`mh_utils.worklist_parser.classes`¶

Main classes for the worklist paser.

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])	Class that 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]¶

Bases: object

Represents an Attribute.

Parameters

attribute_id
attribute_type – Can be System Defined (0), System Used (1), or User Added (2).
field_type – 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.
system_name
header_name
data_type
default_data_value
reorder_id
show_hide_status
column_width

Attributes:

`attribute_id`
`attribute_type`	Can be System Defined (`0`), System Used (`1`), or User Added (`2`).
`column_width`
`data_type`
`default_data_value`
`field_type`	Each of the system defined columns have a field type starting from sampleid = 0 to reserved6 = 24.
`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

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

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]¶

Bases: object

Represents a checksum for a worklist.

The format of the checksum is unknown.

Parameters

SchemaVersion
ALGO_VERSION
HASHCODE

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

Class that 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:

`__repr__`()	Return a string representation of the `Dictable`.
`from_xml`(element[, user_columns])	Construct a `JobData` object from an XML element.

__repr__()[source]¶

Return a string representation of the Dictable.

Return type: str

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]¶

Bases: object

Represents a macro in a worklist.

Parameters

project_name
procedure_name
input_parameter
output_data_type
output_parameter
display_string

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 repr(self).
`as_dataframe`()	Returns the `Worklist` as a `pandas.DataFrame`.
`from_xml`(element)	Construct a `Worklist` object from an XML element.

__repr__()[source]¶

Return repr(self).

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`¶