diff --git a/src/common/db_IO.py b/src/common/db_IO.py index 3a2608a9..08eb0c2b 100644 --- a/src/common/db_IO.py +++ b/src/common/db_IO.py @@ -1242,7 +1242,7 @@ def get_mane_select_for_gene(self, gene, source): """ def get_mane_select_for_gene(self, gene_id): - command = "SELECT name FROM transcript WHERE gene_id = %s AND (is_mane_select=1 or is_mane_plus_clinical=1)" + command = "SELECT name FROM transcript WHERE gene_id = %s AND is_mane_select=1" self.cursor.execute(command, (gene_id, )) result = self.cursor.fetchall() return [x[0] for x in result if x[0].startswith("ENST")] @@ -2088,12 +2088,12 @@ def get_heredicare_center_classifications(self, heredicare_annotation_id): #result = sorted(result, key=lambda x: functions.convert_none_infinite(x[5]), reverse=True) return result - def insert_user(self, username, first_name, last_name, affiliation): + def insert_user(self, username, first_name, last_name, affiliation, api_roles): #command = "INSERT INTO user (username, first_name, last_name, affiliation) \ # SELECT %s FROM DUAL WHERE NOT EXISTS (SELECT * FROM user \ # WHERE `username`=%s LIMIT 1)" - command = "INSERT INTO user (username, first_name, last_name, affiliation) VALUES (%s, %s, %s, %s) ON DUPLICATE KEY UPDATE first_name=%s, last_name=%s, affiliation=%s" - self.cursor.execute(command, (username, first_name, last_name, affiliation, first_name, last_name, affiliation)) + command = "INSERT INTO user (username, first_name, last_name, affiliation, api_roles) VALUES (%s, %s, %s, %s, %s) ON DUPLICATE KEY UPDATE first_name=%s, last_name=%s, affiliation=%s, api_roles=%s" + self.cursor.execute(command, (username, first_name, last_name, affiliation, api_roles, first_name, last_name, affiliation, api_roles)) self.conn.commit() def get_user(self, user_id): @@ -2106,6 +2106,11 @@ def set_api_key(self, username, api_key): command = "UPDATE user SET api_key = %s WHERE username = %s" self.cursor.execute(command, (api_key, username)) self.conn.commit() + + def set_api_roles(self, username, api_roles): + command = "UPDATE user SET api_roles = %s WHERE username = %s" + self.cursor.execute(command, (api_roles, username)) + self.conn.commit() def check_api_key(self, api_key: str, username: str) -> bool: command = "SELECT EXISTS (SELECT * FROM user WHERE api_key = %s AND username = %s)" @@ -2115,6 +2120,16 @@ def check_api_key(self, api_key: str, username: str) -> bool: return True return False + def check_api_roles(self, username: str, roles: list): + command = "SELECT api_roles FROM user WHERE username = %s" + self.cursor.execute(command, (username, )) + result = self.cursor.fetchone()[0] + db_roles = result.split(';') + for role in roles: + if role not in db_roles: + return False, db_roles + return True, db_roles + def parse_raw_user(self, raw_user): return models.User(id = raw_user[0], full_name = raw_user[2] + ' ' + raw_user[3], diff --git a/src/frontend_celery/config.py b/src/frontend_celery/config.py index 76f942cf..6398ba3a 100644 --- a/src/frontend_celery/config.py +++ b/src/frontend_celery/config.py @@ -87,6 +87,9 @@ class Config(object): MAIL_USE_SSL = False MAIL_DEBUG = False + # misc + VCF_FILE_IMPORT_ACTIVE = False + class ProdConfig(Config): diff --git a/src/frontend_celery/webapp/api/api_routes.py b/src/frontend_celery/webapp/api/api_routes.py index 8e853c1a..a975872a 100644 --- a/src/frontend_celery/webapp/api/api_routes.py +++ b/src/frontend_celery/webapp/api/api_routes.py @@ -11,6 +11,7 @@ from ..utils import * from . import api_functions from webapp import tasks +from webapp.variant import variant_functions api_blueprint = Blueprint( 'api', @@ -19,10 +20,10 @@ @api_blueprint.route('/api/v1.0/get/consensus_classification', methods=['GET']) -@accept_token +@require_api_token_permission(["read_only"]) def consensus_classification(): - conn = Connection(roles = ["read_only"]) + conn = get_connection() #Connection(roles = ["read_only"]) variant_id = request.args.get('variant_id') if variant_id is None: @@ -34,11 +35,9 @@ def