model

model Package

The qiprofile REST data model.

The model field choices are listed in the preferred display order, most common to least common.

The data capture client has the following responsibility:

  • Validate the data upon input as determined by the model validation documentation.
  • Resolve conflicts between data capture and the model, e.g. the default value or validation.

admin

The qiprofile administrative Mongodb data model.

class qirest_client.model.admin.User(*args, **values)

Bases: mongoengine.document.Document

The application user.

Initialise a document or embedded document

Parameters:
  • __auto_convert – Try and will cast python objects to Object types
  • values – A dictionary of values for the document

clinical

The qiprofile clinical Mongodb data model.

class qirest_client.model.clinical.Agent(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

A treatment agent, e.g. drug or radiation.

class qirest_client.model.clinical.Biopsy(*args, **kwargs)

Bases: qirest_client.model.common.Encounter

Non-therapeutic tissue extraction resulting in a pathology report.

class qirest_client.model.clinical.BreastGeneticExpression(*args, **kwargs)

Bases: qirest_client.model.common.Outcome

The breast patient genetic expression results.

class qirest_client.model.clinical.BreastNormalizedAssay(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The Breast genomics panel normalized to reference genes.

class qirest_client.model.clinical.BreastNormalizedAssayField(min_value=None, max_value=None, **kwargs)

Bases: mongoengine.fields.IntField

The normalized Breast genomics result in the inclusive range [0, 15].

class qirest_client.model.clinical.BreastPathology(*args, **kwargs)

Bases: qirest_client.model.clinical.TumorPathology

The breast patient pathology summary.

rcb_class(rcb_index)

Returns the RCB class per the cut-offs defined in JCO 25:28 4414-4422.

Parameters:rcb_index – the rcb_index() value
rcb_index()

Returns the RCB index per JCO 25:28 4414-4422.

class qirest_client.model.clinical.BreastSurgery(*args, **kwargs)

Bases: qirest_client.model.clinical.Surgery

Breast tumor extraction.

class qirest_client.model.clinical.Dosage(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The agent dosage.

class qirest_client.model.clinical.Evaluation(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The patient evaluation holds outcomes.

class qirest_client.model.clinical.FNCLCCGrade(*args, **kwargs)

Bases: qirest_client.model.clinical.Grade

The FNCLCC sarcoma tumor grade.

class qirest_client.model.clinical.Grade(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The abstract tumor grade superclass, specialized for each tumor type.

class qirest_client.model.clinical.HormoneReceptorStatus(*args, **kwargs)

Bases: qirest_client.model.common.Outcome

The patient estrogen/progesterone hormone receptor status.

class qirest_client.model.clinical.ModifiedBloomRichardsonGrade(*args, **kwargs)

Bases: qirest_client.model.clinical.Grade

The Modified Bloom Richardson (a.k.a. Nottingham) breast tumor grade.

class qirest_client.model.clinical.NecrosisPercent(*args, **kwargs)

Bases: qirest_client.model.common.Outcome

The necrosis percent value or range.

class qirest_client.model.clinical.NecrosisPercentRange(*args, **kwargs)

Bases: qirest_client.model.clinical.NecrosisPercent

The necrosis percent range.

Note:it is recommended, although not required, that the percent range is a decile range, e.g. [20-30].
Note:A range which spans 50%, e.g. [40-60], results in a necrosis_percent_as_score() ValidationError.
class Bound(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

Necrosis percent upper or lower bound abstract class. The subclass is responsible for adding the inclusive field.

class NecrosisPercentRange.LowerBound(*args, **kwargs)

Bases: qirest_client.model.clinical.Bound

Necrosis percent lower bound.

class NecrosisPercentRange.UpperBound(*args, **kwargs)

Bases: qirest_client.model.clinical.Bound

Necrosis percent upper bound.

class qirest_client.model.clinical.NecrosisPercentValue(*args, **kwargs)

Bases: qirest_client.model.clinical.NecrosisPercent

The necrosis percent absolute value.

class qirest_client.model.clinical.PathologyReport(*args, **kwargs)

Bases: qirest_client.model.clinical.Evaluation

The patient pathology report findings.

class qirest_client.model.clinical.ResidualCancerBurden(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The residual cancer burden after neodjuvant treatment.

class qirest_client.model.clinical.SarcomaPathology(*args, **kwargs)

Bases: qirest_client.model.clinical.TumorPathology

The sarcoma patient pathology summary.

class qirest_client.model.clinical.Surgery(*args, **kwargs)

Bases: qirest_client.model.common.Encounter

Therapeutic tissue extraction which usually results in a pathology report.

class qirest_client.model.clinical.TNM(*args, **kwargs)

Bases: qirest_client.model.common.Outcome

The TNM tumor staging. The TNM fields are as follows:

  • size - primary tumor size (T)
  • lymph_status - regional lymph nodes (N)
  • metastasis - distant metastasis (M)
  • grade - tumor grade (G)
  • serum_tumor_markers (S)
  • resection_boundaries (R)
  • lymphatic_vessel_invasion (L)
  • vein_invasion (V)

The size is an aggregate Size field. See http://www.cancer.gov/cancertopics/factsheet/detection/staging for an overview. See http://en.wikipedia.org/wiki/TNM_staging_system and http://cancerstaging.blogspot.com/ for the value definition.

