pyicat_plus.client.null.IcatNullClient#

class pyicat_plus.client.null.IcatNullClient(expire_datasets_on_close=True)[source]#

Bases: IcatClientInterface

add_files(*args, **kwargs)[source]#

Add missing files to a dataset already ingested.

Parameters:

dataset_id – The ICAT dataset identifier.

Return type:

None

disconnect()[source]#
do_log_in(*args, **kwargs)[source]#

Login to access the restricted part of the API.

Parameters:

  • password

  • username – optional username

  • plugin – authentication plugin, defaults to ‘esrf’

Return type:

None

Returns:

authentication info

download_file_by(*args, **kwargs)[source]#

Download a file associated to a sample.

Parameters:

  • sample_id – Sample identifier.

  • resource_id – Identifier of the resource/file to download.

  • use_chunks – Read the file in chunks or the entire file into memory at once.

  • chunk_size – Size of each chunk in bytes when use_chunks is True. Default is 8192 (8 KB).

Return type:

None

Returns:

The content of the file as bytes.

property expire_datasets_on_close: bool#

A flag indicating whether the dataset expires when it is closed or if it is synchronized with the metadata catalog.

get_datasets_by(investigation_id=None, dataset_ids=None)#

Returns a list of dataset matching the provided criteria.

Parameters:

  • investigation_id (Optional[str]) – an investigationId

  • dataset_ids (Optional[str]) – comma separated list of dataset Ids

Return type:

List[dict]

get_investigations_by(*args, **kwargs)[source]#

Returns a list of investigations matching the provided criteria.

Parameters:

  • filter

  • instrument_name

  • start_date

  • end_date

  • ids

Return type:

None

Returns:

list of investigations

get_parcels_by(*args, **kwargs)[source]#

Returns the list of parcels associated to an investigation.

Parameters:

investigation_id

Return type:

None

Returns:

list of parcel information

get_sample_files_information_by(*args, **kwargs)[source]#

Returns the sample file information for a given sample.

Parameters:

sample_id – Sample identifier.

Return type:

None

Returns:

Sample file information as dict.

get_sample_metadata_by(*args, **kwargs)[source]#

Returns the list of sample metadata associated to a proposal and a beamline.

Parameters:

  • proposal – Proposal identifier (e.g., “hg237”).

  • beamline – Beamline identifier (e.g., “id13”).

  • session_start_date – Experiment session start date (format yyyy-MM-dd).

Return type:

None

Returns:

List of sample metadata.

get_samples_by(investigation_id=None, sample_ids=None)#

Returns a list of samples matching the provided criteria.

Parameters:

  • investigation_id (Optional[str]) – an investigationId

  • sample_ids (Optional[str]) – comma separated list of sampleIds

Return type:

List[dict]

get_session_information(*args, **kwargs)[source]#

Returns the information about a session.

Return type:

None

Returns:

session information

investigation_info(*args, **kwargs)[source]#

Return the information of the experiment session corresponding to a beamline, proposal and date.

Parameters:

  • beamline – The beamline name.

  • proposal – The proposal name.

  • date – The date of the proposal, current date by default.

  • allow_open_ended – If True, enable to select an unofficial experiment session.

  • timeout – Set a timeout for the ICAT request.

Return type:

None

Returns:

If found, return the proposal, beamline, e-logbbok url and data portal url of the experiment session.

investigation_info_string(*args, **kwargs)[source]#

Return the experiment session information as a string.

Parameters:

  • beamline – The beamline name.

  • proposal – The proposal name.

  • date – The date of the proposal, current date by default.

  • allow_open_ended – If True, enable to select an unofficial experiment session.

  • timeout – Set a timeout for the ICAT request.

Return type:

str

Returns:

If found, return the experiment session information from the metadata catalog as a string.

investigation_summary(*args, **kwargs)[source]#

Return the experiment session information as a Tuple.

Parameters:

  • beamline – The beamline name.

  • proposal – The proposal name.

  • date – The date of the proposal, current date by default.

  • allow_open_ended – If True, enable to select an unofficial experiment session.

  • timeout – Set a timeout for the ICAT request.

Return type:

List[Tuple]

Returns:

If found, return the experiment session information from the metadata catalog as a Tuple.

property reason_for_missing_information: str#

A string explaining why some information is missing in the metadata catalog.

registered_dataset_ids(*args, **kwargs)[source]#

Return the dataset list of an experiment session.

Parameters:

  • beamline – The beamline name of the proposal.

  • proposal – The proposal name.

  • date – The date of the proposal, current date by default.

  • allow_open_ended – If True, enable to select an unofficial experiment session.

  • timeout – Set a timeout for the ICAT request.

Return type:

None

Returns:

The list of datasets (name and path).

registered_datasets(*args, **kwargs)[source]#

Return the dataset information list of an experiment session.

Parameters:

  • beamline – The beamline name of the proposal.

  • proposal – The proposal name.

  • date – The date of the proposal, current date by default.

  • allow_open_ended – If True, enable to select an unofficial experiment session.

  • timeout – Set a timeout for the ICAT request.

Return type:

None

Returns:

The list of datasets (name, path, ICAT identifier, and DatasetMetadata).

reschedule_investigation(*args, **kwargs)[source]#

Reschedule an investigation defined by its id.

Parameters:

investigation_id

Return type:

None

send_binary_data(*args, **kw)[source]#

Send an image in base64 format to the proposal or beamline e-logbook.

