+------------+---+-----------------+------------+-------------------------+
| **         |   |                 |            |                         |
| Deployment |   |                 |            |                         |
| specific   |   |                 |            |                         |
| in         |   |                 |            |                         |
| structions |   |                 |            |                         |
| to         |   |                 |            |                         |
| accompany  |   |                 |            |                         |
| every      |   |                 |            |                         |
| [dep       |   |                 |            |                         |
| loyment]{. |   |                 |            |                         |
| underline} |   |                 |            |                         |
| request.** |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **A        |   |                 |            |                         |
| pplication |   |                 |            |                         |
| and        |   |                 |            |                         |
| Submitter  |   |                 |            |                         |
| Inf        |   |                 |            |                         |
| ormation** |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Author     |   | Jim Sun         | Date       | October 21, 2008        |
| Name &     |   |                 |            |                         |
| Phone \#   |   | 301-594-4744    |            |                         |
+------------+---+-----------------+------------+-------------------------+
| A          |   | caBIO API       | Version    | 4.2                     |
| pplication |   |                 | Number     |                         |
| / Product  |   |                 |            |                         |
| Name       |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Government |   | Juli Klemm      | QA Sponsor | Ye Wu                   |
| Sponsor    |   |                 | Name &     |                         |
| Name &     |   | 978-443-2431    | Phone \#   |                         |
| Phone \#   |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **General  |   |                 |            |                         |
| Inf        |   |                 |            |                         |
| ormation** |   |                 |            |                         |
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| beyond     |   |                 |            |                         |
| this point |   |                 |            |                         |
| is         |   |                 |            |                         |
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| Required", |   |                 |            |                         |
| leave the  |   |                 |            |                         |
| field      |   |                 |            |                         |
| blank if   |   |                 |            |                         |
| it does    |   |                 |            |                         |
| not apply  |   |                 |            |                         |
| to the     |   |                 |            |                         |
| product)*  |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
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+------------+---+-----------------+------------+-------------------------+
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+------------+---+-----------------+------------+-------------------------+
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+------------+---+-----------------+------------+-------------------------+
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+------------+---+-----------------+------------+-------------------------+
| **         |   |                 |            |                         |
| Deployment |   |                 |            |                         |
| Units**    |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Archive    |   | output/web      |            |                         |
| files      |   | app/cabio42.war |            |                         |
+------------+---+-----------------+------------+-------------------------+
| JBoss      |   | *Log4j.xml,     |            |                         |
| Property   |   | oracle-ds.xml,  |            |                         |
| File       |   | lo              |            |                         |
| Updates    |   | gin-config.xml, |            |                         |
|            |   | propert         |            |                         |
|            |   | ies-service.xml |            |                         |
|            |   | etc are shared  |            |                         |
|            |   | by all          |            |                         |
|            |   | applications    |            |                         |
|            |   | deployed in the |            |                         |
|            |   | container.      |            |                         |
|            |   | Include the     |            |                         |
|            |   | file name and   |            |                         |
|            |   | specific        |            |                         |
|            |   | updates here.*  |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Other      |   |                 |            |                         |
| Con        |   |                 |            |                         |
| figuration |   |                 |            |                         |
| Files      |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **Con      |   |                 |            |                         |
| figuration |   |                 |            |                         |
| Di         |   |                 |            |                         |
| rectives** |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Container  |   | Classpath, min  |            |                         |
| Con        |   | and max heap    |            |                         |
| figuration |   | size, headless, |            |                         |
|            |   | etc.            |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Logging    |   | Provide the     |            |                         |
|            |   | Log4j.xml (or   |            |                         |
|            |   | appropriate)    |            |                         |
|            |   | configuration   |            |                         |
|            |   | file location.  |            |                         |
|            |   | This is         |            |                         |
|            |   | specific to the |            |                         |
|            |   | deployed        |            |                         |
|            |   | product and not |            |                         |
|            |   | shared or used  |            |                         |
|            |   | for an          |            |                         |
|            |   | application     |            |                         |
|            |   | container, e.g. |            |                         |
|            |   | Jboss, Tomcat,  |            |                         |
|            |   | Apache, etc.    |            |                         |
|            |   |                 |            |                         |
|            |   | If custom       |            |                         |
|            |   | logging is      |            |                         |
