def toggle_prefs():
# if re.search(r'^\d+$', request.form['user_id']) and \
# re.search(r'^[ft]$', request.form['pref_value']):
if re.search(r'^[ft]$', request.form['pref_value']) and \
re.search(r'^(email_pref|lovd_export)$', request.form['field']):
# mobiuser_id = request.form['user_id']
pref = request.form['pref_value']
field = request.form['field']
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"UPDATE mobiuser SET {0} = '{1}' WHERE id = '{2}'".format(field, pref, g.user['id'])
)
db.commit()
return 'ok'
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails error',
'<p>MD failed to modify a user prefs for {0}. User id: {1} to {2}</p>'.format(
request.form['field'],
g.user['id'],
request.form['pref_value']
)
),
'[MobiDetails - User prefs Error]'
)
return md_utilities.danger_panel('', 'Sorry, something went wrong when trying to update your preferences.\
An admin has been warned. Please try again later.')
def test_modif_class(client, app, auth, vf_id, acmg, acmg_com, return_value,
status_code2):
assert client.get('/modif_class').status_code == 405
with app.app_context():
response = client.post('/modif_class',
data=dict(variant_id=vf_id,
acmg_select=acmg,
acmg_comment=acmg_com),
follow_redirects=True)
assert b'check_login_form' in response.get_data(
) # means we are in the login page
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT password FROM mobiuser WHERE email = '*****@*****.**'"
)
res = curs.fetchone()
# login(client, '*****@*****.**', res['password'])
auth.login('*****@*****.**', res['password'])
response = client.post('/modif_class',
data=dict(variant_id=vf_id,
acmg_select=acmg,
acmg_comment=acmg_com),
follow_redirects=True)
assert response.status_code == status_code2
def remove_class():
if re.search(r'^\d+$', request.form['variant_id']) and \
re.search(r'^\d+$', request.form['acmg_class']):
variant_id = request.form['variant_id']
acmg_class = request.form['acmg_class']
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
try:
curs.execute(
"DELETE FROM class_history WHERE \
variant_feature_id = %s AND acmg_class = %s \
AND mobiuser_id = %s",
(variant_id, acmg_class, g.user['id'])
)
db.commit()
return 'ok'
except Exception as e:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails error',
'<p>Variant class deletion failed for {0} with args: {1}</p>'.format(variant_id, e.args)
),
'[MobiDetails - MD variant class Error]'
)
return md_utilities.danger_panel('', 'Sorry, something went wrong with the deletion of this annotation. An admin has been warned.')
def index():
# print(app.config['RUN_MODE'])
# check vv
md_api_url = '{0}{1}'.format(request.host_url[:-1],
url_for('api.check_vv_instance'))
vv_instance = json.loads(
http.request('GET', md_api_url).data.decode('utf-8'))
# count genes
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute("""
SELECT COUNT(DISTINCT(gene_symbol)) AS gene, COUNT(refseq) AS transcript
FROM gene
WHERE variant_creation = 'ok'
""")
res = curs.fetchone()
if res is None:
close_db()
error = 'There is a problem with the number of genes.'
