def setUp(self): self.utils = UtilsForTest() self.curdir = os.path.dirname(os.path.realpath(__file__)) self.examples = os.path.join(self.curdir,'bank') + '/' BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) '''
def setUp(self): self.utils = UtilsForTest() self.curdir = os.path.dirname(os.path.realpath(__file__)) self.examples = os.path.join(self.curdir, 'bank') + '/' BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) '''
def setUp(self): self.utils = UtilsForTest() curdir = os.path.dirname(os.path.realpath(__file__)) BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) #Delete all banks b = Bank('local') b.banks.remove({}) self.config = BiomajConfig('local') data_dir = self.config.get('data.dir') lock_file = os.path.join(data_dir,'local.lock') if os.path.exists(lock_file): os.remove(lock_file)
def setUp(self): self.utils = UtilsForTest() curdir = os.path.dirname(os.path.realpath(__file__)) BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) #Delete all banks b = Bank('local') b.banks.remove({}) self.config = BiomajConfig('local') data_dir = self.config.get('data.dir') lock_file = os.path.join(data_dir, 'local.lock') if os.path.exists(lock_file): os.remove(lock_file)
def setUp(self): BmajIndex.es = None self.utils = UtilsForTest() curdir = os.path.dirname(os.path.realpath(__file__)) BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) if BmajIndex.do_index == False: self.skipTest("Skipping indexing tests due to elasticsearch not available") # Delete all banks b = Bank("local") b.banks.remove({}) self.config = BiomajConfig("local") data_dir = self.config.get("data.dir") lock_file = os.path.join(data_dir, "local.lock") if os.path.exists(lock_file): os.remove(lock_file)
def __init__(self): # If connector type not set, try to get it from the global.properties if not BiomajConfig.global_config: BiomajConfig.load_config() url = BiomajConfig.global_config.get('GENERAL', 'db.url') db = BiomajConfig.global_config.get('GENERAL', 'db.name') if url is None: raise Exception("No connection url set!") if db is None: raise Exception("No connection db set!") driver = split(url, ':')[0] if not driver: raise Exception("Can't determine database driver") Connector.url = url Connector.db = db Connector.driver = driver
def setUp(self): BmajIndex.es = None self.utils = UtilsForTest() curdir = os.path.dirname(os.path.realpath(__file__)) BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) if BmajIndex.do_index == False: self.skipTest( "Skipping indexing tests due to elasticsearch not available") # Delete all banks b = Bank('local') b.banks.remove({}) BmajIndex.delete_all_bank('local') self.config = BiomajConfig('local') data_dir = self.config.get('data.dir') lock_file = os.path.join(data_dir, 'local.lock') if os.path.exists(lock_file): os.remove(lock_file)
database into a PostgreSQL data using Jsonb data typexs """ from __future__ import print_function from pymongo import MongoClient import psycopg2 from psycopg2 import OperationalError, DatabaseError, IntegrityError import json from biomaj.config import BiomajConfig import os import sys __author__ = 'tuco' if __name__ == '__main__': BiomajConfig.load_config() mongo_url = BiomajConfig.global_config.get('GENERAL', 'db.url') mongo_db = BiomajConfig.global_config.get('GENERAL', 'db.name') mc = MongoClient(mongo_url) m_bank = mc[mongo_db].banks banks = [] dbname = 'biomaj' insert_query = "INSERT INTO bank(data) VALUES " for bank in m_bank.find({}, {'_id': 0}): insert_query += "('%s')," % json.dumps(bank) insert_query = insert_query.strip(',') # In case we empty the databble if len(sys.argv) > 1: dbname = sys.argv[1]
def setUp(self): self.utils = UtilsForTest() self.curdir = os.path.dirname(os.path.realpath(__file__)) BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False)
def main(): parser = argparse.ArgumentParser(add_help=False) parser.add_argument('-c', '--config', dest="config",help="Configuration file") parser.add_argument('--check', dest="check", help="Check bank property file", action="store_true", default=False) parser.add_argument('-u', '--update', dest="update", help="Update action", action="store_true", default=False) parser.add_argument('--fromscratch', dest="fromscratch", help="Force a new cycle update", action="store_true", default=False) parser.add_argument('-z', '--from-scratch', dest="fromscratch", help="Force a new cycle update", action="store_true", default=False) parser.add_argument('-p', '--publish', dest="publish", help="Publish", action="store_true", default=False) parser.add_argument('--unpublish', dest="unpublish", help="Unpublish", action="store_true", default=False) parser.add_argument('--release', dest="release", help="release of the bank") parser.add_argument('--from-task', dest="from_task", help="Start cycle at a specific task (init always executed)") parser.add_argument('--process', dest="process", help="Linked to from-task, optionally specify a block, meta or process name to start from") parser.add_argument('-l', '--log', dest="log", help="log level") parser.add_argument('-r', '--remove', dest="remove", help="Remove a bank release", action="store_true", default=False) parser.add_argument('--remove-all', dest="removeall", help="Remove all bank releases and database records", action="store_true", default=False) parser.add_argument('--remove-pending', dest="removepending", help="Remove pending release", action="store_true", default=False) parser.add_argument('-s', '--status', dest="status", help="Get status", action="store_true", default=False) parser.add_argument('-b', '--bank', dest="bank", help="bank name") parser.add_argument('--owner', dest="owner", help="change owner of the bank") parser.add_argument('--stop-before', dest="stop_before", help="Store workflow before task") parser.add_argument('--stop-after', dest="stop_after", help="Store workflow after task") parser.add_argument('--freeze', dest="freeze", help="Freeze a bank