edc-metadata 0.3.5

Add a metadata layer to data entry.

edc_metadata

edc-metadata puts a “metadata” layer on top of your data collection forms, namely CRFs and Requisitions. The “metadata” is used on the data entry dashboard (see also edc_dashboard). The metadata may be queried directly by a data manager to review the completion status of CRF and Requisition forms.

• Metadata is stored in two models, CrfMetaData and RequisitionMetaData. One metadata record is created per form per visit. Metadata is only created for the data collection forms of a visit as defined in the visit schedule.

• Metadata model instances are created for each visit when the visit model is saved. edc_metadata reads from the visit_schedule to decide which data collection form metadata model instances to create for a visit. (Note: See edc_visit_schedule)

• Metadata is guaranteed to exist for every form defined in a visit after the visit form has been submitted.

Note: This module is coupled with edc_metadata_files and edc_reference.

metadata model instances

Each metadata model instance, CrfMetadata or RequisitionMetadata, is managed by an actual CRF or REQUISITION model listed in the visit_schedule. CrfMetadata` model instances are created for each CRF listed in the visit schedule. That is, if the visit schedule schedules a CRF for 5 different visits, 5 ``CrfMetadata` model instances will eventually be created. Metadata model instances are created when the ``visit model for a timepoint is saved. When you save a CRF within a visit, the entry_status of the the metadata instance’s it manages is updated from REQUIRED to KEYED.

The same applies to RequisitionMetadata for REQUISITIONS.

Entry status

By default the entry_status field attribute is set to REQUIRED. You can change the default of each CRF to NOT_REQUIRED in your declaration in the visit schedule. See visit_schedule.crf.

The same applies to REQUISITIONS.

metadata_rules manipulate metadata model instances

metadata_rules are declared to manipulate metadata model instances. The rules change the entry_status field attribute from REQUIRED to NOT_REQUIRED or visa-versa. If the manager of the metadata instance, the CRF or REQUISITION model instance, exists, the entry status is updated to KEYED``and the ``metadata_rules targeting the metadata instance are ignored. metadata rules are run on each save of the visit and managing model instances. If a value on some other form implies that your form should not be completed, your form’s metadata “entry_status” will change from REQUIRED to NOT REQUIRED upon save of the other form. Metadata is updated through a post_save signal that re-runs the metadata rules.

See also edc_metadata_rules

metadata_rules access data through edc_reference

In order to de-couple the metadata rules from each managing model class, metadata rules access the field values for each model via edc_reference instead of directly from the model. It would be too complex and resource intensive to directly query each model separately every time the metadata rules are run. Each managing model class referenced by metadata rules must be declared with the ReferenceModelMixin and the fields list registered with site_reference_configs global. This applies to all managing models, source_model and target_models.

See also edc_reference

Getting started

Models: Visit, Crfs and Requisitions

Let’s prepare the models that will be used in the scheduled data collection. These models are your visit models, crf models and requisition models.

Your application also has one or more Visit models. Each visit model is declared with the CreatesMetadataModelMixin:

class SubjectVisit(CreatesMetadataModelMixin, PreviousVisitMixin, VisitModelMixin,
                   RequiresConsentModelMixin, BaseUuidModel):

    appointment = models.OneToOneField(Appointment)

    class Meta(RequiresConsentModelMixin.Meta):
        app_label = 'example'

Your Crf models are declared with the CrfModelMixin and ReferenceModelMixin:

class CrfOne(CrfModelMixin, ReferenceModelMixin, BaseUuidModel):

    subject_visit = models.ForeignKey(SubjectVisit)

    f1 = models.CharField(max_length=10, default='erik')

    class Meta:
        app_label = 'example'

Your Requisition models are declared with the RequisitionModelMixin and ReferenceModelMixin:

class SubjectRequisition(RequisitionModelMixin, ReferenceModelMixin, BaseUuidModel):

    subject_visit = models.ForeignKey(SubjectVisit)

    f1 = models.CharField(max_length=10, default='erik')

    class Meta:
        app_label = 'example'

metadata_rules

As described above, metadata_rules manipulate the entry_status of CRF and Requisition metadata. metadata_rules are registered to site_metadata_rules in module metadata_rules.py. Place this file in the root of your app. Each app can have one metadata_rules.py.

