all Datasources urls are valid.