def update_data_view(view_id):
user_id = g.current_user_id
view = session.query(View).get(view_id)
# make sure the view was found
if not view:
return jsonify(response="Cannot update data for view {0} from user {1} - view not found".format(view_id,user_id)),404
# make sure the view belongs to the userid
if not view.user_id == int(user_id):
return jsonify(response="Cannot update data view {0} it does not belong to user {1}".format(view_id,user_id)),404
view_json = request.get_json()
# we are only checking the view_track display params
# other updates need to happen through the other end points
view_tracks = view_json.get('view_tracks')
for view_track in view_tracks:
view_track_obj = session.query(ViewTrack).get(view_track.get('view_track_id'))
if not view_track_obj:
return jsonify(response="Cannot update display parameters for view_track {0} it does not exist".format(view_track_id)),404
param_array = view_track.get('display_params')
for param in ['sticky','hidden','y_max']:
val = param_array.get(param)
if val:
setattr(view_track_obj,param,val)
session.add(view_track_obj)
session.commit()
return jsonify(view.to_data())
def update_view(view_id):
user_id = g.current_user_id
json = request.get_json()
view = session.query(View).get(view_id)
if not view:
return jsonify(response="Can't fetch view with id: {}".format(view_id)),404
if not view.user_id == int(user_id):
return jsonify(response="Cant update view {0} for user {1} they do not own it".format(view.id,user.id)),404
# update the view_name if given
view_name = json.get('view_name')
if view_name:
view.view_name = view_name
# update the viewtracks if given
track_ids = json.get('track_ids')
if track_ids is not None:
track_ids = set(track_ids)
existing_ids = set(view_track.track_id for view_track in view.view_tracks)
for new_track_id in track_ids.difference(existing_ids):
app.logger.warning('Adding track {}'.format(new_track_id))
session.add(ViewTrack(track_id=new_track_id, view_id=view.id))
for stale_track_id in existing_ids.difference(track_ids):
app.logger.warning('Removing track {}'.format(stale_track_id))
session.delete(session.query(ViewTrack).filter_by(track_id=stale_track_id,view_id=view.id).first())
session.commit()
return jsonify(view.to_json())
def to_json(self):
track = session.query(Track).get(self.track_id)
data = []
if track.data_type == 'fasta':
fasta = session.query(Fasta).get(track.data_id)
data.append(fasta.header)
data.append("".join(str(base) for base in fasta.base_pairs))
elif track.data_type == 'wig':
wig = session.query(Wig).get(track.data_id)
for wig_val in wig.values:
data.append([wig_val.position, wig_val.value])
elif track.data_type == 'gtf':
gtf = session.query(Gtf).get(track.data_id)
for gtf_val in gtf.values:
data.append(gtf_val.to_json())
elif track.data_type == 'bed':
bed = session.query(Bed).get(track.data_id)
for bed_value in bed.values:
data.append(bed_value.to_json())
return {
'track_name' : track.track_name,
'track_id' : self.track_id,
'data_type' : track.data_type,
'data' : data,
'view_track_id' : self.id,
'display_params': {'sticky': self.sticky, 'hidden': self.hidden, 'y_max' : self.y_max }
}
def to_json(self):
track = session.query(Track).get(self.track_id)
data = []
if track.data_type == 'fasta':
fasta = session.query(Fasta).get(track.data_id)
data.append(fasta.header)
data.append("".join(str(base) for base in fasta.base_pairs))
elif track.data_type == 'wig':
wig = session.query(Wig).get(track.data_id)
for wig_val in wig.values:
data.append([wig_val.position, wig_val.value])
elif track.data_type == 'gtf':
gtf = session.query(Gtf).get(track.data_id)
for gtf_val in gtf.values:
data.append(gtf_val.to_json())
elif track.data_type == 'bed':
bed = session.query(Bed).get(track.data_id)
for bed_value in bed.values:
data.append(bed_value.to_json())
return {
'track_name': track.track_name,
'track_id': self.track_id,
'data_type': track.data_type,
'data': data,
'view_track_id': self.id,
'display_params': {
'sticky': self.sticky,
'hidden': self.hidden,
'y_max': self.y_max
}
}
def new_view():
user_id = g.current_user_id
json = request.get_json()
track_ids = json.get('track_ids')
view_name = json.get('view_name')
for field in [track_ids, view_name]:
if not field:
return jsonify(response="Could not create view, {} is required".format(field)),404
new_view = View(view_name = view_name, user_id = user_id)
session.add(new_view)
session.commit()
view_tracks = []
for track_id in track_ids:
track = session.query(Track).get(track_id)
if not track:
return jsonify(response="Could not create view, {} is not a valid track id".format(track_id)),404
if not track.user_id == int(user_id):
return jsonify(response="Could not create view with track {} is not a owned by user {}".format(track_id,user_id)),404
view_track = ViewTrack(track_id = track_id, view_id = new_view.id)
view_tracks.append(view_track)
session.add_all(view_tracks)
session.commit()
return jsonify(view_id=new_view.id),200
def update_track(track_id):
user_id = g.current_user_id
if not track_id:
return jsonify(response="Can't fetch track, track_id required"), 404
track = session.query(Track).get(track_id)
json = request.get_json()
if not track:
return jsonify(
response="Can't fetch track with id: {}".format(track_id)), 404
if not track.user_id == int(user_id):
return jsonify(
response="Cant update track {0} for user {1} they do not own it".
