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[Treebase-guts] SF.net SVN: treebase:[1112] trunk/treebase-web/src/main/webapp

From: <sfr...@us...> - 2014-04-24 04:36:28

Revision: 1112
          http://sourceforge.net/p/treebase/code/1112
Author:   sfrgpiel
Date:     2014-04-24 04:36:24 +0000 (Thu, 24 Apr 2014)
Log Message:
-----------
Updating links to journals

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/images/journal_files/taxon.jpg

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2014-04-24 04:16:57 UTC (rev 1111)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2014-04-24 04:36:24 UTC (rev 1112)
@@ -339,24 +339,6 @@
 			</a></p>
 			</td>
 		</tr>
-<!-- International Association for Plant Taxonomy -->
-		<tr>
-			<td>
-				<p><a href="http://www.iapt-taxon.org"
-					title="Aquatic Biology"> 
-						<img class="journal"
-						src="images/journal_files/iapt.jpg" alt="IAPT"/> 
-					</a>
-				</p>
-			</td>
-			<td>
-			<p><a
-				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22International%20Association%20for%20Plant%20Taxonomy%22"
-				title="Find records in TreeBASE for articles published in the International Association for Plant Taxonomy">
-			<%=purlBase%>study/find?query=prism.publicationName==&quotInternational+Association+for+Plant+Taxonomy&quot
-			</a></p>
-			</td>
-		</tr>
 
 <!-- ima fungus -->
 		<tr>
@@ -905,6 +887,25 @@
 			<%=purlBase%>study/find?query=prism.publicationName==&quotSystematic+Botany&quot</a></p>
 			</td>
 		</tr>
+<!-- Taxon -->
+		<tr>
+			<td>
+				<p><a href="http://www.iapt-taxon.org"
+					title="Taxon"> 
+						<img class="journal"
+						src="images/journal_files/taxon.jpg" alt="TAXON"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Taxon%22"
+				title="Find records in TreeBASE for articles published in Taxon, the International Association for Plant Taxonomy">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotTaxon&quot
+			</a></p>
+			</td>
+		</tr>
+
 <!-- tropical bryology -->
 		<tr>
 			<td>
@@ -954,8 +955,6 @@
 		title="Proceeding of the National Academy of Sciences of the United States of America">
 	Proceeding of the National Academy of Sciences of the United States of
 	America</a>; <a
-		href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DTaxon"
-		title="Taxon">Taxon</a>; <a
 		href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DZootaxa"
 		title="Zootaxa">Zootaxa</a></p>
 

Added: trunk/treebase-web/src/main/webapp/images/journal_files/taxon.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/taxon.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/taxon.jpg	2014-04-24 04:16:57 UTC (rev 1111)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/taxon.jpg	2014-04-24 04:36:24 UTC (rev 1112)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/taxon.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[1111] trunk/treebase-web/src/main/webapp/images/ journal_files/apps.jpg

From: <sfr...@us...> - 2014-04-24 04:17:00

Revision: 1111
          http://sourceforge.net/p/treebase/code/1111
Author:   sfrgpiel
Date:     2014-04-24 04:16:57 +0000 (Thu, 24 Apr 2014)
Log Message:
-----------
Updating links to journals

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/images/journal_files/apps.jpg

Added: trunk/treebase-web/src/main/webapp/images/journal_files/apps.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/apps.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/apps.jpg	2014-04-24 03:31:38 UTC (rev 1110)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/apps.jpg	2014-04-24 04:16:57 UTC (rev 1111)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/apps.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[1110] trunk/treebase-web/src/main/webapp

From: <sfr...@us...> - 2014-04-24 03:31:42

Revision: 1110
          http://sourceforge.net/p/treebase/code/1110
Author:   sfrgpiel
Date:     2014-04-24 03:31:38 +0000 (Thu, 24 Apr 2014)
Log Message:
-----------
Updating links to journals

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/images/journal_files/ab.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/bl.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/fe.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/iapt.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/je.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/jn.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/jp.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/mee.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/ob.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/prsb.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/pta.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/ptb.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/rchn.jpg

