ReadStore Basic External REST API 1.0.0

OpenAPI 3.1.0 specification for the ReadStore Basic external REST API. This API can be access from program code to automate generation, update and retrieval of elements in ReadStore

Servers

Description	URL
External REST API for Local ReadStore server. Port can vary by deployment.	https://127.0.0.1:8000/api_x_v1/

Endpoints

POST /api_x_v1/auth_token/

Endpoint to validate user credentials through HTTP Basic Authentication.

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No

Response 200 OK

Response 401 Unauthorized

GET /api_x_v1/project/

List all projects

Input parameters

Parameter	In	Type	Default	Nullable
`BasicAuth`	header	string	N/A	No
`project_id`	query	integer		No
`project_name`	query	string		No

Response 200 OK

application/json

Schema of the response body

{
    "type": "array",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "metadata": {
            "type": "dict"
        },
        "dataset_metadata_keys": {
            "type": "dict"
        }
    }
}

POST /api_x_v1/project/

Create a new project

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No

Request body

application/json

{
    "name": "string",
    "description": "string",
    "metadata": {
        "type": "dict"
    },
    "dataset_metadata_keys": {
        "type": "dict"
    }
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "type": "object",
    "properties": {
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "metadata": {
            "type": "dict"
        },
        "dataset_metadata_keys": {
            "type": "dict"
        }
    }
}

Response 201 Created

application/json

Schema of the response body

{
    "type": "array",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "metadata": {
            "type": "dict"
        },
        "dataset_metadata_keys": {
            "type": "dict"
        }
    }
}

GET /api_x_v1/project/{pk}/

Retrieve a project by ID

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No
`pk`	path	integer		No

Response 200 OK

application/json

Schema of the response body

{
    "type": "array",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "metadata": {
            "type": "dict"
        },
        "dataset_metadata_keys": {
            "type": "dict"
        }
    }
}

Response 404 Not Found

DELETE /api_x_v1/project/{pk}/

Delete a project by ID

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No
`pk`	path	integer		No

Response 200 OK

Response 404 Not Found

GET /api_x_v1/project_attachment/

List of project attachments or project attachment object including "body" field

Input parameters

Parameter	In	Type	Default	Nullable
`BasicAuth`	header	string	N/A	No
`attachment_name`	query	string		No
`project_id`	query	integer		No
`project_name`	query	string		No

Response 200 OK

application/json

{
    "id": 0,
    "name": "string",
    "description": "string",
    "owner": 0,
    "created": "string",
    "updated": "string",
    "valid_from": "string",
    "valid_to": "string",
    "project": 0,
    "size_mb": 0,
    "filetype": "string",
    "body": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "owner": {
            "type": "integer"
        },
        "created": {
            "type": "string"
        },
        "updated": {
            "type": "string"
        },
        "valid_from": {
            "type": "string"
        },
        "valid_to": {
            "type": "string"
        },
        "project": {
            "type": "integer"
        },
        "size_mb": {
            "type": "integer"
        },
        "filetype": {
            "type": "string"
        },
        "body": {
            "type": "string"
        }
    }
}

GET /api_x_v1/project_attachment/{pk}/

Retrieve a project attachment by ID

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No
`pk`	path	integer		No

Response 200 OK

application/json

{
    "id": 0,
    "name": "string",
    "description": "string",
    "owner": 0,
    "created": "string",
    "updated": "string",
    "valid_from": "string",
    "valid_to": "string",
    "project": 0,
    "size_mb": 0,
    "filetype": "string",
    "body": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "owner": {
            "type": "integer"
        },
        "created": {
            "type": "string"
        },
        "updated": {
            "type": "string"
        },
        "valid_from": {
            "type": "string"
        },
        "valid_to": {
            "type": "string"
        },
        "project": {
            "type": "integer"
        },
        "size_mb": {
            "type": "integer"
        },
        "filetype": {
            "type": "string"
        },
        "body": {
            "type": "string"
        }
    }
}

