/ 
SimpleFlow-0.161
/ SimpleFlow

NAME

SimpleFlow - easy, simple workflow manager (and logger); for keeping track of and debugging large and complex shell command workflows

VERSION

version 0.161

DESCRIPTION

A tiny workflow manager and logger for Perl, like SnakeMake or NextFlow, but in pure Perl and aimed at making long, error-prone shell pipelines easy to debug and reproduce.

Every step is a single task() call. SimpleFlow checks the inputs before a command runs and the outputs after, times the command, captures its stdout, stderr, exit code and signal, optionally logs a full structured record, and skips work that has already been done. It can also bound a step with a timeout and rebuild out-of-date outputs.

Two subroutines are exported by default: "task" and "say2".

Install

With a CPAN client:

cpanm SimpleFlow

Or from a checkout:

perl Makefile.PL
make
make test
make install

Synopsis

The simplest useful case: run a command and confirm it produced its output:

use SimpleFlow qw(task say2);

my $t = task(
    cmd            => 'which ls',
    'output.files' => '/tmp/AFK3mnEK8L.log',
);

task returns a hash reference describing exactly what happened:

{
    cmd            "which ls",
    die            1,
    dir            "/home/con/Scripts/SimpleFlow",
    done           "now",
    dry.run        0,
    duration       0.00191903114318848,
    exit           0,
    note           "",
    output.files   [
        [0] "/tmp/AFK3mnEK8L.log"
    ],
    overwrite      1,
    signal         0,
    source.file    "t/01.t",
    source.line    29,
    stderr         "",
    stdout         "/usr/bin/ls",
    will.do        "done"
}

> B<Portability note.> SimpleFlow runs whatever shell command you give it via
> C<system()>, so the I<commands themselves> are your responsibility to keep
> cross-platform (e.g. C<which ls> is Unix-only). SimpleFlow's own behaviour
> exit/signal decoding and coloured output is cross-platform; see the
> change log.

task

my $result = task(%args);      # or task(\%args)

Runs one command with checking, timing, capture and logging. Takes either a flat key/value list or a single hash reference; the only required key is cmd.

Arguments

Key Type Default Description
cmd scalar or array undef Required. The command to run. A string is handed to the shell; an array ref is run without a shell.
die bool (0/1) 1 Die if the command fails (non-zero exit, timeout, or a missing output file). Set to 0 to warn and continue instead.
dry.run bool 0 Print the command (and log it) but do not execute it.
input.files scalar or array undef File(s) that must exist and be readable before running; otherwise task dies.
input.file scalar undef Convenience form of input.files for a single file. Must be a plain filename (not a reference). Cannot be combined with input.files.
output.files scalar or array undef File(s) expected to exist after running; used both for the missing-output check and for skip detection.
output.file scalar undef Convenience form of output.files for a single file. Must be a plain filename (not a reference). Cannot be combined with output.files.
log.fh open filehandle undef If given, the full result record is also written here. Must be a real, open filehandle; task switches it to autoflush.
note scalar '' Free-text note copied into the result and the log.
overwrite bool 0 If false and all output.files already exist, the command is skipped. Set true to always run.
quiet bool 0 Suppress the record printed to the terminal. The log and error messages on STDERR are unaffected. See Quiet runs.
stale bool 0 Also re-run when an input file is newer than an output file. See Out-of-date outputs.
timeout whole seconds 0 Kill the command if it runs longer than this. 0 means no limit. See Timeouts.

Passing an unrecognised key, an undefined or empty filename, a cmd that is neither a string nor an array ref, or a non-filehandle log.fh causes task to die: these are usually mistakes worth catching early. Giving both output.file and output.files (or both input.file and input.files), or a reference where a single filename is expected, dies for the same reason.

Return value

task always returns a hash reference. Every field below except the two input.* ones is present on every path, so a caller running under use warnings FATAL => 'all' can read the record after a skip or a dry run without an uninitialized-value warning turning fatal. On those paths the execution-only fields simply hold their empty values (exit and signal are 0, stdout and stderr are '', duration is 0).

Field Meaning
cmd The command that was run. An array-ref cmd is recorded space-joined for readability; that is not a shell-quoted round trip, since it never went near a shell.
dir Working directory at execution time.
done "now" (just ran), "before" (skipped, outputs already existed), or "not yet" (dry run).
will.do "done", "no" (skipped), "no: dry run", or "FAILED". "FAILED" is set whenever the command exited non-zero, timed out, or left a declared output file missing — whether or not die is set.
duration Wall-clock seconds the command took (0 for skips/dry runs).
exit Exit code of the command (-1 if it could not be launched).
signal Signal number if the command process was killed by a signal, else 0. Always 0 on Windows (no POSIX signals).
timed.out 1 if the command was killed for exceeding its timeout, else 0.
out.of.date 1 if stale was set and an input was newer than an output, else 0.
stdout, stderr Captured output, with trailing whitespace stripped.
die, dry.run, overwrite, note, quiet, stale, timeout The (defaulted) argument values used.
output.files Array ref of the output files (a scalar argument, or an output.file, is normalised to a one-element array).
output.file.size Hash of filename => size in bytes for the outputs.
input.files Array ref of the input files, normalised the same way (present only if you passed input.files or input.file).
input.file.size Hash of filename => size in bytes for the inputs (present only if you passed input.files or input.file).
source.file, source.line Where in your code the task was called: handy when debugging a long pipeline.

