tomato package

tomato.set_loglevel(loglevel: int)

tomato.parse_args(parser, verbose, is_tomato=False)

tomato.run_tomato()

tomato.run_ketchup()

tomato.run_passata()

Subpackages

• tomato.daemon package
  • tomato.daemon: module of functions comprising the tomato daemon
  • setup_logging()
  • tomato_daemon()
  • Submodules
    • tomato.daemon.cmd: command parsing for tomato daemon
    • merge_pipelines()
    • status()
    • stop()
    • setup()
    • pipeline()
    • set_job()
    • get_jobs()
    • driver()
    • device()
    • component()
    • tomato.daemon.driver: the driver manager of tomato daemon
    • tomato_driver_bootstrap()
    • tomato_driver()
    • spawn_tomato_driver()
    • stop_tomato_driver()
    • manager()
    • tomato.daemon.io: functions for storing and loading data
    • store()
    • load()
    • merge_netcdfs()
    • data_to_pickle()
    • tomato.daemon.job: the job manager of tomato daemon
    • method_validate()
    • find_matching_pipelines()
    • kill_tomato_job()
    • manage_running_pips()
    • check_queued_jobs()
    • action_queued_jobs()
    • manager()
    • tomato_job()
    • job_thread()
    • job_main_loop()
    • tomato.daemon.jobdb: the sqlite database for jobs in tomato
    • connect_jobdb()
    • jobdb_setup()
    • insert_job()
    • update_job_id()
    • get_job_id()
    • get_jobs_where()
• tomato.driverinterface_1_0 package
  • DriverInterface-1.0
  • in_devmap()
  • Attr
    • Attr.type
    • Attr.rw
    • Attr.status
    • Attr.units
  • ModelInterface
    • ModelInterface.version
    • ModelInterface.DeviceManager
      • ModelInterface.DeviceManager.driver
      • ModelInterface.DeviceManager.key
      • ModelInterface.DeviceManager.task_list
      • ModelInterface.DeviceManager.thread
      • ModelInterface.DeviceManager.data
      • ModelInterface.DeviceManager.running
      • ModelInterface.DeviceManager.datalock
      • ModelInterface.DeviceManager.run()
      • ModelInterface.DeviceManager.task_runner()
      • ModelInterface.DeviceManager.prepare_task()
      • ModelInterface.DeviceManager.do_task()
      • ModelInterface.DeviceManager.stop_task()
      • ModelInterface.DeviceManager.set_attr()
      • ModelInterface.DeviceManager.get_attr()
      • ModelInterface.DeviceManager.get_data()
      • ModelInterface.DeviceManager.attrs()
      • ModelInterface.DeviceManager.capabilities()
      • ModelInterface.DeviceManager.status()
      • ModelInterface.DeviceManager.reset()
    • ModelInterface.CreateDeviceManager()
    • ModelInterface.devmap
    • ModelInterface.settings
    • ModelInterface.dev_register()
    • ModelInterface.dev_teardown()
    • ModelInterface.dev_reset()
    • ModelInterface.dev_set_attr()
    • ModelInterface.dev_get_attr()
    • ModelInterface.dev_status()
    • ModelInterface.task_start()
    • ModelInterface.task_status()
    • ModelInterface.task_stop()
    • ModelInterface.task_data()
    • ModelInterface.status()
    • ModelInterface.reset()
    • ModelInterface.capabilities()
    • ModelInterface.attrs()
• tomato.driverinterface_2_0 package
  • DriverInterface-2.0
  • in_devmap()
  • to_reply()
  • log_errors()
  • Attr
    • Attr.type
    • Attr.rw
    • Attr.status
    • Attr.units
    • Attr.maximum
    • Attr.minimum
  • ModelInterface
    • ModelInterface.version
    • ModelInterface.devmap
    • ModelInterface.constants
    • ModelInterface.settings
    • ModelInterface.DeviceFactory()
    • ModelInterface.dev_register()
    • ModelInterface.dev_teardown()
    • ModelInterface.dev_reset()
    • ModelInterface.dev_set_attr()
    • ModelInterface.dev_get_attr()
    • ModelInterface.dev_status()
    • ModelInterface.dev_capabilities()
    • ModelInterface.dev_attrs()
    • ModelInterface.cmp_register()
    • ModelInterface.cmp_teardown()
    • ModelInterface.cmp_reset()
    • ModelInterface.cmp_set_attr()
    • ModelInterface.cmp_get_attr()
    • ModelInterface.cmp_status()
    • ModelInterface.cmp_capabilities()
    • ModelInterface.cmp_attrs()
    • ModelInterface.cmp_constants()
    • ModelInterface.cmp_last_data()
    • ModelInterface.cmp_measure()
    • ModelInterface.task_start()
    • ModelInterface.task_status()
    • ModelInterface.task_stop()
    • ModelInterface.task_data()
    • ModelInterface.task_validate()
    • ModelInterface.status()
    • ModelInterface.reset()
  • ModelDevice
    • ModelDevice.driver
    • ModelDevice.key
    • ModelDevice.task_list
    • ModelDevice.thread
    • ModelDevice.data
    • ModelDevice.last_data
    • ModelDevice.running
    • ModelDevice.datalock
    • ModelDevice.constants
    • ModelDevice.run()
    • ModelDevice.measure()
    • ModelDevice.task_runner()
    • ModelDevice.meas_runner()
    • ModelDevice.prepare_task()
    • ModelDevice.do_task()
    • ModelDevice.do_measure()
    • ModelDevice.stop_task()
    • ModelDevice.set_attr()
    • ModelDevice.get_attr()
    • ModelDevice.get_data()
    • ModelDevice.get_last_data()
    • ModelDevice.attrs()
    • ModelDevice.capabilities()
    • ModelDevice.status()
    • ModelDevice.reset()
• tomato.ketchup package
  • tomato.ketchup: command line interface to the tomato job queue
  • submit()
  • status()
  • cancel()
  • snapshot()
  • search()
• tomato.passata package
  • status()
  • attrs()
  • capabilities()
  • constants()
  • get_attrs()
  • set_attr()
  • reset()
  • get_last_data()
  • measure()
• tomato.tomato package
  • tomato.tomato: command line interface to the tomato daemon
  • set_loglevel()
  • load_device_file()
  • get_pipelines()
  • status()
  • start()
  • stop()
  • init()
  • reload()
  • pipeline_load()
  • pipeline_eject()
  • pipeline_ready()

