[GENERAL]
conf.dir=/etc/biomaj/db_properties
log.dir=/var/log/biomaj
process.dir=/usr/share/biomaj/conf/process
#The root directory where all databases are stored.
#If your data is not stored under one directory hierarchy
#you can override this value in the database properties file.
data.dir=/var/lib/biomaj
# Optional, lock file directory, defaults to data.dir
lock.dir=/var/lib/biomaj/lock
cache.dir=/var/cache/biomaj

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

# separator between bank name and release for directory
# underscore as default
# biomaj >= 3.0.16
release.separator = _

# List of user admin (linux user id, comma separated)
# biomaj >= 3.0.1
admin=

#Use sudo for Docker, default is 1 (else 0)
docker.sudo=1

#Allow LDAP authentication
use_ldap=0
ldap.host=localhost
ldap.port=389
ldap.dn=dc=example,dc=org

#Use ElasticSearch for index/search capabilities
use_elastic=1
#Comma separated list of elasticsearch nodes  host1,host2:port2
elastic_nodes=localhost
elastic_index=biomaj

# Auto publish on updates (do not need publish flag, can be overriden in bank property file)
auto_publish=0

# Background processing with Celery configuration (for biomaj watcher)
celery.queue=biomaj
celery.broker=mongodb://localhost:27017/biomaj_celery

#Get directory stats (can be time consuming depending on number of files etc...)
data.stats=1

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

#----------------
# Mail Configuration
#---------------

#Uncomment thes lines if you want receive mail when the workflow is finished
mail.smtp.host=
#mail.smtp.port=25
mail.admin=
mail.from=
# tail last X bytes of log in mail body , 0 = no tail
# mail.body.tail=2000000
# attach log file if size < X bytes, 0 for no attach
#mail.body.attach=4000000
# path to jinja template for subject, leave empty for defaults
#mail.template.subject=
# path to jinja template for body, leave empty for default
#mail.template.body=

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

# Number of threads to use for downloading
# set to 0 for no limit in parallelization when using micro services
files.num.threads=4

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

# Optional: do not remove old sessions from database,when removing releases
# >= 3.0.15
# keep.old.sessions = 1
# Default: 0
keep.old.sessions=0

# Can be defined per bank
http.parse.dir.line=<img[\s]+src="[\S]+"[\s]+alt="\[DIR\]"[\s]*/?>[\s]*<a[\s]+href="([\S]+)/"[\s]*>.*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})
http.parse.file.line=<img[\s]+src="[\S]+"[\s]+alt="\[[\s]+\]"[\s]*/?>[\s]<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
# Biomaj >= 3.0.18
# Optional date extract in HTTP protocol following python date regexp format (http://www.tutorialspoint.com/python/time_strptime.htm)
#http.group.file.date_format=%%d-%%b-%%Y %%H:%%M

# Bank default access
visibility.default=public

# Proxy, optional proxy (see format at http://curl.haxx.se/libcurl/c/CURLOPT_PROXY.html)
# Does not work for FTP as library maps FTP to HTTP and HTTP format will differ with proxies.
# biomaj >= 3.0.7
#proxy=myproxyhost:1080
#proxy=myproxyhost
# Set proxy authentication if any, else keep commented
#proxy_auth=user:password

# Computed banks
db.source => depends

#Link copy property
do.link.copy=true

#Needed if data sources are contains in an archive
log.files=true
local.files.excluded=\\.panfs.*

#---------------------
# PROTOCOL
#-------------------
port=21
username=anonymous
password=anonymous@nowhere.com

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

myvar=myvalue
mysupervar=%(myvar)s/additional_value
# properties can be called with the syntax  %(property_name)s

db.fullname="my bank simple description"
# Should be the same than file name mybankname.properties
db.name=mybankname
# Information on the type(s) of the bank, comma separated
db.type=nucleic,protein

# Directory to use for download, must be relative to data.dir and must not start with a /
offline.dir.name=offline/mybankname_tmp
# Directory, relative to data.dir where bank release will be stored, must not start with a /
dir.version=test/mybankname



# Bank dependencies : depends=bankA,bankB
# dependent bank may themselves depend on other banks
depends=
# Optional
#bankA.files.move=**/*
#bankB.files.move=flat/file1 flat/file2

# Optional: If depends is set, optionally specify to use the release of a dependent bank
# eg ref.release=bankA  , new bank will have same release than latest bankA
ref.release=

# ftp, http, local, multi
# none: no expected file download (for computed banks for example), > 3.0.10
#       remote.files and local.files are not necessary in this case
#       however a release must be set (from dependent bank or via a release file)
protocol=ftp
# for non local remote server
# server=
server=ftp.ncbi.nih.gov
# Optional, credentials access to server, format= user:password
server.credentials=
# base url to search in, must start and end with a /
remote.dir=/blast/db/FASTA/

# Download timeout, in seconds.
# From version >=3.0.13
# If timeout is reached, retry the download. If fails again, exit with error
# Default: 24h
# Required if download freezes
timeout.download=300