See also edc_metadata_rules

autodiscovering metadata_rules

AppConfig will autodiscover the rule files and print to the console whatever it finds:

• checking for metadata_rules …

• registered metadata_rules from application ‘edc_example’

Inspect metadata_rules

Inspect metadata_rules from the site registry:

>>> from edc_metadata.rules.site_metadata_rules import site_metadata_rules

>>> for rule_groups in site_metadata_rules.registry.values():
>>>    for rule_group in rule_groups:
>>>        print(rule_group._meta.rules)

(<edc_example.rule_groups.ExampleRuleGroup: crfs_male>, <edc_example.rule_groups.ExampleRuleGroup: crfs_female>)
(<edc_example.rule_groups.ExampleRuleGroup2: bicycle>, <edc_example.rule_groups.ExampleRuleGroup2: car>)

Writing metadata_rules

metadata_rules are declared in a RuleGroup. The syntax is similar to the django model class.

Let’s start with an example from the perspective of the person entering subject data. On a dashboard there are 4 forms (models) to complete. The “rule” is that if the subject is male, only the first two forms should be complete. If the subject is female, only the last two forms should be complete. So the metadata should show:

Subject is Male:

• crf_one - REQUIRED, link to entry screen available

• crf_two - REQUIRED, link to entry screen available

• crf_three - NOT REQUIRED, link to entry screen not available

• crf_four - NOT REQUIRED, link to entry screen not available

Subject is Female:

• crf_one - NOT REQUIRED

• crf_two - NOT REQUIRED

• crf_three - REQUIRED

• crf_four - REQUIRED

A Rule that changes the metadata if the subject is male would look like this:

crfs_male = CrfRule(
    predicate=P('gender', 'eq', 'MALE'),
    consequence=REQUIRED,
    alternative=NOT_REQUIRED,
    target_models=['crfone', 'crftwo'])

The rule above has a predicate that evaluates to True or not. If gender is equal to MALE the consequence is REQUIRED, else NOT_REQUIRED. For this rule, for a MALE, the metadata entry_status for crf_one and crf_two will be updated to REQUIRED. For a FEMALE both will be set to NOT_REQUIRED.

Rules are declared as attributes of a RuleGroup much like fields in a django model:

@register()
class ExampleRuleGroup(CrfRuleGroup):

    crfs_male = CrfRule(
        predicate=P('gender', 'eq', 'MALE'),
        consequence=REQUIRED,
        alternative=NOT_REQUIRED,
        target_models=['crfone', 'crftwo'])

    crfs_female = CrfRule(
        predicate=P('gender', 'eq', FEMALE),
        consequence=REQUIRED,
        alternative=NOT_REQUIRED,
        target_models=['crfthree', 'crffour'])

    class Meta:
        app_label = 'edc_example'

RuleGroup class declarations are placed in file metadata_rules.py in the root of your application. They are registered in the order in which they appear in the file. All rule groups are available from the site_metadata_rules global.

More on Rules

The rule consequence and alternative except these values:

from edc_metadata.constants import REQUIRED, NOT_REQUIRED
from edc_metadata.rules.constants import DO_NOTHING

• REQUIRED

• NOT_REQUIRED

• DO_NOTHING

It is recommended to write the logic so that the consequence is REQUIRED if the predicate evaluates to True.

In the examples above, the rule predicate can only access values that can be found on the subjects’s current visit instance or registered_subject instance. If the value you need for the rule predicate is not on either of those instances, you can pass a source_model. With the source_model declared you would have these data available:

• current visit model instance

• registered subject (see edc_registration)

• source model instance for the current visit

Let’s say the rules changes and instead of refering to gender (male/female) you wish to refer to the value field of favorite_transport on model CrfTransport. favorite_transport can be “car” or “bicycle”. You want the first rule predicate to read as:

• “If favorite_transport is equal to bicycle then set the metadata entry_status for crf_one and crf_two to REQUIRED, if not, set both to NOT_REQUIRED”

and the second to read as:

• “If favorite_transport is equal to car then set the metadata entry_status for crf_three and crf_four to REQUIRED, if not, set both to NOT_REQUIRED”.

The field for car/bicycle, favorite_transport is on model CrfTransport. The RuleGroup might look like this:

@register()
class ExampleRuleGroup(RuleGroup):

    bicycle = CrfRule(
        predicate=P('favorite_transport', 'eq', 'bicycle'),
        consequence=REQUIRED,
        alternative=NOT_REQUIRED,
        target_models=['crfone', 'crftwo'])

    car = CrfRule(
        predicate=P('favorite_transport', 'eq', car),
        consequence=REQUIRED,
        alternative=NOT_REQUIRED,
        target_models=['crfthree', 'crffour'])

    class Meta:
        app_label = 'edc_example'
        source_model = 'CrfTransport'

Note that CrfTransport is a crf model in the Edc. That is, it has a foreign key to the visit model. Internally the query will be constructed like this:

# source model instance for the current visit
visit_attr = 'subject_visit'
source_obj = CrfTansport.objects.get(**{visit_attr: visit})

# queryset of source model for the current subject_identifier
visit_attr = 'subject_visit'
source_qs = CrfTansport.objects.filter(**{'{}__subject_identifier'.format(visit_attr): subject_identifier})

• If the source model instance does not exist, the rules in the rule group will not run.

