def new_track():
user_id = g.current_user_id
# Get json
json = request.get_json()
# Try and get everything
track_name = json.get('track_name')
data_type = json.get('data_type').lower()
data_id = json.get('data_id')
file_name = json.get('file_name')
# Ensure everything was passed
for field in [track_name,user_id,data_type,data_id,file_name]:
if not field:
return jsonify(response="Could not create track, {} field is required".format(track)),404
new_track = Track(
track_name = track_name,
user_id = user_id,
data_type = data_type,
data_id = data_id,
file_name = file_name,
)
session.add(new_track)
session.commit()
# Last check to make sure it was commited properly
if not new_track.id:
return jsonify(response="Could not create track"),404
# Return the user id on success
return jsonify(track_id=new_track.id)
def new_fasta(fasta_file):
position = 0
basepairs = []
header = fasta_file.readline()
if not validate_fasta_header(header):
return jsonify(response="Cannot upload fasta file {} is not a valid header".format(header)),404
fasta = Fasta(header=header)
session.add(fasta)
session.commit()
fasta_id = fasta.id
for line in fasta_file:
line.strip("\n")
for base in line:
bp = BasePair(nucleotide=base,position=position,fasta_id=fasta_id)
position+=1
basepairs.append(bp)
session.add_all(basepairs)
session.commit()
return fasta_id
def new_fasta(fasta_file):
position = 0
basepairs = []
header = fasta_file.readline()
if not validate_fasta_header(header):
return jsonify(
response="Cannot upload fasta file {} is not a valid header".
format(header)), 404
fasta = Fasta(header=header)
session.add(fasta)
session.commit()
fasta_id = fasta.id
for line in fasta_file:
line.strip("\n")
for base in line:
bp = BasePair(nucleotide=base,
position=position,
fasta_id=fasta_id)
position += 1
basepairs.append(bp)
session.add_all(basepairs)
session.commit()
return fasta_id
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 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 new_user():
# Parse the json
json = request.get_json()
u_name = json.get('username')
email = json.get('email')
password = json.get('password')
# Ensure username and email were passed
if not u_name:
return jsonify(response="Could not create user, username field is required"), 404
elif u_name == "default":
return jsonify(response="Invalid username."), 400
if not email:
return jsonify(response="Could not create user. email field is required"),404
# Create user and commit
new_user = User(username=json.get('username'),email=json.get('email'),password=json.get('password'))
session.add(new_user)
session.commit()
# Last check to make sure it was commited properly
if not new_user.id:
return jsonify(response="Could not create user"),404
# Return the user id on success
return jsonify(user_id=new_user.id)
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 new_bed(bed_file):
# create the base record
bed = Bed()
session.add(bed)
session.commit()
bed_vals = []
for line in bed_file:
# skip the header
if line.startswith("#"):
continue
line_vals = line.split("\t")
if len(line_vals) != 12:
app.logger.warning('Invalid bed line - skipping')
continue
[
chrom, start, stop, name, score, strand, thick_start, thick_end,
item_rgb, block_count, bed_block_sizes, bed_block_starts
] = line_vals
bed_val = BedValue(chrom, int(start), int(stop), name, int(score),
strand, int(thick_start), int(thick_end),
int(item_rgb), int(block_count), bed.id)
session.add(bed_val)
session.commit()
index = 0
bed_block_sizes = bed_block_sizes.rstrip(",").split(",")
for size in bed_block_sizes:
bed_block_size = BedBlockSize(index, size, bed_val.id)
index += 1
bed_vals.append(bed_block_size)
index = 0
bed_block_starts = bed_block_starts.rstrip("\n").split(",")
for start in bed_block_starts:
bed_block_start = BedBlockStart(index, start, bed_val.id)
index += 1
bed_vals.append(bed_block_start)
session.add_all(bed_vals)
session.commit()
return bed.id
def new_bed(bed_file):
# create the base record
bed = Bed()
session.add(bed)
session.commit()
bed_vals = []
for line in bed_file:
