BugSeq 0.1.0¶

users¶

GET /v1/users/me¶

Get Current User

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Response 200 OK

application/json

{
    "id": "string",
    "email": "string",
    "first_name": "string",
    "last_name": "string",
    "created": "2022-04-13T15:42:05.901Z",
    "affiliation": "string",
    "billing_account_id": "string",
    "pipeline_version": null,
    "pinned_region": null,
    "enabled_features": [
        "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

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "email": {
            "type": "string",
            "title": "Email"
        },
        "first_name": {
            "type": "string",
            "title": "First Name"
        },
        "last_name": {
            "type": "string",
            "title": "Last Name"
        },
        "created": {
            "type": "string",
            "format": "date-time",
            "title": "Created"
        },
        "affiliation": {
            "type": "string",
            "title": "Affiliation"
        },
        "billing_account_id": {
            "type": "string",
            "title": "Billing Account Id"
        },
        "pipeline_version": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Pipeline Version"
        },
        "pinned_region": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Pinned Region"
        },
        "enabled_features": {
            "items": {
                "type": "string"
            },
            "type": "array",
            "title": "Enabled Features"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "email",
        "first_name",
        "last_name",
        "created",
        "affiliation",
        "billing_account_id",
        "enabled_features"
    ],
    "title": "UserResponse"
}

files¶

POST /v1/files/singlepart/init¶

Initialize Single Part Upload

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "filename": "string",
    "s3_region": null
}

⚠️ 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

{
    "properties": {
        "filename": {
            "type": "string",
            "title": "Filename"
        },
        "s3_region": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "S3 Region"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "filename"
    ],
    "title": "FileCreateS3Request"
}

Response 200 OK

application/json

{
    "id": "string",
    "presigned_s3_data": null
}

⚠️ 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

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "presigned_s3_data": {
            "title": "Presigned S3 Data"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "presigned_s3_data"
    ],
    "title": "FileInitUploadS3Response"
}

POST /v1/files/multipart/init¶

Initialize Multipart Upload

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "filename": "string",
    "s3_region": null
}

⚠️ 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

{
    "properties": {
        "filename": {
            "type": "string",
            "title": "Filename"
        },
        "s3_region": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "S3 Region"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "filename"
    ],
    "title": "FileCreateS3Request"
}

Response 200 OK

application/json

{
    "id": "string",
    "presigned_s3_data": null
}

⚠️ 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

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "presigned_s3_data": {
            "title": "Presigned S3 Data"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "presigned_s3_data"
    ],
    "title": "FileInitUploadS3Response"
}

POST /v1/files/multipart/chunk¶

Presign Multipart Chunk

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "file_id": "string",
    "upload_id": "string",
    "part_number": 0
}

⚠️ 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

{
    "properties": {
        "file_id": {
            "type": "string",
            "title": "File Id"
        },
        "upload_id": {
            "type": "string",
            "title": "Upload Id"
        },
        "part_number": {
            "type": "integer",
            "title": "Part Number"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "file_id",
        "upload_id",
        "part_number"
    ],
    "title": "FileMultipartChunkInitUploadRequest"
}

Response 200 OK

application/json

{
    "id": "string",
    "presigned_s3_data": null
}

⚠️ 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

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "presigned_s3_data": {
            "title": "Presigned S3 Data"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "presigned_s3_data"
    ],
    "title": "FileInitUploadS3Response"
}

POST /v1/files/multipart/complete¶

Complete Multipart Upload

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "file_id": "string",
    "upload_id": "string",
    "parts": null
}

⚠️ 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

{
    "properties": {
        "file_id": {
            "type": "string",
            "title": "File Id"
        },
        "upload_id": {
            "type": "string",
            "title": "Upload Id"
        },
        "parts": {
            "title": "Parts"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "file_id",
        "upload_id",
        "parts"
    ],
    "title": "FileMultipartUploadCompleteRequest"
}

Response 200 OK

application/json

Schema of the response body

jobs¶

POST /v1/jobs/¶

Submit Analysis

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "user_provided_name": null,
    "aws_region": "string",
    "file_ids": [
        "string"
    ],
    "run_options": {
        "platform": "NANOPORE",
        "kit": null,
        "metagenomic_database": "BUGSEQ_DEFAULT",
        "sample_type": "ABSCESS",
        "molecule_type": "DNA",
        "include_in_lab_db": true,
        "filter_animal_reads": null
    },
    "lab_id": null,
    "testmode": true,
    "user_provided_metadata": null,
    "pipeline_version": null
}

