def index():
folder_path = var.music_folder
files = util.get_recursive_filelist_sorted(var.music_folder)
music_library = util.Dir(folder_path)
for file in files:
music_library.add_file(file)
return render_template('index.html',
all_files=files,
music_library=music_library,
os=os,
playlist=var.playlist,
user=var.user,
paused=var.botamusique.is_pause)
p.add_argument('--merge_bams', action='store_true', help='If files need to be merged')
p.add_argument('-T', '--tmp', metavar='DIR', required=True, help='The TMP directory for storing intermediate files (default=output directory')
p.add_argument('--id',metavar='STR', required=True, help="sample id")
p.add_argument('--lb',metavar='STR', required=True, help="library")
p.add_argument('--sm',metavar='STR', required=True, help="sample name (will creat such a folder in TMP dir to hold temp files)")
p.add_argument('--pl',metavar='STR', required=True, help="sequencing platform")
p.add_argument('-j', '--jobfile', metavar='FILE', help='The jobfile name (default: stdout)')
p.add_argument('-m', '--memory', metavar='SIZE', type=int, default=12, help='Memory size (GB) per job (default: 12)')
p.add_argument('-p', '--project', metavar='NAME', default="CompBio", help='Project name for jobs (default: CompBio)')
p.add_argument('-q', '--queue', metavar='NAME', default="normal", help='Queue for jobs (default: normal)')
p.add_argument('-t', '--threads', metavar='COUNT', type=int, default=4, help='Number of threads for BWA alignment, only works for SGE (default: 4)')
p.add_argument('--account', metavar='STR', default="swang", help='Accounting string for the purpose of cluster accounting.')
p.add_argument('--submit', action='store_true', help='Submit the jobs')
args = p.parse_args()
outdir=util.Dir(args.outdir)
outdir.mkdirs()
tmpdir=util.Dir(os.path.join(args.tmp, args.sm))
tmpdir.mkdirs()
if args.jobfile is None:
jobfile=None
else:
jobfile=util.File(args.jobfile)
readgroup = "'@RG\\\\tID:%s\\\\tLB:%s\\\\tSM:%s\\\\tPL:%s'" % (args.id, args.lb, args.sm, args.pl)
sjm.Job.name_prefix="BWA-mapping"+"."
sjm.Job.memory="%sG"%args.memory
sjm.Job.queue="pcgp"
def post():
folder_path = var.music_folder
if request.method == 'POST':
logging.debug("Post request: " + str(request.form))
if 'add_file_bottom' in request.form and ".." not in request.form[
'add_file_bottom']:
path = var.config.get(
'bot', 'music_folder') + request.form['add_file_bottom']
if os.path.isfile(path):
item = {
'type': 'file',
'path': request.form['add_file_bottom'],
'title': '',
'user': '******'
}
var.playlist.append(util.get_music_tag_info(item))
logging.info('web: add to playlist(bottom): ' + item['path'])
elif 'add_file_next' in request.form and ".." not in request.form[
'add_file_next']:
path = var.config.get(
'bot', 'music_folder') + request.form['add_file_next']
if os.path.isfile(path):
item = {
'type': 'file',
'path': request.form['add_file_next'],
'title': '',
'user': '******'
}
var.playlist.insert(var.playlist.current_index + 1,
util.get_music_tag_info(item))
logging.info('web: add to playlist(next): ' + item['path'])
elif ('add_folder' in request.form
and ".." not in request.form['add_folder']) or (
'add_folder_recursively' in request.form
and ".." not in request.form['add_folder_recursively']):
try:
folder = request.form['add_folder']
except:
folder = request.form['add_folder_recursively']
if not folder.endswith('/'):
folder += '/'
print('folder:', folder)
if os.path.isdir(var.config.get('bot', 'music_folder') + folder):
files = util.get_recursive_filelist_sorted(var.music_folder)
music_library = util.Dir(folder_path)
for file in files:
music_library.add_file(file)
if 'add_folder_recursively' in request.form:
files = music_library.get_files_recursively(folder)
else:
files = music_library.get_files(folder)
files = list(
map(
lambda file: util.get_music_tag_info(
{
'type': 'file',
'path': os.path.join(folder, file),
'user': '******'
}), files))
for file in files:
logging.info("web: add to playlist: %s" % file['path'])
var.playlist.extend(files)
elif 'add_url' in request.form:
music = {
'type': 'url',
'url': request.form['add_url'],
'user': '******',
'ready': 'validation'
}
media.url.get_url_info(music)
var.playlist.append(music)
logging.info("web: add to playlist: " + request.form['add_url'])
var.playlist.playlist[-1]['ready'] = "no"
elif 'add_radio' in request.form:
var.playlist.append({
'type': 'radio',
'path': request.form['add_radio'],
'user': "******"
})
logging.info("web: add to playlist: " + request.form['add_radio'])
elif 'delete_music' in request.form:
music = var.playlist.playlist[int(request.form['delete_music'])]
logging.info(
"web: delete from playlist: " +
str(music['path'] if 'path' in music else music['url']))