# skip the header
if line.startswith("#"):
continue
line_vals = line.split("\t")
if len(line_vals) != 12:
app.logger.warning('Invalid bed line - skipping')
continue
[chrom, start, stop, name, score, strand, thick_start,
thick_end, item_rgb, block_count, bed_block_sizes,
bed_block_starts] = line_vals
bed_val = BedValue(chrom, int(start), int(stop), name, int(score), strand, int(thick_start), int(thick_end), int(item_rgb), int(block_count), bed.id)
session.add(bed_val)
session.commit()
index = 0
bed_block_sizes = bed_block_sizes.rstrip(",").split(",")
for size in bed_block_sizes:
bed_block_size = BedBlockSize(index, size, bed_val.id)
index += 1
bed_vals.append(bed_block_size)
index = 0
bed_block_starts = bed_block_starts.rstrip("\n").split(",")
for start in bed_block_starts:
bed_block_start = BedBlockStart(index, start, bed_val.id)
index += 1
bed_vals.append(bed_block_start)
session.add_all(bed_vals)
session.commit()
return bed.id
def new_gtf(gtf_file):
gtf_fields = [
'seqname', 'source', 'feature', 'start', 'end', 'score', 'strand',
'frame', 'attribute'
]
# create the base record
gtf = Gtf()
session.add(gtf)
session.commit()
gtf_values = []
for line in gtf_file:
gtf_dict = dict(zip(gtf_fields, line.split("\t")))
gtf_dict['gtf_id'] = gtf.id
# handle the '.' in score and frame
if gtf_dict['score'] == '.':
gtf_dict['score'] = 0.0
if gtf_dict['frame'] == '.':
gtf_dict['frame'] = 0
# create each value record
gtf_val = GtfValue(seqname=gtf_dict['seqname'],
source=gtf_dict['source'],
feature=gtf_dict['feature'],
start=int(gtf_dict['start']),
end=int(gtf_dict['end']),
score=gtf_dict['score'],
strand=gtf_dict['strand'],
frame=int(gtf_dict['frame']),
attribute=gtf_dict['attribute'],
gtf_id=gtf_dict['gtf_id'])
gtf_values.append(gtf_val)
session.add_all(gtf_values)
session.commit()
return gtf.id
def new_gtf(gtf_file):
gtf_fields = ['seqname','source','feature','start','end','score','strand','frame','attribute']
# create the base record
gtf = Gtf()
session.add(gtf)
session.commit()
gtf_values = []
for line in gtf_file:
gtf_dict = dict(zip(gtf_fields, line.split("\t")))
gtf_dict['gtf_id'] = gtf.id
# handle the '.' in score and frame
if gtf_dict['score'] == '.':
gtf_dict['score'] = 0.0
if gtf_dict['frame'] == '.':
gtf_dict['frame'] = 0
# create each value record
gtf_val = GtfValue(
seqname = gtf_dict['seqname'],
source = gtf_dict['source'],
feature = gtf_dict['feature'],
start = int(gtf_dict['start']),
end = int(gtf_dict['end']),
score = gtf_dict['score'],
strand = gtf_dict['strand'],
frame = int(gtf_dict['frame']),
attribute = gtf_dict['attribute'],
gtf_id = gtf_dict['gtf_id']
)
gtf_values.append(gtf_val)
session.add_all(gtf_values)
session.commit()
return gtf.id
def new_track():
user_id = g.current_user_id
# Get json
json = request.get_json()
# Try and get everything
track_name = json.get('track_name')
data_type = json.get('data_type').lower()
data_id = json.get('data_id')
file_name = json.get('file_name')
# Ensure everything was passed
for field in [track_name, user_id, data_type, data_id, file_name]:
if not field:
return jsonify(
response="Could not create track, {} field is required".format(
track)), 404
new_track = Track(
track_name=track_name,
user_id=user_id,
data_type=data_type,
data_id=data_id,
file_name=file_name,
)
session.add(new_track)
session.commit()
# Last check to make sure it was commited properly
if not new_track.id:
return jsonify(response="Could not create track"), 404
# Return the user id on success
return jsonify(track_id=new_track.id)
def seed_db():
# Setup default user #
default_user = User(username="******", email="*****@*****.**", password="******")
session.add(default_user)
session.commit()
# add the users
user_ids = [default_user.id]
users = ["kyle","karl","coda","max","goof"]
for name in users:
new_user = User(username=name,email="{}@email.com".format(name),password="******")
session.add(new_user)
session.commit()
user_ids.append(new_user.id)
## Give each a track ##
for u_id in user_ids:
view = View(view_name = "Test View", user_id = u_id)