• If the target model instance exists, no rule can change it’s metadata from KEYED.

More Complex Rule Predicates

There are two provided classes for the rule predicate, P and PF. With P you can make simple rule predicates like those used in the examples above. All standard opertors can be used. For example:

predicate = P('gender', 'eq', 'MALE')
predicate = P('referral_datetime', 'is not', None)
predicate = P('age', '<=', 64)

If the logic needs to a bit more complicated, the PF class allows you to pass a lambda function directly:

predicate = PF('age', func=lambda x: True if x >= 18 and x <= 64 else False)

predicate = PF('age', 'gender', func=lambda x, y: True if x >= 18 and x <= 64 and y == MALE else False)

If the logic needs to be more complicated than is recommended for a simple lambda, you can just pass a function. When writing your function just remember that the rule predicate must always evaluate to True or False.

def my_func(visit, registered_subject, source_obj, source_qs):
    if source_obj.married and registered_subject.gender == FEMALE:
        return True
    return False

predicate = my_func

Rule Group Order

IMPORTANT: RuleGroups are evaluated in the order they are registered and the rules within each rule group are evaluated in the order they are declared on the RuleGroup.

Testing

Since the order in which rules run matters, it is essential to test the rules together. See tests for some examples. When writing tests it may be helpful to know the following:

• the standard Edc model configuration assumes you have consent->enrollment->appointments->visit->crfs and requisitions.

• rules can be instected after boot up in the global registry site_metadata_rules.

• all rules are run when the visit is saved.

More examples

See edc_example for working RuleGroups and how models are configured with the edc_metadata mixins. The tests in edc_metadata.rules use the rule group and model classes in edc_example.

Notes on Edc

The standard Edc model configuration assumes you have a data entry flow like this::

consent->enrollment->appointment->visit (1000)->crfs and requisitions
                     appointment->visit (2000)->crfs and requisitions
                     appointment->visit (3000)->crfs and requisitions
                     appointment->visit (4000)->crfs and requisitions

You should also see the other dependencies, edc_consent, edc_visit_schedule, edc_appointment, edc_visit_tracking, edc_metadata, etc.

Signals

In the signals file:

visit model ``post_save``:

• Metadata is created for a particular visit and visit code, e.g. 1000, when the visit model is saved for a subject and visit code using the default entry_status configured in the visit_schedule.

• Immediately after creating metadata, all rules for the app_label are run in order. The app_label is the app_label of the visit model.

crf or requisition model ``post_save``:

• the metadata instance for the crf/requisition is updated and then all rules are run.

crf or requisition model ``post_delete``:

• the metadata instance for the crf/requisition is reset to the default entry_status and then all rules are run.

Changing visit_schedule name and/ or schedule name

If the visit_schedule_name or schedule_name changes, the existing metadata must be manually updated. For example;

update edc_metadata_crfmetadata set visit_schedule_name='visit_schedule'
where visit_schedule_name='old_visit_schedule';

update edc_metadata_crfmetadata set schedule_name='schedule'
where schedule_name='old_schedule';

update edc_metadata_requisitionmetadata set visit_schedule_name='visit_schedule'
where visit_schedule_name='old_visit_schedule';

update edc_metadata_requisitionmetadata set schedule_name='schedule'
where schedule_name='old_schedule';

You also need to update any existing enrollment and disenrollment model data. For example;

update ambition_subject_enrollment set visit_schedule_name='visit_schedule'
where visit_schedule_name='old_visit_schedule';

update ambition_subject_enrollment set schedule_name='schedule'
where schedule_name='old_schedule';

For any other table that use these fields:

SELECT DISTINCT TABLE_NAME
    FROM INFORMATION_SCHEMA.COLUMNS
    WHERE COLUMN_NAME IN ('visit_schedule_name','schedule_name')
        AND TABLE_SCHEMA='edc';

A typical list of tables that need to be updated may look like this:

+------------------------------------------+
| TABLE_NAME                               |
+------------------------------------------+
| ambition_subject_disenrollment           |
| ambition_subject_enrollment              |
| ambition_subject_historicaldisenrollment |
| ambition_subject_historicalenrollment    |
| ambition_subject_historicalsubjectvisit  |
| ambition_subject_subjectvisit            |
| edc_appointment_appointment              |
| edc_appointment_historicalappointment    |
| edc_metadata_crfmetadata                 |
| edc_metadata_requisitionmetadata         |
+------------------------------------------+

In the code you need to update where the visit_schedule or schedule are hard coded.

• visit schedule, schedule

• Meta attributes on the enrollment and disenrollment models.