Sample List
Sample
Samples are handled like Stocks, i.e. we have different predefined types, which are stored in the TypeStore.
As of this writing, we have the default SAMPLE and the ILLUMINALIBRARY.
Each can have different custom properties.
Protocols & Samples
Before being able to add a protocol to a Sample you will first need to create a Protocol.
ProtocolTypes are already defined and extend the TypeStore. For each new ProtocolType a new TypeStore
has to be created with the same name.
Note: Check the /api/v2/protocols/protocols endpoint on how to create them and
the corresponding introduction/explanation on ProtocolTypes
/api/v2/protocols/protocoltypes!
TypeStore:
- id: 1
name: Library Preparation
content_type__model: Protocol
- id: 2
name: ILLUMINALIBRARY
content_type__model: Sample
ProtocolType:
- id: 10
name: Illumina Library Preparation
type: {id: 1}
applicable_model_types: [{id: 2}]
Protocol:
- id: 20
name: Illumina Prep X11
type: {id: 1}
ProtocolList
Samples can have Protocols linked through ProtocolList. ProtocolLists attached to Samples
If the payload contains a ProtocolList value with a ProtocolList ID, then the existing ProtocolList will be
updated.
The payload can not contain a ProtocolList id if you want to update ProtocolList e.g. add a new Protocol.
If an id is provided, we will assume nothing has changed!!
Once a ProtocolList is created - i.e. has an id - it cannot be modified.
When using a predefined ProtocolList (is_template) then this object needs to be send as a whole,
without an id.
i.e. For the UI to enable the edit feature of a ProtocolList on the Sample page, it can simply send/PUT
another ProtocolList object without an id and so a new ProtocolList is created.
The unlinked ProtocolList will be deleted.
POST sample with ProtocolList
Below is a most minimal payload to create a Sample with a to-be-autogenerated ProtocolList with one Protocol
Create a new ProtocolList
{
"results": {
"name": {"value": {"name": "SampleX"}},
"type": {"value": {"id": "SAMPLE_TYPESTORE_UUID"}},
"protocol_list": {
"value": {
"protocols": [{
"order": 0,
"id": "A_PROTOCOL_UUID",
}]
}
}
}
}
» click to learn about Filtering, Ordering and more...
Accepted filters:
- search: Search in the following fields: ^name, ^description. (^startswith, $regex, =exact)
- id: ID (exact)
- created: Created (exact)
- modified: Modified (exact)
- name: Name starts with (istartswith)
- description: Description contains (icontains)
- query: Search filter on the name property (exact)
- owner: Owner Username (exact)
- owned_by: Filter on list of owned by group names [OR] (exact)
- public: Public (exact)
- deleted: Deleted (exact)
- deleted_by: Deleted by (exact)
- deleted_date: Deleted date (exact)
- type: Filter by the protocol type e.g. extract (exact)
- model_type: Filter by the protocol type e.g. extract (exact)
- created_by: Created by Username (exact)
- modified_by: Modified by Username (exact)
- assay: Assay (exact)
- study: [invalid name] (exact)
- project: [invalid name] (exact)
Advanced Filtering
You can also filter using a json object to process all search parameters. Currently this filter supports the syntax as produced/used by the http://summitroute.github.io/react-structured-filter/ search UI.
Example
?query_expression={"category":"name","operator":"contains","value":"Y00"},
{"category":"amount","operator":">","value":"10"},
{"category":"type__name","operator":"exact","value":"ANTIBODY"}
» more info about the query_expression param..
Preset mappings
- specimen: specimen__name
- protocol_list: protocol_list__name
- parents: <function filter_by_parents at 0x7f43648fa3b0>
- children: <function filter_by_children at 0x7f43648fa320>
- stock_locations: stock_locations__name
- used_in_experiments: <function filter_samples_used_in_experiments at 0x7f43648fa290>
- from_experiments: <function filter_samples_from_experiments at 0x7f43648fa200>
- deleted: <function filter_deleted at 0x7f45063b6710>
- deleted_by: deleted_by__username
- type: type__name
- owner: owner__username
- owned_by: owned_by__name
- notes: notes__content
- created_by: created_by__username
- modified_by: modified_by__username
- plate_type: plate_type__name
- primary_project: primary_project__name
- registered_with_assay: registered_with_assay__name
- assay: assay__name
- rt_tem_grid_model: rt_tem_grid_model__name
- cryo_tem_grid_model: cryo_tem_grid_model__name
- grid_prep_instrument: grid_prep_instrument__name
- vitrification_instrument: vitrification_instrument__name
- fibmilling_instrument: fibmilling_instrument__name
Operators
- ==
- =
- >=
- >
- <=
- <
- contains
- icontains
- exact
- iexact
- startswith
- istartswith
- endswith
- iendswith
Permission filtering
Based on the current logged in user you can filter for objects that have a particular permission set:
- can_change: True/False, show objects that you can change
- can_delete: True/False, show objects that you can delete
# not applicable - will raise NotAcceptable:
- can_view: as this is always True, you can only view items you are allowed to see
Ordering
You can order on practically any field even spanning relations.
