mzqc package

Submodules

mzqc.MZQCFile module

class mzqc.MZQCFile.AnalysisSoftware(accession: str = '', name: str = '', description: str = '', value: str = '', unit: str = '', version: str = '', uri: str = '')

Bases: mzqc.MZQCFile.CvParameter

AnalysisSoftware Object representation for mzQC schema type AnalysisSoftware

class mzqc.MZQCFile.BaseQuality(metadata: Optional[mzqc.MZQCFile.MetaDataParameters] = None, qualityMetrics: Optional[List[mzqc.MZQCFile.QualityMetric]] = None)

Bases: mzqc.MZQCFile.jsonobject

BaseQuality Object representation for mzQC schema type BaseQuality

class mzqc.MZQCFile.ControlledVocabulary(name: str = '', uri: str = '', version: str = '')

Bases: mzqc.MZQCFile.jsonobject

ControlledVocabulary Object representation for mzQC schema type ControlledVocabulary

class mzqc.MZQCFile.CvParameter(accession: str = '', name: str = '', description: str = '', value: Optional[Union[int, str, float, List[int], List[str], List[float], List[List[int]], List[List[str]], List[List[float]], Dict[str, List]]] = None, unit: str = '')

Bases: mzqc.MZQCFile.jsonobject

CvParameter Object representation for mzQC schema type CvParameter

class mzqc.MZQCFile.InputFile(location: str = '', name: str = '', fileFormat: Optional[mzqc.MZQCFile.CvParameter] = None, fileProperties: Optional[List[mzqc.MZQCFile.CvParameter]] = None)

Bases: mzqc.MZQCFile.jsonobject

InputFile Object representation for mzQC schema type InputFile

class mzqc.MZQCFile.JsonSerialisable

Bases: object

JsonSerialisable Main structure template for mzQC objects

Sets the foundation for a mzQC object to be readily (de-)serialisable with standard python json handling code. Facilitates reading and writing of complex objects.

classmethod FromJson(json_str, complete=False)

FromJson Main method for deserialisation

Accounts for neccessary object rectification due to same-attribute class footprints. N.B.: for this to work the class init variables must be same name as the corresponding member attributes (self).

Parameters

  • classself (self) – The objects class self

  • json_str (str) – The JSON string to be deserialised

  • complete (bool, optional) – Flag to indicate if the whole JSON is to be returned deserialised, or just the mzQC entry (default).

Returns

The deserialised JSON string

Return type

MzQcFile object

classmethod ToJson(obj, readability=0, complete=True)

ToJson Main method for serialisation

Parameters

  • classself (self) – The objects class self

  • obj (object) – The object to be serialised

  • readability (int, optional) – The indentation level, by default 0 (=no indentation, 1=minor indentation on MZQC objects, >1 heavy indentation for max. human readability)

  • complete (bool, optional) – Flag to indicate if the object is to be left without the enclosing mzQC key or if the JSON is to be amended to full schema compliance (default).

Returns

The serialisation result

Return type

str

classmethod class_mapper(d)

class_mapper Maps incoming objects to their respective definition

Allows every registered object to ‘know’ its type map incuding recursing into its attributes. Can be used as object_hook in the json load process.

Parameters

  • classself (self) – The objects class self

  • d (dict) – The dictionary mapping attributes

Returns

Returns an object of the ‘outer-most’ class

Return type

class object

Raises

ValueError – If expected date strings are invalid.

classmethod complex_handler(obj)

complex_handler Handles the in-depth serialisations necessary

Facilitates the correct serialisation for each type of object (within the registered mzQC JsonSerialisable context).

Parameters

  • classself (self) – The objects class self

  • obj (object) – The object to be deserialised

Returns

The correct object deconstruction into its deserialisable bits

Return type

obj

Raises

TypeError – In case a given object cannot be serialised with the given set of functionalities.

mappings: Dict[str, Any] = {frozenset({'name', 'uri', 'version'}): <class 'mzqc.MZQCFile.ControlledVocabulary'>, frozenset({'accession', 'description', 'name', 'unit', 'value'}): <class 'mzqc.MZQCFile.QualityMetric'>, frozenset({'accession', 'description', 'name', 'unit', 'uri', 'value', 'version'}): <class 'mzqc.MZQCFile.AnalysisSoftware'>, frozenset({'fileFormat', 'fileProperties', 'location', 'name'}): <class 'mzqc.MZQCFile.InputFile'>, frozenset({'analysisSoftware', 'inputFiles', 'label'}): <class 'mzqc.MZQCFile.MetaDataParameters'>, frozenset({'metadata', 'qualityMetrics'}): <class 'mzqc.MZQCFile.SetQuality'>, frozenset({'contactAddress', 'contactName', 'controlledVocabularies', 'creationDate', 'description', 'runQualities', 'setQualities', 'version'}): <class 'mzqc.MZQCFile.MzQcFile'>}
classmethod register(cls)

register The method for class registration in the class mapping process

Each registered class gets mapped.

