Simpler and more efficient CL wrapper

IMP

@@ -3,6 +3,8 @@ from lib.docopt import docopt
 from lib.path import Path
 import subprocess
 import os
+import json
+import shlex
 
 __doc__ = """Integrated Metaomic Pipeline.
  ____  __  __  ____
@@ -11,88 +13,20 @@ __doc__ = """Integrated Metaomic Pipeline.
 (____)(_/\/\_)(__)
 
 Usage:
-  IMP init <data> <output> [<name>]
-  IMP run [VAR ...]
-  IMP -h | --help
+  IMP -d DATA -o OUTPUT [--enter] [-n CONTAINER] [-e ENV] ... [COMMANDS ...]
+  IMP (-h | --help)
   IMP --version
 
 Options:
-  -h --help     Show this help and exit
+  -d DATA             Path to the data
+  -e ENV              Environment variable to pass to the container
+  --enter             Enter the container
+  -h --help           Show this help and exit
+  -n CONTAINER        Name of the container. Useful when you want to run a previous version of IMP.
+  -o OUTPUT           Path to the output directory
 
-Parameters:
-    ** INIT **
-      <data>: the path where your data is stored
-      <output>: the path where IMP will write result files
-      <name>: the name of the configuration file [default:IMP]
-    ** RUN **
-        VAR: any command or flag will be forwarded to the underlying Snakemake.
-        Try '-l' to have a list of all commands available.
 """
 
-DOCKER_COMPOSE_TMPL = """imp:
-    image: imp
-    env_file: {output}/.env
-    volumes:
-        - {data}:/data
-        - {code}:/home/imp/integrated-metaomic-pipeline
-        - {output}:/output
-    environment:
-        - IMP_NAME={name}
-
-"""
-
-IMP_CACHE = Path('.imp')
-IMP_CACHE.makedirs_p()
-IMP_CONFIG_CACHE = IMP_CACHE / 'configs'
-IMP_CONFIG_CACHE.touch()
-
-
-def get_config_cache():
-    cache = None
-    with open(IMP_CONFIG_CACHE, 'r') as rhandle:
-        cache = rhandle.read()
-    return cache
-
-
-def add_to_cache(pth):
-    with open(IMP_CONFIG_CACHE, 'a') as whandle:
-        whandle.write(pth + os.linesep)
-
-
-def write_to_cache(pth):
-    with open(IMP_CONFIG_CACHE, 'w') as whandle:
-        whandle.write(pth + os.linesep)
-
-
-def yes_or_no(question):
-    reply = str(input(question + ' (y/n): ')).lower().strip()
-    if reply[0] == 'y':
-        return True
-    if reply[0] == 'n':
-        return False
-    else:
-        return yes_or_no("Please enter ")
-
-
-def select(title, questions):
-
-    s = os.linesep + title
-    for idx, q in enumerate(questions):
-        s += os.linesep + '%s) %s.' % (idx + 1, q)
-    s += os.linesep + 'Choice: '
-    try:
-        reply = int(input(s))
-    except ValueError:
-        return select("Please type a number: ", questions)
-    except KeyboardInterrupt:
-        print(os.linesep, "Exiting ...")
-        exit(0)
-    if abs(reply) > len(questions) or reply <= 0:
-        return select("Please select one of the following: ", questions)
-    return questions[reply - 1]
-
-CURRENT_PATH = Path('.').abspath()
-
 
 def get_version():
     return subprocess.check_output(
@@ -102,46 +36,30 @@ def get_version():
 if __name__ == '__main__':
     args = docopt(__doc__, version=get_version(), options_first=True)
 
-    # get config file from cache
-    config_files = get_config_cache().split()
-    # delete if some config files are removed
-    cfs = []
-    for cf in config_files:
-        if Path(cf).exists():
-            cfs.append(cf)
-    write_to_cache(os.linesep.join(cfs))
-    config_files = cfs
-
-    # init config
-    if args['init']:
-        data = Path(args['<data>']).abspath()
-        output = Path(args['<output>']).abspath()
-        name = args['<name>']
-        if name is None:
-            name = 'IMP'
-        if not output.exists():
-            output.makedirs()
-        docker_compose_path = Path(output / '%s.yml' % name)
-        env_file = Path(output / '.env').touch()
-        compose = DOCKER_COMPOSE_TMPL.format(data=data, output=output, code=CURRENT_PATH, name=name)
-        if docker_compose_path.exists() and not yes_or_no("Configuration already exist. Overwrite ''%s'?" % docker_compose_path):
-            print("Exiting ... ")
-            exit(0)
-        if docker_compose_path not in config_files:
-            add_to_cache(docker_compose_path)
-            docker_compose_path.parent.makedirs_p()
-        with open(docker_compose_path, 'w') as whandle:
-            whandle.write(compose)
-            print("Configuration written at {}".format(docker_compose_path))
-    # run IMP with docker compose
-    elif args['run']:
-        if not config_files:
-            print("You must init IMP first.")
-            print("Exiting ... ")
-            exit(0)
-        elif len(config_files) > 1:
-            cf = select("Multiple config file found", config_files)
-        else:
-            cf = config_files[0]
-        cmd = ['docker-compose', '-f', cf, 'run', 'imp'] + args['VAR']
-        subprocess.call(cmd)
+    CURRENT_PATH = Path(__file__).parent.abspath()
+    print(args)
+
+    data = Path(args['-d']).abspath()
+    output = Path(args['-o']).abspath()
+    container_name = args['-n'] is not None and args['-n'] or 'imp:latest'
+
+    # configure IMP mount point to the docker container
+    mount_points = [
+        '-v %s:/data' % data,
+        '-v %s:/home/imp/integrated-metaomic-pipeline' % CURRENT_PATH,
+        '-v %s:/output' % output
+    ]
+    # environement variables
+    envs = ['-e {}="{}"'.format(*e.split('=')) for e in args['-e']]
+
+    # CL
+    cmd = ['docker', 'run'] + mount_points + envs
+    # reconfigure entrypoint if --enter flag is specified
+    if args['--enter']:
+        cmd += ['--entrypoint /bin/bash -it']
+    # add container name and commands to pass to snakemake
+    cmd += [container_name] + args['COMMANDS']
+    # parse CL correctly
+    cmd = shlex.split(' '.join(cmd))
+    print("Executing", '"', ' '.join(cmd), '"')
+    subprocess.call(cmd)