GET /api_x_v1/fq_dataset/

List all fq datasets

Input parameters

Parameter	In	Type	Default	Nullable
`BasicAuth`	header	string	N/A	No
`dataset_id`	query	integer		No
`dataset_name`	query	string		No
`project_id`	query	integer		No
`project_name`	query	string		No

Response 200 OK

application/json

{
    "id": 0,
    "name": "string",
    "description": "string",
    "qc_passed": true,
    "paired_end": true,
    "index_read": true,
    "project_ids": [],
    "project_names": [],
    "metadata": {
        "type": "dict"
    },
    "attachments": [],
    "pro_data": []
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "qc_passed": {
            "type": "boolean"
        },
        "paired_end": {
            "type": "boolean"
        },
        "index_read": {
            "type": "boolean"
        },
        "project_ids": {
            "type": "array"
        },
        "project_names": {
            "type": "array"
        },
        "metadata": {
            "type": "dict"
        },
        "attachments": {
            "type": "array"
        },
        "pro_data": {
            "type": "array"
        }
    }
}

POST /api_x_v1/fq_dataset/

Create a new fq dataset

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No

Response 201 Created

application/json

{
    "name": "string",
    "description": "string",
    "qc_passed": true,
    "paired_end": true,
    "index_read": true,
    "project_ids": [],
    "project_names": [],
    "fq_file_r1": 0,
    "fq_file_r2": 0,
    "fq_file_i1": 0,
    "fq_file_i2": 0,
    "metadata": {
        "type": "dict"
    }
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "qc_passed": {
            "type": "boolean"
        },
        "paired_end": {
            "type": "boolean"
        },
        "index_read": {
            "type": "boolean"
        },
        "project_ids": {
            "type": "array"
        },
        "project_names": {
            "type": "array"
        },
        "fq_file_r1": {
            "type": "integer"
        },
        "fq_file_r2": {
            "type": "integer"
        },
        "fq_file_i1": {
            "type": "integer"
        },
        "fq_file_i2": {
            "type": "integer"
        },
        "metadata": {
            "type": "dict"
        }
    }
}

GET /api_x_v1/fq_dataset/{pk}/

Retrieve an fq dataset by ID

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No
`pk`	path	integer		No

Response 200 OK

application/json

{
    "id": 0,
    "name": "string",
    "description": "string",
    "qc_passed": true,
    "paired_end": true,
    "index_read": true,
    "project_ids": [],
    "project_names": [],
    "created": "string",
    "fq_file_r1": 0,
    "fq_file_r2": 0,
    "fq_file_i1": 0,
    "fq_file_i2": 0,
    "metadata": {
        "type": "dict"
    },
    "attachments": [],
    "pro_data": []
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "qc_passed": {
            "type": "boolean"
        },
        "paired_end": {
            "type": "boolean"
        },
        "index_read": {
            "type": "boolean"
        },
        "project_ids": {
            "type": "array"
        },
        "project_names": {
            "type": "array"
        },
        "created": {
            "type": "string"
        },
        "fq_file_r1": {
            "type": "integer"
        },
        "fq_file_r2": {
            "type": "integer"
        },
        "fq_file_i1": {
            "type": "integer"
        },
        "fq_file_i2": {
            "type": "integer"
        },
        "metadata": {
            "type": "dict"
        },
        "attachments": {
            "type": "array"
        },
        "pro_data": {
            "type": "array"
        }
    }
}

Response 404 Not Found

DELETE /api_x_v1/fq_dataset/{pk}/

Delete an fq dataset by ID

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No
`pk`	path	integer		No

Response 204 No Content

Response 404 Not Found

GET /api_x_v1/fq_attachment/

List all fq attachments

Description

List of fq attachments. Specifying a dataset_name or dataset_id plus attachment_name returns a single fq attachment object including "body" field (s. detail view).