Parameters

  • classself (self) – the objects class self

  • cls (object) – the class type

Returns

the class type

Return type

cls

static time_helper(da: str) → datetime.datetime

time_helper Helper method for ISO8601 string of various length consumption

Used on JSON datetime object string representation will handle length and return python datetime objects.

Parameters

da (str) – JSON datetime object string representation

Returns

Python datetime object including the same amount detail provided

Return type

datetime

class mzqc.MZQCFile.MetaDataParameters(label: str = '', inputFiles: Optional[List[mzqc.MZQCFile.InputFile]] = None, analysisSoftware: Optional[List[mzqc.MZQCFile.AnalysisSoftware]] = None)

Bases: mzqc.MZQCFile.jsonobject

MetaDataParameters Object representation for mzQC schema type MetaDataParameters

class mzqc.MZQCFile.MzQcFile(creationDate: Union[datetime.datetime, str] = datetime.datetime(2022, 3, 11, 17, 4, 1), version: str = '1.0.0', contactName: str = '', contactAddress: str = '', description: str = '', runQualities: Optional[List[mzqc.MZQCFile.RunQuality]] = None, setQualities: Optional[List[mzqc.MZQCFile.SetQuality]] = None, controlledVocabularies: Optional[List[mzqc.MZQCFile.ControlledVocabulary]] = None)

Bases: mzqc.MZQCFile.jsonobject

MzQcFile Object representation for mzQC schema type MzQcFile

class mzqc.MZQCFile.MzqcJSONEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Bases: json.encoder.JSONEncoder

MzqcJSONEncoder The encoder used to facilitate indented encoding

Handles the string encoding and formatting of the serialised objects.

iterencode(o, _one_shot=False)

Encode the given object and yield each string representation as available.

For example:

for chunk in JSONEncoder().iterencode(bigobject):
    mysocket.write(chunk)
class mzqc.MZQCFile.QualityMetric(accession: str = '', name: str = '', description: str = '', value: Optional[Union[int, str, float, List[int], List[str], List[float], List[List[int]], List[List[str]], List[List[float]], Dict[str, List]]] = None, unit: str = '')

Bases: mzqc.MZQCFile.CvParameter

QualityMetric Object representation is passed for its more concrete derivatives

class mzqc.MZQCFile.RunQuality(metadata: Optional[mzqc.MZQCFile.MetaDataParameters] = None, qualityMetrics: Optional[List[mzqc.MZQCFile.QualityMetric]] = None)

Bases: mzqc.MZQCFile.BaseQuality

QualityMetric Object representation is passed for its more general basis

class mzqc.MZQCFile.SetQuality(metadata: Optional[mzqc.MZQCFile.MetaDataParameters] = None, qualityMetrics: Optional[List[mzqc.MZQCFile.QualityMetric]] = None)

Bases: mzqc.MZQCFile.BaseQuality

SetQuality Object representation is passed for its more general basis

class mzqc.MZQCFile.jsonobject

Bases: object

jsonobject Proxy object for better integration of mzQC objects

Useful for testing and validity checks as __eq__ is overridden to compare all attributes as well.

mzqc.MZQCFile.rectify(obj)

rectify Rectifies objects according to their position in the local hierarchy

Carries out the neccessary object rectification due to same-attribute class footprints. Rectification depends on the object position in the local object hierarchy.

Parameters

obj (object) – The object to be rectified

Returns

The rectified object

Return type

object

mzqc.SemanticCheck module

class mzqc.SemanticCheck.SemanticCheck(version: str = '')

Bases: object

validate(mzqc_obj: mzqc.MZQCFile.MzQcFile)
exception mzqc.SemanticCheck.SemanticError(message, validator=<unset>, path=(), cause=None, context=(), validator_value=<unset>, instance=<unset>, schema=<unset>, schema_path=(), parent=None)

Bases: jsonschema.exceptions.ValidationError

Base class for exceptions in this module.

mzqc.SyntaxCheck module

class mzqc.SyntaxCheck.SyntaxCheck(version: str = 'main')

Bases: object

SyntaxCheck class for syntax validations of mzQC objects (after JSON dump)

Using member function validate of the SytnaxCheck class, mzQC objects can be checked for correct syntax in its built-in serialisation.

validate(mzqc_str: str)

Module contents