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Read 'Agilent ChemStation' log files

Source: R/read_chemstation_log.R
read_chemstation_logs.Rd

Reads the event log 'Agilent ChemStation' writes to the folder of each sequence, or the RUN.LOG it writes to each .D folder when that file is named in paths. These record instrument errors, aborted runs and routine readings such as pump pressure and column temperature.

Usage

read_chemstation_logs(
  paths,
  what = c("injections", "problems", "events"),
  format_out = "data.frame"
)

Arguments

paths

Paths to 'ChemStation' .LOG files, or to directories to search for sequence logs.

what

What to return: one row per injection (injections, the default), only the events marked as a problem (problems), or every event (events).

format_out

Class of the returned object: data.frame (the default) or data.table.

Value

A data.frame or data.table. For injections, one row per injection, with columns:

  • sequence: the name of the 'ChemStation' sequence, taken from the log's own sequence events or, failing those, from the name of the file. NA for a RUN.LOG, which has neither.

  • folder: the folder the sequence's data are in, which can differ from sequence. This is the folder holding the log, or for a RUN.LOG the folder holding its .D folder.

  • injection: numbers the injections in the order the log starts them.

  • data_file: the .D folder the log names for the injection. The log records it only once the run's data are analyzed, so an aborted injection has none, and its case can differ from the folder on disk.

  • sample: the sample, as the log names it.

  • start: POSIXct, UTC.

  • minutes: from the injection's first event to its last.

  • status: completed, aborted, stopped by user or incomplete.

  • pressure_start, pressure_end: the first and last reading of pump 1, in bar.

  • problems: the injection's problem messages, separated by "; ".

For events, one row per event, with sequence, folder, injection and data_file as above, and:

  • time: POSIXct, UTC, as recorded in the event's header. The local time printed in the log's text is not returned.

  • problem: whether the event reports an alarm from an instrument module (any event from a module with a non-zero event_code, such as a leak or a shutdown), a method that was aborted, timed out, stopped by an instrument error or stopped by the user, or a sequence that was terminated or stopped.

  • event_code, module_id: hexadecimal strings, since 'Agilent' does not document them. The same module always carries the same module_id (for example, 1da6 for the pump in 'Agilent 1100' logs).

  • source: e.g. "1100 PMP 1", "Method" or "Sequence".

  • message: the event's text. The log splits a message longer than 45 characters over several events, which are joined, but stores a message of exactly 45 characters without its last character.

Events of the sequence itself, events between injections such as loading the next method, and method runs that acquire no data, such as a data-analysis-only re-run of the sequence, have no injection or data_file.

For problems, the events marked as a problem, without that column and with incident, which numbers the runs of problem events in the same log that are less than a minute apart, such as a leak and the shutdowns that follow it.

Details

Directories in paths are searched, including their subdirectories, for sequence logs: every .LOG file outside a .D folder. RUN.LOG files are left out, since the sequence log holds their events. A file found this way that is not a 'ChemStation' log is skipped with a warning; a file named in paths that is not one is an error.

Tested on logs from 'ChemStation' revisions A.10.02, B.01.03 and B.04.02.

See also

Other 'Agilent' parsers: read_agilent_d(), read_agilent_dx(), read_agilent_rslt(), read_chemstation_ch(), read_chemstation_csv(), read_chemstation_ms(), read_chemstation_reports(), read_chemstation_uv()

Author

Ethan Bass

Examples

if (FALSE) { # interactive()
read_chemstation_logs("tests/testthat/testdata/chemstation_sequence.LOG")
read_chemstation_logs("path/to/sequences", what = "problems")
}