openapi: 3.2.0 info: title: Genialis base Sample API version: 0.0.0 description: Backend of the Genialis platform. servers: - url: https://app.genialis.com description: Base URL declared by the provider in apis.yml (roadmap#122). tags: - name: Sample paths: /api/sample: get: operationId: api_sample_list description: 'The extended resolwe Entity viewset. It contains method to set predictios.' parameters: - in: query name: annotations schema: type: string - in: query name: basket schema: type: string - in: query name: collection schema: type: integer - in: query name: collection__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: collection__isnull schema: type: boolean - in: query name: collection__name schema: type: string - in: query name: collection__name__contains schema: type: string - in: query name: collection__name__icontains schema: type: string - in: query name: collection__name__iexact schema: type: string - in: query name: collection__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: collection__name__isnull schema: type: boolean - in: query name: collection__name__istartswith schema: type: string - in: query name: collection__name__startswith schema: type: string - in: query name: collection__slug schema: type: string - in: query name: collection__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: contributor schema: type: integer - in: query name: contributor__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: contributor_name schema: type: string - in: query name: created schema: type: string format: date-time - in: query name: created__date schema: type: string format: date - in: query name: created__gt schema: type: string format: date-time - in: query name: created__gte schema: type: string format: date-time - in: query name: created__isnull schema: type: boolean - in: query name: created__lt schema: type: string format: date-time - in: query name: created__lte schema: type: string format: date-time - in: query name: created__time schema: type: string format: time - in: query name: description schema: type: string - in: query name: description__contains schema: type: string - in: query name: description__icontains schema: type: string - in: query name: description__iexact schema: type: string - in: query name: description__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: description__isnull schema: type: boolean - in: query name: description__istartswith schema: type: string - in: query name: description__startswith schema: type: string - in: query name: descriptor__disease_information__disease_status__iexact schema: type: string - in: query name: descriptor__disease_information__disease_type__icontains schema: type: string - in: query name: descriptor__general__biosample_source__icontains schema: type: string - in: query name: descriptor__general__biosample_treatment__icontains schema: type: string - in: query name: descriptor__general__description__icontains schema: type: string - in: query name: descriptor__immuno_oncology_treatment_type__io_drug__iexact schema: type: string - in: query name: descriptor__immuno_oncology_treatment_type__io_treatment__iexact schema: type: string - in: query name: descriptor__response_and_survival_analysis__confirmed_bor__iexact schema: type: string - in: query name: descriptor__response_and_survival_analysis__pfs_event__iexact schema: type: string - in: query name: descriptor__subject_information__batch__exact schema: type: string - in: query name: descriptor__subject_information__group__iexact schema: type: string - in: query name: descriptor__subject_information__sample_label__icontains schema: type: string - in: query name: descriptor__subject_information__subject_id__icontains schema: type: string - in: query name: group schema: type: string - in: query name: id schema: type: integer - in: query name: id__gt schema: type: integer - in: query name: id__gte schema: type: integer - in: query name: id__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: id__isnull schema: type: boolean - in: query name: id__lt schema: type: integer - in: query name: id__lte schema: type: integer - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - in: query name: modified schema: type: string format: date-time - in: query name: modified__date schema: type: string format: date - in: query name: modified__gt schema: type: string format: date-time - in: query name: modified__gte schema: type: string format: date-time - in: query name: modified__isnull schema: type: boolean - in: query name: modified__lt schema: type: string format: date-time - in: query name: modified__lte schema: type: string format: date-time - in: query name: modified__time schema: type: string format: time - in: query name: name schema: type: string - in: query name: name__contains schema: type: string - in: query name: name__icontains schema: type: string - in: query name: name__iexact schema: type: string - in: query name: name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: name__isnull schema: type: boolean - in: query name: name__istartswith schema: type: string - in: query name: name__startswith schema: type: string - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: owners schema: type: integer - in: query name: owners_name schema: type: string - in: query name: permission schema: type: string - in: query name: relation_id schema: type: integer - in: query name: shared_with_me schema: type: boolean - in: query name: slug schema: type: string - in: query name: slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: status schema: type: string - in: query name: status__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: tags schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: type schema: type: string - in: query name: variant_calls__variant schema: type: integer - in: query name: variant_calls__variant__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: variant_calls__variant__isnull schema: type: boolean - in: query name: version schema: type: string - in: query name: version__gt schema: type: string - in: query name: version__gte schema: type: string - in: query name: version__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: version__isnull schema: type: boolean - in: query name: version__lt schema: type: string - in: query name: version__lte schema: type: string tags: - Sample security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedEntitySerializerWithPermissionsList' description: '' summary: Api sample list x-summary-source: derived post: operationId: api_sample_create description: Only authenticated users can create new collections. tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' multipart/form-data: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' required: true security: - cookieAuth: [] responses: '201': content: application/json: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' description: '' summary: Api sample create x-summary-source: derived /api/sample/{id}: get: operationId: api_sample_retrieve description: 'The extended resolwe Entity viewset. It contains method to set predictios.' parameters: - in: path name: id schema: type: integer description: A unique integer value identifying this entity. required: true tags: - Sample security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' description: '' summary: Api sample retrieve x-summary-source: derived put: operationId: api_sample_update description: 'Update an entity. Original queryset produces a temporary database table whose rows cannot be selected for an update. As a workaround, we patch get_queryset function to return only Entity objects without additional data that is not needed for the update.' parameters: - in: path name: id schema: type: integer description: A unique integer value identifying this entity. required: true tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' multipart/form-data: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' required: true security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' description: '' summary: Api sample update x-summary-source: derived patch: operationId: api_sample_partial_update description: 'The extended resolwe Entity viewset. It contains method to set predictios.' parameters: - in: path name: id schema: type: integer description: A unique integer value identifying this entity. required: true tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/PatchedEntitySerializerWithPermissions' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/PatchedEntitySerializerWithPermissions' multipart/form-data: schema: $ref: '#/components/schemas/PatchedEntitySerializerWithPermissions' security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/EntitySerializerWithPermissions' description: '' summary: Api sample partial update x-summary-source: derived delete: operationId: api_sample_destroy description: Delete a resource. parameters: - in: path name: id schema: type: integer description: A unique integer value identifying this entity. required: true tags: - Sample security: - cookieAuth: [] responses: '204': description: No response body summary: Api sample destroy x-summary-source: derived /api/sample/{id}/permissions: get: operationId: api_sample_permissions_retrieve description: Get or set permissions API endpoint. parameters: - in: path name: id schema: type: integer description: A unique integer value identifying this entity. required: true tags: - Sample security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/CurrentUserPermissions' description: '' summary: Api sample permissions retrieve x-summary-source: derived post: operationId: api_sample_permissions_create description: Get or set permissions API endpoint. parameters: - in: path name: id schema: type: integer description: A unique integer value identifying this entity. required: true tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/Permission' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/Permission' multipart/form-data: schema: $ref: '#/components/schemas/Permission' security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/CurrentUserPermissions' description: '' summary: Api sample permissions create x-summary-source: derived /api/sample/{id}/set_annotations: post: operationId: api_sample_set_annotations_create description: Add the given list of AnnotationFields to the given