This guide covers handling INCEpTION from an administrator’s perspective.

Installation

You can run INCEpTION on any major platform supporting Java, i.e. Linux, macOS or Windows. However, we do not provide explicit for setting up a production-ready instance of each of these platforms.

This guide assumes Debian 9.1 (Stretch). It may also work on Ubuntu with some modifications, but we do not test this. Instructions for other Linux distributions and other platforms (i.e. macOS and Windows) likely deviate significantly.

It is further assumed that the use www-data already exists on the system and that it shall be used to run the application.

All commands assume that you are logged in as the root user.

If you cannot log in as root but have to use sudo to become root, then the recommended way to do that is using the command sudo su -.

System Requirements

Table 1. Requirements for users

Browser

Chrome or Safari

Table 2. Requirements to run the standalone version

Java Runtime Environment

version 9 or higher

Table 3. Requirements run the server version

Java Runtime Environment

version 9 or higher

Apache Tomcat

version 8.5 or higher (Servlet API 3.1.0)

MySQL Server

version 5 or higher

Install Java

You can install an Oracle Java 8 JDK using the following commands.

$ apt-get update
$ apt-get install dirmngr
$ echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" | tee /etc/apt/sources.list.d/webupd8team-java.list
$ echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list
$ apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
$ apt-get update
$ apt-get install oracle-java8-installer
$ apt-get install oracle-java8-set-default

Application home folder

The INCEpTION home folder is the place where INCEpTION’s configuration file settings.properties resides and where INCEpTION stores its data. Mind that if you are using a MySQL database server (recommended), then INCEpTION also stores some data in the MySQL database. This is important when you plan to perform a backup, as both the home folder and the database content need to be included in the backup.

Now, let’s go through the steps of setting up a home folder for INCEpTION and creating a configuration file instructing INCEpTION to access the previously prepared MySQL database.

  • Create INCEpTION home folder. This is the directory where INCEpTION settings files and projects (documents, annotations, etc.) are stored

    $ mkdir /srv/inception
  • Edit /srv/inception/settings.properties to define the database connection as well as internal backup properties:

    database.dialect=org.hibernate.dialect.MySQL5InnoDBDialect
    database.driver=com.mysql.jdbc.Driver
    database.url=jdbc:mysql://localhost:3306/inception?useSSL=false&serverTimezone=UTC
    database.username=inception
    database.password=t0t4llYSecreT
    
    # 60 * 60 * 24 * 30 = 30 days
    backup.keep.time=2592000
    
    # 60 * 5 = 5 minutes
    backup.interval=300
    
    backup.keep.number=10
  • Fix permissions in INCEpTION home folder

    $ chown -R www-data /srv/inception

Database

INCEpTION uses an SQL database to store project and user data.

INCEpTION uses by default an embedded HSQLDB database. However, we recommend using the embedded database only for testing purposes. For production use, we recommend using a MySQL server. The reason for this is, that:

  • some users have reported that HSQLDB databases may become corrupt when the computer crashes (note that this could probably also happen with MySQL, but we did so far not have any reports about this);

  • most INCEpTION developers use MySQL when running INCEpTION on their servers;

  • in the past, we had cases where we described in-place upgrade procedures that required performing SQL commands to change the data model as part of the upgrade. We promise to try avoiding this in the future. However, in case we offer advice on fixing anything directly in the database, this advice will refer to a MySQL database.

We try to keep the data model simple, so there should be no significant requirements to the database being used. Theoretically, it should be possible to use any JDBC-compatible database after adding a corresponding driver to the classpath and configuring INCEpTION to use the driver in the settings.properties file.

MySQL

For production use of INCEpTION, it is highly recommended to use a MySQL database. In this section, we briefly describe how to install a MySQL server and how to prepare it for use with the application.

