def index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail = user.email
mail_tmp = mail.split("@")
mail_final = mail_tmp[0] + "AT" + mail_tmp[1]
user_TH_path = trackhubs_path() + "/" + user_lab + "/" + mail_final
trackhubs = []
if os.path.exists(user_TH_path):
list_trackhubs = os.listdir(user_TH_path)
for t in list_trackhubs:
th_path = user_TH_path + "/" + t
#the only one directory into at this th level is named by the assembly used for it
for i in os.listdir(th_path):
path_to_test = th_path + "/" + i
if os.path.isdir(path_to_test):
assembly = i
if not assembly:
break
else:
#hub_url = th_path + "/hub.txt"
hostname = socket.gethostname().lower()
#because of aliasing
if hostname == "ptbbsrv2.epfl.ch":
hostname = "biorepo.epfl.ch"
hub_url = "http://" + hostname + url("/trackHubs/") + user_lab + "/" + mail_final + "/" + t + "/hub.txt"
th = Trackhub(t, 'http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=' + hub_url + "&db=" + assembly)
trackhubs.append(th)
all_trackhubs = [util.to_datagrid(TrackhubGrid(), trackhubs, " UCSC's Trackhub(s)", len(trackhubs) > 0)]
return dict(page='trackhubs', model=trackhubs, items=all_trackhubs, value=kw)
def edit(self, *args, **kw):
th_name = str(args[0])
session["th_name"] = th_name
session.save()
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail_path = str(user._email).lower().replace('@', 'AT')
if user_lab is None:
flash(
"Problem detected with your lab in session. Contact your administrator please",
'error')
raise redirect('/trackhubs')
complementary_path = str(
user_lab) + "/" + mail_path + "/" + th_name + "/"
th_path = trackhubs_path() + "/" + complementary_path
genome_path = th_path + "genomes.txt"
if os.path.exists(genome_path):
#get the final path
with open(genome_path, 'r') as gen:
l = gen.readline()
while l != '':
if l.startswith("trackDb"):
trackdb_path = l.split('trackDb')[1].strip()
l = gen.readline()
final_path = th_path + trackdb_path + "trackDb.txt"
with open(final_path, 'r') as final:
l = final.readline()
dic_colors = {}
cpt = 0
while l != '':
if l.startswith("\ttrack"):
track = l.split("\ttrack")[1].strip()
dic_colors[cpt] = track
cpt += 1
elif l.startswith("\tcolor"):
color = l.split("\tcolor")[1].strip()
dic_colors[cpt] = color
cpt += 1
l = final.readline()
t_length = len(dic_colors.keys())
edit_form = build_form_edit_th(t_length)(
action=url('/trackhubs/post_edit')).req()
for k, v in dic_colors.items():
#even --> track
if (k % 2 == 0):
edit_form.child.children[k].value = v
#odd --> color
else:
edit_form.child.children[k].value = v
return dict(page='trackhubs', widget=edit_form, value=kw)
else:
flash(
"Your trackhub is not accessible right now. Hardware problem on /data. Sorry for this inconvenient, retry in a fiew moment please.",
'error')
raise redirect('/trackhubs')
def edit(self, *args, **kw):
th_name = str(args[0])
session["th_name"] = th_name
session.save()
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail_path = str(user._email).lower().replace('@','AT')
if user_lab is None:
flash("Problem detected with your lab in session. Contact your administrator please", 'error')
raise redirect('/trackhubs')
complementary_path = str(user_lab) + "/" + mail_path + "/" + th_name + "/"
th_path = trackhubs_path() + "/" + complementary_path
genome_path = th_path + "genomes.txt"
if os.path.exists(genome_path):
#get the final path
with open (genome_path, 'r') as gen:
l = gen.readline()
while l!='':
if l.startswith("trackDb"):
trackdb_path = l.split('trackDb')[1].strip()
l = gen.readline()
final_path = th_path + trackdb_path + "trackDb.txt"
with open(final_path, 'r') as final:
l = final.readline()
dic_colors = {}
cpt = 0
while l != '':
if l.startswith("\ttrack"):
track = l.split("\ttrack")[1].strip()
dic_colors[cpt] = track
cpt+=1
elif l.startswith("\tcolor"):
color = l.split("\tcolor")[1].strip()
dic_colors[cpt] = color
cpt += 1
l = final.readline()
t_length = len(dic_colors.keys())
edit_form = build_form_edit_th(t_length)(action=url('/trackhubs/post_edit')).req()
for k, v in dic_colors.items():
#even --> track
if (k % 2 == 0):
edit_form.child.children[k].value = v
#odd --> color
else:
edit_form.child.children[k].value = v
return dict(page='trackhubs', widget=edit_form, value=kw)
else:
flash("Your trackhub is not accessible right now. Hardware problem on /data. Sorry for this inconvenient, retry in a fiew moment please.", 'error')
raise redirect('/trackhubs')
def post_edit(self, *args, **kw):
dic_colors = {}
th_name = session["th_name"]
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail_path = str(user._email).lower().replace('@', 'AT')
for key in kw.keys():
if key.startswith('Color_Track_'):
key_id = key.replace('Color_Track_', '')
dic_colors[int(key_id)] = kw[key] + "\n\n"
#paths...
