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 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 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 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 create(self, *args, **kw):
user = handler.user.get_user_in_session(request)
# get sequence
sequence = None
project_id = None
debug('Create track %s' % kw)
debug('Find sequence', 1)
if 'assembly' in kw and kw.get('assembly'):
assembly = int(kw.get('assembly'))
sequence = DBSession.query(Sequence).filter(Sequence.id == assembly).first()
elif 'sequence_id' in kw and kw.get('sequence_id'):
sequence_id = int(kw.get('sequence_id'))
sequence = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
elif 'sequence_id' in kw and kw.get('sequence_id'):
sequence_id = int(kw.get('sequence_id'))
sequence = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
elif 'project_id' in kw and kw.get('project_id'):
project_id = int(kw.get('project_id'))
project = DBSession.query(Project).filter(Project.id == project_id).first()
if project is None:
return reply.error(request, 'Project with id %s not found on GDV.' % project_id, tg.url('./new', {'pid': project_id}), {})
sequence = DBSession.query(Sequence).filter(Sequence.id == project.sequence_id).first()
if not sequence:
return reply.error(request, 'Sequence not found on GDV.', tg.url('./new'), {'pid': project_id})
debug('%s' % sequence.name, 2)
# know if file is comming from url, fileupload or filsystem
filetoget = None
inputtype = None
debug('Find inputtype', 1)
if 'url' in kw and kw.get('url'):
debug('from url', 2)
filetoget = kw.get('url')
if not filetoget.startswith('http://'):
filetoget = 'http://%s' % filetoget
inputtype = 'url'
elif 'fsys' in kw and kw.get('fsys'):
debug('fsys', 2)
filetoget = kw.get('fsys')
inputtype = 'fsys'
elif 'file_upload' in kw and kw.get('file_upload') is not None and kw['file_upload'] != '':
debug('file upload %s' % kw.get('file_upload'), 2)
filetoget = kw.get('file_upload')
inputtype = 'fu'
if filetoget is None:
return reply.error(request, 'No file to upload', tg.url('./new'), {'pid': project_id})
debug('file2get: %s, intype: %s' % (filetoget, inputtype), 2)
# get file name
debug('Find track name', 1)
trackname = None
if 'trackname' in kw and kw.get('trackname'):
debug('i params', 2)
trackname = kw.get('trackname')
else:
if inputtype == 'url':
debug('trackname from url', 2)
trackname = os.path.split(filetoget)[1].split('?')[0]
elif inputtype == 'fsys':
debug('trackname from fsys', 2)
trackname = os.path.split(filetoget)[-1]
elif inputtype == 'fu':
debug('trackname from fu', 2)
trackname = filetoget.filename
if trackname is None:
return reply.error(request, 'No trackname found', tg.url('./new'), {'pid': project_id})
debug('%s' % trackname, 2)
# get extension
extension = None
if 'extension' in kw and kw.get('extension'):
extension = kw.get('extension')
elif 'ext' in kw and kw.get('ext'):
extension = kw.get('ext')
else:
extension = os.path.splitext(trackname)[-1]
if extension is None or extension == '':
if inputtype == 'url':
debug('extension from url', 2)
extension = os.path.splitext(os.path.split(filetoget)[1].split('?')[0])[-1]
elif inputtype == 'fsys':
debug('extension from fsys', 2)
extension = os.path.splitext(os.path.split(filetoget)[-1])[-1]
elif inputtype == 'fu':
debug('extension from fu', 2)
extension = os.path.splitext(filetoget.filename)[-1]
if extension is None or extension == '':
return reply.error(request, 'No extension found', tg.url('./new'), {'pid': project_id})
if extension.startswith('.'):
extension = extension[1:]
extension = extension.lower()
# is the track "admin"
admin = False
if 'track_admin' in kw and kw.get('track_admin'):
# check if really admin
group_admin = DBSession.query(Group).filter(Group.id == constants.group_admins_id).first()
if user in group_admin.users:
admin = True
debug('admin: %s' % admin, 1)
#store information in a dummy object
out = os.path.join(filemanager.temporary_directory(), trackname)
fileinfo = filemanager.FileInfo(inputtype=inputtype, inpath=filetoget, trackname=trackname, extension=extension, outpath=out, admin=admin)
debug('fileinfo: %s' % fileinfo, 1)
# get additionnal information
user_info = {'id': user.id, 'name': user.name, 'email': user.email}
sequence_info = {'id': sequence.id, 'name': sequence.name}
#upload the track it's from file_upload
if inputtype == 'fu':
debug('Download', 1)
fileinfo.download()
debug('fileinfo: %s' % fileinfo, 1)
# create a track that the user can see something
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, project_id)
t.task_id = async.task_id
DBSession.add(t)
DBSession.flush()
debug('End create')
return reply.normal(request, 'Processing launched.', '/tracks/', {'track_id': t.id, 'pid': project_id})