Prepare database

  • Install MySQL

    $ apt-get install mysql-server
  • make sure your MySQL server is configured for UTF-8. Check the following line is present in /etc/mysql/mariadb.conf.d/50-server.cnf (this is specific to Debian 9; on other systems the relevant file may be /etc/mysql/my.cnf):

    character-set-server = utf8
    collation-server     = utf8_bin
  • also ensure the default settings for client connections to are UTF-8 in /etc/mysql/mariadb.conf.d/50-server.cnf (again Debian 9; likely in /etc/mysql/my.cnf on other systems)

    default-character-set = utf8
  • login to MySQL

    $ mysql -u root -p
  • create a database

    mysql> CREATE DATABASE inception DEFAULT CHARACTER SET utf8 COLLATE utf8_bin ;
  • create a database user called inception with the password t0t4llYSecreT which is later used by the application to access the database (instructions for settings.properties file below).

    mysql> CREATE USER 'inception'@'localhost' IDENTIFIED BY 't0t4llYSecreT';
    mysql> GRANT ALL PRIVILEGES ON inception.* TO 'inception'@'localhost';
    mysql> FLUSH PRIVILEGES;
For production use, make sure you choose a different, secret, and secure password.

Configuration options

This section explains some settings that can be added to the database.url in the settings.properties file when using MySQL. Settings are separated from the host name and database name with a ? character and multiple settings are separated using the & character, e.g.:

database.url=jdbc:mysql://localhost:3306/inception?useSSL=false&serverTimezone=UTC

To suppress the warning about non-SSL database connections with recent MySQL databases, append the following setting to the database.url:

useSSL=false

Recent MySQL drivers may refuse to work unless a database server timezone has been specified. The easiest way to do this is to add the following setting to the database.url:

serverTimezone=UTC

If you plan to use UTF-8 encoding for project name and tagset/tag name, make sure either of the following settings for MySQL database

  • in the settings.properties file, make sure that database.url includes

    useUnicode=true&characterEncoding=UTF-8
  • change the my.conf MySQL databse configuration file to include the following line

    character-set-server = utf8

HSQLDB (embedded)

INCEpTION displays a warning in the user interface when an embedded database is being used. It is not recommended to used an embedded database for various reasons:

  • HSQLDB databases are known to run a risk of becoming corrupt in case of power failures which may render the application inaccessible and your data difficult to recover.

  • In very rare cases it may be necessary to fix the database content which is more inconvenient for embedded databases.

In case that you really want to run INCEpTION with an embedded database in production, you probably want to disable this warning. To do so, please add the following entry to the settings.properties file:

warnings.embeddedDatabase=false

Running via embedded Tomcat (JAR)

The INCEpTION standalone JAR with an embedded Tomcat server and can be easily set up as a UNIX service. This is the recommended way of running INCEpTION on a server.

Installing as a service

To set it up as a service, you can do the following steps. For the following example, I assume that you install INCEpTION in /srv/inception:

  • Copy the standalone JAR file inception-app-standalone-0.7.2.jar to /srv/inception/inception.jar. Note the change of the filename to inception.jar.

  • Create the file /srv/inception/inception.conf with the following content

    JAVA_OPTS="-Djava.awt.headless=true -Dinception.home=/srv/inception"
  • In the previous step, you have already created the /srv/inception/settings.properties file. You may optionally configure the Tomcat port using the following line

    server.port=18080

    If you need to do additional configurations of the embedded Tomcat, best refer to the documentation of Spring Boot itself.

  • Make sure that the file /srv/inception/inception.conf is owned by the root user. If this is not the case, INCEpTION will ignore it and any settings made there will not have any effect. If you start INCEpTION and intead of using the MySQL database, it is using an embedded database, then you should double-check that /srv/inception/inception.conf is owned by the root user.

    $ chown root:root /srv/inception/inception.conf
  • Change the owner/group of /srv/inception/inception.jar to www-data. When the service is started, it will run with the privileges of the user that owns the JAR file, i.e. in this case INCEpTION will run as under the www-data user. Do NOT run INCEpTION as root.

