Frequently Asked Questions

Contacting Specify
Feedback in the Specify application (Top Level Menu: Help > Submit Feedback) is one-way communication from a user to the Specify team. The Specify staff will read and consider these comments but will not answer them specifically. Please use Feedback for any suggestions or thoughts you might have on Specify usability and performance.

The Specify web site Community Forum is a venue for the Specify users to seek and offer advice, make suggestions and provide assistance to other Specify users. The Forum is not the best place to seek answers to specific questions from the Specify Project staff, although we read it from time to time and contribute when we can.

Specific technical issues often require a detailed voice or email conversation. Questions best answered by a Specify staff member can be e-mailed to: specify@ku.edu or better yet, pick up the phone and call us at +1 785 864-4400 (U.S. Central Time Zone, GMT -6) .

Converting from Specify 5

No, one does not need to un-install Specify 5 to use Specify 6. Specify 5 uses Microsoft SQL Server, whereas Specify 6 uses MySQL for the back-end data manager. Installations of these two database management systems are independent and will not interfere with one another. The Specify 6 application is also independent of the Specify 5 software and should pose no conflicts. Any existing Specify 5 data need to be migrated to Specify 6 by the Specify Software Project staff. Contact us for details.

Installing Specify 6 does not update a Specify 5 installation. When you run the Specify Setup Wizard a new, emptly database will be created for Specify 6; any existing Specify 5 databases will remain untouched. Because we made numerous changes to the Specify 6 data model, Specify 5 databases need to be converted by Specify Software Project staff. We are currently developing a queue and scheduling process for conversions of Specify 5 sites to Specify 6. We will also assist with the customization of data entry forms for Specify 6 (there is no forms editor), and with the development of label and report templates for printed outputs.

If you have very little data you may consider exporting your data from Specify 5 into an Excel spreadsheet and bringing it into Specify 6 through the Specify WorkBench Upload tool.

Taxonomic Records
Taxonomic authority files can be added both when running the Specify Setup Wizard and at the time new Disciplines are added within Specify. These records were converted from the Catalog of Life. The Specify team does not create or edit these records. Users are not obligated to use the files that are provided by Specify, they may create their own authority files and upload them either via the Discipline Wizard or WorkBench Uploader.
MySQL
The process is easy, but varies depending your operating system. The Specify staff has created this page to assist you in the process: Changing the default MySQL engine to InnoDB.
The notorious “Error 0″ with MySQL installations when using the MySQL “Server Instance Configuration Wizard” indicates that the MySQL Wizard was unable to install, start or configure the new server you are attempting to setup. We find “Error 0″ commonly occurs when there is a previous installation of MySQL on a Windows machine, or even hidden file remnants of an earlier MySQL installation. It is easy to conclude that a previous installation of MySQL has been completely expunged from your system, but one has to maniacally hunt down and extirpate all old configuration and data files before the MySQL Server Instance Configuration Wizard will install a new MySQL database and start the Windows MySQL service. We recommend that you try the these steps if you see this error.

One user found that the following worked. We suggest trying this first.

  • 1. Cancel the configuration step. (If you haven’t already).
  • 2. Go back to the configuration wizard on the program list (newly installed.) Follow the “reconfigure” option.
  • 3. Uncheck the “modify security settings” box and reconfigure without changing the password. Make sure the password is blank.
  • 4. When you click “finish” on the final screen, the service fails to start. Click “cancel” and restart the configuration wizard. Reconfigure in the same way as before, but check the “modify” security settings” box and leave the “current password” field blank and fill in and confirm a new password. This time the service starts, security settings are applied, and MySQL works… hopefully.

In house, we found the following was successful.

  • 1. Cancel the configuration step. (If you haven’t already.)
  • 2. Start up the configuration wizard. Delete the previous instance. This will close the configuration wizard.
  • 3. Start up the configuration wizard again. Create a new instance. Usually this step will work and you are done.

