Analyses

The Analyses object represents the Analyses tab in the Chemotion user interface. It contains all measurement data and metadata associated with the elements

API Classes

class chemotion_api.elements.abstract_element.AnalysesList(conn: Connection)

List of chemotion_api.elements.abstract_element.Analyses.

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")
>>> s = instance.get_sample(1)
>>> # Download of all analysis files of data set 'V2024_08_23' from 'Analyses MT 1'
>>> analyses = s.analyses.by_name('Analyses MT 1')
>>> dataset = analyses.dataset_by_name('V2024_08_23')
>>> os.makedirs('./TO_DEL', exist_ok=True)
>>> for atta in dataset.attachments:
>>>     atta.save_file('./dataset_files')
>>> # Change value in the metadate set
>>> dataset['General Information']['Label'] = 'V2024_08_23'
>>> # Create a new
>>> ana = s.analyses.add_analyses("Analyses MT 2")
>>> ana.add_dataset('./V2024_08_24.json')
>>> s.save()

class chemotion_api.elements.abstract_element.Analyses(data: dict, session: Connection)

An analysis consists of a list of metadata schemas and associated data files. The schemas can be edited. And the files can be read and saved to your local device

add_dataset(file_path: str) → Dataset

Loads a datafile up and creates a new dataset. The Chemotion Instance will convert the date file and create a metadate set accordingly. However, this process only works if a Converter profile has been created

Parameters:: file_path – the path on your local device to the datafile
Returns:: A new Dataset object

clean_up_after_save(): Do not use this methode! It is automatically used after the element is saved!

dataset_by_name(name: str) → Dataset

Find a dataset by its name.

Parameters:: name – Name of the dataset
Returns:: A Dataset object

property is_new: bool

Returns true if the analyses has not been saved yet.

Type:: return

preview_image() → bytes | None

Loads the image used as preview for the analyses.

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")
>>> s = instance.get_sample(1)
>>> # Loads analysis 'Analyses MT 1'
>>> analyses = s.analyses.by_name('Analyses MT 1')
>>> with open('./img.svg', 'wb+') as f:
>>>     f.write(analyses.preview_image())
>>> s.save()

Raises:: ConnectionError – If the request fails
Returns:: byte representation of an image

save_attachments(): Do not use this methode! It is automatically used before the element is saved!

to_json(): A savable representation of the Analyses :return: Json representation

class chemotion_api.elements.abstract_element.Dataset(session: Connection, json_data: dict, attachments: MutableAttachments | None = None)

A Dataset is an object that consists of a metadata set and a measurement file. If all components have been configured correctly in Chemotion, a BagIT container is created when a new file is uploaded. This container is then used to automatically fill in the metadata set and forward the measurement data to ChemSpectra.

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")
>>> s = instance.get_sample(1)
>>> # Loads dataset V2024_08_23 from 'Analyses MT 1'
>>> d1 = s.analyses.by_name('Analyses MT 1').dataset_by_name('V2024_08_23')
>>> # Write BagIT zip and metadata set as xlsx file
>>> d1.write_data_set_xlsx('./CWD')
>>> d1.write_zip('./CWD')

property attachments: MutableAttachments

A list of all attached files. It contains the BagIt, the ChemSpectra results: as well as the measurement file

Returns:: A mutable attachment File

to_clean_json(): Cleans the data as perpetration to be saved

write_data_set_xlsx(destination='')

Writes the metadata set as xlsx.

Parameters:: destination – Director where the BagIT should be saved to.
Returns:: Abs filepath of the BagIT zip.

write_zip(destination='')

Writes the BagIT zip file.

Parameters:: destination – Director where the BagIT should be saved to
Returns:: Abs filepath of the BagIT zip