complementary_path = str(
user_lab) + "/" + mail_path + "/" + th_name + "/"
th_path = trackhubs_path() + "/" + complementary_path
genome_path = th_path + "genomes.txt"
if os.path.exists(genome_path):
#get the final path
with open(genome_path, 'r') as gen:
l = gen.readline()
while l != '':
if l.startswith("trackDb"):
trackdb_path = l.split('trackDb')[1].strip()
l = gen.readline()
source_path = th_path + trackdb_path + "trackDb.txt"
final_path_tmp = th_path + trackdb_path + "trackDb_tmp.txt"
with open(source_path, 'r') as source:
with open(final_path_tmp, 'a') as destination:
l = source.readline()
color_cpt = 0
while l != '':
if l.startswith("\tcolor "):
color_cpt += 1
destination.write("\tcolor " +
dic_colors[color_cpt])
else:
destination.write(l)
l = source.readline()
# remove old file
os.remove(source_path)
# rename new one
os.rename(final_path_tmp, source_path)
flash("Trackhub edited !")
raise redirect("/trackhubs")
else:
flash(
"Your trackhub is not accessible right now. Hardware problem on /data. Sorry for this inconvenient, retry in a fiew moment please.",
'error')
raise redirect('/trackhubs')
def delete(self, *args, **kw):
th_name = str(args[0])
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail = user.email
mail_tmp = mail.split("@")
mail_final = mail_tmp[0] + "AT" + mail_tmp[1]
user_path = trackhubs_path() + "/" + user_lab + "/" + mail_final
th_path = user_path + "/" + th_name
try:
shutil.rmtree(th_path)
flash("Your trackhub " + th_name + " was deleted.")
except:
flash("Error : your trackhub was not deleted. Contact the administrator please.", 'error')
raise redirect(url('/trackhubs'))
def post_edit(self, *args, **kw):
dic_colors = {}
th_name = session["th_name"]
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail_path = str(user._email).lower().replace('@','AT')
for key in kw.keys():
if key.startswith('Color_Track_'):
key_id = key.replace('Color_Track_','')
dic_colors[int(key_id)] = kw[key] + "\n\n"
#paths...
complementary_path = str(user_lab) + "/" + mail_path + "/" + th_name + "/"
th_path = trackhubs_path() + "/" + complementary_path
genome_path = th_path + "genomes.txt"
if os.path.exists(genome_path):
#get the final path
with open (genome_path, 'r') as gen:
l = gen.readline()
while l!='':
if l.startswith("trackDb"):
trackdb_path = l.split('trackDb')[1].strip()
l = gen.readline()
source_path = th_path + trackdb_path + "trackDb.txt"
final_path_tmp = th_path + trackdb_path + "trackDb_tmp.txt"
with open (source_path, 'r') as source:
with open(final_path_tmp, 'a') as destination:
l = source.readline()
color_cpt = 0
while l!='':
if l.startswith("\tcolor "):
color_cpt += 1
destination.write("\tcolor " + dic_colors[color_cpt])
else:
destination.write(l)
l = source.readline()
# remove old file
os.remove(source_path)
# rename new one
os.rename(final_path_tmp, source_path)
flash("Trackhub edited !")
raise redirect("/trackhubs")
else:
flash("Your trackhub is not accessible right now. Hardware problem on /data. Sorry for this inconvenient, retry in a fiew moment please.", 'error')
raise redirect('/trackhubs')
def delete(self, *args, **kw):
th_name = str(args[0])
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail = user.email
mail_tmp = mail.split("@")
mail_final = mail_tmp[0] + "AT" + mail_tmp[1]
user_path = trackhubs_path() + "/" + user_lab + "/" + mail_final
th_path = user_path + "/" + th_name
try:
shutil.rmtree(th_path)
flash("Your trackhub " + th_name + " was deleted.")
except:
flash(
"Error : your trackhub was not deleted. Contact the administrator please.",
'error')
raise redirect(url('/trackhubs'))
def index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
mail = user.email
mail_tmp = mail.split("@")
mail_final = mail_tmp[0] + "AT" + mail_tmp[1]
user_TH_path = trackhubs_path() + "/" + user_lab + "/" + mail_final
trackhubs = []
if os.path.exists(user_TH_path):
list_trackhubs = os.listdir(user_TH_path)
for t in list_trackhubs:
th_path = user_TH_path + "/" + t
#the only one directory into at this th level is named by the assembly used for it
for i in os.listdir(th_path):
path_to_test = th_path + "/" + i
if os.path.isdir(path_to_test):
assembly = i
if not assembly:
break
else:
#hub_url = th_path + "/hub.txt"
hostname = socket.gethostname().lower()
#because of aliasing
if hostname == "ptbbsrv2.epfl.ch":
hostname = "biorepo.epfl.ch"
hub_url = "http://" + hostname + url(
"/trackHubs/"
) + user_lab + "/" + mail_final + "/" + t + "/hub.txt"
th = Trackhub(
t, 'http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=' +
hub_url + "&db=" + assembly)
trackhubs.append(th)
all_trackhubs = [
util.to_datagrid(TrackhubGrid(), trackhubs, " UCSC's Trackhub(s)",
len(trackhubs) > 0)
]
return dict(page='trackhubs',
model=trackhubs,
items=all_trackhubs,
value=kw)