flash(error, 'w3-pale-red')
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails PostGreSQL error',
'<p>There is a problem with the number of genes.\
<br /> in {}</p>'.format(os.path.basename(__file__))),
'[MobiDetails - PostGreSQL Error]')
else:
close_db()
return render_template('md/index.html',
run_mode=md_utilities.get_running_mode(),
nb_genes=res['gene'],
nb_isoforms=res['transcript'],
vv_instance=vv_instance)
def favourite():
if re.search(r'^\d+$', request.form['vf_id']):
vf_id = request.form['vf_id']
if vf_id is None:
flash('Cannot mark a variant without id! Please contact us.', 'w3-pale-red')
return 'notok'
# print(vf_id)
# g.user['id']
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
if request.form['marker'] == 'mark':
curs.execute(
"INSERT INTO mobiuser_favourite (mobiuser_id, feature_id) VALUES (%s, %s)",
(g.user['id'], vf_id)
)
else:
curs.execute(
"DELETE FROM mobiuser_favourite WHERE mobiuser_id = %s AND feature_id = %s",
(g.user['id'], vf_id)
)
db.commit()
close_db()
return 'ok'
else:
flash('Cannot mark a variant without id! Please contact us.', 'w3-pale-red')
return 'notok'
def api_variant_exists(variant_ghgvs=None):
if variant_ghgvs is None:
return jsonify(mobidetails_error='No variant submitted')
match_object = re.search(r'^([Nn][Cc]_0000\d{2}\.\d{1,2}):g\.(.+)', urllib.parse.unquote(variant_ghgvs))
if match_object:
db = get_db()
# match_object = re.search(r'^([Nn][Cc]_0000\d{2}\.\d{1,2}):g\.(.+)', variant_ghgvs)
# res_common = md_utilities.get_common_chr_name(db, match_object.group(1))
chrom, genome_version = md_utilities.get_common_chr_name(db, match_object.group(1).upper())
pattern = match_object.group(2)
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT feature_id FROM variant WHERE chr = %s AND g_name = %s AND genome_version = %s",
(chrom, pattern, genome_version)
)
res = curs.fetchone()
if res is not None:
return jsonify(mobidetails_id=res['feature_id'], url='{0}{1}'.format(
request.host_url[:-1], url_for('md.variant', variant_id=res['feature_id'])
))
# return jsonify(mobidetails_id=res['feature_id'])
else:
# return jsonify("SELECT feature_id FROM variant WHERE g_name = 'chr{0}:g.{1}' AND genome_version = '{2}'".format(chrom, pattern, genome_version))
return jsonify(mobidetails_warning='The variant {} does not exist yet in MD'.format(variant_ghgvs))
else:
return jsonify(mobidetails_error='Malformed query {}'.format(variant_ghgvs))
def variant_list(list_name):
if len(list_name) < 31 and \
re.search(r'^[\w]+$', list_name):
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"""
SELECT a.variant_ids, b.username, a.creation_date, a.list_name
FROM variants_groups a, mobiuser b
WHERE a.mobiuser_id = b.id AND list_name = %s
""", (list_name, ))
res = curs.fetchone()
# we've got an ARRAY of variants_ids and want to query on them...
if res:
res_ids_string = "("
for id in res['variant_ids']:
res_ids_string += "{}, ".format(id)
res_ids_string = res_ids_string[:-2]
res_ids_string += ")"
# print(res_ids_string)
curs.execute("""
SELECT a.id, a.c_name, a.p_name, a.gene_symbol, a.refseq, a.creation_user, a.creation_date, b.username
FROM variant_feature a, mobiuser b
WHERE a.creation_user = b.id AND a.id IN {0}
""".format(res_ids_string))
variants = curs.fetchall()
close_db()
return render_template('md/variant_multiple.html',
variants=variants,
unique_url_info=res)
else:
close_db()
return render_template('errors/404.html'), 404
else:
return render_template('errors/404.html'), 404
def test_send_var_message(client, app, auth, receiver_id, message_object,
message, status_code):
assert client.get('/send_var_message').status_code == 405
with app.app_context():
response = client.post('/send_var_message',
data=dict(receiver_id=receiver_id,
message_object=message_object,
message=message),
follow_redirects=True)
assert b'check_login_form' in response.get_data(
) # means we are in the login page
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT password FROM mobiuser WHERE email = '*****@*****.**'"
)
res = curs.fetchone()
# login(client, '*****@*****.**', res['password'])
auth.login('*****@*****.**', res['password'])
response = client.post('/send_var_message',
data=dict(receiver_id=receiver_id,
message_object=message_object,
message=message),
follow_redirects=True)
assert response.status_code == status_code
