Configuring Compliance Checker/cHemTS

# THE DEFAULT DATABASE IS "ccDB". (TO USE THIS, PLEASE UNCOMMENT THE NEXT LINE.)
# use ccDB

db.createUser(
 {
  user:"cxnMongo", 
  pwd:"ccMongoPass", 
  customData: 
   {
    data:"anydata"
   }, 
  roles : [ 
     { 
      role: "clusterAdmin", 
      db: "admin" 
     },
     { 
      role: "readAnyDatabase", 
      db: "admin" 
     },
     "readWrite"
    ] 
 }
)

# Security provider chooses what settings to use for user authentication
## LDAP: uses LDAP server to log in users
## ACTIVE_DIRECTORY: Uses Microsoft's Active Directory service for authentication
## IN_MEMORY: small number of predefined users (recommended only for testing purposes)
## ANONYMOUS: no login required
    common.securityProviderName = IN_MEMORY

# If this setting is set to true then the service only accepts HTTPS connections 
    common.securityProviderSecure = false

# If this is set to false then only HTTPS connections with valid certificates will be accepted.
    common.securityProviderAllowUnsignedCert = true

# This setting is to specify that the URL requires a specific IP address (e.g. 192.168.1.79) or a local subnet (e.g. 192.168.0/24).
# (http://forum.springsource.org/showthread.php?102783-How-to-use-hasIpAddress&p=343971#post343971)
# If it is left empty then every IP can access the services.
    common.securityProviderAllowedIp =

# Host of MongoDB.
    databaseHost = 127.0.0.1

# Port of MongoDB.
    databasePort = 27017

# Name of database in MongoDB.
    databaseName = test

# Name of the user who connects the database.
    mongoUser = cxnMongo

# Name of the user who connects the database.
    mongoPassword = ccMongoPass 

# Set this property to true in case you are using Transport Encryption in your database. 
# https://docs.mongodb.com/v3.0/core/security-transport-encryption/
    mongoEncryptConnection = false

#spring.data.mongodb.uri=<URI PROVIDED BY CLOUD SERVICE>

mongoEncryptConnection = true

# These settings set the maximum size of upload for services. These properties also effect the maximum size of DB update as well.
spring.servlet.multipart.max-file-size=256MB
spring.servlet.multipart.max-request-size=256MB

# Search always runs on all available cores.
# If you use PARALLEL, then the system will distinct executors, one for all cores, that can boost the overall system performance and can cause a massive CPU load on server.
# If you use SEQUENTIAL execution strategy then only one executor will run on the server. (For search this executor will use all cores, but it creates a smaller CPU load.)
executionStrategy=PARALLEL

# The priority of Single check and Batch check can be configured by setting *.threadPriority key values between 1 (minimum) and 10 (maximum) priority.
# Default values are 5 for single 3 for batch.
check.single.threadPriority=5
check.batch.threadPriority=3

# This size determines how many molecules are checked in one run.
# If you upload a file with 1000 molecules, and set this property to 25 then the file will be cut to 40 pieces, and 40 executors can start working simultaneously.
chunkSize=10

# The maximum number of heavy atoms in a molecule that should be checked.
check.structure.maxAtomCount=200

# Speed up of checking Markush structures
searchEngine.enableMarkushAnalyzer=true

# Session timeout settings in seconds or minutes (m)
server.servlet.session.timeout=120m

# If the servers know nothing about a job, then they mark it as dead, and reschedule to process. You can set this checking interval in milliseconds
# through this variable.
common.deadJobTreshold=120000

# Time limit in milliseconds for checking compliance of one target molecule against all selected rules.
# If check reaches this limit then search with the given target is stopped and it is added to the list of errors.
searchEngine.check.timeLimit=60000

# Time limit in milliseconds for checking compliance of one target molecule against one query substance.
# If the check against a substance reaches this limit then checking the given target is stopped and the given target molecule is added to the list of errors.
searchEngine.molSearch.timeLimit=10000

# Communication is load-balanced through Ribbon classes. 
# (https://github.com/Netflix/ribbon/wiki/Programmers-Guide/)
ribbon.ReadTimeout=16000

