def lookup(request):
""" return JSON for autocomplete """
q = request.params.get('q')
g = request.params.get('g','')
dbh = get_dbhandler()
g_key = dbh.get_ekey(g)
if not g_key:
return error_page(request, "Parent EK not found!")
if not q:
return error_page(request, "Please provide the query as q.")
q = '%' + q.lower() + '%'
ekeys = dbh.EK.query(dbh.session()).filter( dbh.EK.key.ilike(q),
dbh.EK.member_of_id == g_key.id)
# formating for select2 consumption
result = [
{ 'id': k.id, 'text': '%s [ %s ]' % (k.key, k.desc) }
for k in ekeys]
return result
def action(request):
method = request.params.get('_method', None)
if method == 'add-assay-files':
if not request.POST:
return error_page(request, 'Only accept POST request!')
sample_id = request.POST.get('sample_id')
sample = get_dbhandler().get_sample_by_id(sample_id)
request.session.flash(
('success', 'Sample code [%s] has been added with %d assay files' %
(sample.code, len(request.params.getall('genaf-assay_file')))))
return HTTPFound(
location=request.route_url('genaf.sample-view', id=sample.id))
elif method == 'delete':
dbh = get_dbhandler()
sample_ids = request.POST.getall('sample-ids')
samples = [dbh.get_sample_by_id(sample_id) for sample_id in sample_ids]
return Response(modal_delete % ''.join('<li>%s | %s</li>' %
(s.code, s.batch.code)
for s in samples))
elif method == 'delete/confirm':
dbh = get_dbhandler()
sample_ids = request.POST.getall('sample-ids')
for sample_id in sample_ids:
sample = dbh.get_sample_by_id(sample_id)
if not sample:
request.session.flash(
('error',
'Sample with ID [%d] does not exists' % sample_id))
continue
if not sample.batch.is_manageable(request.user):
request.session.flash(
('error',
'You are not authorized to delete sample [%s | %s]' %
(sample.code, sample.batch.code)))
continue
sample_code = '%s | %s' % (sample.code, sample.batch.code)
dbh.session().delete(sample)
request.session.flash(
('success', 'Sample [%s] has been deleted.' % sample_code))
return HTTPFound(
location=request.referrer or request.route_url('genaf.batch'))
else:
return error_page(request, 'Unknown method!')
def action(request):
method = request.params.get('_method', None)
if method == 'add-assay-files':
if not request.POST:
return error_page(request, 'Only accept POST request!')
sample_id = request.POST.get('sample_id')
sample = get_dbhandler().get_sample_by_id( sample_id )
request.session.flash(
( 'success',
'Sample code [%s] has been added with %d assay files' % ( sample.code,
len(request.params.getall('genaf-assay_file')) )))
return HTTPFound(location = request.route_url('genaf.sample-view', id=sample.id))
elif method == 'delete':
dbh = get_dbhandler()
sample_ids = request.POST.getall('sample-ids')
samples = [ dbh.get_sample_by_id(sample_id) for sample_id in sample_ids ]
return Response(
modal_delete % ''.join('<li>%s | %s</li>' % (s.code, s.batch.code) for s in samples )
)
elif method == 'delete/confirm':
dbh = get_dbhandler()
sample_ids = request.POST.getall('sample-ids')
for sample_id in sample_ids:
sample = dbh.get_sample_by_id(sample_id)
if not sample:
request.session.flash( ('error',
'Sample with ID [%d] does not exists' % sample_id) )
continue
if not sample.batch.is_manageable( request.user ):
request.session.flash( ('error',
'You are not authorized to delete sample [%s | %s]'
% (sample.code, sample.batch.code) ))
continue
sample_code = '%s | %s' % (sample.code, sample.batch.code)
dbh.session().delete( sample )
request.session.flash(
('success', 'Sample [%s] has been deleted.' % sample_code ) )
return HTTPFound( location = request.referrer or
request.route_url( 'genaf.batch' ) )
else:
return error_page(request, 'Unknown method!')
def action(request):
if not request.POST:
return error_page()
method = request.POST.get('_method')
if method == 'delete':
ids = request.POST.getall('ek-ids')
eks = list( EK.query().filter( EK.id.in_( ids ) ) )
if len(eks) == 0:
return Response(modal_error)
#return Response('Delete Enumerated Keys: ' + str(request.POST))
return Response(modal_delete % ''.join( '<li>%s</li>' % x.key for x in eks ))
elif method == 'delete/confirm':
ids = request.POST.getall('ek-ids')
count = 0
for ek_id in ids:
EK.delete( ek_id )
count += 1
request.session.flash( ('success', 'Successfully removed %d Enumerated Keys' % count) )
return HTTPFound(location = request.referer)
return Response(str(request.POST))
def index(request):
dbh = get_dbhandler()
q = dbh.Sample.query(dbh.session()).join(dbh.Batch)
batch_id = request.params.get('batch_id', False)
location_id = request.params.get('location_id', False)
if batch_id:
batch = dbh.get_batch_by_id(batch_id)
q = q.filter(dbh.Sample.batch_id == batch.id)
else:
batch = None
if location_id:
q = q.filter(dbh.Sample.location_id == location_id)
q = q.order_by(dbh.Sample.code)
samples = q.all()
mode = request.params.get('mode', 'fsa')
if mode == 'meta':
html, jscode = format_sampleinfo(samples, request)
elif mode == 'fsa':
html, jscode = format_samplefsa(samples, request)
else:
return error_page(request, 'No suitable mode provided!')