def activate(mobiuser_id, api_key):
if isinstance(mobiuser_id, int) and \
isinstance(api_key, str):
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT id, api_key, activated FROM mobiuser WHERE id = %s AND api_key = %s",
(mobiuser_id, api_key))
user = curs.fetchone()
if user is None:
message_body = '<p>Account activation exception</p><p>Recived API key: {0} and\
mobiuser_id: {1} from {2}'.format(
api_key, mobiuser_id, request.remote_addr)
md_utilities.send_error_email(
md_utilities.prepare_email_html('MobiDetails error',
message_body),
'[MobiDetails - Activation Error]')
flash(
'API key and user id do not seem to fit. An admin has been warned',
'w3-pale-red')
return render_template('md/index.html')
else:
if user['activated'] is False and \
user['api_key'] == api_key and \
user['id'] == mobiuser_id:
curs.execute(
"UPDATE mobiuser SET activated = 't' WHERE id = %s AND api_key = %s",
(user['id'], user['api_key']))
db.commit()
flash(
'Your account has been activated, you may now log in using your email address.',
'w3-pale-green')
return render_template('auth/login.html')
return render_template('md/unknown.html')
def test_intervar(client, app):
assert client.get('/intervar').status_code == 405
with app.app_context():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT a.genome_version, a.chr, a.pos, a.pos_ref, a.pos_alt, b.gene_name[1] as gene FROM variant a, variant_feature b WHERE \
a.feature_id = b.id AND a.genome_version = 'hg19' AND b.dna_type = 'substitution' AND \
b.start_segment_type = 'exon' AND c_name !~ '^[\*-]' AND p_name !~ '\?' ORDER BY random() LIMIT 5"
)
res = curs.fetchall()
for values in res:
data_dict = dict(genome=values['genome_version'],
chrom=values['chr'],
pos=values['pos'],
ref=values['pos_ref'],
alt=values['pos_alt'],
gene=values['gene'])
response = client.post('/intervar', data=data_dict)
assert response.status_code == 200
possible = [
b'athogenic', b'lassified', b'enign', b'ncertain',
b'wintervar looks down'
]
# https://stackoverflow.com/questions/6531482/how-to-check-if-a-string-contains-an-element-from-a-list-in-python/6531704#6531704
print(res)
print(response.get_data())
assert any(test in response.get_data() for test in possible)
def autocomplete_var():
query = request.form['query_engine']
gene = request.form['gene']
# match_object = re.search(r'^c\.([\w\d>_\*-]+)', query)
variant_regexp = md_utilities.regexp['variant']
match_object = re.search(rf'^c\.({variant_regexp})', query)
if match_object:
md_query = match_object.group(1)
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT c_name FROM variant_feature WHERE gene_name[1] = '{0}' AND c_name LIKE '{1}%' ORDER BY c_name LIMIT 10".format(
gene, md_query
)
)
res = curs.fetchall()
result = []
for var in res:
result.append('c.{}'.format(var[0]))
# print(json.dumps(result))
# print("SELECT c_name FROM variant_feature WHERE gene_name[1] = '{0}' AND c_name LIKE '{1}%' ORDER BY c_name LIMIT 10".format(gene, md_query))
if result is not None:
return json.dumps(result)
else:
return ('', 204)
return ('', 204)
def test_gene_page(client, app):
with app.app_context():
db = get_db()
curs = db.cursor()
curs.execute("SELECT name[1] FROM gene LIMIT 50", )
res = curs.fetchall()
for name in res:
assert client.get('/gene/{}'.format(name[0])).status_code == 200
def test_create_var_vv(client, app):
with app.app_context():
g = fake_g_obj()
error_dict = md_utilities.create_var_vv('NM_206933.2:c.100_101delinsA',
'USH2A', 'NM_206933',
'c.100_101delinsA',
'c.100_101delinsA', '2',
vv_dict, 'test', get_db(), g)
assert isinstance(error_dict['mobidetails_id'], int)
def api_gene(gene_hgnc=None):
if gene_hgnc is None:
return jsonify(mobidetails_error='No gene submitted')
if re.search(r'[^\w\.-]', gene_hgnc):
return jsonify(
mobidetails_error='Invalid gene submitted ({})'.format(gene_hgnc))
research = gene_hgnc
search_id = 1
match_obj = re.search(r'(NM_\d+)\.?\d?', gene_hgnc)
if match_obj:
# we have a RefSeq accession number
research = match_obj.group(1)
search_id = 2
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
if re.search(r'^\d+$', research):
curs.execute("SELECT * FROM gene WHERE hgnc_id = %s", (research, ))
else:
curs.execute("SELECT * FROM gene WHERE name[%s] = %s",
(search_id, research))
res = curs.fetchall()
d_gene = {}
if res:
for transcript in res:
if 'HGNC Name' not in d_gene:
