The cheminfopy API reference#

The manager package#

Sample#

Interface for the sample abstraction in the cheminfo ELN

class cheminfopy.managers.sample.Sample(*args, **kwargs)[source]#

Bases: cheminfopy.managers.manager.Manager

Sample manager handles operations on samples

__init__(*args, **kwargs)[source]#
Parameters

  • instance (str) – URL the the ELN instance, for example https://mydb.cheminfo.org/db/eln for the c6h6.org deployment

  • token (str) – Token string. Can be any kind of token (user/entry) with any rights. If the token does not have suitable rights, the library will raise and Exception. Tokens can be generated in the ELN using the “Access Token” view

  • sample_uuid (str) – UUID of the sample

property creation_date#

Returns the creation date

property em#

Returns the exact mass in Dalton

get_data(data_type, file_name)[source]#

Allows to get a specific spectrum from the ELN. For this you need to select the type and the filename of the spectrum. You can get an overview of all the attached spectra from the table of contents of the sample.

Parameters

  • data_type (str) – spectrum type. Valid types are in VALID_DATA_TYPES

  • file_name (str) – filename (with extension)

Returns

The filecontent of the selected spectrum.

Return type

[str]

Raises

InvalidAttachmentTypeError – If the selected type is not supported by the schema of the ELN. The allowed types are in VALID_DATA_TYPES

has_right(right)[source]#

Checks if the token with which the manager was initialized has certain rights.

Parameters

right (str) – right to test (“write”, “create”, “read”, “addAttachment” are the most relevant ones)

Returns

True if the manager instance has the rights

Return type

[bool]

property id#

ID of the sample

property last_modified_by#

Returns the username who performed the last modification

property mf#

Returns a string with the molecular formula

property modification_date#

Returns the date of the last modification

property molfile#

Return the molfile for this sample

property mw#

Return the molecular weight in g/mol

property owners#

Owners of the sample

put_data(data_type, file_name, file_content, metadata=None, source_info=None)[source]#

This methods allows to add spectra to a sample. Follow the dataschema at https://cheminfo.github.io/data_schema/. In particular, use JCAMP-DX files for spectra. You can use the pytojcamp library (https://github.com/cheminfo-py/pytojcamp) to convert Python dictionaries to JCAMP-DX files.

Parameters

  • data_type (str) – spectrum type. Valid types are in VALID_DATA_TYPES

  • file_name (str) – filename (with extension)

  • file_content (str) – String with the content of the file

  • metadata (str) – Metadata dictionary. Please follow the schema at https://cheminfo.github.io/data_schema/. For example, for gas adsorption isotherms you might want to add the keys ‘adsorptive’ and ‘temperature’. Defaults to None.

  • source_info (Union[dict, None], optional) – You can provide a dictionary with source information. Allowed keys are “name”, “url”, ‘uuid”, “doi”. Use this to describe the source of the data you want to attach to the sample. If you do not provide this dictionary / leave the default value of None, we will default the values in DEFAULT_SOURCE_DICT. Defaults to None.

Raises

InvalidAttachmentTypeError – If the selected type is not supported by the schema of the ELN. The allowed types are in VALID_DATA_TYPES

property revision#

Revision of the document

property spectra#

Lists all spectra that are attached to the sample

property toc#

Get the table of contents entry for this sample

property type#

Type of the document

property uuid#

UUID of the sample

UserManager#

Handle operations on the user level

class cheminfopy.managers.user.User(instance, token, **kwargs)[source]#

Bases: cheminfopy.managers.manager.Manager

User manager handles operations on users

get_experiment(uuid)[source]#

Get a experiment object for an experiment UUID

get_experiment_toc()[source]#

Returns the raw table of all experiments the user has access to

get_sample(uuid)[source]#

Get a sample object for a sample UUID

get_sample_toc()[source]#

Returns the raw table of all samples the user has access to

has_rights(rights)[source]#

Checks if the token with which the manager was initialized has certain rights.