Skipping completed work

If overwrite is false (the default) and every file in output.files already exists, task does not re-run the command. This makes pipelines restartable: re-running the script picks up where it left off.

open my $log, '>', 'logfile.txt';
my $t = task(
    cmd            => 'gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr',
    'input.files'  => ['em.mdp', 'box.gro', 'topol.top'],
    'output.files' => 'em.tpr',
    'log.fh'       => $log,
);
close $log;

On the first run done is "now"; on a re-run (with em.tpr present) done is "before" and will.do is "no". Pass overwrite => 1 to force it.

An output file that exists but cannot be read does not count as done: it is not a usable result, and treating it as one would skip the very step that could replace it.

Out-of-date outputs

Existence alone is a weak test. If an input file has been edited since the output was built, the output is stale even though it is present — and by default task will still skip the step, exactly as earlier versions did.

Pass stale => 1 to get the rule make and snakemake use: re-run whenever the newest input.files mtime is later than the oldest output.files mtime.

my $t = task(
    cmd            => 'gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr',
    'input.files'  => ['em.mdp', 'box.gro', 'topol.top'],
    'output.files' => 'em.tpr',
    stale          => 1,
);

Editing em.mdp now rebuilds em.tpr; leaving it alone still skips. The result's out.of.date field says which of the two happened. This is off by default so that upgrading does not silently start re-running steps in pipelines written against 0.15 and earlier.

Timeouts

timeout gives a step a wall-clock budget in whole seconds:

my $t = task(
    cmd     => 'a command that sometimes wedges',
    timeout => 600,
    die     => 0,
);

The command is run in its own process group and, if the budget is exceeded, the whole group is killed — a shell command is usually a pipeline, not a single process, and killing only the shell would leave its children running. The result then has timed.out => 1 and will.do => "FAILED"; with the default die => 1 the pipeline stops there instead.

timeout needs fork() and POSIX process groups, so it is refused on MSWin32. Leaving it at 0 (the default) changes nothing anywhere.

Running without a shell

Giving cmd an array ref runs the command directly, with no shell in between:

my $t = task(
    cmd           => ['gzip', '-9', $file],   # $file needs no quoting
    'output.file' => "$file.gz",
);

This is the form to reach for when an argument comes from data — a filename with a space, a quote, or a $ in it is passed through untouched instead of being re-parsed by the shell. You lose shell features (>, |, *, &&) in exchange; use the string form when you want them.

Quiet runs

Every task prints its record to the terminal. Over a hundred-step pipeline that is a lot of scrollback, so quiet => 1 suppresses it:

my $t = task(
    cmd      => 'one of very many steps',
    'log.fh' => $log,
    quiet    => 1,
);

The log filehandle still receives the full record, and error messages still go to STDERR: asking for less noise is not the same as asking to be kept in the dark about a failure.

Dry runs

Useful for inspecting a pipeline without executing anything expensive:

my $t = task(
    cmd       => 'a long-running, time-consuming command',
    'dry.run' => 1,
    'log.fh'  => $fh,
);

The command is printed (and logged) but not run; will.do is "no: dry run".

Failure behaviour

By default (die => 1) task dies if the command exits non-zero, exceeds its timeout, or leaves any declared output.files missing afterwards, so a broken step stops the pipeline immediately.

With die => 0, task instead warns and returns its result hash with will.do => "FAILED", letting you decide what to do:

my $t = task(cmd => 'a step that may fail', die => 0);
if ($t->{'will.do'} eq 'FAILED') {
    ...   # $t->{'exit'}, $t->{stderr} and $t->{'timed.out'} say why
}

say2

say2($message, $filehandle);

"Say to two places": prints $message to standard output and to the given log filehandle, prefixed with the calling file and line number so log entries are traceable. The filehandle must be open, or say2 dies.

open my $log, '>', 'run.log';
say2('starting equilibration', $log);   # -> STDOUT and run.log
close $log;

Dependencies

Core/runtime modules used by SimpleFlow:

The test suite additionally uses Test::More and Test::Exception.

Changes

The release notes are in the Changes file at the root of the distribution, in the format CPAN itself reads.

COPYRIGHT AND LICENSE

This software is free. It is licensed under the same terms as Perl itself