Submodules

tomato.drivers: Shim interfacing with tomato driver packages

Code author: Peter Kraus

tomato.drivers.driver_to_interface(drivername: str) → None | ModelInterface

tomato.models: Pydantic models for internal tomato use

Code author: Peter Kraus

pydantic model tomato.models.Driver

Bases: BaseModel

Show JSON schema

{
   "title": "Driver",
   "type": "object",
   "properties": {
      "name": {
         "title": "Name",
         "type": "string"
      },
      "version": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Version"
      },
      "port": {
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Port"
      },
      "pid": {
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Pid"
      },
      "spawned_at": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Spawned At"
      },
      "connected_at": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Connected At"
      },
      "settings": {
         "additionalProperties": true,
         "title": "Settings",
         "type": "object"
      }
   },
   "required": [
      "name"
   ]
}

field name: str [Required]

field version: str | None = None

field port: int | None = None

field pid: int | None = None

field spawned_at: str | None = None

field connected_at: str | None = None

field settings: Mapping[str, Any] [Optional]

pydantic model tomato.models.Device

Bases: BaseModel

Show JSON schema

{
   "title": "Device",
   "type": "object",
   "properties": {
      "name": {
         "title": "Name",
         "type": "string"
      },
      "driver": {
         "title": "Driver",
         "type": "string"
      },
      "address": {
         "title": "Address",
         "type": "string"
      },
      "channels": {
         "items": {
            "type": "string"
         },
         "title": "Channels",
         "type": "array"
      },
      "pollrate": {
         "default": 1,
         "title": "Pollrate",
         "type": "integer"
      }
   },
   "required": [
      "name",
      "driver",
      "address",
      "channels"
   ]
}

