def start(self, passwd, port):
self.process = wx.Process(self.parent)
self.process.Redirect()
p = self.app_path
sys.path.insert(0, self.w2p_path)
os.chdir(self.w2p_path)
if not os.path.isfile('web2py.py'):
self.process = None
raise Exception('%s: Execution failed' % 'web2py.py')
if passwd:
passwd = passwd.strip()
from gluon.main import save_password
save_password(passwd, port)
cmd = '"%s" -u "%s" %s "%s"' % (sys.executable,
opj(p, 'gw2pserver.py'), port, self.w2p_path)
self.pid = wx.Execute(cmd, wx.EXEC_ASYNC, self.process)
if self.pid == 0:
self.process = None
raise Exception('%s: Execution failed' % 'web2py.py')
self.is_running = True
def server(host, port, password):
save_password(password, port)
qdb.init(redirect=False)
qdb.qdb.do_debug()
def wrapped_app(environ, start_response):
"WSGI wrapper to allow debugging"
# hanshake with front-end on each request (update ui)
# not realy needed (request processing is sequential)
##qdb.qdb.startup()
# process the request as usual
return wsgibase(environ, start_response)
httpd2 = make_server(host, port, wrapped_app)
print "THREAD - Serving HTTP on port2 %s..." % port
httpd2.serve_forever(poll_interval=0.01)
def server(host, port, password):
save_password(password, port)
qdb.init(redirect=False)
qdb.qdb.do_debug()
def wrapped_app(environ, start_response):
"WSGI wrapper to allow debugging"
# hanshake with front-end on each request (update ui)
# not realy needed (request processing is sequential)
##qdb.qdb.startup()
# process the request as usual
return wsgibase(environ, start_response)
httpd2 = make_server(host, port, wrapped_app)
print "THREAD - Serving HTTP on port2 %s..." % port
httpd2.serve_forever(poll_interval=0.01)
def OnAttachWebserver(self, event):
"start-up a web2py server instance"
# read configuration with safe defaults
cfg = wx.GetApp().get_config("WEB2PY")
path = cfg.get("path", "../web2py")
password = cfg.get("password", "a")
port = cfg.get("port", 8006)
host = "127.0.0.1"
if path:
# store current directory
prevdir = os.path.abspath(os.curdir)
try:
# update current directory and python path to find web2py:
os.chdir(path)
sys.path.insert(0, os.path.abspath(os.curdir))
from gluon.main import wsgibase, save_password
from gluon.contrib import qdb
# store admin password
save_password(password, port)
web2py_env = {} ##self.build_web2py_environment()
# Start a alternate web2py in a separate thread (for blocking requests)
from threading import Thread
def server(host, port, password):
save_password(password, port)
qdb.init(redirect=False)
qdb.qdb.do_debug()
def wrapped_app(environ, start_response):
"WSGI wrapper to allow debugging"
# hanshake with front-end on each request (update ui)
# not realy needed (request processing is sequential)
##qdb.qdb.startup()
# process the request as usual
return wsgibase(environ, start_response)
httpd2 = make_server(host, port, wrapped_app)
print "THREAD - Serving HTTP on port2 %s..." % port
httpd2.serve_forever(poll_interval=0.01)
thread = Thread(target=server, args=(host, port, password))
thread.daemon = True # close on exit
thread.start()
# open internal browser at default page:
url = "http://%s:%s/" % (host, port)
if self.browser:
self.browser.LoadURL(url)
pass
else:
# no internal browser, open external one
try:
import webbrowser
webbrowser.open(url)
except:
print "warning: unable to detect your browser"
except Exception, e:
self.ShowInfoBar(u"cannot start web2py!: %s" % unicode(e), flags=wx.ICON_ERROR, key="web2py")
web2py_env = {}
finally:
def init_db_helper(db, auth, force=False, admin_email="*****@*****.**", admin_password="******"):
from gluon.main import save_password
from permission_enum import PermissionEnum
if (force) or (db(db.auth_user.id > 0).count() == 0) :
if force:
reset_db(db)
id_first_user=""
## création du premier user
id_first_user=db.auth_user.insert(
password = db.auth_user.password.validate(admin_password)[0],
email = admin_email,
first_name = 'System',
