NIH | National Cancer Institute | NCI Wiki  

Information on this page is based on the install.properties file. All releases are on the Installation and Downloads page.

Application Settings

Property Name

Description

Example

application.base.path.linux

Location where user is installing software on Linux

${user.home}/apps/nbia

application.base.path.windows

Location where user is installing software on Windows

c:/apps/nbia

authentication.type

CSM authentication type; the value should be "ldap" or "ldap-auth"

ldap

Database Settings

Property NameDescriptionExample

database.type

This value specifies whether a MySQL or an Oracle database is being used. Currently only MySQL is supported.

mysql

database.re-create

database.drop-schema

One of these properties must be set to true. 

If re-create is true then the install:database target will wipe out the database instance completely and start from scratch. 

If drop-schema is true, then all the schema and data will be wiped out but the database itself will not be removed.

true or false
database.system.user

The username for an administrator of this database. 


This value should correspond to a MySQL username that has full system privileges.

This must correspond to the administrator account defined when MySQL was configured.
For Oracle, this value will be ignored, but the value must be different than the value of database.user.

Depending on how the install is done, or the value of database.re-create this may not be necessary. 
If re-create=true, then this is necessary, otherwise it isn't.

root
database.system.passwordThe password for an administrator of this database that correlates with the value in database.system.user.

For Oracle, this value will be ignored.

Depending on how the install is done, or the value of database.re-create this may not be necessary. 
If re-create=true, then this is necessary, otherwise it isn't.
Someth!ngSecure

database.server

This value must correspond to the domain name of machine that hosts the Oracle/MySQL database server.

Talk to your database administrator to learn the server name and port.

remotehost.org

database.port

This value must correspond to the port for the database.server.

3306 is the default port, but check with your database administrator to be certain.

3306

database.name

Choose a name for the NCIA MySQL database. This must be different than the UPT database name.

nciadb

database.user

Give the username to access database.name.

nciaop

database.password

Use a password to access database.name for the username identified in database.user

Someth!ngSecure

database.url

URL for connection to a database. This is the standard implementation style.

This if fixed. No change required.

jdbc:mysql://${database.server}:${database.port}/${database.name}

database.system.url

URL for connection to a database. This is the standard implementation style.

This if fixed. No change required.

jdbc:mysql://${database.server}:${database.port}/

database.schemaDatabase schema for Oraclenciadev

TCIA LDAP Settings

These can be ignored for the community version. The property names in this category include ldap.memberOf.attribute.nameldap.mail.attribute.name, ldap.group.ignore.list, public.collection.access.group.name and product.variation.

LDAP Settings

Property Name

Description

Example

ldap.url

Universal Resource Locator address for LightWeight Directory Access Protocol server.

ldaps://university.edu:636

ldap.basedn

LDAP server holding referrals to other server holding a given distinguished name (DN).

u=nci,o=nih

ldap.userUsed only under ldap-auth, otherwise comment out.cn=NCILDAP,ou=nci,o=nih
ldap.passPassword for the authenticated user under ldap-auth, otherwise comment out.somepass

CTP Settings

Property Name

Description

Example

ctp.server.port

The port that the CTP administration console will run on

23080

ctp.server.http_import_service.port

The port that CTP will accept submissions on.  This port should be configured as the port to export to in the CTP client configuration.

23104

ctp.server.admin.password

The password for the CTP server administrator

S0meth!ngSecurE

ctp.server.king.password

The password for the CTP server super administrator who has privilege to shutdown the server

S0meth!ngSecurE

ctp.server.storage_service.root

The directory where the CTP will store submitted files

storage/root

ctp.server.storage_service.index

The directory where the CTP will store the index for submitted files.  This directory must be the direct parent of ctp.storage_service.root.

storage

ctp.server.require_authentication

Whether or not the authentication is required for data submission (HttpImportService)

yes

ctp.server.verifier.port

The port that CTP will listen for verification requests on. 

Verification requests are queries to the (NBIA) database adapter to confirm that a given image was submitted successfully.

 23304

ctp.client.port

The port that the CTP administration console will run on (for the client)

24080

ctp.client.http_import_service.port

The port that CTP will accept submissions on.  This port should be configured as the port to send to in the FileSender.

24104

ctp.client.dicom_import_service.port

The port that CTP will accept submissions on.  This port should be configured as the port to send to in the FileSender.

24304

ctp.client.export_service.port

The port that CTP will export submissions to (to the server).  This should match up with the import service port on the server side.

