def add_user(circle=None, circle_id=None, user=None, user_id=None):
if user is None:
user = DBSession.query(User).filter(User.id == user_id).first()
if circle is None:
circle = DBSession.query(Circle).filter(Circle.id == circle_id).first()
circle.users.append(user)
DBSession.flush()
def after_sha1(self, fname, sha1, force, callback_url, track_id, old_task_id, mail, key, sequence_id, extension, trackname):
"""
Called after a sha1 where calculated on a file.
If the sha1 already exist, only the databases operations are done.
Else the input will go in the second part of the process.
The input can be 'forced' to be recomputed
"""
try:
_input = DBSession.query(Input).filter(Input.sha1 == sha1).first()
do_process = True
if util.str2bool(force) and _input is not None:
handler.track.delete_input(_input.sha1)
DBSession.delete(_input)
DBSession.flush()
elif _input is not None:
do_process = False
handler.track.update(track_id=track_id,
params={'new_input_id': _input.id})
handler.track.finalize_track_creation(track_id=track_id)
if do_process:
handler.track.update(track_id=track_id, params={'sha1': sha1})
sequence = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
async = tasks.track_process.delay(mail, key, old_task_id, fname, sha1, callback_url, track_id, sequence.name, extension, trackname, callback_url)
handler.track.update(track_id=track_id,
params={'new_task_id': async.task_id})
return {'success': 'to second process'}
except Exception as e:
etype, value, tb = sys.exc_info()
traceback.print_exception(etype, value, tb)
return {'error': str(e)}
def can_edit_job(user_id, job_id):
user = DBSession.query(User).filter(User.id == user_id).first()
if is_admin(user):
j = DBSession.query(Job).filter(
and_(Job.id == job_id, Job.user_id == user_id)).first()
return j != None
return True
def change_rights(project_id, circle_id, rights=None):
'''
Modify the right associated to a project to a group.
If any right is added, automatically add read right.
@param project_id : the project id
@param circle_id : the circle id
@param rights : the right to update
'''
project = DBSession.query(Project).filter(Project.id == project_id).first()
rc_assocs = get_circle_right_assocs(circle_id, project_id)
for rc in rc_assocs:
if rc.circle.id == int(circle_id):
project._circle_right.remove(rc)
DBSession.delete(rc)
DBSession.flush()
if rights is not None:
_add_read_right(project, circle_id)
for right_name in rights:
if right_name != constants.right_read:
right = DBSession.query(Right).filter(
Right.name == right_name).first()
cr_assoc = _get_circle_right_assoc(right, circle_id,
project_id)
project._circle_right.append(cr_assoc)
DBSession.add(project)
DBSession.flush()
def change_rights(project_id, circle_id, rights=None):
'''
Modify the right associated to a project to a group.
If any right is added, automatically add read right.
@param project_id : the project id
@param circle_id : the circle id
@param rights : the right to update
'''
project = DBSession.query(Project).filter(Project.id == project_id).first()
rc_assocs = get_circle_right_assocs(circle_id, project_id)
for rc in rc_assocs:
if rc.circle.id == int(circle_id) :
project._circle_right.remove(rc)
DBSession.delete(rc)
DBSession.flush()
if rights is not None:
_add_read_right(project, circle_id)
for right_name in rights:
if right_name != constants.right_read :
right = DBSession.query(Right).filter(Right.name == right_name).first()
cr_assoc = _get_circle_right_assoc(right, circle_id, project_id)
project._circle_right.append(cr_assoc)
DBSession.add(project)
DBSession.flush()
def edit(self, *args, **kw):
user = handler.user.get_user_in_session(request)
if request.method == 'GET':
project_id = args[0]
else:
project_id = kw.get('pid')
debug("check permission", 1)
if not checker.check_permission(user=user, project_id=project_id, right_id=constants.right_upload_id) and not checker.is_admin(user=user):
flash('You must have %s permission to edit the project.' % constants.right_upload, 'error')
raise redirect('/tracks/', {'pid': project_id})
#if checker.is_admin(user=user):
#user = DBSession.query(User).join(Project).filter(Project.id == project_id).first()
widget = form.EditProject(action=url('/projects/edit/%s' % project_id)).req()
widget.value = {'pid': project_id}
project = DBSession.query(Project).filter(Project.id == project_id).first()
# prendre les user tracks du meme sequence id
tracks = DBSession.query(Track).join(User.tracks).filter(
and_(User.id == user.id, Track.sequence_id == project.sequence_id,
not_(Track.id.in_([t.id for t in project.tracks])))
).all()
# prendre les sared tracks du meme sequence id
shared_tracks = handler.user.shared_tracks(user.id, constants.rights['download']['id'])