consensus_classification(): variant_id = conn.get_variant_id(chrom, pos, ref, alt) if variant_id is None: - conn.close() abort(404, "Requested variant does not exist or missing variant information") variant = conn.get_variant(variant_id, include_annotations = False, include_consensus = True, include_user_classifications = False, include_heredicare_classifications=False, include_automatic_classification=False, include_clinvar=False, include_consequences=False, include_assays=False, include_literature=False, include_external_ids=False) - conn.close() v_res = api_functions.prepare_variant(variant) mrcc = variant.get_recent_consensus_classification() @@ -52,10 +51,10 @@ def consensus_classification(): return jsonify(result) -# DEPRECATED - DELETE - use /api/v1.0/check_variant -@api_blueprint.route('/api/v1.0/get/check_hgvs', methods = ['GET']) -@accept_token -def check_hgvs(): + +@api_blueprint.route('/api/v1.0/check_variant', methods = ['GET']) +@require_api_token_permission(["read_only"]) +def check(): variant = { 'VID': None, 'CHROM': None, @@ -76,40 +75,6 @@ def check_hgvs(): 'canon_alt': '', 'comment': '' } - conn = Connection(roles = ["read_only"]) - status, message = tasks.map_hg38(variant, -1, conn, insert_variant = False, perform_annotation = False, external_ids = None) - conn.close() - - result = { - "status": status, - "message": message - } - return jsonify(result) - -# DEPRECATED - DELETE- use /api/v1.0/check_variant -@api_blueprint.route('/api/v1.0/get/check_genomic', methods = ['GET']) -@accept_token -def check_genomic(): - variant = { - 'VID': None, - 'CHROM': None, - 'POS_HG19': None, - 'REF_HG19': None, - 'ALT_HG19': None, - 'POS_HG38': None, - 'REF_HG38': None, - 'ALT_HG38': None, - 'REFSEQ': None, - 'CHGVS': None, - 'CGCHBOC': None, - 'VISIBLE': 1, - 'GEN': None, - 'canon_chrom': '', - 'canon_pos': '', - 'canon_ref': '', - 'canon_alt': '', - 'comment': '' - } genome_build = request.args.get('genome') if genome_build == "GRCh38": @@ -123,9 +88,8 @@ def check_genomic(): variant["REF_HG19"] = request.args.get('ref') variant["ALT_HG19"] = request.args.get('alt') - conn = Connection(roles = ["read_only"]) + conn = get_connection() # Connection(roles = ["read_only"]) status, message = tasks.map_hg38(variant, -1, conn, insert_variant = False, perform_annotation = False, external_ids = None) - conn.close() result = { "status": status, @@ -135,48 +99,16 @@ def check_genomic(): -@api_blueprint.route('/api/v1.0/check_variant', methods = ['GET']) -@accept_token -def check(): - variant = { - 'VID': None, - 'CHROM': None, - 'POS_HG19': None, - 'REF_HG19': None, - 'ALT_HG19': None, - 'POS_HG38': None, - 'REF_HG38': None, - 'ALT_HG38': None, - 'REFSEQ': request.args.get('transcript'), - 'CHGVS': request.args.get('hgvsc'), - 'CGCHBOC': None, - 'VISIBLE': 1, - 'GEN': request.args.get("gene"), - 'canon_chrom': '', - 'canon_pos': '', - 'canon_ref': '', - 'canon_alt': '', - 'comment': '' - } - genome_build = request.args.get('genome') - if genome_build == "GRCh38": - variant["CHROM"] = request.args.get('chrom') - variant["POS_HG38"] = request.args.get('pos') - variant["REF_HG38"] = request.args.get('ref') - variant["ALT_HG38"] = request.args.get('alt') - elif genome_build == "GRCh37": - variant["CHROM"] = request.args.get('chrom') - variant["POS_HG19"] = request.args.get('pos') - variant["REF_HG19"] = request.args.get('ref') - variant["ALT_HG19"] = request.args.get('alt') +@api_blueprint.route('/api/v1.0/post/variant', methods = ['POST']) +@require_api_token_permission(["user"]) +def insert_variant(): + conn = get_connection() + + user = conn.parse_raw_user(conn.get_user(session["user"]["user_id"])) + create_result, do_redirect = variant_functions.create_variant_from_request(request, user, conn) + + return jsonify(create_result) + - conn = Connection(roles = ["read_only"]) - status, message = tasks.map_hg38(variant, -1, conn, insert_variant = False, perform_annotation = False, external_ids = None) - conn.close() - result = { - "status": status, - "message": message - } - return jsonify(result) diff --git a/src/frontend_celery/webapp/auth/auth_routes.py b/src/frontend_celery/webapp/auth/auth_routes.py index 7005c818..06889249 100644 --- a/src/frontend_celery/webapp/auth/auth_routes.py +++ b/src/frontend_celery/webapp/auth/auth_routes.py @@ -55,6 +55,8 @@ def auth(): first_name = user_info['given_name'] last_name = user_info['family_name'] affiliation = user_info.get('affiliation') + roles = user_info['roles'] + # init the session session['user'] = user_info @@ -66,8 +68,9 @@ def auth(): return redirect(url_for('auth.logout', auto_logout='True')) conn = Connection(session['user']['roles']) # this inserts only if the user is not already in the database and updates the information if the information changed (except for username this one has to stay) - conn.insert_user(username, first_name, last_name, affiliation) - user_info['user_id'] = conn.get_user_id(username) + conn.insert_user(username, first_name, last_name, affiliation, ';'.join(roles)) + user_id = conn.get_user_id(username) + user_info['user_id'] = user_id conn.close() current_app.logger.info("User " + user_info['preferred_username'] + ' (' + user_info.get('affiliation') + ") successfully logged in.") @@ -176,10 +179,7 @@ def edit_user(username): flash('Please provide at least one role!', 'alert-danger') return render_template('auth/edit_user.html', user = user, avail_roles = avail_roles, set_roles = set_roles) - if enabled == 'on': - enabled = True - else: - enabled = False + enabled = enabled == 'on' resp = auth_functions.update_user_information(kc_user_id, user['username'], first_name, last_name, e_mail, affiliation, enabled) @@ -187,6 +187,15 @@ def edit_user(username): resp = auth_functions.grant_roles(kc_user_id, added_roles, avail_roles) resp = auth_functions.delete_roles(kc_user_id, deleted_roles, avail_roles) + avail_roles = auth_functions.get_roles() + new_roles = auth_functions.get_roles_of_user(kc_user_id, avail_roles) + final_new_roles = [] + if enabled: + for new_role_index in new_roles: + final_new_roles.append(avail_roles[new_role_index]['name']) + conn = get_connection() + conn.set_api_roles(username, ";".join(final_new_roles)) + if resp.status_code == 204: flash('Successfully changed user information!', 'alert-success') return redirect(url_for('auth.edit_user', username = username)) diff --git a/src/frontend_celery/webapp/tasks.py b/src/frontend_celery/webapp/tasks.py index 5c9af5ea..d43d2d28 100644 --- a/src/frontend_celery/webapp/tasks.py +++ b/src/frontend_celery/webapp/tasks.py @@ -457,8 +457,8 @@ def map_hg38(variant, user_id, conn:Connection, insert_variant = True, perform_a if not was_successful and hgvs_c_valid and gene_valid: gene_id = conn.get_gene_id_by_symbol(gene_symbol) - transcripts = conn.get_gencode_basic_transcripts(gene_id) - #transcripts = conn.get_mane_select_for_gene(gene_id) + #transcripts = conn.get_gencode_basic_transcripts(gene_id) + transcripts = conn.get_mane_select_for_gene(gene_id) if transcripts is not None: #print(transcripts) diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html index a089a405..428f9d4e 100644 --- a/src/frontend_celery/webapp/templates/index.html +++ b/src/frontend_celery/webapp/templates/index.html @@ -93,6 +93,20 @@

Overview

Changelog

+
v 1.13.6 (16.08.2024)
+
+ General changes: + + Bugfixes: + +
+ +
v 1.13.5 (15.08.2024)
Bugfixes: diff --git a/src/frontend_celery/webapp/templates/main/documentation.html b/src/frontend_celery/webapp/templates/main/documentation.html index d4543a26..ecfee8f3 100644 --- a/src/frontend_celery/webapp/templates/main/documentation.html +++ b/src/frontend_celery/webapp/templates/main/documentation.html @@ -568,9 +568,112 @@
Download consensus classification

+
Upload variants
-

+

+

+
+ POST variant +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Endpoint/api/v1.0/post/variant
DescriptionUpload a variant in VCF or HGVSc. notation
Allowed methodsPOST
HeadersRequired "Authorization:" header with apikey and username attributes.
