def test_yaml_file_save(self):
y = fantail.Fantail()
y['a']['b']['c'] = 1
y['d.e'] = '2'
tf = tempfile.NamedTemporaryFile(delete=False)
tf.close()
fantail.yaml_file_save(y, tf.name)
tf.close()
z = fantail.yaml_file_loader(tf.name)
self.assertEqual(y, z)
def load(self, madfile, sha1sum=None):
"""
sha1sum is never used for sidecars
"""
lg.debug("sidecar load: %s", madfile)
if os.path.exists(madfile['madname']):
lg.debug("loading madfile {0}".format(madfile['madname']))
# note the mad file data is in stack[1] - 0 is transient
madfile.mad.update(fantail.yaml_file_loader(madfile['madname']))
def load(self, madfile, sha1sum=None):
"""
sha1sum is never used for sidecars
"""
lg.debug("sidecar load: %s", madfile)
if os.path.exists(madfile['madname']):
lg.debug("loading madfile {0}".format(madfile['madname']))
# note the mad file data is in stack[1] - 0 is transient
madfile.mad.update(
fantail.yaml_file_loader(madfile['madname']))
def _get_recursive_dir_data(pth):
global RECURSE_CACHE
lg.debug("start recursive data load for {}".format(pth))
pth = os.path.abspath(pth)
if os.path.exists(pth) and not os.path.isdir(pth):
here = os.path.dirname(pth)
else:
here = pth
here = here.rstrip('/')
conf = []
# find existing directory configuration from the perspective
# of the madfile
last = here
while True:
if os.path.isdir(here):
here_c = os.path.join(here, 'mad.config')
if os.path.exists(here_c):
conf.append(here_c)
parent = os.path.dirname(here)
if parent == '/': # no config in the root - that would be evil!
break
last = here
here = parent
rv = fantail.Fantail()
for c in conf[::-1]:
lg.debug("read .config file: %s", c)
fullname = os.path.expanduser(os.path.abspath(c))
if fullname in RECURSE_CACHE:
y = RECURSE_CACHE[fullname]
else:
#print('start load dir', fullname)
y = fantail.yaml_file_loader(fullname)
RECURSE_CACHE[fullname] = y
rv.update(y)
lg.debug(rv.pretty())
return rv
def retrieve_template_file(self, template_file):
self.data = fantail.yaml_file_loader(template_file)
assert template_file.exists()
for fref in 'template epilog prolog'.split():
tpath = self.data.get(fref, '')
if tpath.startswith('file://'):
tpath = tpath.replace('file://', '')
if not tpath.startswith('/'):
tpath = Path(template_file).dirname() / tpath
with open(tpath) as FT:
self.data[fref] = FT.read()
if self.transient:
self._template_file = template_file
else:
lg.debug("Copying template_file to %s", self.template_file)
self.save_template()
def retrieve_template_file(self, template_file):
self.data = fantail.yaml_file_loader(template_file)
assert template_file.exists()
for fref in 'template epilog prolog'.split():
tpath = self.data.get(fref, '')
if tpath.startswith('file://'):
tpath = tpath.replace('file://', '')
if not tpath.startswith('/'):
tpath = Path(template_file).dirname() / tpath
with open(tpath) as FT:
self.data[fref] = FT.read()
if self.transient:
self._template_file = template_file
else:
lg.debug("Copying template_file to %s", self.template_file)
self.save_template()
def test_yaml_file_loader(self):
y = fantail.yaml_file_loader(self.tf.name)
self.assertEqual(y['a']['b1']['c2'], 'v2')
self.assertEqual(y['b'], 'v5')
z = fantail.dict_loader(test_dict)
self.assertEqual(y, z)
def madset(app, args):
"""
Set a key/value for one or more files.
Use this command to set a key value pair for one or more files.
This command can take the following forms::
mad set project test genome.fasta
ls *.fasta | mad set project test
find . -size +10k | mad set project test
"""
key = args.key
val = args.value
if args.prompt or args.editor:
if not args.value is None:
# when asking for a prompt - the next item on sys.argv
# is assumed to be a file, and needs to be pushed
# into args.file
args.file = [args.value] + args.file
madfiles = []
# gather all madfiles for later parsing
use_stdin = not (args.prompt or args.editor)
if args.dir:
for m in get_filenames(args, use_stdin, allow_dirs=True):
if not os.path.isdir(m):
continue
fn = os.path.join(m, 'mad.config')
mf = fantail.Fantail()
if os.path.exists(fn):
mf = fantail.yaml_file_loader(fn)
mf._mad_dir_name = m
mf._mad_file_name = fn
madfiles.append(mf)
else:
for m in get_all_mad_files(app, args, use_stdin):
madfiles.append(m)
# check if mad needs to show a prompt or editor
if val is None and not (args.prompt or args.editor):
args.prompt = True
# show prompt or editor
if args.prompt or args.editor:
# get a value from the user
default = ''
# Show a prompt asking for a value
data = madfiles[0]
default = madfiles[0].get(key, "")
if args.prompt:
sys.stdin = open('/dev/tty')
val = mad2.ui.askUser(key, default, data)
sys.stdin = sys.__stdin__
elif args.editor:
editor = os.environ.get('EDITOR', 'vim')
tmp_file = tempfile.NamedTemporaryFile('wb', delete=False)
# write default value to the tmp file
if default:
tmp_file.write(default + "\n")
else:
tmp_file.write("\n")
tmp_file.close()
tty = open('/dev/tty')
subprocess.call('{} {}'.format(editor, tmp_file.name),
stdin=tty, shell=True)
sys.stdin = sys.__stdin__
# read value back in
with open(tmp_file.name, 'r') as F:
# removing trailing space
val = F.read().rstrip()
# remove tmp file
os.unlink(tmp_file.name)
# process key & val
key, val, list_mode = _getkeyval(app, key, val, args.force)
lg.info('set %s to %s', key, val)
if list_mode:
lg.info("List modus")
# Now process madfiles
lg.debug("processing %d files" % len(madfiles))
for madfile in madfiles:
if list_mode:
if not key in madfile:
oldval = []
else:
oldval = madfile.get(key)
if not isinstance(oldval, list):
oldval = [oldval]
if args.dir:
madfile[key] = oldval + [val]
else:
madfile.mad[key] = oldval + [val]
else:
#not listmode
if args.dir:
madfile[key] = val
else:
madfile.mad[key] = val
if args.echo:
if args.dir:
print((madfile._mad_dir_name))
else:
print((madfile['filename']))
if args.dir:
fantail.yaml_file_save(madfile, madfile._mad_file_name)
else:
madfile.save()
def madset(app, args):
"""
Set a key/value for one or more files.