For Windows XP,

  • 1. Run the MySQL Server Instance Configuration Wizard which is installed in the MySQL Program Files subdirectory. If the second Wizard window presents the option to “Remove Instance” choose that and then click NEXT and in the subsequent window click EXECUTE.
  • 2. Use Windows Explorer to navigate to the directory \Documents and Settings\All Users\Application Data. If you do not see the subdirectory \Application Data under All Users, while you are in the All Users directory go to the top menu, choose Tools/Folder Options/View, then click on the option “Show hidden files and folders”, then click OK. You should now see \Application Data in the All Users directory, click on it, see the directory MySQL and delete it.
  • 3. Now go to the \Program Files Directory, see the MySQL subdirectory and delete it.
  • 4. Some users have found that rebooting your machine at this point can make a difference between the next step failing or succeeding. So, let’s reboot Windows just in case …
  • 5. Now go back to the MySQL Server Instance Configuration Wizard and run it. The Wizard should now let you re-installl a new copy of MySQL. Be sure to pick the options for Specify as shown in the MySQL installation guide available on the Specify web server.

For Windows Vista, the process is very similar, delete the \Program Files\MySQL directory, and also unhide and delete the directory \ProgramData\MySQL.

If that does not work for any reason, here are various steps that can be taken:

  • 1. Confirm with Wndows XP’s “My Computer/Properties” that you have Windows Service Pack 3 installed.
  • 2. Specify 6 will only communicate with the MySQL database server if MySQL is configured to run on network port 3306.
  • 3. Remove MySQL via the Windows Control Panel, “add/remove programs” option.
  • 4. Use the Windows Control Panel, choose Administrative Tools, then Services, look for MySQL in the list. If it is there it will need to be stopped *and* deleted. If it is present, highlight it, then right mouse click on it and choose the ‘Properties” menu option. In the MySQL Properties window, click the “Stop” button and change the “Startup Type” to “Disabled”. This stops an existing MySQL service if it is running, and prevents it from automatically starting up. Now the service has to be removed from Windows using a text command window. Go to the Windows XP Start menu and choose “Run”. Type “cmd” in the run window, and click “OK”. The command window will pop open, in it type: sc delete MySQL. You should see either a SUCCESS message that the service was deleted, or a Service not found message, either is what you want. Exit the window.
  • 5. Confirm again that all of your MySQL data and configuration directories are deleted as described above.
  • 6. Then try reinstalling MySQL with the downloadable installation package from the MySQL web site.

If all of that fails, we commend you to your local systems administrator if you can grab one, and refer you to the MySQL help forums to help debug system and server issues: http://forums.mysql.com/read.php?11,19373,246717. If you’ve repeatedly failed to solve this MySQL problem, call or e-mail us, we will work with you to get it fixed.

Plugins
1) UI plugins that can be used within the form system and a standard UI control, will not work. We have developed several for use within Specify (e.g. the Latitude/Longitude data entry widget). The following table describes the interfaces and classes that are used for UI plugins:

Name Description Required
UIPluginable The main interface for a UI plugin. Yes
GetSetValueIFace Provides an interface for getting/setting data to/from the plugin for the form system. No
UIValidatable Enables the UI Plugin to participate in the validation system. No
UIPluginBase This is a handy abstract implementation base class that makes creating plugins easy. No

 

2) All the main components within Specify are called “task” plugins, this includes all the tools on the tool bar and other components. There are only two required interfaces that need to be implemented to create a Specify plugin. Below is a list of the interfaces that can be used:

Name Description Required
SecurityOtionIFace This enables the plugin to adequately paticipate within the security system. Yes
Taskable This defines the Task plugin Yes
CommandListener Enables the plugin to listen to application level message (e.g. shutdown) No
SubPaneMgrListener This interface should be implemented if the plugin will display UI. No
BaseTask This is a handy abstract implementation base class that makes creating plugins easy. No

At this time there is only a manual registration within an XML file. In the future there will be UI for installing and managing plugins.
 

WorkBench Uploader
The Specify 6 WorkBench was designed as a streamlined data entry tool and Specify 6 uploading tool for batches of 2,000 or fewer records. The WorkBench is limited to 2,000 records to prevent the program from hitting a memory constraint imposed by Java. Although there is interest in using the WorkBench as a whole database migration tool with tens of thousands of records, it is not designed to work with more than 2,000.