Default settings in application.properties
Other settings in application.properties
Merge specific rules into the Knowledge Base
Your license.cxl file(s) should be installed as described in the License Management section.
Config Server is a service of Compliance Checker to populate your settings to other servers (cc-web, cc-api, cc-bigdata and cc-backend). On startup, all of these services require the Config server to load their settings from it. Config server can update some settings runtime, but others need to be updated by restarting the servers.
To customize the application the configuration can be modified by editing the application.properties file.
Any property changed in the application.properties file will affect the appropriate services.
At the clean install, the settings in application.properties.default will be copied to the application.properties file.
At upgrading the software - i.e. installing the new software version - the application.properties file will never be overwritten. So your already customized configuration will not be changed.
Creating user in MongoDB
# 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"
]
}
)The following default settings in application.properties.default can be modified in the application.properties file (in this format, # stands for comments):
# 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
The following default database connection settings can also be modified in the application.properties file :
# 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 = falseConnection to a MongoDB cluster cloud (MongoDB Atlas, Amazon DocumentDB) can be configured by inserting the provided mongoDB URI to the application.properties file:
#spring.data.mongodb.uri=<URI PROVIDED BY CLOUD SERVICE>For DocumentDB the PEM file should be downloaded, too. (See https://docs.aws.amazon.com/documentdb/latest/developerguide/getting-started.connect.html )
This PEM file should be added to the trusted store:
keytool -import -keystore cacerts -file
The new certificate should be added to the default trusted certificate.
To enable secure database transactions (which is default with db in the cloud), set the following property to true:
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 explicit 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
You can configure other settings for Compliance Checker in the application.properties file.
# The URL of eureka service
eureka.client.serviceUrl.defaultZone=http://localhost:8761/eureka/# The URL of the latest Conpliance Checker knowledge base file:
common.autoUpdateUrl=https://dl.chemaxon.com/cchecker/cc-database.jar
#The URL of the latest cHemTS knowledge abase file
common.htsAutoUpdateUrl:https://dl.chemaxon.com/hts/hts-knowledge-base.jar
# The URL of the text file containing the version of the latest Compliance Checker knowledge base file.
common.autoUpdateVersionUrl=https://dl.chemaxon.com/cchecker/cc-version.txt
#The URL of the text file containing the version of the latest cHemTS knowledge base file
common.htsAutoUpdateVersionUrl:https://dl.chemaxon.com/hts/hts-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
# Enables to schedule the cHemTS knowledge base update automatically.
#common.htsAutoUpdateScheduler=0 0 1 * * MON-FRIRoles - with special privileges - can be assigned to different user groups :.
Compliance Checker
Category group access can be controlled according to ROLES.
CHemTS
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. (E.g.: roles.username=HTS_USER,HTS_CONTENT_MANAGER)
# 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>Admin can select Available countries or Selected check levels to be displayed in Regulation categories by setting check.default.regulationCategories key to COUNTRIES or CHECK_LEVELS in application.properties.
By adding/setting the check.hideCountries key value to true (default is false ) Available countries will not be displayed at all.
(On the System monitor page the Reload settings from config file button should be clicked after editing application.properties.)
Default regulation categories
# 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=trueThe default Report format can be set by the Admin by adding HTML , PDF , SDF , MRV or XLSX value to the batch.default.reportFormat key in application.properties.
(User's last selection is saved in the mongo DB and will not be modified.) Default report format
# 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,IDThe report.xlsx.max-image-count parameter sets the maximum number of images generated in .XSXL reports. The default number is 10000. Setting this parameter may prevent the service going down with out of memory error.
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 * * *cHemTS leverages advanced mixture algorithm in order to be able to decide whether a particular multi-fragment input structure can be classified as a pure form, a salt or a mixture.
The algorithm can be fine-tuned by amending the list of known ignorable fragments. These fragments are either entirely discarded (in case of solvents or additives) or their salt characters are taken into consideration by the algorithm.
Ignorable fragments can be excluded or included on demand, the following configuration options need to be changed accordingly:
hts.search.mixture.ignorablefragments.included=[...]
hts.search.mixture.ignorablefragments.excluded=[...]Multiple structures can be listed separated by comma. E.g.
hts.search.mixture.ignorablefragments.excluded=Br,CC(O)=OEach structure must be represented by SMILES format. In case of including new salts, their characters must be also set. Salt characters can be separated from the structure by semicolon. E.g.
hts.search.mixture.ignorablefragments.included=SC#N;acidic
Our LDAP configuration object is a list of configurations of LDAP servers.
Each server configuration can hold several attributes. Each of them can be left empty, left out from configuration string or can be set to null.
In this case, they will be used by their default values.
