def favourite():
if re.search(r'^\d+$', request.form['vf_id']):
vf_id = request.form['vf_id']
if vf_id is None:
flash('Cannot mark a variant without id! Please contact us.', 'w3-pale-red')
return 'notok'
# print(vf_id)
# g.user['id']
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
if request.form['marker'] == 'mark':
curs.execute(
"INSERT INTO mobiuser_favourite (mobiuser_id, feature_id) VALUES (%s, %s)",
(g.user['id'], vf_id)
)
else:
curs.execute(
"DELETE FROM mobiuser_favourite WHERE mobiuser_id = %s AND feature_id = %s",
(g.user['id'], vf_id)
)
db.commit()
close_db()
return 'ok'
else:
flash('Cannot mark a variant without id! Please contact us.', 'w3-pale-red')
return 'notok'
def index():
# print(app.config['RUN_MODE'])
# check vv
md_api_url = '{0}{1}'.format(request.host_url[:-1],
url_for('api.check_vv_instance'))
vv_instance = json.loads(
http.request('GET', md_api_url).data.decode('utf-8'))
# count genes
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute("""
SELECT COUNT(DISTINCT(gene_symbol)) AS gene, COUNT(refseq) AS transcript
FROM gene
WHERE variant_creation = 'ok'
""")
res = curs.fetchone()
if res is None:
close_db()
error = 'There is a problem with the number of genes.'
flash(error, 'w3-pale-red')
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails PostGreSQL error',
'<p>There is a problem with the number of genes.\
<br /> in {}</p>'.format(os.path.basename(__file__))),
'[MobiDetails - PostGreSQL Error]')
else:
close_db()
return render_template('md/index.html',
run_mode=md_utilities.get_running_mode(),
nb_genes=res['gene'],
nb_isoforms=res['transcript'],
vv_instance=vv_instance)
def variant_list(list_name):
if len(list_name) < 31 and \
re.search(r'^[\w]+$', 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 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 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,}$',
email):
error = 'The email address does not look valid.'
flash(error, 'w3-pale-red')
return render_template('auth/forgot_pass.html')
else:
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute("SELECT * FROM mobiuser WHERE email = %s", (email, ))
user = curs.fetchone()
if user is None:
close_db()
error = """
Your email address {} seems to be unknown by the system.
""".format(email)
flash(error, 'w3-pale-red')
return render_template('auth/forgot_pass.html')
# message, mail_object, receiver
md_utilities.send_email(
md_utilities.prepare_email_html(
'MobiDetails - Reset your password', """
Dear {0},
<p>please follow the link below to reset your MobiDetails password:</p>
<p><a href="{1}{2}" title="Reset your MD password">
Reset your MD password</a></p>
<p>If you do not know why you receive this email,
do not follow the link and please alert
[email protected].</p><br />
""".format(
user['username'], request.host_url.rstrip('/'),
url_for('auth.reset_password',
mobiuser_id=user['id'],
api_key=user['api_key'],
ts=datetime.timestamp(datetime.now()))),
False), '[MobiDetails - Password reset]', [email])
flash(
"""
Please check your e-mail inbox.
You should have received a message with a link
to reset your password
""", 'w3-pale-green')
close_db()
return render_template('auth/forgot_pass.html')
return render_template('md/unknown.html')
def genes():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute("""
SELECT DISTINCT(gene_symbol)
FROM gene
ORDER BY gene_symbol
""")
genes = curs.fetchall()
close_db()
if genes:
return render_template('md/genes.html',
run_mode=md_utilities.get_running_mode(),
genes=genes)
else:
return render_template('md/unknown.html',
run_mode=md_utilities.get_running_mode())
def defgen():
genome_regexp = md_utilities.regexp['genome']
if re.search(r'^\d+$', 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 activate(mobiuser_id, api_key):
if (md_utilities.get_running_mode() == 'maintenance'):
return render_template('md/index.html',
run_mode=md_utilities.get_running_mode())
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')
close_db()
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')
close_db()
return render_template('auth/login.html')
return render_template('md/unknown.html')
def api_variant_create_rs(rs_id=None, caller=None, api_key=None):
# get params
if request.args.get('rs_id') and \
request.args.get('caller') and \
request.args.get('api_key'):
rs_id = request.args.get('rs_id', type=str)
caller = request.args.get('caller', type=str)
api_key = request.args.get('api_key', type=str)
elif 'rs_id' in request.form and \
'caller' in request.form and \
'api_key' in request.form:
rs_id = request.form['rs_id']
caller = request.form['caller']
api_key = request.form['api_key']
else:
if caller == 'cli':
return jsonify(mobidetails_error='I cannot fetch the right parameters')
else:
flash('I cannot fetch the right parameters for MD API.', 'w3-pale-red')
return redirect(url_for('md.index'))
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# check api key
res_check_api_key = md_utilities.check_api_key(db, api_key)
if 'mobidetails_error' in res_check_api_key:
if caller == 'cli':
return jsonify(res_check_api_key)
else:
flash(res_check_api_key['mobidetails_error'], 'w3-pale-red')
return redirect(url_for('md.index'))
else:
g.user = res_check_api_key['mobiuser']
# check caller
if md_utilities.check_caller(caller) == 'Invalid caller submitted':
if caller == 'cli':
return jsonify(mobidetails_error='Invalid caller submitted')
else:
flash('Invalid caller submitted to the API.', 'w3-pale-red')
return redirect(url_for('md.index'))
# check rs_id
trunc_rs_id = None
match_obj = re.search(r'^rs(\d+)$', rs_id)
if match_obj:
trunc_rs_id = match_obj.group(1)
# check if rsid exists
curs.execute(
"SELECT a.c_name, a.id, b.name[2] as nm, b.nm_version FROM variant_feature a, gene b WHERE a.gene_name = b.name AND a.dbsnp_id = %s",
(trunc_rs_id,)
)
res_rs = curs.fetchall()
if res_rs:
vars_rs = {}
for var in res_rs:
current_var = '{0}.{1}:c.{2}'.format(var['nm'], var['nm_version'], var['c_name'])
vars_rs[current_var] = {
'mobidetails_id': var['id'],
'url': '{0}{1}'.format(
request.host_url[:-1],
url_for('md.variant', variant_id=var['id'])
)
}
if caller == 'cli':
return jsonify(vars_rs)
else:
if len(res_rs) == 1:
return redirect(url_for('md.variant', variant_id=res_rs['id']))
else:
return redirect(url_for('md.variant_multiple', vars_rs=vars_rs))
# use putalyzer to get HGVS noemclatures
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED', ca_certs=certifi.where())
mutalyzer_url = "{0}getdbSNPDescriptions?rs_id={1}".format(
md_utilities.urls['mutalyzer_api_json'], rs_id
)
# returns sthg like
# ["NC_000011.10:g.112088901C>T", "NC_000011.9:g.111959625C>T", "NG_012337.3:g.7055C>T", "NM_003002.4:c.204C>T", "NM_003002.3:c.204C>T", "NM_001276506.2:c.204C>T", "NM_001276506.1:c.204C>T", "NR_077060.2:n.239C>T", "NR_077060.1:n.288C>T", "NM_001276504.2:c.87C>T", "NM_001276504.1:c.87C>T", "NG_033145.1:g.2898G>A"]
try:
mutalyzer_data = json.loads(http.request('GET', mutalyzer_url).data.decode('utf-8'))
except Exception:
close_db()
if caller == 'cli':
return jsonify(mobidetails_error='Mutalyzer did not return any value for the variant {}.'.format(rs_id))
else:
flash('Mutalyzer did not return any value for the variant {}'.format(rs_id), 'w3-pale-red')
return redirect(url_for('md.index'))
# print(mutalyzer_data)
md_response = {}
# md_nm = list of NM recorded in MD, to be sure not to consider unexisting NM acc no
# md_nm = []
hgvs_nc = []
gene_names = []
# can_nm = None
for hgvs in mutalyzer_data: # works for exonic variants because mutalyzer returns no NM for intronic variants
variant_regexp = md_utilities.regexp['variant']
# match_nm = re.search(rf'^(NM_\d+)\.\d+:c\.({variant_regexp})$', hgvs)
# if match_nm:
# current_nm = match_nm.group(1)
# # get list of NM recorded in MD
# if not md_nm:
# curs.execute(
# "SELECT name[2] as nm FROM gene WHERE name[1] = (SELECT name[1] FROM gene WHERE name[2] = %s)",
# (current_nm,)
# )
# res_nm_all = curs.fetchall()
# if res_nm_all:
# for nm in res_nm_all:
# md_nm.append(nm[0])
# if current_nm in md_nm:
# # check if variant with same name already recorded => at least we do not query multiple times for these
# curs.execute(
# "SELECT id FROM variant_feature WHERE dbsnp_id = %s AND c_name = %s",
# (trunc_rs_id, match_nm.group(2),)
# )
# res_known = curs.fetchall()
# if not res_known:
# # get gene and MD current NM version
# curs.execute(
# "SELECT nm_version FROM gene WHERE name[2] = %s",
# (current_nm,)
# )
# res_nm = curs.fetchone()
# if res_nm:
# md_api_url = '{0}{1}'.format(request.host_url[:-1], url_for('api.api_variant_create'))
# variant_chgvs = '{0}.{1}:c.{2}'.format(current_nm, res_nm['nm_version'], match_nm.group(2))
# data = {
# 'variant_chgvs': urllib.parse.quote(variant_chgvs),
# 'caller': 'cli',
# 'api_key': api_key
# }
# try:
# md_response[variant_chgvs] = json.loads(http.request('POST', md_api_url, headers=md_utilities.api_agent, fields=data).data.decode('utf-8'))
# except Exception:
# md_response[variant_chgvs] = {'mobidetails_error': 'MobiDetails returned an unexpected error for your request {0}: {1}'.format(rs_id, variant_chgvs)}
