Troubleshooting

 

As stated in the Agilent Literature Search License Agreement, Agilent Literature Search is provided without support. 

However, here are some useful hints for dealing with potential problems that may occur.

 

Agilent Literature Search does not show up on Cytoscape plugins menu.

Check to see that the file AgilentLiteratureSearch.jar exists in Cytoscape's plugin directory.    It is possible that you may have installed Agilent Literature Search to the wrong directory.  If that is the case, move the AgilentLiteratureSearch.jar file to Cytoscape's plugin directory.  When in doubt, run the installation again.

 

A Search Engine Not Found Warning Appears

It is likely that your proxy settings are incorrect.  Check them via the Edit -> Preferences menu item.

 

Search Engine Performance is Slow

USPTO and OMIM search engines can be slow, particularly during daytime hours.  An alternative is to try longer searches during evening hours.

 

You get different results from multiple search executions

Agilent Literature Search performs run-time aliasing and adds the new aliases to its data structure.  You may get different results on multiple runs when you use aliases.  We provide the aliases in the concept lexicon files as a utility.    They may not work for your specific needs, in which case you should edit the concept lexicon files to provide aliases that work for you. 

 

Lexicon and/or Settings files not found

Agilent Literature Search utilizes a number of settings, configuration, and data files which are installed into the folder <user.home>/.cytoscape/<Cytoscape-version>/plugins/ <AgilentLiteratureSearch-version>/data .     If the creation of this folder of copying of these files fails for any reason, e.g. permissions problems, then Agilent Literature Search will not operate properly.   You should check that file permissions are set to allow files to be written to your <user.home> folder (on Microsoft Windows systems this will often be C:\Documents and Settings\<your user name> ).  Then re-install Agilent Literature Search.

 


When you do a search, a warning dialog pops up saying "Engines Unavailable".

Possible Causes: The engine(s) are actually not available (e.g., heavy load, down for maintenence, etc.), your proxy settings are incorrect, your connection to the Internet is not working.

Solutions:

1) First check that your internet connection is working by trying to browse to a page. Use your browser's "refresh" button for the page, to ensure your browser has not locally cached the page.

2) If your Internet connection is working, ensure your proxy settings are correct within Agilent Literature Search. Your proxy settings are correct, if you got some results from other search engines. In this case, go to step 4. If you only searched using one search engine, retry your search with all three engines selected (use View-->Engine Selections). If you *don't*  get an engine down message for any of the other engines, then see step 4.  If all engines return the "Engines Unavailable" warning, see step 3.

3) If you use a proxy server to connect to the Internet, ensure your proxy settings are correct within Agilent Literature Search. Use your Internet browser proxy settings for Agilent Literature Search. If you are not sure if you use a proxy server, then check with your System Administrator. Set your Agilent Literature Search proxy settings using the Edit-->Preferences... menu, Internet tab.

4) Your engine(s) of interest are probably truly unavailable.  Retry your search later.

 

If all else fails, you can send email to mailto:sysbio@labs.agilent.com.  We are not set up to provide support for Agilent Literature Search, but we will try to answer your questions when we can.

 

Clicking on in the Query Matches Window has no Effect

Under certain situations, the in the Query Matches window get asynchronized with the current network under view. Clicking on the under these circumstances will not highlight the corresponding Nodes and Edges in Cytoscape. Click on the Refresh button in the Query Matches window to re-synchronize the icons in the Query Matches to the currently viewed network.

 

 

Warning Dialog Messages


Engines Unavailable

Items under this heading are the names of the engines that Agilent Literature Search could not communicate with (see troubleshooting question).

 

Unreadable Matches

Items under this heading are the URLs of the matches found that could not be read. This may be caused by the search engine becoming unavailable, or your internet connection failing *after* Agilent Literature Search initially gathered matches from the search engines. Items under this heading imply your proxy setting *are correct*--no need to check them.


Maximum Documents Exceeded

Items under this heading are the names of the engines where you have exceeded your document limit for that engine.  The document limit is the total number of matching documents that can be returned for a search from that search engine. To avoid this, split up your searches into smaller pieces with a smaller value for 'Max Engine Matches' .