# reverse order on owner username
?ordering=-owner
# order on related field
?ordering=category__version
## Sample
`Samples` are handled like `Stocks`, i.e. we have different predefined types, which are stored in the `TypeStore`.
As of this writing, we have the default `SAMPLE` and the `ILLUMINALIBRARY`.
Each can have different custom properties.
### Protocols & Samples
Before being able to add a protocol to a Sample you will first need to create a Protocol.
`ProtocolTypes` are already defined and extend the `TypeStore`. For **each new `ProtocolType`** a new `TypeStore`
has to be created with the same name.
**Note**: Check the [/api/v2/protocols/protocols](/api/v2/protocols/protocols) endpoint on how to create them and
the corresponding introduction/explanation on `ProtocolTypes`
[/api/v2/protocols/protocoltypes](/api/v2/protocols/protocoltypes)!
```
TypeStore:
- id: 1
name: Library Preparation
content_type__model: Protocol
- id: 2
name: ILLUMINALIBRARY
content_type__model: Sample
ProtocolType:
- id: 10
name: Illumina Library Preparation
type: {id: 1}
applicable_model_types: [{id: 2}]
Protocol:
- id: 20
name: Illumina Prep X11
type: {id: 1}
```
## ProtocolList
`Samples` can have `Protocols` linked through `ProtocolList`. `ProtocolLists` attached to `Samples`
If the payload contains a `ProtocolList` value with a `ProtocolList ID`, then the existing ProtocolList will be
updated.
The payload can not contain a `ProtocolList` id if you want to update `ProtocolList` e.g. add a new `Protocol`.
If an `id` is provided, we will assume nothing has changed!!
Once a `ProtocolList` is created - i.e. has an `id` - it cannot be modified.
When using a predefined `ProtocolList` (`is_template`) then this object needs to be send as a whole,
without an `id`.
i.e. For the UI to enable the edit feature of a `ProtocolList` on the `Sample` page, it can simply send/`PUT`
another `ProtocolList` object without an `id` and so a new `ProtocolList` is created.
The unlinked `ProtocolList` will be deleted.
### POST sample with ProtocolList
Below is a most minimal payload to create a `Sample` with a to-be-autogenerated `ProtocolList` with one `Protocol`
#### Create a new ProtocolList
```
{
"results": {
"name": {"value": {"name": "SampleX"}},
"type": {"value": {"id": "SAMPLE_TYPESTORE_UUID"}},
"protocol_list": {
"value": {
"protocols": [{
"order": 0,
"id": "A_PROTOCOL_UUID",
}]
}
}
}
}
```
None None
The default modelviewset used in this project
Add JSONPatch like functionality to bulk update items.