One server holds the following possible settings:
| Attribute name | Attribute type | Default value | Example | Explanation |
|---|---|---|---|---|
| serverUrl | String | ldap://localhost:389 | "ldaps://ldap.mycompany.com:621" or "ldap://ldap2.cmp.com/dc=cmp,dc=com" | The URL where the system can reach the LDAP server. |
| userDNPatterns | List of Strings | [ ] | [ "uid={0},dc=mycompany,dc=com", "uid={0},ou=internal,dc=mycompany,dc=com" ] | These patterns will be used to find the User by its distinguished name.The part between the curly brackets will be replaced by the username.If this setting is left empty, then user distinguished name won't be used in the user authentication. |
| groupSearchBase | String | "" | "ou=InternalGroups,dc=mycompany,dc=com" | The base DN from which the search for group membership should be performed. |
| groupSearchFilter | String | "" | "(member={0})" | The pattern to be used for the user search. {0} is the user's DN |
| userSearchBase | String | "" | "ou=Users,dc=mycompany,dc=com" | This element of the LDAP tree will be used as the root element during user search. In case it is left empty, the root of the LDAP tree will be used. If you use userSearchFilter, than you must provide userSearchBase as well. |
| userSearchFilter | String | "" | "sAMAccountName={0}" | In case the users are not found by their distinguished name, user search will happen. The part with the curly brackets will be replaced with the username that used to log in. In case of **Active Directory, ** usually sAMAccountName is required to log in. You can not use userSearchFilter without userSearchBase. |
| managerDN | String | "" | "dn=admin,dc=mycompany,dc=com" or "admin@mycompany.com" | This is the name of the manager user. This name will be used to bind to the LDAP server. The second format can be used to log in to Active Directory through LDAP. |
| managerPassword | String | "" | "s3cr3tp455w0rd" | This is the password of the manager user. |
| root | String | "" | "dc=mycompany,dc=com" | In case the serverURL does not contain the root of the LDAP search, then it can be set here. If it is left empty, then root from URL will be used. Active Directory usually requests root to be set separately for binding. |
This configuration uses two servers (an LDAP and an Active Directory) and has all attributes: LDAP config
{
"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"
}
]
}This means the same as the following: Shorter Config
{
"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"
}
]
}Consider using the shorter config format because in application.properties, the config must be in one single line , like this: Config in one line
{"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"}]}Example settings for 2 Active Directory servers
{
"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.Chemical substances can be checked against some special (e.g. company-specific) rules, too.
MRV files should be created from these rules - with the same data structure as the main Knowledge Base. An MRV file for the specific rules ( rule_structures.mrv ) and another MRV file for the specific exceptions ( exclusion_structures.mrv ).
These files should be copied to the Chemaxon_home/compliancechecker/user folder. (I.e. to the "user" subfolder of the "database" folder. The cc_backend startup process creates that folder with empty MRV files - but these files will never be overwritten automatically.)
Compliance Checker should be restarted to merge these specific rules into the main Knowledge Base.
If you distribute the system you should set the following settings to the services:
Config server is the route of the hierarchy. It should register with Eureka service. If Eureka does not run in localhost:8761 (8761 is the default Eureka port) then you have to set the following property in the application.properties file:
eureka.client.serviceUrl.defaultZone=http\://<eureka-hostname>\:<eureka-port>/eureka/
If Eureka runs locally for the Config Server , but it is a remote service for the other services, then you should set the above property with an address that is available for all services, because this setting will be populated to all services.
Eureka server is used by all the services. It uses the Config Server to init itself. If the Config Server does not run in localhost:8888 (8888 is the default Config Server port), then you can have to set the following property in bootstrap.properties file:
spring.cloud.config.uri=http\://<config-server-host>\:<config-server-port>/
The main components of the application come in 4 war files: cc-backend.war, cc-bigdata.war, cc-web.war, cc-api.
Every war file uses the Config Server to init itself. If the Config Server does not run in localhost:8888, then you have to set for the components where to find the Config Server. One opportunity is to set the CONFIG_SERVER_URI environment variable, or to edit the bootstrap.properties file next to each war file. Or you can set in it in their .vmoptions file. Setting environment variable in unix
export CONFIG_SERVER_URI = http://<config-server-host>:<config-server-port>/
Setting environment variable in windows command line
CONFIG_SERVER_URI = http://<config-server-host>:<config-server-port>/
Set environment variables in .vmoption file
-DCONFIG_SERVER_URI=http://<config-server-host>:<config-server-port>/
Editing bootstrap.properties file
spring.cloud.config.uri=http\://<config-server-host>\:<config-server-port>/
This property will be used in startup time to connect to the Config Server and receive all the properties to use in initialization.