    $ chown www-data:www-data /srv/inception/inception.jar
  • Create a symlink from /etc/init.d to the /srv/inception/inception.jar:

    $ ln -s /srv/inception/inception.jar /etc/init.d/inception
  • Enable the INCEpTION service using

    $ systemctl enable inception
  • Start INCEpTION using

    $ service inception start
  • Stop INCEpTION using

    $ service inception stop

Running the standalone behind HTTPD

These are optional instructions if you want to run INCEpTION behind an Apache web-server instead of accessing it directly. This assumes that you already have the following packages installed:

  • Apache Web Server

  • mod_proxy

  • mod_proxy_ajp

  • Add the following lines to /srv/inception/settings.properties:

    tomcat.ajp.port=18009
    server.contextPath=/inception
    server.use-forward-headers=true
  • Edit /etc/apache2/conf.d/inception.local.conf

    ProxyPreserveHost On
    
    <Proxy ajp://localhost/inception >
      Order Deny,Allow
      Deny from none
      Allow from all
    </Proxy>
    
    <Location /inception >
      ProxyPass ajp://localhost:18009/inception timeout=1200
      ProxyPassReverse http://localhost/inception
    </Location>
  • Restart Apache web server

    $ service apache2 restart

Upgrading

In general, it is possible to perform an in-place upgrade of the application. However, before doing an upgrade, it is recommender to create a backup of the application and data to allow coming back to a working system if case of a problem during the upgrade. Mind that the upgrade is only completed once the new version has successfully started because during startup, the application may make changes to the database schema or to the data on disk.

Backup your data

  • Make a copy of your INCEpTION home folder

  • If you are using MySQL, make a backup of your INCEpTION database, e.g. using the mysqldump command.

Upgrading with embedded Tomcat

  • Stop the INCEpTION service

  • Replace the inception.jar file with the new version

  • Ensure that the file has the right owner/group (usually www-data)

  • Start the INCEpTION service again

Remote API

In order to programmatically manage annotation project, a REST-like remote API is offered. This API is disabled by default. In order to enable it, add the setting remote-api.enabled=true to the settings.properties file.

Once the remote API is enabled, it becomes possible to assign the role ROLE_REMOTE to a user. Create a new user, e.g. remote-api via the user management page and assign at least the roles ROLE_USER and ROLE_REMOTE. Most of the actions accessible through the remote API require administrator access, so adding the ROLE_ADMIN is usually necessary as well.

Once the remote API has been enabled, it offers a convenient and self-explanatory web-based user interface under <APPLICATION_URL>/swagger-ui.html which can be accessed by any user with the role ROLE_REMOTE. Here, you can browse the different operations, their parameters, and even try them out directly via a web browser. The actual AERO remote API uses <APPLICATION_URL/api/aero/v1 as the base URL for its operations.

Table 4. Remote API settings
Setting Description Default Example

remote-api.enabled

Enable remote API

false

true

Webhooks

Webhooks allow INCEpTION to notify external services about certain events. For example, an external service can be triggered when an annotator marks a document as finished or when all documents in a project have been completely curated.

Webhooks are declared in the settings.properties file. For every webhook, it is necessary to specify an URL (url) and a set of topics (topics) about with the remote service listening at the given URL is notified. If the remote service is accessible via https and the certificate is not known to the JVM running INCEpTION, the certificate verification can be disabled (verify-certificates).

The following topics are supported:

  • DOCUMENT_STATE - events related to the change of a document state such as when any user starts annotating or curating the document.

  • ANNOTATION_STATE - events related to the change of an annotation state such as when a user starts or completes the annotation of a document.

  • PROJECT_STATE - events related to the change of an entire project such as when all documents have been curated.