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2014-04-24 03:31:38 UTC (rev 1110)
@@ -80,6 +80,44 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- Applications in Plant Sciences -->
+		<tr>
+			<td>
+				<p><a href="http://botany.org/APPS/"
+					title="Applications in Plant Sciences"> 
+						<img class="journal"
+						src="images/journal_files/apps.jpg" alt="APS"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Applications%20in%20Plant%20Sciences%22"
+				title="Find records in TreeBASE for articles published in Applications in Plant Sciences">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotApplications+in+Plant+Sciences&quot
+			</a></p>
+			</td>
+		</tr>
+
+<!-- Aquatic Biology -->
+		<tr>
+			<td>
+				<p><a href="http://www.int-res.com/journals/ab/ab-home"
+					title="Aquatic Biology"> 
+						<img class="journal"
+						src="images/journal_files/ab.jpg" alt="AB"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aquatic%20Biology%22"
+				title="Find records in TreeBASE for articles published in the Aquatic Biology">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotAquatic+Biology&quot
+			</a></p>
+			</td>
+		</tr>
+
 <!-- basic and applied ecology -->
 		<tr>
 			<td>
@@ -98,6 +136,26 @@
 			</a></p>
 			</td>
 		</tr>
+
+<!-- Biology Letters -->
+		<tr>
+			<td>
+				<p><a href="http://rsbl.royalsocietypublishing.org"
+					title="Biology Letters"> 
+						<img class="journal"
+						src="images/journal_files/bl.jpg" alt="BL"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Biology%20Letters%22"
+				title="Find records in TreeBASE for articles published in the Biology Letters">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotBiology+Letters&quot
+			</a></p>
+			</td>
+		</tr>
+
 <!-- the bryologist -->
 		<tr>
 			<td>
@@ -243,6 +301,25 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- Functional Ecology -->
+		<tr>
+			<td>
+				<p><a href="http://www.functionalecology.org"
+					title="Functional Ecology"> 
+						<img class="journal"
+						src="images/journal_files/fe.jpg" alt="FE"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Functional%20Ecology%22"
+				title="Find records in TreeBASE for articles published in the Functional Ecology">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotFunctional+Ecology&quot
+			</a></p>
+			</td>
+		</tr>
+
 <!-- fungal biology -->
 		<tr>
 			<td>
@@ -262,6 +339,25 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- International Association for Plant Taxonomy -->
+		<tr>
+			<td>
+				<p><a href="http://www.iapt-taxon.org"
+					title="Aquatic Biology"> 
+						<img class="journal"
+						src="images/journal_files/iapt.jpg" alt="IAPT"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22International%20Association%20for%20Plant%20Taxonomy%22"
+				title="Find records in TreeBASE for articles published in the International Association for Plant Taxonomy">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotInternational+Association+for+Plant+Taxonomy&quot
+			</a></p>
+			</td>
+		</tr>
+
 <!-- ima fungus -->
 		<tr>
 			<td>
@@ -300,6 +396,24 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- Journal of Ecology -->
+		<tr>
+			<td>
+				<p><a href="http://www.journalofecology.org"
+					title="Journal of Ecology"> 
+						<img class="journal"
+						src="images/journal_files/je.jpg" alt="JE"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal%20of%20Ecology%22"
+				title="Find records in TreeBASE for articles published in the Journal of Ecology">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotJournal+of+Ecology&quot
+			</a></p>
+			</td>
+		</tr>
 <!-- journal of fish and wildlife management -->
 		<tr>
 			<td>
@@ -337,6 +451,61 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- Journal of Neurochemistry -->
+		<tr>
+			<td>
+				<p><a href="http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1471-4159"
+					title="Journal of Neurochemistry"> 
+						<img class="journal"
+						src="images/journal_files/jn.jpg" alt="JN"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal%20of%20Neurochemistry%22"
+				title="Find records in TreeBASE for articles published in the Journal of Neurochemistry">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotJournal+of+Neurochemistry&quot
+			</a></p>
+			</td>
+		</tr>
+<!-- Journal of Paleontology -->
+		<tr>
+			<td>
+				<p><a href="http://www.journalofpaleontology.org/"
+					title="Journal of Paleontology"> 
+						<img class="journal"
+						src="images/journal_files/jp.jpg" alt="JP"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal%20of%20Paleontology%22"
+				title="Find records in TreeBASE for articles published in the Journal of Paleontology">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotJournal+of+Paleontology&quot
+			</a></p>
+			</td>
+		</tr>
+<!-- Methods in Ecology and Evolution -->
+		<tr>
+			<td>
+				<p><a href="http://www.methodsinecologyandevolution.org"
+					title="Methods in Ecology and Evolution"> 
+						<img class="journal"
