def test_mc_init(self):
proj_list = mcapi.get_all_projects()
proj_dict = {p.name:p for p in proj_list}
self.assertFalse('CLITest' in proj_dict)
testargs = ['mc', 'init']
with captured_output(wd=self.proj_path) as (sout, serr):
init_subcommand(testargs)
#print_stringIO(sout)
out = sout.getvalue().splitlines()
remote = mcapi.use_remote()
url = remote.config.mcurl
self.assertEqual(out[0], "Created new project at: " + url)
testargs = ['mc', 'init']
with captured_output(wd=self.proj_path) as (sout, serr):
init_subcommand(testargs)
#print_stringIO(sout)
out = sout.getvalue().splitlines()
self.assertTrue(re.match("Already in project. name: CLITest", out[0]))
proj_list = mcapi.get_all_projects()
proj_dict = {p.name:p for p in proj_list}
self.assertTrue('CLITest' in proj_dict)
with working_dir(self.proj_path):
proj = make_local_project()
self.assertEqual(proj.name, 'CLITest')
def get_all_objects(self, args):
if self.requires_project and _proj_path() is None:
raise Exception("Not in any Materials Commons project directory")
if not self.proj_member:
data = self.get_all()
else:
proj = make_local_project()
if self.expt_member and args.expt:
expt = make_local_expt(proj)
data = self.get_all_from_experiment(expt)
else:
data = self.get_all_from_project(proj)
def _any_match(value):
for n in args.expr:
if re.match(n, value):
return True
return False
if args.expr:
if args.id:
objects = [d for d in data if _any_match(d.id)]
elif self.has_owner and args.owner:
objects = [d for d in data if _any_match(d.owner)]
else:
objects = [d for d in data if _any_match(d.name)]
else:
objects = data
return objects
def up_subcommand(argv=sys.argv):
"""
upload files to Materials Commons
mc up [-r] [<pathspec> ...]
"""
parser = argparse.ArgumentParser(
description='upload files',
prog='mc up')
parser.add_argument('paths', nargs='*', default=None, help='Files or directories')
parser.add_argument('-r', '--recursive', action="store_true", default=False, help='Upload directory contents recursively')
parser.add_argument('--limit', nargs=1, type=float, default=[50], help='File size upload limit (MB). Default=50MB.')
# ignore 'mc up'
args = parser.parse_args(argv[2:])
limit = args.limit[0]
proj = make_local_project()
local_abspaths = set([os.path.abspath(p) for p in args.paths])
if not args.recursive:
dirs = [p for p in local_abspaths if os.path.isdir(p)]
for d in dirs:
local_abspaths.remove(d)
files = [os.path.join(p, f) for f in os.listdir(d) if os.path.isfile(os.path.join(p,f))]
local_abspaths.update(files)
if args.recursive and proj.local_path in local_abspaths:
# treat upload of everything specially
local_abspaths = set([os.path.join(proj.local_path, f) for f in os.listdir(proj.local_path) if f != ".mc"])
for p in local_abspaths:
if os.path.isfile(p):
#print "uploading:", p
try:
result = proj.add_file_by_local_path(p, verbose=True, limit=limit)
except Exception as e:
print "Could not upload:", p
print "Error:"
print e
elif os.path.isdir(p) and args.recursive:
#print "uploading:", p
result, error = proj.add_directory_tree_by_local_path(p, verbose=True, limit=limit)
if len(error):
for file in error:
print "Could not upload:", file
print "Error:"
print error[file]
return
def get_proj(cls):
return make_local_project(cls.proj_path)
def expt_subcommand(argv=sys.argv):
"""
List, create, delete, and modify experiments
mc expt
mc expt [-c] <exptname>
"""
parser = argparse.ArgumentParser(
description='List, create, delete, and modify experiments',
prog='mc expt')
parser.add_argument('expts', nargs='*', default=None, help='Experiment names (or id if --id given)')
parser.add_argument('-l', '--list', action="store_true", default=True, help='List experiments (default)')
parser.add_argument('-c', '--create', action="store_true", default=False, help='Create experiments')
parser.add_argument('-d', '--delete', action="store_true", default=False, help='Delete experiments')
parser.add_argument('-s', '--set', action="store_true", default=False, help='Set current experiment')