Example webhook configuration
webhooks.globalHooks[0].url=http://localhost:3333/
webhooks.globalHooks[0].topics[0]=DOCUMENT_STATE
webhooks.globalHooks[0].topics[1]=ANNOTATION_STATE
webhooks.globalHooks[0].topics[2]=PROJECT_STATE
webhooks.globalHooks[0].verify-certificates=false

Settings

Application settings are managed via a file called settings.properties which must reside in the application home folder. The file is optional. If it does not exist, default values are assumed.

General Settings

Table 5. General settings
Setting Description Default Example

warnings.unsupportedBrowser

Warn about unsupported browser

true

false

debug.showExceptionPage

Show a page with a stack trace instead of an "Internal error" page. Do not use in production!

false

true

login.message

Custom message to appear on the login page, such as project web-site, annotation guideline link, …​ The message can be an HTML content.

unset

<span style="color:red; font-size: 200%;">Use are your own risk.</span>

user.profile.accessible

Whether regular users can access their own profile to change their password and other profile information. This setting has no effect when running in pre-authentication mode.

false

true

Database connection

Table 6. Database settings in the settings.properties file
Setting Description Default Example

database.dialect

Database dialect

org.hibernate.dialect.HSQLDialect

org.hibernate.dialect.MySQL5InnoDBDialect

database.driver

Database driver

org.hsqldb.jdbc.JDBCDriver

com.mysql.jdbc.Driver

database.url

JDBC connection string

location in application home

jdbc:mysql://localhost:3306/weblab?useUnicode=true&characterEncoding=UTF-8&serverTimezone=UTC

database.username

Database username

sa

user

database.password

Database password

unset

pass

database.initial-pool-size

Initial database connection pool size

4

database.min-pool-size

Minimum database connection pool size

4

database.max-pool-size

Maximum database connection pool size

10

warnings.embeddedDatabase

Warn about using an embedded database

true

false

The basic database connection details can also be configured via environment variables. When these environment variables are present, they are preferred over the settings.properties file. The following environment variables can be used:

Table 7. Database configuration via environment variables
Setting Description Default Example

INCEPTION_DB_DIALECT

Database dialect

org.hibernate.dialect.HSQLDialect

org.hibernate.dialect.MySQL5InnoDBDialect

INCEPTION_DB_DRIVER

Database driver

org.hsqldb.jdbc.JDBCDriver

com.mysql.jdbc.Driver

INCEPTION_DB_URL

JDBC connection string

location in application home

jdbc:mysql://localhost:3306/inception?useUnicode=true&characterEncoding=UTF-8

INCEPTION_DB_USERNAME

Database username

sa

user

INCEPTION_DB_PASSWORD

Database password

unset

pass

Internal backup

INCEpTION stores its annotations internally in files. Whenever a user performs an action on a document, the file is updated. It is possible to configure INCEpTION to keep internal backups of these files, e.g. to safeguard against crashes or bugs.

The internal backups are controlled through three properties:

Table 8. Database settings in the settings.properties file
Setting Description Default Example

backup.interval

Time between backups (seconds)

0 (disabled)

300 (60 * 5 = 5 minutes)

backup.keep.number

Maximum number of backups to keep

0 (unlimited)

5

backup.keep.time

Maximum age of backups to keep (seconds)

0 (unlimited)

2592000 (60 * 60 * 24 * 30 = 30 days)

By default, backups are disabled (backup.interval is set to 0). Changing this properties to any positive number enables internal backups. The interval controls the minimum time between changes to a document that needs to have elapsed in order for a new backup to be created.

When backups are enabled, either or both of the properties backup.keep.number and backup.keep.time should be changed as well, because their default values will cause the backups to be stored indefinitely and they will eventually fill up the disk.

The properties backup.keep.number and backup.keep.time control how long backups are keep and the maximal number of backups to keep. These settings are effective simultaneously.