release", action="store_true", default=False) parser.add_argument('--unfreeze', dest="unfreeze", help="Unfreeze a bank release", action="store_true", default=False) parser.add_argument('-f', '--force', dest="force", help="Force action", action="store_true", default=False) parser.add_argument('-h', '--help', dest="help", help="Show usage", action="store_true", default=False) parser.add_argument('--search', dest="search", help="Search by format and types", action="store_true", default=False) parser.add_argument('--formats', dest="formats", help="List of formats to search, comma separated") parser.add_argument('--types', dest="types", help="List of types to search, comma separated") parser.add_argument('--query', dest="query", help="Lucene query syntax to search in index") parser.add_argument('--show', dest="show", help="Show format files for selected bank", action="store_true", default=False) parser.add_argument('-n', '--change-dbname', dest="newbank", help="Change old bank name to this new bank name") parser.add_argument('-e', '--move-production-directories', dest="newdir",help="Change bank production directories location to this new path, path must exists") parser.add_argument('--visibility', dest="visibility", help="visibility status of the bank") parser.add_argument('--maintenance', dest="maintenance", help="Maintenance mode (on/off/status)") parser.add_argument('--version', dest="version", help="Show version", action="store_true", default=False) parser.add_argument('--status-ko', dest="statusko", help="Get bank in KO status", action="store_true", default=False) options = Options() parser.parse_args(namespace=options) options.no_log = False if options.help: print(''' --config: global.properties file path --status: list of banks with published release [OPTIONAL] --bank xx / bank: Get status details of bank --status-ko: list of banks in error status (last run) --log DEBUG|INFO|WARN|ERR [OPTIONAL]: set log level in logs for this run, default is set in global.properties file --check: Check bank property file [MANDATORY] --bank xx: name of the bank to check (will check xx.properties) --owner yy: Change owner of the bank (user id) [MANDATORY] --bank xx: name of the bank --visibility public|private: change visibility public/private of a bank [MANDATORY] --bank xx: name of the bank --change-dbname yy: Change name of the bank to this new name [MANDATORY] --bank xx: current name of the bank --move-production-directories yy: Change bank production directories location to this new path, path must exists [MANDATORY] --bank xx: current name of the bank --update: Update bank [MANDATORY] --bank xx: name of the bank(s) to update, comma separated [OPTIONAL] --publish: after update set as *current* version --from-scratch: force a new update cycle, even if release is identical, release will be incremented like (myrel_1) --stop-before xx: stop update cycle before the start of step xx --stop-after xx: stop update cycle after step xx has completed --from-task xx --release yy: Force an re-update cycle for bank release *yy* or from current cycle (in production directories), skipping steps up to *xx* --process xx: linked to from-task, optionally specify a block, meta or process name to start from --release xx: release to update --publish: Publish bank as current release to use [MANDATORY] --bank xx: name of the bank to update --release xx: release of the bank to publish --unpublish: Unpublish bank (remove current) [MANDATORY] --bank xx: name of the bank to update --remove-all: Remove all bank releases and database records [MANDATORY] --bank xx: name of the bank to update [OPTIONAL] --force: remove freezed releases --remove-pending: Remove pending releases [MANDATORY] --bank xx: name of the bank to update --remove: Remove bank release (files and database release) [MANDATORY] --bank xx: name of the bank to update --release xx: release of the bank to remove Release must not be the *current* version. If this is the case, publish a new release before. --freeze: Freeze bank release (cannot be removed) [MANDATORY] --bank xx: name of the bank to update --release xx: release of the bank to remove --unfreeze: Unfreeze bank release (can be removed) [MANDATORY] --bank xx: name of the bank to update --release xx: release of the bank to remove --search: basic search in bank production releases, return list of banks --formats xx,yy : list of comma separated format AND/OR --types xx,yy : list of comma separated type --query "LUCENE query syntax": search in index (if activated) --show: Show bank files per format [MANDATORY] --bank xx: name of the bank to show [OPTIONAL] --release xx: release of the bank to show --maintenance on/off/status: (un)set biomaj in maintenance mode to prevent updates/removal ''') return if options.version: version = pkg_resources.require('biomaj')[0].version print('Version: '+str(version)) return if options.stop_after or options.stop_before or options.from_task: available_steps = [] for flow in UpdateWorkflow.FLOW: available_steps.append(flow['name']) for flow in RemoveWorkflow.FLOW: available_steps.append(flow['name']) if options.stop_after: if options.stop_after not in available_steps: print('Invalid step: '+options.stop_after) sys.exit(1) if options.stop_before: if options.stop_before not in available_steps: print('Invalid step: '+options.stop_before) sys.exit(1) if options.from_task: if options.from_task not in available_steps: print('Invalid step: '+options.from_task) sys.exit(1) bmaj = None try: if options.config is not None: BiomajConfig.load_config(options.config) else: BiomajConfig.load_config() except Exception as e: print(str(e)) sys.exit(1) try: if options.maintenance: if options.maintenance not in ['on', 'off', 'status']: print("Wrong maintenance value [on,off,status]") sys.exit(1) data_dir = BiomajConfig.global_config.get('GENERAL', 'data.dir') if BiomajConfig.global_config.has_option('GENERAL', 'lock.dir'): lock_dir = BiomajConfig.global_config.get('GENERAL', 'lock.dir') else: lock_dir = data_dir maintenance_lock_file = os.path.join(lock_dir,'biomaj.lock') if options.maintenance == 'status': if os.path.exists(maintenance_lock_file): print("Maintenance: On") else: print("Maintenance: Off") sys.exit(0) if options.maintenance == 'on': f = open(maintenance_lock_file, 'w') f.write('1') f.close() print("Maintenance set to On") sys.exit(0) if options.maintenance == 'off': if os.path.exists(maintenance_lock_file): os.remove(maintenance_lock_file) print("Maintenance set to Off") sys.exit(0) if options.owner: if not options.bank: print("Bank option is missing") sys.exit(1) bank = Bank(options.bank, no_log=True) bank.set_owner(options.owner) sys.exit(0) if options.visibility: if not options.bank: print("Bank option is missing") sys.exit(1) if options.visibility not in ['public', 'private']: print("Valid values are public|private") sys.exit(1) bank = Bank(options.bank, no_log=True) bank.set_visibility(options.visibility) print("Do not forget to update accordingly the visibility.default parameter in the configuration file") sys.exit(0) if options.newdir: if not options.bank: print("Bank option is missing") sys.exit(1) if not os.path.exists(options.newdir): print("Destination directory does not exists") bank = Bank(options.bank, options=options, no_log=True) if not bank.bank['production']: print("Nothing to move, no production directory") sys.exit(0) bank.load_session(Workflow.FLOW, None) w = Workflow(bank) res = w.wf_init() if not res: sys.exit(1) for prod in bank.bank['production']: session = bank.get_session_from_release(prod['release']) bank.load_session(Workflow.FLOW, session) prod_path = bank.session.get_full_release_directory() if os.path.exists(prod_path): shutil.move(prod_path, options.newdir) prod['data_dir'] = options.newdir bank.banks.update({'name': options.bank}, {'$set' : { 'production': bank.bank['production'] }}) print("Bank production directories moved to " + options.newdir) print("WARNING: do not forget to update accordingly the data.dir and dir.version properties") w.wf_over() sys.exit(0) if options.newbank: if not options.bank: print("Bank option is missing") sys.exit(1) bank = Bank(options.bank, no_log=True) conf_dir = BiomajConfig.global_config.get('GENERAL', 'conf.dir') bank_prop_file = os.path.join(conf_dir,options.bank+'.properties') config_bank = configparser.SafeConfigParser() config_bank.read([os.path.join(conf_dir,options.bank+'.properties')]) config_bank.set('GENERAL', 'db.name', options.newbank) newbank_prop_file = open(os.path.join(conf_dir,options.newbank+'.properties'),'w') config_bank.write(newbank_prop_file) newbank_prop_file.close() bank.banks.update({'name': options.bank}, {'$set' : { 'name': options.newbank }}) os.remove(bank_prop_file) print("Bank "+options.bank+" renamed to "+options.newbank) sys.exit(0) if options.search: if options.query: res = Bank.searchindex(options.query) print("Query matches for :"+options.query) results = [["Release", "Format(s)", "Type(s)", "Files"]] for match in res: results.append([match['_source']['release'], str(match['_source']['format']), str(match['_source']['types']), ','.join(match['_source']['files'])]) print(tabulate(results, headers="firstrow", tablefmt="grid")) else: formats = [] if options.formats: formats = options.formats.split(',') types = [] if options.types: types = options.types.split(',') print("Search by formats="+str(formats)+", types="+str(types)) res = Bank.search(formats, types, False) results = [["Name", "Release", "Format(s)", "Type(s)", 'Current']] for bank in sorted(res, key=lambda bank: (bank['name'])): b = bank['name'] bank['production'].sort(key=lambda n: n['release'], reverse=True) for prod in bank['production']: iscurrent = "" if prod['session'] == bank['current']: iscurrent = "yes" results.append([b if b else '', prod['release'], ','.join(prod['formats']), ','.join(prod['types']), iscurrent]) b = None print(tabulate(results, headers="firstrow", tablefmt="grid")) sys.exit(0) if options.show: if not options.bank: print("Bank option is required") sys.exit(1) bank = Bank(options.bank, no_log=True) results = [["Name", "Release", "Format(s)", "Type(s)", "Tag(s)", "File(s)"]] current = None fformat = None if 'current' in bank.bank and bank.bank['current']: current = bank.bank['current'] for prod in bank.bank['production']: include = True release = prod['release'] if current == prod['session']: release += ' (current)' if options.release and (prod['release'] != options.release and prod['prod_dir'] != options.release): include =False if include: session = bank.get_session_from_release(prod['release']) formats = session['formats'] afiles = [] atags = [] atypes = [] for fformat in list(formats.keys()): for elt in formats[fformat]: atypes.append(','.join(elt['types'])) for tag in list(elt['tags'].keys()): atags.append(elt['tags'][tag]) for eltfile in elt['files']: afiles.append(eltfile) results.append([bank.bank['name'], release, fformat, ','.join(atypes), ','.join(atags), ','.join(afiles)]) print(tabulate(results, headers="firstrow", tablefmt="grid")) sys.exit(0) if options.check: if not options.bank: print("Bank name is missing") sys.exit(1) bank = Bank(options.bank, no_log=True) print(options.bank+" check: "+str(bank.check())+"\n") sys.exit(0) if options.status: if options.bank: bank = Bank(options.bank, no_log=True) info = bank.get_bank_release_info(full=True) print(tabulate(info['info'], headers='firstrow', tablefmt='psql')) print(tabulate(info['prod'], headers='firstrow', tablefmt='psql')) # do we have some pending release(s) if 'pend' in info and len(info['pend']) > 1: print(tabulate(info['pend'], headers='firstrow', tablefmt='psql')) else: banks = Bank.list() # Headers of output table banks_list = [["Name", "Type(s)", "Release", "Visibility"]] for bank in sorted(banks, key=lambda k: k['name']): bank = Bank(bank['name'], no_log=True) banks_list.append(bank.get_bank_release_info()['info']) print(tabulate(banks_list, headers="firstrow", tablefmt="psql")) sys.exit(0) if