### Bulk Delete
This view also allows for one to bulk delete items. The url needs to be appended by ``/bulk_delete/`` and the ids
need to be given by multiple query_params:
```
{current_url}/bulk_delete/?id=<id_1>,id=<id_2>
```
GET /api/v2/stocks/samples/?format=api&ordering=-deleted
{
"previous": null,
"next": null,
"current": 1,
"total": 7,
"total_pages": 1,
"results": [
{
"code": {
"name": "code",
"value": "",
"category": "property"
},
"created_on_data_registration": {
"name": "created_on_data_registration",
"category": "property",
"value": false
},
"produced": {
"name": "produced",
"value": "",
"category": "property"
},
"model_type": {
"name": "model_type",
"category": "property",
"value": "SEQUENCINGLIBRARY"
},
"parents": {
"name": "parents",
"value": [
{
"id": "cdb44868-fee0-43f0-b5c9-615002aabe4c",
"name": "Merged RNA Extracts _test_",
"label": null,
"deleted": false,
"model_name": "sample",
"app_name": "stocks",
"model_type": "GENERICSAMPLE"
}
],
"category": "property"
},
"children": {
"name": "children",
"value": [],
"category": "property"
},
"organism": {
"name": "organism",
"value": {},
"category": "property"
},
"is_used_in_assay": {
"name": "is_used_in_assay",
"category": "property",
"value": false
},
"specimen": {
"name": "specimen",
"value": {},
"category": "property"
},
"type": {
"name": "type",
"value": {
"name": "SEQUENCINGLIBRARY",
"id": "562efa5b-5dd4-4452-b1b3-808226ed3182"
},
"category": "property"
},
"material_type": {
"name": "material_type",
"value": {},
"category": "property"
},
"stock_locations": {
"name": "stock_locations",
"value": [],
"category": "property"
},
"protocol_list": {
"name": "protocol_list",
"category": "property",
"value": {}
},
"sample_status": {
"name": "sample_status",
"value": {
"value": "CREATED",
"label": "CREATED"
},
"category": "property"
},
"sample_qc": {
"name": "sample_qc",
"value": {
"value": null,
"label": "None"
},
"category": "property"
},
"is_pool": {
"name": "is_pool",
"category": "property",
"value": false
},
"is_control": {
"name": "is_control",
"category": "property",
"value": false
},
"control_name": {
"name": "control_name",
"category": "property",
"value": ""
},
"control_type": {
"name": "control_type",
"value": {},
"category": "property"
},
"is_single_cell": {
"name": "is_single_cell",
"category": "property",
"value": false
},
"single_cell_type": {
"name": "single_cell_type",
"value": {},
"category": "property"
},
"cell_number": {
"name": "cell_number",
"category": "property",
"value": null
},
"has_plate_position": {
"name": "has_plate_position",
"category": "property",
"value": false
},
"plate_name": {
"name": "plate_name",
"category": "property",
"value": ""
},
"plate_code": {
"name": "plate_code",
"category": "property",
"value": ""
},
"plate_type": {
"name": "plate_type",
"value": {},
"category": "property"
},
"plate_position": {
"name": "plate_position",
"category": "property",
"value": ""
},
"primary_project": {
"name": "primary_project",
"value": {},
"category": "property"
},
"used_in_experiments": {
"name": "used_in_experiments",
"value": [],
"category": "property"
},
"from_experiments": {
"name": "from_experiments",
"value": [],
"category": "property"
},
"owner": {
"name": "owner",
"value": {
"id": 3,
"username": "demo",
"full_name": "Demo User"
},
"category": "property"
},
"owned_by": {
"name": "owned_by",
"value": {
"id": 2,
"name": "Demo"
},
"category": "property"
},
"deleted": {
"name": "deleted",
"value": false,
"category": "property"
},
"deleted_by": {
"name": "deleted_by",
"value": null,
"category": "property"
},
"deleted_date": {
"name": "deleted_date",
"value": null,
"category": "property"
},
"public": {
"name": "public",
"value": true,
"category": "property"
},
"permissions": {
"name": "permissions",
"value": {
"public": true,
"actions": {},
"allowed": [
"view"
]
},
"category": "property"
},
"notes": {
"name": "notes",
"category": "property",
"value": 0
},
"choice_label": {
"name": "choice_label",
"category": "property",
"value": "HiSeq polyA library _test_"
},
"model_name": {
"name": "model_name",
"category": "property",
"value": "sample"
},
"app_name": {
"name": "app_name",
"category": "property",
"value": "stocks"
},
"name": {
"name": "name",
