Merge from dev branch (#125)

* updating Tethys help

* added help details server connection & calibration

* Reporting outputs to user

Use Pamguard WarnOnce system to show a message of success or failure
after attempting to output to Tethys.

* Removing empty fields

Start of implementation of code that can remove empty fields from
objects before they are written.

* More help documentation

Continued writing general export help.
Added new css style
Added image

* Fix type in Deployment export

* Prevent single deployment export

For now, disable the option to export a single Deployment document for
multiple recording periods.

* System to search species codes

Search the ITIS species codes in Tethys to find ITIS codes. Search can
be on a common or scientific name.

* Data blocks help + species codes

More help documentation on exporting detections/localization as well as mapping detection species codes to TSNs.  Includes supporting images

* Improved dialog for finding species codes

Now has a progress bar to block GUI while searching database.

* Add species codes TOC in help

* Documented new species search in help

* Nilus Checker

Can check a Nilus class to see if it's missing required objects and be
used to remove empty fields (e.g. zero length strings) from an object.

* fixed anchor html problem

* Messing around with checking of required fields in nilus objects.

* split Tethys help files into smaller chunks

* Update button enablers

And reinstate output of a single deployment document, with non-recording
periods stores in the QA section

And update help TOC for latest help documents.

---------

Co-authored-by: Marie <marie.roch@sdsu.edu>

src/PamView/wizard/PamWizardCard.java

@@ -1,7 +1,5 @@
 package PamView.wizard;
 
-import java.io.Serializable;
-
 import javax.swing.JPanel;
 
 

src/clickDetector/ClickClassifiers/ClickBlockSpeciesManager.java

@@ -15,7 +15,7 @@ public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetec
 	public ClickBlockSpeciesManager(ClickControl clickControl, ClickDataBlock clickDataBlock) {
 		super(clickDataBlock);
 		this.clickControl = clickControl;
-		setDefaultDefaultSpecies(new SpeciesMapItem(ITISTypes.UNKNOWN, "Unknown", "Unknown"));
+		setDefaultDefaultSpecies(new SpeciesMapItem(ITISTypes.OTHER, "Unknown", "Unknown"));
 		setDefaultSpeciesCode("Unknown");
 	}
 

src/help/JavaHelpSearch/SCHEMA

@@ -1,2 +1,2 @@
 JavaSearch 1.0
-TMAP bs=2048 rt=1 fl=-1 id1=6727 id2=1
+TMAP bs=2048 rt=1 fl=-1 id1=6882 id2=1

src/help/Map.jhm

@@ -54,6 +54,8 @@
 
 <mapID target="classifiers.whistleClassifierHelp.docs.whistleClassifier_Output" url="classifiers/whistleClassifierHelp/docs/whistleClassifier_Output.html"/>
 
+<mapID target="utilities.tethys.docs.calibrations" url="utilities/tethys/docs/calibrations.html"/>
+
 <mapID target="utilities.hydrophoneArrayManagerHelp.docs.Array_Configuration_sec1" url="utilities/hydrophoneArrayManagerHelp/docs/Array_Configuration.html#sec1"/>
 
 <mapID target="sound_processing.fftManagerHelp.docs.noise_removal_medianfilter" url="sound_processing/fftManagerHelp/docs/noise_removal.html#medianfilter"/>
@@ -138,6 +140,8 @@
 
 <mapID target="sound_processing.NoiseBands.Docs.NoiseBands" url="sound_processing/NoiseBands/Docs/NoiseBands.html"/>
 
+<mapID target="utilities.tethys.docs.detect_localize" url="utilities/tethys/docs/detect_localize.html"/>
+
 <mapID target="visual_methods.videoRangeHelp.docs.videoRange_Calibrating" url="visual_methods/videoRangeHelp/docs/videoRange_Calibrating.html"/>
 
 <mapID target="detectors.gpl.docs.detection" url="detectors/gpl/docs/detection.html"/>
@@ -198,6 +202,8 @@
 
 <mapID target="displays.userDisplayHelp.docs.userDisplayPanel" url="displays/userDisplayHelp/docs/userDisplayPanel.html"/>
 
+<mapID target="utilities.tethys.docs.tethys_speciescodes_TSNLookup" url="utilities/tethys/docs/tethys_speciescodes.html#TSNLookup"/>
+
 <mapID target="classifiers.roccaHelp.docs.rocca_Configure_SchoolStats" url="classifiers/roccaHelp/docs/rocca_Configure.html#SchoolStats"/>
 
 <mapID target="visual_methods.loggerFormsHelp.docs.SUBTABS" url="visual_methods/loggerFormsHelp/docs/SUBTABS.html"/>
@@ -276,8 +282,6 @@
 
 <mapID target="detectors.clickDetectorHelp.docs.offline_Tools_AmplSel" url="detectors/clickDetectorHelp/docs/offline_Tools.html#AmplSel"/>
 
-<mapID target="utilities.tethys.docs.tethys_quickstart" url="utilities/tethys/docs/tethys_quickstart.html"/>
-
 <mapID target="displays.spectrogramDisplayHelp.docs.UserDisplay_Spectrogram_Overlays" url="displays/spectrogramDisplayHelp/docs/UserDisplay_Spectrogram_Overlays.html"/>
 
 <mapID target="displays.radarDisplayHelp.docs.UserDisplay_Radar_Creating" url="displays/radarDisplayHelp/docs/UserDisplay_Radar_Creating.html"/>
@@ -290,6 +294,8 @@
 
 <mapID target="classifiers.roccaHelp.docs.rocca_Spectrogram_rocca_RecalcContour" url="classifiers/roccaHelp/docs/rocca_Spectrogram.html#rocca_RecalcContour"/>
 
+<mapID target="utilities.tethys.docs.tethys_speciescodes" url="utilities/tethys/docs/tethys_speciescodes.html"/>
+
 <mapID target="overview.PamMasterHelp.docs.performanceTests" url="overview/PamMasterHelp/docs/performanceTests.html"/>
 
 <mapID target="overview.PamMasterHelp.docs.xmloutput" url="overview/PamMasterHelp/docs/xmloutput.html"/>
@@ -388,6 +394,8 @@
 
 <mapID target="localisation.group3d.docs.3dsimplex" url="localisation/group3d/docs/3dsimplex.html"/>
 
+<mapID target="utilities.tethys.docs.connection" url="utilities/tethys/docs/connection.html"/>
+
 <mapID target="visual_methods.loggerFormsHelp.docs.NOCLEAR" url="visual_methods/loggerFormsHelp/docs/NOCLEAR.html"/>
 
 <mapID target="sound_processing.beamformer.docs.Beamformer_Settings_BF_SourceTab" url="sound_processing/beamformer/docs/Beamformer_Settings.html#BF_SourceTab"/>
@@ -456,6 +464,8 @@
 
 <mapID target="sound_processing.seismicveto.docs.veto_configuration" url="sound_processing/seismicveto/docs/veto_configuration.html"/>
 
+<mapID target="utilities.tethys.docs.deployments" url="utilities/tethys/docs/deployments.html"/>
+
 <mapID target="detectors.whistleMoanHelp.docs.whistleMoan_ConfigNoise_averagesubtraction" url="detectors/whistleMoanHelp/docs/whistleMoan_ConfigNoise.html#averagesubtraction"/>
 
 <mapID target="localisation.largeAperture3D.docs.meal_exercise3_localise" url="localisation/largeAperture3D/docs/meal_exercise3_localise.html"/>
@@ -592,6 +602,8 @@
 
 <mapID target="detectors.gpl.docs.notes" url="detectors/gpl/docs/notes.html"/>
 
+<mapID target="utilities.tethys.docs.tethys_module" url="utilities/tethys/docs/tethys_module.html"/>
+
 <mapID target="sound_processing.fftManagerHelp.docs.FFTEngine_Creating" url="sound_processing/fftManagerHelp/docs/FFTEngine_Creating.html"/>
 
 <mapID target="sound_processing.fftManagerHelp.docs.noise_removal_clickremoval" url="sound_processing/fftManagerHelp/docs/noise_removal.html#clickremoval"/>

src/help/PAMGUARDIndex.xml

@@ -2,6 +2,8 @@
 <!DOCTYPE index PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Index Version 1.0//EN" "http://java.sun.com/products/javahelp/index_2_0.dtd"><!--generated by JHelpDev Version: 0.63, 14 May 2008, see jhelpdev.sourceforge.net-->
 
 <index version="1.0">
+ <indexitem text="ITIS Species Codes " target="utilities.tethys.docs.tethys_speciescodes"/>
+
  <indexitem text="Tethys server " target="utilities.tethys.docs.tethys_server"/>
 
  <indexitem text="Tethys database interface " target="utilities.tethys.docs.tethys_overview"/>

src/help/PAMGUARDTOC.xml

@@ -198,10 +198,20 @@
   <tocitem text="Tethys Interface ">
    <tocitem text="Tethys Overview " target="utilities.tethys.docs.tethys_overview" image="topic"/>
 
-   <tocitem text="Quick Start " target="utilities.tethys.docs.tethys_quickstart" image="topic"/>
+   <tocitem text="Tethys Module " target="utilities.tethys.docs.tethys_module" image="topic"/>
 
    <tocitem text="Tethys Server " target="utilities.tethys.docs.tethys_server" image="topic"/>
 
+   <tocitem text="Connecting to Tethys " target="utilities.tethys.docs.connection" image="topic"/>
+
+   <tocitem text="Instrument Calibrations " target="utilities.tethys.docs.calibrations" image="topic"/>
+
+   <tocitem text="Instrument Deployments " target="utilities.tethys.docs.deployments" image="topic"/>
+
+   <tocitem text="Detections and Localizations " target="utilities.tethys.docs.detect_localize" image="topic"/>
+
+   <tocitem text="ITIS Species Codes " target="utilities.tethys.docs.tethys_speciescodes" image="topic"/>
+
   </tocitem>
  </tocitem>
  <tocitem text="Sensors ">

src/help/pamHelpStylesheet.css

@@ -55,6 +55,14 @@ ol {
 
 img.wrap {float: left}
 img.wrapright {float: right}
+img.wrapcenter {float: center}
+
+.center {
+    display: block;
+    margin-left: auto;
+    margin-right: auto;
+    width: 85%;
+}
 
 table, th, td {
   border: 1px solid black;

src/help/utilities/tethys/docs/calibrations.html

@@ -0,0 +1,147 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+    "http://www.w3.org/TR/html4/loose.dtd">
+<html lang="en">
+<head>
+
+<link href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<title>Instrument Calibration Information</title>
+<style type="text/css">
+img.wrap {
+	float: left
+}
+
+img.wrapright {
+	float: right
+}
+
+img {
+	float: right;
+}
+</style>
+</head>
+
+<body>
+      
+
+  <h1>Instrument calibration information</h1>
+
+  <p>
+    Most of the calibration data is taken from the array manager and
+    from the sound acquisition module. However, PAMGuard will ask a
+    few questions about HOW the instrument was calibrated, when it was
+    done and who is responsible.
+  </p>
+  <p>
+    There are two dialogs associated with calibration.  The first
+    asks for a calibration method and has the following fields:
+  </p>
+
+  <ul>
+    <li>
+      Method:  Must be one of the following options:
+      <ul>
+	<li>Reference hydrophone</li>
+	<li>Manufacturer’s specification</li>
+	<li>Piston phone</li>
+	<li>Other calibrated source</li>
+	<li>Unknown</li>
+      </ul>
+    </li>
+    
+    <li>
+      Serial number:  Hydrophone serial number
+    </li>
+
+    <li>
+      Quality:  Quality assurance value:
+      <ul>
+	<li> unverified:  The calibration has not been verified </li>
+	<li> valid:  The calibration has been validated as per the quality assurance process </li>
+	<li> invalid:  The calibration was found to be invalid during quality assurance </li>
+      </ul>
+    </li>
+    
+    <li>
+      QA Comment:  Textual description of the quality assurance
+      process.
+    </li>
+    
+    
+    <li>
+      Calibration method:  Textual description of the Method.
+    </li>
+  </ul>
+  
+  <p>
+    The second calibrations dialog asks for:
+  </p>
+  
+  <ul>
+    <li>
+      Calibration date:  Date the calibration was performed.
+    </li>
+    
+    <li>
+	Update frequency:  Must be one of the following:
+	<ul>
+	  <li>
+	    as-needed:  No updates are planned, but if a change is needed the calibration will be updated (defaul)t
+	  </li>
+	  <li>
+	    unplanned:  There are no plans to ever update the record.
+	  </li>
+	  <li>
+	    yearly:  A yearly review will be conducted to ensure that the record is valid.
+	  </li>
+	</ul>
+      </li>
+      
+      <li>
+	Technical Person / Data Manager: These two types of data have
+	the same fields and detail who was responsible for the
+	calibration and who is responsible for maintaining the record
+	of the calibration.  In many cases, this may be the same
+	person and copy buttons allow the fields to be duplicated.
+
+	<ul>
+	  <li>
+	    Name:  Responsible party’s naem
+	  </li>
+	  <li>
+	    Organisation:  Organisation to which the party reports
+	  </li>
+	  <li>
+	    Position:  Responsible party’s title
+	  </li>
+	  <li>
+	    Email:  Email contact information 
+	  </li>
+	</ul>
+      </li>
+      
+    </ul>
+
+    <p>
+      Fill in as much information as you can! 
+      If the export is successful, a record will show for each
+      hydrophone (or sensor) in your instrument array in the
+      calibration information table:
+    </p>
+    
+    <div>
+      <img src="./images/calibration_information.png" class=".center"
+	   alt="Panel with information about instrument calibration"/>
+    </div>
+
+
+    <br>
+    <br>
+    <p class="prevLink"><a href="tethys_module.html">Previous: Module overview
+    <p class="nextLink"><a href="deployments.html">Next: Instrument deployments
+    </a></p>
+    <br>
+
+
+</body>
+</html>

