edc-identifier


Nameedc-identifier JSON
Version 0.3.11 PyPI version JSON
download
home_pagehttps://github.com/clinicedc/edc-identifier
SummaryManage participant and other identifiers in the clinicedc/edc projects
upload_time2022-06-23 20:55:08
maintainer
docs_urlNone
authorErik van Widenfelt
requires_python>=3.9
licenseGPL license, see LICENSE
keywords django edc participant identifier clinicedc clinical trials
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage
            |pypi| |actions| |coverage|

edc-identifier
--------------

Add research subject identifiers and other useful identifiers to your project

Installation
------------

Add to settings:

.. code-block:: python

    INSTALLED_APPS = [
        ...
        'edc_identifier.apps.AppConfig',
        ...
    ]

Identifiers for research subjects
---------------------------------

Create subject identifiers.

.. code-block:: python

    from edc_identifier.subject_identifier import SubjectIdentifier

    subject_identifier = SubjectIdentifier(
        subject_type_name='subject',
        model='edc_example.enrollment',
        protocol='000',
        device_id='99',
        study_site='40')
    >>> subject_identifier.identifier
    '000-40990001-6'


Maternal and Infant Identifiers
-------------------------------

See also, ``edc_pregnancy`` model mixins ``DeliveryMixin``, ``BirthMixin``.

For example:

.. code-block:: python

    from edc_identifier.maternal_identifier import MaternalIdentifier

    maternal_identifier = MaternalIdentifier(
        subject_type_name='maternal',
        model='edc_example.enrollment',
        study_site='40',
        last_name='Carter')

    >>> maternal_identifier.identifier
    '000-40990001-6'

Add infants

.. code-block:: python

    >>> maternal_identifier.deliver(2, model='edc_example.maternallabdel')
    >>> [infant.identifier for infant in maternal_identifier.infants]
    ['000-40990001-6-25', '000-40990001-6-26']

``maternal_identifier.infants`` is a list of ``InfantIdentifier`` instances

Reload class:

.. code-block:: python

    >>> maternal_identifier = MaternalIdentifier(identifier='000-40990001-6')
    >>> maternal_identifier.identifier
    '000-40990001-6'
    >>> [infant.identifier for infant in maternal_identifier.infants]
    ['000-40990001-6-25', '000-40990001-6-26']

Only allocate an identifier to one infant of twins:

.. code-block:: python

    >>> maternal_identifier.deliver(2, model='edc_example.maternallabdel', birth_orders='2')
    >>> [infant.identifier for infant in maternal_identifier.infants]
    [None, '000-40990001-6-26']

Of triplets, allocate identifiers to the 2nd and 3rd infants only:

.. code-block:: python

    >>> maternal_identifier.deliver(3, model='edc_example.maternallabdel', birth_orders='2,3')
    >>> [infant.identifier for infant in maternal_identifier.infants]
    [None, '000-40990001-6-37', '000-40990001-6-38']


Research subject identifier classes can create a Registered Subject instance

See also ``edc_registration``

``SubjectIdentifier`` by default does not create a ``RegisteredSubject`` instance unless ``create_registration=True``.

By default, ``MaternalIdentifier`` and ``InfantIdentifier`` create ``RegisteredSubject`` instances that can be updated with full details later with the Delivery and Birth models. Continuing from above:

.. code-block:: python

    maternal_identifier = MaternalIdentifier(identifier='000-40990001-6')
    maternal_identifier.deliver(1, model='edc_example.maternallabdel', create_registration=True)

    # mother
    >>> RegisteredSubject.objects.get(subject_identifier='000-40990001-6')
    <RegisteredSubject '000-40990001-6'>

    # infant is linked to the mother
    >>> RegisteredSubject.objects.get(linked_identifier='000-40990001-6')
    <RegisteredSubject '000-40990001-6-10'>

    # infant
    >>> obj = RegisteredSubject.objects.get(subject_identifier='000-40990001-6-10')
    >>> obj.first_name
    'Baby1Carter'  ## generates a temp name until Birth form is added with complete information.
    >>> obj.relative_identifier
    '000-40990001-6'


Subject type "Caps" are enforced by the research subject identifier classes

See also ``edc_protocol``

Limits on the number of identifiers that can be allocated per subject type are enforced when identifiers are created. ``edc_identifier`` reads the "caps" from ``edc_protocol.apps.AppConfig`` linking the subject type, e.g. ``subject``, or ``maternal`` or ``infant``, to the relevant cap and not allowing the number of allocated identifiers to exceed the cap.

(Subject type "Caps" still working? needs to be verified)

Numeric Identifiers
-------------------

The numeric identifier uses a check-digit and may have a separator if specified.