shared_tracks = [t for t in shared_tracks if (t.sequence_id == project.sequence_id and t.id not in [tr.id for tr in project.tracks])]
tracks.extend(shared_tracks)
if request.method == 'GET':
debug("GET", 2)
widget.child.children[1].value = project.name
widget.child.children[2].options = [('', '')] + [(t.id, t.name) for t in tracks] + [(t.id, t.name, {'selected': True}) for t in project.tracks]
return dict(page='tracks', widget=widget, project_id=project_id)
debug("POST", 2)
try:
debug("validate post", 2)
widget.validate(kw)
except twc.ValidationError as e:
debug("error", 2)
w = e.widget
w.child.children[1].value = project.name
w.child.children[2].options = [(t.id, t.name) for t in tracks] + [(t.id, t.name, {'selected': True}) for t in project.tracks]
return dict(page='tracks', widget=w, project_id=project_id)
debug("validation passed")
track_ids = kw.get('tracks', [])
if not track_ids:
track_ids = []
if not isinstance(track_ids, list):
track_ids = [track_ids]
if len(track_ids) > 0 and '' in track_ids:
track_ids.remove('')
# if the project is shared, some track cannot be removed
for t in project.tracks:
if not checker.user_own_track(user.id, track=t) and t.id not in track_ids and t.id in [s.id for s in shared_tracks]:
track_ids.append(t.id)
handler.project.e(project_id=project_id, name=kw.get('name'), track_ids=track_ids)
raise redirect('/tracks/', {'pid': project_id})
def delete_user(self, user_id, sequence_id):
user = handler.user.get_user_in_session(request)
s = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
u = DBSession.query(User).filter(User.id == user_id).first()
s.users.remove(u)
DBSession.flush()
raise redirect('/sequences/edit/%s' % sequence_id)
def delete_track(self, sequence_id, track_id):
user = handler.user.get_user_in_session(request)
s = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
t = DBSession.query(Track).filter(Track.id == track_id).first()
s.default_tracks.remove(t)
DBSession.flush()
raise redirect('/sequences/edit/%s' % sequence_id)
def e(project=None, project_id=None, name=None, track_ids=None, circle_ids=None):
if project is None:
project = DBSession.query(Project).filter(Project.id == project_id).first()
if name is not None:
project.name = name
if track_ids is not None:
project.tracks = []
for tid in track_ids:
t = DBSession.query(Track).filter(Track.id == tid).first()
project.tracks.append(t)
if circle_ids is not None:
if not isinstance(circle_ids, list):
circle_ids = [circle_ids]
circle_ids = [int(i) for i in circle_ids]
to_del = []
for shared in project._circle_right:
if shared.circle.id not in circle_ids:
to_del.append(shared)
for d in to_del:
DBSession.delete(d)
project._circle_right.remove(d)
DBSession.flush()
shared_ids = [c.id for c in project.shared_circles]
read_right = DBSession.query(Right).filter(Right.id == constants.rights['read']['id']).first()
for new_id in circle_ids:
if new_id not in shared_ids:
add_right(project=project, circle_id=new_id, right=read_right)
DBSession.flush()
DBSession.add(project)
DBSession.flush()
return project
def get(self, project_key=None, project_id=None, **kw):
# get all user projects
if not project_key and not project_id:
user = handler.user.get_user_in_session(request)
projects = DBSession.query(Project).filter(
Project.user_id == user.id).all()
return reply.normal(request,
'You can upload track on these projects',
'/tracks', {'projects': projects})
project = None
# get one specific user project
if project_id is not None and project_id:
user = handler.user.get_user_in_session(request)
project = DBSession.query(Project).filter(
Project.id == int(project_id)).first()
if project is not None and not project.user_id == user.id:
reply.error(request, 'Not your project', '/tracks', {})
return reply.normal(request,
'You can upload track on this project',
'/tracks', {'project': project})
# get a project by it's key
project = DBSession.query(Project).filter(
Project.key == project_key).first()
if project is None:
return reply.error(request, 'Wrong key', '/tracks', {})
return reply.normal(request, 'You can upload track on this project',
'/tracks', {'project': project})
def validation(*args, **kw):
for arg in args_list:
if arg not in kw:
raise Exception('Missing args for the validation %s' % kw)
user = DBSession.query(User).filter(
User.email == str(kw['mail'])).first()
if user.key != str(kw['key']):
raise Exception('User not valid %s' % kw)
project = DBSession.query(Project).filter(
Project.id == int(kw['pid'])).first()
if project.key != str(kw['pkey']):
raise Exception('Project not valid %s' % kw)
job = Job()
job.user_id = user.id
job.project_id = project.id
job.status = 'PENDING'
job.ext_task_id = kw['task_id']
job.bioscript_url = handler.job.task_url(kw['task_id'])
if 'plugin_info' in kw:
info = json.loads(kw['plugin_info'])
