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

The Developer Panel

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  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)

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Entering Developer Mode

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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.

The "General" tab

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Freemarker settings

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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. For example:

Code Block
languagexml
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<!-- 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

Full documentation for the logging RDF Service is available here, including detailed explanation of an example log excerpt.

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.

Note

The configuration models (display, user accounts) and the TBox models are memory-mapped. This means that any "read" operations are run against a cached copy of the model, and are not logged. For these models, only "write" operations are logged.

The ABox models are not memory-mapped; both "read" and "write" operations will be logged.

In the panelShow stack trace
In the filedeveloper.loggingRDFService.stackTrace
EffectEach log entry will include a stack trace. The trace is abridged so it starts after the ApplicationFilterChain, omits any Jena classes, and ends at the RDFService.

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Link textShow background threads
URL/admin/showThreads
The pageDisplays information about the active background threads. These threads may be rebuilding the search index, re-inferencing the knowledge base, or rebuilding the Class Cache.
Link textShow RDF data sources
URL/admin/showSources
The pageDisplays information about the triple stores, and the layers of adapters that the application wraps around them, including ModelMakers, OntModels, etc.

The "Search" tab

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Search query settings

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In the panelRestrict by calling stack
In the filedeveloper.searchEngine.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.

Search indexing settings

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In the panelLog indexing
In the filedeveloper.searchIndex.enable
Effect

Write an entry to the log each time that documents are added to the Search index, assuming that INFO-level logging is enabled for the SearchEngineLogger. Note that documents are not changed in the Search index: instead, old documents are deleted and new documents are added. Each entry includes

  • The time taken to add the documents.
  • The number of documents added.
  • The URIs of the individuals being indexed in the documents.

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

 

In the panel Show document contents
In the filedeveloper.searchIndex.showDocuments
Effect Each entry will include the contents of the documents being added. This includes the document identifiers, the boost level, and the contents of each of the fields in the document.
In the panel Restrict by URI or name
In the filedeveloper.searchIndex.uriOrNameRestriction
Effect Set this to a regular expression. An addition will be logged only if the list of document identifiers matches the regular expression, in whole or in part. The document identifiers are the URI and the Name fields.
In the panel Restrict by document contents
In the filedeveloper.searchIndex.documentRestriction
EffectSet this to a regular expression. An addition will be logged only if the contents of the documents matches the regular expression, in whole or in part.
In the panel Log breakdown timings for indexing operations
In the filedeveloper.searchIndex.logIndexingBreakdownTimings
Effect

When an indexing operation completed, write entries to the log showing how much time was taken by each indexing object: Excluders, DocumentModifiers, and UriFinders. Each entry includes

 
  • The display label of the indexing object
  • The number of times that the indexing object was invoked
  • The total time required for the indexing object
  • The average time for each invocation of the indexing object


In the panel Log deletions
In the filedeveloper.searchDeletions.enable
Effect

Write an entry to the log each time documents are deleted from the Search index, assuming that INFO-level logging is enabled for the SearchEngineLogger. Each entry includes

  • The time spent deleting the documents
  • Either
    • the list of URIs being deleted, or
    • the search query that was used to find documents for deletion.
In the panel Suppress the automatic indexing of changed triples.
In the filedeveloper.searchIndex.suppressModelChangeListener
Effect

If this is selected, the search indexer will not automatically adjust to changes in the data model. This means that you can ingest data much more quickly, but you must manually request a full re-indexing when your ingests are complete.

Note

This doesn't really belong in the developer panel, since it changes the way VIVO operates. It was put here to answer an urgent requirement.

 

Links

Link textRebuild search index
URL/SearchIndex
The pageAllows you to request a rebuild of the search index, and to monitor its progress.

The "Authorization" tab

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Warning

TBD

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In the panelWrite policy decisions to the log
In the filedeveloper.authorization.logDecisions.enable
Effect

Write an entry to the log for each policy decision that is made for any requested action, assuming that INFO-level logging is enabled for the PolicyDecisionLogger. Each entry includes

  • The requested action
  • The name of the policy
  • The decision and message.

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

In the panelInclude the user identifiers in the log record
In the filedeveloper.authorization.logDecisions.addIdentifiers
EffectEach log entry will include the identifiers assigned to the currently logged-in user.
In the panel Skip inconclusive decisions
In the filedeveloper.authorization.logDecisions.skipInconclusive
Effect Do not log INCONCLUSIVE decisions. If all policies return INCONCLUSIVE for a request, this is treated as UNAUTHORIZED, and will be logged.
In the panel Restrict by requested action
In the filedeveloper.authorization.logDecisions.actionRestriction
EffectSet this to a regular expression. A decision will be logged only if the string value of the requested action matches the regular expression, in whole or in part.
In the panel Restrict by policy name
In the filedeveloper.authorization.logDecisions.policyRestriction
EffectSet this to a regular expression. A decision will be logged only if the string value of the policy matches the regular expression, in whole or in part.
In the panel Restrict by user identifiers
In the filedeveloper.authorization.logDecisions.userRestriction
EffectSet this to a regular expression. A decision will be logged only if the list of user identifiers matches the regular expression, in whole or in part.

What if the developer panel doesn't appear?

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