# Compliance Checker services use Hystrix circuit breaker to protect servers from overload.
# You can read more about hystrix settings here: https://github.com/Netflix/Hystrix/wiki/Configuration
hystrix.command.default.execution.timeout.enabled=true
hystrix.threadpool.default.coreSize=10
hystrix.threadpool.default.maxQueueSize=100
hystrix.threadpool.default.queueSizeRejectionThreshold=90
hystrix.command.default.execution.isolation.thread.timeoutInMilliseconds=15000
hystrix.shareSecurityContext=true
feign.hystrix.enabled=true

# The URL of config server
spring.cloud.config.uri=http://localhost:8888/

# The URL of eureka service
eureka.client.serviceUrl.defaultZone=http://localhost:8761/eureka/

# The URL of the latest database file: 
common.autoUpdateUrl=https://dl.chemaxon.com/cchecker/cc-database.jar 

# The URL of the text file containing the version of the latest database file. common.autoUpdateVersionUrl=https://dl.chemaxon.com/cchecker/cc-version.txt 
common.autoUpdateEnabled=true 

# Enables to schedule the knowledge base update automatically.
# The value should be a cron-like expression, which extends the usual UN*X definition to include triggers
# on the second as well as minute, hour, day of month, month and day of week.
# Example patterns:
# "0 0 * * * *" = the top of every hour of every day.
# "*/10 * * * * *" = every ten seconds.
# "0 0 8-10 * * *" = 8, 9 and 10 o'clock of every day.
# "0 * 6,19 * * *" = 6:00 AM and 7:00 PM every day.
# "0 0/30 8-10 * * *" = 8:00, 8:30, 9:00, 9:30 and 10 o'clock every day.
# "0 0 9-17 * * MON-FRI" = on the hour nine-to-five weekdays
# "0 0 0 25 12 ?" = every Christmas Day at midnight
common.autoUpdateScheduler=0 0 0 * * MON-FRI

# You can map user groups to ROLEs in CC and cHemTS by this setting.
 # CC ROLES - We have 5 CC Roles
 # User groups can be mapped to the following Roles:
 # - USER: Can execute Single and File checks - against all Countries and those User-defined category groups
 # which are not restricted for the USER by the CONTENT_MANAGER or by the ADMIN.
 # - EXPERT_USER: Can execute Single and File checks - against all Countries and those User-defined category groups
 # which are not restricted for the EXPERT_USER by the CONTENT_MANAGER or by the ADMIN.
 # - CONTENT_MANAGER: Has limited access to the Administration functions:
 #   -- User-defined category group editor: Select categories and make restrictions for the USER and/or EXPERT_USER roles,
 #   -- User-defined category editor
 #   -- Database update history
 #   -- Report template editor
 # - ADMIN: Has access to all administration functions
 # cHemTS ROLES - We have 3 cHemTS Roles
 # - HTS_USER: Can execute cHemTS Single and File checks
 # - HTS_CONTENT_MANAGER : Can execute Single and File checks and has limited access to the Administration functions: -- Report template editor
 # - HTS_ADMIN : Has access to all administration functions.
 # COMMON ROLES
 # - SYSTEM: A special group to run automatic system checks
 # CC and cHemTS roles can be combined, so for example a user could have both USER and HTS_USER roles.
 # For automated system communication we need to have a SYSTEM user that can log in to the services.
 # The SYSTEM user - with very limited privileges - will use one of the authentication providers 
 # mentioned below, so you must register it in your LDAP / AD server.
     common.systemUser=system
     common.systemPassword=system

 # Roles - with special privileges - can be assigned to different user groups:
     common.rolesToGroupsMap={"userGroups":[],"userPattern":".*","adminGroups":["cc-admin"],"adminPattern":"","contentManagerGroups":["cc-content-manager"],"contentManagerPattern":"","expertUserGroups":["cc-expert-user"],"expertUserPattern":"","systemGroups":["cc-system"],"htsAdminGroups":["hts-admin"],"htsAdminPattern":"","htsContentManagerGroups":["hts-content-manager"],"htsContentManagerPattern":"","htsUserGroups":["hts-user"],"htsUserPattern":"","systemPattern":""}

