Collection

Collections are the main tool given by the Chemotion system to organize elements. In the Python APi Collection are seperated in different classes. The root collection is the basic element to work with collections.

class chemotion_api.collection.RootCollection(session: Connection)

The root collection is the foundation of working with collections. It serves with methods to navigate through the collections and creating new collections

Usage:

>>> from chemotion_api import Instance
>>> import logging
>>> try:
>>>     instance = Instance('http(d)://xxx.xxx.xxx').test_connection().login('<USER>', "<PASSWORD>")
>>> except ConnectionError as e:
>>>     logging.error(f"A connection to Chemotion ({instance.host_url}) cannot be established")
>>> rc = instance.get_root_collection(True)
>>> # Navigate to collection 'Team One' in 'Projects'
>>> col = rc.get_collection('/Projects/Team One')
>>> # Create collection 'P 123' in '/Project/Team One'
>>> col.get_or_create_collection('./P 123')
>>> # Move collection P 122 into collection '/Done Projects'
>>> col.get_collection('./P 122').move('/Done Projects')
>>> for sample in col.get_samples():
>>>     pass # Do something
add_collection(path_to_new: str | list[str])

Creates a new collection at the path_to_new path. The collection is not saved. Please reload the collection after saving it.

Parameters:

path_to_new – is either a string based on a unix path or a list

Returns:

new Collection (not saved)

property all: dict[slice(<class 'str'>, <built-in function any>, None)]

Returns all information of the ‘All’ collections

Returns:

information of the ‘All’ collection

property children: list[TAbstractCollection]

A list of all children collection

Returns:

A list of all children collection

delete(src: str | list[str], case_insensitive: bool = False)

Deletes a collection at the src path.

Parameters:

  • src – is either a string based on a unix path or a list

  • case_insensitive – If true the cases of path are taken into account

find(label: str | None = None, **kwargs) → list[TAbstractCollection]

Finds a collection by its label or other properties. Path is not needed.

Parameters:

  • label – String or None.

  • kwargs – Other properties used to search Collections

Returns:

All found Collections

get_collection(col_path: str | list[str], case_insensitive: bool = False) → TAbstractCollection

Gets a collection a path points to.

Parameters:

  • col_path – is either a string based on a unix path or a list

  • case_insensitive – If true the cases of path are taken into account

Returns:

Collection the path points to

get_elements_of_iri(element_type: str, per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

Gets all elements of given IRI type.

Parameters:

  • element_type – IRI string chemotion:xxx/xxx/xxx

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet based on the IRI

get_generics_by_label(label: str, per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all generic elements of a given label.

Parameters:

  • label – generic element’s label

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of generic elements of a given name

get_generics_by_name(name: str, per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all generic elements of a given name.

Parameters:

  • name – generic element’s name

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of generic elements of a given name

get_or_create_collection(col_path: str | list[str], case_insensitive: bool = False) → TAbstractCollection

Gets or creates a collection the col_path path points to. If the collection needs to be created the collection is saved right away.

Parameters:

  • col_path – is either a string based on a unix path or a list

  • case_insensitive – If true the cases of path are taken into account

Returns:

Collection the path points to

get_path() → str

Generates the absolut path of collection

Returns:

Absolut path of a collection

get_reactions(per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all reactions.

Parameters:

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of reactions

get_research_plans(per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all research plans.

Parameters:

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of research plans

get_root() → TRootCollection

Get root Collection

Returns:

Instance of the RootCollection

get_samples(per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None, product_only: bool = False) → ElementSet

List of all samples.

Parameters:

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

  • product_only – If True only samples which are products in a reaction are returned

Returns:

ElementSet of samples

get_wellplates(per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all well plates.

Parameters:

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of well plates

property id: int

The ‘All’ collection ID

Returns:

Ihe ID of the ‘All’ collection

property label: str | None

The collection label

Returns:

The collection label

load_collection() → dict[slice(<class 'str'>, <built-in function any>, None)]

Load collection information

Returns:

A collection off all collection information

load_sync_collection() → RootSyncCollection

Loads the RootSyncCollection. The RootSyncCollection collection can be used to access all collection synced with you.

Returns:

instance of RootSyncCollection

move(src: str | list[str], dest: str | list[str], case_insensitive: bool = False)

Moves a collection from a src path to a dest path.

Parameters:

  • src – is either a string based on a unix path or a list

  • dest – is either a string based on a unix path or a list

  • case_insensitive – If true the cases of path are taken into account

Returns:

Collection the path points to

prepare_label(case_insensitive: bool) → str

Prepares the label of a collection

Parameters:

case_insensitive – If true it returns teh lower case label

Returns:

The collection’s label

save()

Saves ALL updates of done to owned (not synced) collection.

set_element_manager(element_manager: ElementManager)

Set the ElementManager class

Parameters:

element_manager – instance of ElementManager

property sync_root: RootSyncCollection

The RootSyncCollection collection can be used to access all collection synced with you.

Returns:

instance of RootSyncCollection

to_json() → dict[slice(<class 'str'>, <class 'list'>, None)]

Generates a dict containing all list of all children collection

Returns:

list of children as savable JSON

The root collection organizes the standard Collections:

class chemotion_api.collection.Collection(collection_json: dict | None = None)

The collection object represents the standard collection owned by the current user

add_collection(name: str)

Creates a new child collection. The collection is not saved. Please reload the collection after saving it.

