Metadata Registration Api documentation¶

A microservice which provides an API to access the Metadata Registration Tool.

Installation¶

This chapter describes how to install and setup the metadata registration API (hereafter API). Before you can install the project, make sure that you meet the requisites:

Prerequisites¶

Database The API uses MongoDB as data store. Independent on how you install the API, make sure you have the necessary credentials to access your MongoDB instance.

Dependencies The API has two internal dependencies. These dependencies are the ‘State Machine’ and the ‘Dynamic Form’. Both projects are listed as git repositories in the requirements.txt document. To download them, you must be able to access github with a SSH key. Check here for a better description.

Credentials / Configuration A configuration done through environment variables, make sure they’re all defined as needed.

Setup¶

The API can be installed in three different ways:

As a podman container
As a docker container
In a conda environment

Although all three approaches work, we recommend running it either as a docker or podman container since it usually takes longer and is more error prone when installing the API in a conda environment.

Run as podman container¶

After, we have met the prerequisites, clone the git repository into our preferred directory. Change into the root directory of the project and copy the ssh private key (i. e. id_rsa) and the .credentials.yaml. Finally execute the following command:

$ ./start_podman.sh

The script checks if an identical container is already running. If this is the case, the container is stopped and removed, and a new container is build and executed.

Run as docker container¶

After, we have met the prerequisites, clone the git repository into our preferred directory. Change into the root directory of the project and copy the ssh private key (i. e. id_rsa) and the .credentials.yaml. Finally execute the following command:

$ ./start_docker.sh

The script checks if an identical container is already running. If this is the case, the container is stopped and removed, and a new container is build and executed.

Run in a conda environment¶

[Documentation not available]

Getting started¶

The API consists of multiple resources. An overview of the resources is available as swagger documentation. The swagger documentation is accessible via the index of the url. If you run the software locally, the swagger documentation is found under `http://127.0.0.1:5001`_.

Resources¶

The API has several resources including properties, controlled vocabularies, forms, studies and users. The API follows the REST principle.

Access¶

Some API commands require an access token. As a registered user you can generate an access token by sending your email address and password as a post request to `user/login`_. The server will response with an access token.

The access token has to be transmitted in the header of each restricted request as value of x-access-token.

{"x-access-token": "eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJ1c2VyX2lkIjoiNWRmMjMyMzE2MzI4MzdiYmU2YmFmODY4IiwiaWF0IjoxNTc4NTg3MjczLCJleHAiOjE1Nzg1ODkwNzN9.PGB-jyqdcpz3LmwOeMP1rxa9a7tVizHqh3EceFWy9dI"}

The access token is only limited for a limited time span. Afterwards, a new token has to be generated.

Metadata_Registration_API¶

metadata_registration_api package¶

Subpackages¶

metadata_registration_api.api package¶

Submodules¶

metadata_registration_api.api.api_ctrl_voc module¶

class metadata_registration_api.api.api_ctrl_voc.ApiControlledVocabulary(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(user=None)¶: Delete all entries

get()¶: Fetch a list with all entries

get_parser = <flask_restx.reqparse.RequestParser object>¶

methods: Optional[List[str]] = {'DELETE', 'GET', 'POST'}¶: A list of methods this view can handle.

post(user=None)¶: Add a new entry

class metadata_registration_api.api.api_ctrl_voc.ApiControlledVocabularyId(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(id, user=None)¶: Delete an entry given its unique identifier

get(id)¶: Fetch an entry given its unique identifier

methods: Optional[List[str]] = {'DELETE', 'GET', 'PUT'}¶: A list of methods this view can handle.

put(id, user=None)¶: Update an entry given its unique identifier

class metadata_registration_api.api.api_ctrl_voc.ApiControlledVocabularyItemsMap(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

get()¶: Get a map for CV items: cv_name: {item_key: item_value}

methods: Optional[List[str]] = {'GET'}¶: A list of methods this view can handle.

metadata_registration_api.api.api_form module¶

class metadata_registration_api.api.api_form.ApiForm(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(user=None)¶: Delete all entries

get()¶: Fetch a list with all entries

get_parser = <flask_restx.reqparse.RequestParser object>¶

methods: Optional[List[str]] = {'DELETE', 'GET', 'POST'}¶: A list of methods this view can handle.

post(user=None)¶: Add a new entry

class metadata_registration_api.api.api_form.ApiFormId(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(id, user=None)¶: Delete an entry given its unique identifier

get(id)¶: Fetch an entry given its unique identifier

get_parser = <flask_restx.reqparse.RequestParser object>¶

methods: Optional[List[str]] = {'DELETE', 'GET', 'PUT'}¶: A list of methods this view can handle.

put(id, user=None)¶: Update an entry given its unique identifier

class metadata_registration_api.api.api_form.ArgsField(default=None, attribute=None, title=None, description=None, required=None, readonly=None, example=None, mask=None, **kwargs)¶

Bases: flask_restx.fields.Raw

Custom field for args field. If the value contains a DataObject, it is modeled with the objects model

format(value)¶

Formats a field’s value. No-op by default - field classes that modify how the value of existing object keys should be presented should override this and apply the appropriate formatting.