.. code-block:: python

	from edc_identifier import NumericIdentifier

	class MyIdentifier(NumericIdentifier):
		pass

	>>> id = MyIdentifier(None)
	>>> id
	MyIdentifier('00000000018')
	>>> next(id)
	'00000000026'
	>>> next(id)
	'00000000034'


	# add a separator
	class MyIdentifier(NumericIdentifier):
    	identifier_pattern = r'^[0-9]{4}\-[0-9]{4}\-[0-9]{4}$'
    	checkdigit_pattern = r'^\-[0-9]{1}$'
    	separator = '-'
    	seed = ['3200-0000-0000']

	>>> id = MyIdentifier(None)
	>>> id
	MyIdentifier('3200-0000-0001-1')
	>>> next(id)
	'3200-0000-0002-9'
	>>> next(id)
	'3200-0000-0003-7'

	# start from the last identifier, increment is immediate and automatic
	>>> id = MyIdentifier('3200-0000-3222-0')
	>>> id
	MyIdentifier('3200-0000-3223-8')


Alphanumeric Identifiers
------------------------

.. code-block:: python

	from edc_identifier import AlphanumericIdentifier

	class MyIdentifier(AlphanumericIdentifier):
		alpha_pattern = r'^[A-Z]{3}$'
		numeric_pattern = r'^[0-9]{4}$'
		seed = ['AAA', '0000']

	>>> id = MyIdentifier(None)
	>>> id
	MyIdentifier('AAA00015')

Your identifier will starts with 'AAA0001' plus the checkdigit "5". Subsequent calls to next increment like this:

.. code-block:: python

	>>> print(next(id))
	AAA00023
	>>> print(next(id))
	AAA00031
	>>> print(next(id))
	AAA00049


The identifier increments on the numeric sequence then the alpha:

.. code-block:: python

	>>> id = MyIdentifier('AAA99991)
	>>> id
	MyIdentifier('AAB00013')

	>>> next(id)
	'AAB00021'
	>>> next(id)
	'AAB00039'
	>>> next(id)
	'AAB00047'

	>>> id = MyIdentifier('AAB99999')
	>>> id
	MyIdentifier('AAC00010')
	...

See ``getresults-receive`` for sample usage with ``settings`` and a ``History`` model.

Short Identifiers
-----------------

Creates a small identifier that is almost unique, for example, across 25 Edc devices in a community. We use these as sample requisition identifiers that are transcribed manually onto a tube from the Edc screen in a household. Once the sample is received at the local lab it is allocated a laboratory-wide unique specimen identifier.

.. code-block:: python

    from edc_identifier import ShortIdentifier

    >>> ShortIdentifier()
    ShortIdentifier('46ZZ2')

Add a static prefix -- ``prefix(2) + identifier(5)``:

.. code-block:: python

	from edc_identifier import ShortIdentifier

	class MyIdentifier(ShortIdentifier):
    	prefix_pattern = r'^[0-9]{2}$'

    >>> options = {'prefix': 22}
    >>> id = MyIdentifier(options=options)
	>>> id
	MyIdentifier('22UYMBT')
	>>> next(id)
	'22KM84G'

Add a checkdigit -- ``prefix(2) + identifier(5) + checkdigit(1)``:

.. code-block:: python

	from edc_identifier import ShortIdentifier

	class MyIdentifier(ShortIdentifier):
    	prefix_pattern = r'^[0-9]{2}$'
    	checkdigit_pattern = r'^[0-9]{1}$'

    >>> options = {'prefix': 22}
    >>> id = MyIdentifier(options=options)
	>>> id
	MyIdentifier('223GF8A3')
	>>> next(id)
	'22DXVW23'

We use this in edc-quota to get a confirmation code:

.. code-block:: python

	from edc_identifier import ShortIdentifier

	class ConfirmationCode(ShortIdentifier):

	    identifier_type = 'confirmation'
	    prefix_pattern = ''

	>>> code = ConfirmationCode()
	>>> print(code)
	CAT33
	>>> next(code)
	3FU7D

Add more to the prefix, such as device code and community code.

