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 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 test_check_caller(caller, result):
assert md_utilities.check_caller(caller) == result
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 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'))