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Table of Contents

Panel
Excerpt

Diagnostic tools that can help you figure out what VIVO is doing.

 

 

toc

Introduction

Are you developing code for VIVO? Are you doing some extreme customization? You might benefit from VIVO's set of built-in diagnostic tools.

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The diagnostic tools are enabled and controlled by settings within VIVO. These settings may be changed interactively, without restarting VIVO. The settings may also be read from a file, so they will be in effect as VIVO is starting up.

Terms

Developer Mode

When the diagnostic tools are enabled, VIVO is said to be running in "Developer Mode".  This reflects the fact that all of the developer settings are ignored unless the tools as a whole are enabled.

Developer Settings

These are parameters that control the diagnostic tools. They may be set interactively, using the Developer Panel, or read from the developer.settings file at startup.

The Developer Panel

When VIVO is in developer mode, the Developer Panel appears on every page. This serves two purposes:

  1. It enables you to change the Developer Settings without navigating away from your current page.
  2. It provides a visual reminder that VIVO is in Developer Mode. If a production instance were accidentally configured to run in Developer Mode, it would be easily noticed.

No Developer PanelDeveloper Panel (closed)

 

Entering Developer Mode

developer.properties file

When VIVO starts up, it looks for a file in the home directory, named developer.properties. If the file is found, the settings are read from it. Any settings that are not found in the file keep their default values. If the file is not found, then all settings keep their default values until set interactively.

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The VIVO distribution includes an example.developer.properties file.  It contains descriptions of all of the settings, with examples. You can rename example.developer.properties to developer.properties, and uncomment the settings you want to use.

Interactively entering developer mode

Log in as a system administrator (or root). Go to the Site Administration page. Click on Activate developer panel.

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The Developer Panel will immediately appear below the page header. You may click on the panel to open it and change the settings. The Developer Panel will continue to appear in every page (except for some "back-end" pages for editing the ontology).

The settings

When open, the developer panel looks like this:

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The following tables show the meaning of each setting in the developer panel, and how to specify it in the developer.properties file.

General settings

In the panelEnable developer mode
In the filedeveloper.enabled
EffectCauses the developer panel to be displayed on each VIVO page. Enables all of the other developer settings. If this is false, other settings will retain their values, but will not take effect.
In the panelAllow anonymous user to see and modify developer settings
In the filedeveloper.permitAnonymousControl
EffectIf true, any VIVO user may change the developer settings. If false, only a system administrator (or root) may change the settings.

Freemarker settings

In the panelDefeat the template cache
In the filedeveloper.defeatFreemarkerCache
EffectIf true, each Freemarker template is loaded from disk each time it is used. If false, a template change may be on disk for up to one minute before it is loaded.
In the panelInsert HTML comments and start and end of templates
In the filedeveloper.insertFreemarkerDelimiters
Effect

If true, you may view the HTML source for a VIVO page to see which Freemarker templates were used to create each portion of the page.

Code Block
languagexml
...
<!-- FM_BEGIN view-search-default.ftl -->
<a href="/vivo/display/n2252" title="individual name">Oswald, Jeremiah</a>
        <span class="display-title">Faculty Member</span>
<p class="snippet"></p><!-- FM_END view-search-default.ftl -->
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SPARQL Query settings

In the panelLOG each query
In the filedeveloper.loggingRDFService.enable
Effect

Write an entry to the log for each SPARQL query, assuming that INFO-level logging is enabled for the RDFServiceLogger. Each entry includes

  • The time spent executing the query
  • The name of the method on RDFService that received the query
  • The format of the result stream from RDFService
  • The text of the query.

The remaining settings in this area can be used to restrict which queries are logged, or to include more information for each query.

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In the panelRestrict by calling stack
In the filedeveloper.loggingRDFService.stackRestriction
EffectSet this to a regular expression. A query will be logged only if the abridged calling stack matches the regular expression, in whole or in part.

Page configuration settings

In the panelLog the use of custom list view XML files.
In the filedeveloper.pageContents.logCustomListView
EffectWrite an entry to the log each time a property is displayed using a list view other than the default lists view.
In the panelLog the use of custom short views in search, index and browse pages.
In the filedeveloper.pageContents.logCustomShortView
EffectWrite an entry to the log each time a search result is displayed using a short view other than the default view for that context.

Language support settings

In the panelDefeat the cache of language property files
In the filedeveloper.i18n.defeatCache
EffectIf true, the language property files are re-loaded each time they are called for. If false, the language property files are loaded only once, when VIVO starts up.
In the panelLog the retrieval of language strings
In the filedeveloper.i18n.logStringRequests.
EffectWrite an entry to the log each time a language-specific string is retrieved from one of the language property files.

The links

The developer panel also contains several links to special VIVO pages that may be helpful to developers.

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