# else:
# continue
# else:
# continue
# else:
# continue
# intronic variant?
# we need HGVS genomic to launch the API but also the gene - got from NG
# f-strings usage https://stackoverflow.com/questions/6930982/how-to-use-a-variable-inside-a-regular-expression
# https://www.python.org/dev/peps/pep-0498/
match_nc = re.search(rf'^(NC_0000\d{{2}}\.\d{{1,2}}):g\.({variant_regexp})$', hgvs)
if match_nc and \
not md_response:
# if hg38, we keep it in a variable that can be useful later
curs.execute(
"SELECT name, genome_version FROM chromosomes WHERE ncbi_name = %s",
(match_nc.group(1),)
)
res_chr = curs.fetchone()
if res_chr and \
res_chr['genome_version'] == 'hg38':
hgvs_nc.append(hgvs)
# look for gene name
positions = md_utilities.compute_start_end_pos(match_nc.group(2))
# print("SELECT a.name[1] as hgnc FROM gene a, segment b WHERE a.name = b.gene_name AND a.chr = {0} AND {1} BETWEEN SYMMETRIC # b.segment_start AND b.segment_end".format(res_chr['name'], positions[0]))
if not gene_names:
curs.execute(
"SELECT DISTINCT(a.name[1]) as hgnc FROM gene a, segment b WHERE a.name = b.gene_name AND a.chr = %s AND %s BETWEEN SYMMETRIC b.segment_start AND b.segment_end",
(res_chr['name'], positions[0])
)
res_gene = curs.fetchall()
if res_gene:
for hgnc_name in res_gene:
gene_names.append(hgnc_name[0])
# match_ng = re.search(rf'^(NG_\d+)\.\d+:g\.{variant_regexp}$', hgvs)
# if match_ng and \
# not gene_name and \
# not md_response:
# # we need to get the gene name that can be useful later
# curs.execute(
# "SELECT name[1] as hgnc FROM gene WHERE ng LIKE %s AND canonical = 't'",
# ('{}%'.format(match_ng.group(1)),)
# )
# res_gene = curs.fetchone()
# if res_gene:
# gene_name = res_gene['hgnc']
else:
continue
# do we have an intronic variant?
if hgvs_nc and \
gene_names: # and \
# not md_response:
md_api_url = '{0}{1}'.format(request.host_url[:-1], url_for('api.api_variant_g_create'))
for var_hgvs_nc in hgvs_nc:
for gene_hgnc in gene_names:
data = {
'variant_ghgvs': urllib.parse.quote(var_hgvs_nc),
'gene_hgnc': gene_hgnc,
'caller': 'cli',
'api_key': api_key
}
try:
# print('{0}-{1}'.format(var_hgvs_nc, gene_hgnc))
md_response[var_hgvs_nc] = json.loads(http.request('POST', md_api_url, headers=md_utilities.api_agent, fields=data).data.decode('utf-8'))
except Exception as e:
md_response[var_hgvs_nc] = {'mobidetails_error': 'MobiDetails returned an unexpected error for your request {0}: {1}'.format(rs_id, var_hgvs_nc)}
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails API error',
'<p>Error with MDAPI file writing for {0} ({1})<br /> - from {2} with args: {3}</p>'.format(
rs_id,
var_hgvs_nc,
os.path.basename(__file__),
e.args
)
),
'[MobiDetails - MDAPI Error]'
)
if md_response:
if caller == 'cli':
return jsonify(md_response)
else:
if len(md_response) == 1:
for var in md_response:
if 'mobidetails_error' in md_response[var]:
flash(md_response[var]['mobidetails_error'], 'w3-pale-red')
return redirect(url_for('md.index'))
return redirect(url_for('md.variant', variant_id=md_response[var]['mobidetails_id']))
else:
return render_template('md/variant_multiple.html', vars_rs=md_response)
# md_utilities.api_end_according_to_caller(
# caller=caller,
# message='Using Mutalyzer, we did not find any suitable variant corresponding to your request {}'.format(rs_id),
# url=url_for('md.index')
# )
if caller == 'cli':
return jsonify(mobidetails_error='Using Mutalyzer, we did not find any suitable variant corresponding to your request {}'.format(rs_id))
else:
flash('Using <a href="https://www.mutalyzer.nl/snp-converter?rs_id={0}", target="_blank">Mutalyzer</a>, we did not find any suitable variant corresponding to your request {0}'.format(rs_id), 'w3-pale-red')
return redirect(url_for('md.index'))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Invalid rs id provided')
else:
flash('Invalid rs id provided', 'w3-pale-red')
return redirect(url_for('md.index'))
def api_variant_g_create(variant_ghgvs=None, gene=None, caller=None, api_key=None):
# get params
if request.args.get('variant_ghgvs') and \
request.args.get('gene_hgnc') and \
request.args.get('caller') and \
request.args.get('api_key'):
variant_ghgvs = request.args.get('variant_ghgvs', type=str)
gene = request.args.get('gene_hgnc', type=str)
caller = request.args.get('caller', type=str)
api_key = request.args.get('api_key', type=str)
elif 'variant_ghgvs' in request.form and \
'gene_hgnc' in request.form and \
'caller' in request.form and \
'api_key' in request.form:
variant_ghgvs = request.form['variant_ghgvs']
gene = request.form['gene_hgnc']
caller = request.form['caller']
api_key = request.form['api_key']
else:
if caller == 'cli':
return jsonify(mobidetails_error='I cannot fetch the right parameters')
else:
flash('I cannot fetch the right parameters', 'w3-pale-red')
return redirect(url_for('md.index'))
if variant_ghgvs is not None and \
gene is not None and \
caller is not None and \
api_key is not None:
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# mobiuser_id = None
res_check_api_key = md_utilities.check_api_key(db, api_key)
if 'mobidetails_error' in res_check_api_key:
if caller == 'cli':
return jsonify(res_check_api_key)
else:
flash(res_check_api_key['mobidetails_error'], 'w3-pale-red')
return redirect(url_for('md.index'))
else:
g.user = res_check_api_key['mobiuser']
if md_utilities.check_caller(caller) == 'Invalid caller submitted':
if caller == 'cli':
return jsonify(mobidetails_error='Invalid caller submitted')
else:
flash('Invalid caller submitted to API.', 'w3-pale-red')
return redirect(url_for('md.index'))
# check gene exists
curs.execute(
"SELECT name, nm_version FROM gene WHERE name[1] = %s AND canonical = 't'",
(gene,)
)
res_gene = curs.fetchone()
if res_gene:
variant_regexp = md_utilities.regexp['variant']
match_object = re.search(rf'^([Nn][Cc]_0000\d{{2}}\.\d{{1,2}}):g\.({variant_regexp})', urllib.parse.unquote(variant_ghgvs))
if match_object:
ncbi_chr, g_var = match_object.group(1), match_object.group(2)
# 1st check hg38
curs.execute(
"SELECT * FROM chromosomes WHERE ncbi_name = %s",
(ncbi_chr,)
)
res = curs.fetchone()
if res and \
res['genome_version'] == 'hg38':
genome_version, chrom = res['genome_version'], res['name']
# check if variant exists
curs.execute(
"SELECT feature_id FROM variant WHERE genome_version = %s AND g_name = %s AND chr = %s",
(genome_version, g_var, chrom)
)
res = curs.fetchone()
if res:
if caller == 'cli':
return jsonify(
mobidetails_id=res['feature_id'],
url='{0}{1}'.format(
request.host_url[:-1],
url_for('md.variant', variant_id=res['feature_id'])
)
)
else:
return redirect(url_for('md.variant', variant_id=res['feature_id']))
else:
# creation
vv_base_url = md_utilities.get_vv_api_url()
if not vv_base_url:
close_db()
if caller == 'cli':
return jsonify(mobidetails_error='Variant Validator looks down!.')
else:
flash('Variant Validator looks down!.', 'w3-pale-red')
return redirect(url_for('md.index'))
vv_url = "{0}VariantValidator/variantvalidator/GRCh38/{1}/all?content-type=application/json".format(
vv_base_url, variant_ghgvs
)
# print(vv_url)
# vv_key_var = "{0}.{1}:c.{2}".format(acc_no, acc_version, new_variant)
try:
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED', ca_certs=certifi.where())
vv_data = json.loads(http.request('GET', vv_url).data.decode('utf-8'))
except Exception:
close_db()
if caller == 'cli':
return jsonify(mobidetails_error='Variant Validator did not return any value for the variant {}.'.format(urllib.parse.unquote(variant_ghgvs)))
else:
try:
flash('There has been a issue with the annotation of the variant via VariantValidator. \
The error is the following: {}'.format(vv_data['validation_warning_1']['validation_warnings']), 'w3-pale-red')
except Exception:
flash('There has been a issue with the annotation of the variant via VariantValidator. \
Sorry for the inconvenience. You may want to try directly in MobiDetails.', 'w3-pale-red')
return redirect(url_for('md.index'))
# look for gene acc #
# print(vv_data)
new_variant = None
vv_key_var = None
res_gene_non_can_list = []
# we still need a list of non canonical NM for the gene of interest
curs.execute(
"SELECT name, nm_version FROM gene WHERE name[1] = %s AND canonical = 'f'",
(gene,)
)
res_gene_non_can = curs.fetchall()
for transcript in res_gene_non_can:
res_gene_non_can_list.append('{0}.{1}'.format(transcript['name'][1], transcript['nm_version']))
for key in vv_data.keys():
variant_regexp = md_utilities.regexp['variant']
match_obj = re.search(rf'^([Nn][Mm]_\d+)\.(\d{{1,2}}):c\.({variant_regexp})', key)
if match_obj:
new_variant = match_obj.group(3)
# print("{0}-{1}-{2}-{3}".format(match_obj.group(1), res_gene['name'][1], match_obj.group(2), res_gene['nm_version']))
if match_obj.group(1) == res_gene['name'][1] and \
str(match_obj.group(2)) == str(res_gene['nm_version']):