Note:The size and lymph_status choices can be further constrained by tumor type. Since TNM is a generic class, these constraints are not enforced in this TNM class. Rather, the REST client is responsible for enforcing additional choice constraints. The TNM.lymph_status_choices() helper method can be used for tumor type specific choices. See TNM.Size` for a discussion of the size constraints.
class Size(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The TNM primary tumor size field.

Note:The size score choices can be further constrained by tumor type. For example, the sarcoma tumor_size choices are 0, 1 or 2 and suffix choices are a or b. See TNM for a discussion of choice constraints. The TNM.Size.tumor_size_choices() and TNM.Size.suffix_choices() helper methods can be used for tumor type specific choices.
clean()

Peforms document-level validation.

Raises:ValidationError – if the in_situ flag is set but there is a tumor_size or suffix field
classmethod parse(klass, value)

Parses the given string into a new Size. The size must match the SIZE_REGEX regular expression.

Parameters:value – the input string
Returns:the new Size object
Raises:ValidationError – it the size value string does not match SIZE_REGEX
static suffix_choices(tumor_type=None)
Parameters:tumor_type – the optional tumor type, e.g. Breast
Returns:the suffix choices for the given type
static tumor_size_choices(tumor_type=None)
Parameters:tumor_type – the optional tumor type, e.g. Breast
Returns:the tumor_size choices for the given type
static TNM.lymph_status_choices(tumor_type=None)
Parameters:tumor_type – the optional tumor type, e.g. Breast
Returns:the lymph_status choices for the given type
class qirest_client.model.clinical.Treatment(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The patient therapy, e.g. adjuvant. Treatment is one of the Treatment.TYPE_CHOICES types, and occurs over a period of time. The treatment consists of dosages, which may be pharmocological or radiological.

class qirest_client.model.clinical.TumorLocation(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The tumor body part and directional orientation.

class qirest_client.model.clinical.TumorPathology(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The tumor-specific pathology.

qirest_client.model.clinical.necrosis_percent_as_score(necrosis_percent)

Calculates the necrosis score from the necrosis percent according to the Stanford Synovial Sarcoma Guideline<http://surgpathcriteria.stanford.edu/softmisc/synovial_sarcoma/grading.html> as follows: * If the percent is None, then None * Otherwise, if the percent is 0, then 0 * Otherwise, if the percent is less than 50, then 1 * Otherwise, 2

Parameters:necrosis_percent – the integer percent, NecrosisPercentValue or NecrosisPercentRange
Returns:the necrosis score
Raises:ValidationError – if the percent is a range that spans 50%

imaging

The qiprofile imaging Mongodb data model.

class qirest_client.model.imaging.Image(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The image file encapsulation.

class qirest_client.model.imaging.ImageSequence(*args, **kwargs)

Bases: qirest_client.model.common.Outcome

The Scan or Registration.

class qirest_client.model.imaging.LabelMap(*args, **kwargs)

Bases: qirest_client.model.imaging.Image

A label map with an optional associated color lookup table.

class qirest_client.model.imaging.Modeling(*args, **kwargs)

Bases: qirest_client.model.common.Outcome

The pharmicokinetic modeling run on an image sequence.

class ParameterResult(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The output for a given modeling run result parameter.

class Modeling.Source(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

This Modeling.Source embedded class works around the following mongoengine limitation:

  • mongoengine does not allow heterogeneous collections, i.e. a domain model Document subclass cannot have subclasses. Furthermore, the domain model Document class cannot be an inner class.

Consequently, the Modeling.source field cannot represent an abstract superclass with subclasses RegistrationSource and ScanSource. The work-around is to introduce this Source embedded document disambiguation by creating a disjunction object that can either hold a scan reference or a registration reference.

class qirest_client.model.imaging.MultiImageResource(*args, **kwargs)

Bases: qirest_client.model.imaging.Resource

A resource with several files.

class qirest_client.model.imaging.Point(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The 3D point in the volume voxel space.

class qirest_client.model.imaging.Protocol(*args, **values)

Bases: mongoengine.document.Document

The image acquisition or processing protocol abstract class.

Initialise a document or embedded document

Parameters:
  • __auto_convert – Try and will cast python objects to Object types
  • values – A dictionary of values for the document
class qirest_client.model.imaging.Region(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The 3D region in volume voxel space.

class qirest_client.model.imaging.Registration(*args, **kwargs)

Bases: qirest_client.model.imaging.ImageSequence

The patient image registration that results from processing a scan.

class qirest_client.model.imaging.Resource(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

The image store file access abstraction.

class qirest_client.model.imaging.Scan(*args, **kwargs)

Bases: qirest_client.model.imaging.ImageSequence

The the concrete subclass of the abstract ImageSequence class for scans.

class qirest_client.model.imaging.Session(*args, **kwargs)

Bases: qirest_client.model.common.Encounter

The MR session (a.k.a. study in DICOM terminology).

acquisition_parameters

alias of DictField

classmethod pre_delete(sender, document, **kwargs)

Cascade delete this Session’s detail.

class qirest_client.model.imaging.SessionDetail(*args, **values)

Bases: mongoengine.document.Document

The MR session detailed content.