last_name = 'Administrator'
)
# set web2py administration interface password to the same as vidjil admin password
save_password(admin_password, 443)
## création des groupes de base
id_admin_group=db.auth_group.insert(role='admin')
id_sa_group=db.auth_group.insert(role='user_1')
id_public_group=db.auth_group.insert(role="public")
db.auth_membership.insert(user_id=id_first_user, group_id=id_admin_group)
db.auth_membership.insert(user_id=id_first_user, group_id=id_sa_group)
db.auth_membership.insert(user_id=id_first_user, group_id=id_public_group)
### Base config classification
db.classification.insert(
name = 'Vidjil-algo',
info = 'Vidjil-algo'
)
db.classification.insert(
name = 'Sub groups',
info = 'Sub groups'
)
db.classification.insert(
name = 'Other germlines',
info = 'Other germlines'
)
db.classification.insert(
name = 'Other species',
info = 'Other species'
)
db.classification.insert(
name = 'Experimentals',
info = 'Experimentals'
)
## base Vidjil configs
db.config.insert(
name = 'default + extract reads',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g -e 1 -2 -d -w 50 -U ',
fuse_command = '-t 100',
info = 'Same as the default "multi+inc+xxx" (multi-locus, with some incomplete/unusual/unexpected recombinations), and extract analyzed reads in the "out" temporary directory.',
classification = 1
)
db.config.insert(
name = 'multi+inc+xxx',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g -e 1 -2 -d -w 50 ',
fuse_command = '-t 100',
info = 'multi-locus, with some incomplete/unusual/unexpected recombinations',
classification = 1
)
db.config.insert(
name = 'multi+inc',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g -e 1 -w 50 ',
fuse_command = '-t 100',
info = 'multi-locus, with some incomplete/unusual recombinations',
classification = 1
)
db.config.insert(
name = 'multi',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g:IGH,IGK,IGL,TRA,TRB,TRG,TRD -e 1 -d -w 50 ',
fuse_command = '-t 100',
info = 'multi-locus, only complete recombinations',
classification = 2
)
db.config.insert(
name = 'TRG',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g:TRG ',
fuse_command = '-t 100',
info = 'TRG, VgJg',
classification = 2
)
db.config.insert(
name = 'IGH',
program = 'vidjil',
command = '-c clones -w 60 -d -3 -z 100 -r 1 -g germline/h**o-sapiens.g:IGH ',
fuse_command = '-t 100',
info = 'IGH, Vh(Dh)Jh',
classification = 2
)
## permission
## system admin have admin/read/create rights on all patients, groups and configs
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.run, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.pre_process, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.run, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin_group.value, db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin_config.value, db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin_pre_process.value, db.pre_process, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.run, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.read_group.value, db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.read_config.value, db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.read_pre_process.value, db.pre_process, 0)
auth.add_permission(id_admin_group, PermissionEnum.create.value, db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.create_group.value, db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.create_config.value, db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.create_pre_process.value, db.pre_process, 0)
auth.add_permission(id_admin_group, 'impersonate', db.auth_user, 0)
auth.add_permission(id_public_group, PermissionEnum.read_config.value, db.config, 0)
for config in db(db.config.id > 0).select():
auth.add_permission(id_public_group, PermissionEnum.access.value, db.config, config.id)
auth.add_permission(id_public_group, PermissionEnum.read_pre_process.value, db.pre_process, 0)
for pre_process in db(db.pre_process.id > 0).select():
