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 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 index(self, *args, **kw):
seq_form = form.NewSequenceForm(action=url('/sequences')).req()
species = genrep.get_species()
m = {}
sp_to_add = []
for sp in species:
assemblies = genrep.get_assemblies_not_created_from_species_id(sp.id)
if len(assemblies) > 0:
m[sp.id] = [(ass.id, ass.name) for ass in assemblies]
sp_to_add.append(sp)
sp_opts = [(sp.id, sp.species) for sp in sp_to_add]
seq_form.child.children[1].options = sp_opts
value = {'smapping' : json.dumps(m)}
seq_form.value = value
grid = datagrid.sequences_grid
if request.method == 'GET':
sequences = DBSession.query(Sequence).all()
seq_grid = [util.to_datagrid(grid, sequences, "Sequences", len(sequences)>0)]
return dict(page="sequences", widget=seq_form, grid=seq_grid)
else :
species_id = kw['species']
assembly_id = kw['assembly']
# look if the species already exist in GDV, else create it
species = DBSession.query(Species).filter(Species.id == species_id).first()
if not species:
species = handler.genrep.get_species_by_id(species_id)
current_sp = Species()
current_sp.id = species.id
current_sp.name = species.species
DBSession.add(current_sp)
DBSession.flush()
current_sp = DBSession.query(Species).filter(Species.id == species_id).first()
flash( '''Species created: %s'''%( current_sp ))
# look if the assembly not already created, else create it
if not DBSession.query(Sequence).filter(Sequence.id == assembly_id).first():
assembly = handler.genrep.get_assembly_by_id(assembly_id)
seq = Sequence()
seq.id = assembly_id
seq.name = assembly.name
seq.species_id = species_id
DBSession.add(seq)
DBSession.flush()
seq = DBSession.query(Sequence).filter(Sequence.id == assembly_id).first()
handler.sequence.add_new_sequence(seq)
flash( '''Sequence created: %s'''%( seq ))
DBSession.flush()
sequences = DBSession.query(Sequence).all()
seq_grid = [util.to_datagrid(grid, sequences, "Sequences", len(sequences)>0)]
return dict(page="sequences", widget=seq_form, grid=seq_grid)
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 export(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 export any tracks which is not yours")
raise redirect('../')
data = util.to_datagrid(track_grid, [trac])
tmpl_context.form = track_export
kw['track_id'] = track_id
return dict(page='tracks', model='Track', info=data, form_title='', value=kw)
def index(self, *args, **kw):
kw['page'] = 'circle'
user = handler.user.get_user_in_session(request)
data = util.to_datagrid(datagrid.circle_grid, user.circles_owned, grid_display=len(user.circles) > 0)
t = handler.help.help_address(url('/help'), 'circles', 'help about circles')
widget = form.NewCircle(action=url('/circles/index')).req()
if request.method == 'GET':
return dict(page='circles', item=data, tooltip=t, widget=widget)
else:
try:
widget.validate(kw)
except twc.ValidationError as e:
return dict(page='circles', item=data, tooltip=t, widget=e.widget, ac_error=True)
user = handler.user.get_user_in_session(request)
handler.circle.create(kw['name'], kw['description'], user)
data = util.to_datagrid(datagrid.circle_grid, user.circles_owned, grid_display=len(user.circles) > 0)
return dict(page='circles', model='circle', item=data, widget=widget, tooltip=t)
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 admin(self):
projects = DBSession.query(Project).all()
data_projects = [
util.to_datagrid(project_admin_grid, projects, "All projects",
len(projects) > 0)
]
t = handler.help.tooltip['project']
return dict(page='projects',
model='project',
tooltip=t,
form_title="new project",
projects=data_projects,
value={})
def index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
if request.method == 'POST':
jid = kw.get('id', None)
if jid is not None and checker.can_edit_job(user.id, jid):
handler.job.delete(jid)
else:
flash('not authorized')
jobs = DBSession.query(Job).filter(Job.user_id == user.id).all()
data = util.to_datagrid(datagrid.job_grid, jobs, "Job Listing", grid_display=len(jobs) > 0)
t = handler.help.help_address(url('/help'), 'jobs', 'How to compute new data')
return dict(page='jobs', model='job', form_title="new job", item=data, value=kw, tooltip=t)
def index(self, *args, **kw):
user = handler.user.get_user_in_session(request)
if request.method == 'POST':
jid = kw.get('id', None)
if jid is not None and checker.can_edit_job(user.id, jid):
handler.job.delete(jid)
else:
flash('not authorized')
jobs = DBSession.query(Job).filter(Job.user_id == user.id).all()
data = util.to_datagrid(datagrid.job_grid,
jobs,
"Job Listing",
grid_display=len(jobs) > 0)
t = handler.help.help_address(url('/help'), 'jobs',
'How to compute new data')
return dict(page='jobs',
model='job',
form_title="new job",
item=data,
value=kw,
tooltip=t)
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 admin(self):
projects = DBSession.query(Project).all()
data_projects = [util.to_datagrid(project_admin_grid, projects, "All projects", len(projects) > 0)]
t = handler.help.tooltip['project']
return dict(page='projects', model='project', tooltip=t, form_title="new project", projects=data_projects, value={})
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 index(self, *args, **kw):
seq_form = form.NewSequenceForm(action=url('/sequences')).req()
species = genrep.get_species()
m = {}
sp_to_add = []
for sp in species:
assemblies = genrep.get_assemblies_not_created_from_species_id(
sp.id)
if len(assemblies) > 0:
m[sp.id] = [(ass.id, ass.name) for ass in assemblies]
sp_to_add.append(sp)
sp_opts = [(sp.id, sp.species) for sp in sp_to_add]
seq_form.child.children[1].options = sp_opts
value = {'smapping': json.dumps(m)}
seq_form.value = value
grid = datagrid.sequences_grid
if request.method == 'GET':
sequences = DBSession.query(Sequence).all()
seq_grid = [
util.to_datagrid(grid, sequences, "Sequences",
len(sequences) > 0)
]
return dict(page="sequences", widget=seq_form, grid=seq_grid)
else:
species_id = kw['species']
assembly_id = kw['assembly']
# look if the species already exist in GDV, else create it
species = DBSession.query(Species).filter(
Species.id == species_id).first()
if not species:
species = handler.genrep.get_species_by_id(species_id)
current_sp = Species()
current_sp.id = species.id
current_sp.name = species.species
DBSession.add(current_sp)
DBSession.flush()
current_sp = DBSession.query(Species).filter(
Species.id == species_id).first()
flash('''Species created: %s''' % (current_sp))
# look if the assembly not already created, else create it
if not DBSession.query(Sequence).filter(
Sequence.id == assembly_id).first():
assembly = handler.genrep.get_assembly_by_id(assembly_id)
seq = Sequence()
seq.id = assembly_id
seq.name = assembly.name
seq.species_id = species_id
DBSession.add(seq)
DBSession.flush()
seq = DBSession.query(Sequence).filter(
Sequence.id == assembly_id).first()
handler.sequence.add_new_sequence(seq)
flash('''Sequence created: %s''' % (seq))
DBSession.flush()
sequences = DBSession.query(Sequence).all()
seq_grid = [
util.to_datagrid(grid, sequences, "Sequences",
len(sequences) > 0)
]
return dict(page="sequences", widget=seq_form, grid=seq_grid)
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)
def admin(self):
c = DBSession.query(Circle).all()
dc = [util.to_datagrid(circle_grid, c, "All circles", len(c) > 0)]
t = handler.help.tooltip['circle']
return dict(page='circles', model='circle', tooltip=t, items=dc, value={})