Parameters:

name – new collection`s name

Returns:

new Collection (not saved)

property children: list[TAbstractCollection]

A list of all children collection

Returns:

A list of all children collection

delete()

Deletes this collection.

find(label: str | None = None, **kwargs) → list[TAbstractCollection]

Finds a collection by its label or other properties. Path is not needed.

Parameters:

  • label – String or None.

  • kwargs – Other properties used to search Collections

Returns:

All found Collections

get_collection(col_path: str | list[str], case_insensitive: bool = False) → TAbstractCollection

Gets a collection a path points to.

Parameters:

  • col_path – is either a string based on a unix path or a list

  • case_insensitive – If true the cases of path are taken into account

Returns:

Collection the path points to

get_elements_of_iri(element_type: str, per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

Gets all elements of given IRI type.

Parameters:

  • element_type – IRI string chemotion:xxx/xxx/xxx

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet based on the IRI

get_generics_by_label(label: str, per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all generic elements of a given label.

Parameters:

  • label – generic element’s label

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of generic elements of a given name

get_generics_by_name(name: str, per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all generic elements of a given name.

Parameters:

  • name – generic element’s name

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of generic elements of a given name

get_or_create_collection(col_path: str | list[str], case_insensitive: bool = False) → TAbstractCollection

Gets or creates a collection the col_path path points to. If the collection needs to be created the collection is saved right away.

Parameters:

  • col_path – is either a string based on a unix path or a list

  • case_insensitive – If true the cases of path are taken into account

Returns:

Collection the path points to

get_path() → str

Generates the absolut path of collection

Returns:

Absolut path of a collection

get_reactions(per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all reactions.

Parameters:

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of reactions

get_research_plans(per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all research plans.

Parameters:

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of research plans

get_root() → TRootCollection

Get root Collection

Returns:

Instance of the RootCollection

get_samples(per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None, product_only: bool = False) → ElementSet

List of all samples.

Parameters:

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

  • product_only – If True only samples which are products in a reaction are returned

Returns:

ElementSet of samples

get_wellplates(per_page: int | None = 10, updated_to_date: datetime | None = None, updated_from_date: datetime | None = None) → ElementSet

List of all well plates.

Parameters:

  • per_page – How many Elements per page

  • updated_to_date – Set date time to fetch only elements which are updated before ‘updated_to_date’

  • updated_from_date – Set date time to fetch only elements which are updated after ‘updated_from_date’

Returns:

ElementSet of well plates

property id: int | None

The chemotion DB ID

Returns:

The chemotion DB ID

property label: str | None

The collection label

Returns:

The collection label

move(dest: str | list[str], case_insensitive: bool = False)

Moves this collection to a dest path.

Parameters:

  • dest – is either a string based on a unix path or a list

  • case_insensitive – If true the cases of path are taken into account

Returns:

Collection the path points to

new_element_by_iri(element_type: str) → AbstractElement

Creates a new element of given IRI type. However, if the type is generic the generated element is of the newest type.

Parameters:

element_type – IRI string chemotion:xxx/xxx/xxx

Returns:

AbstractElement

new_generic(type_name: str) → GenericElement

Creates a new element of given type name in this collection.

Parameters:

type_name – Generic element’s type name

Returns:

New (unsaved) GenericElement

new_generic_by_label(label: str) → GenericElement

Creates a new element of given label in this collection.

Parameters:

label – Generic element’s label

Returns:

GenericElement

new_reaction() → Reaction

Creates a new reaction in this collection.

Returns:

New (unsaved) Reaction

new_research_plan() → ResearchPlan

Creates a new research plan in this collection.

Returns:

New (unsaved) ResearchPlan

new_sample() → Sample

Creates a new sample in this collection.

Returns:

New (unsaved) Sample

new_sample_smiles(smiles_code: str) → Sample

Creates a new sample with a molecule generated with a smiles code in this collection.

Returns:

New (unsaved) Sample

new_solvent(name) → Sample

Creates a new solvent in this collection.

Returns:

New (unsaved) solvent as Sample

new_wellplate() → Wellplate

Creates a new well plate in this collection.

Returns:

New (unsaved) Wellplate

prepare_label(case_insensitive: bool) → str

Prepares the label of a collection

Parameters:

case_insensitive – If true it returns teh lower case label

Returns:

The collection’s label

set_json(collection_json)

Set the json data received from the server

Parameters:

collection_json – JSON object representing the collection

share(permission_level: SyncPermission, *users: Person | Group)

To synchronize a collection with a set of users or groups

Parameters:

  • permission_level – Element from SyncPermission

  • users – a list of users or groups

to_json()

Generates a dict containing all list of all children collection

Returns:

list of children as savable JSON

enum chemotion_api.collection.SyncPermission(value)

An enumeration.

Valid values are as follows:

Read = <SyncPermission.Read: 0>
Write = <SyncPermission.Write: 1>
Share = <SyncPermission.Share: 2>
Delete = <SyncPermission.Delete: 3>
ImportElements = <SyncPermission.ImportElements: 4>
PassOwnership = <SyncPermission.PassOwnership: 5>

The RootCollection as also a property to get the RootSyncCollection

class chemotion_api.collection.RootSyncCollection(session: Connection, element_manager: ElementManager)

This can be used amost like the root collection object. However, you cannot move, delete or create its child collections