def login():
if request.method == 'POST':
username = request.form['username']
password = request.form['password']
print("Trying to log in: %s" % username)
db = get_db()
error = None
user = db.execute(
'SELECT * FROM users WHERE username = ?', (username,)
).fetchone()
if user is None:
error = 'Incorrect username.'
elif not check_password_hash(user['password'], password):
error = 'Incorrect password. |%s| |%s|' % (user['password'],password)
if error is None:
session.clear()
session['user_id'] = user['id']
print(user['id'])
return redirect(url_for('home.index'))
flash(error)
return render_template('auth/login.html')
def register():
if request.method == 'POST':
print(request.form)
forename = request.form['forename'].title()
surname = request.form['surname'].title()
institution = request.form['institution'].lower()
country = request.form['country'].title()
username = request.form['email_address']
password = request.form['password']
password_redo = request.form['password_redo']
db = get_db()
error = None
if None in [forename,surname,institution,country,username,password,password_redo]:
error = 'Please fill in all boxes'
elif password!=password_redo:
error = 'Passwords do not match'
elif db.execute(
'SELECT id FROM user WHERE username = ?', (username,)
).fetchone() is not None:
error = 'User {} is already registered.'.format(username)
if error is None:
db.execute(
'INSERT INTO users (username, forename, surname, password, institution, country) VALUES (?, ?, ?, ?, ?, ?)',
(username, forename, surname, generate_password_hash(password), institution, country)
)
db.commit()
return redirect(url_for('auth.login'))
flash(error)
return render_template('auth/register.html')
def load_logged_in_user():
user_id = session.get('user_id')
if user_id is None:
g.user = None
else:
g.user = get_db().execute(
'SELECT * FROM users WHERE id = ?', (user_id,)
).fetchone()
def user_home():
db = get_db()
data = {}
sql_query = "select id,sample_name,created,status,lineage,drtype from results WHERE user_id = '%s'" % g.user[
"username"]
raw_data = db.execute(sql_query).fetchall()
data["num_samples"] = len(raw_data)
data["top_lineage"] = Counter([x["lineage"]
for x in raw_data]).most_common(1)[0][0]
data["top_drtype"] = Counter([x["drtype"]
for x in raw_data]).most_common(1)[0][0]
return render_template('user/user_home.html', data=data)
def run_result(sample_id):
db = get_db()
tmp = db.execute("SELECT * FROM results WHERE id = ?",
(str(sample_id), )).fetchone()
if tmp == None:
error = "Run does not exist"
abort(404)
run = dict(tmp)
run["result"] = json.loads(tmp["result"])
if request.method == 'POST':
json_results = run["result"]
csv_strings = {}
csv_strings["id"] = json_results["id"]
csv_strings["date"] = run["created"]
csv_strings["strain"] = json_results["sublin"]
csv_strings["drtype"] = json_results["drtype"]
csv_strings["dr_report"] = tbp.dict_list2csv(
json_results["drug_table"],
["Drug", "Genotypic Resistance", "Mutations"] + [])
csv_strings["lineage_report"] = tbp.dict_list2csv(
json_results["lineage"],
["lin", "frac", "family", "spoligotype", "rd"], {
"lin": "Lineage",
"frac": "Estimated fraction"
})
csv_strings["other_var_report"] = tbp.dict_list2csv(
json_results["other_variants"],
["genome_pos", "locus_tag", "change", "freq"], {
"genome_pos": "Genome Position",
"locus_tag": "Locus Tag",
"freq": "Estimated fraction"
})
csv_strings["pipeline"] = tbp.dict_list2csv(
json_results["pipline_table"], ["Analysis", "Program"])
csv_strings["version"] = json_results["tbprofiler_version"]
csv_strings["db_version"] = json_results["db_version"]
csv_text = tbp.load_csv(csv_strings)
return Response(csv_text,
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=%s.csv" % sample_id
})
return render_template('results/run_result.html', run=run)
def upload():
db = get_db()
if request.method == 'POST':
print(request.form)
error=None
username = g.user['username'] if g.user else 'private'
if "single_sample_submit" in request.form:
platform=request.form["platform"]
uniq_id = str(uuid.uuid4())
if "sample_name" in request.form:
sample_name = request.form["sample_name"] if request.form["sample_name"]!="" else uniq_id
else:
sample_name = uniq_id
if request.files['file1'].filename=="":
error = "No file found for read 1, please try again!"