# treat canonical as priority
vv_key_var = "{0}.{1}:c.{2}".format(match_obj.group(1), match_obj.group(2), match_obj.group(3))
break
elif not vv_key_var:
# take into account non canonical isoforms
# print('{0}.{1}'.format(match_obj.group(1), match_obj.group(2)))
# print(res_gene_non_can_list)
if '{0}.{1}'.format(match_obj.group(1), match_obj.group(2)) in res_gene_non_can_list:
vv_key_var = "{0}.{1}:c.{2}".format(match_obj.group(1), match_obj.group(2), match_obj.group(3))
if vv_key_var:
# print(vv_key_var)
creation_dict = md_utilities.create_var_vv(
vv_key_var, res_gene['name'][0], res_gene['name'][1],
'c.{}'.format(new_variant), new_variant,
res_gene['nm_version'], vv_data, 'api', db, g
)
if caller == 'cli':
return jsonify(creation_dict)
else:
return redirect(url_for('md.variant', variant_id=creation_dict['mobidetails_id']))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Could not create variant {} (possibly considered as intergenic).'.format(urllib.parse.unquote(variant_ghgvs)), variant_validator_output=vv_data)
else:
try:
flash('There has been a issue with the annotation of the variant via VariantValidator. \
The error is the following: {}'.format(vv_data['validation_warning_1']['validation_warnings']), 'w3-pale-red')
except Exception:
flash('There has been a issue with the annotation of the variant via VariantValidator. \
Sorry for the inconvenience. You may want to try directly in MobiDetails.', 'w3-pale-red')
return redirect(url_for('md.index'))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Unknown chromosome {} submitted or bad genome version (hg38 only)'.format(ncbi_chr))
else:
flash('The submitted chromosome or genome version looks corrupted (hg38 only).', 'w3-pale-red')
return redirect(url_for('md.index'))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Malformed query {}'.format(urllib.parse.unquote(variant_ghgvs)))
else:
flash('The query seems to be malformed: {}.'.format(urllib.parse.unquote(variant_ghgvs)), 'w3-pale-red')
return redirect(url_for('md.index'))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Unknown gene {} submitted'.format(gene))
else:
flash('Unknown gene {} submitted'.format(gene), 'w3-pale-red')
return redirect(url_for('md.index'))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Invalid parameters')
else:
flash('The submitted parameters looks invalid!!!', 'w3-pale-red')
return redirect(url_for('md.index'))
def file_upload():
if request.method == 'POST':
if request.files:
uploaded_file = request.files['file']
if uploaded_file.filename == "":
flash('No filename.', 'w3-pale-red')
return redirect(request.url)
if allowed_file(uploaded_file.filename):
# filename = secure_filename(uploaded_file.filename)
lines = uploaded_file.read().decode().replace(
'\r\n', '\n').replace('\r', '\n').split('\n')
# print(lines)
# ok we've got the file
# get user API key or use MD
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED',
ca_certs=certifi.where())
# headers
header = md_utilities.api_agent
result = []
api_key = md_utilities.get_api_key(g, curs)
if api_key is None:
flash('There is an issue in obtaining an API key')
return redirect(request.url)
# we need to check the format and send a proper query to the API
for line in lines:
# print('-{}-'.format(line))
# cDNA format
md_response = []
if re.search(r'^#', line) or \
line == '':
continue
line = line.replace(' ', '')
variant_regexp = md_utilities.regexp['variant']
match_obj_c = re.search(
rf'^([Nn][Mm]_\d+)\.(\d+):(c\.{variant_regexp})$',
line)
if match_obj_c:
# check NM number and version
curs.execute(
"SELECT nm_version FROM gene WHERE name[2] = %s",
(match_obj_c.group(1), ))
res_nm = curs.fetchone()
if res_nm:
# send var to api
md_api_url = '{0}{1}'.format(
request.host_url[:-1],
url_for('api.api_variant_create'))
# md_api_url = '{0}/api/variant/create'.format(md_api_base_url)
# print(md_api_url)
data = {
'variant_chgvs':
urllib.parse.quote('{0}.{1}:{2}'.format(
match_obj_c.group(1), match_obj_c.group(2),
match_obj_c.group(3))),
'caller':
'cli',
'api_key':
api_key
}
try:
md_response = json.loads(
http.request(
'POST',
md_api_url,
headers=header,
fields=data).data.decode('utf-8'))
# print(md_response)
result.append({
'variant':
line,
'id':
md_response['mobidetails_id'],
'url':
md_response['url']
})
except Exception:
if 'mobidetails_error' in md_response:
result.append({
'variant':
line,
'error':
md_response['mobidetails_error']
})
else:
result.append({
'variant': line,
'error': 'MDAPI call failed'
})
else:
result.append({
'variant':
line,
'error':
'Unknown NCBI NM accession number'
})
continue
# genomic format
match_obj_g = re.search(
rf'^([Nn][Cc]_\d+\.\d+:g\.{variant_regexp});([\w-]+)$',
line)
if match_obj_g:
# check NM number and version
curs.execute(
"SELECT nm_version FROM gene WHERE name[1] = %s",
(match_obj_g.group(2), ))
res_nm = curs.fetchone()
if res_nm:
# send var to api
md_api_url = '{0}{1}'.format(
request.host_url[:-1],
url_for('api.api_variant_g_create'))
# print(md_api_url)
data = {
'variant_ghgvs':
urllib.parse.quote(match_obj_g.group(1)),
'gene_hgnc':
match_obj_g.group(2),
'caller':
'cli',
'api_key':
api_key
}
try:
md_response = json.loads(
http.request(
'POST',
md_api_url,
headers=header,
fields=data).data.decode('utf-8'))
# print(md_response)
result.append({
'variant':
line,
'id':
md_response['mobidetails_id']
})
except Exception:
if 'variant_validator_output' in md_response and \
'validation_warning_1' in md_response['variant_validator_output'] and \
'validation_warnings' in md_response['variant_validator_output']['validation_warning_1']:
result.append({
'variant':
line,
'error':
md_response['variant_validator_output']
['validation_warning_1']
['validation_warnings'][0]
})
elif 'mobidetails_error' in md_response:
result.append({
'variant':
line,
'error':
md_response['mobidetails_error']
})
v
else:
result.append({
'variant': line,
'error': 'MDAPI call failed'
})
else:
result.append({
'variant': line,
'error': 'Unknown gene'
})
continue
if re.search(rf'^rs\d+$', line):
md_api_url = '{0}{1}'.format(
request.host_url[:-1],
url_for('api.api_variant_create_rs'))
# md_api_url = '{0}/api/variant/create'.format(md_api_base_url)
# print(md_api_url)
data = {
'rs_id': line,
'caller': 'cli',
'api_key': api_key
}
try:
md_response = json.loads(
http.request('POST',
md_api_url,
headers=header,
fields=data).data.decode('utf-8'))
for var in md_response:
print(md_response[var])
if 'mobidetails_error' in md_response[var]:
result.append({
'variant':
'{0} - {1}'.format(line, var),
'error':
md_response[var]['mobidetails_error']
})
elif var == 'mobidetails_error':
result.append({
'variant': line,
'error': md_response[var]
})
else:
result.append({
'variant':
'{0} - {1}'.format(line, var),
'id':
md_response[var]['mobidetails_id'],
'url':
md_response[var]['url']
})
except Exception:
result.append({
'variant': line,
'error': 'MDAPI call failed'
})
continue
result.append({'variant': line, 'error': 'Bad format'})
close_db()
flash('File correctly uploaded', 'w3-pale-green')
if g.user:
# send an email
# print(g.user)
result_list = ''
for resul in result:
result_list = '{0}<li>{1}'.format(
result_list, resul['variant'])
if 'error' in resul:
result_list = '{0} - {1}</li>'.format(
result_list, resul['error'])
else:
result_list = '{0} - <a href="{1}{2}">success</a></li>'.format(
result_list, request.host_url[:-1],
url_for('md.variant', variant_id=resul['id']))
message = 'Dear {0},<br /><p>Your batch job returned the following results:</p><ul>{1}</ul><p>You can have a direct acces to the successfully annotated variants at your <a href="{2}{3}">profile page</a>.'.format(
g.user['username'], result_list, request.host_url[:-1],
url_for('auth.profile', mobiuser_id=0))
md_utilities.send_email(
md_utilities.prepare_email_html(
'MobiDetails - Batch job', message, False),
'[MobiDetails - Batch job]', [g.user['email']])
return render_template('md/variant_multiple.html',
upload=result)
else:
flash('That file extension is not allowed', 'w3-pale-red')
return redirect(request.url)
return render_template("upload/upload_form.html")
def gene(gene_symbol=None):
if gene_symbol is None:
return render_template('md/unknown.html', query='No gene provided')
gene_match_obj = re.search(r'^([\w-]+)$', gene_symbol)
if not gene_match_obj:
return render_template('md/unknown.html', query=gene_symbol)
gene_symbol = gene_match_obj.group(1)
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# main isoform? now canonical is stored in db
curs.execute(
"""
SELECT *
FROM gene
WHERE gene_symbol = %s
AND canonical = 't'
""", (gene_symbol, ))
main = curs.fetchone()
if main:
curs.execute("""
SELECT *
FROM gene
WHERE gene_symbol = %s
ORDER BY number_of_exons DESC
""", (gene_symbol, )) # get all isoforms
result_all = curs.fetchall()
num_iso = len(result_all)