options.statusko: banks = Bank.list() banks_list = [["Name", "Type(s)", "Release", "Visibility"]] for bank in sorted(banks, key=lambda k: k['name']): try: bank = Bank(bank['name'], no_log=True) bank.load_session(UpdateWorkflow.FLOW) if bank.session is not None: if bank.use_last_session and not bank.session.get_status(Workflow.FLOW_OVER): wf_status = bank.session.get('workflow_status') if wf_status is None or not wf_status: banks_list.append(bank.get_bank_release_info()['info']) except Exception as e: print(str(e)) print(tabulate(banks_list, headers="firstrow", tablefmt="psql")) if options.update: if not options.bank: print("Bank name is missing") sys.exit(1) banks = options.bank.split(',') gres = True for bank in banks: options.bank = bank bmaj = Bank(bank, options) print('Log file: '+bmaj.config.log_file) check_status = bmaj.check() if not check_status: print('Skip bank ' + options.bank + ': wrong config') gres = False continue res = bmaj.update(depends=True) if not res: gres = False Notify.notifyBankAction(bmaj) if not gres: sys.exit(1) if options.freeze: if not options.bank: print("Bank name is missing") sys.exit(1) if not options.release: print("Bank release is missing") sys.exit(1) bmaj = Bank(options.bank, options) res = bmaj.freeze(options.release) if not res: sys.exit(1) if options.unfreeze: if not options.bank: print("Bank name is missing") sys.exit(1) if not options.release: print("Bank release is missing") sys.exit(1) bmaj = Bank(options.bank, options) res = bmaj.unfreeze(options.release) if not res: sys.exit(1) if options.remove or options.removeall: if not options.bank: print("Bank name is missing") sys.exit(1) if options.remove and not options.release: print("Bank release is missing") sys.exit(1) if options.removeall: bmaj = Bank(options.bank, options, no_log=True) print('Log file: '+bmaj.config.log_file) res = bmaj.removeAll(options.force) else: bmaj = Bank(options.bank, options) print('Log file: '+bmaj.config.log_file) res = bmaj.remove(options.release) Notify.notifyBankAction(bmaj) if not res: sys.exit(1) if options.removepending: if not options.bank: print("Bank name is missing") sys.exit(1) bmaj = Bank(options.bank, options, no_log=True) print('Log file: '+bmaj.config.log_file) res = bmaj.remove_pending(options.release) if not res: sys.exit(1) if options.unpublish: if not options.bank: print("Bank name is missing") sys.exit(1) bmaj = Bank(options.bank, options, no_log=True) bmaj.load_session() bmaj.unpublish() sys.exit(0) if options.publish: if not options.bank: print("Bank name or release is missing") sys.exit(1) bmaj = Bank(options.bank, options, no_log=True) print('Log file: '+bmaj.config.log_file) bmaj.load_session() bank = bmaj.bank session = None if options.get_option('release') is None: # Get latest prod release if len(bank['production'])>0: prod = bank['production'][len(bank['production'])-1] for s in bank['sessions']: if s['id'] == prod['session']: session = s break else: # Search production release matching release for prod in bank['production']: if prod['release'] == options.release or prod['prod_dir'] == options.release: # Search session related to this production release for s in bank['sessions']: if s['id'] == prod['session']: session = s break break if session is None: print("No production session could be found for this release") sys.exit(1) bmaj.session._session = session bmaj.publish() except Exception as e: print(str(e))
def setUp(self): self.utils = UtilsForTest() BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) self.config = BiomajConfig('testhttp')
def main(): parser = argparse.ArgumentParser(add_help=False) parser.add_argument('-c', '--config', dest="config", help="Configuration file") parser.add_argument('--check', dest="check", help="Check bank property file", action="store_true", default=False) parser.add_argument('-u', '--update', dest="update", help="Update action", action="store_true", default=False) parser.add_argument('--fromscratch', dest="fromscratch", help="Force a new cycle update", action="store_true", default=False) parser.add_argument('-z', '--from-scratch', dest="fromscratch", help="Force a new cycle update", action="store_true", default=False) parser.add_argument('-p', '--publish', dest="publish", help="Publish", action="store_true", default=False) parser.add_argument('--unpublish', dest="unpublish", help="Unpublish", action="store_true", default=False) parser.add_argument('--release', dest="release", help="release of the bank") parser.add_argument( '--from-task', dest="from_task", help="Start cycle at a specific task (init always executed)") parser.add_argument( '--process', dest="process", help= "Linked to from-task, optionally specify a block, meta or process name to start from" ) parser.add_argument('-l', '--log', dest="log", help="log level") parser.add_argument('-r', '--remove', dest="remove", help="Remove a bank release", action="store_true", default=False) parser.add_argument('--remove-all', dest="removeall", help="Remove all bank releases and database records", action="store_true", default=False) parser.add_argument('--remove-pending', dest="removepending", help="Remove pending release", action="store_true", default=False) parser.add_argument('-s', '--status', dest="status", help="Get status", action="store_true", default=False) parser.add_argument('-b', '--bank', dest="bank", help="bank name") parser.add_argument('--owner', dest="owner", help="change owner of the bank") parser.add_argument('--stop-before', dest="stop_before", help="Store workflow before task") parser.add_argument('--stop-after', dest="stop_after", help="Store workflow after task") parser.add_argument('--freeze', dest="freeze", help="Freeze a bank release", action="store_true", default=False) parser.add_argument('--unfreeze', dest="unfreeze", help="Unfreeze a bank release", action="store_true", default=False) parser.add_argument('-f', '--force', dest="force", help="Force