24204

ctp.client.admin.password

The password for the CTP client administrator

S0meth!ngSecurE

ctp.client.king.password

The password for the CTP client super administrator who has privilege to shutdown the server

S0meth!ngSecurE

ctp.client.exportService.usernameSpecifies the user name at the submitting site to ensure that all transmitted data made it into the NBIA database S0meth!ngSecurE
ctp.client.exportService.password Specifies the password at the submitting site to ensure that all transmitted data made it into the NBIA database S0meth!ngSecurE

NBIA Application Properties

Property Name

Description

Example

gov.nih.nci.ncia.imaging.server.url

Publicly visible URL for the Tomcat container hosting NBIA.

This URL should contain the proxy name instead of the host name if there is a proxy.

If this property is not configured properly, then thumbnails images may not appear in the web application search results.

http://locahost:45210

gov.nih.nci.ncia.mapped.image.path.head

\\\\\\\\cbiofs502.nci.nih.gov\\\\nciaimages\\\\,\\\\\\\\cbiofs502.nci.nih.gov\\\\nciaproddataset\\\\dataset_p01\\\\,\\\\\\\\nfs-ncia-d.nci.nih.gov\\\\nciadevdataset\\\\dataset_d01\\\\

gov.nih.nci.ncia.image.path.pattern
NCICBIMAGE/documents/,data/dataset_p01/,data/dataset_d01/

gov.nih.nci.ncia.zip.location

Location to place zipped files created by the NBIA web application for download.

/data/ncia_data/ncia_ftp

gov.nih.nci.ncia.ftp.location

Location to place files for download through an external FTP server. 

/data/ncia_data/ncia_ftp

gov.nih.nci.ncia.grid.local.node.name

If remote search is enabled, this is the name that will be used in the search form to search THIS node.

There is a separate property that governs the name of this node but as  viewed from other instances of NBIA. 

It is likely that these two properties should agree, but it isn't mandatory.

See: grid.poc.tech.researchCenter.displayname

NCI-1

gov.nih.nci.ncia.ui.uid.display.length

Determines the max character length of data representation in the UI tier

100

gov.nih.nci.ncia.ftp.url

FTP server URL used for informing users about where to download the larger size files

localhost

gov.nih.nci.ncia.installationSite

This property determines whether the installation is at ncicb or somewhere else (other). 

This governs certain aspects of the UI such as where the link to reset a password will point to.

ncicb, other

gov.nih.nci.ncia.admin.email

The email address of the user administrator

ncicbmb@mail.nih.gov

gov.nih.nci.ncia.jboss.public.urlNBIA's URL for the portalhttp://localhost:45210/ncia/
gov.nih.nci.ncia.download.server.url

This is the URL that the Download Manager will use to retrieve DICOM images from. 

This should typically be the same host and port of the Tomcat server. 

The webapp context and file path should always be the same unless deployment has been customized.

http://localhost:45210/nbia-download/servlet/DownloadServlet

enabled_guest_account

Whether or not public search will be enabled for this instance.

yes or no

guest_username

If enabled_guest_account=yes then this is the name of the CSM user that will blessed as the user for all public searches. 

This user should likely only be provisioned to be associated with PUBLIC protection elements.

nbia_guest

enable_classic_download

If this is set to no, then only the WebStart based Download Manager will be available to all users. 

If this is set to yes, then the "classic" download feature will still be available that allows downloading zip
 files of DICOM images through HTTP and/or HTTP

yes or no

registration.email.subjectSubject for the email sent to CBIITUser registration to LDAP to access the National Biomedical Imaging Archive (NBIA)
show.collection.search.criteria

If User wants to see Collections such as MR, CT, US etc in the Simple Search Page. By default it's set to false.

true or false
discover.remote.nodesWhat remote nodes the user want to see i.e., Dev, Stage, Prod etc. Deprecated after NBIA 5.2 Version.true or false
show.anatomical.search.criteriaVarious body parts the User wants to Search for such as Abdomen, Brain, Chest etc.true or false

local.grid.uri

For a given installation, this is the URL to the grid service FOR THAT INSTALLATION itself.
 
If this is not set properly, and remote search is enabled, then the local node will appear twice in the
 list of searchable nodes. 

Once for the "local" search, and additionally for its grid interface (if it is registered with the index service).

http://imaging.company.com:45210/wsrf/services/cagrid/NBIAService

show.collection.search.criteria

If set to false, the collection criteria selection control will not appear in the classic search UI. 