Parameters

rights (Collection[str]) – right to test (“write”, “create”, “read”, “addAttachment” are the most relevant ones)

Returns

True if the manager instance has the rights

Return type

[bool]

property is_valid_token#

Checks if the token is actually a user token

ExperimentManager#

Dealing with experiments/reactions

class cheminfopy.managers.experiment.Experiment(*args, **kwargs)[source]#

Bases: cheminfopy.managers.manager.Manager

Experiment manager handles operations on experiments

__init__(*args, **kwargs)[source]#
Parameters

  • instance (str) – URL the the ELN instance, for example https://mydb.cheminfo.org/db/eln for the c6h6.org deployment

  • token (str) – Token string. Can be any kind of token (user/entry) with any rights. If the token does not have suitable rights, the library will raise and Exception. Tokens can be generated in the ELN using the “Access Token” view

  • experiment_uuid (str) – UUID of the experiment

property date#

Date of the experiment

property id#

UUID of the reaction

property kind#

Kind of the entry

property owners#

Owners of the reaction

property procedure#

Procedure of the reaction

property products#

Products of the reaction

property reactionRXN#

Reaction RXN file

property reagents#

Reagents of the reaction

property remarks#

Remarks of the reaction

property revision#

Revision of the reaction

property title#

Title of the reaction

property toc#

Get the table of contents entry for this experiment

Manager base class#

Base manager class

class cheminfopy.managers.manager.Manager(instance, token, **kwargs)[source]#

Bases: object

Base class for all managers

__init__(instance, token, **kwargs)[source]#

A manager instance provides the basic functionality to interact with the rest-on-couch API

Parameters

  • instance (str) – URL the the ELN instance, for example https://mydb.cheminfo.org/ for the c6h6.org deployment

  • token (str) – Token string. Can be any kind of token (user/entry) with any rights. If the token does not have suitable rights, the library will raise and Exception. Tokens can be generated in the ELN using the “Access Token” view

__weakref__#

list of weak references to the object (if defined)

property instance#

Provide the eln database URL

Requester#

Implementing the basic logic for requests the rest-on-couch API

class cheminfopy.request.ELNRequest(token)[source]#

Bases: object

Class that runs the actual request using token authentication.

__init__(token)[source]#
Parameters

token (str) – Token string. Can be any kind of token (user/entry) with any rights. If the token does not have suitable rights, the library will raise and Exception. Tokens can be generated in the ELN using the “Access Token” view

__weakref__#

list of weak references to the object (if defined)

get(url)[source]#

Make a GET request to the URL

Parameters

url (str) – URL to which the request should be made

Returns

Response of the request

Return type

requests.Response

get_file(url)[source]#

Alias for GET request

Return type

Response

post()[source]#

Make a POST request.

put(url, data=None, json_payload=None)[source]#

Make a PUT request to the URL with the provided data

Parameters

  • url (str) – URL to which the request should be made

  • data (object) – Some data to be sent with the request. Defaults to None

  • json_payload (dict) – JSON payload. If not None, this method will default to using the JSON payload instead of the data

Returns

Response of the request

Return type

[requests.Response]

Errors#

Custom error types for cheminfopy

exception cheminfopy.errors.AuthenticationError[source]#

Bases: ValueError

Raised if authentication fails

__weakref__#

list of weak references to the object (if defined)

exception cheminfopy.errors.InvalidAttachmentTypeError[source]#

Bases: ValueError

Raised in case of incompatible attachment type

__weakref__#

list of weak references to the object (if defined)

exception cheminfopy.errors.InvalidInstanceUrlError[source]#

Bases: ValueError

Raised if the provided instance URL seems invalid

__weakref__#

list of weak references to the object (if defined)

exception cheminfopy.errors.InvalidSourceError[source]#

Bases: ValueError

Raised if a “data_type”/”source” key does not match the schema

__weakref__#

list of weak references to the object (if defined)

exception cheminfopy.errors.RequestFailed[source]#

Bases: ValueError

Raised if the request failed

__weakref__#

list of weak references to the object (if defined)

Constants#

Globals to be reused across the cheminfopy package

Zenodo#