"value": {
"id": "41400a50-90ca-4721-b9fd-352aad7cdafa",
"name": "HiSeq polyA library _test_",
"model_name": "sample",
"app_name": "stocks",
"model_type": "SEQUENCINGLIBRARY"
},
"category": "property"
},
"description": {
"name": "description",
"category": "property",
"value": ""
},
"id": {
"name": "id",
"category": "property",
"value": "41400a50-90ca-4721-b9fd-352aad7cdafa"
},
"created": {
"name": "created",
"value": "2025-12-16T09:33:23.222924+01:00",
"category": "property"
},
"modified": {
"name": "modified",
"value": "2025-12-16T09:33:23.230069+01:00",
"category": "property"
},
"created_by": {
"name": "created_by",
"value": {
"id": 3,
"username": "demo",
"full_name": "Demo User"
},
"category": "property"
},
"modified_by": {
"name": "modified_by",
"value": {
"id": 3,
"username": "demo",
"full_name": "Demo User"
},
"category": "property"
}
},
{
"code": {
"name": "code",
"value": "",
"category": "property"
},
"created_on_data_registration": {
"name": "created_on_data_registration",
"category": "property",
"value": false
},
"produced": {
"name": "produced",
"value": "",
"category": "property"
},
"model_type": {
"name": "model_type",
"category": "property",
"value": "SEQUENCINGLIBRARY"
},
"parents": {
"name": "parents",
"value": [
{
"id": "cdb44868-fee0-43f0-b5c9-615002aabe4c",
"name": "Merged RNA Extracts _test_",
"label": null,
"deleted": false,
"model_name": "sample",
"app_name": "stocks",
"model_type": "GENERICSAMPLE"
}
],
"category": "property"
},
"children": {
"name": "children",
"value": [],
"category": "property"
},
"organism": {
"name": "organism",
"value": {},
"category": "property"
},
"is_used_in_assay": {
"name": "is_used_in_assay",
"category": "property",
"value": false
},
"specimen": {
"name": "specimen",
"value": {},
"category": "property"
},
"type": {
"name": "type",
"value": {
"name": "SEQUENCINGLIBRARY",
"id": "562efa5b-5dd4-4452-b1b3-808226ed3182"
},
"category": "property"
},
"material_type": {
"name": "material_type",
"value": {},
"category": "property"
},
"stock_locations": {
"name": "stock_locations",
"value": [],
"category": "property"
},
"protocol_list": {
"name": "protocol_list",
"category": "property",
"value": {}
},
"sample_status": {
"name": "sample_status",
"value": {
"value": "CREATED",
"label": "CREATED"
},
"category": "property"
},
"sample_qc": {
"name": "sample_qc",
"value": {
"value": null,
"label": "None"
},
"category": "property"
},
"is_pool": {
"name": "is_pool",
"category": "property",
"value": false
},
"is_control": {
"name": "is_control",
"category": "property",
"value": false
},
"control_name": {
"name": "control_name",
"category": "property",
"value": ""
},
"control_type": {
"name": "control_type",
"value": {},
"category": "property"
},
"is_single_cell": {
"name": "is_single_cell",
"category": "property",
"value": false
},
"single_cell_type": {
"name": "single_cell_type",
"value": {},
"category": "property"
},
"cell_number": {
"name": "cell_number",
"category": "property",
"value": null
},
"has_plate_position": {
"name": "has_plate_position",
"category": "property",
"value": false
},
"plate_name": {
"name": "plate_name",
"category": "property",
"value": ""
},
"plate_code": {
"name": "plate_code",
"category": "property",
"value": ""
},
"plate_type": {
"name": "plate_type",
"value": {},
"category": "property"
},
"plate_position": {
"name": "plate_position",
"category": "property",
"value": ""
},
"primary_project": {
"name": "primary_project",
"value": {},
"category": "property"
},
"used_in_experiments": {
"name": "used_in_experiments",
"value": [],
"category": "property"
},
"from_experiments": {
"name": "from_experiments",
"value": [],
"category": "property"
},
"owner": {
"name": "owner",
"value": {
"id": 3,
"username": "demo",
"full_name": "Demo User"
},
"category": "property"
},
"owned_by": {
"name": "owned_by",
"value": {
"id": 2,
"name": "Demo"
},
"category": "property"
},
"deleted": {
"name": "deleted",
"value": false,
"category": "property"
},
"deleted_by": {
"name": "deleted_by",
"value": null,
"category": "property"
},
"deleted_date": {
"name": "deleted_date",
"value": null,
"category": "property"
},
"public": {
"name": "public",
"value": true,
"category": "property"
},
"permissions": {