.. code-block:: python

	from edc_identifier.short_identifier import ShortIdentifier

	class RequisitionIdentifier(ShortIdentifier):

		identifier_type = 'requisition'
		prefix_pattern = r'^[0-9]{4}$'
		template = '{device_id}{community_id}{random_string}'

		@property
		def options(self):
			if 'prefix' not in self._options:
				self._options.update(
					{'prefix': str(self._options.get('device_id')) + str(self._options.get('community_id'))})
			return self._options

    >>> options = {'device_id': 22, 'community_id': '12'}
    >>> id = RequisitionIdentifier(options=options)
	>>> id
	RequisitionIdentifier('22126MZXD')
	>>> next(id)
	'2212Y899C'

... if you prefer not to use the ``IdentifierHistory`` model, for example, if you are filling in a model field on ``save()``:

.. code-block:: python

	from my_app.models import Requisition

	class RequisitionIdentifier(ShortIdentifier):

	    identifier_type = 'requisition'
	    requisition_model = Requisition

	    def is_duplicate(self, identifier):
	        try:
	            self.requisition_model.get(requisition_identifier=identifier)
	            return True
	        except self.requisition_model.DoesNotExist:
	            pass
	        return False

		def update_history(self):
			pass


Batch Identifier
----------------

To have an identifier prefixed by the current date stamp:


.. code-block:: python

	from edc_identifier.batch_identifier import BatchIdentifier

	>>> datetime.today().strftime('%Y%m%d)
	20150817
	>>> id = BatchIdentifier()
	>>> id
	BatchIdentifier('201508170001')
	>>> next(id)
	'201508170002'


.. |pypi| image:: https://img.shields.io/pypi/v/edc-identifier.svg
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.. |actions| image:: https://github.com/clinicedc/edc-identifier/workflows/build/badge.svg?branch=develop
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.. |coverage| image:: https://coveralls.io/repos/github/clinicedc/edc-identifier/badge.svg?branch=develop
    :target: https://coveralls.io/github/clinicedc/edc-identifier?branch=develop

            