format(track.id, user.id)), 404
for field in ['track_name', 'data_type', 'data_id']:
val = json.get(field)
if val:
setattr(track, field, val)
session.commit()
return jsonify(track.to_json())
def get_user():
user_id = g.current_user_id
user = session.query(User).get(user_id)
if user:
return jsonify( username=user.username, user_id=user.id, email=user.email )
else:
return jsonify(response="Can't fetch user with id: {}".format(user_id)),404
def get_all_tracks():
user_id = g.current_user_id
# look up all the tracks
tracks = session.query(Track).filter_by(user_id=user_id).all()
if not tracks:
return jsonify(response="user {} has no tracks".format(user_id)), 404
return jsonify(tracks=[track.to_json() for track in tracks])
def delete_user():
user_id = g.current_user_id
user = session.query(User).get(user_id)
if not user:
return jsonify(response="Could not fetch user with id: "+user_id),404
session.delete(user)
session.commit()
return jsonify()
def get_all_tracks():
user_id = g.current_user_id
# look up all the tracks
tracks = session.query(Track).filter_by(user_id=user_id).all()
if not tracks:
return jsonify(response="user {} has no tracks".format(user_id)),404
return jsonify(tracks=[ track.to_json() for track in tracks])
def get_views():
user_id = g.current_user_id
views = session.query(View).filter_by(user_id=user_id).all()
# make sure the view was found
if not views:
return jsonify(response="Cannot fetch views from user {0}".format(user_id)),404
# otherwise return it
return jsonify(views=[ view.to_json() for view in views])
def delete_view(view_id):
user_id = g.current_user_id
view = session.query(View).get(view_id)
if not view:
return jsonify(response="Could not fetch view with id: {}".format(view_id)),404
if not view.user_id == int(user_id):
return jsonify(response="Could not delete view {0} it is not owned by user {1}".format(view.id,user_id)),404
session.delete(view)
session.commit()
return jsonify()
def delete_track(track_id):
user_id = g.current_user_id
track = session.query(Track).get(track_id)
if not track:
return jsonify(response="Could not fetch track with id: {}".format(track_id)),404
if not track.user_id == int(user_id):
return jsonify(response="Could not delete track {0} it is not owned by user {1}".format(track.id,user_id)),404
session.delete(track)
session.commit()
return jsonify()
def get_data_view(view_id):
user_id = g.current_user_id
view = session.query(View).get(view_id)
# make sure the view was found
if not view:
return jsonify(response="Cannot fetch view {0} from user {1}".format(view_id,user_id)),404
# make sure the view belongs to the userid
if not view.user_id == int(user_id):
return jsonify(response="Cannot return view {0} it does not belong to user {1}".format(view_id,user_id)),404
# otherwise return it
return jsonify(view.to_data())
def get_one_track(track_id):
user_id = g.current_user_id
# get the track
track = session.query(Track).get(track_id)
# make sure the track was found
if not track:
return jsonify(response="Cannot fetch track {0} from user {1}".format(track_id,user_id)),404
# make sure the track belongs to the userid
if not track.user_id == int(user_id):
return jsonify(response="Cannot return track {0} it does not belong to user {1}".format(track_id,user_id)),404
# otherwise return it
return jsonify(track.to_json())
def delete_track(track_id):
user_id = g.current_user_id
track = session.query(Track).get(track_id)
if not track:
return jsonify(
response="Could not fetch track with id: {}".format(track_id)), 404
if not track.user_id == int(user_id):
return jsonify(
response="Could not delete track {0} it is not owned by user {1}".
format(track.id, user_id)), 404
session.delete(track)
session.commit()
return jsonify()
def get_one_track(track_id):
user_id = g.current_user_id
# get the track
track = session.query(Track).get(track_id)
# make sure the track was found
if not track:
return jsonify(response="Cannot fetch track {0} from user {1}".format(
track_id, user_id)), 404
# make sure the track belongs to the userid
if not track.user_id == int(user_id):
return jsonify(
response="Cannot return track {0} it does not belong to user {1}".
format(track_id, user_id)), 404
# otherwise return it
return jsonify(track.to_json())
def update_user():
user_id = g.current_user_id
json = request.get_json()
user = session.query(User).get(user_id)
if not user:
return jsonify(response="Can't fetch user with id: "+user_id),404
if json.get('username'):
user.username = json.get('username')
if json.get('email'):
user.email = json.get('email')
if json.get('password'):
user.password = user.hash_password(json.get('password'))
session.commit()
return jsonify(username=user.username, user_id=user.id, email=user.email)
def update_track(track_id):
user_id = g.current_user_id
if not track_id:
return jsonify(response="Can't fetch track, track_id required"),404
track = session.query(Track).get(track_id)
json = request.get_json()
if not track:
return jsonify(response="Can't fetch track with id: {}".format(track_id)),404
if not track.user_id == int(user_id):
return jsonify(response="Cant update track {0} for user {1} they do not own it".format(track.id,user.id)),404
for field in ['track_name','data_type','data_id']:
val = json.get(field)
if val:
setattr(track,field,val)
session.commit()
return jsonify(track.to_json())