 # Configuring ROLES
 # - FOR LDAP
 # If you use LDAP, then you can set it's configuration like this: 
 #   {"servers":[{"serverUrl":"ldap://ldap.server.com:389/dc=test,dc=tld","userDNPatterns":["uid={0},cn=users,cn=accounts"],"groupSearchBase":"","managerDN":"uid=cchecker,cn=sysaccounts","managerPassword":"<password>"}]}
 # This is a standard JSON but it has to be in one line. The "servers" property references an array. In this array you can set as many LDAP servers as you want. 
 # These servers will be checked in this specified order, and the first LDAP server that can authenticate the user will authenticate it.
 # The properties stands for the following:
 # "serverURL" -- The URL of the LDAP server
 # "userDNPatterns" -- The domain name of the users in the LDAP tree
 # "groupSearchBase" -- Domain name of groups in LDAP tree
 # "managerDN' -- The domain name of the manager user to query LDAP tree.
 # "managerPassword" -- The password of manager user.
     common.ldapConfig = {"servers":[{"serverUrl":"ldap://ldap.server.com:389/dc=test,dc=tld","userDNPatterns":["uid={0},cn=users,cn=accounts"],"groupSearchBase":"","managerDN":"uid=cchecker,cn=sysaccounts","managerPassword":"<password>"}]}

 # - FOR ACTIVE_DIRECTORY
 # If you use ACTIVE_DIRECTORY, then you can set you can set it's configuration like this: 
 #   {"servers":[{"domain":"your.domain","url":"ldap://server.domain.com"}]}
 # This is a standard JSON but it has to be in one line. The "servers" property references an array. 
 # In this array you can set as many Active Directory servers as you want. 
 # These servers will be checked in this specified order, and the first AD server that can authenticate the user will authenticate.
     common.activeDirectoryConfig={"servers":[{"domain":"your.domain","url":"ldap://server.domain.com"}]}

 # - FOR IN_MEMORY
 # If you are using IN_MEMORY authentication manager, you can configure it like this:
 #   {"users":[{"name":"<user>","password":"<userpwd>","roles":["USER"]}, {"name":"<admin>","password":"<adminpwd>","roles":["ADMIN"]}, {"name":"contentmanager", "<password>": "<contentmanagerpwd>", "roles":["CONTENT_MANAGER"]}, {"name":"expertuser", "<password>": "<expertuserpwd>", "roles":["EXPERT_USER"]}, {"name":"system","<password>":"system","roles":["SYSTEM"]}]}
 # This is a standard JSON but it has to be in one line. The "servers" property references an array. 
     common.inMemoryConfig = {"users":[{"name":"user","password":"password","roles":["USER"]},{"name":"admin","password":"adminPass","roles":["ADMIN"]},{"name":"contentmanager","password":"password","roles":["CONTENT_MANAGER"]},{"name":"expertuser","password":"password","roles":["EXPERT_USER"]},{"name":"system","password":"system","roles":["SYSTEM"]},{"name":"hts_user","password":"hts_password","roles":["HTS_USER"]},{"name":"hts_admin","password":"hts_adminPass","roles":["HTS_ADMIN"]},{"name":"hts_contentmanager","password":"hts_password","roles":["HTS_CONTENT_MANAGER"]}]}

 # - DIRECT ROLE ASSIGN
 # Roles can be assigned directly to special users by setting the value of the config key.
 # The value should be a comma separated list of ROLES. 
 # Currently available roles are: USER, EXPERT_USER, CONTENT_MANAGER, ADMIN, SYSTEM.
#   roles.<username>=<roles>

# The default view for Regulation Categories. Valid values are: COUNTRIES, CHECK_LEVELS
#check.default.regulationCategories=CHECK_LEVELS

# Setting this to true will only display the check levels as selectable categories on the check pages
#check.hideCountries=true

# The default report format for batch checks. Valid values are: HTML,PDF,SDF,MRV,XLSX
#batch.default.reportFormat=HTML

# Comma separated list of fields to be included in the JSON reports.

# Including only needed fields in JSON reports can greatly increase the speed of report generation

# To include child fields, parent fields also have to be listed

# If none of the listed fields are present in the result or the config key is not set
# then the full result will be added to the report

# Example: 
# [ 
#    [
#       { 
#          "segments":[ 
#             { 
#                "categoryName":"catName", 
#                "categoryCode":1234 
#             } 
#          ], 
#          "inputProperties":{ 
#             "ID":"123", 
#             "Name":"Name" 
#          } 
#       } 
#    ] 
# ] 

#
 To include only the categoryCode and ID in the JSON report from the above example result 
# the following configuration has to be made: 
#json.report.fields=segments,categoryCode,inputProperties,ID

report.xlsx.max-image-count=10000

# Enables to schedule the removal of all check related data from the database.
# The value should be a cron-like expression, which extends the usual UN*X definition to include triggers
# on the second as well as minute, hour, day of month, month and day of week.