auth.add_permission(id_public_group, PermissionEnum.access.value, db.pre_process, pre_process.id)
tags = ['ALL', 'T-ALL', 'B-ALL',
'pre-B-ALL','pro-B-ALL', 'mature-B-ALL',
'CML', 'HCL', 'MZL', 'T-PLL',
'CLL', 'LGL',
'lymphoma',
'MCL', 'NHL', 'HL', 'FL', 'DLBCL',
'WM', 'MAG',
'MM',
'diagnosis', 'MRD', 'relapse', 'CR', 'deceased',
'pre-BMT', 'post-BMT', 'pre-SCT', 'post-SCT',
'dilution', 'standard',
'QC', 'EuroMRD',
'marrow', 'blood',
'repertoire',
'TIL', 'CAR-T', 'scFv',
'FR1', 'FR2', 'FR3',
'TRA', 'TRB', 'TRG', 'TRD',
'IGH', 'IGK', 'KDE', 'IGL',
'IKAROS',
'BCR-ABL', 'TEL-AML1', 'E2A-PBX',
'BCL2',
'PAX5']
for tag in tags:
tid = db.tag.insert(name=tag)
db.group_tag.insert(group_id=id_public_group, tag_id=tid)
def f(host, port, password):
save_password(password, port)
httpd2 = make_server(host, port, wsgibase)
print "THREAD - Serving HTTP on port2 %s..." % port
httpd2.serve_forever()
def __init__(self, path="../web2py", port=8006, password="******"):
"start-up a web2py server instance"
self.menu['run'].Append(ID_ATTACH, "Attach &webserver\tCtrl-W",
"Connect to remote web2py debugger")
self.Bind(wx.EVT_MENU, self.OnAttachWebserver, id=ID_ATTACH)
# read configuration with safe defaults
cfg = wx.GetApp().get_config("WEB2PY")
path = cfg.get("path", path)
password = cfg.get("password", password)
port = cfg.get("port", port)
host = "127.0.0.1"
if path:
# store current directory
prevdir = os.path.abspath(os.curdir)
try:
os.chdir(path)
sys.path.insert(0, path)
from gluon.main import wsgibase, save_password
# store admin password
save_password(password, port)
# create a wsgi server
self.web2py_httpd = make_server(host, port, wsgibase)
print "Serving HTTP on port %s..." % port
# connect to idle event to poll and serve requests
##self.Bind(wx.EVT_IDLE, self.OnIdleServeWeb2py)
# open internal browser at default page:
url = "http://%s:%s/" % (host, port)
if self.browser:
#self.browser.LoadURL(url)
pass
else:
# no interna browser, open external one
try:
import webbrowser
webbrowser.open(url)
except:
print 'warning: unable to detect your browser'
web2py_env = self.build_web2py_environment()
if False:
# Start a alternate web2py in a separate thread (for blocking requests)
from threading import Thread
def f(host, port, password):
save_password(password, port)
httpd2 = make_server(host, port, wsgibase)
print "THREAD - Serving HTTP on port2 %s..." % port
httpd2.serve_forever()
p = Thread(target=f, args=("127.0.0.1", 8000, password))
p.start()
except Exception, e:
self.ShowInfoBar(u"cannot start web2py!: %s" % unicode(e),
flags=wx.ICON_ERROR,
key="web2py")
web2py_env = {}
finally:
def init_db_helper(db, auth, force=False, admin_email="*****@*****.**", admin_password="******"):
from gluon.main import save_password
from permission_enum import PermissionEnum
if (force) or (db(db.auth_user.id > 0).count() == 0) :
if force:
reset_db(db)
id_first_user=""
## création du premier user
id_first_user=db.auth_user.insert(
password = db.auth_user.password.validate(admin_password)[0],
email = admin_email,
first_name = 'System',
last_name = 'Administrator'
)
# set web2py administration interface password to the same as vidjil admin password
save_password(admin_password, 443)
## création des groupes de base
id_admin_group=db.auth_group.insert(role='admin')
id_sa_group=db.auth_group.insert(role='user_1')
id_public_group=db.auth_group.insert(role="public")
db.auth_membership.insert(user_id=id_first_user, group_id=id_admin_group)
db.auth_membership.insert(user_id=id_first_user, group_id=id_sa_group)
db.auth_membership.insert(user_id=id_first_user, group_id=id_public_group)
## base Vidjil configs
db.config.insert(
name = 'default + extract reads',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g -e 1 -2 -d -w 50 -U ',
fuse_command = '-t 100',
info = 'Same as the default "multi+inc+xxx" (multi-locus, with some incomplete/unusual/unexpected recombinations), and extract analyzed reads in the "out" temporary directory.'
