amp_build.py

#!/bin/env python3
#
# Build the amp-mgms tarball for distribution
#

import argparse
import logging
import tempfile
from pathlib import Path
import sys
import os
import subprocess

from amp.package import *

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('--debug', default=False, action='store_true', help="Turn on debugging")
    parser.add_argument('--package', default=False, action='store_true', help="build a package instead of installing")
    parser.add_argument('destdir', help="Output directory for package or tool directory root")
    args = parser.parse_args()
    logging.basicConfig(format="%(asctime)s [%(levelname)-8s] (%(filename)s:%(lineno)d)  %(message)s",
                        level=logging.DEBUG if args.debug else logging.INFO)

    # build anything that needs to be built...
    # Apptainer builds need a lot of disk space. If 
    # APPTAINER_TMPDIR isn't set, we'll use the temp
    # directory next to this script.  Same for the
    # apptainer cache.
    tempdir = Path(sys.path[0], 'temp')
    logging.info(f"Setting tempdir to {tempdir}")
    tempdir.mkdir(exist_ok=True)
    if 'APPTAINER_TMPDIR' not in os.environ:
        os.environ['APPTAINER_TMPDIR'] = sys.path[0] + "/temp"
        Path(os.environ['APPTAINER_TMPDIR']).mkdir(exist_ok=True)
        logging.info(f"Setting APPTAINER_TMPDIR = {os.environ['APPTAINER_TMPDIR']}")
    if 'APPTAINER_CACHEDIR' not in os.environ:
        os.environ['APPTAINER_CACHEDIR'] = sys.path[0] + "/temp/apptainer_cache"
        Path(os.environ['APPTAINER_CACHEDIR']).mkdir(exist_ok=True, parents=True)
        logging.info(f"Setting APPTAINER_CACHEDIR = {os.environ['APPTAINER_CACHEDIR']}")



    logging.info("Building MGMs")
    here = Path.cwd().resolve()
    destdir = Path(args.destdir).resolve()
    for buildscript in here.glob(f"tools/*/mgm_build.sh"):
        # figure out where we're building this
        if args.package:
            buildtmp = tempfile.TemporaryDirectory(prefix='amp_mgms_build-', dir=tempdir)
            builddir = Path(buildtmp.name).resolve()
        else:
            builddir = destdir
    
        logging.info(f"Running build script {buildscript}")
        os.chdir(buildscript.parent)
        cmd = [str(buildscript), str(builddir)]
        if args.debug:
            cmd.append('--debug')
        logging.debug(f"Running command: {cmd}")
        p = subprocess.run(cmd)
        if p.returncode:
            logging.error(f"Build command ({buildscript}) failed with return code {p.returncode}")            
            exit(1)
        os.chdir(here)

        if args.package:        
            # get the version          
            if (buildscript.parent / "mgm_version").exists():
                with open(buildscript.parent / "mgm_version") as f:
                    version = f.readline().strip()
            else:
                version = "0.0"

            # Find optional things
            options = {}
            # defaults
            for dtype in ('user', 'system'):
                cfile = buildscript.parent / f"amp_config.{dtype}_defaults"
                if cfile.exists():
                    options[f"{dtype}_defaults"] = cfile

            # hooks
            options['hooks'] = {}
            for hook in ('pre', 'post', 'config', 'start', 'stop'): 
                hfile = buildscript.parent / f"amp_hook_{hook}.py"
                if hfile.exists():
                    options['hooks'][hook] = hfile

            # arch specific
            options['arch_specific'] = (buildscript.parent / f"amp_arch_specific").exists()


            pkgname = buildscript.parent.stem
            pfile = create_package(f"amp_mgms-{pkgname}", version, "galaxy",
                                   Path(destdir), builddir,
                                   depends_on=['galaxy', 'amp_python'],
                                   **options)
            logging.info(f"New package in {pfile!s}")


if __name__ == "__main__":
    main()