Parameters: value – The value to format
Raises: MarshallingError – In case of formatting problem

Ex:

class TitleCase(Raw):
    def format(self, value):
        return unicode(value).title()

class metadata_registration_api.api.api_form.SubformAddField(default=None, attribute=None, title=None, description=None, required=None, readonly=None, example=None, mask=None, **kwargs)¶

Bases: flask_restx.fields.Raw

Custom field for subforms

format(value)¶

Formats a field’s value. No-op by default - field classes that modify how the value of existing object keys should be presented should override this and apply the appropriate formatting.

Parameters: value – The value to format
Raises: MarshallingError – In case of formatting problem

Ex:

class TitleCase(Raw):
    def format(self, value):
        return unicode(value).title()

class metadata_registration_api.api.api_form.SubformField(default=None, attribute=None, title=None, description=None, required=None, readonly=None, example=None, mask=None, **kwargs)¶

Bases: flask_restx.fields.Raw

Custom field for subforms

format(value)¶

Formats a field’s value. No-op by default - field classes that modify how the value of existing object keys should be presented should override this and apply the appropriate formatting.

Parameters: value – The value to format
Raises: MarshallingError – In case of formatting problem

Ex:

class TitleCase(Raw):
    def format(self, value):
        return unicode(value).title()

metadata_registration_api.api.api_props module¶

class metadata_registration_api.api.api_props.ApiProperties(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(user=None)¶: Deprecates all entries

get()¶: Fetch a list with all entries

get_parser = <flask_restx.reqparse.RequestParser object>¶

methods: Optional[List[str]] = {'DELETE', 'GET', 'POST'}¶: A list of methods this view can handle.

post(user=None)¶

Add a new entry

The name has to be unique and is internally used as a variable name. The passed string is preprocessed before it is inserted into the database. Preprocessing: All characters are converted to lower case, the leading and trailing white spaces are removed, and intermediate white spaces are replaced with underscores (“_”).

Do not pass a unique identifier since it is generated internally.

synonyms (optional)

deprecated (default=False)

If a data type other than “cv” is added, the controlled_vocabullary is not considered.

class metadata_registration_api.api.api_props.ApiPropertyId(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(id, user=None)¶: Deprecates an entry given its unique identifier

get(id)¶: Fetch an entry given its unique identifier

methods: Optional[List[str]] = {'DELETE', 'GET', 'PUT'}¶: A list of methods this view can handle.

put(id, user=None)¶: Update entry given its unique identifier

metadata_registration_api.api.api_props.check_synonyms_unicity(new_property_payload, exclude_id=None)¶

metadata_registration_api.api.api_props.validate_controlled_vocabulary(entry)¶

metadata_registration_api.api.api_study module¶

class metadata_registration_api.api.api_study.ApiStudy(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(user=None)¶: Deprecates all entries

get(user=None)¶: Fetch a list with all entries

methods: Optional[List[str]] = {'DELETE', 'GET', 'POST'}¶: A list of methods this view can handle.

post(user=None)¶: Add a new entry

class metadata_registration_api.api.api_study.ApiStudyId(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(id, user=None)¶: Delete an entry given its unique identifier

get(id, user=None)¶: Fetch an entry given its unique identifier

methods: Optional[List[str]] = {'DELETE', 'GET', 'PUT'}¶: A list of methods this view can handle.

put(id, user=None)¶: Update an entry given its unique identifier

metadata_registration_api.api.api_study.check_alternate_pk_unicity(entries, pseudo_apks, prop_map)¶: Another dirty mongoDB aggregation to enforce unicity of certain entry properties.

metadata_registration_api.api.api_study.index_study_if_es(study, entries, action)¶

metadata_registration_api.api.api_study.update_study(study, study_converter, payload, message, user=None)¶: Steps to update study state, metadata and upload to DB

metadata_registration_api.api.api_study.validate_form_format_against_form(form_name, form_data, form_cls=None)¶

metadata_registration_api.api.api_user module¶

class metadata_registration_api.api.api_user.ApiUser(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(user=None)¶: Delete all entries

get()¶: Fetch a list with all entries

methods: Optional[List[str]] = {'DELETE', 'GET', 'POST'}¶: A list of methods this view can handle.

parser = <flask_restx.reqparse.RequestParser object>¶

post(user=None)¶: Add a new entry

class metadata_registration_api.api.api_user.ApiUserId(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

delete(id, user=None)¶: Delete an entry given its unique identifier

get(id)¶: Fetch an entry given its unique identifier

methods: Optional[List[str]] = {'DELETE', 'GET', 'PUT'}¶: A list of methods this view can handle.

put(id, user=None)¶: Update an entry given its unique identifier

class metadata_registration_api.api.api_user.Login(api=None, *args, **kwargs)¶

Bases: flask_restx.resource.Resource

methods: Optional[List[str]] = {'POST'}¶: A list of methods this view can handle.

