def candidate_set_probe(routes, self, query_id, candidate_id, probe_id):
'''Candidate output page.
Args:
self (App): ProbeDesigner.App instance.
query_id (string): query folder name.
candidate_id (string): candidate folder name.
'''
d = self.vd
d['title'] = '%s Query: %s' % (self.tprefix, query_id)
d['custom_stylesheets'] = ['query.css', 'style.css']
d['custom_root_stylesheets'] = []
d['query'] = Query(query_id, self.qpath).data
d['queryRoot'] = self.qpath
d['query']['candidate_table'] = pd.read_csv(
os.path.join(self.qpath, query_id, "set_candidates.tsv"), "\t")
d['candidate'] = {'id': candidate_id}
d['probe'] = {'id': probe_id}
configPath = os.path.join(self.qpath, query_id,
f"probe_set_{candidate_id}",
f"probe_{probe_id}",
f"probe_{probe_id}.config")
with open(configPath, 'r') as IH:
config = configparser.ConfigParser()
config.read_string("".join(IH.readlines()))
d['probe'].update(config['REGION'].items())
d['probe'].update(config['PROBE'].items())
d['probe'].update(config['FEATURES'].items())
return (d)
def query(routes, self, query_id):
'''Query output page.
Args:
self (App): ProbeDesigner.App instance.
query_id (string): query folder name.
'''
d = self.vd
d['title'] = '%s Query: %s' % (self.tprefix, query_id)
d['custom_stylesheets'] = ['query.css', 'style.css']
d['custom_root_stylesheets'] = []
d['query'] = Query(query_id, self.qpath).data
d['queryRoot'] = self.qpath
if 'done' == d['query']['status']:
if 'single' == d['query']['type']:
fpath = os.path.join(self.qpath, query_id, "candidates.tsv")
elif 'spotting' == d['query']['type']:
fpath = os.path.join(self.qpath, query_id,
"set_candidates.tsv")
if not os.path.isfile(fpath):
d['query']['status'] = 'error'
else:
d['query']['candidate_table'] = pd.read_csv(fpath, "\t")
d['queryTimeout'] = 24 * 60 * 60 # 1 day timeout
d['admin_email'] = self.admin_email
return (d)
def candidate_probe(routes, self, query_id, candidate_id):
"""Candidate output page.
Args:
self (App): ProbeDesigner.App instance.
query_id (string): query folder name.
candidate_id (string): candidate folder name.
"""
d = self.vd
d["title"] = "%s Query: %s" % (self.tprefix, query_id)
d["custom_stylesheets"] = ["query.css", "style.css"]
d["custom_root_stylesheets"] = []
d["query"] = Query(query_id, self.qpath).data
d["queryRoot"] = self.qpath
d["candidate"] = {"id": candidate_id}
configPath = os.path.join(
self.qpath,
query_id,
f"candidate_{candidate_id}",
f"candidate_{candidate_id}.config",
)
with open(configPath, "r") as IH:
config = configparser.ConfigParser()
config.read_string("".join(IH.readlines()))
d["candidate"].update(config["REGION"].items())
d["candidate"].update(config["PROBE"].items())
d["candidate"].update(config["FEATURES"].items())
return d
def query(routes, self, query_id):
"""Query output page.
Args:
self (App): ProbeDesigner.App instance.
query_id (string): query folder name.
"""
d = self.vd
d["title"] = "%s Query: %s" % (self.tprefix, query_id)
d["custom_stylesheets"] = ["query.css", "style.css"]
d["custom_root_stylesheets"] = []
d["query"] = Query(query_id, self.qpath).data
d["queryRoot"] = self.qpath
if d["query"]["status"] == "done":
if d["query"]["type"] == "single":
fpath = os.path.join(self.qpath, query_id, "candidates.tsv")
elif d["query"]["type"] == "spotting":
fpath = os.path.join(self.qpath, query_id,
"set_candidates.tsv")
if not os.path.isfile(fpath):
d["query"]["status"] = "error"
else:
d["query"]["candidate_table"] = pd.read_csv(fpath, "\t")
d["queryTimeout"] = 24 * 60 * 60 # 1 day timeout
d["admin_email"] = self.admin_email
return d
def queueStatus(routes, self):
taskList = []
for task in self.queue.queue:
query_id = os.path.basename(task[5])
data = Query(query_id, self.qpath).data
taskList.append(os.path.basename(task[1]) + f' @{data["isotime"]}')
if not taskList:
return '{"queue":[]}'
return '{"queue": ["%s"]}' % '", "'.join(taskList)
def queueStatus(routes, self):
taskList = []
for task in self.queue.queue:
if 'ifpd_query_set' == task[0]:
outdir_id = 4
elif 'ifpd_query_probe' == task[0]:
outdir_id = 3
query_id = os.path.basename(task[outdir_id])
data = Query(query_id, self.qpath).data
taskList.append(os.path.basename(task[1]) + f' @{data["isotime"]}')
if 0 == len(taskList): return '{"queue":[]}'
return '{"queue": ["%s"]}' % '", "'.join(taskList)
def hide_alert(routes, self):
'''Hide bookmark alert for a specific query.