Input parameters

Parameter	In	Type	Default	Nullable
`BasicAuth`	header	string	N/A	No
`attachment_name`	query	string		No
`dataset_id`	query	integer		No
`dataset_name`	query	string		No

Response 200 OK

application/json

{
    "id": 0,
    "name": "string",
    "description": "string",
    "owner": 0,
    "created": "string",
    "updated": "string",
    "valid_from": "string",
    "valid_to": "string",
    "fq_dataset": 0,
    "size_mb": 0,
    "filetype": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "owner": {
            "type": "integer"
        },
        "created": {
            "type": "string"
        },
        "updated": {
            "type": "string"
        },
        "valid_from": {
            "type": "string"
        },
        "valid_to": {
            "type": "string"
        },
        "fq_dataset": {
            "type": "integer"
        },
        "size_mb": {
            "type": "integer"
        },
        "filetype": {
            "type": "string"
        }
    }
}

GET /api_x_v1/fq_attachment/{pk}/

Retrieve an fq attachment by ID

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No
`pk`	path	integer		No

Response 200 OK

application/json

{
    "id": 0,
    "name": "string",
    "description": "string",
    "owner": 0,
    "created": "string",
    "updated": "string",
    "valid_from": "string",
    "valid_to": "string",
    "fq_dataset": 0,
    "size_mb": 0,
    "filetype": "string",
    "body": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "description": {
            "type": "string"
        },
        "owner": {
            "type": "integer"
        },
        "created": {
            "type": "string"
        },
        "updated": {
            "type": "string"
        },
        "valid_from": {
            "type": "string"
        },
        "valid_to": {
            "type": "string"
        },
        "fq_dataset": {
            "type": "integer"
        },
        "size_mb": {
            "type": "integer"
        },
        "filetype": {
            "type": "string"
        },
        "body": {
            "type": "string"
        }
    }
}

POST /api_x_v1/fq_file_upload/

Upload an fq file

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No

Request body

application/json

{
    "fq_file_path": "string",
    "fq_file_name": "string",
    "read_type": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "type": "object",
    "properties": {
        "fq_file_path": {
            "type": "string"
        },
        "fq_file_name": {
            "type": "string"
        },
        "read_type": {
            "type": "string"
        }
    }
}

Response 201 Created

GET /api_x_v1/fq_file/

List all fq files

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No

Response 200 OK

application/json

{
    "id": 0,
    "name": "string",
    "read_type": "string",
    "qc_passed": true,
    "read_length": 0,
    "num_reads": 0,
    "size_mb": 0,
    "qc_phred_mean": 10.12,
    "creator": "string",
    "upload_path": "string",
    "md5_checksum": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "read_type": {
            "type": "string"
        },
        "qc_passed": {
            "type": "boolean"
        },
        "read_length": {
            "type": "integer"
        },
        "num_reads": {
            "type": "integer"
        },
        "size_mb": {
            "type": "integer"
        },
        "qc_phred_mean": {
            "type": "number",
            "format": "float"
        },
        "creator": {
            "type": "string"
        },
        "upload_path": {
            "type": "string"
        },
        "md5_checksum": {
            "type": "string"
        }
    }
}

POST /api_x_v1/fq_file/

Create a new fq file

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No

Request body

application/json

{
    "name": "string",
    "read_type": "string",
    "qc_passed": true,
    "read_length": 0,
    "num_reads": 0,
    "size_mb": 0,
    "qc_phred_mean": 10.12,
    "qc_phred": {
        "type": "dict"
    },
    "upload_path": "string",
    "md5_checksum": "string",
    "staging": true,
    "pipeline_version": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "type": "object",
    "properties": {
        "name": {
            "type": "string"
        },
        "read_type": {
            "type": "string"
        },
        "qc_passed": {
            "type": "boolean"
        },
        "read_length": {
            "type": "integer"
        },
        "num_reads": {
            "type": "integer"
        },
        "size_mb": {
            "type": "integer"
        },
        "qc_phred_mean": {
            "type": "number",
            "format": "float"
        },
        "qc_phred": {
            "type": "dict"
        },
        "upload_path": {
            "type": "string"
        },
        "md5_checksum": {
            "type": "string"
        },
        "staging": {
            "type": "boolean"
        },
        "pipeline_version": {
            "type": "string"
        }
    }
}