src/help/utilities/tethys/docs/connection.html

@@ -0,0 +1,121 @@
+
+<html>
+<head>
+<LINK href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<title>Tethys Connection and Project Details </title>
+</head>
+
+<body>
+
+    <h1> Connection and Project Details </h1>
+    
+    <p>
+      Make sure you have a <a href = "tethys_server.html">Tethys Server</a> running.  The PAMGuard interface will 
+      only work with <a href="https://tethys.sdsu.edu/tethys3/">Tethys
+      3</a> or later.  The section below specifies how to set the
+      address of Tethys server address as well as determine if
+      PAMGuard can communicate successfully with Tethys.  (The top
+      panel will be orange if communication is not working.
+    </p>
+    
+    <h2>Tethys Server</h2>
+    
+
+    <p>
+      The Tethys Server field next to the picture of the goddess Tethys
+      indicates the address of the Tehtys server. To change this field,
+      click on the gear icon. You will be prompted to provide a computer
+      address (URL) and a port. The address should start with http://
+      followed by the machine name or internet protocol address unless
+      the Tethys server has been configured to use an encrypted
+      connection. In this case, start the address with https://.
+    </p>
+
+    <p>
+      By default, PAMGuard will use http://localhost:9779 which
+      assumes that your Tethys server is running on the same computer as
+      PAMGuard and that it expects communication on port 9779, the
+      default port (administrators may change this).
+    </p>
+
+    <p>
+      If PAMGuard can communicate with the Tethys server, the
+      Connection and Project panel will be light grey. If
+      communication is not possible, the panel will be colored
+      orange. Likely causes for communication failure are:
+    </p>
+    <ul>
+      <li>
+	The server address or port is incorrect.
+      </li>
+      
+      <li>
+	Tethys has not been started on the server machine. One of the
+	main reasons that we see this is when the administrator has
+	not configured Tethys to run automatically as a service. In
+	that case, when a machine reboots (e.g., for automatic
+	operaing system updates) the server will not start
+	automatically. The Tethys manual explains how to configure
+	Tethys as a service that starts automatically when the machine
+	boots.
+      </li>
+      
+      <li>
+	Firewall rules do not permit traffic between the machine
+	executing PAMGuard and the one hosting Tethys on the selected
+	port. If you do not have adminstrative privileges, you will
+	need to contact your support team for help.
+      </li>
+    </ul>
+    
+    <h2>Project and Instrument Information</h2>
+
+    <p>
+      Projects are names used by Tethys to help track work that should
+      be considered together, such as a series of deployments designed
+      to answer a specific question or funded under a specific
+      grant. If you do not already have a project defined in your
+      PAMGuard database, you can click the "New Project" button in the
+      "Connection and Project details" section of the Tethys
+      module. This will start a dialog that asks for a case-sensitive
+      project name and a geographic region. The geographic region is
+      for convenience, PAMGuard and Tethys track information by
+      longitude and latitude, but sometimes it is helpful to query for
+      information with respect to a geographic name such as Channel
+      
+      Islands National Marine Sanctuary.
+    </p>
+
+    <p>
+      The array instrumentation is selected from a drop-down menu next
+      to the Instruments label.  A dropdown menu next to the label
+      “Instruments” shows the list of hydrophone arrays.  These are
+      likely to have been previously established prior to starting
+      analysis of your data by using the menu Settings -> Hydrophone
+      Array.
+
+    </p>
+    
+    <p>
+      If you are a long-time user of PAMGuard, you will notice  
+      additional fields are required for instrumentation: Instrument
+      Type and Instrument Id.  The type indicates what type of
+      instrument is being used and may be generic such as a mooring or
+      array or denote a specific instrument such as a HARP, Rock
+      Hopper, SoundTrap, etc.  The Id is a unique identifier for the
+      instrument such as a serial number.  Note that if you are using
+      an older PAMGuard database, you may see a blank entry in the
+      instruments list as these new fields will not have been
+      populated.  Press new/edit to access the instrument settings
+      from the Tethys module page.
+    </p>
+
+    <br>
+    <br>
+    <p class="prevLink"><a href="tethys_module.html">Previous:
+    Tethys module</a></p>
+    <p class="nextLink"><a href="calibrations.html">Next: Instrument calibrations</a></p>
+    <br>
+
+</body>

src/help/utilities/tethys/docs/deployments.html

@@ -0,0 +1,143 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+    "http://www.w3.org/TR/html4/loose.dtd">
+<html lang="en">
+<head>
+
+<link href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<title>Deployments</title>
+<style type="text/css">
+img.wrap {
+	float: left
+}
+
+img.wrapright {
+	float: right
+}
+
+img {
+	float: right;
+}
+</style>
+</head>
+
+<body>
+      
+  <h1>Deployments</h1>
+
+  <p>
+    Tethys uses deployment records to register information about
+    when instruments have been deployed as well as their
+    characteristics.  Examples of characteristics that are recorded
+    include sample rate and the number of quantization bits,
+    description of duty cycles (if applicable), hydrophone geometry,
+    and enough details to be able find calibration data for specific
+    hydrophones.
+  </p>
+
+  <p>
+    PAMGuard will examine the       
+    <a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard
+      database</a>
+    and <a href="../../BinaryStore/docs/binarystore_overview.html">
+    binary Store</a> to determine what records should be generated for
+    your instrumentation.
+  </p>
+    
+    <p>
+      Where data were collected continuously or on a regular duty
+      cycle, PAMGuard will create a single deployment record.  If data
+      were collected on a more "ad-hoc" basis, where the instrument
+      has been deployed multiple times or has irregular recording,
+      PAMGuard will generate a deployment record for each period of
+      recording.
+    </p>
+
+    <p>
+      The figure below shows an example of ad-hoc recording periods
+      identified by PAMGuard:
+    </p>
+    <div>
+      <img src="./images/deploymentspanel.png" class=".center"
+	   alt="Panel showing recording times/deployments for this PAMGuard database"/>
+    </div> 
+
+    <p>
+      Occasionally, there may be short recording periods (e.g. while
+    you were testing kit on deck) that you do not want to export. Use
+    the select checkbox to pick all of the rows that you wish to
+    export, or right click on the table and "Select All."
+    </p>
+
+    <p>
+      When one or more deployment records are selected, the
+    "Export..."  button will become available.  Selecting the export
+    button will start a dialog that asks for additional information
+    about the deployments and then write records to Tethys.
+    </p>
+    <p>
+      The first page of the dialog asks for the project and geographic
+      region which will be automatically populated if they have been
+      previously specified. In addition, the following fields are
+      requested:
+    </p>
+    <ul>
+      <li>Cruise name - Optional name of the deployment cruise</li>
+      <li>Site - Case-sensitive name for the deployment site,
+	e.g. "Tanner Banks" or a letter designation "T".  This can
+	provide a simple way to identify multiple deployments at the
+	same general location.
+      </li>
+      <li>Responsible Party - A set of fields describing who was
+	responsible for the deployment and how they may be
+	contacted.
+      </li>
+    </ul>
+
+    <p>
+      The next page of the dialog asks whether you would like to
+      export a single deployment document or multiple deployments.
+      <strong>todo:  add more detail here</strong>
+    </p>
+    
+
+    <p>
+      Finally, you are prompted to provide optional textual descriptions of:
+      <ul>
+	<li> Objectives - What were your objectives when deploying the
+	  instrument?  Example: Determine population estimates for
+	  critically endangered populations of vaquita (<em>Phocoena
+	  sinus</em>).
+	</li>
+	<li> Abstract - A textual description of the deployment.
+	  Example:  A set of high frequency recorders  were deployed across the
+	  northern portion of the Sea of Cortez in the historical range
+	  of the vaquita (<em>Phocoena sinus</em>).  These recordings will
+	  support detection and density estimation efforts.	  
+	</li>
+	<li>
+	  Method - A description of the methods used.  Example:
+	  Small boat deployment of bottom moored SoundTrap recorders
+	  with acoustic releases.  
+	</li>
+      </ul>
+
+      Press Finish to export the records.  Once the
+      document(s) have been successuflly exported, the document name
+      associated with each recording period will be shown in the
+      Tethys Deployment column.
+    </p>
+
+    
+	  
+    <br></br>
+    <br></br>
+
+  <p class="prevLink">
+    <a href="calibrations.html">Previous: Calibrations</a>
+  </p>
+  <p class="nextLink">
+    <a href="detect_localize.html">Next: Detections & Localizations</a>
+  </p>
+</body>
+</html>

src/help/utilities/tethys/docs/detect_localize.html

@@ -0,0 +1,161 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+    "http://www.w3.org/TR/html4/loose.dtd">
+<html lang="en">
+<head>
+
+<link href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<title>Detections/Localizations</title>
+<style type="text/css">
+img.wrap {
+	float: left
+}
+
+img.wrapright {
+	float: right
+}
+
+img {
+	float: right;
+}
+</style>
+</head>
+
+<body>
+      
+  <h1>Exporting Detections/Localizations (PAMGuard data blocks)</h1>
+    
+  <p>
+    The bottom left panel of the Tethys module shows a list of
+    different types of PAMGuard data that can be exported.  The data
+    in this list correspond to the various PAMGuard modules that have
+    been configured.  See the
+    <a href="../../../overview/PamMasterHelp/docs/modelViewer.html">
+      data model viewer</a>
+    help for an example of how PAMGuard might be configured.
+  </p> 
+  
+  <h2>Species information</h2>
+
+  <p>
+    Some of these data represent detections of specific species or
+    phenomena that must be translated to Tethys.  A context menu
+    (right-click on most computers) will show the option "Species
+    info..." that will allow you to specify the
+    <a href="./tethys_speciescodes.html">translation of events</a>
+    to species identifiers and call/sound types.  If you try to export
+    without having done this, the species info dialog will be started
+    automatically prior to export.
+  </p>
+
+  <h2>Selecting data blocks for import</h2>
+  
+  <p>
+    In the sample data blocks below, four modules have been
+    configured, but only one of them has been run.  Column "N Pam
+    Data" indicates the number of data records that have been
+    produced, and "PAMGuard Time" tells us when the data were
+    processed.  "Tethys Documents" indicates how many Tethys records
+    have been produced, and should be 0 until the data are exported.
+  </p>
+    
+  <div>
+    <img src="./images/data_blocks.png" class=".center"
+	 alt="List of results showing detections and other module processing events"/>
+  </div>
+  
+  <p>
+    Select the data blocks to be exported by clicking on them.
+    Multiple lines can be selected by using keyboard modifiers such as
+    holding the shift while clicking to select all data blocks between
+    the last clicked block and where you click.  Holding the alternate
+    (ALT) key will allow selection or de-selection of a single item
+    without affecting the selection state of other blocks.
+  <p>
+
+  <p>
+    <em>
+      SUGGESTION:  It looks like we have to highlight these by clicking
+      on them.  As we use select boxes for recording periods, we might
+      want to do the same thing here...  We might want to rename
+      N PAM Datas to N PAM Data as data are already plural.
+    </em>
+  </p>
+
+  <h2> Exporting data blocks </h2>
+
+  <p>
+    Once the data blocks have been selected, press export.  A series
+    of dialogs will guide you through the export process.  The first
+    set of dialogs simply display a summary of information about what 
+    will be exported.
+  </p>
+
+  <div>
+    <img src="./images/stream_algo_info.png" class=".center"
+	 alt="List of details describing the mechanism, parameters, and version of modules used in processing"/>
+  </div>
+    
+  <p>
+    There is nothing to change in this summary.  Press Next once you
+    have reviewed it.  The second panel allows specification of your
+    objectives, abstract, and method.  Many modules will have
+    pre-populated the method for you.  While it is recommended to populate
+    the objectives and abstract, these fields are optional.
+  </p>
+    
+  <p>
+    Press Next to proceed to the next step of the dialog.  You will be asked
+    what details you wish to store within the parameters that were used to
+    produce these data.  Your must select one of the following:
+  </p>
+  
+  <ul>
+    <li> 
+      None - Do not report any of parameters used to produce these
+      detections. This option is <strong>not recommended</strong> as
+      it severely limits your ability to reproduce your results at a
+      later date or know whether or not the results of different
+      studies can be used together. 
+    </li>
+    <li> Data selector only - <strong>not sure what this is</strong> </li>
+    <li>
+      Module only - Report the parameters that were set with this
+      module.  Only parameters associated with the specific module
+      will be reported.  Examples include score and duration thresholds
+      as well as any other type of criterion used to determine whether
+      or not an event is associated with a specific phenomenon or species.
+    </li>
+    <li>
+      Full process chain (default) - This is the most verbose option.  It includes the module
+      parameters as well as anything else that is part of the signal processing chain that leads
+      to the module.  As an example, a module only setting would not report the parameters that were
+      used to generate a spectrogram that was presented to a module for classification, but the
+      full process chain would record these details as well.  Use this option will dramatically
+      increase the potential to reproduce your results, but it will generate a large amount of data
+      about the signal processing chain, much of which might not be useful.
+    </li>
+  </ul>
+  
+  <p>
+    The final page of the dialog has an "Export data" button.  Press
+    this to export the data.  The system will begin generating the
+    Tethys document and the "Export data" button will be relabeled "Export complete"
+    once it is done.  At this point, you can press "Finish" to close
+    the dialog.
+
+    <em>Would it make more sense to export when the user presses
+    Finish (or change the Finish button Export)?</em>
+  </p>
+  
+    
+  <p class="prevLink">
+    <a href="deployments.html">Previous: Deployments</a>
+  </p>
+  <p class="nextLink">
+    <a href="./tethys_speciescodes.html">Translating species to
+    taxonomic serial numbers</a> (species encoding)
+  </p>
+
+</body>
+</html>