d_gene['HGNC Name'] = transcript['name'][0]
if 'HGNC ID' not in d_gene:
d_gene['HGNC ID'] = transcript['hgnc_id']
if 'chr' not in d_gene:
d_gene['Chr'] = transcript['chr']
if 'strand' not in d_gene:
d_gene['Strand'] = transcript['strand']
if 'ng' not in d_gene:
if transcript['ng'] == 'NG_000000.0':
d_gene['RefGene'] = 'No RefGene in MobiDetails'
else:
d_gene['RefGene'] = transcript['ng']
refseq = '{0}.{1}'.format(transcript['name'][1],
transcript['nm_version'])
d_gene[refseq] = {
'canonical': transcript['canonical'],
}
if 'RefProtein' not in d_gene[refseq]:
if transcript['np'] == 'NP_000000.0':
d_gene[refseq][
'RefProtein'] = 'No RefProtein in MobiDetails'
else:
d_gene[refseq]['RefProtein'] = transcript['np']
if 'UNIPROT' not in d_gene[refseq]:
d_gene[refseq]['UNIPROT'] = transcript['uniprot_id']
if 'variantCreationTag' not in d_gene[refseq]:
d_gene[refseq]['variantCreationTag'] = transcript[
'variant_creation']
return jsonify(d_gene)
else:
return jsonify(
mobidetails_warning='Unknown gene ({})'.format(gene_hgnc))
def get_generic_api_key():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT api_key FROM mobiuser WHERE email = '*****@*****.**'"
)
res = curs.fetchone()
if res is not None:
return res['api_key']
def autocomplete():
query = request.form['query_engine']
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# match_object = re.search(r'^c\.([\w\d>_\*-]+)', query)
match_obj = re.search(rf'^rs(\d+)$', query)
if match_obj:
md_query = match_obj.group(1)
curs.execute(
"SELECT dbsnp_id FROM variant_feature WHERE dbsnp_id LIKE '{}%' ORDER BY dbsnp_id LIMIT 10".format(md_query)
)
res = curs.fetchall()
result = []
for var in res:
result.append('rs{}'.format(var[0]))
if result is not None:
return json.dumps(result)
else:
return ('', 204)
variant_regexp = md_utilities.regexp['variant']
match_object = re.search(rf'^c\.({variant_regexp})', query)
if match_object:
md_query = match_object.group(1)
curs.execute(
"SELECT DISTINCT(c_name) FROM variant_feature WHERE c_name LIKE '{}%' ORDER BY c_name LIMIT 10".format(md_query)
)
res = curs.fetchall()
result = []
for var in res:
result.append('c.{}'.format(var[0]))
# print(json.dumps(result))
# print("SELECT c_name FROM variant_feature WHERE gene_name[1] = '{0}' AND c_name LIKE '{1}%' ORDER BY c_name LIMIT 10".format(gene, md_query))
if result is not None:
return json.dumps(result)
else:
return ('', 204)
i = 1
if re.search(r'^[Nn][Mm]_.+', query):
i = 2
query = query.upper()
elif not re.search(r'orf', query):
query = query.upper()
curs.execute(
"SELECT DISTINCT name[1] FROM gene WHERE name[{0}] LIKE '%{1}%' ORDER BY name[1] LIMIT 5".format(i, query)
)
res = curs.fetchall()
result = []
for gene in res:
result.append(gene[0])
# print("SELECT DISTINCT name[1] FROM gene WHERE name[{0}] LIKE '%{1}%' ORDER BY name[1] LIMIT 5".format(i, query))
if result is not None:
return json.dumps(result)
else:
return ('', 204)
def load_logged_in_user():
user_id = session.get('user_id')
if user_id is None:
g.user = None
else:
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute("SELECT * FROM mobiuser WHERE id = %s", (user_id, ))
g.user = curs.fetchone()
close_db()
def test_variant_page(client, app):
with app.app_context():
db = get_db()
curs = db.cursor()
curs.execute(
"SELECT id FROM variant_feature WHERE c_name <> 'c.1A>T' ORDER BY random() LIMIT 100" # WHERE prot_type = 'missense'", # ORDER BY random() LIMIT 500
)
res = curs.fetchall()
for variant_id in res:
print(variant_id)
assert client.get('/variant/{}'.format(
variant_id[0])).status_code == 200
def forgot_pass():
if (md_utilities.get_running_mode() == 'maintenance'):
return render_template('md/index.html',
run_mode=md_utilities.get_running_mode())
if request.method == 'GET':
return render_template('auth/forgot_pass.html')
elif request.method == 'POST':
error = None
email = request.form['email']
if not re.search(r'^[a-zA-Z0-9\._%\+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}$',
email):
error = 'The email address does not look valid.'
flash(error, 'w3-pale-red')
return render_template('auth/forgot_pass.html')
else:
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute("SELECT * FROM mobiuser WHERE email = %s", (email, ))
user = curs.fetchone()
if user is None:
close_db()
error = """
Your email address {} seems to be unknown by the system.