|            |   | performed,      |            |                         |
|            |   | include         |            |                         |
|            |   | instructions on |            |                         |
|            |   | where the log   |            |                         |
|            |   | file format and |            |                         |
|            |   | output file     |            |                         |
|            |   | locations are   |            |                         |
|            |   | configured as   |            |                         |
|            |   | well as         |            |                         |
|            |   | examples on how |            |                         |
|            |   | to specify the  |            |                         |
|            |   | configuration   |            |                         |
|            |   | values.         |            |                         |
+------------+---+-----------------+------------+-------------------------+
| External   |   | The             |            |                         |
| Datasource |   | cabi            |            |                         |
|            |   | o-oracle-ds.xml |            |                         |
|            |   | file must       |            |                         |
|            |   | contain         |            |                         |
|            |   | connection      |            |                         |
|            |   | information for |            |                         |
|            |   | caBIO database  |            |                         |
|            |   | with JNDI name  |            |                         |
|            |   | "cabio".        |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Auth       |   | N/A             |            |                         |
| entication |   |                 |            |                         |
| Module     |   |                 |            |                         |
| (e.g.      |   |                 |            |                         |
| JAAS)      |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Java       |   | N/A             |            |                         |
| Message    |   |                 |            |                         |
| Service    |   |                 |            |                         |
| (JMS)      |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Propertie  |   | The             |            |                         |
| s-services |   | propert         |            |                         |
|            |   | ies-service.xml |            |                         |
|            |   | file must       |            |                         |
|            |   | contain the     |            |                         |
|            |   | following       |            |                         |
|            |   | inside the      |            |                         |
|            |   | S               |            |                         |
|            |   | ystemProperties |            |                         |
|            |   | \<mbean\>       |            |                         |
|            |   | configuration   |            |                         |
|            |   | element:        |            |                         |
|            |   |                 |            |                         |
|            |   | \<attribute     |            |                         |
|            |   | name=\          |            |                         |
|            |   | "Properties\"\> |            |                         |
|            |   | gov.nih         |            |                         |
|            |   | .nci.cacore.cac |            |                         |
|            |   | oreProperties=/ |            |                         |
|            |   | path/to/data/ca |            |                         |
|            |   | core.properties |            |                         |
|            |   |                 |            |                         |
|            |   | \</attribute\>  |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Setup &    |   | The             |            |                         |
| Configure  |   | ca              |            |                         |
| Ex         |   | core.properties |            |                         |
| ternalized |   | file (see       |            |                         |
| Properties |   | "Prope          |            |                         |
|            |   | rties-services" |            |                         |
|            |   | section above)  |            |                         |
|            |   | must contain    |            |                         |
|            |   | the following   |            |                         |
|            |   | line:           |            |                         |
|            |   |                 |            |                         |
|            |   | handler_pat     |            |                         |
|            |   | h=/absolute/pat |            |                         |
|            |   | h/to/data/svr_1 |            |                         |
|            |   |                 |            |                         |
|            |   | The config.dct  |            |                         |
|            |   | file must be    |            |                         |
|            |   | present in the  |            |                         |
|            |   | *handler_path*  |            |                         |
|            |   | (defined        |            |                         |
|            |   | above). The     |            |                         |
|            |   | Oracle          |            |                         |
|            |   | connection      |            |                         |
|            |   | information     |            |                         |
|            |   | inside the      |            |                         |
|            |   | config.dct file |            |                         |
|            |   | must be         |            |                         |
|            |   | configured      |            |                         |
|            |   | identically to  |            |                         |
|            |   | the             |            |                         |
|            |   | cabi            |            |                         |
|            |   | o-oracle-ds.xml |            |                         |
|            |   | file that is    |            |                         |
|            |   | used (see       |            |                         |
|            |   | "External       |            |                         |
|            |   | Datasource"     |            |                         |
|            |   | section above). |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **CSM      |   |                 |            |                         |
| Confi      |   |                 |            |                         |
| guration** |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| CSM        |   | N/A             |            |                         |
| Con        |   |                 |            |                         |
| figuration |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| UPT        |   | N/A             |            |                         |
| Con        |   |                 |            |                         |
| figuration |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **         |   |                 |            |                         |