Args:
self (App): ProbeDesigner.App instance.
'''
formData = bot.request.forms
query = Query(formData.query_id, self.qpath).data
config = configparser.ConfigParser()
configPath = os.path.join(self.qpath, f'{formData.query_id}.config')
with open(configPath, 'r') as IH:
config.read_string("".join(IH.readlines()))
config['GENERAL']['hidden_bookmark_alter'] = "True"
with open(configPath, 'w+') as OH:
config.write(OH)
return 'Done'
def hide_alert(routes, self):
"""Hide bookmark alert for a specific query.
Args:
self (App): ProbeDesigner.App instance.
"""
formData = bot.request.forms
Query(formData.query_id, self.qpath).data
config = configparser.ConfigParser()
configPath = os.path.join(self.qpath, f"{formData.query_id}.config")
with open(configPath, "r") as IH:
config.read_string("".join(IH.readlines()))
config["GENERAL"]["hidden_bookmark_alter"] = "True"
with open(configPath, "w+") as OH:
config.write(OH)
return "Done"
def single_queries(routes, self):
'''Single probe queries reception route.
Args:
self (App): ProbeDesigner.App instance.
'''
# Read uploaded file
data = bot.request.files.data
raw = [row.decode('utf-8') for row in data.file.readlines()]
# Submit query
for row in raw:
args = row.strip().split('\t')
# Build query command line
cmd = ['fprode_dbquery']
cmd.extend([Query.get_next_id(self.qpath, self.queue)])
cmd.extend([shlex.quote(args[0])])
cmd.extend([shlex.quote(e) for e in args[3:6]])
cmd.extend([shlex.quote('%s/db/%s' % (self.static_path, args[2]))])
cmd.extend(['--n_oligo', shlex.quote(args[6])])
cmd.extend(['--f1_thr', shlex.quote(args[7])])
cmd.extend(['--max_probes', shlex.quote(args[8])])
cmd.extend(['--feat_order', shlex.quote(args[9])])
cmd.extend(['--outdir', '%s/query/' % self.static_path])
cmd.extend(['--description', shlex.quote(args[1])])
# Add query to the queue
self.queue.put(cmd)
# Redirect
bot.response.status = 303
bot.response.set_header('Location',
"%s%s" % (self.root_uri, self.app_uri))
# Output
return ('Query received.')
def candidate_set(routes, self, query_id, candidate_id):
'''Candidate output page.
Args:
self (App): ProbeDesigner.App instance.
query_id (string): query folder name.
candidate_id (string): candidate folder name.
'''
d = self.vd
d['title'] = '%s Query: %s' % (self.tprefix, query_id)
d['custom_stylesheets'] = ['query.css', 'style.css']
d['custom_root_stylesheets'] = []
d['query'] = Query(query_id, self.qpath).data
d['queryRoot'] = self.qpath
d['query']['candidate_table'] = pd.read_csv(
os.path.join(self.qpath, query_id, "set_candidates.tsv"), "\t")
d['candidate'] = {'id': candidate_id}
return (d)
def candidate_set(routes, self, query_id, candidate_id):
"""Candidate output page.
Args:
self (App): ProbeDesigner.App instance.
query_id (string): query folder name.
candidate_id (string): candidate folder name.
"""
d = self.vd
d["title"] = "%s Query: %s" % (self.tprefix, query_id)
d["custom_stylesheets"] = ["query.css", "style.css"]
d["custom_root_stylesheets"] = []
d["query"] = Query(query_id, self.qpath).data
d["queryRoot"] = self.qpath
d["query"]["candidate_table"] = pd.read_csv(
os.path.join(self.qpath, query_id, "set_candidates.tsv"), "\t")
d["candidate"] = {"id": candidate_id}
return d