session.add(view)
session.commit()
# Create a fasta
fasta = Fasta(header=">EBV1")
session.add(fasta)
session.commit()
i = 0
for base in "ATTATTAGCATGCATGATCAGTAGCTAGGGGATGCATGCAACTGATCGATCGATGCATGCAT":
bp = BasePair(nucleotide=base,position=i,fasta_id=fasta.id)
i+=1
session.add(bp)
session.commit()
# Add a fasta track
fasta_track = Track(
track_name = "Fasta Test Track",
user_id = u_id,
data_type = "fasta",
data_id = fasta.id,
file_name = "testFasta.fasta"
)
session.add(fasta_track)
session.commit()
session.add(ViewTrack(fasta_track.id,view.id))
# Create a wig track
wig = Wig(chrom='EBV1')
session.add(wig)
session.commit()
for pos in range(1,10):
wig_val = WigValue(
position = pos,
value = 1,
wig_id = wig.id
)
session.add(wig_val)
# add the track
wig_track = Track(
track_name = "Wig Test Track",
user_id = u_id,
data_type = "wig",
data_id = wig.id,
file_name = "testWig.wig"
)
session.add(wig_track)
session.commit()
session.add(ViewTrack(wig_track.id,view.id))
# Create a GTF track
gtf = Gtf()
session.add(gtf)
session.commit()
for pos in range(1,10):
gtf_val = GtfValue(
seqname = "EBV1",
source = "mRNA-Seq",
feature = "exon",
start = pos,
end = pos + 10,
score = 0,
strand = "+",
frame = 0,
attribute = "spanning-juncs=false;host=hg19",
gtf_id = gtf.id
)
session.add(gtf_val)
gtf_track = Track(
track_name = "Gtf Test Track",
user_id = u_id,
data_type = "gtf",
data_id = gtf.id,
file_name = "testGtf.gtf"
)
session.add(gtf_track)
session.commit()
session.add(ViewTrack(gtf_track.id,view.id))
# last make a bed
bed = Bed()
session.add(bed)
session.commit()
for pos in range(1,10):
bed_val = BedValue(
chrom = "EBV1",
start = pos,
end = pos+9,
name = "BED-THING",
score = 0,
strand = "+",
thick_start = pos,
thick_end = pos+9,
item_rgb = 10,
block_count = 1,
bed_id = bed.id
)
session.add(bed_val)
session.commit()
bb_size = BedBlockSize(
index = pos,
value = pos+9,
bed_value_id = bed_val.id
)
bb_start = BedBlockStart(
index = pos,
value = pos,
bed_value_id = bed_val.id
)
session.add_all([bb_size, bb_start])
session.commit()
bed_track = Track(
track_name = "Bed Test Track",
user_id = u_id,
data_type = "bed",
data_id = bed.id,
file_name = "testBED.bed"
)
session.add(bed_track)
session.commit()
session.add(ViewTrack(bed_track.id,view.id))
session.commit()
def new_wigs(wig_file):
current_id = -1
current_dict = None
current_data = []
wig_ids = []
for line in wig_file:
if line.startswith("track"):
continue
# this line starts a wig block
elif line.startswith("variableStep") or line.startswith("fixedStep"):
# validate the wig header is valid
if not valid_wig_header(line):
return jsonify(response="Wig format incorrect"), 404
# get the values from the header
header_dict = parse_header(line)
# commit the bases from the the previous wig
if current_data:
session.add_all(current_data)
session.commit()
# create the new wig
wig = Wig(chrom=header_dict['chrom'])
session.add(wig)
session.commit()
current_id = wig.id
wig_ids.append(current_id)
current_dict = header_dict
current_data = []
# we have a data line
else:
# parse a var step line
if current_dict['stepType'] == "variableStep":
(position, score) = (int(val) for val in line.split())
# if there is no span it is easy
if 'span' not in current_dict:
wig_val = WigValue(position=position,
value=score,
wig_id=current_id)
current_data.append(wig_val)
# handle the span
else:
span = int(current_dict['span'])
for pos in range(position, position + span):
wig_val = WigValue(position=pos,
value=score,
wig_id=current_id)
current_data.append(wig_val)
# parse a fix step line
else:
score = int(line.strip())
# if there is no span it is easy
if 'span' not in current_dict:
wig_val = WigValue(position=current_dict['start'],
value=score,
wig_id=current_id)
current_data.append(wig_val)
current_dict['start'] += current_dict['step']
# handle the span
else:
span = current_dict['span']
for pos in range(current_dict['start'],
current_dict['start'] + span):
wig_val = WigValue(position=pos,
value=score,
wig_id=current_id)
current_data.append(wig_val)