)
db.config.insert(
name = 'multi+inc+xxx',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g -e 1 -2 -d -w 50 ',
fuse_command = '-t 100',
info = 'multi-locus, with some incomplete/unusual/unexpected recombinations'
)
db.config.insert(
name = 'multi+inc',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g -e 1 -w 50 ',
fuse_command = '-t 100',
info = 'multi-locus, with some incomplete/unusual recombinations'
)
db.config.insert(
name = 'multi',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g:IGH,IGK,IGL,TRA,TRB,TRG,TRD -e 1 -d -w 50 ',
fuse_command = '-t 100',
info = 'multi-locus, only complete recombinations'
)
db.config.insert(
name = 'TRG',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g:TRG ',
fuse_command = '-t 100',
info = 'TRG, VgJg'
)
db.config.insert(
name = 'IGH',
program = 'vidjil',
command = '-c clones -w 60 -d -3 -z 100 -r 1 -g germline/h**o-sapiens.g:IGH ',
fuse_command = '-t 100',
info = 'IGH, Vh(Dh)Jh'
)
## permission
## system admin have admin/read/create rights on all patients, groups and configs
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.run, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.pre_process, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value, db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.run, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin_group.value, db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin_config.value, db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin_pre_process.value, db.pre_process, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.run, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.read_group.value, db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.read_config.value, db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.read_pre_process.value, db.pre_process, 0)
auth.add_permission(id_admin_group, PermissionEnum.create.value, db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.create_group.value, db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.create_config.value, db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.create_pre_process.value, db.pre_process, 0)
auth.add_permission(id_admin_group, 'impersonate', db.auth_user, 0)
auth.add_permission(id_public_group, PermissionEnum.read_config.value, db.config, 0)
for config in db(db.config.id > 0).select():
auth.add_permission(id_public_group, PermissionEnum.access.value, db.config, config.id)
auth.add_permission(id_public_group, PermissionEnum.read_pre_process.value, db.pre_process, 0)
for pre_process in db(db.pre_process.id > 0).select():
auth.add_permission(id_public_group, PermissionEnum.access.value, db.pre_process, pre_process.id)
tags = ['ALL', 'T-ALL', 'B-ALL',
'pre-B-ALL','pro-B-ALL', 'mature-B-ALL',
'CML', 'HCL', 'MZL', 'T-PLL',
'CLL', 'LGL',
'lymphoma',
'MCL', 'NHL', 'HL', 'FL', 'DLBCL',
'WM', 'MAG',
'MM',
'diagnosis', 'MRD', 'relapse', 'CR', 'deceased',
'pre-BMT', 'post-BMT', 'pre-SCT', 'post-SCT',
'dilution', 'standard',
'QC', 'EuroMRD',
'marrow', 'blood',
'repertoire',
'TIL', 'CAR-T', 'scFv',
'FR1', 'FR2', 'FR3',
'TRA', 'TRB', 'TRG', 'TRD',
'IGH', 'IGK', 'KDE', 'IGL',
'IKAROS',
'BCR-ABL', 'TEL-AML1', 'E2A-PBX',
'BCL2',
'PAX5']
for tag in tags:
tid = db.tag.insert(name=tag)
db.group_tag.insert(group_id=id_public_group, tag_id=tid)
os.chdir("/home/www-data/smc/web2py/")
#print os.getcwd()
from gluon.main import save_password
# RUN THIS FROM DOCKER CONTAINER
# TODO - make this pull from preset repository on boot?
# : docker exec -it ope_ope-smc_1 python /home/www-data/web2py/applications/smc/set_admin_password.py
# or: docker exec -it ope_ope-smc_1 /set_admin_password
password = ""
match = False
#if (len(sys.argv) >=2):
# password = sys.argv[1]
while (match != True):
pw = getpass("Please enter new admin password for SMC: ")
pw2 = getpass("Enter password again to confirm: ")
if (pw != pw2):
print "\t\tPasswords don't match, try again!!!!"
