metadata_registration_api package

Submodules

metadata_registration_api.app module

metadata_registration_api.app.clear_environmental_variables()
metadata_registration_api.app.config_app(app, credentials)
metadata_registration_api.app.create_app(config='DEVELOPMENT')

metadata_registration_api.errors module

exception metadata_registration_api.errors.ApiBaseException

Bases: Exception

exception metadata_registration_api.errors.IdenticalPropertyException

Bases: metadata_registration_api.errors.ApiBaseException

exception metadata_registration_api.errors.RequestBodyException

Bases: metadata_registration_api.errors.ApiBaseException

exception metadata_registration_api.errors.TokenException

Bases: metadata_registration_api.errors.ApiBaseException

metadata_registration_api.model module

class metadata_registration_api.model.ControlledVocabulary(*args, **values)

Bases: metadata_registration_api.model.TopLevelDocument

Model for a controlled vocabulary.

A controlled vocabulary contains a list of possible items. See Property.

exception DoesNotExist

Bases: mongoengine.errors.DoesNotExist

exception MultipleObjectsReturned

Bases: mongoengine.errors.MultipleObjectsReturned

description

A unicode string field.

id

A field wrapper around MongoDB’s ObjectIds.

items

A list field that wraps a standard field, allowing multiple instances of the field to be used as a list in the database.

If using with ReferenceFields see: one-to-many-with-listfields

Note

Required means it cannot be empty - as the default for ListFields is []

objects

The default QuerySet Manager.

Custom QuerySet Manager functions can extend this class and users can add extra queryset functionality. Any custom manager methods must accept a Document class as its first argument, and a QuerySet as its second argument.

The method function should return a QuerySet , probably the same one that was passed in, but modified in some way.

class metadata_registration_api.model.CvItem(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

An item in the list of controlled vocabularies

description

A unicode string field.

label

A unicode string field.

name

A unicode string field.

synonyms

A list field that wraps a standard field, allowing multiple instances of the field to be used as a list in the database.

If using with ReferenceFields see: one-to-many-with-listfields

Note

Required means it cannot be empty - as the default for ListFields is []

class metadata_registration_api.model.DataObject(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

args

A dictionary field that wraps a standard Python dictionary. This is similar to an embedded document, but the structure is not defined.

Note

Required means it cannot be empty - as the default for DictFields is {}

New in version 0.3.

Changed in version 0.5: - Can now handle complex / varying types of data

class_name

A unicode string field.

fields

A list field that wraps a standard field, allowing multiple instances of the field to be used as a list in the database.

If using with ReferenceFields see: one-to-many-with-listfields

Note

Required means it cannot be empty - as the default for ListFields is []

kwargs

A dictionary field that wraps a standard Python dictionary. This is similar to an embedded document, but the structure is not defined.

Note

Required means it cannot be empty - as the default for DictFields is {}

New in version 0.3.

Changed in version 0.5: - Can now handle complex / varying types of data

property

A reference to a document that will be automatically dereferenced on access (lazily).

Note this means you will get a database I/O access everytime you access this field. This is necessary because the field returns a Document which precise type can depend of the value of the _cls field present in the document in database. In short, using this type of field can lead to poor performances (especially if you access this field only to retrieve it pk field which is already known before dereference). To solve this you should consider using the LazyReferenceField.

Use the reverse_delete_rule to handle what should happen if the document the field is referencing is deleted. EmbeddedDocuments, DictFields and MapFields does not support reverse_delete_rule and an InvalidDocumentError will be raised if trying to set on one of these Document / Field types.

The options are:

  • DO_NOTHING (0) - don’t do anything (default).

  • NULLIFY (1) - Updates the reference to null.

  • CASCADE (2) - Deletes the documents associated with the reference.

  • DENY (3) - Prevent the deletion of the reference object.

  • PULL (4) - Pull the reference from a ListField of references

Alternative syntax for registering delete rules (useful when implementing bi-directional delete rules)

class Org(Document):
    owner = ReferenceField('User')

class User(Document):
    org = ReferenceField('Org', reverse_delete_rule=CASCADE)

User.register_delete_rule(Org, 'owner', DENY)

Changed in version 0.5: added reverse_delete_rule

class metadata_registration_api.model.DataObjects(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

objects

A ListField designed specially to hold a list of embedded documents to provide additional query helpers.