Initialise a document or embedded document

Parameters:
  • __auto_convert – Try and will cast python objects to Object types
  • values – A dictionary of values for the document
class qirest_client.model.imaging.SingleImageResource(*args, **kwargs)

Bases: qirest_client.model.imaging.Resource

A resource with one file.

subject

The qiprofile subject Mongodb data model.

class qirest_client.model.subject.ImagingCollection(*args, **values)

Bases: mongoengine.document.Document

The imaging collection.

Initialise a document or embedded document

Parameters:
  • __auto_convert – Try and will cast python objects to Object types
  • values – A dictionary of values for the document
class qirest_client.model.subject.Project(*args, **values)

Bases: mongoengine.document.Document

The imaging project.

Initialise a document or embedded document

Parameters:
  • __auto_convert – Try and will cast python objects to Object types
  • values – A dictionary of values for the document
class qirest_client.model.subject.Subject(*args, **values)

Bases: mongoengine.document.Document

The patient.

Initialise a document or embedded document

Parameters:
  • __auto_convert – Try and will cast python objects to Object types
  • values – A dictionary of values for the document
add_encounter(encounter)

Inserts the given encounter to this Subject encounters list in temporal order by encounter date.

clinical_encounters
Returns:the non-qirest_client.imaging.Session encounters
pre_delete(sender, document, **kwargs)

Cascade delete the subject’s sessions.

sessions
Returns:the qirest_client.imaging.Session encounters

uom

The qiprofile unit of measurement MongoDB data model.

This uom module is an advisory module for quantity display and conversion. Quantities are always stored in a canonical unit documented in the field.

class qirest_client.model.uom.Decimal(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

This Decimal document class is a work-around for the broken MongoEngine DecimalField (cf. https://github.com/MongoEngine/mongoengine/issues?q=is%3Aissue+is%3Aopen+decimal).

Decimal has a float value and an optional precision. The default precision is determined as follows:

  • If the Decimal value is initialized with a python decimal.Decimal or string, then the default precision is the number of decimal places expressed in that value, e.g.:

    Decimal('1.24').precision #=> 2
Decimal(decimal.Decimal('1.4')).precision #=> 1
  • If the Decimal value is initialized with an integer, then the default

    precision is zero, e.g.:

    Decimal(1).precision #=> 0
__init__(*args, **kwargs)
canonical()
Returns:the python decimal.Decimal equivalent of this Decimal
class qirest_client.model.uom.Measurement(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

A scientific measurement.

The measurement is a quantitative amount associated with a unit. The unit is the Unit as captured and displayed. The amount is expressed as a python Decimal in unscaled units. If the constructor is called with a non-Decimal numeric amount, then the value is converted to a Decimal, e.g.:

Measurement(amount=0.006, unit=Weight())

is equivalent to:

from decimal import Decimal
Measurement(amount=Decimal(0.006), unit=Weight())

The measurement unit can be qualified by a second per_unit dimension, e.g. 2 mg/kg dosage per patient weight is expressed as:

Measurement(amount=0.002, unit=Weight(), per_unit=Weight(scale='k'))
Note:the amount is a Decimal embedded object rather than the broken MongoEngine DecimalField (see the Decimal comment).

Initializes the Measurement document. The amount can be either a positional or a keyword argument. The amount is converted to a Decimal.

Parameters:
  • args – the amount as a positional argument
  • kwargs – the following keyword arguments:
  • amount – the amount as a keyword argument
__init__(*args, **kwargs)

Initializes the Measurement document. The amount can be either a positional or a keyword argument. The amount is converted to a Decimal.

Parameters:
  • args – the amount as a positional argument
  • kwargs – the following keyword arguments:
  • amount – the amount as a keyword argument
class qirest_client.model.uom.Radiation(*args, **kwargs)

Bases: qirest_client.model.uom.Unit

The radiation unit is always an unscaled Gray.

class qirest_client.model.uom.Unit(*args, **kwargs)

Bases: mongoengine.document.EmbeddedDocument

Unit is an abstract class for the supported measurement units. Each unit has a scaling factor with the default scaling factor defined in the concrete Unit subclass. Each Unit subclass has the following class variables:

  • BASE - the standard unscaled metric unit abbreviation, e.g. m for the meter Extent unit.
  • SCALES - the recommended scaling factors, e.g. m for
    milli and c for centi.

The scales are a list in preference order, e.g. the Extent.SCALES value ['c', 'm'] implies that the preferred extent unit display is cm (centimeter) and an edit form should show the scales c and m, in that order, defaulting to c. A scale of None signifies the scaling factor 1, e.g. the the Radiation.SCALES value [None, 'c'] implies that the preferred radiation unit display is Gy (Gray) and an edit form should show the scales blank and c, in that order, defaulting to blank (scaling factor 1).

These class variables are advisory. The client is responsible for displaying the base and scales and converting from a scaled value to an unscaled value before saving the measurement to the database.

facade