示例#1
0
def biomaj_owner(options):
    '''
    Bank ownership management
    '''
    if not options.bank:
        return (False, "Bank option is missing")
    bank = Bank(options.bank, options=options, no_log=True)
    bank.set_owner(options.owner)
    return (True, None)
示例#2
0
 def test_owner(self):
     '''
 test ACL with owner
 '''
     b = Bank('local')
     res = b.update()
     self.assertTrue(res)
     b.set_owner('sample')
     b2 = Bank('local')
     try:
         res = b2.update()
         self.fail('not owner, should not be allowed')
     except Exception as e:
         pass
示例#3
0
 def test_owner(self):
   '''
   test ACL with owner
   '''
   b = Bank('local')
   res = b.update()
   self.assertTrue(res)
   b.set_owner('sample')
   b2 = Bank('local')
   try:
     res = b2.update()
     self.fail('not owner, should not be allowed')
   except Exception as e:
     pass
示例#4
0
 def test_owner(self):
     """
 test ACL with owner
 """
     b = Bank("local")
     res = b.update()
     self.assertTrue(res)
     b.set_owner("sample")
     b2 = Bank("local")
     try:
         res = b2.update()
         self.fail("not owner, should not be allowed")
     except Exception as e:
         pass
示例#5
0
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))
示例#6
0
def update_bank_config(request):
  settings = request.registry.settings
  user = is_authenticated(request)
  if user is None:
      return HTTPForbidden('Not authenticated')

  name = request.matchdict['id']
  body = request.body
  if sys.version_info >= (3,):
    body = request.body.decode()
  props = json.loads(body)
  newprops = copy.deepcopy(props)

  if 'db.post.process' in newprops:
    del newprops['db.post.process']

  for key,value in props.iteritems():
    if key == 'no.extract':
      if props['no.extract']:
        newprops['no.extract'] = 'true'
      else:
        newprops['no.extract'] = 'false'
    elif 'depends' in props and props['depends']:
      depnames = []
      for dep in props['depends']:
        depnames.append(dep['name'])
        newprops[dep['name']+'.files.move'] = dep['files.move']
      newprops['depends'] = ','.join(depnames)
    elif 'multi' in props and props['multi']:
      count = 0
      for m in props['multi']:
        newprops['remote.file.'+str(count)+'name'] = m['name']
        newprops['remote.file.'+str(count)+'method'] = m['method']
        newprops['remote.file.'+str(count)+'protocol'] = m['protocol']
        newprops['remote.file.'+str(count)+'server'] = m['server']
        newprops['remote.file.'+str(count)+'path'] = m['path']
        newprops['remote.file.'+str(count)+'credentials'] = m['credentials']
        count += 1
      del newprops['multi']
    elif 'db.pre.process' in props and props['db.pre.process']:
        metas = set_metas(newprops, props['db.pre.process'])
        newprops['db.pre.process'] = ','.join(metas)
    elif 'db.remove.process' in props and props['db.remove.process']:
        metas = set_metas(newprops, props['db.remove.process'])
        newprops['db.remove.process'] = ','.join(metas)
    elif 'blocks' in props and props['blocks']:
        blocks = set_blocks(newprops, props['blocks'])
        newprops['blocks'] = ','.join(blocks)

  bank = None
  try:
    config = BiomajConfig(name, options)
  except Exception:
    # config does not exists, create it
    conf_dir = BiomajConfig.global_config.get('GENERAL', 'conf.dir')
    config_bank = ConfigParser.SafeConfigParser()
    config_bank.add_section('GENERAL')
    for key,value in newprops.iteritems():
      if value is None:
        value = ""
      config_bank.set('GENERAL',key,value)
    config_bank_file = open(os.path.join(conf_dir,name+".properties"),'w')
    config_bank.write(config_bank_file)
    config_bank_file.close()
  finally:
    bank = Bank(name, no_log=True)
    # Force owner to user logged in
    bank.set_owner(user['id'])
    test = bank.config.check()
    if not test:
      return {'msg': 'invalid configuration'}
  if bank is None or not can_edit_bank(request, bank.bank):
    return HTTPForbidden('Not authorized to access this resource')

  return {'msg': 'bank created/updated'}
示例#7
0
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))