Use this command to set a key value pair for one or more files.
This command can take the following forms::
mad set project test genome.fasta
ls *.fasta | mad set project test
find . -size +10k | mad set project test
"""
key = args.key
val = args.value
if args.prompt or args.editor:
if not args.value is None:
# when asking for a prompt - the next item on sys.argv
# is assumed to be a file, and needs to be pushed
# into args.file
args.file = [args.value] + args.file
madfiles = []
# gather all madfiles for later parsing
use_stdin = not (args.prompt or args.editor)
if args.dir:
for m in get_filenames(args, use_stdin, allow_dirs=True):
if not os.path.isdir(m):
continue
fn = os.path.join(m, 'mad.config')
mf = fantail.Fantail()
if os.path.exists(fn):
mf = fantail.yaml_file_loader(fn)
mf._mad_dir_name = m
mf._mad_file_name = fn
madfiles.append(mf)
else:
for m in get_all_mad_files(app, args, use_stdin):
madfiles.append(m)
# check if mad needs to show a prompt or editor
if val is None and not (args.prompt or args.editor):
args.prompt = True
# show prompt or editor
if args.prompt or args.editor:
# get a value from the user
default = ''
# Show a prompt asking for a value
data = madfiles[0]
default = madfiles[0].get(key, "")
if args.prompt:
sys.stdin = open('/dev/tty')
val = mad2.ui.askUser(key, default, data)
sys.stdin = sys.__stdin__
elif args.editor:
editor = os.environ.get('EDITOR', 'vim')
tmp_file = tempfile.NamedTemporaryFile('wb', delete=False)
# write default value to the tmp file
if default:
tmp_file.write(default + "\n")
else:
tmp_file.write("\n")
tmp_file.close()
tty = open('/dev/tty')
subprocess.call('{} {}'.format(editor, tmp_file.name),
stdin=tty,
shell=True)
sys.stdin = sys.__stdin__
# read value back in
with open(tmp_file.name, 'r') as F:
# removing trailing space
val = F.read().rstrip()
# remove tmp file
os.unlink(tmp_file.name)
# process key & val
key, val, list_mode = _getkeyval(app, key, val, args.force)
lg.info('set %s to %s', key, val)
if list_mode:
lg.info("List modus")
# Now process madfiles
lg.debug("processing %d files" % len(madfiles))
for madfile in madfiles:
if list_mode:
if not key in madfile:
oldval = []
else:
oldval = madfile.get(key)
if not isinstance(oldval, list):
oldval = [oldval]
if args.dir:
madfile[key] = oldval + [val]
else:
madfile.mad[key] = oldval + [val]
else:
#not listmode
if args.dir:
madfile[key] = val
else:
madfile.mad[key] = val
if args.echo:
if args.dir:
print((madfile._mad_dir_name))
else:
print((madfile['filename']))
if args.dir:
fantail.yaml_file_save(madfile, madfile._mad_file_name)
else:
madfile.save()
def load_template(self):
"""
Load the local template.
"""
self.data = fantail.yaml_file_loader(self.template_file)
def _get_recursive_dir_data(pth):
global RECURSE_CACHE
lg.debug("start recursive data load for {}".format(pth))
pth = os.path.abspath(pth)
if os.path.exists(pth) and not os.path.isdir(pth):
here = os.path.dirname(pth)
else:
here = pth
here = here.rstrip('/')
conf = []
# find existing directory configuration from the perspective
# of the madfile
last = here
while True:
if os.path.isdir(here):
here_c = os.path.join(here, 'mad.config')
if os.path.exists(here_c):
conf.append(here_c)
parent = os.path.dirname(here)
if parent == '/': # no config in the root - that would be evil!
break
last = here
here = parent
# now again from the current directory
here = os.getcwd().rstrip('/')
last = here
cwdconf = []
while True:
assert(os.path.isdir(here))
here_c = os.path.join(here, 'mad.config')
if os.path.exists(here_c):
if here_c in conf:
break # overlap with tree from the madfile's location
else:
cwdconf.append(here_c)
parent = os.path.dirname(here)
if parent == '/': # no config in the root - that would be evil!
break
last = here
here = parent
conf = cwdconf + conf
# load (or get from cache)
rv = fantail.Fantail()
for c in conf[::-1]:
fullname = os.path.expanduser(os.path.abspath(c))
if fullname in RECURSE_CACHE:
y = RECURSE_CACHE[fullname]
else:
#print('start load dir', fullname)
y = fantail.yaml_file_loader(fullname)
RECURSE_CACHE[fullname] = y
rv.update(y)
return rv
def load_template(self):
"""
Load the local template.
"""
self.data = fantail.yaml_file_loader(self.template_file)
def get_local_config_file(name):
fn = get_local_config_filename(name)
if os.path.exists(fn):
return fantail.yaml_file_loader(fn)
else:
return fantail.Fantail()
