def result(self, id):
res = DBSession.query(Bresults).filter(Bresults.id == id).first()
checker.check_permission(user=handler.user.get_user_in_session(request),
project=res.job.project, right_id=constants.right_download_id)
if res.rtype in constants.track_types:
raise redirect(url('/tracks/links/%s' % res.track_id))
src = constants.extra_url() + '/' + res.rpath
return dict(page='jobs', model='Job', src=src)
def result(self, id):
res = DBSession.query(Bresults).filter(Bresults.id == id).first()
checker.check_permission(
user=handler.user.get_user_in_session(request),
project=res.job.project,
right_id=constants.right_download_id)
if res.rtype in constants.track_types:
raise redirect(url('/tracks/links/%s' % res.track_id))
src = constants.extra_url() + '/' + res.rpath
return dict(page='jobs', model='Job', src=src)
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 view(self, project_id, *args, **kw):
debug('VIEW')
user = handler.user.get_user_in_session(request)
if not checker.check_permission(project_id=project_id, user=user, right_id=constants.rights['read']['id']):
flash('You must have %s permission to view the project.' % constants.right_read, 'error')
raise redirect(url('/'))
d = handler.view.prepare_view(project_id, *args, **kw)
response.headerlist.append(('Access-Control-Allow-Origin', '*'))
return d
def delete(self, *args, **kw):
user = handler.user.get_user_in_session(request)
if len(args) > 0:
project_id = args[0]
if not checker.check_permission(user=user, project_id=project_id, right_id=constants.right_upload_id) and not checker.is_admin(user=user):
return reply.error(request, "You must have %s permission to delete the project." % constants.right_upload,
'/tracks', {'error': 'wrong credentials'})
handler.project.delete(project_id=project_id)
return reply.normal(request, 'Project successfully deleted.', '/tracks', {'success': 'project deleted'})
def delete(self, project_id, selection_id):
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 {'delete': 'failed'}
selection = DBSession.query(Selection).filter(Selection.id == selection_id).first()
if not selection.project_id == project_id:
flash('Bad project_id: %s' % project_id, 'error')
return {'delete': 'failed'}
DBSession.delete(selection)
DBSession.flush()
return {'delete': 'success'}
def share(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')
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 share the project', 'error') % constants.right_upload
raise redirect('/tracks', {'pid': project_id})
project = DBSession.query(Project).filter(Project.id == project_id).first()
widget = form.ShareProject(action=url('/projects/share/%s' % project_id))
# public url
pub = url('/public/project', {'id': project_id, 'k': project.key})
# download url
if project.download_key is None:
project.download_key = project.setdefaultkey()
down = url('/public/project', {'id': project_id, 'k': project.download_key})
widget.value = {'pid': project_id}
tl = handler.help.help_address(url('help'), '#share', 'sharing projects')
if request.method == 'POST':
if kw.has_key('rights'):
rights_checkboxes = kw.get('rights_checkboxes', None)
if rights_checkboxes is not None:
if not isinstance(rights_checkboxes,list):
rights_checkboxes = [rights_checkboxes]
handler.project.change_rights(kw.get('pid'), kw.get('cid'), rights=rights_checkboxes)
else: handler.project.change_rights(kw.get('pid'), kw.get('cid'))
else:
circle_ids = kw.get('circles', [])
if not circle_ids: circle_ids = []
if not isinstance(circle_ids, list):
circle_ids = [circle_ids]
if len(circle_ids) > 0 and '' in circle_ids: circle_ids.remove('')
handler.project.e(project=project, circle_ids=circle_ids)
debug(project.get_circle_with_right_display)
cr_data = [util.to_datagrid(datagrid.project_sharing, project.circles_rights, "Sharing", len(project.circles_rights)>0)]
widget.child.children[1].options = [('','')] + [(c.id, c.name) for c in user.circles_sharing if c not in project.shared_circles] +\
[(c.id, c.name, {'selected': True}) for c in project.shared_circles]
return dict(page='projects', public=pub, download=down, name=project.name,
tooltip_links=tl, widget=widget, items=cr_data, project_id=project_id)
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 view(self, project_id, *args, **kw):
debug('VIEW')
user = handler.user.get_user_in_session(request)
if not checker.check_permission(
project_id=project_id,
user=user,
right_id=constants.rights['read']['id']):
flash(
'You must have %s permission to view the project.' %
constants.right_read, 'error')
raise redirect(url('/'))
d = handler.view.prepare_view(project_id, *args, **kw)
response.headerlist.append(('Access-Control-Allow-Origin', '*'))
return d
def delete(self, project_id, selection_id):
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 {'delete': 'failed'}
selection = DBSession.query(Selection).filter(
Selection.id == selection_id).first()
if not selection.project_id == project_id:
flash('Bad project_id: %s' % project_id, 'error')
return {'delete': 'failed'}
DBSession.delete(selection)