job.name = info['title']
job.description = info['description']
else:
job.name = 'Job %s from bioscript' % kw['task_id']
job.description = 'Description available at %s' % handler.job.task_url(
kw['task_id'])
DBSession.add(job)
DBSession.flush()
return {}
def validation(*args, **kw):
for arg in args_list:
if arg not in kw:
raise Exception('Missing args for the validation %s' % kw)
user = DBSession.query(User).filter(User.email == str(kw['mail'])).first()
if user.key != str(kw['key']):
raise Exception('User not valid %s' % kw)
project = DBSession.query(Project).filter(Project.id == int(kw['pid'])).first()
if project.key != str(kw['pkey']):
raise Exception('Project not valid %s' % kw)
job = Job()
job.user_id = user.id
job.project_id = project.id
job.status = 'PENDING'
job.ext_task_id = kw['task_id']
job.bioscript_url = handler.job.task_url(kw['task_id'])
if 'plugin_info' in kw:
info = json.loads(kw['plugin_info'])
job.name = info['title']
job.description = info['description']
else:
job.name = 'Job %s from bioscript' % kw['task_id']
job.description = 'Description available at %s' % handler.job.task_url(kw['task_id'])
DBSession.add(job)
DBSession.flush()
return {}
def admin(self, **kw):
# view on a specific project
grid = datagrid.track_admin_grid
if kw.has_key('pid'):
project_id = kw.get('pid')
project = DBSession.query(Project).filter(Project.id == project_id).first()
tracks = project.tracks
kw['upload'] = True
kw['pn'] = project.name
track_list = [util.to_datagrid(grid, tracks, "Track Listing", len(tracks)>0)]
else:
if 'user_id' in kw:
tracks = DBSession.query(Track).filter(Track.user_id == kw['user_id']).all()
else:
tracks = DBSession.query(Track).all()
track_list = [util.to_datagrid(grid, tracks, "Track Listing", len(tracks)>0)]
kw['upload'] = True
# track list
t = handler.help.tooltip['admin']
# project list
all_projects = DBSession.query(Project).all()
project_list = [(p.id, p.name,) for p in all_projects]
return dict(page='tracks', model='track', form_title="new track", track_list=track_list,
project_list=project_list, shared_project_list=[], value=kw,
tooltip=t, project_id=kw.get('pid', None), upload=kw.get('upload', None), project_name=kw.get('pn', None))
def delete_track(self, sequence_id, track_id):
user = handler.user.get_user_in_session(request)
s = DBSession.query(Sequence).filter(
Sequence.id == sequence_id).first()
t = DBSession.query(Track).filter(Track.id == track_id).first()
s.default_tracks.remove(t)
DBSession.flush()
raise redirect('/sequences/edit/%s' % sequence_id)
def delete_user(self, user_id, sequence_id):
user = handler.user.get_user_in_session(request)
s = DBSession.query(Sequence).filter(
Sequence.id == sequence_id).first()
u = DBSession.query(User).filter(User.id == user_id).first()
s.users.remove(u)
DBSession.flush()
raise redirect('/sequences/edit/%s' % sequence_id)
def edit(self, *args, **kw):
user = handler.user.get_user_in_session(request)
# get circle id
if request.method == 'GET':
sequence_id = args[0]
else :
sequence_id = kw.get('cid')
sequence_id=int(sequence_id)
sequence = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
if not sequence:
abort(404, 'Sequence with id %s not found' % sequence_id)
if not sequence.public:
add_user_widget = form.AddUser(action=url('/sequences/edit/%s' % sequence_id)).req()
if request.method == 'POST':
# add an user
mail = kw.get('mail')
try:
add_user_widget.validate({'cid' : sequence_id, 'mail' : mail})
except twc.ValidationError as e:
users = ', '.join(['%s' % u.email for u in sequence.users])
default_tracks = ', '.join(['%s' % t.name for t in sequence.default_tracks])
kw['cid'] = sequence_id
users = sequence.users
for u in users:
u.__dict__['sid'] = sequence_id
widget = e.widget
widget.value = kw
return dict(page='sequences', users=users, add_user=add_user, add_user_widget=add_user_widget, default_tracks=default_tracks, au_error=True, seq_id=sequence_id)
to_add = DBSession.query(User).filter(User.email == mail).first()
if to_add is None:
to_add = handler.user.create_tmp_user(mail)
sequence.users.append(to_add)
DBSession.flush()
kw['cid'] = sequence_id
add_user_widget.value = kw
else:
add_user_widget = None
users = sequence.users
for u in users:
u.__dict__['sid'] = sequence_id
tracks = sequence.default_tracks
for t in tracks:
t.__dict__['sid'] = sequence_id
add_user = util.to_datagrid(datagrid.sequence_user_grid, users, "Users", len(users)>0)
def_tracks = util.to_datagrid(datagrid.sequence_default_tracks, tracks, "Default tracks", len(tracks)>0)
return dict(page='sequences', users=users, add_user=add_user, add_user_widget=add_user_widget, default_tracks=def_tracks, au_error=False, seq_id=sequence_id)
def get_permissions(admin):
'''
Get the right permissions for an user.