This should only be set to false if a given instance of NBIA has, and only will ever have, 
only one collection/project to search through.

true or false

discover.remote.nodes

If set to false, the NBIA web application will not attempt to discover other instances of NBIA to search through the caGrid Index Service.

In other words, no remote nodes will appear at the top of the classic search page if this is set to false.

true or false

gov.nih.nci.ncia.download.no.retryMaximum number of retry to download images for NBIA Download Manager
4

Log4J Settings

Property Name

Description

Example

log4j.maxFileSize
100MB
log4j.maxDays
7
log4j.level
WARN

Mail Settings

Property Name

Description

Example

mail.smtp.server

Location of mail server to send emails for application to forward emails to users, notify users of the location of the download files

mail.university.edu

Download Manager Digital Signature Settings

Property Name

Description

Example

jar-signing.keystore.location

The location of the keystore to find a key to sign the download manager jars with. 

If (file://\\If) generate-selfsigned is set to true, then this location will be where the installation process CREATES the keystore. 

Otherwise (file://\\Otherwise), the keystore should already exist at this location.

c:/keystores/nbia_keystore

jar-signing.keystore.password

The password for the keystore pointed to by keystore.location.

If (file://\\If) generate-selfsigned is set to true, then this password will be set when the installation process CREATES the keystore.  \ (file://\\Otherwise)

Otherwise, the password should apply to the existing keystore.

something_secure

jar-signing.keystore.alias

The alias for the key to use when signing the download manager jars.

If (file://\\If) generate-selfsigned is set to true, then this alias will be set when the installation process CREATES the key and keystore. 

Otherwise (file://\\Otherwise), the alias should exist in the existing keystore.

alias1

jar-signing.execution.time

Whether to sign the jars at build time or install time.  If not at NCICB, this value should always be install.

build or install

jar-signing.generate-selfsigned

If set to true, the install process will generate a self-signed certificate to sign the jars with. 

If (file://\\If) false, there must be an existing certificate to use when signing.

true or false

gov.nih.nci.ncia.encrypt.keyAlphanumeric key for password encryption ABCD12346598AYE2

Exclusions

Property Name

Description

Example

exclude.start.servers

If you want to exclude starting server after the completion of installation. Default is set to false.true or false

exclude.ctp

If you want to exclude CTP. Default is set to false.true or false

exclude.ctp-client

If ctp-client should be excluded or not. Default is set to false.true or false

exclude.database

If you want to exclude database or not. Default is set to false.  For the first time installation, please leave this property commented out so that database schema can be created.
true or false

exclude.ctp.client.backup

If CTP Client backup is excluded. Default is set to false.true or false

exclude.ctp.server.backup

If CTP server backup should be excluded. Default is set to false.true or false

exclude.nbia-api

Exclude NBIA API or not. Default is false.true or false

User Guide Settings

Property Name

Description

Example

gov.nih.nci.ncia.wiki.context.sensitive.help.urlwiki tiny URL for context sensitive help

https://wiki.nci.nih.gov/display/NBIA/NBIA+Help+Topics#NBIAHelpTopics

SOLR Settings

Property Name

Description

Example

gov.nih.nci.ncia.solr.homeLocation to keep Solr indexesc:/apps/nbia/solr-home/
gov.nih.nci.ncia.solr.updateintervalThis will defines how often in minutes Solr will update indexes60

Workflow Settings

Property Name

Description

Example

gov.nih.nci.ncia.workflow.updateintervalThis will defines how often in minutes the workflow will be updated60

REST API Settings

Property Name

Description

Example

nbia.api.oauth2.client.idUnique ID given by authorization server during registration to the client application

Contact 

nbia.api.oauth2.client.secretThe password supplied to identify the client

Contact 

nbia.api.oauth2.token.validity.in.secondsThe expiration time in seconds before which the transaction has to be performed7200

Tomcat Configuration Properties

Property Name

Description

example

gov.nih.nci.ncia.tomcat.homeWhere tomcat is installed/local/content/apache-tomcat-7.0.68
database.driverThe database driver. Please do not change the value of the property. If the database used is MySQL, just comment out the same property for Oracle and un-comment out the property for MySQL.  Vise versa for Oracle database.

For MySQL database:

com.mysql.jdbc.Driver

For Oracle database:

oracle.jdbc.driver.OracleDriver

database.driver.jarThe jar name of database driver. Please do not change the value of the property.  If the database used is MySQL, just comment out the same property for Oracle and un-comment out the property for MySQL. Vise versa for Oracle database.