src/help/utilities/tethys/docs/tethys_module.html

@@ -0,0 +1,92 @@
+<html>
+<head>
+<LINK href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<title>Tethys Module Overview</title>
+</head>
+
+<body>
+    <h1>Tethys Module Overview</h1>
+
+    <p>
+      It is assumed that you are familiar with PAMGuard and have some
+      knowledge about Tethys.  
+      <a href="https://tethys.sdsu.edu/documentation">Documentation</a>
+      and <a href="https://tethys.sdsu.edu/tutorials/">tutorials</a>
+      are available at the Tethys
+      <a href="https://tethys.sdsu.edu">web site</a>.
+    </p>
+
+    <h1>Launch PAMGuard in viewer mode</h1>
+    <p>
+      Tethys export is only available in 
+      <a href="../../../overview/PamMasterHelp/docs/viewerMode.html">PAMGuard
+	Viewer mode</a>
+      and is used to archive project data to a centralised
+      database.  It is NOT a replacement for the
+      existing <a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard
+	database</a>.  Open the PAMGuard database that you wish to use
+      in viewer mode.
+    </p>
+     
+    <h1>PAMGuard Tethys Module</h1>
+
+    <p>
+      Add a Tethys module to PAMGuard from the File / Add Modules /
+      Utilities menu.  A new tab panel will show the Tethys interface
+    </p>
+    
+    <div>
+      <img src = "./images/TethysGUI_1.png" class=".center"/>
+    </div>
+    
+    <p>
+      The tab shows a number of panes for the connection to the server
+      and the various types of data that will be output to the
+      database. Some of these panes summarize information on what's in
+      the current PAMGuard dataset (consisting of your PAMGuard
+      database and binary store), others may be empty until you start
+      to export to Tethys.
+    </p>
+    
+    <p>
+      The Tethys module consists of several panels:
+    </p>
+    <ul>
+      <li>
+	<a href="connection.html">Connection and Project Details</a> -
+	Specifies the location of the Tethys server and metadata about
+	the project.
+      </li>
+      <br>
+      <li>Data Export - There are several panes that are responsible
+      for exporting information about instrument deployments, their
+      calibrations, and what they detected/localized.
+	<ul>
+	  <li>
+	    Instrument <a href="calibrations.html">calibration</a>
+	    information
+	  </li>
+	  
+	  <li>
+	    Recording periods
+	    and <a href="deployments.html">deployments</a> information.
+	  </li>
+	  
+	  <li>
+	    <a href="detect_localize.html">Detections and
+	    localizations</a>.  A final panel next to this one lists
+	    exported detection/localization documents.
+	  </li>
+	</ul>
+      </li>
+    </ul>
+    
+    <br>
+    <br>
+    <p class="prevLink"><a href="tethys_overview.html">Previous: Overview</a></p>
+    <p class="nextLink"><a href="connection.html">Next: Connection
+    & Project Details</a></p>
+    <br>
+</body>
+</html>

src/help/utilities/tethys/docs/tethys_overview.html

@@ -21,48 +21,68 @@ img {
 </style>
 </head>
 <body>
-	<h1>Tethys Interface</h1>
+  <h1>Tethys Interface</h1>
-	<h2>Overview</h2>
+  <p></p>
+  <h2>Overview</h2>
 
-	<p align="right">
+  <div>
-				<img class="wrap" SRC="images/Tethys-200.png" alt="Tethys mosaic">
+    <img SRC="images/Tethys-200.png" alt="Tethys mosaic"
-				</p>
+	 style="float: right; margin 10px;"/>
-		<p>
+  </div>
   
-		<a	href="https://tethys.sdsu.edu/">Tethys</a> is a freely
+  <p>
-		available open source temporal-spatial database for metadata related
+    PAMGuard is compatible
-		to acoustic recordings. The database is intended to house the metadata
+    with <a href="https://tethys.sdsu.edu/tethys3/">Tethys 3.0</a> or
-		from marine mammal detection and localization studies, allowing the
+    later.
-		user to perform meta analyses or to aggregate data from many
+    <a href="https://tethys.sdsu.edu/">Tethys</a> is a freely
-		experimental efforts based on a common attribute. This resulting
+    available open source temporal-spatial database for metadata
-		database can then be queried based on time, space, or any desired
+    related to acoustic recordings. The database is intended to house
-		attribute and the results can be integrated with external datasets
+    the metadata from marine mammal detection and localization
-		such as NASA's Ocean Color, lunar illumination, etc. in a consistent
+    studies, allowing the user to perform meta analyses or to
-		manner. While Tethys is designed primarily for acoustic metadata from
+    aggregate data from many experimental efforts based on a common
-		marine mammals, the design is general enough to permit use in other
+    attribute. This resulting database can then be queried based on
-		areas as well.
+    time, space, or any desired attribute and the results can be
-		
+    integrated with external datasets such as NASA's Ocean Color,
-	</p>
+    lunar illumination, etc. in a consistent manner. While Tethys is
-	<p>PAMGuard is compatible with <a href="https://tethys.sdsu.edu/tethys3/">Tethys 3.0</a> or above, released early in 2024. </p>
+    designed primarily for acoustic metadata from marine mammals, the
-	<p>The Tethys database is not a replacement for the existing 	
+    design is general enough to permit use in other areas as well.
-	<a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard Database.</a> 
+  </p>
-	Where the PAMGuard database only contains data from a single instrument or cruise, the Tethys
-	database contains data from many cruises and projects and can be used to hold a summary of all data 
-	from a lab or organisation.
-	</p>
-	
-	<p>Before using the module in PAMGuard, you should install the Tethys Server, which runs under 
-	Windows. <a href="https://tethys.sdsu.edu/install/">
-	Instructions for installing the Tethys Server can be found here.</a></p>
 
 
-	<br><br>
+  <p>
+    The Tethys database is not a replacement for the existing
+    <a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard
+    Database.</a>  Where the PAMGuard database only contains data from
+    a single instrument or cruise, the Tethys database contains data
+    from many cruises and projects and can be used to hold a summary
+    of all data from a lab or organisation.  PAMGuard's Tethys module
+    provides an interface for exporting detailed or summary
+    information about acoustic detections to the Tethys database.
+  </p>
+	
+  <p>
+    Before using the module in PAMGuard, you should install the Tethys
+    Server.  While clients that communicate with Tethys can run on a
+    variety of computer operating systems, there are a small number of
+    dependencies on Microsoft technologies that require the server to
+    be installed on a Microsoft Windows machine.
+    <a href="https://tethys.sdsu.edu/install/"> Instructions
+    for installing the Tethys Server can be found here.</a></p>
+
+  <br><br>
+	
+  <p>
+    Module help:
+  </p>
+  <ol>
+    <li> The <a href="tethys_module.html">Tethys module</a> (start here)</li>
+    <li> The <a href="connection.html">Connecting to Tethys</a> </li>
+    <li> The <a href="calibrations.html">Instrument calibrations</a> </li>
+    <li> The <a href="deployments.html">Instrument deployments</a> </li>
+    <li> The <a href="detect_localize.html">Detections & Localizations</a> </li>
+    <li> Guide to specifying <a href="tethys_speciescodes.html">species names</li>
+  </ol>
 
 
-		<a href="tethys_quickstart.html">Next: Quick Start</a>
-	</p>
-	<br>
-	<br>
-	<br>
 </body>
 </html>

src/help/utilities/tethys/docs/tethys_quickstart.html

@@ -1,80 +0,0 @@
-<html>
-<head>
-<LINK href="../../../pamHelpStylesheet.css" type="text/css"
-	rel="STYLESHEET">
-<title>Tethys</title>
-</head>
-
-<body>
-    <h1>Tethys Quick Start</h1>
-    
-    <p>This 'Quick Start' guide is aimed at people who are already familiar with both Tethys and PAMGuard</p>
-    <p>The Tethys database is only used in 
-    <a href="../../../overview/PamMasterHelp/docs/viewerMode.html">PAMGUard Viewer mode</a> and is only used to archive project data to a single 
-    centralised database. 
-    It is NOT a replacement for the existing <a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard database</a>.</p>
-     
-    <h3>PAMGuard Tethys Module</h3>
-    <p>Launch PAMGuard in Viewer Mode with an existing set of data.</p> 
-    <p>Add a Tethys module to PAMGuard from the File / Add Modules / Utilities menu. </p>
-    <p>A new tab panel will show the Tethys interface</p>
-    <center><img src = "./images/TethysGUI_1.png" width="100%" height="auto"></center>
-    <p>The tab shows a number of panels for the connection to the server and the various types 
-    of data that will be output to the database. Some of these should summary information on what's in the
-    current PAMGuard dataset (consisting of your PAMGuard database and binary store), others may be empty until you start to 
-    export to Tethys. </p>
-    
-    
-    
-    <h3>Tethys Server</h3>
-    <p>Make sure you have a <a href = "tethys_server.html">Tethys Server</a> running.  The PAMGuard interface will 
-    only work with <a href="https://tethys.sdsu.edu/tethys3/">Tethys 3.</a> </p>
-    <p>Check the server connection. If PAMGuard has correctly connected to the Tethys server, the top panel of the display will be a normal
-    grey colour. If the connection cannot be made, the panel will be orange.</p>
-    <p>If required, change the server settings using the "Select Sever" button</p>
-    
-    
-    <h4>Project and Instrument Information</h4>
-    <p>Either select an existing "Project", or create a new one.</p>
-    <p>You also need to give Tethys more information about the instrument(s) or arrays you've deployed than in previous PAMGuard versions. Again, select an 
-    existing instrument, or set up a new one. You'll notice that this information is held with the rest of the PAMGuard array management information.</p>
-    
-    <h3>Data Export</h3>
-    <p>It's best to export data in the sequence the panels are laid out in on the PAMGuard display, i.e. Calibrations, then Deployments, and finally Detections.</p>
-
-    <h4>Calibrations</h4>
-    <p>To export the calibration data, press the "Export..." button at the top of the "Instrument Calibration Information" panel. 
-    <p>Most of the calibration data is taken from the array manager and from the sound acquisition module. However, PAMGuard will ask a few questions about
-    HOW the instrument was calibrated, when it was done and who is responsible. Fill in as much information as you can! 
-    IF the export is successful, a record will show for each hydrophone (or sensor) in your instrument array in the calibration information table:</p>
-    
-    <center><img src="./images/calibration_information.png"></center>
-    
-    <h4>Deployments</h4>
-    <p>PAMGuard will have done it's best to work out the temporal extent of your data by looking in the 
-	<a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard database</a> and    
-   	<a href= "../../BinaryStore/docs/binarystore_overview.html">binary Store</a>. Where data were collected on a regular duty 
-   	cycle, or continuously, there should be a single record in the table of recording periods. If data were collected on a more
-   	"ad-hoc" basis, for instance during a boat based survey, there might be many different records in the table.
-   	Occasionally, there may be short recording periods (e.g. while you were testing kit on deck) that you don't want to export. Either select
-   	individual rows that you want to export, or right click on the table and "Select All".</p>
- 
-   	<p>Press the "Export..." button and work through the questions to provide additional information about your data, why it was collected, etc. </p>
-   	<p>Once the document(s) have been exported, the document names will be shown alongside each PAMGuard deployment period</p>
-   	<center><img src="./images/deploymentspanel.png"></center> 
-    
-    <h4>Detections</h4>
-    <p>The bottom left panel shows a list of different types of PAMGuard data that can be exported and should also show the total numbers of each type of data that are available
-    within the PAMGuard storage systems. Select the datablock you want to export from and press "Export...". </p>
-    <p><strong>You really don't want to try to export zillions of data to Tethys</strong> , in the options that will appear you can opt to just export certain types of detections
-    or summary counts.</p>
-    
-    <br>
-    <br>
-    <p class="prevLink"><a href="tethys_overview.html">Previous: Overview</a></p>
-    <p class="nextLink"><a href="tethys_server.html">Next: Tethys Server</a></p>
-    <br>
-    <br>
-    <br>
-</body>
-</html>