@param admin : True if the user is an admin.
@type admin : a boolean.
'''
if admin :
return DBSession.query(Permission).all()
return DBSession.query(Permission).filter(Permission.name != 'admin').all()
def get_permissions(admin):
'''
Get the right permissions for an user.
@param admin : True if the user is an admin.
@type admin : a boolean.
'''
if admin:
return DBSession.query(Permission).all()
return DBSession.query(Permission).filter(Permission.name != 'admin').all()
def delete_user(self, id, user_id):
user = handler.user.get_user_in_session(request)
if not checker.user_own_circle(user.id, id):
flash('you have no rights to delete users from this circle: you are not the creator of it')
raise redirect('/circles')
circle = DBSession.query(Circle).filter(Circle.id == id).first()
to_delete = DBSession.query(User).filter(User.id == user_id).first()
circle.users.remove(to_delete)
DBSession.flush()
raise redirect('/circles/edit/%s' % id)
def add_right(project=None, project_id=None, circle=None, circle_id=None, right=None, right_id=None):
if project is None:
project = DBSession.query(Project).filter(Project.id == project_id).first()
if circle_id is None:
circle_id = circle.id
if right is None:
right = DBSession.query(Right).filter(Right.id == right_id).first()
cr_assoc = _get_circle_right_assoc(right, circle_id, project.id)
project._circle_right.append(cr_assoc)
def index(self, came_from='/'):
'''
Redirect user on tequila page in order to log him
'''
if tg.config.get('authentication.disable').lower() in ['t', 'true']:
print constants.admin_user_email()
environ = request.environ
authentication_plugins = environ['repoze.who.plugins']
identifier = authentication_plugins['ticket']
secret = identifier.secret
cookiename = identifier.cookie_name
remote_addr = environ['REMOTE_ADDR']
user = DBSession.query(User).filter(
User.email == constants.admin_user_email()).first()
admins = tg.config.get('admin.mails')
group_admins = DBSession.query(Group).filter(
Group.id == constants.group_admins_id).first()
if user.email in admins:
user not in group_admins.users and group_admins.users.append(
user)
else:
user in group_admins.users and group_admins.users.remove(user)
DBSession.flush()
userdata = "%s|%s" % (user.id, user in group_admins.users)
ticket = auth_tkt.AuthTicket(secret,
user.email,
remote_addr,
tokens=token,
user_data=userdata,
time=None,
cookie_name=cookiename,
secure=True)
val = ticket.cookie_value()
# set it in the cookies
response.set_cookie(cookiename,
value=val,
max_age=None,
path='/',
domain=None,
secure=False,
httponly=False,
comment=None,
expires=None,
overwrite=False)
raise redirect(came_from)
u = resolve_relative_url(url(), request.environ)
res = tequila.create_request(u + '/login/auth', 'tequila.epfl.ch')
raise redirect(
'https://tequila.epfl.ch/cgi-bin/tequila/requestauth?request' +
res)
def user_own_circle(user_id, circle_id):
'''
Look if the user own the circle.
'''
circle = DBSession.query(Circle).filter(Circle.id == circle_id).first()
if circle.creator_id == user_id:
return True
if circle.admin:
user = DBSession.query(User).filter(User.id == user_id).first()
admin_group = DBSession.query(Group).filter(Group.name == constants.group_admins).first()
return user in admin_group.users
return False
def save(self, project_id, color, description, locations):
user = handler.user.get_user_in_session(request)
if not checker.check_permission(user=user,
project_id=project_id,
right_id=constants.right_upload_id):
flash(
'You must have %s permission to delete the project.' %
constants.right_upload, 'error')
return {'save': 'failed'}
#print "save %s, color %s, desc %s loc %s" % (project_id, color, description, locations)
''' For the moment, there is only one selection per project'''
sel = DBSession.query(Selection).filter(
Selection.project_id == project_id).first()
if sel is None:
sel = Selection()
sel.project_id = project_id
sel.description = description
sel.color = color
DBSession.add(sel)
DBSession.flush()
locations_ids = []
# add locations
for loc in json.loads(locations):
obj = None
if 'id' in loc:
obj = DBSession.query(Location).join(
Selection.locations).filter(
and_(Selection.id == sel.id,
Location.id == loc.get('id'))).first()
if obj is None:
obj = Location()
obj.chromosome = loc.get('chr')
obj.start = loc.get('start')
obj.end = loc.get('end')
obj.description = loc.get('desc', 'No description')
obj.selection = sel
DBSession.add(obj)
DBSession.flush()
locations_ids.append(obj.id)
# remove not saved ones
loc_to_remove = DBSession.query(Location).filter(
not_(Location.id.in_(locations_ids))).all()
for l in loc_to_remove:
DBSession.delete(l)
DBSession.flush()
return {"saved": "ok"}
def user_own_circle(user_id, circle_id):
'''
Look if the user own the circle.