# get metadome json?
enst_ver = {}
# if not json metadome file on filesystem, create it in
# radboud server, then next time get it - it will then be
# available for future requests
# if we have the main => next step
if not os.path.isfile('{0}{1}.json'.format(
md_utilities.local_files['metadome']['abs_path'],
main['enst'])):
for gene in result_all:
if not os.path.isfile('{0}{1}.json'.format(
md_utilities.local_files['metadome']['abs_path'],
gene['enst'])):
if gene['enst'] not in enst_ver:
# get enst versions in a dict
metad_ts = None
try:
metad_ts = json.loads(
http.request(
'GET', '{0}get_transcripts/{1}'.format(
md_utilities.urls['metadome_api'],
gene['gene_symbol'])).data.decode(
'utf-8'))
if metad_ts is not None and \
'trancript_ids' in metad_ts:
for ts in metad_ts['trancript_ids']:
if ts['has_protein_data']:
match_obj = re.search(
r'^(ENST\d+)\.\d',
ts['gencode_id'])
enst_ver[match_obj.group(
1)] = ts['gencode_id']
except Exception as e:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails API error', """
<p>MetaDome first block code failed for gene {0} ({1})<br /> - from {2} with args: {3}</p>
""".format(gene_symbol, gene['enst'],
os.path.basename(__file__),
e.args)),
'[MobiDetails - API Error]')
break
# we check if data exist at metadome
# we have a set of metadome transcripts
for enst in enst_ver:
# print('enst: {}'.format(enst_ver[enst]))
# print('--{}--'.format(app.debug))
# print(json.dumps({'transcript_id': enst_ver[enst]}))
if not os.path.isfile('{0}{1}.json'.format(
md_utilities.local_files['metadome']['abs_path'], enst)):
metad_data = None
try:
metad_data = json.loads(
http.request(
'GET', '{0}status/{1}/'.format(
md_utilities.urls['metadome_api'],
enst_ver[enst])).data.decode('utf-8'))
except Exception as e:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails API error', """
<p>MetaDome second block code failed for gene {0} ({1})<br /> - from {2} with args: {3}</p>
""".format(gene_symbol, enst,
os.path.basename(__file__), e.args)),
'[MobiDetails - API Error]')
if metad_data is not None:
if metad_data['status'] == 'PENDING':
# get transcript_ids ?? coz of the version number
# send request to build visualization to metadome
vis_request = None
# find out how to get app object
try:
# enst_metadome = {transcript_id: enst_ver[enst]}
header = md_utilities.api_agent
header['Content-Type'] = 'application/json'
vis_request = json.loads(
http.request(
'POST',
'{0}submit_visualization/'.format(
md_utilities.urls['metadome_api']),
# headers={'Content-Type': 'application/json'},
headers=header,
body=json.dumps({
'transcript_id':
enst_ver[enst]
})).data.decode('utf-8'))
if not app.debug:
app.logger.info(
'{} submitted to metadome'.format(
vis_request['transcript_id']))
else:
print('{} submitted to metadome'.format(
vis_request['transcript_id']))
except Exception as e:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails API error', """
<p>Error with metadome submission for {0} ({1})<br /> - from {2} with args: {3}</p>
""".format(gene_symbol, enst,
os.path.basename(__file__),
e.args)),
'[MobiDetails - API Error]')
# print('Error with metadome
# submission for {}'.format(enst))
elif metad_data['status'] == 'SUCCESS':
# get_request = None
try:
get_request = json.loads(
http.request(
'GET', '{0}result/{1}/'.format(
md_utilities.urls['metadome_api'],
enst_ver[enst])).data.decode('utf-8'))
# copy in file system
with open('{0}{1}.json'.format(
md_utilities.local_files['metadome']
['abs_path'], enst),
"w",
encoding='utf-8') as metad_file:
json.dump(get_request,
metad_file,
ensure_ascii=False,
indent=4)
if not app.debug:
app.logger.info(
'saving metadome {} into local file system'
.format(enst_ver[enst]))
else:
print(
'saving metadome {} into local file system'
.format(enst_ver[enst]))
except Exception as e:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails API error', """
<p>Error with metadome file writing for {0} ({1})<br /> - from {2} with args: {3}</p>
""".format(gene_symbol, enst,
os.path.basename(__file__),
e.args)),
'[MobiDetails - API Error]')
# print('error saving metadome json
# file for {}'.format(enst))
if result_all is not None:
# get annotations
curs.execute(
"""
SELECT *
FROM gene_annotation
WHERE gene_symbol = %s
""", (gene_symbol, ))
annot = curs.fetchone()
if annot is None:
annot = {'nognomad': 'No values in gnomAD'}
curs.execute(
"""
SELECT MAX(prot_size) AS size
FROM gene
WHERE gene_symbol = %s
""", (gene_symbol, ))
res_size = curs.fetchone()
# get refseq select, mane, etc from vv json file
no_vv_file = 0
try:
json_file = open(
'{0}{1}.json'.format( # lgtm [py/path-injection]
md_utilities.local_files['variant_validator']
['abs_path'], gene_symbol))
except IOError:
no_vv_file = 1
if no_vv_file == 0:
transcript_road_signs = {}
vv_json = json.load(json_file)
if 'error' in vv_json \
or ('message' in vv_json and
vv_json['message'] == 'Internal Server Error'):
no_vv_file = 1
curs.execute(
"""
UPDATE gene
SET variant_creation = 'not_in_vv_json'
WHERE gene_symbol = %s
AND variant_creation <> 'not_in_vv_json'
""", (gene_symbol, ))
db.commit()
curs.execute("""
SELECT *
FROM gene
WHERE gene_symbol = %s
ORDER BY number_of_exons DESC
""", (gene_symbol, )) # get all isoforms
result_all = curs.fetchall()
num_iso = len(result_all)
if no_vv_file == 0:
for vv_transcript in vv_json['transcripts']:
for res in result_all:
# need to check vv isoforms against MD isoforms to keep only relevant ones
if vv_transcript['reference'] == res['refseq']:
if 'mane_select' in vv_transcript['annotations'] and \
'mane_plus_clinical' in vv_transcript['annotations'] and \
'refseq_select' in vv_transcript['annotations']:
transcript_road_signs[res['refseq']] = {
'mane_select':
vv_transcript['annotations']
['mane_select'],
'mane_plus_clinical':
vv_transcript['annotations']
['mane_plus_clinical'],
'refseq_select':
vv_transcript['annotations']
['refseq_select']
}
# print(transcript_road_signs)
close_db()
clingen_criteria_specification_id = md_utilities.get_clingen_criteria_specification_id(
gene_symbol)
return render_template('md/gene.html',
run_mode=md_utilities.get_running_mode(),
urls=md_utilities.urls,
gene_symbol=gene_symbol,
num_iso=num_iso,
main_iso=main,
res=result_all,
annotations=annot,
max_prot_size=res_size['size'],
clingen_criteria_specification_id=
clingen_criteria_specification_id,
transcript_road_signs=transcript_road_signs)
else:
close_db()
return render_template('md/unknown.html',
run_mode=md_utilities.get_running_mode(),
query=gene_symbol)
else:
close_db()
return render_template('md/unknown.html',
run_mode=md_utilities.get_running_mode(),
query=gene_symbol)
def search_engine():
# print("--{}--".format(request.form['search']))
query_engine = request.form['search']
# query_engine = query_engine.upper()
error = None
variant_regexp = md_utilities.regexp['variant']
variant_regexp_flexible = md_utilities.regexp['variant_flexible']
amino_acid_regexp = md_utilities.regexp['amino_acid']
nochr_captured_regexp = md_utilities.regexp['nochr_captured']
ncbi_transcript_regexp = md_utilities.regexp['ncbi_transcript']
vcf_str_regexp = md_utilities.regexp['vcf_str']
if query_engine is not None and \
query_engine != '':
pattern = ''
query_type = ''
sql_table = 'variant_feature'
col_names = 'id, c_name, gene_symbol, refseq, p_name'
semaph_query = 0
query_engine = re.sub(r'\s', '', query_engine)
query_engine = re.sub(r"'", '', query_engine)
if re.search(r'^last$', query_engine):
# get variant annotated the last 7 days
if 'db' not in locals():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
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.creation_date > CURRENT_DATE - 7
ORDER BY creation_date DESC
""")
variants = curs.fetchall()
close_db()
return render_template('md/variant_multiple.html',
variants=variants)
match_object = re.search(
rf'^([Gg]*[rR]*[hHcC][gGhH][13][978])[:_-]({vcf_str_regexp})$',
query_engine)
# match_object = re.search(rf'^{vcf_str_regexp}$', query_engine)
if match_object:
genome_version = md_utilities.translate_genome_version(
match_object.group(1))
if genome_version != 'wrong_genome_input':
if 'db' not in locals():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
api_key = md_utilities.get_api_key(g, curs)
if api_key is not None:
close_db()
return redirect(url_for('api.api_create_vcf_str',
genome_version=genome_version,
vcf_str=match_object.group(2),
caller='browser',
api_key=api_key),
code=307)
else:
error = 'Your genome version looks suspicious ({}). Supported are hg19, hg38, GRCh37, GRCh38'.format(
match_object.group(1))
else:
match_object = re.search(rf'^{vcf_str_regexp}$', query_engine)
if match_object:
if 'db' not in locals():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
api_key = md_utilities.get_api_key(g, curs)
if api_key is not None:
close_db()
return redirect(url_for('api.api_create_vcf_str',
vcf_str=query_engine,
caller='browser',
api_key=api_key),
code=307)
match_object = re.search(
rf'^([{amino_acid_regexp}]{{1}})(\d+)([{amino_acid_regexp}\*]{{1}})$',
query_engine) # e.g. R34X
if match_object:
confusing_genes = [
'C1R', 'C8G', 'S100G', 'F11R', 'C1S', 'A2M', 'C1D', 'S100P',
'F2R', 'C8A', 'C4A'
]
# list of genes that look like the query
if query_engine.upper() in confusing_genes:
sql_table = 'gene'
query_type = 'gene_symbol'
col_names = 'gene_symbol'
pattern = query_engine.upper()
else:
query_type = 'p_name'
pattern = md_utilities.one2three_fct(query_engine)
elif re.search(r'^rs\d+$', query_engine):
query_type = 'dbsnp_id'
match_object = re.search(r'^rs(\d+)$', query_engine)
pattern = match_object.group(1)
elif re.search(r'^p\..+', query_engine):
query_type = 'p_name'
var = md_utilities.clean_var_name(query_engine)
match_object = re.search(r'^(\w{1})(\d+)([\w\*]{1})$',
var) # e.g. p.R34X
match_object_inter = re.search(r'^(\w{1})(\d+)([d][ue][pl])',
var) # e.g. p.L34del
match_object_long = re.search(r'^(\w{1})(\d+_)(\w{1})(\d+.+)$',
var) # e.g. p.R34_E68del
if match_object or match_object_inter or match_object_long:
pattern = md_utilities.one2three_fct(var)
else:
if re.search('X', var):
pattern = re.sub(r'X', 'Ter', var)
elif re.search(r'\*', var):
pattern = re.sub(r'\*', 'Ter', var)
else:
pattern = var
elif re.search(rf'^{ncbi_transcript_regexp}:c\.{variant_regexp}$', query_engine) or \
re.search(rf'^{ncbi_transcript_regexp}\([A-Za-z0-9-]+\):c\.{variant_regexp}$', query_engine): # NM acc_no variant
# f-strings usage https://stackoverflow.com/questions/6930982/how-to-use-a-variable-inside-a-regular-expression
# API call
if 'db' not in locals():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
api_key = md_utilities.get_api_key(g, curs)
match_obj = re.search(
rf'^({ncbi_transcript_regexp})\(*[A-Za-z0-9-]*\)*(:c\.{variant_regexp})$',
query_engine)
if api_key is not None:
close_db()
return redirect(url_for('api.api_variant_create',
variant_chgvs='{0}{1}'.format(
match_obj.group(1),
match_obj.group(2)),
caller='browser',
