datasafe.loi module

Lab Object Identifiers (LOIs)

Accessing objects in a laboratory via unique identifiers (here: a Lab Object Identifier, LOI) is a key concept of the LabInform framework. “Object” may be thought of in a very broad and general way, ranging from (physically existing) samples via datasets represented as files on a computer storage system to abstract concepts such as projects.

Currently, the classes implemented in this module can check a LOI for consistency and compliance to the LOI scheme developed so far.

Todo

structure of the LOI that is implemented in this module needs to be described.

Note

This module should probably eventually be moved to a separate subpackage dealing with LOIs. See the LabInform documentation containing already hints of such a subpackage of the LabInform package for details.

class datasafe.loi.LoiMixin[source]

Bases: object

Define basic properties for LOIs.

Every class handling LOIs should inherit/mixin this class.

separator

Character that separates different parts of the LOI. Defaults to /.

Type:: str

root

Number identifying a LOI; default: 42

Type:: str

root_issuer_separator

Character separating root and issuer; default: .

Type:: str

class datasafe.loi.AbstractChecker[source]

Bases: object

Base class for different types of checkers.

A given string is analysed using basic checkers that look for specific elements or patterns.

Derived classes should implement the concrete and private method check(). This method returns a Boolean value depending on the test results.

check(string)[source]

Return result of private method _check()

Parameters:: string (str) – string to check
Returns:: Bool True if string fulfills criteria.
Return type:: bool

class datasafe.loi.InListChecker[source]

Bases: AbstractChecker

Check whether the given string is contained in a given list.

list

List of strings that are possible options for the given string.

Type:: list

class datasafe.loi.StartsWithChecker[source]

Bases: AbstractChecker

Check whether a string starts with the given string.

string

Pattern the string should start with

Type:: str

class datasafe.loi.IsPatternChecker[source]

Bases: AbstractChecker

Check whether a string matches the given pattern.

pattern

Pattern the string should match

Type:: str

class datasafe.loi.IsNumberChecker[source]

Bases: IsPatternChecker

Check whether a string contains only numbers.

pattern

Pattern defining numbers: “d+”

Type:: str

class datasafe.loi.IsDateChecker[source]

Bases: IsPatternChecker

Check for date in given form (YYYY-MM-DD).

Note that currently, the checker doesn’t validate if the date is valid date.

class datasafe.loi.IsFriendlyStringChecker[source]

Bases: IsPatternChecker

Check whether the string contains only “friendly” characters.

class datasafe.loi.AbstractLoiChecker[source]

Bases: LoiMixin

Abstract checker class to check if LOI is supposed to exist.

The Laboratory Object Identifier (LOI) is a persistent identifier or handle to identify various samples, objects and projects that are linked to a laboratory and its working group. The aim of it is a unique connection between those objects and actions performed on or with them. The LOI is part of the LabInform framework. For more information see https://www.labinform.de/

The checker works recursive-like: If the attribute next_checker is given in the respective class, checking continues.

This class contains the public method check() which calls the private method _check() that is to be overwritten in derived checkers.

property ignore_check: Check that should be ignored.

property next_checker: Next checker class that should be called.

check(string)[source]

Split string, check first part, give the rest over to next checker.

Initiates checking cascade by checking the first part of the LOI and pass the following string to the next checker (if given) which performs the next checking step in a recursive-like way. Key element of the LOI validating cascade.

Parameters:: string (str) – Part of the LOI to check.
Returns:: result – Returns true if part of the string is valid.
Return type:: bool

class datasafe.loi.LoiChecker[source]