DBSession.flush()
return {'delete': 'success'}
def delete(self, *args, **kw):
user = handler.user.get_user_in_session(request)
if len(args) > 0:
project_id = args[0]
if not checker.check_permission(
user=user,
project_id=project_id,
right_id=constants.right_upload_id
) and not checker.is_admin(user=user):
return reply.error(
request,
"You must have %s permission to delete the project." %
constants.right_upload, '/tracks',
{'error': 'wrong credentials'})
handler.project.delete(project_id=project_id)
return reply.normal(request, 'Project successfully deleted.',
'/tracks', {'success': 'project deleted'})
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 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 share(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')
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 share the project',
'error') % constants.right_upload
raise redirect('/tracks', {'pid': project_id})
project = DBSession.query(Project).filter(
Project.id == project_id).first()
widget = form.ShareProject(action=url('/projects/share/%s' %
project_id))
# public url
pub = url('/public/project', {'id': project_id, 'k': project.key})
# download url
if project.download_key is None:
project.download_key = project.setdefaultkey()
down = url('/public/project', {
'id': project_id,
'k': project.download_key
})
widget.value = {'pid': project_id}
tl = handler.help.help_address(url('help'), '#share',
'sharing projects')
if request.method == 'POST':
if kw.has_key('rights'):
rights_checkboxes = kw.get('rights_checkboxes', None)
if rights_checkboxes is not None:
if not isinstance(rights_checkboxes, list):
rights_checkboxes = [rights_checkboxes]
handler.project.change_rights(kw.get('pid'),
kw.get('cid'),
rights=rights_checkboxes)
else:
handler.project.change_rights(kw.get('pid'), kw.get('cid'))
else:
circle_ids = kw.get('circles', [])
if not circle_ids: circle_ids = []
if not isinstance(circle_ids, list):
circle_ids = [circle_ids]
if len(circle_ids) > 0 and '' in circle_ids:
circle_ids.remove('')
handler.project.e(project=project, circle_ids=circle_ids)
debug(project.get_circle_with_right_display)
cr_data = [
util.to_datagrid(datagrid.project_sharing, project.circles_rights,
"Sharing",
len(project.circles_rights) > 0)
]
widget.child.children[1].options = [('','')] + [(c.id, c.name) for c in user.circles_sharing if c not in project.shared_circles] +\
[(c.id, c.name, {'selected': True}) for c in project.shared_circles]
return dict(page='projects',
public=pub,
download=down,
name=project.name,
tooltip_links=tl,
widget=widget,
items=cr_data,
project_id=project_id)
def index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
shared_by = None
# view on a specific project
if 'pid' in kw and kw.get('pid'):
project_id = kw.get('pid')
project = DBSession.query(Project).filter(Project.id == project_id).first()
if project is None:
flash("Project doesn't exists", "error")
raise redirect('/tracks')
if not checker.check_permission(user=user, project=project, right_id=constants.right_read_id):
flash('You must have %s permission to view the project.' % constants.right_read, 'error')
raise redirect('/tracks')
tracks = project.tracks
# view on user project
if checker.own(user=user, project=project):
kw['own'] = True
kw['upload'] = True
grid = datagrid.track_grid_user(user, project)
# view from a shared user
else:
rights = handler.project.get_rights(project=project, user=user)
debug('find %s' % rights, 2)
if constants.right_upload_id in [r.id for r in rights]:
kw['upload'] = True
debug('view from a shared user %s' % rights)
grid = datagrid.track_grid_permissions(user=user, rights=rights, project=project)
shared_by = "%s %s" % (project.user.firstname, project.user.name[0].upper())
kw['pn'] = project.name
track_list = [util.to_datagrid(grid, tracks, "Track Listing", len(tracks) > 0)]
shared_with = project.get_circle_with_right_display
# view all user tracks
else:
if 'pid' in kw:
del kw['pid']
shared_with = ''
tracks = list(user.tracks)
# shared tracks
shared_tracks = handler.user.shared_tracks(user.id, constants.rights['download']['id'])
tracks.extend(shared_tracks)
debug('shared tracks : %s' % ', '.join((str(x) for x in shared_tracks)))
track_list = [util.to_datagrid(datagrid.track_grid_user(user), tracks, "Track Listing", len(tracks) > 0)]
kw['upload'] = True
t = handler.help.help_address(url('/help'), 'main', 'track list help')
# project list
project_list = [(p.id, p.name,) for p in user.projects]
# shared projects
shared_with_rights = handler.project.get_shared_projects(user)
sorted_projects = sorted(shared_with_rights.iteritems(), key=lambda k: k[0].name)
shared_project_list = [(p.id, p.name, ''.join([r[0] for r in rights])) for p, rights in sorted_projects]
return dict(page='tracks', model='track', form_title="new track", track_list=track_list,
project_list=project_list, shared_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),
shared_with=shared_with, owner=kw.get('own', False), shared=not kw.get('own', False), shared_by=shared_by)