Note

The only valid list values are subclasses of EmbeddedDocument.

New in version 0.9.

class metadata_registration_api.model.Form(*args, **values)

Bases: metadata_registration_api.model.TopLevelDocument

MongoDB representation of a FlaskForm

The form contains multiple fields.

exception DoesNotExist

Bases: mongoengine.errors.DoesNotExist

exception MultipleObjectsReturned

Bases: mongoengine.errors.MultipleObjectsReturned

description

A unicode string field.

fields

A ListField designed specially to hold a list of embedded documents to provide additional query helpers.

Note

The only valid list values are subclasses of EmbeddedDocument.

New in version 0.9.

id

A field wrapper around MongoDB’s ObjectIds.

objects

The default QuerySet Manager.

Custom QuerySet Manager functions can extend this class and users can add extra queryset functionality. Any custom manager methods must accept a Document class as its first argument, and a QuerySet as its second argument.

The method function should return a QuerySet , probably the same one that was passed in, but modified in some way.

class metadata_registration_api.model.FormField(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

args

A generic embedded document field - allows any EmbeddedDocument to be stored.

Only valid values are subclasses of EmbeddedDocument.

Note

You can use the choices param to limit the acceptable EmbeddedDocument types

class_name

A unicode string field.

clean()

Hook for doing document level data cleaning before validation is run.

Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

description

A unicode string field.

fields

A list field that wraps a standard field, allowing multiple instances of the field to be used as a list in the database.

If using with ReferenceFields see: one-to-many-with-listfields

Note

Required means it cannot be empty - as the default for ListFields is []

kwargs

A dictionary field that wraps a standard Python dictionary. This is similar to an embedded document, but the structure is not defined.

Note

Required means it cannot be empty - as the default for DictFields is {}

New in version 0.3.

Changed in version 0.5: - Can now handle complex / varying types of data

label

A unicode string field.

name

A unicode string field.

property

A reference to a document that will be automatically dereferenced on access (lazily).

Note this means you will get a database I/O access everytime you access this field. This is necessary because the field returns a Document which precise type can depend of the value of the _cls field present in the document in database. In short, using this type of field can lead to poor performances (especially if you access this field only to retrieve it pk field which is already known before dereference). To solve this you should consider using the LazyReferenceField.

Use the reverse_delete_rule to handle what should happen if the document the field is referencing is deleted. EmbeddedDocuments, DictFields and MapFields does not support reverse_delete_rule and an InvalidDocumentError will be raised if trying to set on one of these Document / Field types.

The options are:

  • DO_NOTHING (0) - don’t do anything (default).

  • NULLIFY (1) - Updates the reference to null.

  • CASCADE (2) - Deletes the documents associated with the reference.

  • DENY (3) - Prevent the deletion of the reference object.

  • PULL (4) - Pull the reference from a ListField of references

Alternative syntax for registering delete rules (useful when implementing bi-directional delete rules)

class Org(Document):
    owner = ReferenceField('User')

class User(Document):
    org = ReferenceField('Org', reverse_delete_rule=CASCADE)

User.register_delete_rule(Org, 'owner', DENY)

Changed in version 0.5: added reverse_delete_rule

class metadata_registration_api.model.History(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

action

A unicode string field.

manual_user

A unicode string field.

timestamp

Datetime field.

Uses the python-dateutil library if available alternatively use time.strptime to parse the dates. Note: python-dateutil’s parser is fully featured and when installed you can utilise it to convert varying types of date formats into valid python datetime objects.

Note: To default the field to the current datetime, use: DateTimeField(default=datetime.utcnow)

Note: Microseconds are rounded to the nearest millisecond.

Pre UTC microsecond support is effectively broken. Use ComplexDateTimeField if you need accurate microsecond support.

user_id

A reference to a document that will be automatically dereferenced on access (lazily).

Note this means you will get a database I/O access everytime you access this field. This is necessary because the field returns a Document which precise type can depend of the value of the _cls field present in the document in database. In short, using this type of field can lead to poor performances (especially if you access this field only to retrieve it pk field which is already known before dereference). To solve this you should consider using the LazyReferenceField.