For MySQL database:

${mysql.driver.jar}

For Oracle database:

${oracle.driver.jar}

database.driver.jar.src.urlThe URL for downloading database driver library. Please do not change the value of the property. If the database used is MySQL, just comment out the same property for Oracle and un-comment out the property for MySQL. Do the same for the Oracle database.

For MySQL database:

${mysql.driver.jar.src.url}

For Oracle database:

${oracle.driver.jar.src.url}


csm.api.jarThe name of CSM API jar. Do not change the value of the property.csmapi-5.2.jar
csm.api.jar.src.urlThe source URL for CSM API jar. Do not change the value of the property.https://ncimvn.nci.nih.gov/nexus/service/local/repositories/thirdparty/content/gov/nih/nci/csm/csmapi/5.2/${csm.api.jar}
bouncy.castle.jarThe name of bouncy castle jar. Do not change the value of the property.bcprov-jdk15on-1.51.jar
bouncy.castle.jar.src.urlThe source URL for bouncy.castle.jar. Do not change the value of the property.https://ncimvn.nci.nih.gov/nexus/service/local/repositories/central/content/org/bouncycastle/bcprov-jdk15on/1.51/${bouncy.castle.jar}
mysql.driver.jarThe jar name of MySQL Driver. Do not change the value of the property.mysql-connector-java-5.1.34.jar
mysql.driver.jar.src.urlThe source URL for MySQL driver.  Do not change the value of the property.https://ncimvn.nci.nih.gov/nexus/service/local/repositories/central/content/mysql/mysql-connector-java/5.1.34/${mysql.driver.jar}
oracle.driver.jarThe jar name of Oracle driver. Do not change the value of the property.ojdbc14-10.2.0.3.0.jar
oracle.driver.jar.src.urlThe source URL for Oracle driver. Do not change the value of the property.https://ncimvn.nci.nih.gov/nexus/service/local/repositories/thirdparty/content/oracle/ojdbc14/10.2.0.3.0/${oracle.driver.jar}

GUI Link Properties

Property Name

Description

Example

gui.textText for button linking out to beta search applicationLeave blank in community version
gui.linkURL for beta application, ignored in community versiongui.link=http//google.com

NBIA Data Retriever Properties

Property Name

Description

Example

win.downloader.installer.pathThe URL for downloading NBIA Data Retriever Installer for Windows 7 and 10https://cbiit-download.nci.nih.gov/nbia/releases/ForTCIA/NBIADataRetriever_4.0/NBIA%20Data%20Retriever-4.0.msi
mac.downloader.installer.pathThe URL for downloading/installing NBIA Data Retriever Installer from Mac App Storehttps://itunes.apple.com/us/app/downloader-app/id1399207860?mt=12
centos.downloader.installer.pathThe URL for downloading NBIA Data Retriever Installer for CentOS and RedHathttps://cbiit-download.nci.nih.gov/nbia/releases/ForTCIA/NBIADataRetriever_4.0/NBIADataRetriever-4.0-1.x86_64.rpm

ubuntu.downloader.installer.path

The URL for downloading NBIA Data Retriever Installer for Ubuntuhttps://cbiit-download.nci.nih.gov/nbia/releases/ForTCIA/NBIADataRetriever_4.0/nbia-data-retriever-4.0.deb
latest.TCIA.downloader.versionThe latest version of NBIA Data Retriever supported by the download server4.0
latest.manifest.versionThe latest version of manifest file supported by the download server3.0

force.downloader.upgrade

A flag to send to NBIA Data Retriever for disabling "Remind me later" button

false

help.desk.urlURL to access help desk page from NBIA Data Retrieverhttps://cbiit.cancer.gov/application-support
online.help.urlURL to access online help wiki page from NBIA Data Retrieverhttps://wiki.cancerimagingarchive.net/display/NBIA/TCIA+Current+Help+Topics#TCIACurrentHelpTopics-DownloadingTCIAImages

Species Properties

Property Name

Description

Example

species.descriptionThe species description for human in DICOMHomo sapiens
species.codeThe species code for human in DICOM337915000

User Authentication Tool (UAT) Properties

Property Name

Description

uat.enable.creating.newCollectionSite

If set to True, this property shows the Protection Element tab in UAT. If this property is set to True, it is recommended that ctp.block.creating.newCollectionSite should also be set to true. This requires that a new collection and site must be created first before managing these elements in UAT.