action", action="store_true", default=False) parser.add_argument('-h', '--help', dest="help", help="Show usage", action="store_true", default=False) parser.add_argument('--search', dest="search", help="Search by format and types", action="store_true", default=False) parser.add_argument('--formats', dest="formats", help="List of formats to search, comma separated") parser.add_argument('--types', dest="types", help="List of types to search, comma separated") parser.add_argument('--query', dest="query", help="Lucene query syntax to search in index") parser.add_argument('--show', dest="show", help="Show format files for selected bank", action="store_true", default=False) parser.add_argument('-n', '--change-dbname', dest="newbank", help="Change old bank name to this new bank name") parser.add_argument( '-e', '--move-production-directories', dest="newdir", help= "Change bank production directories location to this new path, path must exists" ) parser.add_argument('--visibility', dest="visibility", help="visibility status of the bank") parser.add_argument('--maintenance', dest="maintenance", help="Maintenance mode (on/off/status)") parser.add_argument('--version', dest="version", help="Show version", action="store_true", default=False) parser.add_argument('--status-ko', dest="statusko", help="Get bank in KO status", action="store_true", default=False) options = Options() parser.parse_args(namespace=options) options.no_log = False if options.help: print(''' --config: global.properties file path --status: list of banks with published release [OPTIONAL] --bank xx / bank: Get status details of bank --status-ko: list of banks in error status (last run) --log DEBUG|INFO|WARN|ERR [OPTIONAL]: set log level in logs for this run, default is set in global.properties file --check: Check bank property file [MANDATORY] --bank xx: name of the bank to check (will check xx.properties) --owner yy: Change owner of the bank (user id) [MANDATORY] --bank xx: name of the bank --visibility public|private: change visibility public/private of a bank [MANDATORY] --bank xx: name of the bank --change-dbname yy: Change name of the bank to this new name [MANDATORY] --bank xx: current name of the bank --move-production-directories yy: Change bank production directories location to this new path, path must exists [MANDATORY] --bank xx: current name of the bank --update: Update bank [MANDATORY] --bank xx: name of the bank(s) to update, comma separated [OPTIONAL] --publish: after update set as *current* version --from-scratch: force a new update cycle, even if release is identical, release will be incremented like (myrel_1) --stop-before xx: stop update cycle before the start of step xx --stop-after xx: stop update cycle after step xx has completed --from-task xx --release yy: Force an re-update cycle for bank release *yy* or from current cycle (in production directories), skipping steps up to *xx* --process xx: linked to from-task, optionally specify a block, meta or process name to start from --release xx: release to update --publish: Publish bank as current release to use [MANDATORY] --bank xx: name of the bank to update --release xx: release of the bank to publish --unpublish: Unpublish bank (remove current) [MANDATORY] --bank xx: name of the bank to update --remove-all: Remove all bank releases and database records [MANDATORY] --bank xx: name of the bank to update [OPTIONAL] --force: remove freezed releases --remove-pending: Remove pending releases [MANDATORY] --bank xx: name of the bank to update --remove: Remove bank release (files and database release) [MANDATORY] --bank xx: name of the bank to update --release xx: release of the bank to remove Release must not be the *current* version. If this is the case, publish a new release before. --freeze: Freeze bank release (cannot be removed) [MANDATORY] --bank xx: name of the bank to update --release xx: release of the bank to remove --unfreeze: Unfreeze bank release (can be removed) [MANDATORY] --bank xx: name of the bank to update --release xx: release of the bank to remove --search: basic search in bank production releases, return list of banks --formats xx,yy : list of comma separated format AND/OR --types xx,yy : list of comma separated type --query "LUCENE query syntax": search in index (if activated) --show: Show bank files per format [MANDATORY] --bank xx: name of the bank to show [OPTIONAL] --release xx: release of the bank to show --maintenance on/off/status: (un)set biomaj in maintenance mode to prevent updates/removal ''') return if options.version: version = pkg_resources.require('biomaj')[0].version print('Version: ' + str(version)) return if options.stop_after or options.stop_before or options.from_task: available_steps = [] for flow in UpdateWorkflow.FLOW: available_steps.append(flow['name']) for flow in RemoveWorkflow.FLOW: available_steps.append(flow['name']) if options.stop_after: if options.stop_after not in available_steps: print('Invalid step: ' + options.stop_after) sys.exit(1) if options.stop_before: if options.stop_before not in available_steps: print('Invalid step: ' + options.stop_before) sys.exit(1) if options.from_task: if options.from_task not in available_steps: print('Invalid step: ' + options.from_task) sys.exit(1) bmaj = None try: if options.config is not None: BiomajConfig.load_config(options.config) else: BiomajConfig.load_config() except Exception as e: print(str(e)) sys.exit(1) try: if options.maintenance: if options.maintenance not in ['on', 'off', 'status']: print("Wrong maintenance value [on,off,status]") sys.exit(1) data_dir = BiomajConfig.global_config.get('GENERAL', 'data.dir') if BiomajConfig.global_config.has_option('GENERAL', 'lock.dir'): lock_dir = BiomajConfig.global_config.get( 'GENERAL', 'lock.dir') else: lock_dir = data_dir maintenance_lock_file = os.path.join(lock_dir, 'biomaj.lock') if options.maintenance == 'status': if os.path.exists(maintenance_lock_file): print("Maintenance: On") else: print("Maintenance: Off") sys.exit(0) if options.maintenance == 'on': f = open(maintenance_lock_file, 'w') f.write('1') f.close() print("Maintenance set to On") sys.exit(0) if options.maintenance == 'off': if os.path.exists(maintenance_lock_file): os.remove(maintenance_lock_file) print("Maintenance set to Off") sys.exit(0) if options.owner: if not options.bank: print("Bank option is missing") sys.exit(1) bank = Bank(options.bank, no_log=True) bank.set_owner(options.owner) sys.exit(0) if options.visibility: if not options.bank: print("Bank option is missing") sys.exit(1) if options.visibility not in ['public', 'private']: print("Valid values are public|private") sys.exit(1) bank = Bank(options.bank, no_log=True) bank.set_visibility(options.visibility) print( "Do not forget to update accordingly the visibility.default parameter in the configuration file" ) sys.exit(0) if options.newdir: if not options.bank: print("Bank option is missing") sys.exit(1) if not os.path.exists(options.newdir): print("Destination directory does not exists") bank = Bank(options.bank, options=options, no_log=True) if not bank.bank['production']: print("Nothing to move, no production directory") sys.exit(0) bank.load_session(Workflow.FLOW, None) w = Workflow(bank) res = w.wf_init() if not res: sys.exit(1) for prod in bank.bank['production']: session = bank.get_session_from_release(prod['release']) bank.load_session(Workflow.FLOW, session) prod_path = bank.session.get_full_release_directory() if os.path.exists(prod_path): shutil.move(prod_path, options.newdir) prod['data_dir'] = options.newdir bank.banks.update( {'name': options.bank}, {'$set': { 'production': bank.bank['production'] }}) print("Bank production directories moved to " + options.newdir) print( "WARNING: do not forget to update accordingly the data.dir and dir.version properties" ) w.wf_over() sys.exit(0) if options.newbank: if not options.bank: print("Bank option is missing") sys.exit(1) bank = Bank(options.bank, no_log=True) conf_dir = BiomajConfig.global_config.get('GENERAL', 'conf.dir') bank_prop_file = os.path.join(conf_dir, options.bank + '.properties') config_bank = configparser.SafeConfigParser() config_bank.read( [os.path.join(conf_dir, options.bank + '.properties')]) config_bank.set('GENERAL', 'db.name', options.newbank) newbank_prop_file = open( os.path.join(conf_dir, options.newbank + '.properties'), 'w') config_bank.write(newbank_prop_file) newbank_prop_file.close() bank.banks.update({'name': options.bank}, {'$set': { 'name': options.newbank }}) os.remove(bank_prop_file) print("Bank " + options.bank + " renamed to " + options.newbank) sys.exit(0) if options.search: if options.query: res = Bank.searchindex(options.query) print("Query matches for :" + options.query) results = [["Release", "Format(s)", "Type(s)", "Files"]] for match in res: results.append([ match['_source']['release'], str(match['_source']['format']), str(match['_source']['types']), ','.join(match['_source']['files']) ]) print(tabulate(results, headers="firstrow", tablefmt="grid")) else: formats = [] if options.formats: formats = options.formats.split(',') types = [] if options.types: types = options.types.split(',') print("Search by formats=" + str(formats) + ", types=" + str(types)) res = Bank.search(formats, types, False) results = [[ "Name", "Release", "Format(s)", "Type(s)", 'Published' ]] for bank in sorted(res, key=lambda bank: (bank['name'])): b = bank['name'] bank['production'].sort(key=lambda n: n['release'], reverse=True) for prod in bank['production']: iscurrent = "" if prod['session'] == bank['current']: iscurrent = "yes" results.append([ b if b else '', prod['release'], ','.join(prod['formats']), ','.join(prod['types']), iscurrent ]) print(tabulate(results, headers="firstrow", tablefmt="grid")) sys.exit(0) if options.show: if not options.bank: print("Bank option is required") sys.exit(1) bank = Bank(options.bank, no_log=True) results = [[ "Name", "Release", "Format(s)", "Type(s)", "Tag(s)", "File(s)" ]] current = None fformat = None if 'current' in bank.bank and bank.bank['current']: current = bank.bank['current'] for prod in bank.bank['production']: include = True release = prod['release'] if current == prod['session']: release += ' (current)' if options.release and (prod['release'] != options.release and prod['prod_dir'] != options.release): include = False if include: session = bank.get_session_from_release(prod['release']) formats = session['formats'] afiles = [] atags = [] atypes = [] for fformat in list(formats.keys()): for elt in formats[fformat]: atypes.append(','.join(elt['types'])) for tag in list(elt['tags'].keys()): atags.append(elt['tags'][tag]) for eltfile in elt['files']: afiles.append(eltfile) results.append([ bank.bank['name'], release, fformat, ','.join(atypes), ','.join(atags), ','.join(afiles) ]) print(tabulate(results, headers="firstrow", tablefmt="grid")) sys.exit(0) if options.check: if not options.bank: print("Bank name is missing") sys.exit(1) bank = Bank(options.bank, no_log=True) print(options.bank + " check: " + str(bank.check()) + "\n") sys.exit(0) if options.status: if options.bank: bank = Bank(options.bank, no_log=True) info = bank.get_bank_release_info(full=True) print( tabulate(info['info'], headers='firstrow', tablefmt='psql')) print( tabulate(info['prod'], headers='firstrow', tablefmt='psql')) # do we have some pending release(s) if 'pend' in info and len(info['pend']) > 1: print( tabulate(info['pend'], headers='firstrow', tablefmt='psql')) else: banks = Bank.list() # Headers of output table banks_list = [["Name", "Type(s)", "Release", "Visibility"]] for bank in sorted(banks, key=lambda k: k['name']): bank = Bank(bank['name'], no_log=True) banks_list.append(bank.get_bank_release_info()['info']) print(tabulate(banks_list, headers="firstrow", tablefmt="psql")) sys.exit(0) if options.statusko: banks = Bank.list() banks_list = [[ "Name", "Type(s)", "Release", "Visibility", "Last