current_dict['start'] += current_dict['step']
session.add_all(current_data)
session.commit()
return wig_ids
def new_file():
user_id = g.current_user_id
file = request.files['file']
type = request.form['type']
track_name = request.form['track_name'] if request.form.has_key('track_name') else file.filename
if not file:
return jsonify(response="Can't create upload file! No file found in form data"),404
if not type in ['wig','bed','gtf','fasta']:
return jsonify(response="Can't create upload file! {} is not a valid file type".format(type)),404
if type == 'fasta':
fasta_id = new_fasta(file)
new_track = Track(
track_name = track_name,
user_id = user_id,
data_type = type,
data_id = fasta_id,
file_name = file.filename,
)
session.add(new_track)
session.commit()
return jsonify(track_id = new_track.id)
elif type == 'wig':
wig_ids = new_wigs(file)
new_tracks = []
count = 1
for wig_id in wig_ids:
curr_name = "{}-{}".format(track_name, count)
count += 1
new_track = Track(
track_name = curr_name,
user_id = user_id,
data_type = type,
data_id = wig_id,
file_name = file.filename,
)
new_tracks.append(new_track)
session.add_all(new_tracks)
session.commit()
return jsonify(track_ids = [new_track.id for new_track in new_tracks])
elif type == 'gtf':
gtf_id = new_gtf(file)
new_track = Track(
track_name = track_name,
user_id = user_id,
data_type = type,
data_id = gtf_id,
file_name = file.filename,
)
session.add(new_track)
session.commit()
return jsonify(track_id = new_track.id)
elif type == 'bed':
bed_id = new_bed(file)
new_track = Track(
track_name = track_name,
user_id = user_id,
data_type = type,
data_id = bed_id,
file_name = file.filename,
)
session.add(new_track)
session.commit()
return jsonify(track_id = new_track.id)
def new_wigs(wig_file):
current_id = -1
current_dict = None
current_data = []
wig_ids = []
for line in wig_file:
if line.startswith("track"):
continue
# this line starts a wig block
elif line.startswith("variableStep") or line.startswith("fixedStep"):
# validate the wig header is valid
if not valid_wig_header(line):
return jsonify(response="Wig format incorrect"),404
# get the values from the header
header_dict = parse_header(line)
# commit the bases from the the previous wig
if current_data:
session.add_all(current_data)
session.commit()
# create the new wig
wig = Wig(chrom=header_dict['chrom'])
session.add(wig)
session.commit()
current_id = wig.id
wig_ids.append(current_id)
current_dict = header_dict
current_data = []
# we have a data line
else:
# parse a var step line
if current_dict['stepType'] == "variableStep":
(position, score) = (int(val) for val in line.split())
# if there is no span it is easy
if 'span' not in current_dict:
wig_val = WigValue(
position = position,
value = score,
wig_id = current_id
)
current_data.append(wig_val)
# handle the span
else:
span = int(current_dict['span'])
for pos in range(position, position+span):
wig_val = WigValue(
position = pos,
value = score,
wig_id = current_id
)
current_data.append(wig_val)
# parse a fix step line
else:
score = int(line.strip())
# if there is no span it is easy
if 'span' not in current_dict:
wig_val = WigValue(
position = current_dict['start'],
value = score,
wig_id = current_id
)
current_data.append(wig_val)
current_dict['start'] += current_dict['step']
# handle the span
else:
span = current_dict['span']
for pos in range(current_dict['start'], current_dict['start']+span):
wig_val = WigValue(
position = pos,
value = score,
wig_id = current_id
)
current_data.append(wig_val)
current_dict['start'] += current_dict['step']
session.add_all(current_data)
session.commit()
return wig_ids
def new_file():
user_id = g.current_user_id
file = request.files['file']
type = request.form['type']
track_name = request.form['track_name'] if request.form.has_key(
'track_name') else file.filename
if not file:
return jsonify(
response="Can't create upload file! No file found in form data"
), 404
if not type in ['wig', 'bed', 'gtf', 'fasta']:
return jsonify(
response="Can't create upload file! {} is not a valid file type".