"name": "permissions",
"value": {
"public": true,
"actions": {},
"allowed": [
"view"
]
},
"category": "property"
},
"notes": {
"name": "notes",
"category": "property",
"value": 0
},
"choice_label": {
"name": "choice_label",
"category": "property",
"value": "HiSeq total RNA library _test_"
},
"model_name": {
"name": "model_name",
"category": "property",
"value": "sample"
},
"app_name": {
"name": "app_name",
"category": "property",
"value": "stocks"
},
"name": {
"name": "name",
"value": {
"id": "eaf1571f-d40e-4a7b-bf3d-a42d39f6da9a",
"name": "HiSeq total RNA library _test_",
"model_name": "sample",
"app_name": "stocks",
"model_type": "SEQUENCINGLIBRARY"
},
"category": "property"
},
"description": {
"name": "description",
"category": "property",
"value": ""
},
"id": {
"name": "id",
"category": "property",
"value": "eaf1571f-d40e-4a7b-bf3d-a42d39f6da9a"
},
"created": {
"name": "created",
"value": "2025-12-16T09:33:23.428721+01:00",
"category": "property"
},
"modified": {
"name": "modified",
"value": "2025-12-16T09:33:23.437030+01:00",
"category": "property"
},
"created_by": {
"name": "created_by",
"value": {
"id": 3,
"username": "demo",
"full_name": "Demo User"
},
"category": "property"
},
"modified_by": {
"name": "modified_by",
"value": {
"id": 3,
"username": "demo",
"full_name": "Demo User"
},
"category": "property"
}
},
{
"code": {
"name": "code",
"value": "",
"category": "property"
},
"created_on_data_registration": {
"name": "created_on_data_registration",
"category": "property",
"value": false
},
"produced": {
"name": "produced",
"value": "",
"category": "property"
},
"model_type": {
"name": "model_type",
"category": "property",
"value": "GENERICSAMPLE"
},
"parents": {
"name": "parents",
"value": [],
"category": "property"
},
"children": {
"name": "children",
"value": [
{
"id": "ae49754c-7eb4-46d6-a44f-b911f93b6d9d",
"name": "RNA Extract Mouse 1 _test_",
"label": null,
"deleted": false,
"model_name": "sample",
"app_name": "stocks",
"model_type": "GENERICSAMPLE"
}
],
"category": "property"
},
"organism": {
"name": "organism",
"value": {},
"category": "property"
},
"is_used_in_assay": {
"name": "is_used_in_assay",
"category": "property",
"value": false
},
"specimen": {
"name": "specimen",
"value": {
"id": "a7ea1cb8-d07a-4193-a4eb-e0e5e3292275",
"name": "Balb/c",
"label": null,
"deleted": false,
"model_name": "specimen",
"app_name": "stocks",
"model_type": "CELLLINE"
},
"category": "property"
},
"type": {
"name": "type",
"value": {
"name": "GENERICSAMPLE",
"id": "7809ac0d-a07a-47d6-b828-880ad6241777"
},
"category": "property"
},
"material_type": {
"name": "material_type",
"value": {},
"category": "property"
},
"stock_locations": {
"name": "stock_locations",
"value": [],
"category": "property"
},
"protocol_list": {
"name": "protocol_list",
"category": "property",
"value": {}
},
"sample_status": {
"name": "sample_status",
"value": {
"value": "CREATED",
"label": "CREATED"
},
"category": "property"
},
"sample_qc": {
"name": "sample_qc",
"value": {
"value": null,
"label": "None"
},
"category": "property"
},
"is_pool": {
"name": "is_pool",
"category": "property",
"value": false
},
"is_control": {
"name": "is_control",
"category": "property",
"value": false
},
"control_name": {
"name": "control_name",
"category": "property",
"value": ""
},
"control_type": {
"name": "control_type",
"value": {},
"category": "property"
},
"is_single_cell": {
"name": "is_single_cell",
"category": "property",
"value": false
},
"single_cell_type": {
"name": "single_cell_type",
"value": {},
"category": "property"
},
"cell_number": {
"name": "cell_number",
"category": "property",
"value": null
},
"has_plate_position": {
"name": "has_plate_position",
"category": "property",
"value": false
},
"plate_name": {
"name": "plate_name",
"category": "property",
"value": ""
},
"plate_code": {
"name": "plate_code",
"category": "property",
"value": ""
},
"plate_type": {
"name": "plate_type",
"value": {},
"category": "property"
},
"plate_position": {
"name": "plate_position",
"category": "property",
"value": ""
},
"primary_project": {
"name": "primary_project",
"value": {},
"category": "property"
},
"used_in_experiments": {
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