Validators:

• coerce_channels » channels

field name: str [Required]

field driver: str [Required]

field address: str [Required]

field channels: Sequence[str] [Required]

Validated by:

• coerce_channels

field pollrate: int = 1

validator coerce_channels  »  channels

pydantic model tomato.models.Component

Bases: BaseModel

Show JSON schema

{
   "title": "Component",
   "type": "object",
   "properties": {
      "name": {
         "title": "Name",
         "type": "string"
      },
      "driver": {
         "title": "Driver",
         "type": "string"
      },
      "device": {
         "title": "Device",
         "type": "string"
      },
      "address": {
         "title": "Address",
         "type": "string"
      },
      "channel": {
         "title": "Channel",
         "type": "string"
      },
      "role": {
         "title": "Role",
         "type": "string"
      },
      "capabilities": {
         "anyOf": [
            {
               "items": {
                  "type": "string"
               },
               "type": "array",
               "uniqueItems": true
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Capabilities"
      }
   },
   "required": [
      "name",
      "driver",
      "device",
      "address",
      "channel",
      "role"
   ]
}

Validators:

• coerce_channel » channel

field name: str [Required]

field driver: str [Required]

field device: str [Required]

field address: str [Required]

field channel: str [Required]

Validated by:

• coerce_channel

field role: str [Required]

field capabilities: set[str] | None = None

validator coerce_channel  »  channel

pydantic model tomato.models.Pipeline

Bases: BaseModel

Show JSON schema

{
   "title": "Pipeline",
   "type": "object",
   "properties": {
      "name": {
         "title": "Name",
         "type": "string"
      },
      "ready": {
         "default": false,
         "title": "Ready",
         "type": "boolean"
      },
      "jobid": {
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Jobid"
      },
      "sampleid": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Sampleid"
      },
      "components": {
         "items": {
            "type": "string"
         },
         "title": "Components",
         "type": "array"
      }
   },
   "required": [
      "name"
   ]
}

field name: str [Required]

field ready: bool = False

field jobid: int | None = None

field sampleid: str | None = None

field components: Sequence[str] [Optional]