Use the reverse_delete_rule to handle what should happen if the document the field is referencing is deleted. EmbeddedDocuments, DictFields and MapFields does not support reverse_delete_rule and an InvalidDocumentError will be raised if trying to set on one of these Document / Field types.

The options are:

  • DO_NOTHING (0) - don’t do anything (default).

  • NULLIFY (1) - Updates the reference to null.

  • CASCADE (2) - Deletes the documents associated with the reference.

  • DENY (3) - Prevent the deletion of the reference object.

  • PULL (4) - Pull the reference from a ListField of references

Alternative syntax for registering delete rules (useful when implementing bi-directional delete rules)

class Org(Document):
    owner = ReferenceField('User')

class User(Document):
    org = ReferenceField('Org', reverse_delete_rule=CASCADE)

User.register_delete_rule(Org, 'owner', DENY)

Changed in version 0.5: added reverse_delete_rule

class metadata_registration_api.model.MetaInformation(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

change_log

A ListField designed specially to hold a list of embedded documents to provide additional query helpers.

Note

The only valid list values are subclasses of EmbeddedDocument.

New in version 0.9.

deprecated

Boolean field type.

New in version 0.1.2.

state

A unicode string field.

class metadata_registration_api.model.Property(*args, **values)

Bases: metadata_registration_api.model.TopLevelDocument

Model for a property

A property is assigned to a level.

exception DoesNotExist

Bases: mongoengine.errors.DoesNotExist

exception MultipleObjectsReturned

Bases: mongoengine.errors.MultipleObjectsReturned

clean()

Hook for doing document level data cleaning before validation is run.

Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

description

A unicode string field.

id

A field wrapper around MongoDB’s ObjectIds.

level

A unicode string field.

objects

The default QuerySet Manager.

Custom QuerySet Manager functions can extend this class and users can add extra queryset functionality. Any custom manager methods must accept a Document class as its first argument, and a QuerySet as its second argument.

The method function should return a QuerySet , probably the same one that was passed in, but modified in some way.

synonyms

A list field that wraps a standard field, allowing multiple instances of the field to be used as a list in the database.

If using with ReferenceFields see: one-to-many-with-listfields

Note

Required means it cannot be empty - as the default for ListFields is []

value_type

An embedded document field - with a declared document_type. Only valid values are subclasses of EmbeddedDocument.

class metadata_registration_api.model.Study(*args, **values)

Bases: mongoengine.document.Document

exception DoesNotExist

Bases: mongoengine.errors.DoesNotExist

exception MultipleObjectsReturned

Bases: mongoengine.errors.MultipleObjectsReturned

entries

A ListField designed specially to hold a list of embedded documents to provide additional query helpers.

Note

The only valid list values are subclasses of EmbeddedDocument.

New in version 0.9.

id

A field wrapper around MongoDB’s ObjectIds.

meta_information

An embedded document field - with a declared document_type. Only valid values are subclasses of EmbeddedDocument.

objects

The default QuerySet Manager.

Custom QuerySet Manager functions can extend this class and users can add extra queryset functionality. Any custom manager methods must accept a Document class as its first argument, and a QuerySet as its second argument.

The method function should return a QuerySet , probably the same one that was passed in, but modified in some way.

class metadata_registration_api.model.StudyEntry(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

property

A reference to a document that will be automatically dereferenced on access (lazily).

Note this means you will get a database I/O access everytime you access this field. This is necessary because the field returns a Document which precise type can depend of the value of the _cls field present in the document in database. In short, using this type of field can lead to poor performances (especially if you access this field only to retrieve it pk field which is already known before dereference). To solve this you should consider using the LazyReferenceField.

Use the reverse_delete_rule to handle what should happen if the document the field is referencing is deleted. EmbeddedDocuments, DictFields and MapFields does not support reverse_delete_rule and an InvalidDocumentError will be raised if trying to set on one of these Document / Field types.

The options are:

  • DO_NOTHING (0) - don’t do anything (default).

  • NULLIFY (1) - Updates the reference to null.

  • CASCADE (2) - Deletes the documents associated with the reference.

  • DENY (3) - Prevent the deletion of the reference object.