'''
circle = DBSession.query(Circle).filter(Circle.id == circle_id).first()
if circle.creator_id == user_id:
return True
if circle.admin:
user = DBSession.query(User).filter(User.id == user_id).first()
admin_group = DBSession.query(Group).filter(
Group.name == constants.group_admins).first()
return user in admin_group.users
return False
def link(self, track_id, *args, **kw):
user = handler.user.get_user_in_session(request)
trac = DBSession.query(Track).filter(Track.id == track_id).first()
if not checker.can_download(user, trac):
flash("You haven't the right to download any tracks which is not yours", 'error')
raise redirect('/tracks/')
track = DBSession.query(Track).filter(Track.id == track_id).first()
if track.status == constants.ERROR:
flash("The track processing failed. You cannot download it.", 'error')
raise redirect('/tracks/')
response.content_type = 'application/x-sqlite3'
response.headerlist.append(('Content-Disposition', 'attachment;filename=%s.sqlite' % track.name))
return open(track.path).read()
def get_rights(project=None, project_id=None, user=None, user_id=None):
if project is None:
project = DBSession.query(Project).filter(Project.id == project_id).first()
if user is None:
user = DBSession.query(User).filter(User.id == user_id).first()
debug('get rights %s' % project.get_circle_with_right_display)
r = []
for circle, rights in project.circles_with_rights.iteritems():
debug('circle %s with rights %s' % (circle, rights), 1)
if circle in user.circles:
r.extend(rights)
return r
def edit(self, *args, **kw):
user = handler.user.get_user_in_session(request)
t = handler.help.tooltip['circledesc']
# get circle id
if request.method == 'GET':
circle_id = args[0]
else:
circle_id = kw.get('cid')
circle_id = int(circle_id)
if circle_id not in [c.id for c in user.circles_owned]:
flash('You have no right to edit this circle', 'error')
raise redirect('/circles/')
circle = DBSession.query(Circle).filter(Circle.id == circle_id).first()
widget = form.AddUser(action=url('/circles/edit/%s' % circle_id)).req()
if request.method == 'POST':
# add user
mail = kw.get('mail')
try:
widget.validate({'cid': circle_id, 'mail': mail})
except twc.ValidationError as e:
for u in circle.users:
u.__dict__['cid'] = circle_id
wrappers = [u for u in circle.users if u.id != user.id]
data = [util.to_datagrid(datagrid.circle_description_grid, wrappers, grid_display=len(wrappers) > 0)]
return dict(page='circles', name=circle.name, widget=e.widget, items=data, value=kw, tooltip=t, au_error=True)
mail = mail.lower()
to_add = DBSession.query(User).filter(User.email == mail).first()
if to_add is None:
to_add = handler.user.create_tmp_user(mail)
handler.circle.add_user(circle_id=circle_id, user=to_add)
# build common parameters
if not checker.user_own_circle(user.id, circle_id):
flash('you have no right to edit this circle: you are not the creator of it')
raise redirect('/circles')
for u in circle.users:
u.__dict__['cid'] = circle_id
wrappers = [u for u in circle.users if u.id != user.id]
data = [util.to_datagrid(datagrid.circle_description_grid, wrappers, grid_display=len(wrappers) > 0)]
kw['cid'] = circle_id
widget.value = kw
return dict(page='circles', name=circle.name, widget=widget, items=data, tooltip=t)
def callback(self, *args, **kw):
print kw
job = DBSession.query(Job).filter(Job.ext_task_id == kw['task_id']).first()
project = DBSession.query(Project).filter(Project.id == int(kw['pid'])).first()
if project is None or project.key != str(kw['pkey']):
raise Exception('Project not valid')
if job.project_id != project.id:
raise Exception('Job not valid')
status = str(kw['status'])
job.status = status
if status.lower() in ['error', 'failed']:
job.traceback = kw['error']
elif status == 'SUCCESS':
results = json.loads(kw['results'])
for result in results:
bres = Bresults()
bres.job_id = job.id
bres.output_type = str(result.get('type', 'not defined'))
bres.is_file = result.get('is_file', False)
path = str(result.get('path', ''))
bres.path = path
bres.data = str(result.get('value', ''))
is_track = result.get('type', '') == 'track'
if is_track:
out = os.path.join(filemanager.temporary_directory(), os.path.split(path)[-1])