parser.add_argument('--id', action="store_true", default=False, help='Input experiment id instead of name')
parser.add_argument('--desc', type=str, default="", help='Experiment description')
parser.add_argument('-n', '--dry-run', action="store_true", default=False, help='Dry run deletion')
parser.add_argument('-a', '--all', action="store_true", default=False, help='Delete all samples and processes')
#parser.add_argument('-m', '--rename', type=str, default='origin', help='Rename experiment')
# ignore 'mc expt'
args = parser.parse_args(argv[2:])
proj = make_local_project()
expt_list = proj.get_all_experiments()
expts = {e.name:e for e in expt_list}
expt_ids = {e.id:e for e in expt_list}
if args.create:
if len(args.expts) != 1:
print 'create one experiment at a time'
print 'example: mc expt -c ExptName --desc "short description"'
parser.print_help()
exit(1)
for name in args.expts:
if name not in expts:
expt = proj.create_experiment(name, args.desc)
print 'Created experiment:', expt.name
set_current_experiment(proj, expt)
print "Set current experiment: '" + expt.name + "'"
else:
print 'experiment: \'' + name + '\' already exists'
elif args.delete:
for name in args.expts:
if args.id:
_expts = expt_ids
else:
_expts = expts
_expts[name].delete(dry_run=args.dry_run, delete_processes_and_samples=args.all)
print 'Deleted experiment:', name
for key, val in _expts[name].delete_tally.__dict__.iteritems():
print key, val
print ""
elif args.set:
if len(args.expts) != 1:
print 'set one current experiment at a time'
print 'example: mc expt -s ExptName'
parser.print_help()
exit(1)
if args.id:
set_current_experiment(proj, expt_ids[args.expts[0]])
print "Set current experiment: '" + expt_ids[args.expts[0]].name + "'"
else:
set_current_experiment(proj, expts[args.expts[0]])
print "Set current experiment: '" + expts[args.expts[0]].name + "'"
elif args.list:
_print_experiments(proj.get_all_experiments(), make_local_expt(proj))
return
def get_proj(self):
return make_local_project(self.proj_path)
def ls_subcommand(argv=sys.argv):
"""
'ls' a project directory to see local and remote files and directories.
mc ls [<pathspec> ...]
"""
parser = argparse.ArgumentParser(
description='List local & remote directory contents',
prog='mc ls')
parser.add_argument('paths', nargs='*', default=[os.getcwd()], help='Files or directories')
parser.add_argument('--checksum', action="store_true", default=False, help='Calculate MD5 checksum for local files')
parser.add_argument('--json', action="store_true", default=False, help='Print JSON exactly')
# ignore 'mc ls'
args = parser.parse_args(argv[2:])
local_abspaths = [os.path.abspath(p) for p in args.paths]
proj = make_local_project()
# act on local paths
(df, files, dirs, remotes) = _ls_group(proj, local_abspaths,
files_only=True, checksum=args.checksum, json=args.json)
# print warnings for type mismatches
for file in files:
if file in dirs and os.path.isfile(file):
print "warning!", file, "is a local file and remote directory!"
if file in dirs and os.path.isdir(file):
print "warning!", file, "is a local directory and remote file!"
if args.json:
for r in remotes:
print r.input_data
else:
if df.shape[0]:
print df.to_string(index=False)
print ""
for d in dirs:
_locals = []
if os.path.exists(d):
_locals = [os.path.join(d, f) for f in os.listdir(d)]
if os.path.abspath(d) == proj.local_path:
remote_dir = proj.get_top_directory()
else:
remote_dir = proj.get_by_local_path(d)
_remotes = []
if remote_dir is not None:
_remotes = [os.path.join(d, child.name) for child in remote_dir.get_children()]
_local_abspaths = SortedSet(_locals + _remotes)
(df, files, dirs, remotes) = _ls_group(proj, _local_abspaths,
files_only=False, checksum=args.checksum, json=args.json)
if args.json:
for r in remotes:
print r.input_data
else:
if df.shape[0]:
print os.path.relpath(d, os.getcwd()) + ":"
#print df.to_string(index=False)
print tabulate(df, showindex=False, headers=df.columns, tablefmt="plain")
print ""
return