Example: Make backups every 5 minutes and keep 10 backups irrespective of age
backup.interval    = 300
backup.keep.number = 10
backup.keep.time   = 0
Example: Make backups every 5 minutes and all not older than 7 days (60 * 60 * 24 * 7 seconds)
backup.interval    = 300
backup.keep.number = 0
backup.keep.time   = 604800
Example: Make backups every 5 minutes and keep at most 10 backups that are not older than 7 days
backup.interval    = 300
backup.keep.number = 10
backup.keep.time   = 604800

Custom header icons

INCEpTION allows adding custom icons to the page header. You can declare such custom icons in the settings.properties file as shown in the example below. Each declaration begins with the prefix style.header.icon. followed by an identifier (here myOrganization and mySupport). The suffixes .linkUrl and .imageUrl indicate the URL of the target page and of the icon image respectively. Images are automatically resized via CSS. However, to keep loading times low, you should point to a reasonably small image.

The order of the icons is controlled by the ID, not by the order in the configuration file!

Example: Custom header icon
style.header.icon.myOrganization.linkUrl=http://my.org
style.header.icon.myOrganization.imageUrl=http://my.org/logo.png
style.header.icon.mySupport.linkUrl=http://my.org/support
style.header.icon.mySupport.imageUrl=http://my.org/help.png
Setting Description Default Example

style.logo

Logo image displayed in the upper-right corner

unset

path to an image file

style.header.icon…​

Icons/links to display in the page header. For details, see below.

unset

Annotation editor

Setting Description Default Example

ui.brat.autoScroll

Whether to scroll the annotation being edited into the center of the page

true

ui.brat.pageSize

The number of sentences to display per page

5

ui.brat.singleClickSelection

Whether to select annotations with a single click

false

ui.brat.rememberLayer

Whether "remember layer" is activated by default

false

annotation.feature-support.string.autoCompleteThreshold

If the tagset is larger than the threshold, an auto-complete field is used instead of a standard combobox.

75

100

annotation.feature-support.string.autoCompleteMaxResults

When an auto-complete field is used, this determines the maximum number of items shown in the dropdown menu.

100

1000

External pre-authentication

INCEpTION can be used in conjunction with header-based external per-authentication. In this mode, the application looks for a special HTTP header (by default remote_user) and if that header exists, it is taken for granted that this user has been authenticated. The application will check its internal database if a user by the given name exists, otherwise it will create the user.

Pre-authentication can be enabled by setting the property auth.mode to preauth. When enabling pre-authentication mode, the default roles for new users can be controlled using the auth.preauth.newuser.roles property. The ROLE_USER is always added, even if not specified explicitly. Adding also the role ROLE_PROEJCT_CREATOR allows all auto-created users also to create their own projects.

Since the default administrator user is not created in pre-authentication, it is useful to also declare at least one user as an administrator. This is done through the property auth.user.<username>.roles where <username> must be replaced with the name of the user. The example below shows how the user Franz is given administrator permissions.

Example: Authenticate using the remote_user header, new users can create projects, user Franz is always admin.
auth.mode                     = preauth
auth.preauth.header.principal = remote_user
auth.preauth.newuser.roles    = ROLE_PROJECT_CREATOR
auth.user.Franz.roles         = ROLE_ADMIN
The roles specified through auth.preauth.newuser.roles are saved in the database when a user logs in for the first time and can be changed after creation through the user interface.
The roles added through auth.user.<username>.roles properties are not saved in the database and cannot be edited through the user interface.
Setting Description Default Example

auth.mode

Authentication mode

database

preauth

auth.preauth.header.principal

Principal header

remote_user

some other header

auth.preauth.newuser.roles

Default roles for new users (comma separated)

<none>

ROLE_PROJECT_CREATOR

auth.user.<username>.roles

Extra roles for user (comma separated)

<none>

ROLE_ADMIN

Concept Linking

There are several configurable parameters related to the Concept Linking functionality:

Cache size

This parameter controls the size of the Candidate Cache, which stores a set of candidates for a mention. Increasing the cache size will reduce the number of queries that have to be made against the KB and therefore increase average retrieval time.

