scidatacontainer_db API

Models

class scidatacontainer_db.models.DataSet(*args, **kwargs)

Bases: DataSetBase

Representation of a ZDC dataset after parsing.

Parameters:

id (UUIDField) – UUID primary key
_replaced_by_field_id (OneToOneField) – Other instance that replaces this instance. Don’t use this field but the getter and setter functions
datasetbase_ptr_id (OneToOneField) – Datasetbase ptr
owner_id (ForeignKey) – Owner of the dataset
upload_time (DateTimeField) – Datetime of server uplaod
complete (BooleanField) – Complete flag to ensure overwrite protection
valid (BooleanField) – Valid flag to mark erroneous datasets
invalidation_comment (TextField) – Comment to describe why this dataset is invalid
size (IntegerField) – Size of the dataset in bytes
server_path (CharField) – File path to find the file on the server
created (DateTimeField) – Creation timestamp of the container
storage_time (DateTimeField) – Timestamp of storage of the container
static (BooleanField) – Flag for static containers
container_type_id (ForeignKey) – ContainerType of this dataset
hash (CharField) – Hash of the container
model_version (CharField) – Version of the data model
author (CharField) – Author
email (EmailField) – Email
organization (CharField) – Affiliation of the author
comment (TextField) – Comment
title (CharField) – Title
description (TextField) – Description
timestamp (DateTimeField) – Timestamp
doi (CharField) – Doi
license (TextField) – Name or text of the license

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

get_read_perm_group_list(): Get a list of groups that have read only permission for this object.

get_read_perm_user_list(): Get a list of users that have read only permission for this object.

get_write_perm_group_list(): Get a list of groups that have read and write permission for this object.

get_write_perm_user_list(): Get a list of users that have read and write permission for this object.

update_attributes(d, user): Update a :model:`scidatacontainer_db.DataSet` instance with the information in the dictionary d. It first ensures that the user is the owner of the DataSet.

class scidatacontainer_db.models.DataSetBase(*args, **kwargs)

Bases: Model

Base Model of a :model:`scidatacontainer_db.DataSet`. It is required for DataSets that are unknown to the server. For example if an unknown ID is found in the :model:`scidatacontainer_db.DataSetBase`.replaces attribute, an instance of DataSetBase is created. It can be later on replaced by uploading this dataset without breaking the relations imposed by replaced_by or replaces.

Parameters:

id (UUIDField) – UUID primary key
_replaced_by_field_id (OneToOneField) – Other instance that replaces this instance. Don’t use this field but the getter and setter functions

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

property is_replaced: bool: Returna true if the model instance is replaced by another DataSet.

property replaced_by: Other object that replaces this instance. This might be None.

property replaces: Other object that is replaced by this instance. This might by None.

class scidatacontainer_db.models.ContainerType(*args, **kwargs)

Bases: Model

Model to represent the container type of a dataset.

Parameters:

dbid (UUIDField) – UUID primary key
name (CharField) – Name of the container type
id (CharField) – Identifier of the container type
version (CharField) – Version of the container type

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

classmethod to_ContainerType(pt): Convert a dictionary as found in a ZDC container into a :model:`scidatacontainer_db.ContainerType` instance.

class scidatacontainer_db.models.File(*args, **kwargs)

Bases: Model

Model to represent a File from the content of a dataset. If the file is a JSON file, the content will be saved, too.

Parameters:

id (UUIDField) – UUID primary key
name (CharField) – File name inside the ZDC dataset
size (IntegerField) – File size in bytes
content (JSONField) – Dictionary containing the content of a JSON file

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

class scidatacontainer_db.models.Keyword(*args, **kwargs)

Bases: Model

Model to represent a Keyword of a DataSet.

Parameters:

id (UUIDField) – UUID primary key
name (CharField) – String representation of a keyword

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

class scidatacontainer_db.models.Software(*args, **kwargs)

Bases: Model

Model to represent a Software package used in a dataset.

Parameters:

dbid (UUIDField) – UUID primary_key
name (CharField) – Name of the Software package
version (CharField) – Version of the software package
id (CharField) – Identifier of the software package
id_type (CharField) – Type of the given identifier

exception DoesNotExist: Bases: ObjectDoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

classmethod to_Software(pt): Convert a dictionary as found in a ZDC container into a :model:`scidatacontainer_db.Software` instance.

Views

class scidatacontainer_db.views.IndexView(**kwargs)

Bases: LoginRequiredMixin, ListView

Display a list of :model:`scidatacontainer_db.DataSet`

Template :template:`scidatacontainer_db/index.html`

get_context_data(**kwargs): Context Data function to enable pagination.

get_queryset(): Get the list of :model:`scidatacontainer_db.DataSet` objects to display. It only provides :model:`scidatacontainer_db.DataSet` objects that the user is allowed to read and filters for the search query.

model: alias of DataSet

class scidatacontainer_db.views.DetailView(**kwargs)

Bases: LoginRequiredMixin, DetailView

Display the detailed information of a single :model:`scidatacontainer_db.DataSet`.

Template :template:`scidatacontainer_db/detail.html`

get(request, pk): Handle a GET request. If this :model:`scidatacontainer_db:DataSet` is marked invalid, a warning message will be shown. If it was replaced by a successor :model:`scidatacontainer_db.DataSet`, a warning message will be shown and the user is redirected to the successor.

get_object(): Get a :model:`scidatacontainer_db.DataSet` instance and make sure the requesting user has read permissions.

model: alias of DataSet

class scidatacontainer_db.views.UploadFileView(**kwargs)

Bases: LoginRequiredMixin, View

Upload a file and parse its content.

class scidatacontainer_db.views.DownloadFileView(**kwargs)

Bases: LoginRequiredMixin, DetailView

Provide a ::model::scidatacontainer_db.DataSet as a FileResponse.

model: alias of DataSet

class scidatacontainer_db.views.UpdatePermissionsView(**kwargs)

Bases: LoginRequiredMixin, UpdateView

Display a permission modification page and handle a POST request to change them.