⚠️ 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

{
    "properties": {
        "user_provided_name": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "User Provided Name"
        },
        "aws_region": {
            "type": "string",
            "title": "Aws Region"
        },
        "file_ids": {
            "items": {
                "type": "string"
            },
            "type": "array",
            "title": "File Ids"
        },
        "run_options": {
            "$ref": "#/components/schemas/RunOptionsRequest"
        },
        "lab_id": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Lab Id"
        },
        "testmode": {
            "type": "boolean",
            "title": "Testmode",
            "default": false
        },
        "user_provided_metadata": {
            "anyOf": [
                {
                    "items": {
                        "additionalProperties": {
                            "anyOf": [
                                {
                                    "type": "boolean"
                                },
                                {
                                    "type": "string"
                                }
                            ]
                        },
                        "type": "object"
                    },
                    "type": "array"
                },
                {
                    "type": "null"
                }
            ],
            "title": "User Provided Metadata"
        },
        "pipeline_version": {
            "anyOf": [
                {
                    "$ref": "#/components/schemas/PipelineVersion"
                },
                {
                    "type": "null"
                }
            ]
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "aws_region",
        "file_ids",
        "run_options"
    ],
    "title": "JobRunSubmitRequest"
}

Response 200 OK

application/json

{
    "id": "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

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id"
    ],
    "title": "JobRunSubmitResponse"
}

GET /v1/jobs/¶

List Analyses

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`ids`	query	None		No
`lab_ids`	query	None		No
`limit`	query	integer	20	No
`owner_ids`	query	None		No
`skip`	query	integer	0	No
`user_provided_name`	query	None		No

Response 200 OK

application/json

{
    "job_runs": [
        {
            "id": "string",
            "user_provided_name": null,
            "owner_id": "string",
            "created": "2022-04-13T15:42:05.901Z",
            "end_time": null,
            "job_status": "created",
            "results_url": "string",
            "org_id": null,
            "pipeline_version": "latest"
        }
    ],
    "has_more": true
}

⚠️ 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

{
    "properties": {
        "job_runs": {
            "items": {
                "$ref": "#/components/schemas/JobRunResponse"
            },
            "type": "array",
            "title": "Job Runs"
        },
        "has_more": {
            "type": "boolean",
            "title": "Has More"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "job_runs",
        "has_more"
    ],
    "title": "JobRunListResponse"
}

GET /v1/jobs/{job_id}/results¶

Get Analysis Results

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`job_id`	path	string		No

Response 200 OK

application/json

{
    "id": "string",
    "user_provided_name": null,
    "owner_id": "string",
    "created": "2022-04-13T15:42:05.901Z",
    "end_time": null,
    "job_status": "created",
    "inputs": [
        {
            "filename": "string",
            "size": null
        }
    ],
    "outputs": null,
    "org_id": null,
    "pipeline_version": "latest"
}

⚠️ 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

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "user_provided_name": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "User Provided Name"
        },
        "owner_id": {
            "type": "string",
            "title": "Owner Id"
        },
        "created": {
            "type": "string",
            "format": "date-time",
            "title": "Created"
        },
        "end_time": {
            "anyOf": [
                {
                    "type": "string",
                    "format": "date-time"
                },
                {
                    "type": "null"
                }
            ],
            "title": "End Time"
        },
        "job_status": {
            "$ref": "#/components/schemas/JobStatus"
        },
        "inputs": {
            "items": {
                "$ref": "#/components/schemas/JobRunFileResponse"
            },
            "type": "array",
            "title": "Inputs"
        },
        "outputs": {
            "anyOf": [
                {
                    "items": {
                        "$ref": "#/components/schemas/JobRunFileResponse"
                    },
                    "type": "array"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Outputs"
        },
        "org_id": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Org Id"
        },
        "pipeline_version": {
            "$ref": "#/components/schemas/PipelineVersion"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "owner_id",
        "created",
        "job_status",
        "inputs",
        "outputs",
        "org_id",
        "pipeline_version"
    ],
    "title": "JobRunResultsResponse"
}

GET /v1/jobs/{job_id}/results/download¶

Download Analysis Result

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`filename`	query	string		No
`job_id`	path	string		No