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    "description": "|pypi| |actions| |coverage|\n\nedc-identifier\n--------------\n\nAdd research subject identifiers and other useful identifiers to your project\n\nInstallation\n------------\n\nAdd to settings:\n\n.. code-block:: python\n\n    INSTALLED_APPS = [\n        ...\n        'edc_identifier.apps.AppConfig',\n        ...\n    ]\n\nIdentifiers for research subjects\n---------------------------------\n\nCreate subject identifiers.\n\n.. code-block:: python\n\n    from edc_identifier.subject_identifier import SubjectIdentifier\n\n    subject_identifier = SubjectIdentifier(\n        subject_type_name='subject',\n        model='edc_example.enrollment',\n        protocol='000',\n        device_id='99',\n        study_site='40')\n    >>> subject_identifier.identifier\n    '000-40990001-6'\n\n\nMaternal and Infant Identifiers\n-------------------------------\n\nSee also, ``edc_pregnancy`` model mixins ``DeliveryMixin``, ``BirthMixin``.\n\nFor example:\n\n.. code-block:: python\n\n    from edc_identifier.maternal_identifier import MaternalIdentifier\n\n    maternal_identifier = MaternalIdentifier(\n        subject_type_name='maternal',\n        model='edc_example.enrollment',\n        study_site='40',\n        last_name='Carter')\n\n    >>> maternal_identifier.identifier\n    '000-40990001-6'\n\nAdd infants\n\n.. code-block:: python\n\n    >>> maternal_identifier.deliver(2, model='edc_example.maternallabdel')\n    >>> [infant.identifier for infant in maternal_identifier.infants]\n    ['000-40990001-6-25', '000-40990001-6-26']\n\n``maternal_identifier.infants`` is a list of ``InfantIdentifier`` instances\n\nReload class:\n\n.. code-block:: python\n\n    >>> maternal_identifier = MaternalIdentifier(identifier='000-40990001-6')\n    >>> maternal_identifier.identifier\n    '000-40990001-6'\n    >>> [infant.identifier for infant in maternal_identifier.infants]\n    ['000-40990001-6-25', '000-40990001-6-26']\n\nOnly allocate an identifier to one infant of twins:\n\n.. code-block:: python\n\n    >>> maternal_identifier.deliver(2, model='edc_example.maternallabdel', birth_orders='2')\n    >>> [infant.identifier for infant in maternal_identifier.infants]\n    [None, '000-40990001-6-26']\n\nOf triplets, allocate identifiers to the 2nd and 3rd infants only:\n\n.. code-block:: python\n\n    >>> maternal_identifier.deliver(3, model='edc_example.maternallabdel', birth_orders='2,3')\n    >>> [infant.identifier for infant in maternal_identifier.infants]\n    [None, '000-40990001-6-37', '000-40990001-6-38']\n\n\nResearch subject identifier classes can create a Registered Subject instance\n\nSee also ``edc_registration``\n\n``SubjectIdentifier`` by default does not create a ``RegisteredSubject`` instance unless ``create_registration=True``.\n\nBy default, ``MaternalIdentifier`` and ``InfantIdentifier`` create ``RegisteredSubject`` instances that can be updated with full details later with the Delivery and Birth models. Continuing from above:\n\n.. code-block:: python\n\n    maternal_identifier = MaternalIdentifier(identifier='000-40990001-6')\n    maternal_identifier.deliver(1, model='edc_example.maternallabdel', create_registration=True)\n\n    # mother\n    >>> RegisteredSubject.objects.get(subject_identifier='000-40990001-6')\n    <RegisteredSubject '000-40990001-6'>\n\n    # infant is linked to the mother\n    >>> RegisteredSubject.objects.get(linked_identifier='000-40990001-6')\n    <RegisteredSubject '000-40990001-6-10'>\n\n    # infant\n    >>> obj = RegisteredSubject.objects.get(subject_identifier='000-40990001-6-10')\n    >>> obj.first_name\n    'Baby1Carter'  ## generates a temp name until Birth form is added with complete information.\n    >>> obj.relative_identifier\n    '000-40990001-6'\n\n\nSubject type \"Caps\" are enforced by the research subject identifier classes\n\nSee also ``edc_protocol``\n\nLimits on the number of identifiers that can be allocated per subject type are enforced when identifiers are created. ``edc_identifier`` reads the \"caps\" from ``edc_protocol.apps.AppConfig`` linking the subject type, e.g. ``subject``, or ``maternal`` or ``infant``, to the relevant cap and not allowing the number of allocated identifiers to exceed the cap.\n\n(Subject type \"Caps\" still working? needs to be verified)\n\nNumeric Identifiers\n-------------------\n\nThe numeric identifier uses a check-digit and may have a separator if specified.