web.xml is a text
file that lives in /var/www/html/recipnet/WEB-INF
, but most users find it convenient to edit the symlinked copy of the file in /etc/recipnet
. The file controls the operation of the
web application, the portion of the Reciprocal Net site software that’s hosted
by the Apache Tomcat web application server.
The contents of the text file are eXtensible Markup Language (XML)
syntax. The
Each <context-param> element, which contains a single configuration directive, is expressed in a syntax similar to the following:
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. In this example, the text between <param-name> and </param-name> identifies this setting as the hostname directive. The description of the directive is present for this directive only as a convenience for the system administrator; it serves no functional purpose. The current value of the hostname directive is localhost .
The web.xml contains a number of configuration directives, each of which already has a value assigned. System administrators may change a directive’s value, but should not alter its name or description. Syntax of the file should be preserved. Positioning of directives within the file is significant.
Currently the following configuration directives are defined in the file:
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adminEmail |
SMTP e-mail address of the server’s administrator. In a default installation the value is blank, which implies that the administrator’s e-mail address is root@ your server’s DNS name. It is not necessary to specify a value for this directive unless you wish to override the default behavior. |
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childPath |
Specifies the PATH environment variable that should be used when by the web application when it launches external subprocesses. These programs might be spawned to perform specific scientific calculations or generate images, for example. The current release depends upon the programs cjpeg, gs, pnmcrop, pnmdepth, pnmmargin, pnmscale, recipnet-ortep3, recipnet-renderclient, recipnet-vort2ppm, and sh; each of these programs must reside within the path specified. In a default installation this value is PATH=/bin:/usr/bin:/usr/local/bin . |
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darterServer |
The DNS name of a server offering molecular image rendering services (so-called “darter” services) to Reciprocal Net partner sites. At the time of this writing only once such server exists, the central rendering service hosted by IUMSC. The name of their server is iumsc-beowulf.reciprocalnet.org . |
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defaultAuthenticatedApplet |
Controls which molecular visualization applet authenticated users should see by default when they first visit a Sample detail page. Possible values are minijamm , jamm1 , and jamm2 . The suggested value is jamm2 . |
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defaultAuthenticatedLevel |
The default “detail level” for samples to be used for authenticated users. This is not a security feature, because users are able to switch their level freely, but rather an educational one. The suggested value is 65536, which is intended for use by “researchers”. Another possible value is 8192, which equates to “generic Common Molecules level”. |
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defaultUnauthenticatedApplet |
Similar to defaultAuthenticatedApplet above, except this setting controls the default molecular visualization applet for unauthenticated users. The suggested value is minijamm because it is compatible with the widest range of web browser programs. |
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defaultUnauthenticatedLevel |
Similar to defaultAuthenticatedLevel above, except this setting controls the default detail level for unauthenticated users. The suggested value is 65536. |
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externalProcessTimeout |
The maximum number of milliseconds an external program spawned by the web application (to perform a specific computation, for example) may run before it’s assumed to have stalled and is forcibly terminated. The suggested value is 30000 (30 seconds). |
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fileCacheTimeout |
The minimum number of seconds after having been generated that a molecular image or diagram is available for download by the user who requested it. Once this time has elapsed the image may no longer be available. The suggested value is 1800 seconds (30 minutes). |
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hostname |
DNS or other name of the system on which recipnetd is running. It is possible to run recipnetd on one computer and the web application on potentially many other computers in order to improve performance. The suggested value localhost is correct for environments where recipnetd and the web application run on the same system. |
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languageCacheParameterString |
These are performance tuning parameters used for a cache of localization resources. The default value is 64,0,4,0,0,0,true . |
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languagePackJar |
The complete path of a jar file containing localization information for status codes, file codes, or action codes. The default value is blank, which means that Reciprocal Net site software’s own language facilities are employed. |
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maxFileCacheSize |
Specifies the maximum number of megabytes that temporary files generated in response to molecular diagramming or rendering requests may consume on the local filesystem. When this limit is approached, temporary files are deleted via a least-recently-used scheme. The suggested value is 512 megabytes. |
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maxOaiPmhSamples |
The maximum number of samples to return in response to a single request from a digital library harvesting agent via the OAI-PMH protocol. Harvesting agents desiring more samples than this value are expected to send multiple consecutive requests. Setting this value too high might expose your system to possible denial-of-service (DoS) attacks. Setting this value to 0 causes no limit to be enforced – all matching samples are returned in response to a single request – and poses an even greater DoS risk. The suggested value is 512. |
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newUserInitialPreferences |