src/help/utilities/tethys/docs/tethys_speciescodes.html

@@ -0,0 +1,192 @@
+<html>
+<head>
+<LINK href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<title>Species coding</title>
+</head>
+
+<body>
+
+  <h1> Species and Call Type Names </h1>
+
+  When exporting data from PAMGuard to Tethys, some PAMGuard records
+  will require additional information indicating what type of animal
+  or phenomena were detected.  If a specific call-type was detected,
+  e.g. "Clicks" or "Whistles", these should be noted as well.
+  
+  <h2> Species Names </h2>
+  <p>
+    Tethys uses the <a href="https:itis.gov">Integrated Taxonomic
+    Information System</a> (ITIS) to encode species names as taxonomic
+    serial numbers (TSNs), unique numeric identifiers for species.
+    These data conform with several international coding systems which
+    are described on the <a href="https://itis.gov/standard.html">ITIS
+    standards</a> page.  
+  </p>
+
+  <p>
+    It is not uncommon to be unable to describe a call to the genus
+    level.  In such cases, one can use a higher taxonomic level.  For
+    example, beaked whale echolocation clicks are distinctive from the
+    clicks of other toothed whales as their pulses have a
+    frequency-modulated component.  While they can frequently be
+    associated with the family Hyperodontidae, it is not always
+    possible to associate a click to a specific species as many of the
+    at least twenty-two species remain understudied.  In such a case,
+    we would use the TSN for Hyperodontidae, 770799.  While not
+    currently supported by PAMGuard, each species identifier has an
+    optional Group attribute that can be used in an ad-hoc manner to
+    provide additional information.  This can be used to add
+    population markers, tentative genus groups, etc.
+  </p>
+
+  <p>
+    ITIS does not describe abiotic sounds, Tethys records such sounds as follows:
+    <ol>
+      <li>
+	For anthropogenic signals, the Tethys convention is to
+	use <em>Homo sapiens</em>, TSN 180092, for the species code
+	and describe the human-generated signal via a call type,
+	e.g. ship, mid-frequency active sonar, etc.
+      </li>
+      <li>
+	Tethys reserves the TSN -10 for geophonic signals.
+	The call type is used to describe the source.  Examples
+	include ambient sound, earthquake, rain, etc.  Note that negative TSNs
+	are not part of the ITIS standard.
+      </li>
+    </ol>
+  </p>
+
+  Note that in general, you do not have to worry about remembering
+  TSNs.  Tethys uses TSNs internally, but will translate TSNs to/from
+  Latin names or user-defined abbreviations both when querying and
+  presenting results.
+
+  <h2> Call types </h2>
+
+  <p>
+    Some detectors identify specific call types.  When this is the
+    case, users will need to specify the call type name.  While
+    species names are standardized in Tethys, call names do not have a
+    well-defined standard and experts frequently use different names
+    for the same type of call.  Consequently, Tethys does not provide a
+    standard coding for call types and users are free to choose the call
+    type names with which they feel most comfortable.
+  </p>
+
+  <p>
+    That said, the authors of Tethys do however provide a list of recommend call
+    types for many species.  These recommendations can be accessed in the
+    <a href="https://ars.els-cdn.com/content/image/1-s2.0-S1574954115001983-mmc1.docx">
+    supplemental information</a> of the open access article "Management of acoustic metadata
+    for bioacoustics," Roch et al. (2016),
+    (<a href="https://doi.org/10.1016/j.ecoinf.2015.12.002">DOI:10.1016/j.ecoinf.2015.12.002</a>).
+  </p>
+  
+  <h2>
+    Export dialog
+  </h2>
+
+  <p>
+    During export of records that are species-specific, a dialog will
+    appear that lists the types of events that were found by PAMGuard
+    modules.  This dialog permits users to specify how the ad-hoc species
+    species/call encoding scheme used by PAMGuard modules can be systematically
+    translated to the TSNs and call types are stored in Tethys.
+  </p>
+
+  <p>
+    PAMGuard events typically are a short name that represents the
+    species and/or potentially a call.  Knowledge of the PAMGuard
+    modules that were run and the data on which they executed will let
+    a user infer what should be recorded.
+    
+    The dialog below shows a sample set of events produced by one or more PAMGuard modules
+    using the names:  HP, DO, SON, KW, UNK, and PHP:
+
+  <div>
+      <img src="./images/species_codes.png" class=".center"/>
+  </div>
+
+  The dialog above was produced from detections on data that were
+  recorded near the mouth of the River Tay in Scotland.  Consequently,
+  we can infer that the harbour porpoise that is denoted by "HP" is
+  <em>Phocena phocena</em>, the only harbour porpoise endemic to
+  Scottish waters.
+  </p>
+  
+  An ITIS code and call/sound type can be associated with each event.  The dialog lists:
+  <ul>
+    <li>
+      Name - The ad-hoc name given by the PAMGuard module.  This may not be changed.
+    </li>
+
+    <li>
+      ITIS code -This is the ITIS TSN that is associated with PAMGuard
+      event code.  Click on Find to inovke the TSN
+      search dialog whose behavior is described in the <a href="#TSNLookup">next
+	section</a>.
+      <p>
+	If you happen to know the TSN, you
+	can enter it directly.  Pressing Find after typing the TNS will
+	populate the Latin and English vernauclar names so that you may
+	verify your TSN was entered correctly.
+      </p>
+    </li>
+
+    <li> Call / sound type - This will default to the code provided by
+      the module but should be updated to specify an appropriate call
+      type or left blank to indicate that the detection is not related
+      to a specific call type.  In the case of a porpoise detector,
+      the likely call type would be "Clicks".
+      <strong>We should double check that no Call element is generated when this is blank.</strong>
+    </li>
+  </ul>
+
+  <p>
+  Once all species names and call/sound types have been identified, press the Okay button.
+  </p>
+
+
+  
+  <a name="TSNLookup"></a>
+  <h2> Searching for ITIS Taxonomic Serial Numbers (TSNs) </h2>
+
+  <p>
+    As noted above, pressing Find without typing a TSN will bring up a
+    search dialog:
+  </p>
+
+  <div>
+    <image src="./images/species_search.png" class=".center"/>
+  </div>
+  
+  <p>
+    The top of this dialog has a search box where one can enter either
+    a Latin name or the common name for a species.  The Tethys server
+    will search for all species that match the search-box contents.
+    For many species, there are common name entries in languages
+    other than English, and these are searched as well.
+  </p>
+  <p>
+    Once you press the search button, a list will appear with all
+    matches for your search term.  If there are too many, a scroll bar
+    will permit you to look through the list.  Select the entry that
+    you wish and press OK.  The TSN on the species dialog will be
+    populated along with the Latin name and common names from the ITIS
+    database.
+  </p>
+
+
+    <br></br>
+    <br></br>
+
+  <p class="prevLink">
+    <a href="detect_localize.html">Previous: Detections & Localizations</a>
+  </p>
+  <p class="nextLink">
+    <a href="tethys_overview.html">Returrn to overview</a>
+  </p>
+  
+</body>

src/tethys/TethysControl.java

@@ -491,9 +491,10 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 	public ServerStatus checkServer() {
 		ServerStatus serverState = dbxmlConnect.pingServer();
 		if (lastServerStatus == null || lastServerStatus.ok != serverState.ok) {
+			lastServerStatus = serverState; // set before sending notification!
 			sendStateUpdate(new TethysState(StateType.UPDATESERVER));
 		}
-		lastServerStatus = serverState;
+//		lastServerStatus = serverState;
 		return serverState;
 	}
 
@@ -699,5 +700,23 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 		return calibrationHandler;
 	}
 
+	/**
+	 * @return the lastServerStatus
+	 */
+	public ServerStatus getLastServerStatus() {
+		return lastServerStatus;
+	}
+	
+	/**
+	 * Quick way for any controls to see that the server is probably OK
+	 * without actually pinging it. 
+	 * @return true if last ping of server was OK
+	 */
+	public boolean isServerOk() {
+		if (lastServerStatus == null) {
+			return false;
+		}
+		return lastServerStatus.ok;
+	}
 
 }

src/tethys/calibration/CalibrationHandler.java

@@ -1,5 +1,6 @@
 package tethys.calibration;
 
+import java.lang.reflect.Field;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
@@ -45,9 +46,11 @@ import tethys.TethysTimeFuncs;
 import tethys.calibration.swing.CalibrationsExportWizard;
 import tethys.dbxml.DBXMLConnect;
 import tethys.dbxml.TethysException;
+import tethys.niluswraps.NilusChecker;
 import tethys.niluswraps.NilusSettingsWrapper;
 import tethys.niluswraps.NilusUnpacker;
 import tethys.pamdata.AutoTethysProvider;
+import tethys.reporter.TethysReporter;
 
 public class CalibrationHandler implements TethysStateObserver {
 
@@ -186,6 +189,7 @@ public class CalibrationHandler implements TethysStateObserver {
 		int nExport = 0;
 		boolean overwrite = false;
 		boolean exists;
+		TethysReporter.getTethysReporter().clear();
 		for (int i = 0; i < nPhone; i++) {
 //			String docName = getHydrophoneId(i);
 			NilusSettingsWrapper<Calibration> clonedWrap = wrappedSample.clone();
@@ -195,11 +199,24 @@ public class CalibrationHandler implements TethysStateObserver {
 				calDoc.setMetadataInfo(sampleCal.getMetadataInfo());				
 				calDoc.setProcess(sampleCal.getProcess());
 				calDoc.setQualityAssurance(sampleCal.getQualityAssurance());
-				calDoc.setResponsibleParty(sampleCal.getResponsibleParty());
+				if (NilusChecker.isEmpty(sampleCal.getResponsibleParty()) == false) {
+					calDoc.setResponsibleParty(sampleCal.getResponsibleParty());
+				}
 				calDoc.setTimeStamp(sampleCal.getTimeStamp());
 			}
+			// check the contact info in the metadata. 
+			// can't so because it's required. 
+//			MetadataInfo metaData = calDoc.getMetadataInfo();
+//			if (metaData != null) {
+//				if (NilusChecker.isEmpty(metaData.getContact())) {
+//					metaData.setContact(null);
+//				}
+//			}
 			
 			addParameterDetails(calDoc, i);
+			// run some checks of completeness of the data
+			NilusChecker.removeEmptyFields(calDoc);
+//			ArrayList<Field> emptyFields = NilusChecker.checkEmptyFields(calDoc);
 			
 			String calDocName = createDocumentName(calDoc, i);
 			exists = calDocumentExists(calDocName);
@@ -233,6 +250,7 @@ public class CalibrationHandler implements TethysStateObserver {
 			}
 		}
 		tethysControl.sendStateUpdate(new TethysState(TethysState.StateType.EXPORTRDATA, Collection.Calibrations));
+		TethysReporter.getTethysReporter().showReport(true);
 		return nExport;
 	}
 	
@@ -405,6 +423,10 @@ public class CalibrationHandler implements TethysStateObserver {
 		hz.add(Double.valueOf(0));
 		db.add(Double.valueOf(hSens+preampGain));
 		
+		if (NilusChecker.isEmpty(calibration.getResponsibleParty())) {
+			calibration.setResponsibleParty(null);
+		}
+		
 		MetadataInfo metaInf = calibration.getMetadataInfo();
 		if (metaInf == null) {
 			metaInf = new MetadataInfo();
@@ -417,6 +439,12 @@ public class CalibrationHandler implements TethysStateObserver {
 			contact = new ResponsibleParty();
 			metaInf.setContact(contact);
 		}
+		if (NilusChecker.isEmpty(metaInf.getContact())) {
+			metaInf.setContact(null);
+		}
+		if (NilusChecker.isEmpty(metaInf)) {
+			calibration.setMetadataInfo(null);
+		}
 		contact.setIndividualName("Unknown");
 		contact.setOrganizationName("unknown");
 		

src/tethys/calibration/swing/CalibrationProcessCard.java

@@ -4,6 +4,8 @@ import java.awt.BorderLayout;
 import java.awt.Dimension;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.JComboBox;
@@ -15,6 +17,7 @@ import javax.swing.JTextArea;
 import javax.swing.JTextField;
 import javax.swing.border.TitledBorder;
 
+import PamView.dialog.PamDialog;
 import PamView.dialog.PamGridBagContraints;
 import PamView.panel.WestAlignedPanel;
 import PamView.wizard.PamWizard;
@@ -23,9 +26,17 @@ import nilus.AlgorithmType.Parameters;
 import nilus.AlgorithmType.SupportSoftware;
 import nilus.Calibration;
 import nilus.Calibration.QualityAssurance;
+import nilus.Helper;
 import nilus.QualityValueBasic;
 import tethys.calibration.CalibrationHandler;
+import tethys.niluswraps.NilusChecker;
 
+/**
+ * Calibrations Process card attempts to fill in the 
+ * calibration data for the Quality Assurance and Process fields. 
+ * @author dg50
+ *
+ */
 public class CalibrationProcessCard extends CalibrationsCard {
 	
 	private JPanel processPanel;
@@ -123,9 +134,13 @@ public class CalibrationProcessCard extends CalibrationsCard {
 		}
 		process.setMethod((String) calMethod.getSelectedItem());
 		process.setVersion(version.getText());
-		process.setSoftware(software.getText());
+		String soft = warnNotNull(getPamWizard(), software, "Calibration Method");
+		if (soft == null) {
+			return false;
+		}
+		process.setSoftware(soft);
 		if (software.getText() == null) {
-			getPamWizard().showWarning("You must specify the calibratin method used");
+			getPamWizard().showWarning("You must specify the calibration method used");
 		}
 		
 		QualityAssurance qa = calibration.getQualityAssurance();
@@ -133,7 +148,11 @@ public class CalibrationProcessCard extends CalibrationsCard {
 			qa = new QualityAssurance();
 			calibration.setQualityAssurance(qa);
 		}
-		qa.setComment(qaComment.getText());
+		String t = warnNotNull(getPamWizard(), qaComment, "QA Comment");
+		if (t == null) {
+			return false;
+		}
+		qa.setComment(t);
 		qa.setQuality(QualityValueBasic.fromValue((String) qaQuality.getSelectedItem()));
 		