pydantic model tomato.models.Job

Bases: BaseModel

Show JSON schema

{
   "title": "Job",
   "type": "object",
   "properties": {
      "id": {
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Id"
      },
      "payload": {
         "$ref": "#/$defs/Payload"
      },
      "jobname": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Jobname"
      },
      "pid": {
         "anyOf": [
            {
               "type": "integer"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Pid"
      },
      "status": {
         "default": "q",
         "enum": [
            "q",
            "qw",
            "r",
            "rd",
            "c",
            "cd",
            "ce"
         ],
         "title": "Status",
         "type": "string"
      },
      "submitted_at": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Submitted At"
      },
      "executed_at": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Executed At"
      },
      "completed_at": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Completed At"
      },
      "jobpath": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Jobpath"
      },
      "respath": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Respath"
      },
      "snappath": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Snappath"
      }
   },
   "$defs": {
      "Output": {
         "additionalProperties": false,
         "description": "Provide the ``path`` and ``prefix`` for the final FAIR-data archive of the *job*.",
         "properties": {
            "path": {
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Path"
            },
            "prefix": {
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Prefix"
            }
         },
         "title": "Output",
         "type": "object"
      },
      "Payload": {
         "additionalProperties": false,
         "properties": {
            "version": {
               "const": "2.0",
               "title": "Version",
               "type": "string"
            },
            "settings": {
               "$ref": "#/$defs/Settings"
            },
            "sample": {
               "$ref": "#/$defs/Sample"
            },
            "method": {
               "items": {
                  "$ref": "#/$defs/Task"
               },
               "title": "Method",
               "type": "array"
            }
         },
         "required": [
            "version",
            "sample",
            "method"
         ],
         "title": "Payload",
         "type": "object"
      },
      "Sample": {
         "additionalProperties": true,
         "description": "Additional attributes for each :class:`Sample` may be required, depending on the\nmethod within the payload.",
         "properties": {
            "name": {
               "title": "Name",
               "type": "string"
            }
         },
         "required": [
            "name"
         ],
         "title": "Sample",
         "type": "object"
      },
      "Settings": {
         "additionalProperties": false,
         "description": "Specification of *job* configuration for tomato.",
         "properties": {
            "unlock_when_done": {
               "default": false,
               "title": "Unlock When Done",
               "type": "boolean"
            },
            "verbosity": {
               "default": "WARNING",
               "enum": [
                  "DEBUG",
                  "INFO",
                  "WARNING",
                  "ERROR",
                  "CRITICAL"
               ],
               "title": "Verbosity",
               "type": "string"
            },
            "output": {
               "$ref": "#/$defs/Output"
            },
            "snapshot": {
               "anyOf": [
                  {
                     "$ref": "#/$defs/Snapshot"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null
            }
         },
         "title": "Settings",
         "type": "object"
      },
      "Snapshot": {
         "additionalProperties": false,
         "description": "Provide the ``frequency``, ``path`` and ``prefix`` to configure the snapshotting\nfunctionality of tomato.",
         "properties": {
            "path": {
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Path"
            },
            "prefix": {
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Prefix"
            },
            "frequency": {
               "default": 3600.0,
               "title": "Frequency",
               "type": "number"
            }
         },
         "title": "Snapshot",
         "type": "object"
      },
      "Task": {
         "additionalProperties": false,
         "description": "The :class:`Task` is a driver/device-independent abstraction describing the\nmeasurement steps. The driver-specific information for the :class:`Task` can be\nprovided via the :obj:`technique_name` and :obj:`task_params` parameters.",
         "properties": {
            "component_tag": {
               "title": "Component Tag",
               "type": "string"
            },
            "max_duration": {
               "title": "Max Duration",
               "type": "number"
            },
            "sampling_interval": {
               "title": "Sampling Interval",
               "type": "number"
            },
            "polling_interval": {
               "anyOf": [
                  {
                     "type": "number"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Polling Interval"
            },
            "technique_name": {
               "title": "Technique Name",
               "type": "string"
            },
            "task_params": {
               "anyOf": [
                  {
                     "additionalProperties": true,
                     "type": "object"
                  },
                  {
                     "type": "null"
                  }
               ],
               "title": "Task Params"
            }
         },
         "required": [
            "component_tag",
            "max_duration",
            "sampling_interval",
            "technique_name"
         ],
         "title": "Task",
         "type": "object"
      }
   },
   "required": [
      "payload"
   ]
}

Validators:

• coerce_payload » payload

field id: int | None = None

field payload: Payload [Required]

Validated by:

• coerce_payload

field jobname: str | None = None

field pid: int | None = None

field status: Literal['q', 'qw', 'r', 'rd', 'c', 'cd', 'ce'] = 'q'