| Standalone |   |                 |            |                         |
| modules or |   |                 |            |                         |
| scripts**  |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Automated  |   | N/A             |            |                         |
| Scripts    |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Manual     |   | N/A             |            |                         |
| Scripts    |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **De       |   |                 |            |                         |
| pendencies |   |                 |            |                         |
| and        |   |                 |            |                         |
| Children** |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Database   |   | Is there a      |            |                         |
| Dependency |   | database        |            |                         |
|            |   | component for   |            |                         |
|            |   | this            |            |                         |
|            |   | deployment?\    |            |                         |
|            |   | [X]{.underline} |            |                         |
|            |   | Yes\            |            |                         |
|            |   | No              |            |                         |
|            |   |                 |            |                         |
|            |   | If Yes, provide |            |                         |
|            |   | instructions in |            |                         |
|            |   | the sections    |            |                         |
|            |   | below.          |            |                         |
+------------+---+-----------------+------------+-------------------------+
| APIs and   |   | CBIIT Services  |            |                         |
| Services   |   | required for    |            |                         |
|            |   | this            |            |                         |
|            |   | application:    |            |                         |
|            |   | (select all     |            |                         |
|            |   | that apply).\   |            |                         |
|            |   | CSM (specify    |            |                         |
|            |   | version)\       |            |                         |
|            |   | RMI (explain)\  |            |                         |
|            |   | caCORE API      |            |                         |
|            |   | (specify        |            |                         |
|            |   | version)\       |            |                         |
|            |   | EVS Services    |            |                         |
|            |   | (explain)\      |            |                         |
|            |   | Analysis        |            |                         |
|            |   | Services        |            |                         |
|            |   | (explain)\      |            |                         |
|            |   | caGRID          |            |                         |
|            |   | Framework       |            |                         |
|            |   | (explain)\      |            |                         |
|            |   | Other (please   |            |                         |
|            |   | specify)        |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Child      |   | Identify other  |            |                         |
| services   |   | applications or |            |                         |
|            |   | services        |            |                         |
|            |   | dependant on    |            |                         |
|            |   | this            |            |                         |
|            |   | deployment.     |            |                         |
|            |   | This exposes    |            |                         |
|            |   | the deployment  |            |                         |
|            |   | environment and |            |                         |
|            |   | potential       |            |                         |
|            |   | impact of       |            |                         |
|            |   | restarts.       |            |                         |
|            |   | Identify static |            |                         |
|            |   | connection      |            |                         |
|            |   | dependencies    |            |                         |
|            |   | which may       |            |                         |
|            |   | require child   |            |                         |
|            |   | services        |            |                         |
|            |   | restart, for    |            |                         |
|            |   | example, RMI    |            |                         |
|            |   | server and      |            |                         |
|            |   | webServices, or |            |                         |
|            |   | R servers and   |            |                         |
|            |   | Portal.         |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **System   |   |                 |            |                         |
| I          |   |                 |            |                         |
| nteraction |   |                 |            |                         |
| Details**  |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Cache      |   | Lucene caching  |            |                         |
|            |   | (EHCache) is    |            |                         |
|            |   | used by the     |            |                         |
|            |   | FreestyleLM     |            |                         |
|            |   | search. The     |            |                         |
|            |   | cache directory |            |                         |
|            |   | must exist at   |            |                         |
|            |   | the location    |            |                         |
|            |   | configured      |            |                         |
|            |   | during the      |            |                         |
|            |   | build with the  |            |                         |
|            |   | CACHE_PATH      |            |                         |
|            |   | property.       |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Hibernate  |   | *Details about  |            |                         |
| ( ORM )    |   | hibernate or    |            |                         |
|            |   | other ORM       |            |                         |
|            |   | product.        |            |                         |
|            |   | Externalize     |            |                         |
|            |   | this property   |            |                         |
|            |   | if you want to  |            |                         |
|            |   | control         |            |                         |
|            |   | hibernate       |            |                         |
|            |   | logging. **If   |            |                         |
|            |   | not             |            |                         |
|            |   | externalized,   |            |                         |
|            |   | disable         |            |                         |
|            |   | sql_query       |            |                         |
|            |   | logging for     |            |                         |
|            |   | stage/prod      |            |                         |
