Starting Materials

pydatalab.models.starting_materials

StartingMaterial

Bases: Item, HasSynthesisInfo

A model for representing an experimental sample, based on the connection with cheminventory.net, which mixes container-level and substance-level information.

Attributes:

Name	Type	Description
CAS	str | None	The CAS Registry Number for the substance described by this entry.
GHS_codes	str | None	A string describing any GHS hazard codes associated with this item. See https://pubchem.ncbi.nlm.nih.gov/ghs/ for code definitions.
barcode	str | None	A unique barcode provided by an external source, e.g., cheminventory.
blocks_obj	dict[str, Any]	A mapping from block ID to block data.
chemform	str | None	A string representation of the chemical formula associated with this sample.
chemical_purity	str | None	The chemical purity of this container with regards to the defined substance.
collections	list[Collection]	Inlined info for the collections associated with this item.
comment	str | None	Any additional comments or notes about the container.
creator_ids	list[PyObjectId]	The database IDs of the user(s) who created the item.
creators	list[Person] | None	Inlined info for the people associated with this item.
date	IsoformatDateTime | None	The date the item was acquired
date_opened	IsoformatDateTime | None	The date the item was opened
description	str | None	A description of the item, either in plain-text or a markup language.
display_order	list[str]	The order in which to display block data in the UI.
file_ObjectIds	list[PyObjectId]	Links to object IDs of files stored within the database.
files	list[File] | None	Any files attached to this sample.
full_percent	str | None	The amount of the defined substance remaining in the container, expressed as a percentage.
immutable_id	PyObjectId	The immutable database ID of the entry.
item_id	HumanReadableIdentifier	A locally unique, human-readable identifier for the entry. This ID is mutable.
last_modified	IsoformatDateTime | None	The timestamp at which the entry was last modified.
location	str | None	The place where the container is located.
molar_mass	float | None	Mass per formula unit, in g/mol.
name	str | None	The name of the substance in the container.
refcode	Refcode	A globally unique immutable ID comprised of the deployment prefix (e.g., grey)
relationships	list[TypedRelationship] | None	A list of related entries and their types.
revision	int	The revision number of the entry.
revisions	dict[int, Any] | None	An optional mapping from old revision numbers to the model state at that revision.
size	str | None	The total size of the container, in units of size_unit.
size_unit	str | None	Units for the 'size' field.
smiles_representation	str | None	A SMILES string representation of a chemical structure associated with this substance.
supplier	str | None	Supplier or manufacturer of the chemical.
synthesis_constituents	list[Constituent]	A list of references to constituent materials giving the amount and relevant inlined details of consituent items.
synthesis_description	str | None	Free-text details of the procedure applied to synthesise the sample
type	str

CAS: str | None = Field(alias='Substance CAS')

The CAS Registry Number for the substance described by this entry.

GHS_codes: str | None = Field(alias='GHS H-codes', examples=['H224', 'H303, H316, H319'])

A string describing any GHS hazard codes associated with this item. See https://pubchem.ncbi.nlm.nih.gov/ghs/ for code definitions.

barcode: str | None = Field(alias='Barcode')

A unique barcode provided by an external source, e.g., cheminventory.

blocks_obj: dict[str, Any] = Field({})

A mapping from block ID to block data.

chemform: str | None = Field(alias='Molecular Formula')

A string representation of the chemical formula associated with this sample.

chemical_purity: str | None = Field(alias='Chemical purity')

The chemical purity of this container with regards to the defined substance.

collections: list[Collection] = Field([])

Inlined info for the collections associated with this item.

comment: str | None = Field(alias='Comments')

Any additional comments or notes about the container.

creator_ids: list[PyObjectId] = Field([])

The database IDs of the user(s) who created the item.

creators: list[Person] | None = Field(None)

Inlined info for the people associated with this item.

date: IsoformatDateTime | None = Field(alias='Date Acquired')

The date the item was acquired

date_opened: IsoformatDateTime | None = Field(alias='Date opened')

The date the item was opened

description: str | None

A description of the item, either in plain-text or a markup language.

display_order: list[str] = Field([])

The order in which to display block data in the UI.

file_ObjectIds: list[PyObjectId] = Field([])

Links to object IDs of files stored within the database.

files: list[File] | None

Any files attached to this sample.

full_percent: str | None = Field(alias='Full %')

The amount of the defined substance remaining in the container, expressed as a percentage.