field submitted_at: str | None = None

field executed_at: str | None = None

field completed_at: str | None = None

field jobpath: str | None = None

field respath: str | None = None

field snappath: str | None = None

validator coerce_payload  »  payload

pydantic model tomato.models.Daemon

Bases: BaseModel

Show JSON schema

{
   "title": "Daemon",
   "type": "object",
   "properties": {
      "status": {
         "enum": [
            "bootstrap",
            "running",
            "stop"
         ],
         "title": "Status",
         "type": "string"
      },
      "port": {
         "title": "Port",
         "type": "integer"
      },
      "verbosity": {
         "title": "Verbosity",
         "type": "integer"
      },
      "appdir": {
         "title": "Appdir",
         "type": "string"
      },
      "settings": {
         "additionalProperties": true,
         "title": "Settings",
         "type": "object"
      },
      "pips": {
         "additionalProperties": {
            "$ref": "#/$defs/Pipeline"
         },
         "title": "Pips",
         "type": "object"
      },
      "devs": {
         "additionalProperties": {
            "$ref": "#/$defs/Device"
         },
         "title": "Devs",
         "type": "object"
      },
      "drvs": {
         "additionalProperties": {
            "$ref": "#/$defs/Driver"
         },
         "title": "Drvs",
         "type": "object"
      },
      "cmps": {
         "additionalProperties": {
            "$ref": "#/$defs/Component"
         },
         "title": "Cmps",
         "type": "object"
      }
   },
   "$defs": {
      "Component": {
         "properties": {
            "name": {
               "title": "Name",
               "type": "string"
            },
            "driver": {
               "title": "Driver",
               "type": "string"
            },
            "device": {
               "title": "Device",
               "type": "string"
            },
            "address": {
               "title": "Address",
               "type": "string"
            },
            "channel": {
               "title": "Channel",
               "type": "string"
            },
            "role": {
               "title": "Role",
               "type": "string"
            },
            "capabilities": {
               "anyOf": [
                  {
                     "items": {
                        "type": "string"
                     },
                     "type": "array",
                     "uniqueItems": true
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Capabilities"
            }
         },
         "required": [
            "name",
            "driver",
            "device",
            "address",
            "channel",
            "role"
         ],
         "title": "Component",
         "type": "object"
      },
      "Device": {
         "properties": {
            "name": {
               "title": "Name",
               "type": "string"
            },
            "driver": {
               "title": "Driver",
               "type": "string"
            },
            "address": {
               "title": "Address",
               "type": "string"
            },
            "channels": {
               "items": {
                  "type": "string"
               },
               "title": "Channels",
               "type": "array"
            },
            "pollrate": {
               "default": 1,
               "title": "Pollrate",
               "type": "integer"
            }
         },
         "required": [
            "name",
            "driver",
            "address",
            "channels"
         ],
         "title": "Device",
         "type": "object"
      },
      "Driver": {
         "properties": {
            "name": {
               "title": "Name",
               "type": "string"
            },
            "version": {
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Version"
            },
            "port": {
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Port"
            },
            "pid": {
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Pid"
            },
            "spawned_at": {
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Spawned At"
            },
            "connected_at": {
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Connected At"
            },
            "settings": {
               "additionalProperties": true,
               "title": "Settings",
               "type": "object"
            }
         },
         "required": [
            "name"
         ],
         "title": "Driver",
         "type": "object"
      },
      "Pipeline": {
         "properties": {
            "name": {
               "title": "Name",
               "type": "string"
            },
            "ready": {
               "default": false,
               "title": "Ready",
               "type": "boolean"
            },
            "jobid": {
               "anyOf": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Jobid"
            },
            "sampleid": {
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "null"
                  }
               ],
               "default": null,
               "title": "Sampleid"
            },
            "components": {
               "items": {
                  "type": "string"
               },
               "title": "Components",
               "type": "array"
            }
         },
         "required": [
            "name"
         ],
         "title": "Pipeline",
         "type": "object"
      }
   },
   "required": [
      "status",
      "port",
      "verbosity",
      "appdir",
      "settings"
   ]
}

Config:

• arbitrary_types_allowed: bool = True

field status: Literal['bootstrap', 'running', 'stop'] [Required]

field port: int [Required]

field verbosity: int [Required]

field appdir: str [Required]

field settings: dict [Required]

field pips: Mapping[str, Pipeline] [Optional]

field devs: Mapping[str, Device] [Optional]

field drvs: Mapping[str, Driver] [Optional]

field cmps: Mapping[str, Component] [Optional]

pydantic model tomato.models.Reply

Bases: BaseModel

Show JSON schema

{
   "title": "Reply",
   "type": "object",
   "properties": {
      "success": {
         "title": "Success",
         "type": "boolean"
      },
      "msg": {
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Msg"
      },
      "data": {
         "anyOf": [
            {},
            {
               "type": "null"
            }
         ],
         "default": null,
         "title": "Data"
      }
   },
   "required": [
      "success"
   ]
}

field success: bool [Required]

field msg: str | None = None

field data: Any | None = None