Parameters:

  • data – The binary message content.

  • mimetype – {‘text/plain’, ‘text/html’}, optional.

  • beamline – The beamline name of the proposal or beamline e-logbook.

  • proposal – The proposal name of the e-logbook. Ignored if beamline_only is True.

  • investigation_id – The investigation identifier in the ICAT database.

  • beamline_only – if True, the message will be stored in the beamline e-logbook.

  • payload – Additional payload for the e-logbook message. It can contain tags (list of strings or list of dictionaries), the machine, the software.

send_binary_file(*args, **kw)[source]#

Send the content of a file as a binary image to the proposal or beamline e-logbook.

Parameters:

  • filename – The filename of the image to be sent.

  • beamline – The beamline name of the proposal or beamline e-logbook.

  • proposal – The proposal name of the e-logbook. Ignored if beamline_only is True.

  • beamline_only – if True, the message will be stored in the beamline e-logbook.

  • payload – Additional payload for the e-logbook message. It can contain tags (list of strings or list of dictionaries), the machine, the software.

send_message(*args, **kw)[source]#

Send a message to the proposal or beamline e-logbook.

Parameters:

  • msg – The message content.

  • msg_type – {‘comment’, ‘debug’, ‘info’, ‘error’, ‘commandLine’}, optional.

  • beamline – The beamline name of the proposal or beamline e-logbook.

  • proposal – The proposal name of the e-logbook. Ignored if beamline_only is True.

  • investigation_id – The investigation identifier in the ICAT database.

  • dataset – The specific dataset name to link the message to.

  • beamline_only – if True, the message will be stored in the beamline e-logbook.

  • editable – Used with the formatted field, to determine the category of message. Annotation characterizes editable and unformatted messages, while Notification charaterizes non-editable and formatted messages.

  • formatted – Used with the editable field, to determine the category of message. Annotation characterizes editable and unformatted messages, while Notification charaterizes non-editable and formatted messages.

  • mimetype – {‘text/plain’, ‘text/html’}, optional.

  • payload – Additional payload for the message. It can contain tags (list of strings or list of dictionaries), the machine, the software.

send_text_file(*args, **kw)[source]#

Send the content of a text file as a message to the proposal or beamline e-logbook.

Parameters:

  • filename – The filename containing the message to be sent.

  • beamline – The beamline name of the proposal or beamline e-logbook.

  • proposal – The proposal name of the e-logbook. Ignored if beamline_only is True.

  • investigation_id – The investigation identifier in the ICAT database.

  • beamline_only – if True, the message will be stored in the beamline e-logbook.

  • payload – Additional payload for the e-logbook message. It can contain tags (list of strings or list of dictionaries), the machine, the software.

start_investigation(*args, **kw)[source]#

Send a message to ActiveMQ to either synchronize the experiment session from the User Portal in ICAT or to create a test experiment session in ICAT.

Parameters:

  • beamline – The beamline name of the proposal.

  • proposal – The proposal name.

  • start_datetime – The start date of the experiment session, timezone local time. Current date time by default.

  • end_datetime – The end date of the experiment session, timezone local time.

store_dataset(*args, **kw)[source]#

Request icat to store raw dataset.

Parameters:

  • str (proposal) – beamline name like id01, id15a, bm18…

  • str – proposal name like in1169, blc14795, ihma429…

  • dataset (str) – dataset name.

  • path (str) – path to the raw dataset to store. Must be a folder.

  • metadata (dict) – metadata to associate with the dataset. Must contain keys defined by the appropriate application definition, available at https://icat-esrf-definitions.readthedocs.io.

  • store_filename (str) – xml file with metadata to be stored.

store_dataset_from_file(*args, **kw)[source]#

Send a message to ActiveMQ to store a dataset and the associated metadata from a xml file stored on the disk.

Parameters:

store_filename – The XML filename containing all dataset metadata.

store_processed_data(*args, **kw)[source]#

Request icat to store a processed dataset.

Parameters:

  • str (proposal) – beamline name like id01, id15a, bm18…

  • str – proposal name like in1169, blc14795, ihma429…

  • dataset (str) – dataset name like sample_XYZ.

  • path (str) – path to the processed dataset to store. Can be a file or a folder.

  • metadata (dict) – metadata to associate with the dataset. Must contain keys defined by the appropriate application definition, available at https://icat-esrf-definitions.readthedocs.io.

  • raw (tuple) – Path(s) to the raw dataset(s). Should point to the ‘bliss dataset’ folder(s). If processing relies on multiple datasets, all corresponding folders must be provided.

  • store_filename (str) – xml file with metadata to be stored.

update_archive_restore_status(*args, **kwargs)[source]#

DEPRECATED: This method is deprecated and may be removed in future versions. Update the archiving or restore status of a dataset.

Parameters:

  • dataset_id – The ICAT dataset identifier.

  • type – The type of the status, possible options are {‘archiving’, ‘restoration’}.

  • level – The level of the status message; possible options are {‘info’, ‘warning’, ‘error’}.

  • message – The optional status’ message.

Return type:

None

update_metadata(*args, **kwargs)[source]#

Update or create datasets metadata.

Parameters:

  • proposal – The proposal name.

  • beamline – The beamline name of the proposal.

  • dataset_paths – Comma-separated list of the dataset locations.

  • metadata_name – The name of the metadata to update.

  • metadata_value – The new value of the metadata.

Return type:

None