""".format(email)
flash(error, 'w3-pale-red')
return render_template('auth/forgot_pass.html')
# message, mail_object, receiver
md_utilities.send_email(
md_utilities.prepare_email_html(
'MobiDetails - Reset your password', """
Dear {0},
<p>please follow the link below to reset your MobiDetails password:</p>
<p><a href="{1}{2}" title="Reset your MD password">
Reset your MD password</a></p>
<p>If you do not know why you receive this email,
do not follow the link and please alert
[email protected].</p><br />
""".format(
user['username'], request.host_url.rstrip('/'),
url_for('auth.reset_password',
mobiuser_id=user['id'],
api_key=user['api_key'],
ts=datetime.timestamp(datetime.now()))),
False), '[MobiDetails - Password reset]', [email])
flash(
"""
Please check your e-mail inbox.
You should have received a message with a link
to reset your password
""", 'w3-pale-green')
close_db()
return render_template('auth/forgot_pass.html')
return render_template('md/unknown.html')
def test_lovd(client, app):
assert client.get('/lovd').status_code == 405
with app.app_context():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT a.genome_version, a.chr, a.g_name, b.c_name FROM variant a, variant_feature b WHERE \
a.feature_id = b.id AND a.genome_version = 'hg19' ORDER BY random() LIMIT 5"
)
res = curs.fetchall()
for values in res:
data_dict = dict(genome=values['genome_version'], chrom=values['chr'], g_name=values['g_name'], c_name='c.{}'.format(values['c_name']))
assert client.post('/lovd', data=data_dict).status_code == 200
def test_defgen(client, app):
assert client.get('/defgen').status_code == 405
with app.app_context():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT feature_id, genome_version FROM variant OFFSET RANDOM() * (SELECT COUNT(*) FROM variant) LIMIT 50"
)
res = curs.fetchall()
for values in res:
data_dict = dict(vfid=values['feature_id'], genome=values['genome_version'])
response = client.post('/defgen', data=data_dict)
assert response.status_code == 200
assert b'Export Variant data to DEFGEN' in response.get_data()
def test_favourite(client, app, auth, vf_id, status_code):
assert client.get('/favourite').status_code == 405
with app.app_context():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT password FROM mobiuser WHERE email = '*****@*****.**'"
)
res = curs.fetchone()
response = client.post('/favourite', data=dict(vf_id=vf_id), follow_redirects=True)
print(response.get_data())
assert b'check_login_form' in response.get_data() # means we are in the login page
auth.login('*****@*****.**', res['password'])
assert client.post('/favourite', data=dict(vf_id=vf_id), follow_redirects=True).status_code == status_code
def genes():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute("""
SELECT DISTINCT(gene_symbol)
FROM gene
ORDER BY gene_symbol
""")
genes = curs.fetchall()
close_db()
if genes:
return render_template('md/genes.html',
run_mode=md_utilities.get_running_mode(),
genes=genes)
else:
return render_template('md/unknown.html',
run_mode=md_utilities.get_running_mode())
def test_check_api_key(app, api_key, result):
with app.app_context():
db = get_db()
if api_key == '':
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT api_key FROM mobiuser WHERE email = '*****@*****.**'"
)
res = curs.fetchone()
if res is not None:
api_key = res['api_key']
check = md_utilities.check_api_key(db, api_key)
if 'mobidetails_error' in check:
assert result == check['mobidetails_error']
else:
print(check['mobiuser'])
assert result == check['mobiuser'][4]
def send_var_message():
if re.search(r'^\d+$', request.form['receiver_id']):
if request.form['message'] != '' and \
re.search(r'Query\svia\sMobiDetails\sfrom', request.form['message_object']):
# sender = {}
receiver = {}
# variant = request.form['variant_mes']
# sender['id'] = request.form['sender_id']
receiver['id'] = request.form['receiver_id']
message = request.form['message']
message_object = request.form['message_object']
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# get username and email
curs.execute(
"SELECT id, username, email FROM mobiuser WHERE id = %s",
(receiver['id'])
)
# res = curs.fetchall()
receiver = curs.fetchone()
message.replace("\n", "<br />")
message += "<br /><br /><p>You can contact user {0} directly at {1}</p>".format(
g.user['username'],
g.user['email']
)
md_utilities.send_email(
md_utilities.prepare_email_html(message_object, message, False),
message_object,
[receiver['email']]
)
return md_utilities.info_panel('Your email has just been sent.', '', '', 'w3-pale-green')
else:
return md_utilities.danger_panel('', 'Please complete the message part of the form.')