 		// need to add a few fixed things for this to work...
@@ -142,11 +161,27 @@ public class CalibrationProcessCard extends CalibrationsCard {
 		if (params == null) {
 			params = new Parameters();
 			process.setParameters(params);
+//			params.getAny().
 		}
+		try {
+			Helper.createRequiredElements(params);
+		} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		
+//		if (checkEmptyFields(qa) == false) {
+//			return false;
+//		}
+//		if (checkEmptyFields(process) == false) {
+////			return false;
+//		}
 		
 		return true;
 	}
 	
+
+
 	@Override
 	public void setParams(Calibration calibration) {
 		if (calibration == null) {

src/tethys/calibration/swing/CalibrationsCard.java

@@ -3,8 +3,9 @@ package tethys.calibration.swing;
 import PamView.wizard.PamWizard;
 import PamView.wizard.PamWizardCard;
 import nilus.Calibration;
+import tethys.swing.TethysWizardCard;
 
-abstract public class CalibrationsCard extends PamWizardCard<Calibration> {
+abstract public class CalibrationsCard extends TethysWizardCard<Calibration> {
 
 	public CalibrationsCard(PamWizard pamWizard, String title) {
 		super(pamWizard, title);

src/tethys/calibration/swing/CalibrationsContactCard.java

@@ -28,6 +28,7 @@ import nilus.MetadataInfo;
 import nilus.ResponsibleParty;
 import tethys.TethysTimeFuncs;
 import tethys.calibration.CalibrationHandler;
+import tethys.niluswraps.NilusChecker;
 import tethys.swing.export.ResponsiblePartyPanel;
 
 public class CalibrationsContactCard extends CalibrationsCard {
@@ -125,6 +126,11 @@ public class CalibrationsContactCard extends CalibrationsCard {
 		}
 		metaData.setContact(checkRPChildren(metaData.getContact()));
 		dataManager.getParams(metaData.getContact());
+		ResponsibleParty metaContact = metaData.getContact();
+		NilusChecker.removeEmptyFields(metaData);
+		if (metaData.getContact() == null) {
+			return PamDialog.showWarning(getPamWizard(), "Missing data", "The Data Manager fields must be completed");
+		}		
 		
 		metaData.setUpdateFrequency((String) updateInterval.getSelectedItem());
 		metaData.setDate(TethysTimeFuncs.xmlGregCalFromMillis(System.currentTimeMillis()));
@@ -136,6 +142,10 @@ public class CalibrationsContactCard extends CalibrationsCard {
 		long millis = date.getTime();
 		cardParams.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(millis));
 		
+		
+		checkEmptyFields(rp);
+		checkEmptyFields(metaData);
+		
 		return true;
 	}
 	

src/tethys/calibration/swing/CalibrationsMainPanel.java

@@ -13,6 +13,7 @@ import javax.swing.border.TitledBorder;
 
 import PamView.panel.PamPanel;
 import tethys.TethysControl;
+import tethys.TethysState;
 import tethys.calibration.CalibrationHandler;
 import tethys.swing.TethysGUIPanel;
 
@@ -63,4 +64,14 @@ public class CalibrationsMainPanel extends TethysGUIPanel {
 		return mainPanel;
 	}
 
+	@Override
+	public void updateState(TethysState tethysState) {
+		super.updateState(tethysState);
+		enableControls();
+	}
+
+	private void enableControls() {
+		exportButton.setEnabled(getTethysControl().isServerOk());
+	}
+
 }

src/tethys/dbxml/DBXMLConnect.java

@@ -22,7 +22,10 @@ import tethys.Collection;
 import tethys.TethysControl;
 import tethys.database.TethysActions;
 import tethys.database.TethysLogger;
+import tethys.niluswraps.NilusChecker;
 import tethys.output.TethysExportParams;
+import tethys.reporter.TethysReport;
+import tethys.reporter.TethysReporter;
 
 /**
  * Class containing functions for managing the database connection. Opening, closing,
@@ -144,6 +147,9 @@ public class DBXMLConnect {
 	 */
 	public boolean postAndLog(Object nilusObject, String documentName) throws TethysException 
 	{	
+		boolean ok = NilusChecker.warnEmptyFields(tethysControl.getGuiFrame(), nilusObject);
+		
+		
 		TethysException e = null;
 		boolean success = false;
 		try {
@@ -207,6 +213,8 @@ public class DBXMLConnect {
 		 */
 		boolean error = importReturn.contains("<Error");
 		boolean success = importReturn.contains("<Success>");
+		String name = tempFile.getName();
+		TethysReporter.getTethysReporter().addReport(new TethysReport(success, collection, name, name));
 //		error = !success; might be a better options. 
 		if (error) {
 			throw new TethysException("Error posting to Tethys", importReturn);

src/tethys/deployment/DeploymentHandler.java

@@ -45,6 +45,9 @@ import dataMap.OfflineDataMapPoint;
 import generalDatabase.DBControlUnit;
 import metadata.MetaDataContol;
 import metadata.PamguardMetaData;
+import nilus.AcousticDataQAType;
+import nilus.AcousticDataQAType.Quality;
+import nilus.AcousticDataQAType.Quality.FrequencyRange;
 import nilus.Audio;
 import nilus.ChannelInfo;
 import nilus.ChannelInfo.DutyCycle;
@@ -84,6 +87,7 @@ import tethys.deployment.swing.RecordingGapDialog;
 import tethys.niluswraps.PDeployment;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.AutoTethysProvider;
+import tethys.reporter.TethysReporter;
 import tethys.swing.DeploymentTableObserver;
 
 /**
@@ -387,12 +391,14 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
 	 * @param selectedDeployments
 	 */
 	public void exportDeployments(ArrayList<RecordingPeriod> selectedDeployments) {
+		TethysReporter.getTethysReporter().clear();
 		if (deploymentExportOptions.separateDeployments) {
 			exportSeparateDeployments(selectedDeployments);
 		}
 		else {
 			exportOneDeploymnet(selectedDeployments);
 		}
+		TethysReporter.getTethysReporter().showReport(tethysControl.getGuiFrame(), true);
 	}
 	
 	/**
@@ -400,6 +406,14 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
 	 */
 	private void exportOneDeploymnet(ArrayList<RecordingPeriod> selectedDeployments) {
 		// do the lot, whatever ...
+		Float sampleRate = null;
+		AcquisitionControl daq = (AcquisitionControl) PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
+		if (daq != null) {
+			DaqSystem system = daq.findDaqSystem(null);
+			AcquisitionParameters daqParams = daq.acquisitionParameters;
+			sampleRate = daqParams.sampleRate;
+		}
+		
 		selectedDeployments = getDeploymentOverview().getRecordingPeriods();
 		int freeId = getTethysControl().getDeploymentHandler().getFirstFreeDeploymentId();
 		RecordingPeriod onePeriod = new RecordingPeriod(selectedDeployments.get(0).getRecordStart(), 
@@ -412,11 +426,37 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
 		deployment.setCruise(globalMeta.getCruise());
 		deployment.setSite(globalMeta.getSite());
 		if (selectedDeployments.size() > 1) {
-			// now need to remove the 
+//			// now need to remove the sampling details - don't though, add invalid periods instead. 
-			SamplingDetails samplingDetails = deployment.getSamplingDetails();
+//			SamplingDetails samplingDetails = deployment.getSamplingDetails();
-			samplingDetails.getChannel().clear();
+//			samplingDetails.getChannel().clear();
-			for (int i = 0; i < selectedDeployments.size(); i++) {
+//			for (int i = 0; i < selectedDeployments.size(); i++) {
-				addSamplingDetails(deployment, selectedDeployments.get(i));
+//				addSamplingDetails(deployment, selectedDeployments.get(i));
+//			}
+			/*
+			 * Instead, we're putting invalid periods into the QA section. 
+			 */
+			AcousticDataQAType qa = deployment.getQualityAssurance();
+			if (qa == null) {
+				deployment.setQualityAssurance(qa = new AcousticDataQAType());
+			}
+			List<Quality> qualityList = qa.getQuality();
+			for (int i = 1; i < selectedDeployments.size(); i++) {
+				long end = selectedDeployments.get(i-1).getRecordStop();
+				long start = selectedDeployments.get(i).getRecordStart();
+				Quality q = new Quality();
+				q.setStart(TethysTimeFuncs.xmlGregCalFromMillis(end));
+				q.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(start));
+				q.setCategory("unusable");
+				if (sampleRate != null) {
+					FrequencyRange f = q.getFrequencyRange();
+					if (f == null) {
+						q.setFrequencyRange(f = new FrequencyRange());
+					}
+					f.setLowHz(0);
+					f.setHighHz(sampleRate/2);
+				}
+				q.setComment("No data (probably off or out of water)");
+				qualityList.add(q);
 			}
 		}
 		DBXMLConnect dbxmlConnect = getTethysControl().getDbxmlConnect();

src/tethys/deployment/swing/DeploymentDataCard.java

@@ -39,11 +39,12 @@ public class DeploymentDataCard extends PamWizardCard {
 		this.tethysControl = tethysControl;
 		deploymentHandler = tethysControl.getDeploymentHandler();
 		ButtonGroup bg = new ButtonGroup();
-		exportOne = new JRadioButton("Export a single detection document for all data");
+		exportOne = new JRadioButton("Export a single deployment document for all data");
-		exportMany = new JRadioButton("Export separate documents for each ad-hoc recording period");
+		exportMany = new JRadioButton("Export separate deployment documents for each ad-hoc recording period");
 		bg.add(exportOne);
 		bg.add(exportMany);
 		
+		
 		JPanel optsPanel = new JPanel(new GridBagLayout());
 		optsPanel.setBorder(new TitledBorder("Number of documents"));
 		GridBagConstraints c = new PamGridBagContraints();
@@ -95,6 +96,15 @@ public class DeploymentDataCard extends PamWizardCard {
 	}
 
 	public void setParams(DeploymentExportOpts exportOptions, Deployment deployment) {
+
+		/* 
+		 * temp code to only allow export of multiple documents. 
+		 */
+//		exportOptions.separateDeployments = true;
+//		exportOne.setEnabled(false);
+//		exportOne.setToolTipText("Feature not yet enabled");
+		
+		
 		exportOne.setSelected(exportOptions.separateDeployments == false);
 		exportMany.setSelected(exportOptions.separateDeployments == true);
 		setParams(deployment);

src/tethys/detection/DetectionsHandler.java

@@ -43,6 +43,7 @@ import tethys.output.DatablockSynchInfo;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.TethysDataProvider;
+import tethys.reporter.TethysReporter;
 import tethys.species.DataBlockSpeciesManager;
 import tethys.swing.export.DetectionsExportWizard;
 
@@ -587,6 +588,7 @@ public class DetectionsHandler {
 			this.dataBlock = dataBlock;
 			this.exportParams = exportParams;
 			this.exportObserver = exportObserver;
+			TethysReporter.getTethysReporter().clear();
 		}
 
 		public void publish(DetectionExportProgress exportProgress) {
@@ -617,6 +619,7 @@ public class DetectionsHandler {
 			DetectionExportProgress prog = new DetectionExportProgress(null, null, 0, 0, 0, 0, DetectionExportProgress.STATE_COMPLETE);
 			tethysControl.exportedDetections(dataBlock);
 			exportObserver.update(prog);
+			TethysReporter.getTethysReporter().showReport(tethysControl.getGuiFrame(), true);
 		}
 