if var.playlist.length() >= int(request.form['delete_music']):
if int(request.form['delete_music']
) == var.playlist.current_index:
var.playlist.remove(int(request.form['delete_music']))
var.botamusique.stop()
var.botamusique.launch_music(
int(request.form['delete_music']))
else:
var.playlist.remove(int(request.form['delete_music']))
elif 'play_music' in request.form:
music = var.playlist.playlist[int(request.form['play_music'])]
logging.info(
"web: jump to: " +
str(music['path'] if 'path' in music else music['url']))
if len(var.playlist.playlist) >= int(request.form['play_music']):
var.botamusique.stop()
var.botamusique.launch_music(int(request.form['play_music']))
elif 'delete_music_file' in request.form and ".." not in request.form[
'delete_music_file']:
path = var.config.get(
'bot', 'music_folder') + request.form['delete_music_file']
if os.path.isfile(path):
logging.info("web: delete file " + path)
os.remove(path)
elif 'delete_folder' in request.form and ".." not in request.form[
'delete_folder']:
path = var.config.get(
'bot', 'music_folder') + request.form['delete_folder']
if os.path.isdir(path):
logging.info("web: delete folder " + path)
shutil.rmtree(path)
time.sleep(0.1)
elif 'action' in request.form:
action = request.form['action']
if action == "randomize":
var.botamusique.stop()
var.playlist.randomize()
var.botamusique.resume()
elif action == "stop":
var.botamusique.stop()
elif action == "pause":
var.botamusique.pause()
elif action == "resume":
var.botamusique.resume()
elif action == "clear":
var.botamusique.clear()
elif action == "volume_up":
if var.botamusique.volume_set + 0.03 < 1.0:
var.botamusique.volume_set = var.botamusique.volume_set + 0.03
else:
var.botamusique.volume_set = 1.0
logging.info("web: volume up to %d" %
(var.botamusique.volume_set * 100))
elif action == "volume_down":
if var.botamusique.volume_set - 0.03 > 0:
var.botamusique.volume_set = var.botamusique.volume_set - 0.03
else:
var.botamusique.volume_set = 0
logging.info("web: volume up to %d" %
(var.botamusique.volume_set * 100))
if (var.playlist.length() > 0):
return jsonify({
'ver': var.playlist.version,
'empty': False,
'play': not var.botamusique.is_pause
})
else:
return jsonify({
'ver': var.playlist.version,
'empty': True,
'play': False
})
def index():
folder_path = var.music_folder
files = util.get_recursive_filelist_sorted(var.music_folder)
music_library = util.Dir(folder_path)
for file in files:
music_library.add_file(file)
if request.method == 'POST':
print(request.form)
if 'add_file' in request.form and ".." not in request.form['add_file']:
item = {'type': 'file',
'path' : request.form['add_file'],
'user' : 'Web'}
var.playlist.append(item)
elif ('add_folder' in request.form and ".." not in request.form['add_folder']) or ('add_folder_recursively' in request.form and ".." not in request.form['add_folder_recursively']):
try:
folder = request.form['add_folder']
except:
folder = request.form['add_folder_recursively']
if not folder.endswith('/'):
folder += '/'
print('folder:', folder)
if 'add_folder_recursively' in request.form:
files = music_library.get_files_recursively(folder)
else:
files = music_library.get_files(folder)
files = list(map(lambda file: {'type':'file','path': os.path.join(folder, file), 'user':'******'}, files))
print('Adding to playlist: ', files)
var.playlist.extend(files)
elif 'add_url' in request.form:
var.playlist.append({'type':'url',
'url': request.form['add_url'],
'user': '******',
'ready': 'validation'})
media.url.get_url_info()
var.playlist[-1]['ready'] = "no"
elif 'add_radio' in request.form:
var.playlist.append({'type': 'radio',
'path': request.form['add_radio'],
'user': "******"})
elif 'delete_music' in request.form:
if len(var.playlist) >= request.form['delete_music']:
var.playlist.pop(request.form['delete_music'])
elif 'action' in request.form:
action = request.form['action']
if action == "randomize":
random.shuffle(var.playlist)
return render_template('index.html',
all_files=files,
music_library=music_library,
os=os,
playlist=var.playlist,
user=var.user)
help='Final single vcf output file if choose joint call')
g2.add_argument('--skip_realn_recal',
action='store_true',
help='Skip GATK relingment and recalibration')
g2.add_argument('--skip_recal',
action='store_true',
help='Skip GATK recalibration only')
p.add_argument('--submit', action='store_true', help='Submit the jobs')
args = p.parse_args()
if args.jobfile is None:
jobfile = None
else:
jobfile = util.File(args.jobfile)
outdir = util.Dir(args.output)
logdir = util.Dir(outdir, 'log')
tmpdir = outdir
if args.tmp: tmpdir = util.Dir(args.tmp)
tmpdir.mkdirs()
outdir.mkdirs()
sjm.Job.name_prefix = "GATK" + "."