if not request.user.has_roles(GUEST):
if batch:
add_button = ('New sample',
request.route_url('genaf.sample-edit',
id=0,
_query={'batch_id': batch.id}))
others = p()[
'Batch code:',
a(batch.code,
href=request.route_url('genaf.batch-view', id=batch.id))]
else:
add_button = others = None
bar = selection_bar('sample-ids',
action=request.route_url('genaf.sample-action'),
add=add_button,
others=others)
html, jscode = bar.render(html, jscode)
return render_to_response("genaf:templates/sample/index.mako", {
'samples': samples,
'batch': batch,
'html': str(html),
'code': jscode,
},
request=request)
def view(request):
""" view a EnumKey along with its members """
ek_id = int(request.matchdict.get('id', -1))
dbh = get_dbhandler()
ek = dbh.EK.get(ek_id, dbh.session())
if not ek:
return error_page(request)
return render_to_response('rhombus:templates/ek/view.mako',
{ 'ek': ek }, request = request )
def index(request):
dbh = get_dbhandler()
q = dbh.Sample.query(dbh.session()).join(dbh.Batch)
batch_id = request.params.get('batch_id', False)
location_id = request.params.get('location_id', False)
if batch_id:
batch = dbh.get_batch_by_id( batch_id )
q = q.filter( dbh.Sample.batch_id == batch.id )
else:
batch = None
if location_id:
q = q.filter( dbh.Sample.location_id == location_id )
q = q.order_by( dbh.Sample.code )
samples = q.all()
mode = request.params.get('mode','fsa')
if mode == 'meta':
html, jscode = format_sampleinfo(samples, request)
elif mode == 'fsa':
html, jscode = format_samplefsa(samples, request)
else:
return error_page(request, 'No suitable mode provided!')
if not request.user.has_roles(GUEST):
if batch:
add_button = ( 'New sample',
request.route_url('genaf.sample-edit', id=0, _query={ 'batch_id': batch.id })
)
others = p()[ 'Batch code:',
a(batch.code, href=request.route_url('genaf.batch-view', id=batch.id))
]
else:
add_button = others = None
bar = selection_bar('sample-ids', action=request.route_url('genaf.sample-action'),
add=add_button, others=others)
html, jscode = bar.render(html, jscode)
return render_to_response("genaf:templates/sample/index.mako",
{ 'samples': samples,
'batch': batch,
'html': str(html),
'code': jscode,
},
request = request)
def edit(request):
""" edit a EnumKey """
dbh = get_dbhandler()
ek_id = int(request.matchdict.get('id', -1))
if ek_id < 0:
return error_page(request)
if ek_id == 0:
ek = dbh.EK()
ek.id = 0
ek.member_of_id = int(request.params.get('member_of_id', 0))
else:
ek = dbh.EK.get(ek_id)
eform = edit_form(ek, dbh, request)
return render_to_response('rhombus:templates/ek/edit.mako',
{ 'ek': ek, 'form': eform }, request = request )
def lookup(request):
""" return JSON for autocomplete """
q = request.params.get('q')
if not q:
return error_page(request)
q = '%' + q.lower() + '%'
dbh = get_dbhandler()
users = dbh.User.query(dbh.session()).filter( or_( dbh.User.login.ilike(q),
dbh.User.lastname.ilike(q), dbh.User.firstname.ilike(q)) )
# formating for select2 consumption
result = [
{ 'id': u.id, 'text': u.render()}
for u in users]
return result
def save(request):
""" save a EnumKey """
ek_id = int(request.matchdict.get('id', -1))
dbh = get_dbhandler()
ek = parse_form(request.POST, dbh)
if ek_id == 0:
session = dbh.session()
session.add( ek )
session.flush()
db_ek = ek
else:
db_ek = dbh.EK.get(ek_id)
if not db_ek:
return error_page(request)
db_ek.update( ek )
if ek_id != 0:
location = request.route_url('rhombus.ek-view', id=ek_id)
elif ek.member_of_id:
location = request.route_url('rhombus.ek-view', id = ek.member_of_id)
else:
location = request.route_url('rhombus.ek-view', id = ek.id)
return HTTPFound( location = location )
def edit(request):
""" editing sample metadata """
sample_id = int(request.matchdict.get('id'))
if sample_id < 0:
return error_page(request, 'Please provide valid sample ID')
dbh = get_dbhandler()
if request.method == 'GET':
sample = dbh.get_sample_by_id(sample_id)
batch = sample.batch
# XXX: check authorization here: whether current user belongs to batch owner group
if not request.user.in_group(batch.group):
return error_page(request,
'User is not a member of batch: %s' % batch.code)
# prepare form
eform = edit_form(sample, dbh, request)
return render_to_response("genaf:templates/sample/edit.mako", {
'sample': sample,
'eform': eform,
},
request=request)
elif request.method == 'POST':
sample_d = parse_form(request.POST)
if sample_d['id'] != sample_id:
return error_page(request, 'Inconsistent sample ID!')