 		@Override

src/tethys/niluswraps/NilusChecker.java

@@ -0,0 +1,417 @@
+package tethys.niluswraps;
+
+import java.awt.Window;
+import java.lang.annotation.Annotation;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.renjin.methods.Methods;
+
+import PamView.dialog.warn.WarnOnce;
+import nilus.Calibration;
+import nilus.Calibration.QualityAssurance;
+import nilus.Helper;
+import nilus.ResponsibleParty;
+
+/**
+ * A few static checks of some nilus classes to see if it's 
+ * worth writing them or not. 
+ * @author dg50
+ *
+ */
+public class NilusChecker {
+	
+	public static void main(String args[]) {
+		Calibration cal = new Calibration();
+		try {
+			Helper.createRequiredElements(cal);
+		} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		
+		QualityAssurance qa;
+		cal.setQualityAssurance(qa = new QualityAssurance());
+		qa.setComment("Nothing to comment on ");
+		
+		int removed = removeEmptyFields(cal);
+		System.out.printf("%d fields removed from object %s\n", removed, cal);
+
+		
+		ArrayList<Field> missing = checkEmptyFields(cal);
+		for (Field field : missing) {
+			System.out.printf("Field %s is required but empty in %s\n", field.getName(), field.getDeclaringClass().toString());
+		}
+	}
+	
+	public static boolean warnEmptyFields(Window owner, Object nilusObject) {
+		ArrayList<Field> emptyFields = findEmptyFields(nilusObject, true);
+		if (emptyFields == null || emptyFields.size() == 0) {
+			return true;
+		}
+		String msg = String.format("<html>One or more fields in the nilus object %s are required but empty:<br>", nilusObject.getClass().getName());
+		for (Field f : emptyFields) {
+			msg += String.format("<br>Field %s in object %s", f.getName(), f.getDeclaringClass().getName());
+		}
+		msg += "<br><br>It is likely that this document will fail to write to the Tethys database.</html>";
+		String tit = "Incomplete Tethys data";
+		WarnOnce.showWarning(owner, tit, msg, WarnOnce.WARNING_MESSAGE);
+		return false;
+	}
+	
+	/**
+	 * Find empty fields
+	 * @param nilusObject object to search
+	 * @param onlyRequired only list required fields. 
+	 * @return list of empty, and optionally also required, fields. 
+	 */
+	public static ArrayList<Field> findEmptyFields(Object nilusObject, boolean onlyRequired) {
+		return findEmptyFields(nilusObject, new ArrayList<Field>(), onlyRequired);
+	}
+	
+	private static ArrayList<Field> findEmptyFields(Object nilusObject, ArrayList<Field> found, boolean onlyRequired) {
+		if (nilusObject == null) {
+			return found;
+		}
+		int removed = 0;
+
+		Class<? extends Object> nilusClass = nilusObject.getClass();
+		if (nilusClass.getCanonicalName().contains("java.lang")) {
+			return found;
+		}
+		Method[] methods = nilusClass.getDeclaredMethods();
+		Field[] fields = nilusClass.getDeclaredFields();
+		for (int i = 0; i < fields.length; i++) {
+			Method getter = findGetter(fields[i], methods);
+			if (getter == null) {
+//				System.out.printf("Unable to find getter for field %s in %s\n", fields[i].getName(), nilusClass.getName());
+				continue;
+			}
+			boolean required = isRequired(fields[i]);
+//			System.out.printf("Field %30s is %s required\n", fields[i].getName(), required ? "   " : "NOT");
+			Object gotObj = null;
+			try {
+				gotObj = getter.invoke(nilusObject, new Object[0]);
+			} catch (IllegalAccessException | InvocationTargetException e) {
+//				System.out.printf("Unable to invoce getter %s on %s\n", getter.getName(), nilusObject);
+				continue;
+			}
+			boolean empty = isEmpty(gotObj);
+			if (empty) {
+				if (required || !onlyRequired) {
+					found.add(fields[i]);
+				}
+			}
+			else {
+				found = findEmptyFields(gotObj, found, onlyRequired);
+			}
+		}
+		return found;		
+	}
+	
+	/**
+	 * Remove empty fields from a nilus object. <br>
+	 * An empty field is a field that is null, or has a String that is empty, or 
+	 * only contains elements which are all themselves empty. i.e. an object that references
+	 * empty objects will be considered empty.
+	 * @param nilusObject
+	 * @return number of empty fields removed. 
+	 */
+	public static int removeEmptyFields(Object nilusObject) {
+		if (nilusObject == null) {
+			return 0;
+		}
+		int removed = 0;
+
+		Class<? extends Object> nilusClass = nilusObject.getClass();
+		if (nilusClass.getCanonicalName().contains("java.lang")) {
+			return 0;
+		}
+		Method[] methods = nilusClass.getDeclaredMethods();
+		Field[] fields = nilusClass.getDeclaredFields();
+		for (int i = 0; i < fields.length; i++) {
+			Method getter = findGetter(fields[i], methods);
+			Method setter = findSetter(fields[i], methods);
+			if (getter == null) {
+//				System.out.printf("Unable to find getter for field %s in %s\n", fields[i].getName(), nilusClass.getName());
+				continue;
+			}
+			if (setter == null) {
+//				System.out.printf("Unable to find setter for field %s in %s\n", fields[i].getName(), nilusClass.getName());
+				continue;
+			}
+			boolean required = isRequired(fields[i]);
+//			System.out.printf("Field %30s is %s required\n", fields[i].getName(), required ? "   " : "NOT");
+			Object gotObj = null;
+			try {
+				gotObj = getter.invoke(nilusObject, null);
+			} catch (IllegalAccessException | InvocationTargetException e) {
+//				System.out.printf("Unable to invoce getter %s on %s\n", getter.getName(), nilusObject);
+				continue;
+			}
+			boolean empty = isEmpty(gotObj);
+			if (empty && gotObj != null && canRemove(fields[i])) {
+				try {
+//					System.out.printf("Removing empty field %s in object %s\n", fields[i].getName(), nilusObject);
+//					Object args = new Object[1];
+					setter.invoke(nilusObject, new Object[1]);
+					removed++;
+				} catch (IllegalAccessException | InvocationTargetException e) {
+					System.out.printf("Unable to invoce setter %s on %s\n", getter.getName(), nilusObject);
+					continue;
+				}
+			}
+			else {
+				removed += removeEmptyFields(gotObj);
+			}
+		}
+		return removed;		
+	}
+	
+	/**
+	 * Fields that can be removed. 
+	 * @param field
+	 * @return
+	 */
+	private static boolean canRemove(Field field) {
+		if (field == null) {
+			return true;
+		}
+		Class fClass = field.getType();
+		if (fClass == String.class) {
+			return true;
+		}
+		if (List.class.isAssignableFrom(fClass)) {
+			return false;
+		}
+		if (fClass.isPrimitive()) {
+			return false;
+		}
+		String className = fClass.getCanonicalName();
+		if (className.contains("nilus.")) {
+			return true;
+		}
+		return false;
+	}
+
+	/**
+	 * Check an object for empty and required fields. 
+	 * @param nilusObject
+	 * @return a list of required empty fields in the nilusObjec and any objects references by that object. 
+	 */
+	public static ArrayList<Field> checkEmptyFields(Object nilusObject) {
+		return checkEmptyFields(nilusObject, new ArrayList<Field>());
+	}
+	
+	/**
+	 * Check an object for empty and required fields. 
+	 * @param nilusObject
+	 * @param emptyFields
+	 * @return
+	 */
+	private static ArrayList<Field> checkEmptyFields(Object nilusObject, ArrayList<Field> emptyFields) {
+		if (nilusObject == null) {
+			return emptyFields;
+		}
+
+		Class<? extends Object> nilusClass = nilusObject.getClass();
+		if (nilusClass.isPrimitive()) {
+			return emptyFields;
+		}
+		if (nilusClass.getCanonicalName().contains("java.lang")) {
+			return emptyFields;
+		}
+		Method[] methods = nilusClass.getDeclaredMethods();
+		Field[] fields = nilusClass.getDeclaredFields();
+		for (int i = 0; i < fields.length; i++) {
+			Method getter = findGetter(fields[i], methods);
+			Method setter = findSetter(fields[i], methods);
+			if (getter == null) {
+//				System.out.printf("Unable to find getter for field %s in %s\n", fields[i].getName(), nilusClass.getName());
+				continue;
+			}
+			if (setter == null) {
+//				System.out.printf("Unable to find setter for field %s in %s\n", fields[i].getName(), nilusClass.getName());
+				continue;
+			}
+			boolean required = isRequired(fields[i]);
+//			System.out.printf("Field %30s is %s required\n", fields[i].getName(), required ? "   " : "NOT");
+			Object gotObj = null;
+			try {
+				gotObj = getter.invoke(nilusObject, null);
+			} catch (IllegalAccessException | InvocationTargetException e) {
+//				System.out.printf("Unable to invoce getter %s on %s\n", getter.getName(), nilusObject);
+				continue;
+			}
+			boolean empty = isEmpty(gotObj);
+			if (empty) {
+				if (required) {
+					emptyFields.add(fields[i]);
+				}
+			}
+			else {
+				checkEmptyFields(gotObj, emptyFields);
+			}
+//			if (required == true && empty == true) {
+//				System.out.printf("Field %s is required but empty in %s\n", fields[i].getName(), nilusObject.toString());
+//			}
+		}
+		return emptyFields;
+	}
+	
+	/**
+	 * See if a field has an annotation that indicates it's required. 
+	 * @param field field
+	 * @return required
+	 */
+	private static boolean isRequired(Field field) {
+		Annotation[] annots = field.getAnnotations();
+		for (int a = 0; a < annots.length; a++) {
+//			System.out.printf("Field %s has annotation %d %s\n", fields[i].getName(), a, annots[a].toString());
+			String str = annots[a].toString();
+			if (str.contains("required=true")) {
+				return true;
+			}
+		}
+		return false;
+	}
+	
+	/**
+	 * Find a getter for a field. This will either be get... or is...
+	 * @param field
+	 * @param methods list of methods to search
+	 * @return found method or null
+	 */
+	private static Method findGetter(Field field, Method[] methods) {
+		String name = field.getName();
+		String poss = "get"+name;
+		Method found = findMethod(poss, methods);
+		if (found != null) {
+			return found;
+		}
+		poss = "is" + name;
+		return findMethod(poss, methods);
+	}
+	
+	/**
+	 * Fine a setter for a field. This will always be set...
+	 * @param field field
+	 * @param methods list of methods to search
+	 * @return found method or null
+	 */
+	private static Method findSetter(Field field, Method[] methods) {
+		String name = field.getName();
+		String poss = "set" + name;
+		return findMethod(poss, methods);
+	}
+	
+	/**
+	 * Find a method based on it's name (case insensitive). 
+	 * @param name name of method
+	 * @param methods list of methods to search
+	 * @return found method or null
+	 */
+	private static Method findMethod(String name, Method[] methods) {
+		for (int i = 0; i < methods.length; i++) {
+			if (methods[i].getName().equalsIgnoreCase(name)) {
+				return methods[i];
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * Test if an object is empty. <br>
+	 * An object is considered empty if any of the following criteria are met:
+	 * <ul>
+	 * <li>The object is null</li>
+	 * <li>The object is a zero length string</li>
+	 * <li>The object is not null, but all of it's fields satisfy this same criteria of being empty</li>
+	 * <li>The object is a list which has no elements</li>
+	 * </ul>
+	 * Primitive types are never empty. 
+	 * @param nilusObject
+	 * @return true if it's empty
+	 */
+	public static boolean isEmpty(Object nilusObject) {
+		if (nilusObject == null) {
+			return true;
+		}
+		if (nilusObject instanceof String) {
+			String str = (String) nilusObject;
+			return (str.length() == 0);
+		}
+		if (nilusObject instanceof List) {
+			return isEmptyList((List) nilusObject);
+		}
+		if (nilusObject.getClass().isPrimitive()) {
+			return false;
+		}
+		boolean empty = true;
+		// and check all getters 
+		Class<? extends Object> nilusClass = nilusObject.getClass();
+		Method[] methods = nilusClass.getDeclaredMethods();
+		// searching for getters. 
+		int nGet = 0;
+		for (int i = 0; i < methods.length; i++) {
+			Method method = methods[i];
+			if (method.getName().startsWith("get") && method.getParameterCount() == 0) {
+				nGet ++;
+				try {
+					Object got = method.invoke(nilusObject, null);
+					if (got != null) {
+						if (got instanceof String) {
+							if (isEmptyString((String) got) == false) {
+								empty = false;
+							}
+						}
+						else if (got instanceof List<?>) {
+							if (isEmptyList((List) got) == false) {
+								empty = false;
+							}
+						}
+						else if (isEmpty(got) == false) {// it's some other class type, so recurecively ask back here.
+							empty = false;
+						}
+						
+					}
+				} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+					return false; // better save than sorry if we don't understand. 
+				}
+			}
+		}
+		if (nGet == 0) {
+			// there weren't any understandable getters, so assume not empty. May be some other primitive type. 
+			empty = false;
+		}
+			
+		return empty;
+	}
+	
+	/**
+	 * A list is considered empty if it has no elements
+	 * @param list
+	 * @return true if empty
+	 */
+	private static boolean isEmptyList(List list) {
+		if (list == null) {
+			return true;
+		}
+		return list.size() == 0;
+	}
+
+	/**
+	 * A String is empty if it is null or of zero length
+	 * @param string string
+	 * @return true if empty
+	 */
+	public static boolean isEmptyString(String string) {
+		if (string == null || string.length() == 0) {
+			return true;
+		}
+		return false;
+	}
+}

src/tethys/reporter/TethysReport.java

@@ -0,0 +1,56 @@
+package tethys.reporter;
+
+import tethys.Collection;
+
+public class TethysReport {
+
+	private boolean success;
+	
+	private Collection collection;
+	 
+	private String docName;
+	
+	private String docId;
+
+	/**
+	 * @param success
+	 * @param collection
+	 * @param docName
+	 * @param docId
+	 */
+	public TethysReport(boolean success, Collection collection, String docName, String docId) {
+		this.success = success;
+		this.collection = collection;
+		this.docName = docName;
+		this.docId = docId;
+	}
+
+	/**
+	 * @return the success
+	 */
+	public boolean isSuccess() {
+		return success;
+	}
+
+	/**
+	 * @return the collection
+	 */
+	public Collection getCollection() {
+		return collection;
+	}
+
+	/**
+	 * @return the docName
+	 */
+	public String getDocName() {
+		return docName;
+	}
+
+	/**
+	 * @return the docId
+	 */
+	public String getDocId() {
+		return docId;
+	}
+	
+}

