nexusLIMS.builder package

Submodules

nexusLIMS.builder.record_builder module

Attributes

nexusLIMS.builder.record_builder.XSLT_PATH

The path to cal_events_to_nx_record.xsl, which is used to translate the calender event response XML to a format compatible with the Nexus Schema

Type:

str

nexusLIMS.builder.record_builder.build_acq_activities(instrument, dt_from, dt_to, sample_id, generate_previews)[source]

Build an XML string representation of each AcquisitionActivity for a single microscopy session. This includes setup parameters and metadata associated with each dataset obtained during a microscopy session. Unique AcquisitionActivities are delimited via clustering of file collection time to detect "long" breaks during a session.

Parameters:

  • instrument (Instrument) -- One of the NexusLIMS instruments contained in the database. Controls what instrument calendar is used to get events.

  • dt_from (datetime.datetime) -- The starting timestamp that will be used to determine which files go in this record

  • dt_to (datetime.datetime) -- The ending timestamp used to determine the last point in time for which files should be associated with this record

  • sample_id (str) -- An identifier for the sample from which data was collected

  • generate_previews (bool) -- Whether or not to create the preview thumbnail images

Returns:

  • acq_activities (str) -- A string representing the XML output for each AcquisitionActivity associated with a given reservation/experiment on a microscope.

  • activities (list of AcquisitionActivity:) -- The list of AcquisitionActivity objects generated for the record

nexusLIMS.builder.record_builder.build_new_session_records()[source]

Fetches new records that need to be built from the database (using get_sessions_to_build()), builds those records using build_record() (saving to the NexusLIMS folder), and returns a list of resulting .xml files to be uploaded to CDCS.

Returns:

xml_files -- A list of record files that were successfully built and saved to centralized storage

Return type:

list of str

nexusLIMS.builder.record_builder.build_record(instrument, dt_from, dt_to, user=None, sample_id=None, generate_previews=True)[source]

Construct an XML document conforming to the NexusLIMS schema from a directory containing microscopy data files. For calendar parsing, currently no logic is implemented for a query that returns multiple records

Parameters:

  • instrument (Instrument) -- One of the NexusLIMS instruments contained in the database. Controls what instrument calendar is used to get events.

  • dt_from (datetime or None) --

  • dt_to (datetime or None) -- The

  • dt_from -- A datetime object representing the starting timestamp that will be used to determine which files go in this record, as in fetch_xml().

  • dt_to -- A datetime object representing the ending timestamp used to determine the last point in time for which files should be associated with this record, as in fetch_xml().

  • user (str or None) -- A valid NIST username (the short format: e.g. "ear1" instead of ernst.august.ruska@nist.gov). Controls the results returned from the calendar - value is as specified in get_events()

  • sample_id (str or None) -- A unique identifier pointing to a sample identifier for data collected in this record. If None, a UUIDv4 will be generated

  • generate_previews (bool) -- Whether or not to create the preview thumbnail images

Returns:

xml_record -- A formatted string containing a well-formed and valid XML document for the data contained in the provided path

Return type:

str

nexusLIMS.builder.record_builder.dry_run_file_find(s)[source]

Get the files that would be included for any records to be created based off the supplied session

Parameters:

s (Session) -- A session read from the database

Returns:

files -- A list of strings containing the files that would be included for the record of this session (if it were not a dry run)

Return type:

list of str

nexusLIMS.builder.record_builder.dry_run_get_calendar_event(s)[source]

Get the calendar event that would be used to create a record based off the supplied session

Parameters:

s (Session) -- A session read from the database

Returns:

cal_event -- A list of strings containing the files that would be included for the record of this session (if it were not a dry run)

Return type:

CalendarEvent

nexusLIMS.builder.record_builder.dump_record(instrument, dt_from, dt_to, filename=None, user=None, generate_previews=True)[source]

Writes an XML record composed of information pulled from the Sharepoint calendar as well as metadata extracted from the microscope data (e.g. dm3 files).

Parameters:

  • instrument (Instrument) -- One of the NexusLIMS instruments contained in the database. Controls what instrument calendar is used to get events.

  • dt_from (datetime.datetime) -- The starting timestamp that will be used to determine which files go in this record

  • dt_to (datetime.datetime) -- The ending timestamp used to determine the last point in time for which files should be associated with this record

  • filename (None or str) -- The filename of the dumped xml file to write. If None, a default name will be generated from the other parameters

  • user (str) -- A string which corresponds to the NIST user who performed the microscopy experiment

  • generate_previews (bool) -- Whether or not to create the preview thumbnail images

Returns:

filename -- The name of the created record that was returned

Return type:

str

nexusLIMS.builder.record_builder.get_files(path, dt_from, dt_to)[source]

Get list of files under a path that were last modified between the two given timestamps.

Parameters:

  • path (str) -- The file path in which to search for files

  • dt_from (datetime.datetime) -- The starting timestamp that will be used to determine which files go in this record

  • dt_to (datetime.datetime) -- The ending timestamp used to determine the last point in time for which files should be associated with this record

Returns:

files -- A list of the files that have modification times within the time range provided (sorted by modification time)

Return type:

list of str

nexusLIMS.builder.record_builder.process_new_records(dry_run=False)[source]

Using build_new_session_records(), process new records, save them to disk, and upload them to the NexusLIMS CDCS instance.

nexusLIMS.builder.record_builder.validate_record(xml_filename)[source]

Validate an .xml record against the Nexus schema

Parameters:

xml_filename (str or io.StringIO or io.BytesIO) -- The path to the xml file to be validated (can also be a file-like object like StringIO or BytesIO)

Returns:

validates -- Whether or not the record validates against the Nexus schema

Return type:

bool