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Merge pull request #281 from thehyve/update_cancer_types
Update cancer types
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| Original file line number | Diff line number | Diff line change |
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| #!/usr/bin/env python2.7 | ||
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| # Copyright (c) 2018 The Hyve B.V. | ||
| # This code is licensed under the GNU Affero General Public License (AGPL), | ||
| # version 3, or (at your option) any later version. | ||
| # | ||
| # This file is part of cBioPortal. | ||
| # | ||
| # cBioPortal is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU Affero General Public License as | ||
| # published by the Free Software Foundation, either version 3 of the | ||
| # License. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU Affero General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU Affero General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| # | ||
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| """Update cancer types script - updates cancer types from OncoTree API to an empty cBioPortal database | ||
| http://oncotree.mskcc.org/#/home?tab=api | ||
| Run with the command line option --help for usage information. | ||
| """ | ||
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| from __future__ import print_function | ||
| import requests | ||
| import MySQLdb | ||
| import sys | ||
| import argparse | ||
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| def eprint(*args, **kwargs): | ||
| """Print error message and exit""" | ||
| print(*args, file=sys.stderr, **kwargs) | ||
| sys.exit(1) | ||
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| def retrieve_oncotree_cancer_types(): | ||
| """Retrieve cancer types from OncoTree API""" | ||
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| print('Retrieving cancer types from OncoTree API') | ||
| request_url = 'http://oncotree.mskcc.org/api/tumorTypes/tree?version=oncotree_latest_stable' | ||
| request_headers = {'Accept': 'application/json'} | ||
| # request_data = '{ "transcriptIds" : ["%s"] }' % ('", "'.join(self.transcript_set)) | ||
| request = requests.get(url=request_url, headers=request_headers) | ||
| if request.ok: | ||
| # Parse transcripts and exons from JSON | ||
| result_json = request.json() | ||
| return result_json | ||
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| else: | ||
| if request.status_code == 404: | ||
| print('Error 404') | ||
| sys.exit(1) | ||
| else: | ||
| request.raise_for_status() | ||
| return | ||
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| def parse_cancer_types_json(cancer_types_json): | ||
| """Parse JSON formatted cancer types received from OncoTree API""" | ||
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| print('Parsing JSON formatted cancer types received from OncoTree API') | ||
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| def flatten_oncotree(node, node_name): | ||
| """Recursive function to flatten the JSON formatted cancer types""" | ||
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| type_of_cancer_id = node_name | ||
| name = node['name'] | ||
| clinical_trial_keywords = node['name'].lower() | ||
| dedicated_color = node['color'] | ||
| short_name = node_name | ||
| parent = node['parent'] | ||
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| cancer_type = [type_of_cancer_id, name, clinical_trial_keywords, dedicated_color, short_name, parent] | ||
| cancer_types.append(cancer_type) | ||
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| if len(node['children'].values()) > 0: | ||
| for child_node in node['children'].keys(): | ||
| flatten_oncotree(node['children'][child_node], child_node) | ||
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| # Save cancer types as tuples in a list | ||
| cancer_types = list() | ||
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| # The root node, 'TISSUE' can be skipped | ||
| for child in cancer_types_json['TISSUE']['children'].keys(): | ||
| # print child | ||
| flatten_oncotree(cancer_types_json['TISSUE']['children'][child], child) | ||
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| return cancer_types | ||
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| def get_portal_properties(portal_properties_filename): | ||
| """Retrieve database settings from portal.properties""" | ||
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| print('Retrieving database settings from portal.properties') | ||
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| portal_properties = {} | ||
| with open(portal_properties_filename, 'r') as portal_properties_file: | ||
| for line in portal_properties_file: | ||
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| # Skip line if its blank or a comment | ||
| line = line.strip() | ||
| if len(line) == 0 or line.startswith('#'): | ||
| continue | ||