src/tethys/reporter/TethysReporter.java

@@ -0,0 +1,118 @@
+package tethys.reporter;
+
+import java.awt.Window;
+import java.util.ArrayList;
+
+import PamController.PamController;
+import PamView.dialog.warn.WarnOnce;
+
+/**
+ * Set of functions to provide mesage reports on Tethys output. This 
+ * will work with the existing WarnOnce type pop-up, the primary purpose
+ * of the functions here being to collate information, possibly from 
+ * several document writes, before issuing an overall report. 
+ * @author dg50
+ *
+ */
+public class TethysReporter {
+
+	private static TethysReporter singleInstance;
+	
+	private ArrayList<TethysReport> tethysReports;
+
+	private TethysReporter() {
+		tethysReports = new ArrayList<TethysReport>();
+	}
+	
+	/**
+	 * Get the reporter. 
+	 * @return
+	 */
+	public static final TethysReporter getTethysReporter() {
+		if (singleInstance == null) {
+			singleInstance = new TethysReporter();
+		}
+		return singleInstance;
+	}
+	
+	/**
+	 * Clear all reports
+	 */
+	synchronized public void clear() {
+		tethysReports.clear();
+	}
+	
+	/**
+	 * Add a report after attempting to write a document
+	 * @param report
+	 */
+	synchronized public void addReport(TethysReport report) {
+		tethysReports.add(report);
+	}
+	
+	/**
+	 * Get the current number of reports
+	 * @return number of reports
+	 */
+	synchronized public int getSize() {
+		return tethysReports.size();
+	}
+	
+	/**
+	 * Get a summary string of all reported writes using html to separate each ont a separat eline
+	 * @return
+	 */
+	synchronized public String getReportString() {
+		if (tethysReports.size() == 0) {
+			return "No reports";
+		}
+		String str = "<html>";
+		for (int i = 0; i < tethysReports.size(); i++) {
+			TethysReport aReport = tethysReports.get(i);
+			String res = aReport.isSuccess() ? "Success" : "Failure";
+			if (i > 0) {
+				str += "<br>";
+			}
+		    str += String.format("%s writing %s document %s to Tethys", res, aReport.getCollection().collectionName(), aReport.getDocName());	
+		}
+		
+		
+		str += "</html>";
+		return str;
+	}
+	
+	/**
+	 * Get a count of failed document writes
+	 * @return failure count
+	 */
+	public int countFails() {
+		int fails = 0;
+		for (TethysReport aReport : tethysReports) {
+			if (aReport.isSuccess() == false) {
+				fails++;
+			}
+		}
+		return fails;
+	}
+
+	/**
+	 * Show a report in a popup window
+	 * @param clear clear the list of reports afterwards
+	 */
+	public void showReport(boolean clear) {
+		showReport(PamController.getMainFrame(), clear);
+	}
+	
+	/**
+	 * Show a report on a popup window
+	 * @param window parent frame
+	 * @param clear clear the list of reports afterwards
+	 */
+	public void showReport(Window window, boolean clear) {
+		boolean probs = countFails() > 0;
+		WarnOnce.showNamedWarning("TethysReporter", window, "Tethys Document Writer", getReportString(), WarnOnce.WARNING_MESSAGE);
+		if (clear) {
+			clear();
+		}
+	}
+}

src/tethys/species/DataBlockSpeciesCodes.java

@@ -21,7 +21,7 @@ public class DataBlockSpeciesCodes {
 	/**
 	 * Probably only to be used when there are no defined names, but helpful if it's set. 
 	 */
-	private int itisDefault = ITISTypes.UNKNOWN;
+	private int itisDefault = ITISTypes.OTHER;
 	
 	/**
 	 * A default sound type, which can be used for all 'species', but can get 

src/tethys/species/ITISFunctions.java

@@ -1,14 +1,23 @@
 package tethys.species;
 
+import java.io.StringReader;
+import java.util.ArrayList;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
 
 import PamController.settings.output.xml.PAMGuardXMLPreview;
 import PamController.settings.output.xml.PamguardXMLWriter;
+import dbxml.Queries;
 import tethys.TethysControl;
 import tethys.dbxml.DBQueryResult;
+import tethys.dbxml.DBXMLConnect;
 import tethys.dbxml.DBXMLQueries;
 import tethys.dbxml.TethysQueryException;
 
@@ -81,4 +90,83 @@ public class ITISFunctions {
 		
 		return new TethysITISResult(itisCode, taxunit, latin, vernacular);
 	}
+	
+	public ArrayList<SpeciesMapItem> searchSpecies(String searchTerm) {
+		ArrayList<SpeciesMapItem> items = new ArrayList<SpeciesMapItem>();		
+		String xQ = "let $target := \"thespeciessearchterm\" \r\n"
+				+ "return\r\n"
+				+ "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
+				+ "\r\n"
+				+ "  for $ranks0 in collection(\"ITIS_ranks\")/ranks/rank[\r\n"
+				+ "          dbxml:contains(completename, $target) or \r\n"
+				+ "                 vernacular[dbxml:contains(name,$target)]]\r\n"
+				+ "return\r\n"
+				+ "  <Record> {\r\n"
+				+ "    $ranks0/tsn,\r\n"
+				+ "            $ranks0/completename,\r\n"
+				+ "            <vernacular>\r\n"
+				+ "              {string-join($ranks0/vernacular/name, \", \")}\r\n"
+				+ "            </vernacular>\r\n"
+				+ "  } </Record>\r\n"
+				+ "} </Result>\r\n"
+				+ "";
+		xQ = xQ.replace("thespeciessearchterm", searchTerm);
+		DBXMLConnect dbXMLConnect = tethysControl.getDbxmlConnect();
+		DBXMLQueries dbxmlQueries = tethysControl.getDbxmlQueries();
+		Queries queries = dbXMLConnect.getTethysQueries();
+
+		String queryResult = null;
+		try {
+			 queryResult = queries.QueryTethys(xQ);
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+//			e.printStackTrace();
+			return items;
+		}
+		
+
+		DocumentBuilder builder = null;
+		Document doc = null;
+		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+		try {
+			//Create DocumentBuilder with default configuration
+			builder = factory.newDocumentBuilder();
+
+			//Parse the content to Document object
+			doc = builder.parse(new InputSource(new StringReader(queryResult)));
+		} catch (Exception e) {
+//			e.printStackTrace();
+//			System.out.println(queryResult);
+			return items;
+		}
+		// print for now, then comment this out.. 
+//		PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
+//		String fDoc = pamXMLWriter.getAsString(doc, true);
+//		System.out.println(fDoc);
+		// now unpack the xml document. 
+		NodeList els = doc.getElementsByTagName("Record");
+		int n = els.getLength();
+		for (int i = 0; i < n; i++) {
+			Node aNode = els.item(i);
+			if (aNode instanceof Element) {
+				Element anEl = (Element) aNode;
+				String tsn = dbxmlQueries.getElementData(anEl, "tsn");
+				int nTSN = 0;
+				try {
+					nTSN = Integer.valueOf(tsn);
+				}
+				catch (NumberFormatException ex) {
+					System.out.println("Invalid TSN read from Tethys: " + tsn);
+					continue;
+				}
+				
+				String completeName = dbxmlQueries.getElementData(anEl, "completename");
+				String vernacular = dbxmlQueries.getElementData(anEl, "vernacular");
+				SpeciesMapItem mapItem = new SpeciesMapItem(nTSN, "", "", completeName, vernacular);
+				items.add(mapItem);
+			}
+			
+		}
+		return items;
+	}
 }

src/tethys/species/ITISTypes.java

@@ -7,12 +7,12 @@ package tethys.species;
  */
 public class ITISTypes {
 
-	public static final int UNKNOWN = 0;
+	public static final int OTHER = 0;
 	public static final int ANTHROPOGENIC = 1;
 	
 	public static final String getName(int code) {
 		switch (code) {
-		case UNKNOWN:
+		case OTHER:
 			return "Unknown";
 		case ANTHROPOGENIC:
 			return "Anthropogenic";

src/tethys/species/SpeciesTest.java

@@ -21,11 +21,11 @@ public class SpeciesTest {
 	public static void main(String[] args) {
 		
 		SpeciesTest st = new SpeciesTest();
-		st.runJson();
+//		st.runJson();
 		
 //		int spermWhale = 180488;
 //		st.getCodeInfo(spermWhale);
-//		st.runXQuery();
+		st.runXQuery();
 
 	}
 	private  void getCodeInfo(int itisCode) {
@@ -86,14 +86,31 @@ public class SpeciesTest {
 //				+ "    }</Deployment>\r\n"
 //				+ "} </Result>";
 
-		String xQ = "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
+//		String xQ = "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
-				+ "  for $rank0 in collection(\"ITIS_ranks\")/rank[tsn = \"180488\"]\r\n"
+//				+ "  for $rank0 in collection(\"ITIS_ranks\")/rank[tsn = \"180488\"]\r\n"
-				+ "  return\r\n"
+//				+ "  return\r\n"
-				+ "    <rank>{\r\n"
+//				+ "    <rank>{\r\n"
-				+ "      $rank0/completename\r\n"
+//				+ "      $rank0/completename\r\n"
-				+ "    }</rank>\r\n"
+//				+ "    }</rank>\r\n"
-				+ "} </Result>";
+//				+ "} </Result>";
-		
+		String xQ = "let $target := \"physeter\" \r\n"
+				+ "return\r\n"
+				+ "<Result xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"> {\r\n"
+				+ "\r\n"
+				+ "  for $ranks0 in collection(\"ITIS_ranks\")/ranks/rank[\r\n"
+				+ "          dbxml:contains(completename, $target) or \r\n"
+				+ "                 vernacular[dbxml:contains(name,$target)]]\r\n"
+				+ "return\r\n"
+				+ "  <Record> {\r\n"
+				+ "    $ranks0/tsn,\r\n"
+				+ "            $ranks0/completename,\r\n"
+				+ "            <vernacular>\r\n"
+				+ "              {string-join($ranks0/vernacular/name, \", \")}\r\n"
+				+ "            </vernacular>\r\n"
+				+ "  } </Record>\r\n"
+				+ "} </Result>\r\n"
+				+ "";
+		System.out.println(xQ);
 		
 		JerseyClient jerseyClient = new JerseyClient(uri);
 		Queries queries = new Queries(jerseyClient);

src/tethys/species/swing/DataBlockSpeciesDialog.java

@@ -7,12 +7,14 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
 import javax.swing.JButton;
+import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.border.TitledBorder;
 
 import PamController.PamController;
 import PamView.PamGui;
 import PamView.dialog.PamDialog;
+import PamView.panel.PamNorthPanel;
 import PamguardMVC.PamDataBlock;
 import tethys.species.SpeciesMapManager;
 
@@ -38,7 +40,16 @@ public class DataBlockSpeciesDialog extends PamDialog {
 		});
 		JPanel nPanel = new JPanel(new BorderLayout());
 		nPanel.setBorder(new TitledBorder("Code management"));
-		nPanel.add(BorderLayout.EAST, itisButton);
+		nPanel.add(BorderLayout.EAST, new PamNorthPanel(itisButton));
+		String otherMsg = 
+				"<html>Specify an ITIS taxonomic serial number (coding)."
+				+ "<br>Press the Find button to look up TSNs by Latin or common name.  "
+				+ "<br>Anthropogenic signals should be coded as Homo sapiens (180092). "
+				+ "<br>Noise Measurements and geophonic sounds should be coded as " 
+				+ "\"Other Phenomena\" (-10).  "
+				+ "<br>When known, a call or sound type should "
+				+ "be specified (see help for more information).</html>";
+		nPanel.add(BorderLayout.CENTER, new JLabel(otherMsg , JLabel.LEFT));
 //		JPanel nwBit = new JPanel(new FlowLayout());
 //		JButton exportButton = new JButton("Export");
 //		exportButton.addActionListener(SpeciesMapManager.getInstance().getExportAction(parentFrame));
@@ -52,6 +63,7 @@ public class DataBlockSpeciesDialog extends PamDialog {
 		mainPanel.add(BorderLayout.NORTH, nPanel);
 		setDialogComponent(mainPanel);
 		setResizable(true);
+		setHelpPoint("utilities.tethys.docs.tethys_speciescodes");
 	}
 	