|            |   | builds.***      |            |                         |
+------------+---+-----------------+------------+-------------------------+
| File       |   | Setup and       |            |                         |
| System     |   | configuration   |            |                         |
|            |   | of the file     |            |                         |
|            |   | system. Include |            |                         |
|            |   | size, expected  |            |                         |
|            |   | growth, file    |            |                         |
|            |   | retention       |            |                         |
|            |   | plans, static   |            |                         |
|            |   | vs. dynamic     |            |                         |
|            |   | content,        |            |                         |
|            |   | performance     |            |                         |
|            |   | c               |            |                         |
|            |   | haracteristics, |            |                         |
|            |   | cleanup method, |            |                         |
|            |   | la              |            |                         |
|            |   | yout/structure, |            |                         |
|            |   | configured      |            |                         |
|            |   | directory       |            |                         |
|            |   | references,     |            |                         |
|            |   | coded directory |            |                         |
|            |   | references,     |            |                         |
|            |   | Apache          |            |                         |
|            |   | accessible,     |            |                         |
|            |   | etc.            |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Mail       |   | SMTP            |            |                         |
| Forwarding |   | configuration.  |            |                         |
|            |   | This must be    |            |                         |
|            |   | included for    |            |                         |
|            |   | any and all     |            |                         |
|            |   | application     |            |                         |
|            |   | e-mail uses.    |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **Grid     |   |                 |            |                         |
| Services** |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Grid       |   | Service         |            |                         |
| Details    |   | offered, grid   |            |                         |
|            |   | version, grid   |            |                         |
|            |   | dependencies.   |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **Detailed |   |                 |            |                         |
| Inst       |   |                 |            |                         |
| ructions** |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| EAR, WAR,  |   | Place           |            |                         |
| JAR, TAR   |   | cabio42.war     |            |                         |
| and ZIP    |   | file in JBoss   |            |                         |
| Deployment |   | deploy          |            |                         |
|            |   | directory and   |            |                         |
|            |   | restart JBoss.  |            |                         |
+------------+---+-----------------+------------+-------------------------+
| RMI        |   | N/A             |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Database   |   | Database        |            |                         |
| I          |   | population      |            |                         |
| nteraction |   | scripts are run |            |                         |
|            |   | by the caBIO    |            |                         |
|            |   | Data Architect. |            |                         |
|            |   | During          |            |                         |
|            |   | deployment of   |            |                         |
|            |   | the API, the    |            |                         |
|            |   | system only     |            |                         |
|            |   | needs to be     |            |                         |
|            |   | pointed to the  |            |                         |
|            |   | correct         |            |                         |
|            |   | database using  |            |                         |
|            |   | a JNDI          |            |                         |
|            |   | connection      |            |                         |
|            |   | specification,  |            |                         |
|            |   | with the name   |            |                         |
|            |   | "cabio".        |            |                         |
+------------+---+-----------------+------------+-------------------------+
| File Copy  |   | A base          |            |                         |
|            |   | directory for   |            |                         |
|            |   | the Freestyle   |            |                         |
|            |   | indexes needs   |            |                         |
|            |   | to be created   |            |                         |
|            |   | locally. The    |            |                         |
|            |   | location is     |            |                         |
|            |   | configured      |            |                         |
|            |   | during the      |            |                         |
|            |   | build, with the |            |                         |
|            |   | INDEX_BASE      |            |                         |
|            |   | parameter. This |            |                         |
|            |   | directory will  |            |                         |
|            |   | hold the        |            |                         |
|            |   | indexes         |            |                         |
|            |   | generated by    |            |                         |
|            |   | the caBIO       |            |                         |
|            |   | IndexGenerator. |            |                         |
|            |   |                 |            |                         |
|            |   | The indexes     |            |                         |
|            |   | should be       |            |                         |
|            |   | retrieved off   |            |                         |
|            |   | the previous    |            |                         |
|            |   | tier (i.e. for  |            |                         |
|            |   | Stage           |            |                         |
|            |   | deployment,     |            |                         |
|            |   | take indexes    |            |                         |
|            |   | from QA in the  |            |                         |
|            |   | /loc            |            |                         |
|            |   | al/content/cabi |            |                         |
|            |   | oapi/42/indexes |            |                         |
|            |   | directory).     |            |                         |
|            |   |                 |            |                         |
|            |   | The folder for  |            |                         |