if error==None:
run_sample(db,username,uniq_id,sample_name,platform,request.files['file1'],request.files['file2'])
return redirect(url_for('results.run_result', sample_id=uniq_id))
elif "multi_sample_submit" in request.form:
x = request.form
if request.form["r1_suffix"]!="" and request.form["r2_suffix"]!="":
print("Setting suffix")
r1_suffix = request.form["r1_suffix"].strip()
r2_suffix = request.form["r2_suffix"].strip()
elif request.form["r1_suffix"]=="" and request.form["r2_suffix"]=="":
r1_suffix = "_1.fastq.gz"
r2_suffix = "_2.fastq.gz"
else:
error = "If you would like to change the file suffix please fill in for both the forward and reverse"
if error==None:
files = {f.filename:f for f in list(request.files.lists())[0][1]}
if len(files)%2!=0:
error = "Odd number of files. There should be two files per sample, please check."
if error==None:
prefixes = set()
for f in files.keys():
tmp1 = re.search("(.+)%s" % r1_suffix,f)
tmp2 = re.search("(.+)%s" % r2_suffix,f)
if tmp1==None and tmp2==None:
error = "%s does not contain '_1.fastq.gz' or '_2.fastq.gz' as the file ending. Please revise your file names" % f
break
if tmp1:
prefixes.add(tmp1.group(1))
if tmp2:
prefixes.add(tmp2.group(1))
if error==None:
runs = []
for p in prefixes:
uniq_id = str(uuid.uuid4())
r1 = p + r1_suffix
r2 = p + r2_suffix
if r1 not in files:
error = "%s is present in data file but not %s. Please check." % (r2,r1)
if r2 not in files:
error = "%s is present in data file but not %s. Please check." % (r1,r2)
sample_name = p if g.user else uniq_id
runs.append({"ID":uniq_id,"sample_name":sample_name,"R1":r1,"R2":r2})
if error==None:
csv_text = "ID,Name,R1,R2\n" + "\n".join(["%(ID)s,%(sample_name)s,%(R1)s,%(R2)s" % d for d in runs])
for run in runs:
run_sample(db,username,run["ID"],run["sample_name"],request.form["platform"],files[run["R1"]],files[run["R2"]])
return Response(csv_text,mimetype="text/csv",headers={"Content-disposition": "attachment; filename=tb-profiler-IDs.csv"})
flash(error)
return render_template('upload/upload.html')
def result_table(request, user):
db = get_db()
if request.method == 'POST':
if "search_strains_button" in request.form:
sql_query = "select id,sample_name,created,status,lineage,drtype from results WHERE user_id = '%s'" % user
filters = []
key_values = list(request.form.lists())
for key, values in list(request.form.lists()):
if values == [""]:
continue
elif key == "sample_name":
filters.append("( %s )" % (" OR ".join([
"sample_name = '%s'" % (run_id.strip())
for run_id in values[0].split(",")
])))
elif key == "project_id":
pass
# filters.append("( %s )" % (" OR ".join(["project_id = '%s'" % (run_id.strip()) for run_id in values[0].split(",")])))
elif key == "drtype":
filters.append("( %s )" % (" OR ".join(
["drtype = '%s'" % (drtype) for drtype in values])))
elif key == "lineage":
filters.append("( %s )" % (" OR ".join([
"lineage LIKE 'lineage%s%%'" %
(lineage.strip().replace("lineage", ""))
for lineage in values[0].split(",")
])))
else:
pass
if len(filters) > 0:
sql_query = sql_query + " AND %s" % (" AND ".join(filters))
tmp = db.execute(sql_query).fetchall()
return render_template('results/result_table.html',
results=tmp,
user=user)
else:
# print(request.form)
if request.form["button"] == "download":
ids = list(json.loads(request.form["ids"]).keys())
cmd = "select * from full_results where id in ( %s )" % ", ".join(
["'%s'" % x for x in ids])
data = db.execute(cmd).fetchall()
fieldnames = [
x["name"] for x in db.execute(
"PRAGMA table_info(full_results)").fetchall()
]
csv_text = ",".join(fieldnames) + "\n"
for row in data:
csv_text = csv_text + ",".join([
'"%s"' % row[c] if
(row[c] != None and row[c] != "") else '"-"'
for c in fieldnames
]) + "\n"
return Response(csv_text,
mimetype="text/csv",
headers={
"Content-disposition":
"attachment; filename=result.csv"
})
elif request.form["button"] == "delete":
ids = list(json.loads(request.form["ids"]).keys())
cmd = "DELETE FROM results WHERE id in ( %s )" % ", ".join(
["'%s'" % x for x in ids])
db.execute(cmd)
db.commit()
return render_template('results/result_table.html', user=user)
def index():
db = get_db()
if request.method == 'POST':
return redirect(url_for('results.run_result', sample_id=request.form["sample_id"]))
return render_template('home/index.html')