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails error',
'<p>An email was not sent from {0} to {1}<br />Variant was {2}<br />Message was:<br />{3}</p>'.format(
g.user['sender_id'],
request.form['receiver_id'],
request.form['variant_mes'],
request.form['message'])
),
'[MobiDetails - Email Error]'
)
return md_utilities.danger_panel('', 'Sorry, something went wrong with this message. An admin has been warned.')
def test_register(client, app):
# test register returns no error
assert client.get('/auth/register').status_code == 200
response = client.post(
'/auth/register', data={
'username': '******', 'password': '******',
'country': 'a', 'institute': 'a', 'email': '*****@*****.**'
}
)
assert response.status_code == 200
# test db returns a value
with app.app_context():
db = get_db()
curs = db.cursor()
curs.execute(
"SELECT * FROM mobiuser WHERE username = '******'",
)
res = curs.fetchone()
assert res is not None
def defgen():
genome_regexp = md_utilities.regexp['genome']
if re.search(r'^\d+$', request.form['vfid']) and \
re.search(rf'^{genome_regexp}$', request.form['genome']):
variant_id = request.form['vfid']
genome = request.form['genome']
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# get all variant_features and gene info
curs.execute(
"SELECT * FROM variant_feature a, variant b, gene c WHERE \
a.id = b.feature_id AND a.gene_name = c.name AND a.id = '{0}'\
AND b.genome_version = '{1}'".format(variant_id, genome)
)
vf = curs.fetchone()
file_content = "GENE;VARIANT;A_ENREGISTRER;ETAT;RESULTAT;VARIANT_P;VARIANT_C;ENST;NM;POSITION_GENOMIQUE;CLASSESUR5;CLASSESUR3;COSMIC;RS;REFERENCES;CONSEQUENCES;COMMENTAIRE;CHROMOSOME;GENOME_REFERENCE;NOMENCLATURE_HGVS;LOCALISATION;SEQUENCE_REF;LOCUS;ALLELE1;ALLELE2\r\n"
file_content += "{0};{1}.{2}:c.{3};;;;p.{4};c.{3};{5};{1}.{2};{6};;;;rs{7};;{8};;chr{9};{10};chr{9}:g.{11};{12} {13};;;;\r\n".format(
vf['gene_name'][0], vf['gene_name'][1], vf['nm_version'], vf['c_name'], vf['p_name'], vf['enst'], vf['pos'],
vf['dbsnp_id'], vf['prot_type'], vf['chr'], genome, vf['g_name'], vf['start_segment_type'], vf['start_segment_number']
)
# print(file_content)
app_path = os.path.dirname(os.path.realpath(__file__))
file_loc = "defgen/{0}-{1}-{2}{3}-{4}.csv".format(genome, vf['chr'], vf['pos'], vf['pos_ref'], vf['pos_alt'])
defgen_file = open("{0}/static/{1}".format(app_path, file_loc), "w")
defgen_file.write(file_content)
close_db()
return render_template('ajax/defgen.html', variant="{0}.{1}:c.{2}".format(
vf['gene_name'][1], vf['nm_version'], vf['c_name']), defgen_file=file_loc, genome=genome)
else:
# close_db()
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails Ajax error',
'<p>DefGen file generation failed in {} (no variant_id)</p>'.format(
os.path.basename(__file__)
)
),
'[MobiDetails - Ajax Error]'
)
return '<div class="w3-blue w3-ripple w3-padding-16 w3-large w3-center" style="width:100%">Impossible to create DEFGEN file</div>'
def test_litvar(client, app):
assert client.get('/litVar').status_code == 405
with app.app_context():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT dbsnp_id FROM variant_feature WHERE dbsnp_id IS NOT NULL ORDER BY random() LIMIT 5"
)
# https://stackoverflow.com/questions/5297396/quick-random-row-selection-in-postgres
# discussion on how to select random rows in postgresql
res = curs.fetchall()
for values in res:
response = client.post('/litVar', data=dict(rsid='rs{0}'.format(values['dbsnp_id'])))
assert response.status_code == 200
possible = [
b'<div class="w3-blue w3-ripple w3-padding-16 w3-large w3-center" style="width:100%;">No match in Pubmed using LitVar API</div>',
b'PubMed links of articles citing this variant'
]