else:
match = True
password = pw
password = password.strip()
if (password != ""):
save_password(password, 80)
save_password(password, 443)
def init_db_helper(force=False,
admin_email="*****@*****.**",
admin_password="******"):
if (force) or (db(db.auth_user.id > 0).count() == 0):
#for table in db :
#table.truncate()
id_first_user = ""
## création du premier user
id_first_user = db.auth_user.insert(
password=db.auth_user.password.validate(admin_password)[0],
email=admin_email,
first_name='System',
last_name='Administrator')
# set web2py administration interface password to the same as vidjil admin password
save_password(admin_password, 443)
## création des groupes de base
id_admin_group = db.auth_group.insert(role='admin')
id_sa_group = db.auth_group.insert(role='user_1')
id_public_group = db.auth_group.insert(role="public")
db.auth_membership.insert(user_id=id_first_user,
group_id=id_admin_group)
db.auth_membership.insert(user_id=id_first_user, group_id=id_sa_group)
db.auth_membership.insert(user_id=id_first_user,
group_id=id_public_group)
## base Vidjil configs
db.config.insert(
name='multi+inc+xxx',
program='vidjil',
command=
'-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g -e 1 -2 -d -w 50 ',
fuse_command='-t 100',
info=
'multi-locus, with some incomplete/unusual/unexpected recombinations'
)
db.config.insert(
name='multi+inc',
program='vidjil',
command=
'-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g -e 1 -w 50 ',
fuse_command='-t 100',
info='multi-locus, with some incomplete/unusual recombinations')
db.config.insert(
name='multi',
program='vidjil',
command=
'-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g:IGH,IGK,IGL,TRA,TRB,TRG,TRD -i -e 1 -d -w 50 ',
fuse_command='-t 100',
info='multi-locus, only complete recombinations')
db.config.insert(
name='TRG',
program='vidjil',
command='-c clones -3 -z 100 -r 1 -g germline/h**o-sapiens.g:TRG ',
fuse_command='-t 100',
info='TRG, VgJg')
db.config.insert(
name='IGH',
program='vidjil',
command=
'-c clones -w 60 -d -3 -z 100 -r 1 -g germline/h**o-sapiens.g:IGH ',
fuse_command='-t 100',
info='IGH, Vh(Dh)Jh')
## permission
## system admin have admin/read/create rights on all patients, groups and configs
auth.add_permission(id_admin_group, PermissionEnum.access.value,
db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value,
db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value,
db.run, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value,
db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value,
db.config, 0)
auth.add_permission(id_admin_group, PermissionEnum.access.value,
db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value,
db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value,
db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value,
db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin.value, db.run,
0)
auth.add_permission(id_admin_group, PermissionEnum.admin_group.value,
db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.admin_config.value,
db.config, 0)
auth.add_permission(id_admin_group,
PermissionEnum.admin_pre_process.value,
db.pre_process, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value,
db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value,
db.patient, 0)
auth.add_permission(id_admin_group, PermissionEnum.read.value, db.run,
0)
auth.add_permission(id_admin_group, PermissionEnum.read.value,
db.generic, 0)
auth.add_permission(id_admin_group, PermissionEnum.read_group.value,
db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.read_config.value,
db.config, 0)
auth.add_permission(id_admin_group,
PermissionEnum.read_pre_process.value,
db.pre_process, 0)
auth.add_permission(id_admin_group, PermissionEnum.create.value,
db.sample_set, 0)
auth.add_permission(id_admin_group, PermissionEnum.create_group.value,
db.auth_group, 0)
auth.add_permission(id_admin_group, PermissionEnum.create_config.value,
db.config, 0)
auth.add_permission(id_admin_group,
PermissionEnum.create_pre_process.value,
db.pre_process, 0)
auth.add_permission(id_admin_group, 'impersonate', db.auth_user, 0)
def OnAttachWebserver(self, event):
"start-up a web2py server instance"
# read configuration with safe defaults
cfg = wx.GetApp().get_config("WEB2PY")
path = cfg.get("path", "../web2py")
password = cfg.get("password", "a")
port = cfg.get("port", 8006)
host = "127.0.0.1"
if path:
# store current directory
prevdir = os.path.abspath(os.curdir)
try:
# update current directory and python path to find web2py:
os.chdir(path)
sys.path.insert(0, os.path.abspath(os.curdir))
from gluon.main import wsgibase, save_password
from gluon.contrib import qdb
# store admin password
save_password(password, port)
web2py_env = {} ##self.build_web2py_environment()
# Start a alternate web2py in a separate thread (for blocking requests)
from threading import Thread
def server(host, port, password):
save_password(password, port)
qdb.init(redirect=False)
qdb.qdb.do_debug()
def wrapped_app(environ, start_response):
"WSGI wrapper to allow debugging"
# hanshake with front-end on each request (update ui)
# not realy needed (request processing is sequential)
##qdb.qdb.startup()
# process the request as usual
return wsgibase(environ, start_response)
httpd2 = make_server(host, port, wrapped_app)
print "THREAD - Serving HTTP on port2 %s..." % port
httpd2.serve_forever(poll_interval=0.01)
thread = Thread(target=server, args=(host, port, password))
thread.daemon = True # close on exit
thread.start()
# open internal browser at default page:
url = "http://%s:%s/" % (host, port)
if self.browser:
self.browser.LoadURL(url)
pass
else:
# no internal browser, open external one
try:
import webbrowser
webbrowser.open(url)
except:
print 'warning: unable to detect your browser'
except Exception, e:
self.ShowInfoBar(u"cannot start web2py!: %s" % unicode(e),
flags=wx.ICON_ERROR,
key="web2py")
web2py_env = {}
finally:
os.chdir(application_path)
check_output(['cp', 'handlers/wsgihandler.py', 'wsgihandler.py'])
update_rights('wsgihandler.py', u_name='nginx', g_name=GROUP_NAME, octal_rights=755)
except CalledProcessError as cpe:
exit('An issue occurred, exiting !')