api_key=api_key),
code=307)
elif re.search(r'^[Nn][Mm]_\d+', query_engine): # NM acc_no
sql_table = 'gene'
query_type = 'refseq'
col_names = 'gene_symbol'
match_object = re.search(r'^(^[Nn][Mm]_\d+)', query_engine)
if match_object:
col_names = 'partial_name'
pattern = match_object.group(1)
elif re.search(
rf'^[Nn][Cc]_0000\d{{2}}\.\d{{1,2}}:g\.{variant_regexp}$',
query_engine): # strict HGVS genomic
sql_table = 'variant'
query_type = 'g_name'
col_names = 'feature_id'
db = get_db()
match_object = re.search(
rf'^([Nn][Cc]_0000\d{{2}}\.\d{{1,2}}):g\.({variant_regexp})$',
query_engine)
# res_common = md_utilities.get_common_chr_name(db, match_object.group(1))
chrom = md_utilities.get_common_chr_name(db,
match_object.group(1))[0]
pattern = match_object.group(2)
close_db()
# res_common = md_utilities.get_common_chr_name(db, )
elif re.search(
rf'^[Nn][Cc]_0000\d{{2}}\.\d{{1,2}}:g\.{variant_regexp};[\w-]+$',
query_engine): # strict HGVS genomic + gene (API call)
# API call
if 'db' not in locals():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
api_key = md_utilities.get_api_key(g, curs)
match_obj = re.search(
rf'^([Nn][Cc]_0000\d{{2}}\.\d{{1,2}}:g\.{variant_regexp});([\w-]+)$',
query_engine)
if api_key is not None:
close_db()
return redirect(url_for('api.api_variant_g_create',
variant_ghgvs=match_obj.group(1),
gene_hgnc=match_obj.group(2),
caller='browser',
api_key=api_key),
code=307)
elif re.search(
rf'^[Cc][Hh][Rr]({nochr_captured_regexp}):g\.{variant_regexp_flexible}$',
query_engine): # deal w/ genomic
sql_table = 'variant'
query_type = 'g_name'
col_names = 'feature_id'
match_object = re.search(
rf'^[Cc][Hh][Rr]({nochr_captured_regexp}):g\.({variant_regexp_flexible})$',
query_engine)
chrom = match_object.group(1)
pattern = match_object.group(2)
# if re.search(r'>', pattern):
# pattern = pattern.upper()
elif re.search(r'^g\..+', query_engine): # g. ng dna vars
query_type = 'ng_name'
pattern = md_utilities.clean_var_name(query_engine)
elif re.search(r'^c\..+', query_engine): # c. dna vars
query_type = 'c_name'
pattern = md_utilities.clean_var_name(query_engine)
elif re.search(
r'^%\d+$', query_engine
): # only numbers: get matching variants (exact position match) - specific query
match_obj = re.search(r'^%(\d+)$', query_engine)
pattern = match_obj.group(1)
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(r"""
SELECT {0}
FROM {1}
WHERE c_name ~ '^{2}[^\d]'
OR c_name ~ '_{2}[^\d]'
OR p_name ~ '^{2}[^\d]'
OR p_name ~ '_{2}[^\d]'
""".format(col_names, sql_table, pattern))
semaph_query = 1
close_db()
elif re.search(
r'^\d{2,}$', query_engine
): # only numbers: get matching variants (partial match, at least 2 numbers) - specific query
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute("""
SELECT {0}
FROM {1}
WHERE c_name LIKE '%{2}%'
OR p_name LIKE '%{2}%'
""".format(col_names, sql_table, query_engine))
semaph_query = 1
close_db()
elif re.search(r'^[A-Za-z0-9-]+$', query_engine): # genes
sql_table = 'gene'
query_type = 'gene_symbol'
col_names = 'gene_symbol'
pattern = query_engine
if not re.search(r'[oO][rR][fF]', pattern):
pattern = pattern.upper()
else:
# from experience the only low case in gene is 'orf'
pattern = re.sub(r'O', 'o', pattern)
pattern = re.sub(r'R', 'r', pattern)
pattern = re.sub(r'F', 'f', pattern)
pattern = pattern.capitalize()
else:
error = 'Sorry I did not understand this query ({}).'.format(
query_engine)
# return render_template('md/unknown.html', query=query_engine, transformed_query=pattern)
if error is None:
# print(semaph_query)
if semaph_query == 0:
if 'db' not in locals():
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# sql_query = "SELECT {0} FROM {1} WHERE {2} = '{3}'".format(col_names, sql_table, query_type, pattern)
# return render_template('md/search_engine.html', query=text)
# a little bit of formatting
if re.search('variant', sql_table) and \
re.search('>', pattern):
# upper for the end of the variant, lower for genomic chr
var_match = re.search(
r'^(.*)(\d+)([ACTGactg]>[ACTGactg])$', pattern)
if var_match:
pattern = var_match.group(1).lower() + var_match.group(
2) + var_match.group(3).upper()
else:
close_db()
error = 'You submitted a forbidden character in "{}".'.format(
pattern)
flash(error, 'w3-pale-red')
return render_template('md/unknown.html',
run_mode=app.config['RUN_MODE'])
# print(pattern)
if pattern == 'g_name':
curs.execute("""
SELECT {0}
FROM {1}
WHERE chr = {2}
AND {3} = '{4}'
""".format(col_names, sql_table, chrom, query_type,
pattern))
else:
if col_names == 'partial_name':
col_names = 'gene_symbol'
curs.execute("""
SELECT {0}
FROM {1}
WHERE {2} LIKE '{3}%'
""".format(col_names, sql_table, query_type,
pattern))
else:
curs.execute("""
SELECT {0}
FROM {1}
WHERE {2} = '{3}'
""".format(col_names, sql_table, query_type,
pattern))
result = None
if sql_table == 'gene':
result = curs.fetchone()
if result is None:
query_type = 'second_name'
# https://www.postgresql.org/docs/9.3/functions-matching.html#POSIX-ESCAPE-SEQUENCES
curs.execute(r"""
SELECT {0}
FROM {1}
WHERE {2} ~* '\m[;,]?{3}[;,]?\M'
""".format(col_names, sql_table, query_type, pattern))
result_second = curs.fetchone()
close_db()
if result_second is None:
error = """
Sorry the gene does not seem to exist yet in MD or cannot be annotated for some reason ({}).
""".format(query_engine)
else:
return redirect(
url_for('md.gene',
gene_symbol=result_second[col_names]))
else:
close_db()
return redirect(
url_for('md.gene', gene_symbol=result[col_names]))
else:
result = curs.fetchall()
if not result:
if query_type == 'dbsnp_id':
# api call to create variant from rs id
api_key = md_utilities.get_api_key(g, curs)
if api_key is not None:
close_db()
return redirect(url_for(
'api.api_variant_create_rs',
rs_id='rs{}'.format(pattern),
caller='browser',
api_key=api_key),
code=307)
error = """
Sorry the variant or gene does not seem to exist yet in MD or cannot be annotated for some reason ({}).<br />
You can annotate it directly at the corresponding gene page.
""".format(query_engine)
else:
if len(result) == 1:
close_db()
return redirect(
url_for('api.variant',
variant_id=result[0][0],
caller='browser'))
else:
variants = result
if query_type == 'g_name':
# coming from a query type: NC_000001.11:g.216422237G>A
id_tuple = []
for feature_id in result:
id_tuple.append(feature_id['feature_id'])
curs.execute(
"""
SELECT id, c_name, p_name, gene_symbol, refseq
FROM variant_feature
WHERE id IN %s
ORDER BY id
""", (tuple(id_tuple), ))
variants = curs.fetchall()
close_db()
return render_template(
'md/variant_multiple.html',
run_mode=md_utilities.get_running_mode(),
variants=variants)
if 'db' in locals():
close_db()
else:
error = 'Please type something for the search engine to work.'
flash(error, 'w3-pale-red')
return render_template('md/unknown.html',
run_mode=md_utilities.get_running_mode())
def vars(gene_symbol=None):
if gene_symbol is None:
return render_template('md/unknown.html', query='No gene provided')
elif re.search(r'[^\w-]', gene_symbol):
return render_template('md/unknown.html', query=gene_symbol)
gene_symbol = re.escape(gene_symbol)
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# error = None
# main isoform?
curs.execute(
"""
SELECT *
FROM gene
WHERE gene_symbol = %s
AND canonical = 't'
""", (gene_symbol, ))
main = curs.fetchone()
if main is not None:
curs.execute("""
SELECT gene_symbol, refseq, variant_creation
FROM gene
WHERE gene_symbol = %s
""", (gene_symbol, )) # get all isoforms
result_all = curs.fetchall()
num_iso = len(result_all)
# curs.execute(
# """
# SELECT d.variant_creation, d.refseq, b.pos, a.c_name, a.p_name, a.start_segment_type, a.start_segment_number, a.creation_date, c.username, a.prot_type, a.ivs_name, a.id as vf_id
# FROM variant_feature a, variant b, mobiuser c, gene d
# WHERE a.id = b.feature_id
# AND a.gene_symbol = d.gene_symbol
# AND a.refseq = d.refseq
# AND a.creation_user = c.id
# AND b.genome_version = 'hg38'
# AND a.gene_symbol = %s
# """,
# (gene_symbol,)
# )
curs.execute(
"""
SELECT d.variant_creation, d.refseq, a.c_name, a.p_name, a.start_segment_type, a.start_segment_number, a.creation_date, c.username, a.prot_type, a.ivs_name, a.id as vf_id
FROM variant_feature a, mobiuser c, gene d
WHERE a.gene_symbol = d.gene_symbol
AND a.refseq = d.refseq
AND a.creation_user = c.id
AND a.gene_symbol = %s
""", (gene_symbol, ))
variants = curs.fetchall()
curs.execute(
"""
SELECT MAX(prot_size) AS size
FROM gene
WHERE gene_symbol = %s
""", (gene_symbol, ))
res_size = curs.fetchone()
# if vars_type is not None:
close_db()
clingen_criteria_specification_id = md_utilities.get_clingen_criteria_specification_id(
gene_symbol)
return render_template(
'md/vars.html',
run_mode=md_utilities.get_running_mode(),
urls=md_utilities.urls,
gene_symbol=gene_symbol,
num_iso=num_iso,
variants=variants,
gene_info=main,
res=result_all,
max_prot_size=res_size['size'],
clingen_criteria_specification_id=clingen_criteria_specification_id
)
else:
close_db()
return render_template('md/unknown.html',
run_mode=md_utilities.get_running_mode(),
query=gene_symbol)
def register():
if (md_utilities.get_running_mode() == 'maintenance'):
return render_template('md/index.html',
run_mode=md_utilities.get_running_mode())
if request.method == 'POST':
# username = urllib.parse.unquote(request.form['username'])
username = request.form['username']
password = request.form['password']
country = request.form['country']
institute = request.form['institute']
email = request.form['email']
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
error = None
if not username:
error = 'Username is required.'
elif len(username) < 5:
error = 'Username should be at least 5 characters.'
elif not password:
error = 'Password is required.'
elif len(password) < 8 or \
not re.search(r'[a-z]', password) or \
not re.search(r'[A-Z]', password) or \
not re.search(r'[0-9]', password):
error = """
Password should be at least 8 characters and mix at least letters (upper and lower case) and numbers.
"""
elif not country or re.match('--', country):
error = 'Country is required.'
elif not institute:
error = 'Institute is required.'
elif not email:
error = 'Email is required.'
elif 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.'
else:
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED',
ca_certs=certifi.where())
# try:
# read api key for mailboxvalidator
apikey = configuration.mdconfig(section='email_check')['apikey']
mv_url = 'https://api.mailboxvalidator.com/v1/validation/single?key={0}&format=json&email={1}'.format(
apikey, email)
try:
mv_json = json.loads(
http.request('GET', mv_url).data.decode('utf-8'))
except Exception:
mv_json = None
if mv_json is not None:
try:
if mv_json['credits_available'] > 0:
if mv_json['status'] == "False":
if (mv_json['is_high_risk'] == "True"
or mv_json['is_suppressed'] == "True"
or mv_json['is_catchall'] == "True"):
error = """
The email address is reported as risky or suppressed.