run" ]] for bank in sorted(banks, key=lambda k: k['name']): try: bank = Bank(bank['name'], no_log=True) bank.load_session(UpdateWorkflow.FLOW) if bank.session is not None: if bank.use_last_session and not bank.session.get_status( Workflow.FLOW_OVER): wf_status = bank.session.get('workflow_status') if wf_status is None or not wf_status: banks_list.append( bank.get_bank_release_info()['info']) except Exception as e: print(str(e)) print(tabulate(banks_list, headers="firstrow", tablefmt="psql")) if options.update: if not options.bank: print("Bank name is missing") sys.exit(1) banks = options.bank.split(',') gres = True for bank in banks: options.bank = bank bmaj = Bank(bank, options) print('Log file: ' + bmaj.config.log_file) check_status = bmaj.check() if not check_status: print('Skip bank ' + options.bank + ': wrong config') gres = False continue res = bmaj.update(depends=True) if not res: gres = False Notify.notifyBankAction(bmaj) if not gres: sys.exit(1) if options.freeze: if not options.bank: print("Bank name is missing") sys.exit(1) if not options.release: print("Bank release is missing") sys.exit(1) bmaj = Bank(options.bank, options) res = bmaj.freeze(options.release) if not res: sys.exit(1) if options.unfreeze: if not options.bank: print("Bank name is missing") sys.exit(1) if not options.release: print("Bank release is missing") sys.exit(1) bmaj = Bank(options.bank, options) res = bmaj.unfreeze(options.release) if not res: sys.exit(1) if options.remove or options.removeall: if not options.bank: print("Bank name is missing") sys.exit(1) if options.remove and not options.release: print("Bank release is missing") sys.exit(1) if options.removeall: bmaj = Bank(options.bank, options, no_log=True) print('Log file: ' + bmaj.config.log_file) res = bmaj.removeAll(options.force) else: bmaj = Bank(options.bank, options) print('Log file: ' + bmaj.config.log_file) res = bmaj.remove(options.release) Notify.notifyBankAction(bmaj) if not res: sys.exit(1) if options.removepending: if not options.bank: print("Bank name is missing") sys.exit(1) bmaj = Bank(options.bank, options, no_log=True) res = bmaj.remove_pending(options.release) if not res: sys.exit(1) if options.unpublish: if not options.bank: print("Bank name is missing") sys.exit(1) bmaj = Bank(options.bank, options, no_log=True) bmaj.load_session() bmaj.unpublish() sys.exit(0) if options.publish: if not options.bank: print("Bank name or release is missing") sys.exit(1) bmaj = Bank(options.bank, options, no_log=True) bmaj.load_session() bank = bmaj.bank session = None if options.get_option('release') is None: # Get latest prod release if len(bank['production']) > 0: prod = bank['production'][len(bank['production']) - 1] for s in bank['sessions']: if s['id'] == prod['session']: session = s break else: # Search production release matching release for prod in bank['production']: if prod['release'] == options.release or prod[ 'prod_dir'] == options.release: # Search session related to this production release for s in bank['sessions']: if s['id'] == prod['session']: session = s break break if session is None: print("No production session could be found for this release") sys.exit(1) bmaj.session._session = session bmaj.publish() except Exception as e: print(str(e))
def main(): parser = argparse.ArgumentParser() parser.add_argument('-c', '--config', dest="config", help="Biomaj3 Configuration file") parser.add_argument('-o', '--oldconfig', dest="oldconfig", help="Old configuration file") parser.add_argument('-u', '--user', dest="user", help="MySQL user to override global properties") parser.add_argument('-p', '--password', dest="password", help="MySQL password to override global properties") parser.add_argument('-l', '--host', dest="host", help="MySQL host to override global properties") parser.add_argument('-d', '--database', dest="database", help="MySQL database to override global properties") parser.add_argument('-H', '--keep_history', dest="history", action="store_true", default=False, help="Keep bank history, not only production") args = parser.parse_args() biomajconfig = {} banks = [] with open(args.oldconfig, 'r') as old: for line in old: vals = line.split('=') if len(vals) > 1: biomajconfig[vals[0].strip()] = vals[1].strip() BiomajConfig.load_config(args.config, allow_user_config=False) db_properties_dir = os.path.dirname(args.oldconfig) if db_properties_dir == os.path.dirname(args.config): logging.error( "Bank properties use the same directory, please use a different conf.dir" ) sys.exit(1) data_dir = biomajconfig['data.dir'] if data_dir.endswith('/'): data_dir = data_dir[:-1] if not os.path.dirname(data_dir) == os.path.dirname( BiomajConfig.global_config.get('GENERAL', 'data.dir')): logging.error('Data dirs are different, please use the same data dirs') sys.exit(1) prop_files = [] for root, dirnames, filenames in os.walk(db_properties_dir): for filename in fnmatch.filter(filenames, '*.properties'): if filename != 'global.properties': prop_files.append(os.path.join(root, filename)) if not os.path.exists(BiomajConfig.global_config.get( 'GENERAL', 'conf.dir')): os.makedirs(BiomajConfig.global_config.get('GENERAL', 'conf.dir')) for prop_file in prop_files: propbankconfig = {} with open(prop_file, 'r') as old: for line in old: vals = line.split('=') if len(vals) > 1: propbankconfig[vals[0].strip()] = vals[1].strip() newpropfile = os.path.join( BiomajConfig.global_config.get('GENERAL', 'conf.dir'), os.path.basename(prop_file)) newprop = open(newpropfile, 'w') # logging.warn("manage "+prop_file+" => "+newpropfile) newprop.write("[GENERAL]\n") with open(prop_file, 'r') as props: for line in props: if not (line.startswith('*') or line.startswith('/*')): # Replace config variables with new syntax ${xx} => %(xx)s, not other env variables pattern = re.compile("\$\{([a-zA-Z0-9-_.]