print(SColors.OK_BLUE + 'ok' + SColors.END_C)
# set admin password
try:
print(SColors.BOLD + '\nSet application Admin interface password..' + SColors.END_C, end=' ')
os.chdir(application_path)
sys.path.append(application_path)
# noinspection PyUnresolvedReferences,PyUnresolvedReferences
from gluon.main import save_password
save_password(input(SColors.WARNING + '\n\n\tAdmin Password : '******'\n\nRestarting servers..' + SColors.END_C, end=' ')
try:
def f(host, port, password):
save_password(password, port)
httpd2 = make_server(host, port, wsgibase)
print "THREAD - Serving HTTP on port2 %s..." % port
httpd2.serve_forever()
def __init__(self, path="../web2py", port=8006, password="******"):
"start-up a web2py server instance"
self.menu['run'].Append(ID_ATTACH,
"Attach &webserver\tCtrl-W",
"Connect to remote web2py debugger")
self.Bind(wx.EVT_MENU, self.OnAttachWebserver, id=ID_ATTACH)
# read configuration with safe defaults
cfg = wx.GetApp().get_config("WEB2PY")
path = cfg.get("path", path)
password = cfg.get("password", password)
port = cfg.get("port", port)
host = "127.0.0.1"
if path:
# store current directory
prevdir = os.path.abspath(os.curdir)
try:
os.chdir(path)
sys.path.insert(0, path)
from gluon.main import wsgibase, save_password
# store admin password
save_password(password, port)
# create a wsgi server
self.web2py_httpd = make_server(host, port, wsgibase)
print "Serving HTTP on port %s..." % port
# connect to idle event to poll and serve requests
##self.Bind(wx.EVT_IDLE, self.OnIdleServeWeb2py)
# open internal browser at default page:
url = "http://%s:%s/" % (host, port)
if self.browser:
#self.browser.LoadURL(url)
pass
else:
# no interna browser, open external one
try:
import webbrowser
webbrowser.open(url)
except:
print 'warning: unable to detect your browser'
web2py_env = self.build_web2py_environment()
if False:
# Start a alternate web2py in a separate thread (for blocking requests)
from threading import Thread
def f(host, port, password):
save_password(password, port)
httpd2 = make_server(host, port, wsgibase)
print "THREAD - Serving HTTP on port2 %s..." % port
httpd2.serve_forever()
p = Thread(target=f, args=("127.0.0.1", 8000, password))
p.start()
except Exception, e:
self.ShowInfoBar(u"cannot start web2py!: %s" % unicode(e),
flags=wx.ICON_ERROR, key="web2py")
web2py_env = {}
finally:
def load_configuration(self):
"""
Loads the configuration required to build the command-line string
for running web2py. Returns a tuple (command_args, config_dict).