post()¶

Fetch an access token to perform requests which require elevated privileges

Upon successful login, you receive an access token. Pass the token as value of ‘x-access-token’ in the header of every request that requires elevated privileges. The token is only valid for a certain time interval.

metadata_registration_api.api.api_utils module¶

class metadata_registration_api.api.api_utils.ChangeLog(action: str, user_id: str, timestamp: datetime.datetime, manual_user: Union[str, NoneType] = None)¶

Bases: object

action: str¶

manual_user: Optional[str] = None¶

timestamp: datetime.datetime¶

to_dict()¶

user_id: str¶

class metadata_registration_api.api.api_utils.MetaInformation(state: str, change_log=None)¶

Bases: object

add_log(log: metadata_registration_api.api.api_utils.ChangeLog)¶

to_json()¶

metadata_registration_api.api.api_utils.get_cv_items_map(key='name', value='label')¶: Returns a map to find the CV item labels in this format: {cv_name: {item_name: item_label}}

metadata_registration_api.api.api_utils.get_json(url, headers={})¶

metadata_registration_api.api.api_utils.get_mask(request)¶

metadata_registration_api.api.api_utils.get_property_map(key, value, mask=None)¶: Helper to get property mapper

metadata_registration_api.api.decorators module¶

metadata_registration_api.api.decorators.token_required(f)¶: A decorator to ensure that the request contains an access token

Module contents¶

metadata_registration_api.api.general_error_handler(error)¶

metadata_registration_api.api.handle_authorization_error(error)¶

metadata_registration_api.api.handle_does_not_exist_error(error)¶

metadata_registration_api.api.handle_not_unique_error(error)¶

metadata_registration_api.api.http_error_handler(error)¶

metadata_registration_api.api.state_machine_exception(error)¶

Submodules¶

metadata_registration_api.app module¶

metadata_registration_api.app.config_app(app)¶

metadata_registration_api.app.create_app()¶

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: many-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.

validate(*args, **kwargs)¶: Enforce unicity of CV item synonyms

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: many-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 {}

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: many-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 {}

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)

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.

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.

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 (usually validation or assignment) 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: many-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 {}

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)

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)

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.

deprecated¶: Boolean field type.

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 (usually validation or assignment) 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: many-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.

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)

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 (usually validation or assignment) 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.

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.

firstname¶: A unicode string field.

id¶: A field wrapper around MongoDB’s ObjectIds.

is_active¶: Boolean field type.

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)

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¶

Module contents¶

scripts package¶

Submodules¶

scripts.rna_seq_upload module¶

scripts.setup module¶

Module contents¶

test package¶

Submodules¶

test.test_api_base module¶

class test.test_api_base.BaseTestCase(methodName='runTest')¶

Bases: unittest.case.TestCase

Run the WSGI server in separate daemon thread

classmethod setUpClass() → None¶

classmethod tearDownClass() → None¶

test.test_api_cv module¶

test.test_api_form module¶

test.test_api_property module¶

test.test_api_study module¶

test.test_api_user module¶

test.test_api_util module¶

class test.test_api_util.TestAPIUtil(methodName='runTest')¶

Bases: unittest.case.TestCase

test_meta_information_empty_change_log()¶

test.test_main module¶

test.test_main.suite()¶

test.test_utils module¶

Utility function used for only testing

class test.test_utils.ServerThread(config='TESTING')¶

Bases: threading.Thread

run()¶

Method representing the thread’s activity.

You may override this method in a subclass. The standard run() method invokes the callable object passed to the object’s constructor as the target argument, if any, with sequential and keyword arguments taken from the args and kwargs arguments, respectively.

shutdown()¶

test.test_utils.insert(url=None, data=None)¶: Insert a new entry

Metadata Registration Api documentation¶

Installation¶

Prerequisites¶

Setup¶

Run as podman container¶

Run as docker container¶

Run in a conda environment¶

Getting started¶

Resources¶

Access¶

Metadata_Registration_API¶

metadata_registration_api package¶

Subpackages¶

metadata_registration_api.api package¶

Submodules¶

metadata_registration_api.api.api_ctrl_voc module¶

metadata_registration_api.api.api_form module¶

metadata_registration_api.api.api_props module¶

metadata_registration_api.api.api_study module¶

metadata_registration_api.api.api_user module¶

metadata_registration_api.api.api_utils module¶

metadata_registration_api.api.decorators module¶

Module contents¶

Submodules¶

metadata_registration_api.app module¶

metadata_registration_api.errors module¶

metadata_registration_api.model module¶

metadata_registration_api.my_utils module¶

Module contents¶

scripts package¶

Submodules¶

scripts.rna_seq_upload module¶

scripts.setup module¶

Module contents¶

test package¶

Submodules¶

test.test_api_base module¶

test.test_api_cv module¶

test.test_api_form module¶

test.test_api_property module¶

test.test_api_study module¶

test.test_api_user module¶

test.test_api_util module¶

test.test_main module¶

test.test_utils module¶

Module contents¶

Indices and tables¶