\n\n.. code-block:: python\n\n\tfrom edc_identifier import NumericIdentifier\n\n\tclass MyIdentifier(NumericIdentifier):\n\t\tpass\n\n\t>>> id = MyIdentifier(None)\n\t>>> id\n\tMyIdentifier('00000000018')\n\t>>> next(id)\n\t'00000000026'\n\t>>> next(id)\n\t'00000000034'\n\n\n\t# add a separator\n\tclass MyIdentifier(NumericIdentifier):\n    \tidentifier_pattern = r'^[0-9]{4}\\-[0-9]{4}\\-[0-9]{4}$'\n    \tcheckdigit_pattern = r'^\\-[0-9]{1}$'\n    \tseparator = '-'\n    \tseed = ['3200-0000-0000']\n\n\t>>> id = MyIdentifier(None)\n\t>>> id\n\tMyIdentifier('3200-0000-0001-1')\n\t>>> next(id)\n\t'3200-0000-0002-9'\n\t>>> next(id)\n\t'3200-0000-0003-7'\n\n\t# start from the last identifier, increment is immediate and automatic\n\t>>> id = MyIdentifier('3200-0000-3222-0')\n\t>>> id\n\tMyIdentifier('3200-0000-3223-8')\n\n\nAlphanumeric Identifiers\n------------------------\n\n.. code-block:: python\n\n\tfrom edc_identifier import AlphanumericIdentifier\n\n\tclass MyIdentifier(AlphanumericIdentifier):\n\t\talpha_pattern = r'^[A-Z]{3}$'\n\t\tnumeric_pattern = r'^[0-9]{4}$'\n\t\tseed = ['AAA', '0000']\n\n\t>>> id = MyIdentifier(None)\n\t>>> id\n\tMyIdentifier('AAA00015')\n\nYour identifier will starts with 'AAA0001' plus the checkdigit \"5\". Subsequent calls to next increment like this:\n\n.. code-block:: python\n\n\t>>> print(next(id))\n\tAAA00023\n\t>>> print(next(id))\n\tAAA00031\n\t>>> print(next(id))\n\tAAA00049\n\n\nThe identifier increments on the numeric sequence then the alpha:\n\n.. code-block:: python\n\n\t>>> id = MyIdentifier('AAA99991)\n\t>>> id\n\tMyIdentifier('AAB00013')\n\n\t>>> next(id)\n\t'AAB00021'\n\t>>> next(id)\n\t'AAB00039'\n\t>>> next(id)\n\t'AAB00047'\n\n\t>>> id = MyIdentifier('AAB99999')\n\t>>> id\n\tMyIdentifier('AAC00010')\n\t...\n\nSee ``getresults-receive`` for sample usage with ``settings`` and a ``History`` model.\n\nShort Identifiers\n-----------------\n\nCreates a small identifier that is almost unique, for example, across 25 Edc devices in a community. We use these as sample requisition identifiers that are transcribed manually onto a tube from the Edc screen in a household. Once the sample is received at the local lab it is allocated a laboratory-wide unique specimen identifier.\n\n.. code-block:: python\n\n    from edc_identifier import ShortIdentifier\n\n    >>> ShortIdentifier()\n    ShortIdentifier('46ZZ2')\n\nAdd a static prefix -- ``prefix(2) + identifier(5)``:\n\n.. code-block:: python\n\n\tfrom edc_identifier import ShortIdentifier\n\n\tclass MyIdentifier(ShortIdentifier):\n    \tprefix_pattern = r'^[0-9]{2}$'\n\n    >>> options = {'prefix': 22}\n    >>> id = MyIdentifier(options=options)\n\t>>> id\n\tMyIdentifier('22UYMBT')\n\t>>> next(id)\n\t'22KM84G'\n\nAdd a checkdigit -- ``prefix(2) + identifier(5) + checkdigit(1)``:\n\n.. code-block:: python\n\n\tfrom edc_identifier import ShortIdentifier\n\n\tclass MyIdentifier(ShortIdentifier):\n    \tprefix_pattern = r'^[0-9]{2}$'\n    \tcheckdigit_pattern = r'^[0-9]{1}$'\n\n    >>> options = {'prefix': 22}\n    >>> id = MyIdentifier(options=options)\n\t>>> id\n\tMyIdentifier('223GF8A3')\n\t>>> next(id)\n\t'22DXVW23'\n\nWe use this in edc-quota to get a confirmation code:\n\n.. code-block:: python\n\n\tfrom edc_identifier import ShortIdentifier\n\n\tclass ConfirmationCode(ShortIdentifier):\n\n\t    identifier_type = 'confirmation'\n\t    prefix_pattern = ''\n\n\t>>> code = ConfirmationCode()\n\t>>> print(code)\n\tCAT33\n\t>>> next(code)\n\t3FU7D\n\nAdd more to the prefix, such as device code and community code.\n\n.. code-block:: python\n\n\tfrom edc_identifier.short_identifier import ShortIdentifier\n\n\tclass RequisitionIdentifier(ShortIdentifier):\n\n\t\tidentifier_type = 'requisition'\n\t\tprefix_pattern = r'^[0-9]{4}$'\n\t\ttemplate = '{device_id}{community_id}{random_string}'\n\n\t\t@property\n\t\tdef options(self):\n\t\t\tif 'prefix' not in self._options:\n\t\t\t\tself._options.update(\n\t\t\t\t\t{'prefix': str(self._options.get('device_id')) + str(self._options.get('community_id'))})\n\t\t\treturn self._options\n\n    >>> options = {'device_id': 22, 'community_id': '12'}\n    >>> id = RequisitionIdentifier(options=options)\n\t>>> id\n\tRequisitionIdentifier('22126MZXD')\n\t>>> next(id)\n\t'2212Y899C'\n\n... if you prefer not to use the ``IdentifierHistory`` model, for example, if you are filling in a model field on ``save()``:\n\n.. code-block:: python\n\n\tfrom my_app.models import Requisition\n\n\tclass RequisitionIdentifier(ShortIdentifier):\n\n\t    identifier_type = 'requisition'\n\t    requisition_model = Requisition\n\n\t    def is_duplicate(self, identifier):\n\t        try:\n\t            self.requisition_model.get(requisition_identifier=identifier)\n\t            return True\n\t        except self.requisition_model.DoesNotExist:\n\t            pass\n\t        return False\n\n\t\tdef update_history(self):\n\t\t\tpass\n\n\nBatch Identifier\n----------------\n\nTo have an identifier prefixed by the current date stamp:\n\n\n.. code-block:: python\n\n\tfrom edc_identifier.batch_identifier import BatchIdentifier\n\n\t>>> datetime.today().strftime('%Y%m%d)\n\t20150817\n\t>>> id = BatchIdentifier()\n\t>>> id\n\tBatchIdentifier('201508170001')\n\t>>> next(id)\n\t'201508170002'\n\n\n.. |pypi| image:: https://img.shields.io/pypi/v/edc-identifier.svg\n    :target: https://pypi.python.org/pypi/edc-identifier\n\n.. |actions| image:: https://github.com/clinicedc/edc-identifier/workflows/build/badge.svg?branch=develop\n  :target: https://github.com/clinicedc/edc-identifier/actions?query=workflow:build\n\n.. |coverage| image:: https://coveralls.io/repos/github/clinicedc/edc-identifier/badge.svg?branch=develop\n    :target: https://coveralls.io/github/clinicedc/edc-identifier?branch=develop\n",
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