entity. parameters: - in: path name: id schema: type: integer description: A unique integer value identifying this entity. required: true tags: - Sample requestBody: content: application/json: schema: type: array items: $ref: '#/components/schemas/AnnotationsByPath' application/x-www-form-urlencoded: schema: type: array items: $ref: '#/components/schemas/AnnotationsByPath' multipart/form-data: schema: type: array items: $ref: '#/components/schemas/AnnotationsByPath' required: true security: - cookieAuth: [] responses: '200': description: No response body summary: Api sample set annotations create x-summary-source: derived /api/sample/{id}/set_predictions: post: operationId: api_sample_set_predictions_create description: Add the given list of PredictionField to the given entity. parameters: - in: path name: id schema: type: integer description: A unique integer value identifying this entity. required: true tags: - Sample requestBody: content: application/json: schema: type: array items: $ref: '#/components/schemas/PredictionsByPath' application/x-www-form-urlencoded: schema: type: array items: $ref: '#/components/schemas/PredictionsByPath' multipart/form-data: schema: type: array items: $ref: '#/components/schemas/PredictionsByPath' required: true security: - cookieAuth: [] responses: '200': description: No response body summary: Api sample set predictions create x-summary-source: derived /api/sample/bulk_delete: post: operationId: api_sample_bulk_delete_create description: 'Bulk delete objects in the background. The background task is returned.' tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/Delete' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/Delete' multipart/form-data: schema: $ref: '#/components/schemas/Delete' required: true security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/BackgroundTask' description: '' summary: Api sample bulk delete create x-summary-source: derived /api/sample/duplicate: post: operationId: api_sample_duplicate_create description: 'Bulk duplicate objects in the background. The background task is returned.' tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/Duplicate' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/Duplicate' multipart/form-data: schema: $ref: '#/components/schemas/Duplicate' required: true security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/BackgroundTask' description: '' summary: Api sample duplicate create x-summary-source: derived /api/sample/move_to_collection: post: operationId: api_sample_move_to_collection_create description: Move samples from source to destination collection. tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/MoveEntityToCollection' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/MoveEntityToCollection' multipart/form-data: schema: $ref: '#/components/schemas/MoveEntityToCollection' required: true security: - cookieAuth: [] responses: '200': description: No response body summary: Api sample move to collection create x-summary-source: derived /api/sample/slug_exists: get: operationId: api_sample_slug_exists_retrieve description: 'Check if given url slug exists. Check if slug given in query parameter ``name`` exists. Return ``True`` if slug already exists and ``False`` otherwise.' parameters: - in: query name: name schema: type: string minLength: 1 required: true tags: - Sample security: - cookieAuth: [] responses: '200': content: application/json: schema: type: boolean description: '' summary: Api sample slug exists retrieve x-summary-source: derived /api/sample/subscribe: post: operationId: api_sample_subscribe_create description: Register an Observer for a resource. tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/ObserverSubscribeRequest' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/ObserverSubscribeRequest' multipart/form-data: schema: $ref: '#/components/schemas/ObserverSubscribeRequest' required: true security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/ObserverSubscription' description: '' summary: Api sample subscribe create x-summary-source: derived /api/sample/unsubscribe: post: operationId: api_sample_unsubscribe_create description: Unregister a subscription. tags: - Sample requestBody: content: application/json: schema: $ref: '#/components/schemas/ObserverSubscription' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/ObserverSubscription' multipart/form-data: schema: $ref: '#/components/schemas/ObserverSubscription' required: true security: - cookieAuth: [] responses: '200': description: No response body summary: Api sample unsubscribe create x-summary-source: derived components: schemas: BackgroundTaskStatusEnum: enum: - WT - PR - OK - ER type: string description: '* `WT` - Waiting * `PR` - Processing * `OK` - Done * `ER` - Error' Duplicate: type: object description: Deserializer for duplicate endpoint. properties: ids: type: array items: type: integer required: - ids EntitySerializerWithPermissions: type: object description: Serializer for Entity with added collection field. properties: created: type: string format: date-time readOnly: true duplicated: type: - string - 'null' format: date-time readOnly: true id: type: integer readOnly: true