The preference settings given to newly-created user
accounts. The default value is JaMM2,sample,detailed,3,10,true,false,true,false,true,true,false,true,false,false,form-based,false,false, In order, the preferences are: Visualization applet: valid choices are minijamm, jamm1, and jamm2. Sample view: the preferred means of viewing sample records. Valid choices are showsample (for the “Sample Detail” page) and sample (for the “Edit Sample” page). Sample detail: the preferred degree of detail to be shown on samples. Valid choices are basic and detailed . Lab summary day count: the number of days to be displayed on the “Lab Summary” page. Lab summary sample count: the number of samples to be listed in each box on the “Lab Summary” page. Blank fields suppressed: whether blank fields are suppressed from display on the “Edit Sample” page. Valid choices are true and false . Comments suppressed: whether workflow comments are suppressed from display on the “Edit Sample” page. Valid choices are true and false . Empty file boxes suppressed: whether action boxes for file actions that are empty are suppressed from display on the “Edit Sample” page. Valid choices are true and false . Empty correction boxes supressed: whether action boxes for correction boxes that are empty are suppressed from display on the “Edit Sample” page. Valid choices are true and false . Empty action boxes suppressed: whether other action boxes that are empty are suppressed from display on the “Edit Sample” page. Valid choices are true and false . Skipped-by-reversion action boxes suppressed: whether action boxes that were skipped by a reversion are suppressed from display on the “Edit Sample” page. Valid choices are true and false . File descriptions suppressed: whether file descriptions are suppressed from display on the “Edit Sample” page. Valid choices are true and false . Blank file listings suppressed: whether blank listings of files are suppressed from display on the “Edit Sample” page. Valid choices are true and false . Suppression options suppressed: whether the suppression options box is suppressed from display on the “Edit Sample” page. Valid choices are true and false . Files overwritten: whether newly-uploaded files can overwrite existing sample data files. Valid choices are true and false . Upload mechanism: the preferred means of uploading sample data files. Valid choices are form-based and drag-and-drop . Searches limited to non-retracted: whether searches are limited to samples that do not have a retracted status. Valid choices are true and false . Searches limited to finished: whether searches are limited to samples that have a finished status. Valid choices are true and false . Searches limited to local: whether searches are limited to samples with data files hosted at the local site. Valid choices are true and false . Searches limited to provider: whether searches are limited to samples associated with the user’s affiliated provider. Valid choices are true and false . Implicit preference changes: whether the user’s preferences are updated implicitly as he navigates through the web application. Valid choices are true and false . Space group symbol validation: whether space group symbols typed into the web application by the user should be validated. Valid choices are true and false . |
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persistedOperationsCache |
These are performance tuning parameters used for a cache of persisted operations. The default value is 256,128,16,0,30000,.1,false . |
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repositoryManagerName |
The RMI registration name used by Repository Manager, one of the “core modules” contained within recipnetd. This value must match the RepRmiName value defined in recipnetd.conf . In a default installation it is RecipnetRepositoryManager . |
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restrictLargeFilesAvailability |
Specifies whether prior versions of “large” sample data files are restricted to users affiliated with the sample, or whether such files are generally available. The sense of “large” is determined by the RepPriorVersionFileSizeLimit directive in recipnetd.conf. The suggested value is true because making available prior versions of very large sample data files consumes a great deal of server resources; thus, allowing unauthenticated users to do so might pose a security risk. If this value is false, then no file size limit is imposed upon unauthenticated users. |
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rmiPort |
The TCP port number on which recipnetd is listening for connections from the site software web application. The value here must match the directive GenRmiPort in recipnetd.conf . |
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shouldredirectAuthUserToSampleJsp |
Specifies whether authenticated users who execute a search that matches exactly one sample should be redirected to the Sample Details page for that sample (false) or to the Edit Sample page for that sample if they have such authorization (true). The default is false. Unauthenticated users are always redirected to the Sample Details page when a search they execute matches exactly one sample, regardless of this setting. |
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siteManagerName |
Similar to repositoryManagerName above, except this is the name used by Site Manager. In a default installation this value is RecipnetSiteManager. |
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stylesheetName |
The name of the CSS stylesheet that Reciprocal Net pages should reference, as a path name relative to the webapp context root. The value should start with a slash (/) character. The default value is /recipnet.css . |
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tempDir |
The filesystem location in which temporary files generated by the web application such as molecular diagrams and rendered images are stored. No more than maxFileSizeCache bytes will be stored in this directory at any one time. The default value is blank, which instructs the web application to store temporary files using the temporary file facility that Apache Tomcat provides. It is not necessary to specify a value for this directive unless you wish to override the default behavior. |
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unauthenticatedPreferences |
The preference settings given to users who do not
authenticate. The default value is minijamm,sample,detailed,3,10,true,false,true,false, |