sjm.Job.memory = "20G"
sjm.Job.queue = "pcgp"
sjm.Job.project = "CompBio"
if args.account: sjm.Job.sge_options = "-A %s" % args.account
tmpdir = getattr(__builtins__, 'str')(tmpdir)
outdir = getattr(__builtins__, 'str')(outdir)
'--temp_prefix',
metavar='NAME',
required=True,
help='The merged gvcf file prefix')
p.add_argument('-T',
'--tempdir',
metavar='DIR',
required=True,
help='The directory to hold merged gvcfs')
p.add_argument('-j',
'--jobfile',
metavar='FILE',
help='The jobfile name (default: stdout)')
args = p.parse_args()
outdir = util.Dir(args.outdir)
outdir.mkdirs()
tmpdir = util.Dir(args.tempdir)
tmpdir.mkdirs()
if args.jobfile is None:
jobfile = None
else:
jobfile = util.File(args.jobfile)
sjm.Job.name_prefix = "GATK-joint" + "."
sjm.Job.memory = "12G"
sjm.Job.queue = "pcgp"
sjm.Job.project = "CompBio"
outdir = getattr(__builtins__, 'str')(outdir)
p.add_argument(
'-t',
'--threads',
metavar='COUNT',
type=int,
default=4,
help='Number of threads for BWA alignment, only works for SGE (default: 4)'
)
p.add_argument('--account',
metavar='STR',
default="swang",
help='Accounting string for the purpose of cluster accounting.')
p.add_argument('--submit', action='store_true', help='Submit the jobs')
args = p.parse_args()
outdir = util.Dir(args.outdir)
outdir.mkdirs()
tmplett = ''.join(random.sample(string.ascii_letters, 6))
tmpdir = util.Dir(os.path.join(args.tmp, tmplett))
tmpdir.mkdirs()
if args.jobfile is None:
jobfile = None
else:
jobfile = util.File(args.jobfile)
sjm.Job.name_prefix = "BWA-mapping" + "."
sjm.Job.memory = "%sG" % args.memory
sjm.Job.queue = "pcgp"
sjm.Job.project = "CompBio"
def cmd_play_file(bot, user, text, command, parameter):
music_folder = var.config.get('bot', 'music_folder')
# if parameter is {index}
if parameter.isdigit():
files = util.get_recursive_filelist_sorted(music_folder)
if int(parameter) < len(files):
filename = files[int(parameter)].replace(music_folder, '')
music = {'type': 'file',
'path': filename,
'user': user}
logging.info("cmd: add to playlist: " + filename)
var.playlist.append(music)
bot.send_msg(var.config.get('strings', 'file_added') + music['title'], text)
# if parameter is {path}
else:
# sanitize "../" and so on
path = os.path.abspath(os.path.join(music_folder, parameter))
if not path.startswith(os.path.abspath(music_folder)):
bot.send_msg(var.config.get('strings', 'no_file'), text)
return
if os.path.isfile(path):
music = {'type': 'file',
'path': parameter,
'user': user}
logging.info("cmd: add to playlist: " + parameter)
music = var.playlist.append(music)
bot.send_msg(var.config.get('strings', 'file_added') + music['title'], text)
return
# if parameter is {folder}
elif os.path.isdir(path):
if parameter != '.' and parameter != './':
if not parameter.endswith("/"):
parameter += "/"
else:
parameter = ""
files = util.get_recursive_filelist_sorted(music_folder)
music_library = util.Dir(music_folder)
for file in files:
music_library.add_file(file)
files = music_library.get_files(parameter)
msgs = [var.config.get('strings', 'file_added')]
count = 0
for file in files:
count += 1
music = {'type': 'file',
'path': file,
'user': user}
logging.info("cmd: add to playlist: " + file)
music = var.playlist.append(music)
msgs.append("{} ({})".format(music['title'], music['path']))
if count != 0:
send_multi_lines(bot, msgs, text)
else:
bot.send_msg(var.config.get('strings', 'no_file'), text)
else:
# try to do a partial match
files = util.get_recursive_filelist_sorted(music_folder)
matches = [(index, file) for index, file in enumerate(files) if parameter.lower() in file.lower()]
if len(matches) == 0:
bot.send_msg(var.config.get(
'strings', 'no_file'), text)
elif len(matches) == 1:
music = {'type': 'file',
'path': matches[0][1],
'user': user}
logging.info("cmd: add to playlist: " + matches[0][1])
music = var.playlist.append(music)
bot.send_msg(var.config.get( 'strings', 'file_added')
+ "{} ({})".format(music['title'], music['path']), text)
else:
msgs = [ var.config.get('strings', 'multiple_matches') ]
for match in matches:
msgs.append("<b>{:0>3d}</b> - {:s}".format(match[0], match[1]))
send_multi_lines(bot, msgs, text)