feature request: logging

[georgemarselis-nvi]

What has to be done

-[ ] log to syslog so later on we can ship the logs -[ ] log to file log file hierarchy is roughly outlined below

THOUGHTS ABOUT LOGGING

• [x] Logging should be done on every step

• [x] if you set demux.debug on the object, you will get debug information this needs to be expanded and worked on on a separate ticket

• [x] Logging happens on stdout, not stderr

• [x] Errors are logged on stderr, only

• [x] Log to syslog

• [x] stdout as INFO

• [x] stderr as WARNING or ERROR

• [x] sys.exit as CRITICAL

  Files created:

• [x] RunIDDir/demultiplex_log

• [x] RunIDDir/demultiplex_log/00_script.log

• [x] RunIDDir/demultiplex_log/01_blc2fastq.log

• [x] RunIDDir/demultiplex_log/02_FastQC.log

• [x] RunIDDir/demultiplex_log/03_MultiQC.log

• [ ] RunIDDir/demultiplex_log/04_NIRD.log

• [x] RunIDDir/demultiplex_log/05_VIGASP.log /data/log/RunID.log ( copy of RunIDDir/Logs/00_script.log / symlink to RunID/Logs/00_script.log ? )

• [x] /data/log/demultiplex.log (cumulative log) /data/Logs/script.log ( copy of RunIDDir/Logs/00_script.log - gets rotated/overwritten with each run ) /data/Logs/current_run_00.log /data/Logs/current_run_01.log if _00 exists and so on

      ~~Only for current run(s), file(s) do not get saved~~

• [x] overwrite when starting a new run

• [x] /data/log/script_cumulative.log ( cumulative - does not get rotated, append )

  Actions taken

• [ ] Email on parsing configuration file error

• [x] Email send on completion

• [x] Email sent on error

• [x] run did not complete (specific step) disk full (no, belongs to nagios)

• [ ] Email sent on run looping detected

• [ ] Email sent on parsing error of SampleSheet.csv

• [ ] Email on completion of NIRD upload

• [ ] Email on completion of VIGASP upload

• [ ] Email on completion of LIMS upload

  ######################################
  If debug run, indicate so in email
  ######################################

  if you run the script interactively:

• [x] Color:

• [x] Console: console has color

• [x] Files: files do not have color

  Timestamps:

  -[ ] Console: console has "Time since started" and "time since started this step" save to SQL database each time stamp? -[ ] Files: files get regular current timestamp on each step

  if you run the script non-interactively

• [x] Color:

• [x] Console: no console

• [x] Files: files do not have color

• [x] Timestamps:

• [x] Console: no console

• [x] Files: files get regular current timestamp on each step

  End of logging:

• [ ] Time:

• [ ] how much time the whole procedure took

• [ ] how much each step

• [ ] save times to SQL database?

[arvindsundaram]

I am not sure if we need to maintain a SQL database for the logs. Any specific reason for this?

[georgemarselis-nvi]

It will be an sqlite3 file, I mean, not a whole host. And yes, metrics (and some professional curiosity) and if we have enough data, a paper.

[georgemarselis-nvi]

I was agonizing for over a week over this feature request: add proper syslog/logging to this demultiplexing pipeline: Learn how to log things beyond a print() statement, what counts as info, warning and critical^[1] , what is useful and what is not, how to log to multiple locations/destinations, how to log to console with color, while sending the same message unformatted to syslog and file...

... then i just bit the bullet: copied over all the output messages to a new script that prints the same things but does none of the work and said "let me play with that". At last, i got something I can start working with.

... moving right along, i guess. better to produce something imperfect than nothing at all (or worse, wait for your inner davinci to wake up)

[1] at least i knew what counted as debug!

[georgemarselis-nvi]

Lots of good progress tonight.

Tomorrow: figuring out how to write messages using formatters according to destination.

[georgemarselis-nvi]

do we need millisecond stamping, or is second good enough? datefmt = '%Y-%m-%d %H:%M:%S' vs datefmt = '%Y-%m-%d %H:%M:%S.%f'[:-3]

[georgemarselis-nvi]

logging run log, , implemented

cumulative run log, , implemented

syslog log, , implemented

email log, success, implemented, needs testing

email log, failures( many points of ), implemented, needs testing

workplace notifications on the horizon.

[georgemarselis-nvi]

update: only thing left is workplace notifications, for now.

email notifications on failures, need refactoring to modularize then so we can test them

[georgemarselis-nvi]

this is not a blocking issue for version 1.0

if add-ins are needed, we can come back.

removing from starred issues.

[georgemarselis-nvi]

this issue is like a well done steak. Closing.