format(type)), 404
if type == 'fasta':
fasta_id = new_fasta(file)
new_track = Track(
track_name=track_name,
user_id=user_id,
data_type=type,
data_id=fasta_id,
file_name=file.filename,
)
session.add(new_track)
session.commit()
return jsonify(track_id=new_track.id)
elif type == 'wig':
wig_ids = new_wigs(file)
new_tracks = []
count = 1
for wig_id in wig_ids:
curr_name = "{}-{}".format(track_name, count)
count += 1
new_track = Track(
track_name=curr_name,
user_id=user_id,
data_type=type,
data_id=wig_id,
file_name=file.filename,
)
new_tracks.append(new_track)
session.add_all(new_tracks)
session.commit()
return jsonify(track_ids=[new_track.id for new_track in new_tracks])
elif type == 'gtf':
gtf_id = new_gtf(file)
new_track = Track(
track_name=track_name,
user_id=user_id,
data_type=type,
data_id=gtf_id,
file_name=file.filename,
)
session.add(new_track)
session.commit()
return jsonify(track_id=new_track.id)
elif type == 'bed':
bed_id = new_bed(file)
new_track = Track(
track_name=track_name,
user_id=user_id,
data_type=type,
data_id=bed_id,
file_name=file.filename,
)
session.add(new_track)
session.commit()
return jsonify(track_id=new_track.id)
def seed_db():
# Setup default user #
default_user = User(username="******",
email="*****@*****.**",
password="******")
session.add(default_user)
session.commit()
# add the users
user_ids = [default_user.id]
users = ["kyle", "karl", "coda", "max", "goof"]
for name in users:
new_user = User(username=name,
email="{}@email.com".format(name),
password="******")
session.add(new_user)
session.commit()
user_ids.append(new_user.id)
## Give each a track ##
for u_id in user_ids:
view = View(view_name="Test View", user_id=u_id)
session.add(view)
session.commit()
# Create a fasta
fasta = Fasta(header=">EBV1")
session.add(fasta)
session.commit()
i = 0
for base in "ATTATTAGCATGCATGATCAGTAGCTAGGGGATGCATGCAACTGATCGATCGATGCATGCAT":
bp = BasePair(nucleotide=base, position=i, fasta_id=fasta.id)
i += 1
session.add(bp)
session.commit()
# Add a fasta track
fasta_track = Track(track_name="Fasta Test Track",
user_id=u_id,
data_type="fasta",
data_id=fasta.id,
file_name="testFasta.fasta")
session.add(fasta_track)
session.commit()
session.add(ViewTrack(fasta_track.id, view.id))
# Create a wig track
wig = Wig(chrom='EBV1')
session.add(wig)
session.commit()
for pos in range(1, 10):
wig_val = WigValue(position=pos, value=1, wig_id=wig.id)
session.add(wig_val)
# add the track
wig_track = Track(track_name="Wig Test Track",
user_id=u_id,
data_type="wig",
data_id=wig.id,
file_name="testWig.wig")
session.add(wig_track)
session.commit()
session.add(ViewTrack(wig_track.id, view.id))
# Create a GTF track
gtf = Gtf()
session.add(gtf)
session.commit()
for pos in range(1, 10):
gtf_val = GtfValue(seqname="EBV1",
source="mRNA-Seq",
feature="exon",
start=pos,
end=pos + 10,
score=0,
strand="+",
frame=0,
attribute="spanning-juncs=false;host=hg19",
gtf_id=gtf.id)
session.add(gtf_val)
gtf_track = Track(track_name="Gtf Test Track",
user_id=u_id,
data_type="gtf",
data_id=gtf.id,
file_name="testGtf.gtf")
session.add(gtf_track)
session.commit()
session.add(ViewTrack(gtf_track.id, view.id))
# last make a bed
bed = Bed()
session.add(bed)
session.commit()
for pos in range(1, 10):
bed_val = BedValue(chrom="EBV1",
start=pos,
end=pos + 9,
name="BED-THING",
score=0,
strand="+",
thick_start=pos,
thick_end=pos + 9,
item_rgb=10,
block_count=1,
bed_id=bed.id)
session.add(bed_val)
session.commit()
bb_size = BedBlockSize(index=pos,
value=pos + 9,
bed_value_id=bed_val.id)
bb_start = BedBlockStart(index=pos,
value=pos,
bed_value_id=bed_val.id)
session.add_all([bb_size, bb_start])
session.commit()
bed_track = Track(track_name="Bed Test Track",
user_id=u_id,
data_type="bed",
data_id=bed.id,
file_name="testBED.bed")
session.add(bed_track)
session.commit()
session.add(ViewTrack(bed_track.id, view.id))
session.commit()