Response 201 Created

GET /api_x_v1/fq_file/{pk}/

Retrieve an fq file by ID

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No
`pk`	path	integer		No

Response 200 OK

application/json

{
    "id": 0,
    "name": "string",
    "read_type": "string",
    "qc_passed": true,
    "read_length": 0,
    "num_reads": 0,
    "size_mb": 0,
    "qc_phred_mean": 10.12,
    "creator": "string",
    "upload_path": "string",
    "md5_checksum": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "type": "object",
    "properties": {
        "id": {
            "type": "integer"
        },
        "name": {
            "type": "string"
        },
        "read_type": {
            "type": "string"
        },
        "qc_passed": {
            "type": "boolean"
        },
        "read_length": {
            "type": "integer"
        },
        "num_reads": {
            "type": "integer"
        },
        "size_mb": {
            "type": "integer"
        },
        "qc_phred_mean": {
            "type": "number",
            "format": "float"
        },
        "creator": {
            "type": "string"
        },
        "upload_path": {
            "type": "string"
        },
        "md5_checksum": {
            "type": "string"
        }
    }
}

DELETE /api_x_v1/fq_file/{pk}/

Delete an fq file by ID

Input parameters

Parameter	In	Type	Default	Nullable	Description
`BasicAuth`	header	string	N/A	No
`pk`	path	integer		No

Response 200 OK

Response 404 Not Found

Schemas

FqDataset

Name	Type
`attachments`	Array<>
`description`	string
`id`	integer
`index_read`	boolean
`metadata`
`name`	string
`paired_end`	boolean
`pro_data`	Array<>
`project_ids`	Array<>
`project_names`	Array<>
`qc_passed`	boolean

FqDatasetAttachment

Name	Type
`created`	string
`description`	string
`filetype`	string
`fq_dataset`	integer
`id`	integer
`name`	string
`owner`	integer
`size_mb`	integer
`updated`	string
`valid_from`	string
`valid_to`	string

FqDatasetAttachmentDetail

Name	Type
`body`	string
`created`	string
`description`	string
`filetype`	string
`fq_dataset`	integer
`id`	integer
`name`	string
`owner`	integer
`size_mb`	integer
`updated`	string
`valid_from`	string
`valid_to`	string

FqDatasetDetail

Name	Type
`attachments`	Array<>
`created`	string
`description`	string
`fq_file_i1`	integer
`fq_file_i2`	integer
`fq_file_r1`	integer
`fq_file_r2`	integer
`id`	integer
`index_read`	boolean
`metadata`
`name`	string
`paired_end`	boolean
`pro_data`	Array<>
`project_ids`	Array<>
`project_names`	Array<>
`qc_passed`	boolean

FqDatasetPost

Name	Type
`description`	string
`fq_file_i1`	integer
`fq_file_i2`	integer
`fq_file_r1`	integer
`fq_file_r2`	integer
`index_read`	boolean
`metadata`
`name`	string
`paired_end`	boolean
`project_ids`	Array<>
`project_names`	Array<>
`qc_passed`	boolean

FqFile

Name	Type
`creator`	string
`id`	integer
`md5_checksum`	string
`name`	string
`num_reads`	integer
`qc_passed`	boolean
`qc_phred_mean`	number(float)
`read_length`	integer
`read_type`	string
`size_mb`	integer
`upload_path`	string

FqFilePost

Name	Type
`md5_checksum`	string
`name`	string
`num_reads`	integer
`pipeline_version`	string
`qc_passed`	boolean
`qc_phred`
`qc_phred_mean`	number(float)
`read_length`	integer
`read_type`	string
`size_mb`	integer
`staging`	boolean
`upload_path`	string

FqFileUpload

Name	Type
`fq_file_name`	string
`fq_file_path`	string
`read_type`	string

ProjectArray

Type: Array<>

ProjectAttachmentArray

Type: Array<>

ProjectAttachmentObject

Name	Type
`body`	string
`created`	string
`description`	string
`filetype`	string
`id`	integer
`name`	string
`owner`	integer
`project`	integer
`size_mb`	integer
`updated`	string
`valid_from`	string
`valid_to`	string

ProjectPost

Name	Type
`dataset_metadata_keys`
`description`	string
`metadata`
`name`	string