If this is not the case, please send
us an email directly to
mobide
tails
.iurc@
gmail.
com.
"""
# else:valid adressese such as
# [email protected] are reported as False
else:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails email validation error',
'<p>mailboxvalidator credits == 0</p>'),
'[MobiDetails - Email Validation Error]')
except Exception as e:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails email validation error', """
<p>mailboxvalidator validation failed: <br/> {0} <br /> - from {1} with args: {2}</p>
""".format(mv_json, os.path.basename(__file__),
e.args)),
'[MobiDetails - Email Validation Error]')
# 2nd check https://www.stopforumspam.com/
# ex https://www.stopforumspam.com/api?ip=&email=&username=&f=json
sfs_url = 'https://www.stopforumspam.com/api?ip={0}&email={1}&username={2}&f=json'.format(
request.remote_addr, email, username)
# print(sfs_url)
try:
sfs_json = json.loads(
http.request('GET', sfs_url).data.decode('utf-8'))
except Exception:
sfs_json = None
if sfs_json is not None:
try:
print(sfs_json)
if sfs_json['success'] == 1:
# sfs return a boolean for username, ip, email
# if email or ip = 1 => rejected
# username won't be rejected but a warning will be sent
if sfs_json['ip']['appears'] == 1 or \
sfs_json['email']['appears'] == 1:
error = """
Sorry, your input data is reported as risky.
If this is not the case, please send
us an email directly to
mobide
tails
.iurc
@gmail
.com.
"""
elif sfs_json['username']['appears'] == 1:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails stop forum spam \
username validation error', """
<p>Stop forum spam username validation failed (user created but to follow):
<br/> {0} <br /> - from {1} with url: {2}</p>
""".format(sfs_json,
os.path.basename(__file__),
sfs_url)),
'[MobiDetails - Email Validation Error]')
else:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails stop forum spam validation error',
"""
<p>Stop forum spam validation failed:<br/> {0}<br /> - from {1} with url: {2}</p>
""".format(sfs_json,
os.path.basename(__file__),
sfs_url)),
'[MobiDetails - Email Validation Error]')
except Exception as e:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails stop forum spam validation error', """
<p>Stop forum spam validation failed:<br/> {0}<br /> - from {1} with args: {2}</p>
""".format(sfs_json, os.path.basename(__file__),
e.args)),
'[MobiDetails - Email Validation Error]')
if error is None:
# curs.execute(
# "SELECT id FROM mobiuser WHERE username = '******'\
# OR email = '{1}'".format(username, email)
# )
curs.execute(
"""
SELECT id
FROM mobiuser
WHERE username = %s OR email = %s
""", (username, email))
if curs.fetchone() is not None:
error = 'User {0} or email address {1}\
is already registered.'.format(username, email)
if error is None:
key = secrets.token_urlsafe(32)
curs.execute(
"""
INSERT INTO mobiuser (username, password, country, institute, email, api_key, activated)
VALUES (%s, %s, %s, %s, %s, %s, 'f')
RETURNING id
""", (username, generate_password_hash(password), country,
institute, email, key))
user_id = curs.fetchone()[0]
db.commit()
md_utilities.send_email(
md_utilities.prepare_email_html(
'MobiDetails - Account activation', """
Dear {0},
<p>thank you for registering in MobiDetails.
We hope you will find this website useful.</p>
<p>Please follow the link below to activate
your MobiDetails account:</p>
<p><a href="{1}{2}" title="Activate your MD account">
Activate your MD account</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(
username, request.host_url.rstrip('/'),
url_for('auth.activate',
mobiuser_id=user_id,
api_key=key)),
False), '[MobiDetails - Account activation]', [email],
[app.config["MAIL_ERROR_RECIPIENT"]])
flash(
"""
<br /><p>Your account has been created but requires an activation step.
An email has been sent to {} with an activation link.</p><br />
""".format(email), 'w3-pale-green')
close_db()
return redirect(url_for('md.index'), code=302)
flash(error, 'w3-pale-red')
if error is not None and not app.config['TESTING']:
message_body = """
<p>{0}</p><p>Originated from :</p><ul><li>
Remote IP: {1}</li><li>Username: {2}</li>
<li>Country: {3}</li><li>Institute: {4}</li>
<li>Email: {5}</li></ul>
""".format(error, request.remote_addr, username, country,
institute, email)
md_utilities.send_error_email(
md_utilities.prepare_email_html('MobiDetails error',
message_body),
'[MobiDetails - Registering Error]')
close_db()
return render_template('auth/register.html',
countries=md_utilities.countries,
prev_username=username,
prev_institute=institute,
prev_email=email)
return render_template('auth/register.html',
countries=md_utilities.countries)
def create():
# start_time = time.time()
# print(request.form['new_variant'])
variant_regexp = md_utilities.regexp['variant']
if request.form['new_variant'] == '':
return md_utilities.danger_panel('variant creation attempt', 'Please fill in the form before submitting!')
if re.search(r'^[\w-]+$', request.form['gene']) and \
re.search(r'^NM_\d+$', request.form['acc_no']) and \
re.search(rf'^c\.{variant_regexp}$', request.form['new_variant']) and \
re.search(r'^\d+$', request.form['acc_version']):
gene = request.form['gene']
acc_no = request.form['acc_no']
new_variant = request.form['new_variant']
new_variant = new_variant.replace(" ", "").replace("\t", "")
# new_variant = new_variant.replace("\t", "")
original_variant = new_variant
acc_version = request.form['acc_version']
alt_nm = None
if 'alt_iso' in request.form:
alt_nm = request.form['alt_iso']
# return md_utilities.danger_panel(alt_nm, acc_version)
if alt_nm != '' and alt_nm != "{0}.{1}".format(acc_no, acc_version):
acc_no, acc_version = alt_nm.split('.')
# variant already registered?
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
var_db = new_variant.replace("c.", "")
curs.execute(
"SELECT id FROM variant_feature WHERE c_name = %s AND gene_name[2] = %s",
(var_db, acc_no)
)
res = curs.fetchone()
if res:
close_db()
return md_utilities.info_panel('Variant already in MobiDetails: ', var_db, res['id'])
if re.search(r'c\..+', new_variant):
# is vv alive?
# vv_alive = None
vv_base_url = md_utilities.get_vv_api_url()
# try:
# json.loads(http.request('GET', md_utilities.urls['variant_validator_api_hello']).data.decode('utf-8'))
# except Exception as e:
# try:
# json.loads(http.request('GET', md_utilities.urls['variant_validator_api_hello_backup']).data.decode('utf-8'))
# vv_base_url = md_utilities.urls['variant_validator_api_backup']
# except Exception as e:
# md_utilities.send_error_email(
# md_utilities.prepare_email_html(
# 'MobiDetails VariantValidator error',
# '<p>VariantValidator looks down!!<br /> - from {0} with args: {1}</p>'.format(
# os.path.basename(__file__), e.args
# )
# ),
# '[MobiDetails - VariantValidator Error]'
# )
# # vv_data = {'apiVersion': 'Service Unavailable'}
# # vv_alive = {'status': 'Service Unavailable'}
if not vv_base_url:
close_db()
return md_utilities.danger_panel(
new_variant, 'Variant Validator did not answer our call, status: Service Unavailable. \
I have been informed by email. Please retry later.')
# http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED', ca_certs=certifi.where())
if not alt_nm or acc_no == request.form['acc_no']:
vv_url = "{0}VariantValidator/variantvalidator/GRCh38/{1}.{2}:{3}/{1}.{2}?content-type=application/json".format(
vv_base_url, acc_no, acc_version, new_variant
)
else:
vv_url = "{0}VariantValidator/variantvalidator/GRCh38/{1}.{2}:{3}/all?content-type=application/json".format(
vv_base_url, acc_no, acc_version, new_variant
)
vv_key_var = "{0}.{1}:{2}".format(acc_no, acc_version, new_variant)
try:
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED', ca_certs=certifi.where())
vv_data = json.loads(http.request('GET', vv_url).data.decode('utf-8'))
except Exception:
close_db()
return md_utilities.danger_panel(
new_variant,
'Variant Validator did not return any value for the variant.\
Either it is down or your nomenclature is very odd!'
)
if re.search('[di][neu][psl]', new_variant):
# need to redefine vv_key_var for indels as the variant name returned by vv is likely to be different form the user's
for key in vv_data:
if re.search('{0}.{1}'.format(acc_no, acc_version), key):
vv_key_var = key
# print(key)
var_obj = re.search(r':(c\..+)$', key)
if var_obj:
new_variant = var_obj.group(1)
else:
close_db()
return md_utilities.danger_panel(new_variant, 'Please provide the variant name as HGVS c. nomenclature (including c.)')
return md_utilities.create_var_vv(
vv_key_var, gene, acc_no, new_variant,
original_variant, acc_version,
vv_data, 'webApp', db, g
)
else:
close_db()
return md_utilities.danger_panel('variant creation attempt', 'A mandatory argument is lacking or is malformed.')
def reset_password():
if (md_utilities.get_running_mode() == 'maintenance'):
return render_template('md/index.html',
run_mode=md_utilities.get_running_mode())
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')
close_db()
return render_template('auth/forgot_pass.html')
else:
close_db()
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.search(r'[a-z]', password) or \
not re.search(r'[A-Z]', password) or \
not re.search(r'[0-9]', 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')
close_db()
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')
def profile(mobiuser_id=0):
if re.search(r'^\d+$', str(mobiuser_id)):
user_id = g.user['id']
if mobiuser_id != 0:
user_id = mobiuser_id
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"""
SELECT id, username, email, institute, country, api_key, email_pref, lovd_export, academic
FROM mobiuser
WHERE id = %s
""", (user_id, ))
mobiuser = curs.fetchone()
error = None
if mobiuser is None:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails error',
'<p>Bad profile attempt username: from id: {0} file: {1}\
</p>'.format(g.user['id'], os.path.basename(__file__))),
'[MobiDetails - Profile Error]')
error = 'You seem to be unknown by MobiDetails.'
if mobiuser_id != 0:
error = 'This user seems to be unknown by MobiDetails.'