Response 200 OK

application/json

{
    "url": "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

{
    "properties": {
        "url": {
            "type": "string",
            "title": "Url"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "url"
    ],
    "title": "FileDownloadResponse"
}

billing¶

GET /v1/billing/{billing_account_id}/credits/sample¶

List Billing Account Sample Credits

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`billing_account_id`	path	string		No
`include_expired`	query	boolean	True	No
`limit`	query	integer	20	No
`remaining_count_gt`	query	None		No
`skip`	query	integer	0	No
`sort_by`	query	string	expiration	No
`sort_dir`	query	string	asc	No

Response 200 OK

application/json

{
    "items": [
        {
            "id": "string",
            "sample_type": "metagenomic",
            "initial_count": 0,
            "remaining_count": 0,
            "expiration": "2022-04-13T15:42:05.901Z",
            "billing_account_id": "string",
            "created": "2022-04-13T15:42:05.901Z"
        }
    ],
    "has_more": true
}

⚠️ 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

{
    "properties": {
        "items": {
            "items": {
                "$ref": "#/components/schemas/BillingAccountSampleCreditResponse"
            },
            "type": "array",
            "title": "Items"
        },
        "has_more": {
            "type": "boolean",
            "title": "Has More"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "items",
        "has_more"
    ],
    "title": "ListBillingAccountSampleCreditResponse"
}

Schemas¶

BillingAccountSampleCreditResponse¶

Name	Type
`billing_account_id`	string
`created`	string(date-time)
`expiration`	string(date-time)
`id`	string
`initial_count`	integer
`remaining_count`	integer
`sample_type`	SampleType-Output

FileCreateS3Request¶

Name	Type
`filename`	string
`s3_region`

FileDownloadResponse¶

Name	Type
`url`	string

FileInitUploadS3Response¶

Name	Type
`id`	string
`presigned_s3_data`

FileMultipartChunkInitUploadRequest¶

Name	Type
`file_id`	string
`part_number`	integer
`upload_id`	string

FileMultipartUploadCompleteRequest¶

Name	Type
`file_id`	string
`parts`
`upload_id`	string

HTTPValidationError¶

Name	Type
`detail`	Array<ValidationError>

JobRunFileResponse¶

Name	Type
`filename`	string
`size`

JobRunListResponse¶

Name	Type
`has_more`	boolean
`job_runs`	Array<JobRunResponse>

JobRunResponse¶

Name	Type
`created`	string(date-time)
`end_time`
`id`	string
`job_status`	JobStatus
`org_id`
`owner_id`	string
`pipeline_version`	PipelineVersion
`results_url`	string
`user_provided_name`

JobRunResultsResponse¶

Name	Type
`created`	string(date-time)
`end_time`
`id`	string
`inputs`	Array<JobRunFileResponse>
`job_status`	JobStatus
`org_id`
`outputs`
`owner_id`	string
`pipeline_version`	PipelineVersion
`user_provided_name`

JobRunSubmitRequest¶

Name	Type
`aws_region`	string
`file_ids`	Array<string>
`lab_id`
`pipeline_version`
`run_options`	RunOptionsRequest
`testmode`	boolean
`user_provided_metadata`
`user_provided_name`

JobRunSubmitResponse¶

Name	Type
`id`	string

JobStatus¶

Type: string

Kit¶

Type: string

ListBillingAccountSampleCreditResponse¶

Name	Type
`has_more`	boolean
`items`	Array<BillingAccountSampleCreditResponse>

MetagenomicDatabase¶

Type: string

MoleculeType¶

Type: string

PipelineVersion¶

Type: string

Platform¶

Type: string

RunOptionsRequest¶

Name	Type
`filter_animal_reads`
`include_in_lab_db`	boolean
`kit`
`metagenomic_database`	MetagenomicDatabase
`molecule_type`	MoleculeType
`platform`	Platform
`sample_type`	SampleType-Input

SampleType-Input¶

Type: string

SampleType-Output¶

Type: string

UserResponse¶

Name	Type
`affiliation`	string
`billing_account_id`	string
`created`	string(date-time)
`email`	string
`enabled_features`	Array<string>
`first_name`	string
`id`	string
`last_name`	string
`pinned_region`
`pipeline_version`

ValidationError¶

Name	Type
`loc`	Array<>
`msg`	string
`type`	string

Security schemes¶

Name	Type	Scheme	Description
HTTPBearer	http	bearer