  • PULL (4) - Pull the reference from a ListField of references

Alternative syntax for registering delete rules (useful when implementing bi-directional delete rules)

class Org(Document):
    owner = ReferenceField('User')

class User(Document):
    org = ReferenceField('Org', reverse_delete_rule=CASCADE)

User.register_delete_rule(Org, 'owner', DENY)

Changed in version 0.5: added reverse_delete_rule

value

A truly dynamic field type capable of handling different and varying types of data.

Used by DynamicDocument to handle dynamic data

class metadata_registration_api.model.TopLevelDocument(*args, **values)

Bases: mongoengine.document.Document

Base class for all top level documents

All top level documents have a label, a name and a deprecated flag. The label is for displaying to the end user (external representation) and the name is used by the machine (internal representation). The name is expected to be unique for the model. To ensures that the name is converted to snake case before it is inserted into the database. The deprecated flag indicates if a document is no longer needed (alternative to delete it)

clean()

Hook for doing document level data cleaning before validation is run.

Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

deprecated

Boolean field type.

New in version 0.1.2.

label

A unicode string field.

name

A unicode string field.

class metadata_registration_api.model.User(*args, **values)

Bases: mongoengine.document.Document

exception DoesNotExist

Bases: mongoengine.errors.DoesNotExist

exception MultipleObjectsReturned

Bases: mongoengine.errors.MultipleObjectsReturned

clean()

Called before data is inserted into the database

email

A field that validates input as an email address.

New in version 0.4.

firstname

A unicode string field.

id

A field wrapper around MongoDB’s ObjectIds.

is_active

Boolean field type.

New in version 0.1.2.

lastname

A unicode string field.

objects

The default QuerySet Manager.

Custom QuerySet Manager functions can extend this class and users can add extra queryset functionality. Any custom manager methods must accept a Document class as its first argument, and a QuerySet as its second argument.

The method function should return a QuerySet , probably the same one that was passed in, but modified in some way.

password

A unicode string field.

class metadata_registration_api.model.VocabularyType(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

Model which defines the allowed vocabulary.

It is used to validate user input. If the data type is ctrl_voc, only the items of ControlledVocabulary are allowed.

controlled_vocabulary

A reference to a document that will be automatically dereferenced on access (lazily).

Note this means you will get a database I/O access everytime you access this field. This is necessary because the field returns a Document which precise type can depend of the value of the _cls field present in the document in database. In short, using this type of field can lead to poor performances (especially if you access this field only to retrieve it pk field which is already known before dereference). To solve this you should consider using the LazyReferenceField.

Use the reverse_delete_rule to handle what should happen if the document the field is referencing is deleted. EmbeddedDocuments, DictFields and MapFields does not support reverse_delete_rule and an InvalidDocumentError will be raised if trying to set on one of these Document / Field types.

The options are:

  • DO_NOTHING (0) - don’t do anything (default).

  • NULLIFY (1) - Updates the reference to null.

  • CASCADE (2) - Deletes the documents associated with the reference.

  • DENY (3) - Prevent the deletion of the reference object.

  • PULL (4) - Pull the reference from a ListField of references

Alternative syntax for registering delete rules (useful when implementing bi-directional delete rules)

class Org(Document):
    owner = ReferenceField('User')

class User(Document):
    org = ReferenceField('Org', reverse_delete_rule=CASCADE)

User.register_delete_rule(Org, 'owner', DENY)

Changed in version 0.5: added reverse_delete_rule

data_type

A unicode string field.

metadata_registration_api.model.to_snake_case(name)

Convert a string into an internal representation (no leading and trailing whitespace, and intermediate whitespace replaced with underscore)

Parameters

name – a given name

Returns

name in snake_case or None

metadata_registration_api.my_utils module

metadata_registration_api.my_utils.load_credentials(filename='.credentials.yaml')

” Load credential from file.

metadata_registration_api.my_utils.map_key_value(url, key='id', value='name')

Call API at url endpoint and create a dict which maps key to value

If the response contains identical keys, only the last value is stored for this key. The mapping only works for fields in the top level (no nested fields).

Parameters

  • url (str) – API endpoint to call

  • key (str) – The key by which the value will be found

  • value (str) – The value to which the key will map

… :return: A dict with maps key -> value :rtype: dict

Module contents