Candidate Frequency Threshold

This parameter controls after how many concepts the ranking approach should take into account by selecting the n most frequent concepts. Increasing this parameter will lead to a longer ranking time, since more candidates are considered for ranking.

Mention Context Size

This parameter declares the size k of the context, where the context is defined as the words included in a window with k words to both left and right.

Candidate Retrieval Limit

This parameter defines how many concepts should be retrieved for the Candidate Retrieval step. Increasing this parameter will lead to a longer time to retrieve candidates from the KB.

Semantic Signature Query Limit

This parameter defines how many concepts should be retrieved for the Semantic Signature of a candidate. Increasing this parameter will lead to a longer time to retrieve concepts for constructing the Semantic Signature.

Candidate Display Limit

This parameter regulates how many candidates will be displayed for a mention in the Concept Selector UI.

If no value for a parameter is specified, its default value is used. The default values are shown as examples of how the parameters can be configured below:

Table 9. Concept linking settings overview
Setting Description Default Example

inception.entity-linking.cacheSize

Cache size

1024

-

inception.entity-linking.candidateQueryLimit

Candidate Retrieval Limit

2500

-

inception.entity-linking.mentionContextSize

Mention Context Size

5

-

inception.entity-linking.candidateDisplayLimit

Candidate Display Limit

20

-

inception.entity-linking.candidateFrequencyThreshold

Candidate Frequency Threshold

25

-

inception.entity-linking.signatureQueryLimit

Semantic Signature Query Limit

2147483647

-

Resources

In order to improve the quality of suggestions, several additional resources can be incorporated. These are to be put into the .inception/resources folder. These include:

  • properties_with_labels.txt

    • List of properties, each line containing information for one property, tab-separated

ID

Label

Description

Aliases

Data type

Count

P6

head of government

head of the executive power of this town, city, municipality, state, country, or other governmental body

government headed by, executive power headed by, president, chancellor

wikibase-item

17,592

  • property_blacklist.txt

    • A list of properties that are filtered when computing the Semantic Signature, one property ID per line, e.g. P1005, P1014

  • stopwords-en.txt

    • A list of stopwords, one stopword per line, e.g. i, me

  • wikidata_entity_freqs.map

    • Each line consists of a the ID of a concept and its frequency in the KB, tab-separated, e.g. Q4664130 409104, Q30 205747

Knowledge Base Settings

This section describes the global settings related to the knowledge base module.

Default max results

This parameter determines the default value for the maximum number of results that can be retrieved from a SPARQL query. The queries are used to retrieve concepts, statements, properties, etc. from the knowledge base. The maximum number of results can also be configured separately for each knowledge base in the project settings.

Hard max results

A hard limit for the Max results parameter.

If no value for the parameter is specified, its default value is used. The default value is shown as an example of how the parameter can be configured below:

Table 10. Knowledge base settings overview
Setting Description Default Example

inception.knowledge-base.defaultMaxResults

default result limit for SPARQL query

1000

10000

inception.knowledge-base.hardMaxResults

hard limit for the maximum number of results from a query

10000

5000

Recommender Settings

This section describes the global settings related to the recommender module.

Table 11. Recommender settings overview
Setting Description Default Example

show.learning.curve.diagram

Show learning curve diagram on the recommendation sidebar.

false

true

Scheduler Settings

This section describes the global settings related to the scheduler.

Number of threads

This parameter determines the number of threads the scheduler uses. It should be less than hardware threads available on the machine that runs INCEpTION. The higher the number, the more tasks can be run in parallel.

Queue size

This parameter determines the maximum number of tasks that can be waiting in the scheduler queue. If the queue is full, then no new tasks can be scheduled until running tasks are completed.

If no value for the parameter is specified, its default value is used. The default value is shown as an example of how the parameter can be configured below:

Table 12. Scheduler settings overview
Setting Description Default Example

inception.scheduler.numberOfThreads

Number of threads that run tasks

4

8

inception.scheduler.queueSize

Maximum number of tasks waiting for execution

100

200