GET-data + type: The type of data that is going to be used. Must be one of {"vcf", "hgvs"} +
POST-data + One of the following sets is required: +
    +
  1. + genome: The reference genome. Must be one of {GRCh38, GRCh37}
    + chr: The chromosome. Must be one of {chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrMT}
    + pos: The chromosomal position relative to the reference genome provided
    + ref: The genomic sequence at the provided position from the reference genome. Can not be longer than 1000 bp and must contain only ACGT letters.
    + alt: The mutated genomic sequence at the provided position. Can not be longer than 1000 bp and must contain only ACGT letters. +
    2. +
  2. + transcript: The reference transcript. Preferably Ensembl transcript identifiers. The version number is not required
    + hgvsc: The HGVSc. string +
    3. +
+
Response & http status codes +
    +
  • 403: authorization header is missing or was set incorrectly
    • +
  • 200: successful request (get details of the submission from the response)
    • +
+
Examples +
Using the variant id:
+
+ wget --header "Authorization: apikey $apikey username $username" --post-data="chr=chr19&pos=50398920&ref=G&alt=C&genome=GRCh38" "{{url_for('api.insert_variant', type="vcf")}}" +
+
Using chromosomal coordinates with respect to the GRCh38 reference genome
+
+ wget --header "Authorization: apikey $yourkey username $yourusername" {{url_for('api.consensus_classification', chrom=chr2, pos=214730440, ref="G", alt="A")}} +
+
Example output variant already in database:
+
+ { + "flash_class": "alert-danger flash_id:variant_already_in_database", + "flash_link": "/display/1234", + "flash_message": "Variant not imported: chr19-50398920-G-C already in database!", + "status": "skipped" + } +
+
Example output erroneous variant:
+
+ { + "flash_class": "alert-danger flash_id:variant_from_vcf_error", + "flash_link": "", + "flash_message": "VcfCheck runtime ERROR: VcfCheck 2024_02-84-g1b249e47\nVCF check failed - see 'out' file for details! Code: 1 ERROR: Reference base(s) not correct. Is 'A', should be 'G'! - in line 6:\nchr19\t5039892\t.\tA\tC\t.\t.\t.", + "status": "error" + } +
+
Example output success
+
+ { + "flash_class": "alert-success flash_id:successful_variant_from_vcf", + "flash_link": "/display/1234", + "flash_message": "Successfully inserted variant: chr19-5039892-G-C", + "status": "success" + } +
+
+
+
+

diff --git a/src/frontend_celery/webapp/utils/decorators.py b/src/frontend_celery/webapp/utils/decorators.py index 7afab4b5..f02ea66f 100644 --- a/src/frontend_celery/webapp/utils/decorators.py +++ b/src/frontend_celery/webapp/utils/decorators.py @@ -15,23 +15,45 @@ import common.functions as functions from common.db_IO import Connection -# used for api endpoints to check the bearer token header -# similar to require login, but for api endpoints -def accept_token(f): - @wraps(f) - def decorated_function(*args, **kwargs): - - authorization_header = parse_authorization_header(request.headers.get('Authorization')) +## used for api endpoints to check the bearer token header +## similar to require login, but for api endpoints +#def accept_api_token(f): +# @wraps(f) +# def decorated_function(*args, **kwargs): +# +# authorization_header = parse_authorization_header(request.headers.get('Authorization')) +# +# conn = Connection() +# api_key_ok = conn.check_api_key(authorization_header['apikey'], authorization_header['username']) +# conn.close() +# +# if not api_key_ok: +# abort(403, "Invalid credentials") +# +# return f(*args, **kwargs) +# return decorated_function + +def require_api_token_permission(roles): + def decorator(f): + @wraps(f) + def wrapper(*args, **kwargs): + authorization_header = parse_authorization_header(request.headers.get('Authorization')) - conn = Connection() - api_key_ok = conn.check_api_key(authorization_header['apikey'], authorization_header['username']) - conn.close() + conn = Connection() + api_key_ok = conn.check_api_key(authorization_header['apikey'], authorization_header['username']) + roles_ok, api_roles = conn.check_api_roles(authorization_header['username'], roles) + user_id = conn.get_user_id(authorization_header['username']) + conn.close() - if not api_key_ok: - abort(403, "Invalid credentials") + if not api_key_ok: + abort(403, "Invalid credentials") + if not roles_ok: + abort(403, "Insufficient privileges") - return f(*args, **kwargs) - return decorated_function + session['user'] = {'roles': api_roles, 'user_id': user_id,'preferred_username': authorization_header['username']} + return f(*args, **kwargs) + return wrapper + return decorator def parse_authorization_header(authorization_header: str): authorization_header = authorization_header.split(' ') @@ -56,7 +78,8 @@ def parse_authorization_header(authorization_header: str): abort(403, "Incomplete authorization header. Missing keyword: " + kw) return result - + + # a decorator which redirects to the login page if the user is not logged in. diff --git a/src/frontend_celery/webapp/variant/variant_functions.py b/src/frontend_celery/webapp/variant/variant_functions.py index 5cb30bc6..a35a6f95 100644 --- a/src/frontend_celery/webapp/variant/variant_functions.py +++ b/src/frontend_celery/webapp/variant/variant_functions.py @@ -2,6 +2,7 @@ from ..download.download_routes import calculate_class from flask import render_template import io +from webapp import tasks @@ -347,17 +348,10 @@ def summarize_heredicare_status(heredicare_queue_entries, publish_queue): def summarize_clinvar_status(clinvar_queue_entries, publish_queue): summary = {"status": "unknown", "insert_tasks_message": ""} if publish_queue is not None: - if publish_queue.status == 'error': - summary["status"] = "error" - summary["insert_tasks_message"] = publish_queue.insert_tasks_message - if publish_queue.insert_tasks_status == 'pending': - summary["status"] = "waiting" - elif publish_queue.insert_tasks_status == 'progress': - summary["status"] = "requesting" - elif clinvar_queue_entries is not None: + if clinvar_queue_entries is not None: all_skipped = True - for heredicare_queue_entry in clinvar_queue_entries: - current_status = heredicare_queue_entry[3] + for clinvar_queue_entry in clinvar_queue_entries: + current_status = clinvar_queue_entry[3] if current_status == 'skipped': continue all_skipped = False @@ -367,4 +361,147 @@ def summarize_clinvar_status(clinvar_queue_entries, publish_queue): summary["status"] = "multiple stati" if all_skipped: summary["status"] = "skipped" - return summary \ No newline at end of file + else: + if publish_queue.status == 'error': + summary["status"] = "error" + summary["insert_tasks_message"] = publish_queue.insert_tasks_message + if publish_queue.insert_tasks_status == 'pending': + summary["status"] = "waiting" + elif publish_queue.insert_tasks_status == 'progress': + summary["status"] = "requesting" + + return summary + + + + +#user = self.parse_raw_user(conn.get_user(user_id)) +# session["user"]["user_id"] +def create_variant_from_request(request_obj, user, conn): + result = { + "flash_message": "", + "flash_class": "", + "flash_link": "", + "status": "" + } + do_redirect = False + + create_variant_from = request_obj.args.get("type") + + if not create_variant_from: + result["flash_message"] = "Missing type of variant information. Either vcf or hgvs." + result["flash_class"] = "alert-danger" + result["status"] = "error" + + if create_variant_from == 'vcf': + chrom = request_obj.form.get('chr', '') + pos = ''.join(request_obj.form.get('pos', '').split()) + ref = request_obj.form.get('ref', '').upper().strip() + alt = request_obj.form.get('alt', '').upper().strip() + genome_build = request_obj.form.get('genome') + + # we do not have to check the input parameters in depth here because + # they are checked by the validate_and_insert_variant function anyway + # here we just make sure that the user submitted **something** + # -> better understanding/readability of the error message + if not chrom or not pos or not ref or not alt or 'genome' not in request_obj.form: + result["flash_message"] = 'All fields are required!' + result["flash_class"] = 'alert-danger flash_id:missing_data_vcf' + result["status"] = "error" + #flash('All fields are required!', 'alert-danger flash_id:missing_data_vcf') + else: + was_successful, message, variant_id = tasks.validate_and_insert_variant(chrom, pos, ref, alt, genome_build, conn = conn, user_id = user.id) + new_variant = conn.get_variant(variant_id, include_annotations=False, include_consensus = False, include_user_classifications = False, include_heredicare_classifications = False, include_automatic_classification=False, include_clinvar = False, include_consequences = False, include_assays = False, include_literature = False, include_external_ids=False) + if 'already in database' in message: + result["flash_message"] = "Variant not imported: " + new_variant.get_string_repr() + " already in database!" + result["flash_class"] = 'alert-danger flash_id:variant_already_in_database' + result["flash_link"] = url_for("variant.display", variant_id = new_variant.id) + result["status"] = "skipped" + #flash({"message": "Variant not imported: " + new_variant.get_string_repr() + " already in database! View the variant", + # "link": url_for("variant.display", variant_id = new_variant.id)}, "alert-danger flash_id:variant_already_in_database") + elif was_successful: + result["flash_message"] = "Successfully inserted variant: " + new_variant.get_string_repr() + result["flash_class"] = 'alert-success flash_id:successful_variant_from_vcf' + result["flash_link"] = url_for("variant.display", variant_id = new_variant.id) + result["status"] = "success" + #flash({"message": "Successfully inserted variant: " + new_variant.get_string_repr() + ". View your variant", + # "link": url_for("variant.display", variant_id = new_variant.id)}, "alert-success flash_id:successful_variant_from_vcf") + current_app.logger.info(str(user.id) + " successfully created a new variant from vcf which resulted in this vcf-style variant: " + ' '.join([str(new_variant.chrom), str(new_variant.pos), new_variant.ref, new_variant.alt, "GRCh38"])) + do_redirect = True + else: # import had an error + result["flash_message"] = message + result["flash_class"] = 'alert-danger flash_id:variant_from_vcf_error' + result["status"] = "error" + #flash(message, 'alert-danger flash_id:variant_from_vcf_error') + + if create_variant_from == 'hgvsc': + reference_transcript = request_obj.form.get('transcript') + hgvsc = request_obj.form.get('hgvsc') + + if not hgvsc or not reference_transcript: + result["flash_message"] = 'All fields are required!' + result["flash_class"] = 'alert-danger flash_id:missing_data_hgvs' + result["status"] = "error" + #flash('All fields are required!', 'alert-danger flash_id:missing_data_hgvs') + else: + chrom, pos, ref, alt, possible_errors = functions.hgvsc_to_vcf(reference_transcript + ':' + hgvsc) + if possible_errors != '': + flash_message = possible_errors + flash_class = 'alert-danger flash_id:variant_from_hgvs_error' + #flash(possible_errors, "alert-danger flash_id:variant_from_hgvs_error") + else: + was_successful, message, variant_id = tasks.validate_and_insert_variant(chrom, pos, ref, alt, 'GRCh38', conn = conn, user_id = session['user']['user_id']) + new_variant = conn.get_variant(variant_id, include_annotations=False, include_consensus = False, include_user_classifications = False, include_heredicare_classifications = False, include_clinvar = False, include_consequences = False, include_assays = False, include_literature = False) + if 'already in database' in message: + result["flash_message"] = "Variant not imported: " + new_variant.get_string_repr() + " already in database!" + result["flash_class"] = 'alert-danger flash_id:variant_already_in_database' + result["flash_link"] = url_for("variant.display", variant_id = new_variant.id) + result["status"] = "skipped" + #flash({"message": "Variant not imported: " + new_variant.get_string_repr() + " already in database! View your variant", + # "link": url_for("variant.display", variant_id = new_variant.id)}, "alert-danger flash_id:variant_already_in_database") + elif was_successful: + result["flash_message"] = "Successfully inserted variant: " + new_variant.get_string_repr() + result["flash_class"] = 'alert-success flash_id:successful_variant_from_hgvs' + result["flash_link"] = url_for("variant.display", variant_id = new_variant.id) + result["status"] = "success" + #flash({"message": "Successfully inserted variant: " + new_variant.get_string_repr() + ". View your variant", + # "link": url_for("variant.display", variant_id = new_variant.id)}, "alert-success flash_id:successful_variant_from_hgvs") + current_app.logger.info(str(user.id) + " successfully created a new variant from hgvs: " + hgvsc + "Which resulted in this vcf-style variant: " + ' '.join([str(new_variant.chrom), str(new_variant.pos), new_variant.ref, new_variant.alt, "GRCh38"])) + do_redirect = True + else: + result["flash_message"] = message + result["flash_class"] = "alert-danger flash_id:variant_from_hgvs_error" + result["status"] = "error" + #flash(message, 'alert-danger flash_id:variant_from_hgvs_error') + + if create_variant_from == 'vcf_file' and current_app.config["vcf_file_import_active"]: + genome_build = request_obj.form.get('genome') + if 'file' not in request_obj.files or genome_build is None: + result["flash_message"] = 'You must specify the genome build and select a vcf file.' + result["flash_class"] = "alert-danger" + result["status"] = "error" + #flash('You must specify the genome build and select a vcf file.', 'alert-danger') + else: + file = request_obj.files['file'] + filename = file.filename + + if file.filename.strip() == '' or not functions.filename_allowed(file.filename, allowed_extensions = {"vcf", "txt"}): + result["flash_message"] = 'No valid file selected.' + result["flash_class"] = "alert-danger" + result["status"] = "error" + #flash('No valid file selected.', 'alert-danger') + else: + filepath = functions.get_random_temp_file(fileending = "tsv", filename_ext = "import_vcf") + with open(filepath, "w") as f: # file is deleted in task + we have to write to disk because filehandle can not be json serialized and thus, can not be given to a celery task + f.write(file.read().decode("utf-8")) + user_id = session["user"]["user_id"] + user_roles = session["user"]["roles"] + #inserted_variants, skipped_variants = variant_functions.insert_variants_vcf_file(vcf_file, genome_build, conn) + import_queue_id = tasks.start_variant_import_vcf(user_id, user_roles, conn, filename, filepath, genome_build) + result["flash_message"] = 'Successfully submitted vcf file. The import is processed in the background".' + result["flash_class"] = "alert-success" + result["status"] = "success" + #flash("Successfully submitted vcf file. The import is processed in the background", "alert-success") + do_redirect = True + + return result, do_redirect diff --git a/src/frontend_celery/webapp/variant/variant_routes.py b/src/frontend_celery/webapp/variant/variant_routes.py index 3a9775f7..7f4eaa69 100644 --- a/src/frontend_celery/webapp/variant/variant_routes.py +++ b/src/frontend_celery/webapp/variant/variant_routes.py @@ -62,87 +62,21 @@ def search(): def create(): conn = get_connection() chroms = conn.get_enumtypes("variant", "chr") - vcf_file_import_active = False do_redirect = False if request.method == 'POST': - create_variant_from = request.args.get("type") - - if create_variant_from == 'vcf': - chrom = request.form.get('chr', '') - pos = ''.join(request.form.get('pos', '').split()) - ref = request.form.get('ref', '').upper().strip() - alt = request.form.get('alt', '').upper().strip() - genome_build = request.form.get('genome') - - # we do not have to check the input parameters in depth here because - # they are checked by the validate_and_insert_variant function anyway - # here we just make sure that the user submitted **something** - # -> better understanding/readability of the error message - if not chrom or not pos or not ref or not alt or 'genome' not in request.form: - flash('All fields are required!', 'alert-danger flash_id:missing_data_vcf') - else: - was_successful, message, variant_id = tasks.validate_and_insert_variant(chrom, pos, ref, alt, genome_build, conn = conn, user_id = session['user']['user_id']) - new_variant = conn.get_variant(variant_id, include_annotations=False, include_consensus = False, include_user_classifications = False, include_heredicare_classifications = False, include_automatic_classification=False, include_clinvar = False, include_consequences = False, include_assays = False, include_literature = False, include_external_ids=False) - if 'already in database' in message: - flash({"message": "Variant not imported: " + new_variant.get_string_repr() + " already in database! View the variant", - "link": url_for("variant.display", variant_id = new_variant.id)}, "alert-danger flash_id:variant_already_in_database") - elif was_successful: - flash({"message": "Successfully inserted variant: " + new_variant.get_string_repr() + ". View your