UNM_BIOCOMP

Libraries and web apps developed at the UNM Translational Informatics Division (formerly Biocomputing Division). The name UNM_BIOCOMP reflects this provenance.

• Maven multi-module project.
• Modules
  • (JARs): unm_biocomp_convert, unm_biocomp_fp, unm_biocomp_freechart, unm_biocomp_jchemdb, unm_biocomp_mcs, unm_biocomp_molcloud, unm_biocomp_qed, unm_biocomp_react, unm_biocomp_ro5, unm_biocomp_sim2d, unm_biocomp_tautomer
  • (WAR) biocomp_war deploys several web apps, including: Convert, Depict, MolCloud, Ro5, Sim2D and SmartsFilter.

Dependencies

• Java 8
• Maven 3.5+
• ChemAxon 19.3.0+
• Access to ChemAxon Maven repository (see documentation)
  • Requires API key.
• Access to Oracle Maven repository
  • Requires credentials, obtained via maven.oracle.com registration and license agreement acceptance.
• Access to EBI Maven repository
• Separate https://github.com/unmtransinfo/ repos:
  • unm_biocomp_util, unm_biocomp_text, unm_biocomp_smarts, unm_biocomp_depict, unm_biocomp_hscaf, unm_biocomp_sasa, unm_biocomp_grouping, unm_biocomp_cdk, unm_biocomp_biobyte, unm_biocomp_vcclab, unm_biocomp_descriptors
• Many others, including CDK, Derby, MySql, PostgreSql, Oracle, VCCLAB, Freechart, many Apache and other open source libraries.

Issues with repositories

• See configuration example settings.xml.
• Java/SSL-cert issues may result in error: unable to find valid certification path to requested target requiring solutions such as:

openssl s_client -showcerts -connect www.ebi.ac.uk:443

(Edit output, save root.crt and intermediate.crt.)

MacOSX:

sudo keytool -importcert -keystore /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/security/cacerts -storepass changeit -file root.crt -alias "ebi-root"
sudo keytool -importcert -keystore /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/security/cacerts -storepass changeit -file intermediate.crt -alias "ebi-intermediate"

Ubuntu:

sudo keytool -importcert -cacerts -storepass changeit -file root.crt -alias "ebi-root"
sudo keytool -importcert -cacerts -storepass changeit -file intermediate.crt -alias "ebi-intermediate"

Compilation

• See README_REPOS.md for cloning and compiling dependency repos.

mvn clean install

Deploying BIOCOMP_WAR

Ok for Tomcat v8/v9 also, apparently.

Copy ChemAxon license to /biocomp_war/src/main/webapp/.chemaxon/license.cxl for inclusion in the WAR.

mvn --projects biocomp_war tomcat7:deploy

or

mvn --projects biocomp_war tomcat7:redeploy

Testing with Jetty

http://localhost:8080/convert, etc.

mvn --projects biocomp_war jetty:run

Usage

See example commmands in README_APPS.md

Docker

• Dockerfile
• Go_DockerBuild.sh
• Go_DockerRun.sh
• From Docker engine host, applications accessible via http://localhost:9095/biocomp/.
• ChemAxon license must be copied into running container.