|            |   | the indexes     |            |                         |
|            |   | should be       |            |                         |
|            |   | created and     |            |                         |
|            |   | exists before   |            |                         |
|            |   | starting the    |            |                         |
|            |   | application     |            |                         |
|            |   | server.         |            |                         |
|            |   |                 |            |                         |
|            |   | The indexes are |            |                         |
|            |   | approximately 2 |            |                         |
|            |   | GB in size      |            |                         |
|            |   | (expected to    |            |                         |
|            |   | grow up to 5 GB |            |                         |
|            |   | in the next     |            |                         |
|            |   | year).          |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **Web      |   |                 |            |                         |
| Server     |   |                 |            |                         |
| Confi      |   |                 |            |                         |
| guration** |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| DNS        |   | cabioapi-       |            |                         |
| Entries    |   | dev.nci.nih.gov |            |                         |
|            |   |                 |            |                         |
|            |   | cabioapi        |            |                         |
|            |   | -qa.nci.nih.gov |            |                         |
|            |   |                 |            |                         |
|            |   | cabioapi-st     |            |                         |
|            |   | age.nci.nih.gov |            |                         |
|            |   |                 |            |                         |
|            |   | cabio           |            |                         |
|            |   | api.nci.nih.gov |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Apache     |   | Apache          |            |                         |
|            |   | configuration   |            |                         |
|            |   | or redirection, |            |                         |
|            |   | e.g. options,   |            |                         |
|            |   | aliases,        |            |                         |
|            |   | mime-types,     |            |                         |
|            |   | logs, reports,  |            |                         |
|            |   | HTML file       |            |                         |
|            |   | types, Index    |            |                         |
|            |   | files, etc.     |            |                         |
+------------+---+-----------------+------------+-------------------------+
| SSL        |   | N/A             |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Single     |   | N/A             |            |                         |
| Sign On    |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| **Test     |   |                 |            |                         |
| Cases**    |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Pre        |   | N/A             |            |                         |
| Deployment |   |                 |            |                         |
| Tests      |   |                 |            |                         |
+------------+---+-----------------+------------+-------------------------+
| Post       |   | 1\) Connect to  |            |                         |
| Deployment |   | the "Home page" |            |                         |
| Tests\     |   | --              |            |                         |
| \          |   | <http://        |            |                         |
| **         |   | cabioapi.nci.ni |            |                         |
| Required** |   | h.gov/cabio42/> |            |                         |
|            |   |                 |            |                         |
|            |   | 2\) Verify the  |            |                         |
|            |   | webpage appears |            |                         |
|            |   | and click       |            |                         |
|            |   | "Continue"      |            |                         |
|            |   | button.         |            |                         |
|            |   |                 |            |                         |
|            |   | 3\) Select the  |            |                         |
|            |   | "gov.nih.nc     |            |                         |
|            |   | i.cabio.domain" |            |                         |
|            |   | package under   |            |                         |
|            |   | "Domain         |            |                         |
|            |   | Packages"       |            |                         |
|            |   |                 |            |                         |
|            |   | 4\) Select      |            |                         |
|            |   | "Gene"          |            |                         |
|            |   |                 |            |                         |
|            |   | 5\) Enter       |            |                         |
|            |   | 'brca1' for the |            |                         |
|            |   | symbol          |            |                         |
|            |   | attribute       |            |                         |
|            |   | (Note: the '    |            |                         |
|            |   | should not be   |            |                         |
|            |   | included)       |            |                         |
|            |   |                 |            |                         |
|            |   | 6\) Verify that |            |                         |
|            |   | some results    |            |                         |
|            |   | appear          |            |                         |
|            |   |                 |            |                         |
|            |   | 7\) Return to   |            |                         |
|            |   | the "Home       |            |                         |
|            |   | page" -         |            |                         |
|            |   | <http://        |            |                         |
|            |   | cabioapi.nci.ni |            |                         |
|            |   | h.gov/cabio42/> |            |                         |
|            |   |                 |            |                         |
|            |   | 8\) Enter       |            |                         |
|            |   | 'brca1' into    |            |                         |
|            |   | the FreestyleLM |            |                         |
|            |   | search text box |            |                         |
|            |   | and click       |            |                         |
|            |   | "Search"        |            |                         |
|            |   |                 |            |                         |
|            |   | 9\) Verify that |            |                         |
|            |   | some results    |            |                         |
|            |   | appear          |            |                         |
+------------+---+-----------------+------------+-------------------------+