immutable_id: PyObjectId = Field(None, title='Immutable ID', alias='_id', format='uuid')

The immutable database ID of the entry.

item_id: HumanReadableIdentifier

A locally unique, human-readable identifier for the entry. This ID is mutable.

last_modified: IsoformatDateTime | None = None

The timestamp at which the entry was last modified.

location: str | None = Field(alias='Location')

The place where the container is located.

molar_mass: float | None = Field(alias='Molecular Weight')

Mass per formula unit, in g/mol.

name: str | None = Field(alias='Container Name')

The name of the substance in the container.

refcode: Refcode = None

A globally unique immutable ID comprised of the deployment prefix (e.g., grey) and a locally unique string, ideally created with some consistent scheme.

relationships: list[TypedRelationship] | None = None

A list of related entries and their types.

revision: int = 1

The revision number of the entry.

revisions: dict[int, Any] | None = None

An optional mapping from old revision numbers to the model state at that revision.

size: str | None = Field(alias='Container Size')

The total size of the container, in units of size_unit.

size_unit: str | None = Field(alias='Unit')

Units for the 'size' field.

smiles_representation: str | None = Field(alias='SMILES')

A SMILES string representation of a chemical structure associated with this substance.

supplier: str | None = Field(alias='Supplier')

Supplier or manufacturer of the chemical.

synthesis_constituents: list[Constituent] = Field([])

A list of references to constituent materials giving the amount and relevant inlined details of consituent items.

synthesis_description: str | None = None

Free-text details of the procedure applied to synthesise the sample

type: str = Field('starting_materials', const='starting_materials', pattern='^starting_materials$')

Collection

Bases: Entry, HasOwner, HasBlocks

Attributes:

Name	Type	Description
blocks_obj	dict[str, Any]	A mapping from block ID to block data.
collection_id	HumanReadableIdentifier	A short human-readable/usable name for the collection.
creator_ids	list[PyObjectId]	The database IDs of the user(s) who created the item.
creators	list[Person] | None	Inlined info for the people associated with this item.
description	str | None	A description of the collection, either in plain-text or a markup language.
display_order	list[str]	The order in which to display block data in the UI.
immutable_id	PyObjectId	The immutable database ID of the entry.
last_modified	IsoformatDateTime | None	The timestamp at which the entry was last modified.
num_items	int | None	Inlined number of items associated with this collection.
relationships	list[TypedRelationship] | None	A list of related entries and their types.
title	str | None	A descriptive title for the collection.
type	str

blocks_obj: dict[str, Any] = Field({})

A mapping from block ID to block data.

collection_id: HumanReadableIdentifier = Field(None)

A short human-readable/usable name for the collection.

creator_ids: list[PyObjectId] = Field([])

The database IDs of the user(s) who created the item.

creators: list[Person] | None = Field(None)

Inlined info for the people associated with this item.

description: str | None

A description of the collection, either in plain-text or a markup language.

display_order: list[str] = Field([])

The order in which to display block data in the UI.

immutable_id: PyObjectId = Field(None, title='Immutable ID', alias='_id', format='uuid')

The immutable database ID of the entry.

last_modified: IsoformatDateTime | None = None

The timestamp at which the entry was last modified.

num_items: int | None = Field(None)

Inlined number of items associated with this collection.

relationships: list[TypedRelationship] | None = None

A list of related entries and their types.

title: str | None

A descriptive title for the collection.

type: str = Field('collections', const='collections', pattern='^collections$')

check_id_names(values)

Slightly upsetting hack: this case should be covered by the pydantic setting for populating fields by alias names.

check_ids(values)

to_reference(additional_fields: list[str] | None = None) -> EntryReference

Populate an EntryReference model from this entry, selecting additional fields to inline.

Parameters:

Name	Type	Description	Default
additional_fields	list[str] | None	A list of fields to inline in the reference.	None

add_missing_collection_relationships(values)

add_missing_synthesis_relationships(values)

Add any missing sample synthesis constituents to parent relationships

add_molar_mass(v, values)

check_id_names(values)

Slightly upsetting hack: this case should be covered by the pydantic setting for populating fields by alias names.

refcode_validator(v)

Generate a refcode if not provided.

to_reference(additional_fields: list[str] | None = None) -> EntryReference

Populate an EntryReference model from this entry, selecting additional fields to inline.

Parameters:

Name	Type	Description	Default
additional_fields	list[str] | None	A list of fields to inline in the reference.	None