try:
if sample_id == 0:
pass
else:
sample = dbh.get_sample_by_id(sample_id)
batch = sample.batch
# authorisation: current user must belongs to batch owner group
if not request.user.in_group(batch.group):
return error_page(
request,
'User is not a member of batch: %s' % batch.code)
sample.update(sample_d)
dbh.session().flush()
request.session.flash(
('success', 'Sample [%s] has been updated.' % sample.code))
except RuntimeError as err:
return error_Page(request, str(err))
except sqlalchemy.exc.IntegrityError as err:
dbh.session().rollback()
detail = err.args[0]
if not sample.id: sample.id = sample_id
editform = edit_form(sample, dbh, request)
# use constraint name to detect error type
if 'uq_samples_code_batch_id' in detail:
editform.get('genaf-sample_code').add_error(
'The sample code: %s is '
'already being used. Please use other sample code!' %
sample_d['code'])
r = render_to_response("genaf:templates/sample/edit.mako", {
'sample': None,
'eform': editform,
},
request=request)
transaction.abort()
return r
return HTTPFound(
location=request.route_url('genaf.sample-view', id=sample.id))
return error_page(request, 'Invalid method!')
def edit(request):
user_id = int(request.matchdict['id'])
if user_id < 0:
return error_page(request, 'Please provide userclass ID')
dbh = get_dbhandler()
if request.method == 'GET':
if user_id == 0:
user = dbh.User()
user.id = 0
else:
user = dbh.get_user(user_id)
editform = edit_form(user, dbh, request)
return render_to_response( "rhombus:templates/generics/page.mako",
{ 'html': editform,
}, request = request
)
elif request.POST:
user_d = parse_form( request.POST )
if user_d['id'] != user_id:
return error_page(request, "Inconsistent data!")
try:
if user_id == 0:
# create a new user
userclass = dbh.get_userclass( user_d['userclass_id'])
user = userclass.add_user(
login = user_d['login'],
lastname = user_d['lastname'],
firstname = user_d['firstname'],
email = user_d['email'],
primarygroup = user_d['primarygroup_id'],
)
user.institution = user_d['institution']
dbh.session().flush()
request.session.flash(
( 'success',
'User [%s] has been created.' % user.login )
)
else:
user = dbh.get_user(user_id)
user.update( user_d )
dbh.session().flush()
except RuntimeError as err:
return error_page(request, str(err))
except:
raise
return HTTPFound(location = request.route_url('rhombus.user-view', id=user.id))
raise NotImplementedError()
def edit(request):
""" editing sample metadata """
sample_id = int(request.matchdict.get('id'))
if sample_id < 0:
return error_page(request, 'Please provide valid sample ID')
dbh = get_dbhandler()
if request.method == 'GET':
sample = dbh.get_sample_by_id( sample_id )
batch = sample.batch
# XXX: check authorization here: whether current user belongs to batch owner group
if not request.user.in_group( batch.group ):
return error_page(request, 'User is not a member of batch: %s' % batch.code)
# prepare form
eform = edit_form(sample, dbh, request)
return render_to_response("genaf:templates/sample/edit.mako",
{ 'sample': sample,
'eform': eform,
},
request = request)
elif request.method == 'POST':
sample_d = parse_form( request.POST )
if sample_d['id'] != sample_id:
return error_page(request, 'Inconsistent sample ID!')
try:
if sample_id == 0:
pass
else:
sample = dbh.get_sample_by_id( sample_id )
batch = sample.batch
# authorisation: current user must belongs to batch owner group
if not request.user.in_group( batch.group ):
return error_page(request,
'User is not a member of batch: %s' % batch.code)
sample.update(sample_d)
dbh.session().flush()
request.session.flash(
( 'success',
'Sample [%s] has been updated.' % sample.code )
)
except RuntimeError as err:
return error_Page(request, str(err))
except sqlalchemy.exc.IntegrityError as err:
dbh.session().rollback()
detail = err.args[0]
if not sample.id: sample.id = sample_id
editform = edit_form(sample, dbh, request)
# use constraint name to detect error type
if 'uq_samples_code_batch_id' in detail:
editform.get('genaf-sample_code').add_error('The sample code: %s is '
'already being used. Please use other sample code!'
% sample_d['code'])
r = render_to_response( "genaf:templates/sample/edit.mako",
{ 'sample': None,
'eform': editform,
},
request = request )
transaction.abort()
return r
return HTTPFound(location = request.route_url('genaf.sample-view', id = sample.id))
return error_page(request, 'Invalid method!')