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| # Check whether the line contains a single property | ||
| if len(line.split('=')) > 2: | ||
| continue | ||
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| # Read relevant portal properties | ||
| property_key, property_value = line.split('=') | ||
| if property_key == 'db.host': | ||
| # Check if host and port can be read. | ||
| if len(property_value.split(':')) != 2: | ||
| eprint('Unable to read host from db.host in portal.properties.\n' | ||
| 'Expected format: host:port\n' | ||
| 'Found: %s' % property_value) | ||
| host, port = property_value.split(':') | ||
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| # localhost has to be converted to 127.0.0.1 | ||
| if host == 'localhost': | ||
| host = '127.0.0.1' | ||
| portal_properties['host'] = host | ||
| portal_properties['port'] = int(port) | ||
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| elif property_key == 'db.portal_db_name': | ||
| portal_properties['database'] = property_value | ||
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| elif property_key == 'db.user': | ||
| portal_properties['user'] = property_value | ||
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| elif property_key == 'db.password': | ||
| portal_properties['passwd'] = property_value | ||
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| required_properties = ['host', 'user', 'passwd', 'database', 'port'] | ||
| for required_property in required_properties: | ||
| if required_property not in portal_properties: | ||
| eprint('Unable to extract %s from portal.properties') | ||
| return portal_properties | ||
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| def insert_cancer_types(cancer_types, portal_properties): | ||
| """Insert cancer types in cBioPortal database""" | ||
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| print('Inserting cancer types in cBioPortal database') | ||
| db = MySQLdb.connect(host=portal_properties['host'], | ||
| user=portal_properties['user'], | ||
| passwd=portal_properties['passwd'], | ||
| db=portal_properties['database'], | ||
| port=portal_properties['port']) | ||
| cursor = db.cursor() | ||
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| # Check whether the database is empty | ||
| cursor.execute('SELECT * FROM cbioportal.cancer_study') | ||
| cancer_studies = cursor.fetchall() | ||
| if len(cancer_studies) > 0: | ||
| eprint('cancer_study table is not empty. Please use an empty cBioPortal database when updating cancer ' | ||
| 'types. Afterwards this empty database can be exported to create a new seed database.\n' | ||
| 'https://github.com/cBioPortal/datahub/tree/master/seedDB') | ||
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| # Remove foreign key restrictions | ||
| cursor.execute('ALTER TABLE cancer_study DROP FOREIGN KEY cancer_study_ibfk_1') | ||
| cursor.execute('ALTER TABLE sample DROP FOREIGN KEY sample_ibfk_2') | ||
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| # Remove previous cancer types | ||
| cursor.execute('TRUNCATE type_of_cancer') | ||
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| # Insert new cancer types | ||
| sql = 'INSERT INTO type_of_cancer ' \ | ||
| '(TYPE_OF_CANCER_ID, NAME, CLINICAL_TRIAL_KEYWORDS, DEDICATED_COLOR, SHORT_NAME, PARENT) ' \ | ||
| 'VALUES (%s, %s, %s, %s, %s, %s)' | ||
| cursor.executemany(sql, cancer_types) | ||
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| # Restore foreign key restrictions | ||
| cursor.execute('ALTER TABLE cancer_study ADD CONSTRAINT cancer_study_ibfk_1 FOREIGN KEY (TYPE_OF_CANCER_ID) ' | ||
| 'REFERENCES type_of_cancer (TYPE_OF_CANCER_ID)') | ||
| cursor.execute('ALTER TABLE sample ADD CONSTRAINT sample_ibfk_2 FOREIGN KEY (TYPE_OF_CANCER_ID) REFERENCES ' | ||
| 'type_of_cancer (TYPE_OF_CANCER_ID)') | ||
| db.commit() | ||
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| def main(portal_properties_filename): | ||
| # First retrieve data base settings from portal properties file | ||
| cancer_types_json = retrieve_oncotree_cancer_types() | ||
| cancer_types = parse_cancer_types_json(cancer_types_json) | ||
| portal_properties = get_portal_properties(portal_properties_filename) | ||
| insert_cancer_types(cancer_types, portal_properties) | ||
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| if __name__ == '__main__': | ||
| parser = argparse.ArgumentParser(usage='-p <portal_properties_file>', | ||
| description='This code updates the cancer types in an empty cBioPortal database. ' | ||
| 'Afterwards this database can be exported to create a new seed ' | ||
| 'database.') | ||
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| arguments = parser.add_argument_group('Named arguments') | ||
| arguments.add_argument('-p', '--portal_properties_file', | ||
| required=True, | ||
| help='Path to portal.properties file') | ||
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| args = parser.parse_args() | ||
| main(args.portal_properties_file) |