If set to False, this property hides the Protection Element tab in UAT. An NBIA hosting site may chose to set this property to False if the are generating the Protection Element  automatically during the DICOM submission process.

Note: Configure the properties uat.enable.creating.newCollectionSite and ctp.block.creating.newCollectionSite together using one of the following two scenarios.

  1. Set both uat.enable.creating.newCollectionSite and ctp.block.creating.newCollectionSite to False if you want users to submit DICOM data and then let the User Authentication Tool (UAT) create the Protection Element automatically, based on the collection and site in the submission.
  2. Set both uat.enable.creating.newCollectionSite and ctp.block.creating.newCollectionSite to True if you want to create a new collection and site using UAT before users submit DICOM data for that collection and site. This bypasses the NBIA database adapter that would have normally created a new collection and site in the database based on the submission.
ctp.block.creating.newCollectionSite

If set to True, this property prevents a new collection and site from being created automatically when DICOM data is submitted.

If set to False, this property creates a new collection and site when DICOM data is submitted.

See note above for more information.

uat.enable.assign.user.to.userGroupIf set to True, this property allows a user to be assigned to a user group.
uat.enable.assign.user.to.protectionGroupIf set to True, this property allows a user to be assigned to a protection group.

NBIA Classic Help Topic Mapping

The following are the anchors for the context-sensitive help for the NBIA Classic UI. The NBIA Data Portal does not have context-sensitive help.

Base URL=https://wiki.nci.nih.gov/display/NBIA/NBIA+Help+Topics
NBIA Help Topic NameAnchor
Registering a New User#NBIAHelpTopics-RegisteringaNewUser
Logging into NBIA#NBIAHelpTopics-LoggingintoNBIA
Using the NBIA Home Page#NBIAHelpTopics-UsingtheNBIAHomePage
Using NBIA Online Help#NBIAHelpTopics-UsingNBIAOnlineHelp
Performing a Simple Search#NBIAHelpTopics-PerformingaSimpleSearch
Performing a Text Search#NBIAHelpTopics-PerformingaTextSearch
Performing an Advanced Search#NBIAHelpTopics-PerforminganAdvancedSearch
Creating Saved Queries#NBIAHelpTopics-CreatingSavedQueries
Working with Saved Queries#NBIAHelpTopics-WorkingwithSavedQueries
Editing Saved Queries#NBIAHelpTopics-EditingSavedQueries
Viewing a Query History#NBIAHelpTopics-ViewingQueryHistory
Search Results by Subject#NBIAHelpTopics-SearchResultsStudiesforSubject
Managing a Shared List#NBIAHelpTopics-ManagingaSharedList
Creating a Shared List#NBIAHelpTopics-CreatingaSharedList
Searching a Shared List#NBIAHelpTopics-SearchingaSharedList
Editing a Shared List#NBIAHelpTopics-EditingaSharedList
Managing the Data Basket#NBIAHelpTopics-ManagingtheDataBasket
Download Manager#NBIAHelpTopics-DownloadManager
Viewing Submission Reports#NBIAHelpTopics-ViewingSubmissionReports
Accrual Report#NBIAHelpTopics-AccrualReport
Image Submission Report#NBIAHelpTopics-ImageSubmissionReport
Annotation Submission Report#NBIAHelpTopics-AnnotationSubmissionReport
Using the Quality Control Tool#NBIAHelpTopics-UsingtheQualityControlTool
Generating a QC Status Report#NBIAHelpTopics-GeneratingaQCStatusReport
Approving Image Deletions#NBIAHelpTopics-ApprovingImageDeletions
Manually Deleting Image Series#NBIAHelpTopics-ManuallyDeletingImageSeries
Editing a Collection Description#NBIAHelpTopics-EditingaCollectionDescription
Managing Workflow Items#NBIAHelpTopics-ManagingWorkflowItems
Creating Workflow Items#NBIAHelpTopics-CreatingWorkflowitems
Managing Saved Queries#NBIAHelpTopics-ManagingSavedQueries
Managing Users#NBIAHelpTopics-ManagingUsers
Managing Protection Groups#NBIAHelpTopics-ManagingProtectionGroups
Adding Protection Groups and Assigning Roles#NBIAHelpTopics-AddingProtectionGroupsandAssigningRoles
Managing Protection Elements#NBIAHelpTopics-ManagingProtectionElements
  • No labels