# Example patterns:
# "0 0 * * * *" = the top of every hour of every day.
# "*/10 * * * * *" = every ten seconds.
# "0 0 8-10 * * *" = 8, 9 and 10 o'clock of every day.
# "0 * 6,19 * * *" = 6:00 AM and 7:00 PM every day.
# "0 0/30 8-10 * * *" = 8:00, 8:30, 9:00, 9:30 and 10 o'clock every day.
# "0 0 9-17 * * MON-FRI" = on the hour nine-to-five weekdays
# "0 0 0 25 12 ?" = every Christmas Day at midnight
#batch.cleanup.scheduler=0 0 4 * * *

{
    "servers" : [{
            "serverUrl" : "ldap://ldap1.mycompany.com/dc=mycompany,dc=com",
            "userDNPatterns" : ["uid={0},cn=users,dc=mycompany,dc=com", "uid={0},cn=external,dc=mycompany,dc=com"],
            "groupSearchBase" : "",
            "groupSearchFiler" : "",
            "userSearchBase" : "",
            "userSearchFilter" : "",
            "managerDN" : "uid=admin,cn=sysusers,dc=mycompany,dc=com",
            "managerPassword" : "PASSWORD!",
            "root" : ""
        }, {
            "serverUrl" : "ldaps://ad.mycompany.com/dc=cmp,dc=com",
            "userDNPatterns" : [],
            "groupSearchBase" : "",
            "groupSearchFiler" : "",
            "userSearchBase" : "dc=cmp,dc=com",
            "userSearchFilter" : "sAMAccountName={0}",
            "managerDN" : "Administrator@cmp.com",
            "managerPassword" : "other_PASSWORD!",
            "root" : "dc=cmp,dc=com"
        }
    ]
}

{
    "servers" : [{
            "serverUrl" : "ldap://ldap1.mycompany.com/dc=mycompany,dc=com",
            "userDNPatterns" : ["uid={0},cn=users,dc=mycompany,dc=com", "uid={0},cn=external,dc=mycompany,dc=com"],
            "managerDN" : "uid=admin,cn=sysusers,dc=mycompany,dc=com",
            "managerPassword" : "PASSWORD!"
        }, {
            "serverUrl" : "ldaps://ad.mycompany.com/dc=cmp,dc=com",
            "userSearchBase" : "dc=cmp,dc=com",
            "userSearchFilter" : "sAMAccountName={0}",
            "managerDN" : "Administrator@cmp.com",
            "managerPassword" : "other_PASSWORD!",
            "root" : "dc=cmp,dc=com"
        }
    ]
}

{"servers" : [{"serverUrl" : "ldap://ldap1.mycompany.com/dc=mycompany,dc=com", "userDNPatterns" : ["uid={0},cn=users,dc=mycompany,dc=com", "uid={0},cn=external,dc=mycompany,dc=com"], "managerDN" : "uid=admin,cn=sysusers,dc=mycompany,dc=com", "managerPassword" : "PASSWORD!"}, { "serverUrl" : "ldaps://ad.mycompany.com/dc=cmp,dc=com", "userSearchBase" : "dc=cmp,dc=com","userSearchFilter" : "sAMAccountName={0}", "managerDN" : "Administrator@cmp.com", "managerPassword" : "other_PASSWORD!", "root":"dc=cmp,dc=com"}]}

{
    "servers": [
        {
            "domain" : "first.domain",
            "url" : "ldap://first.com"
        } ,
        {
            "domain" : "second.domain",
            "url" : "ldap://second.com"
        } 
    ]
}

// Don't forget that you have to set it in the <code>application.properties</code> file in one line.
// Like this: { "servers": [    {"domain" : "first.domain", "url" : "ldap://first.com"} , {"domain" : "second.domain", "url" : "ldap://second.com"} ]}
// We only used multi line example for better readability.