Context

users: List of all available users.
groups: List of all available groups.
r_users: List of users with read-only permission.
w_users: List of users with read and write permission.
rw_users: List of users with read-only or read-and-write permission.
r_groups: List of groups with read-only permission.
w_groups: List of groups with read and write permission.
rw_groups: List of groups with read-only or read-and-write permission.

Template

:template:`scidatacontainer_db/update_permissions.html`

get_context_data(**kwargs): Prepare context data for the template.

get_object(): Check permission while finding the :model:`scidatacontainer_db.DataSet`.

model: alias of DataSet

post(request, pk): Handle POST requests to update the permissions on an object.

class scidatacontainer_db.views.InvalidationView(**kwargs)

Bases: LoginRequiredMixin, SingleObjectMixin, View

Handle the request from the invalidation modal.

It handles PATCH and POST requests. POST request require _method set to patch to enable PATCH requests even thought web browsers don’t support PATCH requests.

model: alias of DataSet

patch(request, pk)

Handle a PATCH request.

If the user is the owner of a :model:`scidatacontainer_db.DataSet`, store the invalidation reason and unset the valid flag. Afterwards, redirect to the overview page.

post(request, pk): Handle a POST request. This is a forward to the patch method if _method is patch.

class scidatacontainer_db.views.ApiKeyView(**kwargs)

Bases: LoginRequiredMixin, ListView

View to list a users API keys. A post request can be used to generate a new API key.

Template

:template:`scidatacontainer_db/api_keys.html`

get_context_data(**kwargs): Context Data function to enable pagination.

get_queryset(): Filter :model:`knox.AuthToken` instances to show only the ones from the requesting user.

model: alias of AuthToken

post(request): Handle a POST request for key generation or deletion.

class scidatacontainer_db.views.LoginView(**kwargs)

Bases: LoginView

Display a login page.

Template

:template:`scidatacontainer_db/login.html`

class scidatacontainer_db.views.LogoutView(**kwargs)

Bases: LogoutView

Logout a user and redirect to index page.

REST API Views

class scidatacontainer_db.api_views.DataSetViewSet(**kwargs)

Bases: ReadOnlyModelViewSet, CreateModelMixin

get_queryset()

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

serializer_class: alias of DataSetSerializer

class scidatacontainer_db.api_views.DataSetViewSet(**kwargs)

Bases: ReadOnlyModelViewSet, CreateModelMixin

get_queryset()

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

serializer_class: alias of DataSetSerializer

class scidatacontainer_db.api_views.ContainerTypeViewSet(**kwargs)

Bases: PermissionFilteredReadOnlyViewSet

model: alias of ContainerType

serializer_class: alias of ContainerTypeSerializer

class scidatacontainer_db.api_views.FileViewSet(**kwargs)

Bases: PermissionFilteredReadOnlyViewSet

model: alias of File

serializer_class: alias of FileSerializer

class scidatacontainer_db.api_views.KeywordViewSet(**kwargs)

Bases: PermissionFilteredReadOnlyViewSet

model: alias of Keyword

serializer_class: alias of KeywordSerializer

class scidatacontainer_db.api_views.SoftwareViewSet(**kwargs)

Bases: PermissionFilteredReadOnlyViewSet

model: alias of Software

serializer_class: alias of SoftwareSerializer

class scidatacontainer_db.api_views.PermissionFilteredReadOnlyViewSet(**kwargs)

Bases: ReadOnlyModelViewSet

get_queryset()

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

Parsers

class scidatacontainer_db.parsers.BaseParser

Bases: ABC

Base class for file format specific parsers. Parsers should inherit from this class because it ensures the validation of the meta data.

parse(filename: str, user: User) → DataSet

Read the meta data from the file, validate it and store it in the DB.

Parameters:

filename – Filename of the ZDC dataset.
user – User sending the request to validate permissions and to

set ownership.

class scidatacontainer_db.parsers.ZipContainerParser

Bases: BaseParser

Parser implementing the file type specific routines for .ZIP based containers.

Utils

class scidatacontainer_db.utils.ensure_read_permission(user: User, dataset)

Bases:

Checks if the user has read permission for a given DataSet. Raises a PermissionDenied Exception otherwise.

Parameters:

user – User object of requesting user.
dataset – DataSet that the user wants to read.

Raises:

django.core.exceptions.PermissionDenied – If the user doesn’t have

read permissions.

class scidatacontainer_db.utils.ensure_owner(user: User, dataset)

Bases:

Checks if the user is the owner of a given DataSet. Raises a PermissionDenied Exception otherwise.

Parameters:

user – User object of requesting user.
dataset – DataSet to check the ownership.

Raises:

django.core.exceptions.PermissionDenied – If the user isn’t the

owner.

class scidatacontainer_db.utils.APIResponse(data=None, status=None, template_name=None, headers=None, exception=False, content_type=None, reason=None)

Bases: Response

Custom Response derived from rest_framewort.response.Response to set the reason phrase on creation of the response.

class scidatacontainer_db.utils.MetaDBError

Bases: Exception

Excetption raised by various function and caught by the request handling views. The status code and reason_phrase stored in the instances will be part of the response.