client

client is an SPA providing the web interface to site-business.

The client interface is intended for use at sites that intend to configure the AP-Portal to directly query their compound databases.

Dependencies

• Maven (build)
• Java 7 8 [1] or higher (build, deploy)
• Java Servlet Container, e.g. Apache Tomcat (deploy)
• Database (build, deploy)
• A Maven-installed client-parent and client-shared. See client-parent and client-shared

General topics

• Database
• Internationalisation
• User Authentication and Authorisation.
• User Registration.

Initial installation

Download the project source and go to this component’s root directory (i.e. here) and follow the steps below.

• Either …

1. Run tools/one_time_copying.sh

• … or …

1. [ T ] Copy sample.pom.xml to pom.xml
2. [ V ] Copy src/main/resources/bundle/sample.site.properties to src/main/resources/bundle/site.properties
3. [ S ] Copy src/main/resources/META-INF/spring/ctx/config/sample.appCtx.config.site.xml to src/main/resources/META-INF/spring/ctx/config/appCtx.config.site.xml
4. [ T ] Copy src/main/resources/META-INF/spring/ctx/ws/sample.appCtx.ws.security-outgoing.xml to src/main/resources/META-INF/spring/ctx/ws/appCtx.ws.security-outgoing.xml
5. [ T ] Copy src/properties/database/sample.database.filter.properties to src/properties/database/database.filter.properties
6. [ T ] Copy src/properties/database/sample.database.spring.properties to src/properties/database/dev.database.embedded.properties
7. See Database choice
8. [ T ] Copy src/properties/sample.filter.properties to src/properties/filter.properties
9. [ T ] Copy src/properties/sample.spring.properties to src/properties/spring.properties

If you intend to have a client-specific “prepopulated user authentication” user authentication mechanism database then also do the following :

1. [ T ] Copy src/main/resources/META-INF/data/spring-security/local/sample.users.sql to src/main/resources/META-INF/data/spring-security/local/users.sql

• … finally

1. Edit each of the copied files according to your desired configuration.

Configuration

pom.xml

It may necessary in some circumstances, e.g. if there is site-specific access control code being overlayed into the client src/main/java directory, or if using a MySQL driver, to adapt the pom.xml file for Maven-building the component.

src/main/resources/bundle/site.properties

site.compound_identifier=

Adjust the prompt message for compound identifiers (if necessary).

If the site is to be internationalised create all the corresponding language properties files, e.g. src/main/resources/site_(es,zh).properties.

src/main/resources/META-INF/data/spring-security/local/users.sql

Adjust this according to your expected usage requirements :

• If you are using a local client-specific “prepopulated user authentication” mechanism for authentication and authorisation, this file is required.
  Please also check the following Note.
• If you are using a “bespoke user authentication” mechanism, or if “prepopulated user authentication” users are shared between client and client-direct installations (and hence defined in client-shared), then this file is not required.

Note

If there is a new registration request the requesting user’s details are not automatically written to the user database.
New users must be manually added to this users.sql file and the system restarted – for this reason it is better to create a number of unissued usernames and passwords (commensurate with the total anticipated usage) and then distribute them to new registrations as they arrive.

src/main/resources/META-INF/spring/ctx/config/appCtx.config.site.xml

c50Units

Preferred units for displaying inhibitory concentration, e.g. IC50 [nM], IC50 [µM], pIC50.
Cut-and-paste your preferred unit to be the top/first <entry /> value.

configuration -> inputValueDisplay

Choose how to derive the mean of pIC50 ApPredict invocation input values.

Set the value of the ref="" attribute to one of the following :

1. INPUT_VALUE_DISPLAY_ANY_MODIFIER
   Display the mean of all pIC50 values, irrespective of modifier (i.e. include ‘=’, ‘<’, ‘>’).
2. INPUT_VALUE_DISPLAY_EQUALITY_MODIFIER
   Display the mean of pIC50 values only where there was an equality modifier (i.e. use only ‘=’).

Use of INPUT_VALUE_DISPLAY_ANY_MODIFIER.

src/main/resources/META-INF/spring/ctx/ws/appCtx.ws.security-outgoing.xml

Generally no change necessary.

src/properties/database/database.filter.properties

client_direct.database.queryTimeout=

Data query timeout (in milliseconds). Shouldn’t need to be higher than 200?

src/properties/database/dev.database.<deploy.db_vendor>.properties

See also

Database choice

src/properties/filter.properties

log.file.client=

Component log file location on disk, e.g. ‘logs/client.log’

log.level.client=

Component log level, e.g. (trace|debug|info|warn|error|fatal).

log.level.general=

Log level of code from other libraries, e.g. (trace|debug|info|warn|error|fatal).

business_services.ws.url=

WS URL of site-business component, e.g. ‘http://localhost:18080/site_business-0.0.2/bws/’

src/properties/spring.properties

recaptcha.private.key=

reCAPTCHA private key.

recaptcha.public.key=

reCAPTCHA public key. If this field is left empty it will be assumed that no reCAPTCHA is available!

securement.business.username=

site-business WSS username.

securement.business.password=

site-business WSS password.

Build

See also

Database choice and Spring profiles for additional information.

-Dspring.profiles.active=

Options are currently client-shared_(embedded|mysql|oracle10g),client-shared_(bespoke|prepopulated).

Warning

At build time it is important to include the client-shared_embedded spring profile during building because during integration testing rubbish may be written to the database so it is important to use the embedded database during the build process.

-Ddeploy.db_vendor=

The name of the database vendor, e.g. mysql, postgres, used in the intended deployment (not build) environment. The actual name used corresponds exactly to the <deploy.db_vendor> element of the file derived from sample.database.spring.properties during the installation process.

-Ddeploy.env=

The environment name, i.e. dev.

Example build instructions (illustrating use of embedded during the build process, and mysql in the deploy environment):

cd <ap_predict_online>/client
mvn clean verify -Dspring.profiles.active=client-shared_embedded,client-shared_prepopulated -Ddeploy.db_vendor=mysql -Ddeploy.env=dev

Deploy

If the Build command has completed successfully the webapp .war file should be in the target directory. Copy this to the servlet container’s relevant file, e.g. for Tomcat, the webapps directory.

Run

See start.

Start-up problems

See also

Log file troubleshooting.

Footnotes

[1]	Since early 2019.