fileinfo = filemanager.FileInfo(inputtype='fsys', inpath=path, outpath=out, admin=False)
sequence = project.sequence
user = DBSession.query(User).filter(User.key == str(kw['key'])).first()
if user.email != str(kw['mail']):
raise Exception("Wrong user")
user_info = {'id': user.id, 'name': user.name, 'email': user.email}
sequence_info = {'id': sequence.id, 'name': sequence.name}
t = Track()
t.name = fileinfo.trackname
t.sequence_id = sequence.id
t.user_id = user.id
DBSession.add(t)
DBSession.flush()
async = tasks.new_input.delay(user_info, fileinfo, sequence_info, t.id, project.id)
t.task_id = async.task_id
bres.track_id = t.id
bres.is_track = is_track
DBSession.add(bres)
DBSession.flush()
return {}
def get_rights(project=None, project_id=None, user=None, user_id=None):
if project is None:
project = DBSession.query(Project).filter(
Project.id == project_id).first()
if user is None:
user = DBSession.query(User).filter(User.id == user_id).first()
debug('get rights %s' % project.get_circle_with_right_display)
r = []
for circle, rights in project.circles_with_rights.iteritems():
debug('circle %s with rights %s' % (circle, rights), 1)
if circle in user.circles:
r.extend(rights)
return r
def get_tequila_circle(name):
'''
Get the Circle created by Tequila with the specified name
@param name : the name
'''
return DBSession.query(Circle).filter(
and_(Circle.admin == True, Circle.name == name)).first()
def edit(project, name, user_id, sequence_id=None, tracks=None, isPublic=False, circles=None):
'''
Like create but edit an existing project.
'''
project.name=name
if sequence_id is not None:
project.sequence_id = sequence_id
project.user_id = user_id
project.is_public = isPublic
DBSession.add(project)
DBSession.flush()
project.tracks = []
if tracks is not None:
for track_id in tracks :
t = DBSession.query(Track).filter(Track.id == track_id).first()
project.tracks.append(t)
if circles is not None: # adding circle with the read permission by default
project._circle_right = []
for circle in circles : _add_read_right(project, circle.id)
DBSession.add(project)
DBSession.flush()
return project
def get_user(key, mail):
'''
Get the user with the the given mail,
with the given key.
'''
user = DBSession.query(User).filter(and_(User.email == mail, User.key == key)).first()
return user
def edit(self, track_id, **kw):
user = handler.user.get_user_in_session(request)
if track_id is not None:
if not checker.can_edit_track(user, track_id):
flash("You haven't the right to edit any tracks which is not yours", 'error')
raise redirect('/tracks')
widget = form.EditTrack(action=url('/tracks/edit/%s' % track_id)).req()
track = DBSession.query(Track).filter(Track.id == track_id).first()
d = {}
d['name'] = track.name
if track.parameters is None or not 'color' in track.parameters:
cc = constants.default_track_color
else:
cc = track.parameters['color']
d['track_id'] = track_id
d['color'] = cc
if 'pid' in kw:
d['pid'] = kw['pid']
widget.value = d
if request.method == 'GET':
return dict(title='Edit track', page='track', widget=widget, color=cc)
if request.method == 'POST':
try:
widget.validate(kw)
except twc.ValidationError as e:
return dict(title='Edit track', page='track', widget=e.widget, color=cc)
handler.track.edit(track=track, name=kw.get('name', None), color=kw.get('color', None))
raise redirect('/tracks', {'pid': kw.get('pid', None)})
def get(self, *args, **kw):
bsurl = handler.job.bioscript_url
bsrequesturl = bsurl + '/plugins/fetch?oid=' + kw['oid']
user = handler.user.get_user_in_session(request)
project = DBSession.query(Project).filter(Project.id == kw['pid']).first()
# add private parameters
pp = {"key": user.key, "mail": user.email, "pid": project.id, "pkey": project.key}
# add prefill parameters
tracks = list(project.tracks)
selections = list(project.selections)
gtrack = [(json.dumps({'p':handler.track.plugin_link(t), 'n':os.path.split(handler.track.plugin_link(t))[-1]}), t.name) for t in tracks]
if len(selections) > 0:
s = selections[0]
if len(s.locations) > 0:
gtrack.append((handler.track.plugin_link(s, selection_id=s.id), 'selection'))
prefill = {'track': gtrack}
# prepare parameters
parameters = {
