Replicate

pydantic model pyenzyme.enzymeml.core.replicate.Replicate[source]

Bases: pyenzyme.enzymeml.core.enzymemlbase.EnzymeMLBase

Show JSON schema

{
   "title": "Replicate",
   "type": "object",
   "properties": {
      "id": {
         "title": "Id",
         "description": "Unique identifier of the replicate",
         "type": "string"
      },
      "species_id": {
         "title": "Species Id",
         "description": "Unique identifier of the species that has been measured.",
         "pattern": "[s|r|p][\\d]+",
         "type": "string"
      },
      "measurement_id": {
         "title": "Measurement Id",
         "description": "Unique identifier of the measurement that the replicate is part of.",
         "pattern": "m[\\d]+",
         "type": "string"
      },
      "data_type": {
         "description": "Type of data that was measured (e.g. concentration)",
         "default": "conc",
         "allOf": [
            {
               "$ref": "#/definitions/DataTypes"
            }
         ]
      },
      "data_unit": {
         "title": "Data Unit",
         "description": "SI unit of the data that was measured.",
         "type": "string"
      },
      "time_unit": {
         "title": "Time Unit",
         "description": "Time unit of the replicate.",
         "type": "string"
      },
      "time": {
         "title": "Time",
         "description": "Time steps of the replicate.",
         "type": "array",
         "items": {
            "type": "number"
         }
      },
      "data": {
         "title": "Data",
         "description": "Data that was measured.",
         "type": "array",
         "items": {
            "type": "number"
         }
      },
      "is_calculated": {
         "title": "Is Calculated",
         "description": "Whether or not the data has been generated by simulation.",
         "default": false,
         "type": "boolean"
      },
      "uri": {
         "title": "Uri",
         "description": "URI of the protein.",
         "type": "string"
      },
      "creator_id": {
         "title": "Creator Id",
         "description": "Unique identifier of the author.",
         "type": "string"
      }
   },
   "required": [
      "id",
      "species_id",
      "data_unit",
      "time_unit"
   ],
   "definitions": {
      "DataTypes": {
         "title": "DataTypes",
         "description": "String enumeration used to assign replicate type ontologies",
         "enum": [
            "conc",
            "abs",
            "feed",
            "biomass"
         ],
         "type": "string"
      }
   }
}

Config

validate_all: bool = True
validate_assignment: bool = True

Fields

creator_id (Optional[str])
data (List[float])
data_type (pyenzyme.enzymeml.core.ontology.DataTypes)
data_unit (str)
id (str)
is_calculated (bool)
measurement_id (Optional[str])
species_id (str)
time (List[float])
time_unit (str)
uri (Optional[str])

Validators

check_data_completeness » data

field creator_id: Optional[str] = None: Unique identifier of the author.

field data: List[float] = None

Data that was measured.

Validated by

check_data_completeness

field data_type: pyenzyme.enzymeml.core.ontology.DataTypes = DataTypes.CONCENTRATION: Type of data that was measured (e.g. concentration)

field data_unit: str [Required]: SI unit of the data that was measured.

field id: str [Required]: Unique identifier of the replicate

field is_calculated: bool = False: Whether or not the data has been generated by simulation.

field measurement_id: Optional[str] = None

Unique identifier of the measurement that the replicate is part of.

Constraints

pattern = m[d]+

field species_id: str [Required]

Unique identifier of the species that has been measured.

Constraints

pattern = [s|r|p][d]+

field time: List[float] = None: Time steps of the replicate.

field time_unit: str [Required]: Time unit of the replicate.

field uri: Optional[str] = None: URI of the protein.

validator check_data_completeness » data[source]

data_unitdef()[source]: Returns the appropriate unitdef if an enzmldoc is given

getData(sep=False)[source]: Deprecated since version Use: the attribute time’ and ‘data instead.

getDataUnit()[source]: Deprecated since version Use: the attribute data_unit instead.

getIsCalculated()[source]: Deprecated since version Use: the attribute is_calculated instead.

getMeasurement()[source]: Deprecated since version Use: the attribute measurement_id instead.

getReactant()[source]: Deprecated since version Use: the attribute species_id instead.

getReplica()[source]: Deprecated since version Use: the attribute replicate_id instead.

getTimeUnit()[source]: Deprecated since version Use: the attribute time_unit instead.

getType()[source]: Deprecated since version Use: the attribute data_type instead.

time_unitdef()[source]: Returns the appropriate unitdef if an enzmldoc is given