variant", - "link": url_for("variant.display", variant_id = new_variant.id)}, "alert-success flash_id:successful_variant_from_vcf") - current_app.logger.info(session['user']['preferred_username'] + " successfully created a new variant from vcf which resulted in this vcf-style variant: " + ' '.join([str(new_variant.chrom), str(new_variant.pos), new_variant.ref, new_variant.alt, "GRCh38"])) - do_redirect = True - else: # import had an error - flash(message, 'alert-danger flash_id:variant_from_vcf_error') - - if create_variant_from == 'hgvsc': - reference_transcript = request.form.get('transcript') - hgvsc = request.form.get('hgvsc') - - if not hgvsc or not reference_transcript: - flash('All fields are required!', 'alert-danger flash_id:missing_data_hgvs') - else: - chrom, pos, ref, alt, possible_errors = functions.hgvsc_to_vcf(reference_transcript + ':' + hgvsc) - if possible_errors != '': - flash(possible_errors, "alert-danger flash_id:variant_from_hgvs_error") - else: - was_successful, message, variant_id = tasks.validate_and_insert_variant(chrom, pos, ref, alt, 'GRCh38', conn = conn, user_id = session['user']['user_id']) - new_variant = conn.get_variant(variant_id, include_annotations=False, include_consensus = False, include_user_classifications = False, include_heredicare_classifications = False, include_clinvar = False, include_consequences = False, include_assays = False, include_literature = False) - if 'already in database' in message: - flash({"message": "Variant not imported: " + new_variant.get_string_repr() + " already in database! View your variant", - "link": url_for("variant.display", variant_id = new_variant.id)}, "alert-danger flash_id:variant_already_in_database") - elif was_successful: - flash({"message": "Successfully inserted variant: " + new_variant.get_string_repr() + ". View your variant", - "link": url_for("variant.display", variant_id = new_variant.id)}, "alert-success flash_id:successful_variant_from_hgvs") - current_app.logger.info(session['user']['preferred_username'] + " successfully created a new variant from hgvs: " + hgvsc + "Which resulted in this vcf-style variant: " + ' '.join([str(new_variant.chrom), str(new_variant.pos), new_variant.ref, new_variant.alt, "GRCh38"])) - do_redirect = True - else: - flash(message, 'alert-danger flash_id:variant_from_hgvs_error') - - if create_variant_from == 'vcf_file' and vcf_file_import_active: - genome_build = request.form.get('genome') - if 'file' not in request.files or genome_build is None: - flash('You must specify the genome build and select a vcf file.', 'alert-danger') - else: - file = request.files['file'] - filename = file.filename - - if file.filename.strip() == '' or not functions.filename_allowed(file.filename, allowed_extensions = {"vcf", "txt"}): - flash('No valid file selected.', 'alert-danger') - else: - filepath = functions.get_random_temp_file(fileending = "tsv", filename_ext = "import_vcf") - with open(filepath, "w") as f: # file is deleted in task + we have to write to disk because filehandle can not be json serialized and thus, can not be given to a celery task - f.write(file.read().decode("utf-8")) - user_id = session["user"]["user_id"] - user_roles = session["user"]["roles"] - #inserted_variants, skipped_variants = variant_functions.insert_variants_vcf_file(vcf_file, genome_build, conn) - import_queue_id = tasks.start_variant_import_vcf(user_id, user_roles, conn, filename, filepath, genome_build) - flash("Successfully submitted vcf file. The import is processed in the background", "alert-success") - do_redirect = True + user = conn.parse_raw_user(conn.get_user(session["user"]["user_id"])) + create_result, do_redirect = variant_functions.create_variant_from_request(request, user, conn) + if not create_result["flash_link"]: + flash_message = create_result["flash_message"] + else: + flash_message = {"message": create_result["flash_message"] + " view the variant ", "link": create_result["flash_link"]} + flash(flash_message, create_result["flash_class"]) if do_redirect: return redirect(url_for('variant.create')) - return render_template('variant/create.html', chrs=chroms, vcf_file_import_active=vcf_file_import_active) + return render_template('variant/create.html', chrs=chroms, vcf_file_import_active=current_app.config["VCF_FILE_IMPORT_ACTIVE"]) +