'key': handler.job.shared_key,
'bs_private': json.dumps({
'app': pp,
'cfg': handler.job.bioscript_config,
'prefill': prefill
})
}
# TODO fetch tracks & selections
req = urllib2.urlopen(url=bsrequesturl, data=urllib.urlencode(parameters))
# display the form in template
response.headerlist.append(('Access-Control-Allow-Origin', '*'))
data = req.read()
return data
def search(self, project_id, term, *args, **kw):
project = DBSession.query(Project).filter(Project.id == project_id).first()
sequence = project.sequence
default = sequence.default_tracks
if default is None or len(default) < 1:
return {}
t = default[0]
chrs = {}
with track.load(t.path, 'sql', readonly=True) as t:
gene_name_alias = t.find_column_name(['name', 'gene_name', 'gene name', 'gname', 'Name', 'product'])
try:
for row in t.search({gene_name_alias: term}, [gene_name_alias, 'start', 'end']):
chr, name, start, stop = row
if chr not in chrs:
chrs[chr] = {}
names = chrs[chr]
if name in names:
old = names[name]
start = min(old[0], start)
stop = max(old[1], stop)
names[name] = [start, stop]
except Exception:
return {}
#result[chr].append([name, start, stop])
result = {}
for chr, names in chrs.iteritems():
result[chr] = []
for k, v in names.iteritems():
result[chr].append([k, v[0], v[1]])
return result
def add_right(project=None,
project_id=None,
circle=None,
circle_id=None,
right=None,
right_id=None):
if project is None:
project = DBSession.query(Project).filter(
Project.id == project_id).first()
if circle_id is None:
circle_id = circle.id
if right is None:
right = DBSession.query(Right).filter(Right.id == right_id).first()
cr_assoc = _get_circle_right_assoc(right, circle_id, project.id)
project._circle_right.append(cr_assoc)
def edit(project,
name,
user_id,
sequence_id=None,
tracks=None,
isPublic=False,
circles=None):
'''
Like create but edit an existing project.
'''
project.name = name
if sequence_id is not None:
project.sequence_id = sequence_id
project.user_id = user_id
project.is_public = isPublic
DBSession.add(project)
DBSession.flush()
project.tracks = []
if tracks is not None:
for track_id in tracks:
t = DBSession.query(Track).filter(Track.id == track_id).first()
project.tracks.append(t)
if circles is not None: # adding circle with the read permission by default
project._circle_right = []
for circle in circles:
_add_read_right(project, circle.id)
DBSession.add(project)
DBSession.flush()
return project
def _add_read_right(project, circle_id):
'''
Add the ``read`` right to the project % circle specified without flushing
'''
read_right = DBSession.query(Right).filter(Right.name == constants.right_read).first()
cr_assoc = _get_circle_right_assoc(read_right, circle_id, project.id)
project._circle_right.append(cr_assoc)
def new_selection(self, project_id, s, job_name, job_description, *args, **kw):
'''
Called by the browser. Transform a selection to a new track;
'''
user = handler.user.get_user_in_session(request)
sels = json.loads(s)
project = DBSession.query(Project).filter(Project.id == project_id).first()
if project is None :
return {'error' : "project id %s doesn't exist" % project_id}
path = track.common.temporary_path()
with track.new(path, 'sql') as t:
t.fields = simple_fields
for chromosome in sels:
t.write(chromosome, ((marquee['start'], marquee['end'], 0, '', 0 , '') for marquee in sels[chromosome]))
t.datatype = constants.FEATURES
t.assembly = project.sequence.name
task_id, track_id = handler.track.create_track(user.id, project.sequence, f=path, trackname='%s %s'
% (job_name, job_description), project=project)
if task_id == constants.NOT_SUPPORTED_DATATYPE :
return {'error' : "not supported datatype" % project_id}
job_id = handler.job.new_sel(user.id, project.id, job_description, job_name, task_id=task_id)
return {'job_id' : job_id,
'job_name' : job_name,
'job_description' : job_description,
'status' : 'RUNNING'}
def remove_sharing(project=None, project_id=None):
if project is None:
project = DBSession.query(Project).filter(
Project.id == project_id).first()
for rc in project._circle_right:
DBSession.delete(rc)
DBSession.flush()
def add_new_sequence(sequence):
'''
Method called when a new sequence is created on GDV.