modified: type: string format: date-time readOnly: true data_count: type: integer description: Return number of data objects on the collection. readOnly: true status: type: string readOnly: true contributor: $ref: '#/components/schemas/Contributor' description: type: string name: type: string settings: {} slug: type: - string - 'null' tags: type: array items: type: string maxLength: 255 collection: allOf: - $ref: '#/components/schemas/RelationshipDict' type: type: - string - 'null' maxLength: 100 current_user_permissions: type: array items: $ref: '#/components/schemas/CurrentUserPermissions' readOnly: true required: - contributor - created - current_user_permissions - data_count - duplicated - id - modified - status AnnotationsByPath: type: object description: Serializer that reads annotation field and its value. properties: field_path: type: string maxLength: 257 value: {} required: - field_path - value PermissionsEnum: enum: - none - view - edit - share - owner type: string description: '* `none` - none * `view` - view * `edit` - edit * `share` - share * `owner` - owner' Contributor: type: object description: Serializer for contributor User objects. properties: first_name: type: string maxLength: 150 id: type: integer readOnly: true last_name: type: string maxLength: 150 username: type: string description: Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only. pattern: ^[\w.@+-]+$ maxLength: 150 required: - id - username PublicEnum: enum: - VIEW - EDIT - SHARE - OWNER type: string description: '* `VIEW` - VIEW * `EDIT` - EDIT * `SHARE` - SHARE * `OWNER` - OWNER' CurrentUserPermissionsTypeEnum: enum: - user - group - public type: string description: '* `user` - user * `group` - group * `public` - public' BackgroundTask: type: object description: Serialize the BackgroundTask model. properties: id: type: integer readOnly: true started: type: - string - 'null' format: date-time finished: type: - string - 'null' format: date-time status: $ref: '#/components/schemas/BackgroundTaskStatusEnum' description: type: string maxLength: 256 output: {} required: - description - id Permission: type: object description: 'Permission serializer. Dictionary keys for users and groups are either ids or usernames (emails) or group names.' properties: users: type: object additionalProperties: enum: - VIEW - EDIT - SHARE - OWNER type: string description: '* `VIEW` - VIEW * `EDIT` - EDIT * `SHARE` - SHARE * `OWNER` - OWNER' groups: type: object additionalProperties: enum: - VIEW - EDIT - SHARE - OWNER type: string description: '* `VIEW` - VIEW * `EDIT` - EDIT * `SHARE` - SHARE * `OWNER` - OWNER' public: $ref: '#/components/schemas/PublicEnum' ObserverSubscribeRequest: type: object description: Serializer for the subscribe endpoint. properties: ids: type: - array - 'null' items: type: integer session_id: type: string required: - session_id PaginatedEntitySerializerWithPermissionsList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/EntitySerializerWithPermissions' CurrentUserPermissions: type: object description: Current user permissions serializer. properties: id: type: integer type: $ref: '#/components/schemas/CurrentUserPermissionsTypeEnum' name: type: string maxLength: 100 username: type: string maxLength: 150 permissions: type: array items: $ref: '#/components/schemas/PermissionsEnum' required: - permissions - type PredictionsByPath: type: object description: Serializer that reads prediction field and its value. properties: field_path: type: string maxLength: 257 value: {} required: - field_path - value MoveEntityToCollection: type: object description: Serializer for moving entities to a collection. properties: ids: type: array items: type: integer destination_collection: type: integer required: - destination_collection - ids ObserverSubscription: type: object description: Serializer for the subscribe response. properties: subscription_id: type: string format: uuid required: - subscription_id RelationshipDict: type: object description: Serializer for the DictRelatedField relation. properties: id: type: integer slug: type: - string - 'null' PatchedEntitySerializerWithPermissions: type: object description: Serializer for Entity with added collection field. properties: created: type: string format: date-time readOnly: true duplicated: type: - string - 'null' format: date-time readOnly: true id: type: integer readOnly: true modified: type: string format: date-time readOnly: true data_count: type: integer description: Return number of data objects on the collection. readOnly: true status: type: string readOnly: true contributor: $ref: '#/components/schemas/Contributor' description: type: string name: type: string settings: {} slug: type: - string - 'null' tags: type: array items: type: string maxLength: 255 collection: allOf: - $ref: '#/components/schemas/RelationshipDict' type: type: - string - 'null' maxLength: 100 current_user_permissions: type: array items: $ref: '#/components/schemas/CurrentUserPermissions' readOnly: true Delete: type: object description: Bulk delete given objects. properties: ids: type: array items: type: integer required: - ids securitySchemes: cookieAuth: type: apiKey in: cookie name: sessionid