"""
s = os.path.sep
default = dict(
python='python',
web2py=os.path.join(s.join(__file__.split(s)[:-3]), 'web2py.py'),
http_enabled=True,
http_ip='0.0.0.0',
http_port=8000,
https_enabled=True,
https_ip='0.0.0.0',
https_port=8001,
https_key='',
https_cert='',
password='******',
)
config = default
if self.config_file:
try:
f = open(self.config_file, 'r')
lines = f.readlines()
f.close()
for line in lines:
fields = line.split('=', 1)
if len(fields) == 2:
key, value = fields
key = key.strip()
value = value.strip()
config[key] = value
except:
pass
web2py_path = os.path.dirname(config['web2py'])
os.chdir(web2py_path)
args = [config['python'], config['web2py']]
interfaces = []
ports = []
if config['http_enabled']:
ip = config['http_ip']
port = config['http_port']
interfaces.append('%s:%s' % (ip, port))
ports.append(port)
if config['https_enabled']:
ip = config['https_ip']
port = config['https_port']
key = config['https_key']
cert = config['https_cert']
if key != '' and cert != '':
interfaces.append('%s:%s:%s:%s' % (ip, port, cert, key))
ports.append(ports)
if len(interfaces) == 0:
sys.exit(
'Configuration error. Must have settings for http and/or https'
)
password = config['password']
if not password == '<recycle>':
from gluon import main
for port in ports:
main.save_password(password, port)
password = '******'
args.append('-a "%s"' % password)
interfaces = ';'.join(interfaces)
args.append('--interfaces=%s' % interfaces)
if 'log_filename' in config.key():
log_filename = config['log_filename']
args.append('--log_filename=%s' % log_filename)
return (args, config)
def load_configuration(self):
"""
Loads the configuration required to build the command-line string
for running web2py. Returns a tuple (command_args, config_dict).
"""
s = os.path.sep
default = dict(
python = 'python',
web2py = os.path.join(s.join(__file__.split(s)[:-3]), 'web2py.py'),
http_enabled = True,
http_ip = '0.0.0.0',
http_port = 8000,
https_enabled = True,
https_ip = '0.0.0.0',
https_port = 8001,
https_key = '',
https_cert = '',
password = '******',
)
config = default
if self.config_file:
try:
f = open(self.config_file, 'r')
lines = f.readlines()
f.close()
for line in lines:
fields = line.split('=', 1)
if len(fields) == 2:
key, value = fields
key = key.strip()
value = value.strip()
config[key] = value
except:
pass
web2py_path = os.path.dirname(config['web2py'])
os.chdir(web2py_path)
args = [config['python'], config['web2py']]
interfaces = []
ports = []
if config['http_enabled']:
ip = config['http_ip']
port = config['http_port']
interfaces.append('%s:%s' % (ip, port))
ports.append(port)
if config['https_enabled']:
ip = config['https_ip']
port = config['https_port']
key = config['https_key']
cert = config['https_cert']
if key != '' and cert != '':
interfaces.append('%s:%s:%s:%s' % (ip, port, key, cert))
ports.append(ports)
if len(interfaces) == 0:
sys.exit('Configuration error. Must have settings for http and/or https')
password = config['password']
if not password == '<recycle>':
from gluon import main
for port in ports:
main.save_password(password, port)
password = '******'
args.append('-a "%s"' % password)
interfaces = ';'.join(interfaces)
args.append('--interfaces=%s' % interfaces)
if 'log_filename' in config.keys():
log_filename = config['log_filename']
args.append('--log_filename=%s' % log_filename)
return (args, config)
import os
import sys
import getpass
curr_dir = os.path.dirname(os.path.abspath(__file__))
os.chdir(curr_dir)
from gluon.main import save_password
param_file = os.path.join(curr_dir, "parameters_8000.py")
print(param_file)
if os.path.exists(param_file) is True:
print("PW already set")
sys.exit()
pw = getpass.getpass("Enter w2py admin password: ")
save_password(pw, 8000)
admin_group_id = auth.id_group("Administrators")
row = db(db.auth_user.username == "admin").select().first()
admin_id = row["id"]
auth.add_membership(group_id=admin_group_id, user_id=admin_id)
db.commit()
new_admin = False
# Make sure the admin password is setup if we are in a docker container (presence of IT_PW environment variable)
startup = cache.ram('startup', lambda: True, time_expire=600)
if (startup == True):
# Set password
from gluon.main import save_password
pw = ""
if "IT_PW" in os.environ:
pw = str(os.environ["IT_PW"]) + ""
pw = pw.strip()
if (pw != ""):
# print("Resetting admin password...")
# Set pw for w2p admin login (parameters_??.py file)
save_password(pw, 80)
save_password(pw, 443)
# Set pw for smc admin login (in the database)
db(db.auth_user.username == 'admin').update(
password=db.auth_user.password.validate(pw)[0])
db.commit()
# Set the cache with the new value
cache.ram('startup', lambda: False, 0)
if db_init_needed:
# Mark that we did it so we quit doing it on every page view
cache.ram('db_init_needed', lambda: False, 0)