`mh_utils.worklist_parser.classes`

Main classes for the worklist parser.

Classes:

`Attribute`(attribute_id, attribute_type, …)	Represents an Attribute.
`Checksum`(SchemaVersion, ALGO_VERSION, HASHCODE)	Represents a checksum for a worklist.
`JobData`(id, job_type, run_status[, sample_info])	Represents an entry in the worklist.
`Macro`(project_name, procedure_name, …)	Represents a macro in a worklist.
`Worklist`(version, locked_run_mode, …)	Class that represents an Agilent MassHunter worklist.

class Attribute(attribute_id, attribute_type, field_type, system_name, header_name, data_type, default_data_value, reorder_id, show_hide_status, column_width)[source]

Represents an Attribute.

Parameters

attribute_id (int)
attribute_type (AttributeType) – The attribute type identifier.
field_type (int) – The field type identifier.
system_name (str)
header_name (str)
data_type (int)
default_data_value (str)
reorder_id (int)
show_hide_status (Union[str, bool])
column_width (int) – end{multicols}

Attributes:

`attribute_id`
`attribute_type`	The attribute type identifier.
`column_width`
`data_type`
`default_data_value`
`field_type`	The field type identifier.
`header_name`
`reorder_id`
`show_hide_status`
`system_name`

Methods:

`from_dict`(d)	Construct an instance of `Attribute` from a dictionary.
`from_xml`(element)	Construct an `Attribute` object from an XML element.
`to_dict`([convert_values])	Returns a dictionary containing the contents of the `Attribute` object.

attribute_id: Type: int

attribute_type

Type: AttributeType

The attribute type identifier.

Can be System Defined (0), System Used (1), or User Added (2).

column_width: Type: int

data_type: Type: Any

default_data_value: Type: str

field_type

Type: int

The field type identifier.

Each of the system defined columns have a field type starting from sampleid = 0 to reserved6 = 24.

The system used column can be ‘compound param’ = 35, ‘optim param’ = 36, ‘mass param’ = 37 and ‘protein param’ = 38.

The User added columns start from 45.

classmethod from_dict(d)

Construct an instance of Attribute from a dictionary.

Parameters: d (Mapping[str, Any]) – The dictionary.

classmethod from_xml(element)[source]

Construct an Attribute object from an XML element.

Return type: Attribute

header_name: Type: str

reorder_id: Type: int

show_hide_status: Type: bool

system_name: Type: str

to_dict(convert_values=False)

Returns a dictionary containing the contents of the Attribute object.

Parameters: convert_values (bool) – Recursively convert values into dictionaries, lists etc. as appropriate. Default False.
Return type: MutableMapping[str, Any]

class Checksum(SchemaVersion, ALGO_VERSION, HASHCODE)[source]

Represents a checksum for a worklist.

The format of the checksum is unknown.

Parameters

SchemaVersion (int)
ALGO_VERSION (int)
HASHCODE (str)

Attributes:

`ALGO_VERSION`
`HASHCODE`
`SchemaVersion`

Methods:

`from_dict`(d)	Construct an instance of `Checksum` from a dictionary.
`from_xml`(element)	Construct a `Checksum` object from an XML element.
`to_dict`([convert_values])	Returns a dictionary containing the contents of the `Checksum` object.

ALGO_VERSION: Type: int

HASHCODE: Type: str

SchemaVersion: Type: int

classmethod from_dict(d)

Construct an instance of Checksum from a dictionary.

Parameters: d (Mapping[str, Any]) – The dictionary.

classmethod from_xml(element)[source]

Construct a Checksum object from an XML element.

Return type: Checksum

to_dict(convert_values=False)

Returns a dictionary containing the contents of the Checksum object.

Parameters: convert_values (bool) – Recursively convert values into dictionaries, lists etc. as appropriate. Default False.
Return type: MutableMapping[str, Any]

class JobData(id, job_type, run_status, sample_info=None)[source]

Bases: Dictable

Represents an entry in the worklist.

Parameters

id (Union[str, UUID]) – The ID of the job.
job_type (int) – The type of job. TODO: enum of values
run_status (int) – The status of the analysis. TODO: enum of values
sample_info (Optional[dict]) – Optional key: value mapping of information about the sample. Default None.

Methods:

from_xml(element[, user_columns])

Construct a JobData object from an XML element.

classmethod from_xml(element, user_columns=None)[source]

Construct a JobData object from an XML element.

Parameters

element (ObjectifiedElement) – The XML element to parse the data from
user_columns (Optional[Dict[str, Column]]) – Optional mapping of user column labels to Column objects. Default None.

Return type

JobData

class Macro(project_name, procedure_name, input_parameter, output_data_type, output_parameter, display_string)[source]

Represents a macro in a worklist.

Parameters

project_name (str)
procedure_name (str)
input_parameter (str)
output_data_type (int)
output_parameter (str) –
.
display_string (str)

Attributes:

`display_string`
`input_parameter`
`output_data_type`
`output_parameter`
`procedure_name`
`project_name`
`undefined`	Returns whether the macro is undefined.

Methods:

`from_dict`(d)	Construct an instance of `Macro` from a dictionary.
`from_xml`(element)	Construct a `Macro` object from an XML element.
`to_dict`([convert_values])	Returns a dictionary containing the contents of the `Macro` object.

display_string: Type: str

classmethod from_dict(d)

Construct an instance of Macro from a dictionary.

Parameters: d (Mapping[str, Any]) – The dictionary.

classmethod from_xml(element)[source]

Construct a Macro object from an XML element.

Return type: Macro

input_parameter: Type: str

output_data_type: Type: int

output_parameter: Type: str

procedure_name: Type: str

project_name: Type: str

to_dict(convert_values=False)

Returns a dictionary containing the contents of the Macro object.

Parameters: convert_values (bool) – Recursively convert values into dictionaries, lists etc. as appropriate. Default False.
Return type: MutableMapping[str, Any]

property undefined

Returns whether the macro is undefined.

Return type: bool

class Worklist(version, locked_run_mode, instrument_name, params, user_columns, jobs, checksum)[source]

Bases: XMLFileMixin, Dictable

Class that represents an Agilent MassHunter worklist.

Parameters

version (float) – WorklistInfo version number
locked_run_mode (bool) – Flag to indicate whether the data was acquired in locked mode. Yes = -1. No = 0.
instrument_name (str) – The name of the instrument.
params (dict) – Mapping of parameter names to values. TODO: Check
user_columns (dict) – Mapping of user columns to ??? TODO
jobs (Sequence[JobData])
checksum (Checksum) – The checksum of the worklist file. The format is unknown.

Methods:

`__repr__`()	Return a string representation of the `Worklist`.
`as_dataframe`()	Returns the `Worklist` as a `pandas.DataFrame`.
`from_xml`(element)	Construct a `Worklist` object from an XML element.

__repr__()[source]

Return a string representation of the Worklist.

Return type: str

as_dataframe()[source]

Returns the Worklist as a pandas.DataFrame.

Return type: DataFrame

classmethod from_xml(element)[source]

Construct a Worklist object from an XML element.

Return type: Worklist

mh_utils.worklist_parser.classes

`mh_utils.worklist_parser.classes`