global.properties.example

[GENERAL]
root.dir=/var/lib/biomaj
conf.dir=%(root.dir)s/conf
log.dir=%(root.dir)s/log
process.dir=%(root.dir)s/process
cache.dir=%(root.dir)s/cache
lock.dir=%(root.dir)s/lock
#The root directory where all databases are stored.
#If your data is not stored under one directory hirearchy
#you can override this value in the database properties file.
data.dir=%(root.dir)s//data


db.url=mongodb://localhost:27017
db.name=biomaj

use_ldap=0
ldap.host=localhost
ldap.port=389
ldap.dn=nodomain

use_elastic=0
#Comma separated list of elasticsearch nodes  host1,host2:port2
elastic_nodes=localhost
elastic_index=biomaj
# Calculate data.dir size stats
data.stats=1

redis.host=localhost
redis.port=6379
redis.db=0
redis.prefix=biomaj

# options to send to downloaders (protocol dependent)
# options.names=option1,option2
# options.option1=value1
# options.option2=value2
#
# Example supported options for ftp/http
# tcp_keepalive: number of seconds for curl keep alive (maps to curl option TCP_KEEPALIVE, TCP_KEEPINTVL and TCP_KEEPIDLE)
# ssl_verifyhost: boolean, check or skips SSL host  (maps to curl option SSL_VERIFYHOST)
# ssl_verifypeer: boolean, SSL checks (maps to curl option SSL_VERIFYPEER)
# ssl_server_cert: path to certificate (maps to curl option CAINFO).


# Influxdb configuration (optional)
# User and db must be manually created in influxdb before use
influxdb.host=
influxdb.port=8086
influxdb.user=root
influxdb.password=root
influxdb.db=biomaj

# Needed for download remote service (should be a load balancer to services
#micro.biomaj.proxy=http://127.0.0.1:5000
#micro.biomaj.rabbit_mq=127.0.0.1
#micro.biomaj.rabbit_mq_port=5672
#micro.biomaj.rabbit_mq_user=
#micro.biomaj.rabbit_mq_password=
#micro.biomaj.rabbit_mq_virtualhost=
#micro.biomaj.service.download=1
#micro.biomaj.service.process=1
#micro.biomaj.service.user=1
#micro.biomaj.service.daemon=1

## Optional
# micro.biomaj.proxy.[user,cron,release,daemon,download,process]=http://127.0.0.1:5000

auto_publish=1

########################
# Global properties file


#To override these settings for a specific database go to its
#properties file and uncomment or add the specific line you want
#to override.

#----------------
# Mail Configuration
#---------------
#Uncomment thes lines if you want receive mail when the workflow is finished

mail.smtp.host=
mail.admin=
mail.from=
mail.user=
mail.password=
mail.tls=true

mail.body.tail=2000000
mail.body.attach=9000000

#---------------------
#Proxy authentification
#---------------------
#proxyHost=
#proxyPort=
#proxyUser=
#proxyPassword=

#---------------------
# PROTOCOL
#-------------------
#possible values : ftp, http, rsync, local
port=21
username=anonymous
password=anonymous@nowhere.com

#access user for production directories
production.directory.chmod=775

#Number of thread during the download
bank.num.threads=4

#Number of threads to use for downloading and processing
files.num.threads=4

#Timeout for a download, in seconds (applies for each file, not for the whole downloads)
timeout.download=3600

#to keep more than one release increase this value
keep.old.version=0

#Link copy property
do.link.copy=true


#The historic log file is generated in log/
#define level information for output : DEBUG,INFO,WARN,ERR
historic.logfile.level=DEBUG

# Hint: you can use online service https://regex101.com/ to test your regexps
http.parse.dir.line=<a[\\s]+href=\"([\\S]+)/\".*alt=\"\\[DIR\\]\">.*([\\d]{2}-[\\w\\d]{2,5}-[\\d]{4}\\s[\\d]{2}:[\\d]{2})
http.parse.file.line=<a[\\s]+href=\"([\\S]+)\".*([\\d]{2}-[\\w\\d]{2,5}-[\\d]{4}\\s[\\d]{2}:[\\d]{2})[\\s]+([\\d\\.]+[MKG]{0,1})

http.group.dir.name=1
http.group.dir.date=2
http.group.file.name=1
http.group.file.date=2
http.group.file.size=3

#Needed if data sources are contains in an archive
log.files=true

local.files.excluded=\\.panfs.*

#~40mn
ftp.timeout=2000000
ftp.automatic.reconnect=5
ftp.active.mode=false

# Bank default access
visibility.default=public

# use hard links instead of copy
# use_hardlinks=0

[loggers]
keys = root, biomaj

[handlers]
keys = console

[formatters]
keys = generic

[logger_root]
level = DEBUG
handlers = console

[logger_biomaj]
level = DEBUG
handlers = console
qualname = biomaj
propagate=0

[handler_console]
class = StreamHandler
args = (sys.stderr,)
level = DEBUG
formatter = generic

[formatter_generic]
format = %(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s