It should import fast from JBrowse
'''
print 'add new sequence'
file_url = Assembly(sequence).get_sqlite_url()
print file_url
out = os.path.join(filemanager.temporary_directory(), 'Genes.sql')
fileinfo = filemanager.FileInfo(inputtype='url',
inpath=file_url, trackname='Genes', extension='sql', outpath=out, admin=True)
print fileinfo
user = DBSession.query(User).filter(User.key == constants.admin_user_key()).first()
user_info = {'id': user.id, 'name': user.name, 'email': user.email}
sequence_info = {'id': sequence.id, 'name': sequence.name}
# track
t = Track()
t.name = fileinfo.trackname
t.sequence_id = sequence.id
t.user_id = user.id
DBSession.add(t)
DBSession.flush()
# send task
async = tasks.new_input.delay(user_info, fileinfo, sequence_info, t.id)
t.task_id = async.task_id
DBSession.add(t)
sequence.default_tracks.append(t)
DBSession.add(sequence)
DBSession.flush()
def delete(project=None, project_id=None):
if project is None:
project = DBSession.query(Project).filter(
Project.id == project_id).first()
remove_sharing(project=project)
DBSession.delete(project)
DBSession.flush()
def get(self, selection_id):
sel = DBSession.query(Selection).filter(
Selection.id == selection_id).first()
b = ''
for loc in sel.locations:
b += '%s\t%s\t%s' % (loc.chromosome, loc.start, loc.end)
return b
def get_user(key, mail):
'''
Get the user with the the given mail,
with the given key.
'''
user = DBSession.query(User).filter(
and_(User.email == mail, User.key == key)).first()
return user
def get_circle_right_assocs(circle_id, project_id):
'''
Get the ``RightCircleAssociation`` corresponding
to the circle_id & project_id given
'''
return DBSession.query(RightCircleAssociation).filter(
and_(RightCircleAssociation.circle_id == circle_id,
RightCircleAssociation.project_id == project_id)).all()
def _add_read_right(project, circle_id):
'''
Add the ``read`` right to the project % circle specified without flushing
'''
read_right = DBSession.query(Right).filter(
Right.name == constants.right_read).first()
cr_assoc = _get_circle_right_assoc(read_right, circle_id, project.id)
project._circle_right.append(cr_assoc)
def delete(self, _id):
user = handler.user.get_user_in_session(request)
if not checker.can_edit_job(user.id, _id):
return {'error': "You have don't have the right to delete this job"}
job = DBSession.query(Job).filter(Job.id == _id).first()
# TODO delete results (DB + filesystem)
DBSession.delete(job)
raise redirect('/jobs')
def get_circle_right_assocs(circle_id, project_id):
'''
Get the ``RightCircleAssociation`` corresponding
to the circle_id & project_id given
'''
return DBSession.query(RightCircleAssociation).filter(
and_(RightCircleAssociation.circle_id == circle_id,
RightCircleAssociation.project_id == project_id)).all()
def status(self, job_id, *args, **kw):
try :
job_id = int(job_id)
job = DBSession.query(Job).filter(Job.id == job_id).first()
return {'job_id' : job.id, 'status' : job.status, 'output' : job.output, 'error' : job.traceback}
except ValueError:
pass
return {}
def add_tracks(project, track_ids):
'''
Add a list of track to the project specified.
'''
for track_id in track_ids:
track_ = DBSession.query(Track).filter(Track.id == track_id).first()
project.tracks.append(track_)
DBSession.add(project)
DBSession.flush()
def copy(user_id, project_id):
project = DBSession.query(Project).filter(Project.id == project_id).first()
ts = []
for to_copy in project.tracks:
ts.append(track.copy_track(user_id, to_copy))
create('copied ' + project.name,
project.sequence_id,
user_id,
tracks=[t.id for t in ts])
def add_tracks(project, track_ids):
'''
Add a list of track to the project specified.
'''
for track_id in track_ids:
track_ = DBSession.query(Track).filter(Track.id == track_id).first()
project.tracks.append(track_)
DBSession.add(project)
DBSession.flush()
def copy(self, track_id):
user = handler.user.get_user_in_session(request)
if not checker.can_download_track(user.id, track_id):
return reply.error(request, 'You have no right to copy this track in your profile.', './', {})
t = DBSession.query(Track).filter(Track.id == track_id).first()
if not t:
return reply.error(request, 'No track with this id.', './', {})
handler.track.copy_track(user.id, t)
return reply.normal(request, 'Copy successfull', './', {})
def new(self, *args, **kw):
new_form = form.NewProject(action=url('/projects/create')).req()
species = DBSession.query(Species).all()
sp_opts = [(sp.id, sp.name) for sp in species]
new_form.child.children[2].options = sp_opts
mapping = json.dumps(dict([(sp.id, [(seq.id, seq.name) for seq in sp.sequences
if seq.public or handler.genrep.checkright(seq, user)]) for sp in species]))
new_form.value = {'smapping': mapping}
return dict(page='projects', widget=new_form)