def get_all(self, *args, **kw):
user = handler.user.get_user_in_session(request)
# user attributs
#to block to one specific user
attributs = DBSession.query(Attributs).all()
all_attributs = [util.to_datagrid(attribut_grid, attributs, "Attributs Table", len(attributs) > 0)]
return dict(page='attributs', model='attribut', form_title="new attribut", items=all_attributs, value=kw)
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 get_all(self, *args, **kw):
user = handler.user.get_user_in_session(request)
# user attributs
#to block to one specific user
attributs = DBSession.query(Attributs).all()
all_attributs = [
util.to_datagrid(attribut_grid, attributs, "Attributs Table",
len(attributs) > 0)
]
return dict(page='attributs',
model='attribut',
form_title="new attribut",
items=all_attributs,
value=kw)
def index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
admins = tg.config.get('admin.mails')
mail = user.email
if user_lab and mail not in admins:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
projects = [p for p in user.projects if p in lab.projects]
elif mail in admins:
projects = DBSession.query(Projects).all()
else:
projects = None
all_projects = [util.to_datagrid(ProjectGrid(), projects, "Projects Table", len(projects) > 0)]
return dict(page='projects', model='project', form_title="new project", items=all_projects, value=kw)
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 index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
user_lab = session.get("current_lab", None)
admins = tg.config.get('admin.mails')
mail = user.email
if user_lab and mail not in admins:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
attributs = DBSession.query(Attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).all()
projects = [p.id for p in user.projects if p in lab.projects]
samples = []
for a in attributs:
for s in a.samples:
if s not in samples and s.project_id in projects:
samples.append(s)
elif mail in admins:
samples = DBSession.query(Samples).all()
all_samples = [util.to_datagrid(SampleGrid(), samples, "Samples Table", len(samples) > 0)]
return dict(page='samples', model='sample', form_title="new sample", items=all_samples, value=kw)
def search_old(self, *args, **kw):
"""
Handle the searching page
"""
user_lab = session.get("current_lab", None)
if user_lab:
lab = DBSession.query(Labs).filter(Labs.name == user_lab).first()
measurements = DBSession.query(Measurements).join(Measurements.attributs).filter(and_(Attributs.lab_id == lab.id, Attributs.deprecated == False)).distinct().all()
searching = [SW(meas) for meas in measurements]
search_grid, hidden_positions, positions_not_searchable = build_search_grid(measurements)
items = [util.to_datagrid(search_grid, searching, '', grid_display=len(searching) > 0)]
return dict(
page='search_old',
items=items,
searchlists=json.dumps([hidden_positions, positions_not_searchable]),
value=kw,
)
else:
flash("Your lab is not registred, contact the administrator please", "error")
raise redirect("./")