How to diagnose and correct problems when SLAP malfunctions. That is, the web app http://cheminfov.informatics.indiana.edu:8080/slap.
- SLAP the web app depends on Tomcat, Apache-HTTPD, and Postgresql.
Are these services running? Restarting services may correct problem. - Note that SLAP does not depend on Virtuoso [right?].
- The web app depends on the SLAP REST API, as documented at http://slapfordrugtargetprediction.wikispaces.com/API. Test the REST API. Example URLs:
- If the SLAP REST API does work, perhaps the Tomcat web app itself is the problem. Restart Tomcat. If needed, the files are in /usr/share/tomcat5/webapps/slap/.
- If the SLAP REST API does not work, try some other REST requests. These use Apache-HTTPD (port 80). If these fail the problem could be Apache-HTTPD.
- http://cheminfov.informatics.indiana.edu/rest/Chem2Bio2RDF/Bayes\_Model/5880:NR1I2
- http://cheminfov.informatics.indiana.edu/rest/Chem2Bio2RDF/Sea\_Model/5591:PPARG
- Note that REST API testing can be done via various clients (wget, curl, browsers). It seems that error messages are sometimes client dependent, and browsers show mod_python errors which wget does not.
- The REST API depends on Python programs which can be run locally (http://slapfordrugtargetprediction.wikispaces.com/SLAP+interfaces). Files are in /var/www/html/rest/Chem2Bio2RDF/slap/.
- Please do not make any irreversible changes! Document any changes.
| Package | Description |
|---|---|
| Apache HTTPD | webserver |
| Apache Tomcat | Java servlet container |
| JME | Java Molecular Editor (applet) |
| JQuery | JavaScript library |
| CytoscapeWeb | Flash plugin for network visualization |
| CDK | Cheminfo Java kit used by webapp (maybe) |
| BioJava | Java kit used by webapp (maybe) |
| Blast | Used by webapp (maybe) |
| R | Used by webservice (previous to May 2014) |
| Virtuoso | (Not used by SLAP at runtime, I think. However, dir exists at /var/www/html/rest/Chem2Bio2RDF/slap/virtuoso. |
| C++ | (or maybe other compiled language) See compiled binary executables in /var/www/html/rest/Chem2Bio2RDF/slap: findPath_m, pathfinder_m,(maybe not needed, see pathfinder\_m.py), PreProcess (maybe not needed) |
| Psycopg2 | Python API for Postgres |
Jeremy Yang May 22, 2014