+)\}") varmatch = pattern.findall(line) if varmatch: for match in varmatch: if match in biomajconfig or match in propbankconfig: line = line.replace('${' + match + '}', '%(' + match + ')s') newprop.write( line.replace('\\\\', '\\').replace('db.source', 'depends')) newprop.close() b = Bank(os.path.basename(prop_file).replace('.properties', ''), no_log=True) banks.append(b.name) # database.url=jdbc\:mysql\://genobdd.genouest.org/biomaj_log vals = biomajconfig['database.url'].split('/') urllen = len(vals) db_name = vals[urllen - 1] if args.database: db_name = args.database db_host = vals[urllen - 2] if args.host: db_host = args.host db_user = biomajconfig['database.login'] if args.user: db_user = args.user db_password = biomajconfig['database.password'] if args.password: db_password = args.password try: cnx = mysql.connector.connect(host=db_host, database=db_name, user=db_user, password=db_password) cur = cnx.cursor() cur.execute("SELECT name FROM bank") for row in cur.fetchall(): migrate_bank(cur, row[0], history=args.history) except mysql.connector.Error as error: if error.errno == errorcode.ER_ACCESS_DENIED_ERROR: print("Wrong username or password: %s" % error.msg) elif error.errno == errorcode.ER_BAD_DB_ERROR: print("Database does not exist: %s" % error.msg) else: print("Unknown error: %s" % error) finally: cnx.close()
def load_config(request): if BiomajConfig.global_config is None: settings = request.registry.settings global_properties = settings['global_properties'] BiomajConfig.load_config(global_properties)
def main(global_config, **settings): """ This function returns a Pyramid WSGI application. """ #config = Configurator(settings=settings) global_properties = settings.get( 'global_properties', '/etc/biomaj/global.properties') if not os.path.exists(global_properties): print 'global.properties configuration field is not set' sys.exit(1) BiomajConfig.load_config(global_properties) settings['global_properties'] = global_properties config = Configurator(settings=settings) config.include('pyramid_chameleon') config.add_subscriber(before_render, BeforeRender) authentication_policy = AuthTktAuthenticationPolicy('seekrit', callback=None, hashalg='sha512') authorization_policy = ACLAuthorizationPolicy() config.set_authentication_policy(authentication_policy) config.set_authorization_policy(authorization_policy) config.add_static_view('static', 'static', cache_max_age=3600) config.add_static_view('app', 'biomajwatcher:webapp/app') config.add_route('home', '/') config.add_route('user','/user') config.add_route('user_banks','/user/{id}/banks') config.add_route('bank', '/bank') config.add_route('bankdetails', '/bank/{id}') config.add_route('banklocked', '/bank/{id}/locked') config.add_route('bankstatus', '/bank/{id}/status') config.add_route('bankconfig', '/bank/{id}/config') config.add_route('bankreleaseremove', '/bank/{id}/{release}') config.add_route('sessionlog', '/bank/{id}/log/{session}') config.add_route('schedulebank','/schedule') config.add_route('updateschedulebank','/schedule/{name}') config.add_route('search', '/search') config.add_route('search_format', '/search/format/{format}') config.add_route('search_format_type', '/search/format/{format}/type/{type}') config.add_route('search_type', '/search/type/{type}') config.add_route('stat', '/stat') config.add_route('is_auth', '/auth') config.add_route('auth', '/auth/{id}') config.add_route('logout', '/logout') config.add_route('old_api', 'BmajWatcher/GET') config.scan() # automatically serialize bson ObjectId and datetime to Mongo extended JSON json_renderer = JSON() def pymongo_adapter(obj, request): return json_util.default(obj) json_renderer.add_adapter(ObjectId, pymongo_adapter) json_renderer.add_adapter(datetime.datetime, pymongo_adapter) config.add_renderer('json', json_renderer) return config.make_wsgi_app()
def migrate_pendings(): """ Migrate database 3.0.18: Check the actual BioMAJ version and if older than 3.0.17, do the 'pending' key migration """ if BiomajConfig.global_config is None: try: BiomajConfig.load_config() except Exception as err: print("* SchemaVersion: Can't find config file") return None if MongoConnector.db is None: MongoConnector( BiomajConfig.global_config.get('GENERAL', 'db.url'), BiomajConfig.global_config.get('GENERAL', 'db.name')) schema = MongoConnector.db_schema banks = MongoConnector.banks schema_version = schema.find_one({'id': 1}) installed_version = pkg_resources.get_distribution("biomaj").version if schema_version is None: schema_version = {'id': 1, 'version': '3.0.0'} schema.insert(schema_version) moderate = int(schema_version['version'].split('.')[1]) minor = int(schema_version['version'].split('.')[2]) if moderate == 0 and minor <= 17: print("Migrate from release: %s" % schema_version['version']) # Update pending releases bank_list = banks.find() updated = 0 for bank in bank_list: if 'pending' in bank: # Check we have an old pending type if type(bank['pending']) == dict: updated += 1 pendings = [] for release in sorted( bank['pending'], key=lambda r: bank['pending'][r]): pendings.append({ 'release': str(release), 'id': bank['pending'][str(release)] }) if len(pendings) > 0: banks.update({'name': bank['name']}, {'$set': { 'pending': pendings }}) else: # We remove old type for 'pending' banks.update({'name': bank['name']}, {'$unset': { 'pending': "" }}) print("Migration: %d bank(s) updated" % updated) schema.update_one({'id': 1}, {'$set': {'version': installed_version}})
import bcrypt from biomaj.config import BiomajConfig parser = argparse.ArgumentParser(description='Initialize database content.') parser.add_argument('--config') parser.add_argument('--user') parser.add_argument('--pwd') parser.add_argument('--email') args = parser.parse_args() if not args.config: print "config argument is missing" sys.exit(2) BiomajConfig.load_config(args.config) from biomaj.user import BmajUser from hashlib import sha1 if not args.user: print 'user parameter is missing' sys.exit(1) rootuser = BmajUser(args.user) if args.pwd: pwd = args.pwd else: pwd = sha1("%s" % randint(1, 1e99)).hexdigest()