 	protected void gotoITIS() {

src/tethys/species/swing/SpeciesSearchDialog.java

@@ -0,0 +1,282 @@
+package tethys.species.swing;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
+import javax.swing.SwingWorker;
+import javax.swing.border.TitledBorder;
+import javax.swing.table.AbstractTableModel;
+
+import PamUtils.worker.PamWorkDialog;
+import PamUtils.worker.PamWorkProgressMessage;
+import PamView.dialog.PamDialog;
+import PamView.dialog.PamGridBagContraints;
+import PamView.dialog.warn.WarnOnce;
+import PamView.tables.SwingTableColumnWidths;
+import PamView.tables.TableColumnWidthData;
+import tethys.TethysControl;
+import tethys.species.ITISFunctions;
+import tethys.species.SpeciesMapItem;
+
+public class SpeciesSearchDialog extends PamDialog {
+
+	private static final long serialVersionUID = 1L;
+
+	private TethysControl tethysControl;
+	
+	private SpeciesMapItem selectedItem;
+
+	private static SpeciesSearchDialog singleInstance;
+	
+	private JTextField searchText;
+	
+	private JButton searchButton;
+	
+	private JTable resultTable;
+
+	private ArrayList<SpeciesMapItem> speciesMapItems;
+
+	private DataModel tableModel;
+	
+	private volatile PamWorkDialog workDialog;
+	
+	private Object synch = new Object();
+		
+
+	private SpeciesSearchDialog(Window parentFrame, TethysControl tethysControl) {
+		super(parentFrame, "Species search", false);
+		this.tethysControl = tethysControl;
+		JPanel mainPanel = new JPanel(new BorderLayout());
+		mainPanel.setBorder(new TitledBorder("Search Term"));
+		JPanel topPanel = new JPanel(new GridBagLayout());
+		GridBagConstraints c = new PamGridBagContraints();
+		topPanel.add(new JLabel("Latin or common name ", JLabel.RIGHT), c);
+		c.gridx++;
+		topPanel.add(searchText = new JTextField(12), c);
+		c.gridx++;
+		topPanel.add(searchButton = new JButton("search"), c);
+		mainPanel.add(BorderLayout.NORTH, topPanel);
+		searchButton.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				searchTethys();
+			}
+
+		});
+		searchText.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				searchTethys();
+			}
+		});
+		
+		tableModel = new DataModel();
+		resultTable = new JTable(tableModel);
+		JPanel centPanel = new JPanel(new BorderLayout());
+		centPanel.add(BorderLayout.NORTH, new JLabel("Possible matches (select one)", JLabel.LEFT));
+		JScrollPane scrollPane = new JScrollPane(resultTable);
+		centPanel.add(BorderLayout.CENTER, scrollPane);
+		mainPanel.add(BorderLayout.CENTER, centPanel);
+		
+		resultTable.addMouseListener(new TableMouse());
+		SwingUtilities.invokeLater(new Runnable() {
+			@Override
+			public void run() {
+				new SwingTableColumnWidths("Species Search Dialog Table", resultTable);				
+			}
+		});
+		
+		setResizable(true);
+		setDialogComponent(mainPanel);
+	}
+	public static SpeciesMapItem showDialog(Window parentFrame, TethysControl tethysControl) {
+		if (singleInstance == null) {
+			singleInstance = new SpeciesSearchDialog(parentFrame, tethysControl);
+		}
+		singleInstance.setParams();
+		singleInstance.setVisible(true);
+		return singleInstance.selectedItem;
+	}
+
+	
+	private void searchTethys() {
+		clearResults();
+		String str = searchText.getText();
+		if (str == null || str.length() == 0) {
+			return;
+		}
+		SearchWorker searchWorker = new SearchWorker(str);
+		searchWorker.execute();
+		// then open the dialog to block this thread. 
+		synchronized (synch) {
+			workDialog = new PamWorkDialog(getOwner(), 1, "Searching Tethys Database");
+			workDialog.setVisible(true);
+		}
+	}
+	
+	public void setMapItems(ArrayList<SpeciesMapItem> newMapItems) {
+		this.speciesMapItems = newMapItems;
+		tableModel.fireTableDataChanged();
+	}
+
+	private class SearchWorker extends SwingWorker<Integer, PamWorkProgressMessage> {
+
+		private String searchString;
+		private ArrayList<SpeciesMapItem> newMapItems;
+
+		public SearchWorker(String searchString) {
+			this.searchString = searchString;
+		}
+
+		@Override
+		protected Integer doInBackground() throws Exception {
+			String msg = String.format("Searching database for names containing \"%s\"", searchString);
+			PamWorkProgressMessage pm = new PamWorkProgressMessage(null, msg);
+			publish(pm);
+			try {
+				ITISFunctions itisFunctions = tethysControl.getItisFunctions();
+				this.newMapItems = itisFunctions.searchSpecies(searchString);
+			}
+			catch (Exception e) {
+				e.printStackTrace();
+			}
+			if (newMapItems == null) {
+				return 0;
+			}
+			if (workDialog != null) {
+				workDialog.setVisible(false);
+				workDialog.dispose();
+			}
+			return newMapItems.size();
+		}
+
+		@Override
+		protected void done() {
+			if (newMapItems == null || newMapItems.size() == 0) {
+				String msg = String.format("No matching ITIS types for search term %s", searchString);
+				WarnOnce.showNamedWarning("ITIS Lookup failure", getOwner(), "ITIS Code search", msg, WarnOnce.WARNING_MESSAGE);
+				
+			}
+			setMapItems(newMapItems);
+		}
+
+		@Override
+		protected void process(List<PamWorkProgressMessage> chunks) {
+			for (PamWorkProgressMessage msg : chunks) {
+				synchronized (synch) {
+					if (workDialog != null) {
+						workDialog.update(msg);
+					}
+				}				
+			}
+		}
+		
+	}
+	
+	private void setParams() {
+		searchText.setText(null);
+		clearResults();
+	}
+
+	private void clearResults() {
+		speciesMapItems = null;
+		selectedItem = null;
+	}
+	@Override
+	public boolean getParams() {
+		if (selectedItem == null) {
+			return showWarning("You must select a row from the table of species");
+		}
+		return selectedItem != null;
+	}
+
+	@Override
+	public void cancelButtonPressed() {
+		clearResults();
+	}
+
+	@Override
+	public void restoreDefaultSettings() {
+		// TODO Auto-generated method stub
+
+	}
+	
+	private class TableMouse extends MouseAdapter {
+
+		@Override
+		public void mouseClicked(MouseEvent e) {
+			if (speciesMapItems == null) {
+				return;
+			}
+			int selectedRow = resultTable.getSelectedRow();
+			if (selectedRow >= 0 && selectedRow < speciesMapItems.size()) {
+				selectedItem = speciesMapItems.get(selectedRow);
+			}
+			tableModel.fireTableDataChanged();
+		}
+		
+	}
+	private class DataModel extends AbstractTableModel {
+		
+		private String[] colNames = {"Select", "TSN", "Name", "Common Name"};
+
+		@Override
+		public int getRowCount() {
+			if (speciesMapItems == null) {
+				return 0;
+			}
+			return speciesMapItems.size();
+		}
+
+		@Override
+		public int getColumnCount() {
+			return colNames.length;
+		}
+
+		@Override
+		public Object getValueAt(int rowIndex, int columnIndex) {
+			SpeciesMapItem mapItem = speciesMapItems.get(rowIndex);
+			switch (columnIndex) {
+			case 0:
+				return mapItem == selectedItem;
+			case 1:
+				return mapItem.getItisCode();
+			case 2:
+				return mapItem.getLatinName();
+			case 3:
+				return mapItem.getCommonName();
+			}
+			return null;
+		}
+
+		@Override
+		public String getColumnName(int column) {
+			return colNames[column];
+		}
+
+		@Override
+		public Class<?> getColumnClass(int columnIndex) {
+			if (columnIndex == 0) {
+				return Boolean.class;
+			}
+			return super.getColumnClass(columnIndex);
+		}
+		
+	}
+
+}

src/tethys/species/swing/SpeciesSubPanel.java

@@ -85,7 +85,8 @@ public class SpeciesSubPanel {
 		
 		pamguardName.setToolTipText("Internal name within PAMGuard module");
 		itisCode.setToolTipText("ITIS species code");
-		searchButton.setToolTipText("Search for species code");
+		searchButton.setToolTipText("<html>Either enter a code manually and press \"Find\" for additional information,<br>"
+				+ "or leave the code empty and press \"Find\" to search the Tethys database using common or scientific names.</html>" );
 		callType.setToolTipText("Descriptive name for call type or measurement");
 		latinName.setToolTipText("Scientific name");
 		commonName.setToolTipText("Common name");
@@ -112,6 +113,17 @@ public class SpeciesSubPanel {
 			return;
 		}
 		ITISFunctions itisFunctions = tethysControl.getItisFunctions();
+		String itisString = this.itisCode.getText();
+		if (itisString == null || itisString.length() == 0) {
+			searchForCode(tethysControl, itisFunctions);
+		}
+		else {
+			getCodeInformation(tethysControl, itisFunctions, itisString);
+		}
+//		System.out.println(itisInfo);
+	}
+
+	private void getCodeInformation(TethysControl tethysControl, ITISFunctions itisFunctions, String itisString) {
 		int itisCode = 0;
 		try {
 			itisCode = Integer.valueOf(this.itisCode.getText());
@@ -129,7 +141,15 @@ public class SpeciesSubPanel {
 				commonName.setText(itisInfo.getVernacular());
 			}
 		}		
-//		System.out.println(itisInfo);
+	}
+
+	private void searchForCode(TethysControl tethysControl, ITISFunctions itisFunctions) {
+		SpeciesMapItem speciesItem = SpeciesSearchDialog.showDialog(tethysControl.getGuiFrame(), tethysControl);
+		if (speciesItem != null) {
+			itisCode.setText(String.format("%d", speciesItem.getItisCode()));
+			latinName.setText(speciesItem.getLatinName());
+			commonName.setText(speciesItem.getCommonName());
+		}
 	}
 
 	public JComponent getDialogComponent() {

src/tethys/swing/DatablockSynchPanel.java

@@ -147,7 +147,7 @@ public class DatablockSynchPanel extends TethysGUIPanel {
 		if (deployments == null || deployments.size() == 0) {
 			en = false;
 		}
-		exportButton.setEnabled(en);
+		exportButton.setEnabled(getTethysControl().isServerOk() & en);
 	}
 
 	public void showPopup(MouseEvent e, int row) {
@@ -181,6 +181,9 @@ public class DatablockSynchPanel extends TethysGUIPanel {
 //			dataBlockSynchInfo = null;
 //			getSychInfos();
 //			getTethysControl().coun
+			break;
+		case UPDATESERVER:
+			enableExportButton();
 		}
 		
 		synchTableModel.fireTableDataChanged();

src/tethys/swing/DeploymentExportPanel.java

@@ -154,6 +154,9 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
 		case UPDATEMETADATA:
 			setInternal();
 			break;
+		case UPDATESERVER:
+			enableControls();
+			break;
 		}
 	}
 
@@ -244,7 +247,7 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
 
 	private void enableControls() {
 		boolean enable = selectedDeployments != null && selectedDeployments.size() > 0;
-		bigExportButton.setEnabled(enable);
+		bigExportButton.setEnabled(getTethysControl().isServerOk() & enable);
 	}
 
 }

src/tethys/swing/DeploymentsPanel.java

@@ -15,6 +15,7 @@ import javax.swing.border.TitledBorder;
 
 import PamView.panel.PamPanel;
 import tethys.TethysControl;
+import tethys.TethysState;
 import tethys.deployment.DeploymentHandler;
 import tethys.deployment.RecordingPeriod;
 
@@ -97,14 +98,22 @@ public class DeploymentsPanel extends TethysGUIPanel implements DeploymentTableO
 		enableExportButton();
 	}
 	
+	
+
 	private void enableExportButton() {
 		ArrayList<RecordingPeriod> selected = pamDeploymentsTable.getSelectedPeriods();
-		// and see if any warnings are needed: basically if anything selected has an output.
+		if (selected == null) {
+			exportButton.setEnabled(false);
+			return;
+		}
 		boolean existing = false;
-		for (RecordingPeriod aPeriod: selected) {
+		if (selected != null) {
-			if (aPeriod.getMatchedTethysDeployment() != null) {
+			// and see if any warnings are needed: basically if anything selected has an output.
-				existing = true;
+			for (RecordingPeriod aPeriod: selected) {
-				break;
+				if (aPeriod.getMatchedTethysDeployment() != null) {
+					existing = true;
+					break;
+				}
 			}
 		}
 		String warning = null;
@@ -113,7 +122,13 @@ public class DeploymentsPanel extends TethysGUIPanel implements DeploymentTableO
 			exportWarning.setText(warning);
 		}
 
-		exportButton.setEnabled(selected.size()>0 & existing == false);
+		exportButton.setEnabled(selected.size()>0 & existing == false && getTethysControl().isServerOk());
+	}
+
+	@Override
+	public void updateState(TethysState tethysState) {
+		super.updateState(tethysState);
+		enableExportButton();
 	}
 
 

src/tethys/swing/PAMGuardDeploymentsTable.java

@@ -326,6 +326,9 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
 	 * @return
 	 */
 	public ArrayList<RecordingPeriod> getSelectedPeriods() {
+		if (deploymentOverview == null) {
+			return null;
+		}
 		ArrayList<RecordingPeriod> allPeriods = deploymentOverview.getRecordingPeriods();
 		ArrayList<RecordingPeriod> selPeriods = new ArrayList();
 		int n = allPeriods.size();

src/tethys/swing/TethysWizardCard.java

@@ -0,0 +1,80 @@
+package tethys.swing;
+
+import java.awt.Window;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+
+import javax.swing.JTextField;
+import javax.swing.text.JTextComponent;
+
+import PamView.dialog.PamDialog;
+import PamView.dialog.warn.WarnOnce;
+import PamView.wizard.PamWizard;
+import PamView.wizard.PamWizardCard;
+import tethys.niluswraps.NilusChecker;
+
+/**
+ * Wizard card with a few extra functions for Tethys. 
+ * @author dg50
+ *
+ * @param <T>
+ */
+abstract public class TethysWizardCard<T extends Object> extends PamWizardCard<T> {
+
+	private static final long serialVersionUID = 1L;
+
+	public TethysWizardCard(PamWizard pamWizard, String title) {
+		super(pamWizard, title);
+	}
+	
+	/**
+	 * Get a string out of a text component, but if the field is
+	 * empty, return null rather than an empty, 0 length, string. 
+	 * @param textField
+	 * @return string, or null if it's empty. 
+	 */
+	public String getText(JTextComponent textField) {
+		String str = textField.getText();
+		if (str == null) {
+			return null;
+		}
+		if (str.length() == 0) {
+			return null;
+		}
+		return str;
+	}
+	
+	/**
+	 * Get a string from a text component, and warn if it is empty or null. 
+	 * @param owner parent window for warning
+	 * @param textComponent text component
+	 * @param name control name for warning text
+	 * @return String if there was one, or null if it was null or empty.
+	 */
+	public String warnNotNull(Window owner, JTextComponent textComponent, String name) {
+		String str = getText(textComponent);
+		if (str != null) {
+			return str;
+		}
+		String warn = String.format("The field %s cannot be empty", name);
+		PamDialog.showWarning(owner, "Empty or missing data", warn);
+		return null;
+	}
+	
+	/**
+	 * Check for required empty fields. 
+	 * @param nilusObject
+	 * @return true if all OK, false if there are required fields
+	 */
+	public boolean checkEmptyFields(Object nilusObject) {
+		NilusChecker.removeEmptyFields(nilusObject);
+		ArrayList<Field> emptyList = NilusChecker.checkEmptyFields(nilusObject);
+		if (emptyList.size() == 0) {
+			return true;
+		}
+		Field first = emptyList.get(0);
+		String msg = String.format("The field \"%s\" in \"%s\" is required by Tethys and must be completed", first.getName(), first.getDeclaringClass().getCanonicalName());
+		return PamDialog.showWarning(getPamWizard(), "Missing required data", msg);
+	}
+
+}