# https://stackoverflow.com/questions/6531482/how-to-check-if-a-string-contains-an-element-from-a-list-in-python/6531704#6531704
print(values['dbsnp_id'])
print(response.get_data())
assert any(test in response.get_data() for test in possible)
def check_api_key(api_key=None):
api_key = md_utilities.get_post_param(request, 'api_key')
# if request.args.get('api_key'):
# api_key = request.args.get('api_key', type=str)
# elif 'api_key' in request.form:
# api_key = request.form['api_key']
if not api_key:
return jsonify(mobidetails_error='I cannot fetch the right parameters',
api_key_pass_check=False,
api_key_status='irrelevant')
db = get_db()
response = md_utilities.check_api_key(db, api_key)
if 'mobiuser' in response:
if response['mobiuser']['activated'] is True:
return jsonify(api_key_submitted=api_key,
api_key_pass_check=True,
api_key_status='active')
return jsonify(api_key_submitted=api_key,
api_key_pass_check=True,
api_key_status='inactive')
return jsonify(api_key_submitted=api_key,
api_key_pass_check=False,
api_key_status='irrelevant')
def reset_password():
if request.method == 'GET':
if re.search(r'^\d+$', request.args.get('mobiuser_id')) and \
re.search(r'^[\d\.]+$', request.args.get('ts')):
mobiuser_id = request.args.get('mobiuser_id')
api_key = request.args.get('api_key')
original_timestamp = request.args.get('ts')
# we will keep the link alive for 30 minutes i.e. 1800 s
if float(float(datetime.timestamp(datetime.now())) - float(original_timestamp)) > 1800 or \
float(float(datetime.timestamp(datetime.now())) - float(original_timestamp)) < 0:
flash('This link is outdated. Please try again the procedure.',
'w3-pale-red')
return render_template('auth/login.html')
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT id, api_key, activated FROM mobiuser WHERE id = %s AND api_key = %s",
(mobiuser_id, api_key))
user = curs.fetchone()
if user is None:
message_body = '<p>Password reset exception</p><p>Received API key: {0} and\
mobiuser_id: {1} from {2}'.format(
api_key, mobiuser_id, request.remote_addr)
md_utilities.send_error_email(
md_utilities.prepare_email_html('MobiDetails error',
message_body),
'[MobiDetails - Password reset Error]')
flash(
'API key and user id do not seem to fit. An admin has been warned',
'w3-pale-red')
return render_template('auth/forgot_pass.html')
else:
return render_template('auth/reset_pass.html',
mobiuser_id=mobiuser_id,
api_key=api_key)
else:
message_body = '<p>Password reset exception</p><p>Received timestamp: {0} and\
mobiuser_id: {1} from {2}'.format(
request.args.get('ts'), request.args.get('mobiuser_id'),
request.remote_addr)
md_utilities.send_error_email(
md_utilities.prepare_email_html('MobiDetails error',
message_body),
'[MobiDetails - Password reset Error]')
flash('Some parameters are not legal. An admin has been warned',
'w3-pale-red')
return render_template('auth/forgot_pass.html')
elif request.method == 'POST':
mobiuser_id = request.form['mobiuser_id']
api_key = request.form['api_key']
password = request.form['password']
error = None
if len(password) < 8 or not re.match('[a-zA-Z0-9]+', password):
error = 'Password should be at least 8 characters and mix at least letters (upper and lower case) and numbers.'
else:
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"UPDATE mobiuser SET password= %s WHERE id = %s AND api_key = %s",
(generate_password_hash(password), mobiuser_id, api_key))
db.commit()
flash('Your password has just been reset.', 'w3-pale-green')
return render_template('auth/login.html')
if error is not None:
flash(error, 'w3-pale-red')
return render_template('auth/reset_pass.html',
mobiuser_id=mobiuser_id,
api_key=api_key)
return render_template('md/unknown.html')