# Optional
# release.protocol =
# release.server =
# release.url.method =
# release.url.params =
# release.remote.dir =
# release.format = %Y-%m-%d  >= 3.0.15
release.file=
release.regexp=


# No leading slash
# Can use **/* to download all files and directories
# From version >= 3.0.4, for ftp and http protocols, remote.files can include groups to save file without directory structure, or partial directories only, examples:
# remote.files = genomes/fasta/.*\.gz => save files in offline directory, keeping remote structure offlinedir/genomes/fasta/
# remote.files = genomes/fasta/(.*\.gz) => save files in offline directory offlinedir/
# remote.files = genomes/(fasta)/(.*\.gz) => save files in offline directory offlinedir/fasta
# To manage a regexp selection but not use it as final file structure, prepend with :?
# Example: remote.files = genomes/(?:fasta|flat)/.*\.gz => take directories fasta or flat but keep original structure when saving file.
remote.files=^alu.*\.gz$

# Download files using specified file instead of listing remote.dir with remote.files
# From version >= 3.0.20
# remote.files will not be used to match files on remote server
# remote.list is a json text file with format, see Remote file list chapter
# If set, remote.files should be empty
# remote.list = path_to_file.json


# regexp to copy from downloaded files to production directory
# No leading slash
local.files=^alu\.(a|n).*


#Uncomment if you don't want to extract the data files.
#no.extract=true

# File path to release, optionally with regular expression to find file. If regexp is set and release.regexp is not set, extract release from expression in file name
# For this to work, the definition of regexp for release.file needs to start with '^' and end with '$'
# release.file=^filename_release_is_(\d+)_\.txt$
release.file=
# if file is not a regexp, extract release from regexp in downloaded file
release.regexp=
# DEPRECATED release.file.compressed=

[optional, will use by default protocol, server, remote.dir]
release.protocol=
release.server=
release.remote.dir=

protocol = directhttp
=> http://test.org/test/test.fa
server = test.org
remote.dir = test/test.fa
# GET or POST
# Optional, default = GET
url.method = GET
# Optional, save results as mytest.fa
target.name = mytest.fa

protocol = directhttp
=> http://test.org/test/test.fa?key1=val1,key2=val2
server = test.org
remote.dir = test/test.fa
# GET or POST
# Optional, default = GET
url.method = GET
url.params=key1,key2
key1.value=val1
key2.value=val1
# Optional, save results as mytest.fa
target.name = mytest.fa




protocol = directftp
=> ftp://test.org/test/test.fa
server = test.org
remote.dir = test/test.fa

protocol = multi
=> ftp://ftp.ncbi.org//musmusculus/chr1/chr1.fa
remote.file.0.protocol = directftp
remote.file.0.server = ftp.ncbi.org
remote.file.0.path = /musmusculus/chr1/chr1.fa

=> http://ftp2.fr.debian.org/debian/README.html?key1=value&key2=value2
remote.file.1.protocol = directhttp
remote.file.1.server = ftp2.fr.debian.org
remote.file.1.path = debian/README.html
# optional, save file under specified name/path
remote.file.1.name = debian/README.html
remote.file.1.method =  GET
remote.file.1.params.keys = key1,key2
remote.file.1.params.key1 = value1
remote.file.1.params.key2 = value2

=> http://ftp2.fr.debian.org/debian/README.html
    #POST PARAMS:
        key1=value
        key2=value2
remote.file.1.protocol = directhttp
remote.file.1.server = ftp2.fr.debian.org
# optional
remote.file.1.credentials = anonymous:password
remote.file.1.path = debian/README.html
# optional, save file under specified name/path
remote.file.1.name = debian/README.html
remote.file.1.method =  POST
remote.file.1.params.keys = key1,key2
remote.file.1.params.key1 = value1
remote.file.1.params.key2 = value2

release.protocol=directhttp
release.server=plasmodb.org
# For directhttp, remote.dir contains full url
release.remote.dir=common/downloads/Current_Release/Build_number
# Mandatory: save remote url under name release.file
release.file=Build_number
release.regexp=(\d+)

remote.list = path_to_file.json

[{"name": "alu.n.gz", "root": "/blast/db/FASTA/"}, {"name": "alu.n.gz.md5", "root": "/blast/db/FASTA/"}]

[{"save_as": "alu.n.gz", "group": "ftp", "name": "alu.n.gz", "month": 11, "user": "anonymous", "year": 2003, "hash": "027577640cd7f182826abbf83e76050c", "permissions": "-r--r--r--", "root": "/blast/db/FASTA/", "day": 26, "size": 24465}, {"save_as": "alu.n.gz.md5", "group": "ftp", "name": "alu.n.gz.md5", "month": 6, "user": "anonymous", "year": 2009, "hash": "98caf48b2f98cdf0c38bda8a74352266", "permissions": "-r--r--r--", "root": "/blast/db/FASTA/", "day": 15, "size": 43}]