if mobiuser_id == 0:
# curs.execute(
# "SELECT id, c_name, gene_name, p_name, creation_date \
# FROM variant_feature WHERE\
# creation_user = %s ORDER BY creation_date DESC",
# (g.user['id'],)
# )
curs.execute(
"""
SELECT a.id, a.c_name, a.gene_symbol, a.p_name, a.creation_date, b.mobiuser_id
FROM variant_feature a
LEFT JOIN mobiuser_favourite b ON a.id = b.feature_id
WHERE a.creation_user = %s
ORDER BY a.creation_date DESC
""", (g.user['id'], ))
variants = curs.fetchall()
num_var = curs.rowcount
curs.execute(
"""
SELECT * FROM variants_groups
WHERE mobiuser_id = %s
ORDER BY creation_date DESC
""", (g.user['id'], ))
variant_groups = curs.fetchall()
variant_groups_number = curs.rowcount
# we need to modify the username to propose a list name without special characters
clean_username = re.sub(r'[^\w]', '_', mobiuser['username'])
curs.execute(
"""
SELECT a.id, a.c_name, a.ng_name, a.gene_symbol, a.p_name
FROM variant_feature a, mobiuser_favourite b
WHERE a.id = b.feature_id AND b.mobiuser_id = %s
ORDER BY a.gene_symbol, a.ng_name
""", (g.user['id'], ))
variants_favourite = curs.fetchall()
if error is None:
# num_var_fav = curs.rowcount
close_db()
return render_template(
'auth/profile.html',
run_mode=md_utilities.get_running_mode(),
mobiuser=mobiuser,
view='own',
num_var=num_var,
num_var_fav=curs.rowcount,
variants=variants,
variants_favourite=variants_favourite,
variant_groups=variant_groups,
variant_groups_number=variant_groups_number + 1,
clean_username=clean_username)
elif error is None:
# other profile view
close_db()
return render_template('auth/profile.html',
run_mode=md_utilities.get_running_mode(),
mobiuser=mobiuser,
view='other',
num_var=None,
num_var_fav=None,
variants=None,
variants_favourite=None,
variant_groups=None,
variant_groups_number=None,
clean_username=None)
flash(error, 'w3-pale-red')
close_db()
return render_template('md/index.html',
run_mode=md_utilities.get_running_mode())
else:
('Invalid user ID!!', 'w3-pale-red')
return render_template('md/index.html',
run_mode=md_utilities.get_running_mode())
def login():
referrer_page = None
if request.method == 'GET':
referrer_page = request.referrer
# if request.referrer is not None and \
# (url_parse(request.referrer).host ==
# url_parse(request.base_url).host):
# referrer_page = request.referrer
if request.method == 'POST':
email = request.form['email']
password = request.form['password']
try:
referrer_page = request.form['referrer_page']
# if request.form['referrer_page'] is not None and \
# (url_parse(request.form['referrer_page']).host ==
# url_parse(request.base_url).host:
# referrer_page = request.form['referrer_page']
except Exception:
pass
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
error = None
curs.execute(
"""
SELECT *
FROM mobiuser
WHERE email = %s
""", (email, ))
user = curs.fetchone()
if user is None:
error = 'Unknown email.'
elif not check_password_hash(user['password'], password):
error = 'Incorrect password.'
elif user['activated'] is False:
error = """
This account is not activated.
An email to activate your account
has been sent to {}
""".format(user['email'])
# message, mail_object, receiver
md_utilities.send_email(
md_utilities.prepare_email_html(
'MobiDetails - Account activation', """
Dear {0},
<p>please follow the link below to activate your MobiDetails account:</p>
<p><a href="{1}{2}" title="Activate your MD account">
Activate your MD account</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.activate',
mobiuser_id=user['id'],
api_key=user['api_key'])), False),
'[MobiDetails - Account activation]', [email])
if error is None:
session.clear()
close_db()
flash(
'You have successfully been logged in as {}.'.format(
user["username"]), 'w3-pale-green')
session['user_id'] = user['id']
if referrer_page is None or \
(url_parse(referrer_page).host !=
url_parse(request.base_url).host or
re.search(r'(login|register)', referrer_page)):
return redirect(url_for(
'auth.profile',
run_mode=md_utilities.get_running_mode(),
mobiuser_id=0),
code=302)
else:
if referrer_page is not None and \
(url_parse(referrer_page).host ==
url_parse(request.base_url).host):
# not coming from mobidetails
# rebuild redirect URL
return redirect(
md_utilities.build_redirect_url(referrer_page),
code=302)
else:
return redirect(url_for(
'auth.profile',
run_mode=md_utilities.get_running_mode(),
mobiuser_id=0),
code=302)
close_db()
flash(error, 'w3-pale-red')
# not coming from mobidetails
# rebuild redirect URL
return render_template(
'auth/login.html',
run_mode=md_utilities.get_running_mode(),
referrer_page=md_utilities.build_redirect_url(referrer_page))
def api_variant_create(variant_chgvs=None, caller=None, api_key=None):
# print(request.form)
# print(request.args)
# get params
# swagger/curl sends request.args e.g.
# curl -X POST "http://10.34.20.79:5001/api/variant/create?variant_chgvs=NM_005422.2%3Ac.5040G%3ET&api_key=XXX" -H "accept: application/json"
# while
# urllib3 request from create_vars_batch.py sends request.form
if request.args.get('variant_chgvs') and \
request.args.get('caller') and \
request.args.get('api_key'):
variant_chgvs = request.args.get('variant_chgvs', type=str)
caller = request.args.get('caller', type=str)
api_key = request.args.get('api_key', type=str)
elif 'variant_chgvs' in request.form and \
'caller' in request.form and \
'api_key' in request.form:
variant_chgvs = request.form['variant_chgvs']
caller = request.form['caller']
api_key = request.form['api_key']
else:
if caller == 'cli':
return jsonify(mobidetails_error='I cannot fetch the right parameters')
else:
flash('I cannot fetch the right parameters', 'w3-pale-red')
return redirect(url_for('md.index'))
if variant_chgvs is not None and \
caller is not None and \
api_key is not None:
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# mobiuser_id = None
res_check_api_key = md_utilities.check_api_key(db, api_key)
if 'mobidetails_error' in res_check_api_key:
if caller == 'cli':
return jsonify(res_check_api_key)
else:
flash(res_check_api_key['mobidetails_error'], 'w3-pale-red')
return redirect(url_for('md.index'))
else:
g.user = res_check_api_key['mobiuser']
if md_utilities.check_caller(caller) == 'Invalid caller submitted':
if caller == 'cli':
return jsonify(mobidetails_error='Invalid caller submitted')
else:
flash('Invalid caller submitted to API.', 'w3-pale-red')
return redirect(url_for('md.index'))
# if len(api_key) != 43:
# return jsonify(mobidetails_error='Invalid API key')
# else:
# curs.execute(
# "SELECT * FROM mobiuser WHERE api_key = %s",
# (api_key,)
# )
# res = curs.fetchone()
# if res is None:
# return jsonify(mobidetails_error='Unknown API key')
# else:
# g.user = res
# if variant_chgvs is None:
# return jsonify(mobidetails_error='No variant submitted')
variant_regexp = md_utilities.regexp['variant']
match_object = re.search(rf'^([Nn][Mm]_\d+)\.(\d{{1,2}}):c\.({variant_regexp})', urllib.parse.unquote(variant_chgvs))
if match_object:
# match_object = re.search(r'^([Nn][Mm]_\d+)\.(\d{1,2}):c\.(.+)', variant_chgvs)
acc_no, acc_version, new_variant = match_object.group(1), match_object.group(2), match_object.group(3)
new_variant = new_variant.replace(" ", "").replace("\t", "")
# new_variant = new_variant.replace("\t", "")
original_variant = new_variant
curs.execute(
"SELECT id FROM variant_feature WHERE c_name = %s AND gene_name[2] = %s",
(new_variant, acc_no)
)
res = curs.fetchone()
if res is not None:
if caller == 'cli':
return jsonify(
mobidetails_id=res['id'],
url='{0}{1}'.format(
request.host_url[:-1],
url_for('md.variant', variant_id=res['id'])
)
)
else:
return redirect(url_for('md.variant', variant_id=res['id']))
else:
# creation
# get gene
curs.execute(
"SELECT name[1] as gene FROM gene WHERE name[2] = %s",
(acc_no,)
)
res_gene = curs.fetchone()
if res_gene is None:
return jsonify(mobidetails_error='The gene corresponding to {} is not yet present in MobiDetails'.format(acc_no))
vv_base_url = md_utilities.get_vv_api_url()
if not vv_base_url:
close_db()
if caller == 'cli':
return jsonify(mobidetails_error='Variant Validator looks down!.')
else:
flash('TVariant Validator looks down!.', 'w3-pale-red')
return redirect(url_for('md.index'))
vv_url = "{0}VariantValidator/variantvalidator/GRCh38/{1}.{2}:{3}/all?content-type=application/json".format(
vv_base_url, acc_no, acc_version, new_variant
)
vv_key_var = "{0}.{1}:c.{2}".format(acc_no, acc_version, new_variant)
try:
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED', ca_certs=certifi.where())
vv_data = json.loads(http.request('GET', vv_url).data.decode('utf-8'))
except Exception:
close_db()
if caller == 'cli':
return jsonify(mobidetails_error='Variant Validator did not return any value for the variant {}.'.format(new_variant))
else:
try:
flash('There has been a issue with the annotation of the variant via VariantValidator. \
The error is the following: {}'.format(vv_data['validation_warning_1']['validation_warnings']), 'w3-pale-red')
except Exception:
flash('There has been a issue with the annotation of the variant via VariantValidator. \
Sorry for the inconvenience. You may want to try directly in MobiDetails.', 'w3-pale-red')
return redirect(url_for('md.index'))
if re.search('[di][neu][psl]', new_variant):
# need to redefine vv_key_var for indels as the variant name returned by vv is likely to be different form the user's
for key in vv_data.keys():
if re.search('{0}.{1}'.format(acc_no, acc_version), key):
vv_key_var = key
# print(key)
var_obj = re.search(r':c\.(.+)$', key)
if var_obj is not None:
new_variant = var_obj.group(1)
creation_dict = md_utilities.create_var_vv(
vv_key_var, res_gene['gene'], acc_no,
'c.{}'.format(new_variant), original_variant,
acc_version, vv_data, 'api', db, g
)
if caller == 'cli':
return jsonify(creation_dict)
else:
return redirect(url_for('md.variant', variant_id=creation_dict['mobidetails_id']))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Malformed query {}'.format(urllib.parse.unquote(variant_chgvs)))
else:
flash('The query seems to be malformed: {}.'.format(urllib.parse.unquote(variant_chgvs)), 'w3-pale-red')
return redirect(url_for('md.index'))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Invalid parameters')
else:
flash('The submitted parameters looks invalid!!!', 'w3-pale-red')
return redirect(url_for('md.index'))
def intervar():
genome_regexp = md_utilities.regexp['genome']
nochr_chrom_regexp = md_utilities.regexp['nochr_chrom']
if re.search(rf'^{genome_regexp}$', request.form['genome']) and \
re.search(rf'^{nochr_chrom_regexp}$', request.form['chrom']) and \
re.search(r'^\d+$', request.form['pos']) and \
re.search(r'^[ATGC]+$', request.form['ref']) and \
re.search(r'^[ATGC]+$', request.form['alt']) and \
'gene' in request.form:
genome = request.form['genome']
chrom = request.form['chrom']
pos = request.form['pos']
ref = request.form['ref']
alt = request.form['alt']
gene = request.form['gene']
if len(ref) > 1 or len(alt) > 1:
return 'No wintervar for indels'
if ref == alt:
return 'hg19 reference is equal to variant: no wIntervar query'
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED', ca_certs=certifi.where())
intervar_url = "{0}{1}_updated.v.201904&chr={2}&pos={3}&ref={4}&alt={5}".format(
md_utilities.urls['intervar_api'], genome, chrom,
pos, ref, alt
)
try:
intervar_data = [json.loads(http.request('GET', intervar_url).data.decode('utf-8'))]
except Exception:
try:
# intervar can return mutliple json objects, e.g.:
# {"Intervar":"Uncertain significance","Chromosome":1,"Position_hg19":151141512,"Ref_allele":"T","Alt_allele":"A","Gene":"SCNM1","PVS1":0,"PS1":0,"PS2":0,"PS3":0,"PS4":0,"PM1":1,"PM2":1,"PM3":0,"PM4":0,"PM5":0,"PM6":0,"PP1":0,"PP2":0,"PP3":0,"PP4":0,"PP5":0,"BA1":0,"BP1":0,"BP2":0,"BP3":0,"BP4":0,"BP5":0,"BP6":0,"BP7":0,"BS1":0,"BS2":0,"BS3":0,"BS4":0}{"Intervar":"Uncertain significance","Chromosome":1,"Position_hg19":151141512,"Ref_allele":"T","Alt_allele":"A","Gene":"TNFAIP8L2-SCNM1","PVS1":0,"PS1":0,"PS2":0,"PS3":0,"PS4":0,"PM1":1,"PM2":1,"PM3":0,"PM4":0,"PM5":0,"PM6":0,"PP1":0,"PP2":0,"PP3":0,"PP4":0,"PP5":0,"BA1":0,"BP1":0,"BP2":0,"BP3":0,"BP4":0,"BP5":0,"BP6":0,"BP7":0,"BS1":0,"BS2":0,"BS3":0,"BS4":0}
intervar_list = re.split('}{', http.request('GET', intervar_url).data.decode('utf-8'))
i = 0
for obj in intervar_list:
# some housekeeping to get proper strings
obj = obj.replace('{', '').replace('}', '')
obj = '{{{}}}'.format(obj)
intervar_list[i] = obj
i += 1
# if i == 0:
# intervar_list[i] = '{0}}}'.format(obj)
# else:
# intervar_list[i] = '{{{0}'.format(obj)
# if i > 2:
# intervar_list[i-1] = '{0}}}'.format(intervar_list[i-1])
intervar_data = []
for obj in intervar_list:
# print(obj)
intervar_data.append(json.loads(obj))
except Exception as e:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails API error',
'<p>Intervar API call failed for {0}-{1}-{2}-{3}-{4} - url: {5} <br /> - from {6} with args: {7}</p>'.format(
genome, chrom, pos, ref, alt,
intervar_url, os.path.basename(__file__), e.args
)
),
'[MobiDetails - API Error]'
)
return "<span>No wintervar class</span>"
intervar_acmg = None
if len(intervar_data) == 1:
intervar_acmg = intervar_data[0]['Intervar']
else:
for intervar_dict in intervar_data:
# intervar likely returns several json objects
if intervar_dict['Gene'] == gene:
intervar_acmg = intervar_dict['Intervar']
if intervar_acmg is not None:
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
curs.execute(
"SELECT html_code FROM valid_class WHERE acmg_translation = '{}'".format(
intervar_acmg.lower()
)
)
res = curs.fetchone()
close_db()
return "<span style='color:{0};'>{1}</span>".format(res['html_code'], intervar_acmg)
else:
return "<span>No wintervar class</span>"
else:
md_utilities.send_error_email(
md_utilities.prepare_email_html(
'MobiDetails API error',
'<p>Intervar API call failed for {0}-{1}-{2}-{3}-{4}<br /> - from {5} with args: A mandatory argument is missing</p>'.format(
request.form['genome'], request.form['chrom'],
request.form['pos'], request.form['ref'],
request.form['alt'], os.path.basename(__file__)
)
),
'[MobiDetails - API Error]'
)
return "<span>No wintervar class</span>"
def api_variant_create(variant_chgvs=None, caller=None, api_key=None):
# get params
caller = md_utilities.get_post_param(request, 'caller')
variant_chgvs = md_utilities.get_post_param(request, 'variant_chgvs')
api_key = md_utilities.get_post_param(request, 'api_key')
if variant_chgvs and \
caller and \
api_key:
db = get_db()
curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor)
# mobiuser_id = None
res_check_api_key = md_utilities.check_api_key(db, api_key)
if 'mobidetails_error' in res_check_api_key:
if caller == 'cli':
return jsonify(res_check_api_key)
else:
flash(res_check_api_key['mobidetails_error'], 'w3-pale-red')
return redirect(url_for('md.index'))
else:
g.user = res_check_api_key['mobiuser']
if md_utilities.check_caller(caller) == 'Invalid caller submitted':
if caller == 'cli':
return jsonify(mobidetails_error='Invalid caller submitted')
else:
flash('Invalid caller submitted to API.', 'w3-pale-red')
return redirect(url_for('md.index'))
variant_regexp = md_utilities.regexp['variant']
match_object = re.search(
rf'^([Nn][Mm]_\d+)\.(\d{{1,2}}):c\.({variant_regexp})',
urllib.parse.unquote(variant_chgvs))
if match_object:
# match_object = re.search(r'^([Nn][Mm]_\d+)\.(\d{1,2}):c\.(.+)', variant_chgvs)
acc_no, submitted_nm_version, new_variant = match_object.group(
1), match_object.group(2), match_object.group(3)
# acc_no, acc_version, new_variant = match_object.group(1), match_object.group(2), match_object.group(3)
new_variant = new_variant.replace(" ", "").replace("\t", "")
# new_variant = new_variant.replace("\t", "")
original_variant = new_variant
curs.execute(
"SELECT id FROM variant_feature WHERE c_name = %s AND gene_name[2] = %s",
(new_variant, acc_no))
res = curs.fetchone()
if res is not None:
if caller == 'cli':
return jsonify(mobidetails_id=res['id'],
url='{0}{1}'.format(
request.host_url[:-1],
url_for('md.variant',
variant_id=res['id'])))
else:
return redirect(url_for('md.variant',
variant_id=res['id']))
else:
# creation
# get gene
curs.execute(
"SELECT name[1] as gene, nm_version FROM gene WHERE name[2] = %s and variant_creation = 'ok'",
(acc_no, ))
res_gene = curs.fetchone()
if res_gene is None:
if caller == 'cli':
return jsonify(
mobidetails_error=
'The gene corresponding to {} is not yet available for variant annotation in MobiDetails'
.format(acc_no))
else:
flash(
'The gene corresponding to {} is not available for variant annotation in MobiDetails.'
.format(acc_no), 'w3-pale-red')
return redirect(url_for('md.index'))
if int(res_gene['nm_version']) != int(submitted_nm_version):
if caller == 'cli':
return jsonify(
mobidetails_error=
'The RefSeq accession number submitted ({0}) for {1} does not match MobiDetail\'s ({2}).'
.format(submitted_nm_version, acc_no,
res_gene['nm_version']))
else:
flash(
'The RefSeq accession number submitted ({0}) for {1} does not match MobiDetail\'s ({2}).'
.format(submitted_nm_version, acc_no,
res_gene['nm_version']), 'w3-pale-red')
return redirect(url_for('md.index'))
acc_version = res_gene['nm_version']
vv_base_url = md_utilities.get_vv_api_url()
if not vv_base_url:
close_db()
if caller == 'cli':
return jsonify(
mobidetails_error='Variant Validator looks down!.')
else:
flash('Variant Validator looks down!.', 'w3-pale-red')
return redirect(url_for('md.index'))
vv_url = "{0}VariantValidator/variantvalidator/GRCh38/{1}.{2}:{3}/all?content-type=application/json".format(
vv_base_url, acc_no, acc_version, new_variant)
vv_key_var = "{0}.{1}:c.{2}".format(acc_no, acc_version,
new_variant)
try:
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED',
ca_certs=certifi.where())
vv_data = json.loads(
http.request('GET', vv_url).data.decode('utf-8'))
except Exception:
close_db()
if caller == 'cli':
return jsonify(
mobidetails_error=
'Variant Validator did not return any value for the variant {}.'
.format(new_variant))
else:
try:
flash(
'There has been a issue with the annotation of the variant via VariantValidator. \
The error is the following: {}'.format(
vv_data['validation_warning_1']
['validation_warnings']), 'w3-pale-red')
except Exception:
flash(
'There has been a issue with the annotation of the variant via VariantValidator. \
Sorry for the inconvenience. You may want to try directly in MobiDetails.',
'w3-pale-red')
return redirect(url_for('md.index'))
if re.search('[di][neu][psl]', new_variant):
# need to redefine vv_key_var for indels as the variant name returned by vv is likely to be different form the user's
for key in vv_data.keys():
if re.search('{0}.{1}'.format(acc_no, acc_version),
key):
vv_key_var = key
# print(key)
var_obj = re.search(r':c\.(.+)$', key)
if var_obj is not None:
new_variant = var_obj.group(1)
creation_dict = md_utilities.create_var_vv(
vv_key_var, res_gene['gene'], acc_no,
'c.{}'.format(new_variant), original_variant, acc_version,
vv_data, 'api', db, g)
if 'mobidetails_error' in creation_dict:
if caller == 'cli':
return jsonify(creation_dict)
else:
flash(creation_dict['mobidetails_error'],
'w3-pale-red')
return redirect(url_for('md.index'))
if caller == 'cli':
return jsonify(creation_dict)
else:
return redirect(
url_for('md.variant',
variant_id=creation_dict['mobidetails_id']))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Malformed query {}'.format(
urllib.parse.unquote(variant_chgvs)))
else:
flash(
'The query seems to be malformed: {}.'.format(
urllib.parse.unquote(variant_chgvs)), 'w3-pale-red')
return redirect(url_for('md.index'))
else:
if caller == 'cli':
return jsonify(mobidetails_error='Invalid parameters')
else:
flash('The submitted parameters looks invalid!!!', 'w3-pale-red')
return redirect(url_for('md.index'))