+						src="images/journal_files/mee.jpg" alt="MEE"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Methods%20in%20Ecology%20and%20Evolution%22"
+				title="Find records in TreeBASE for articles published in the Methods in Ecology and Evolution">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotMethods+in+Ecology+and+Evolution&quot
+			</a></p>
+			</td>
+		</tr>
+
 <!-- molecular ecology -->
 		<tr>
 			<td>
@@ -369,6 +538,21 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- muelleria -->
+		<tr>
+			<td>
+			<p><a
+				href="http://www.rbg.vic.gov.au/science/information-and-resources/science-publications/muelleria">
+			<img class="journal"
+				src="images/journal_files/image015.jpg" alt="Muelleria"/></a></p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMuelleria"
+				title="Find records in TreeBASE for articles published in Muelleria">
+			<%=purlBase%>study/find?query=prism.publicationName==Muelleria</a></p>
+			</td>
+		</tr>
 <!-- mycologia -->
 		<tr>
 			<td>
@@ -459,6 +643,7 @@
 			<%=purlBase%>study/find?query=prism.publicationName==Mycosphere</a></p>
 			</td>
 		</tr>
+
 <!-- north american fauna -->
 		<tr>
 			<td>
@@ -475,6 +660,25 @@
 			<%=purlBase%>study/find?query=prism.publicationName==&quotNorth+American+Fauna&quot</a></p>
 			</td>
 		</tr>
+<!-- Open Biology -->
+		<tr>
+			<td>
+				<p><a href="http://rsob.royalsocietypublishing.org"
+					title="Open Biology"> 
+						<img class="journal"
+						src="images/journal_files/ob.jpg" alt="OB"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Open%20Biology%22"
+				title="Find records in TreeBASE for articles published in Open Biology">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotOpen+Biology&quot
+			</a></p>
+			</td>
+		</tr>
+
 <!-- organisms, diversity, and evolution -->
 		<tr>
 			<td>
@@ -522,6 +726,44 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- Philosophical Transactions of the Royal Society A -->
+		<tr>
+			<td>
+				<p><a href="http://rsta.royalsocietypublishing.org"
+					title="Philosophical Transactions of the Royal Society A"> 
+						<img class="journal"
+						src="images/journal_files/pta.jpg" alt="PTA"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Philosophical%20Transactions%20of%20the%20Royal%20Society%20A%22"
+				title="Find records in TreeBASE for articles published in the Philosophical Transactions of the Royal Society A">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotPhilosophical+Transactions+of+the+Royal+Society+A&quot
+			</a></p>
+			</td>
+		</tr>
+
+<!-- Philosophical Transactions of the Royal Society B -->
+		<tr>
+			<td>
+				<p><a href="http://rstb.royalsocietypublishing.org"
+					title="Philosophical Transactions of the Royal Society B"> 
+						<img class="journal"
+						src="images/journal_files/ptb.jpg" alt="PTB"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Philosophical%20Transactions%20of%20the%20Royal%20Society%20B%22"
+				title="Find records in TreeBASE for articles published in the Philosophical Transactions of the Royal Society B">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotPhilosophical+Transactions+of+the+Royal+Society+B&quot
+			</a></p>
+			</td>
+		</tr>
+
 <!-- phytopathology -->
 		<tr>
 			<td>
@@ -569,35 +811,58 @@
 			<%=purlBase%>study/find?query=prism.publicationName==&quotPLoS+Currents:+Tree+of+Life&quot</a></p>
 			</td>
 		</tr>
-<!-- rhodora -->
+<!-- Proceedings of the Royal Society B -->
 		<tr>
 			<td>
-			<p><a href="http://www.rhodora.org/rhodora/currentissues.html"><img
-				class="journal"
-				src="images/journal_files/image014.gif" alt="Rhodora"/></a></p>
+				<p><a href="http://rspb.royalsocietypublishing.org"
+					title="Proceedings of the Royal Society B"> 
+						<img class="journal"
+						src="images/journal_files/prsb.jpg" alt="PRSB"/> 
+					</a>
+				</p>
 			</td>
 			<td>
 			<p><a
-				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DRhodora"
-				title="Find records in TreeBASE for articles published in Rhodora">
-			<%=purlBase%>study/find?query=prism.publicationName==Rhodora</a></p>
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Proceedings%20of%20the%20Royal%20Society%20B%22"
+				title="Find records in TreeBASE for articles published in the Proceedings of the Royal Society B">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotProceedings+of+the+Royal+Society+B&quot
+			</a></p>
 			</td>
 		</tr>
-<!-- muelleria -->
+<!-- Revista Chilena de Historia Natural -->
 		<tr>
 			<td>
+				<p><a href="http://rchn.biologiachile.cl/"
+					title="Revista Chilena de Historia Natural"> 
+						<img class="journal"
+						src="images/journal_files/rchn.jpg" alt="RCHN"/> 
+					</a>
+				</p>
+			</td>
+			<td>
 			<p><a
-				href="http://www.rbg.vic.gov.au/science/information-and-resources/science-publications/muelleria">
-			<img class="journal"
-				src="images/journal_files/image015.jpg" alt="Muelleria"/></a></p>
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Revista%20Chilena%20de%20Historia%20Natural%22"
+				title="Find records in TreeBASE for articles published in Revista Chilena de Historia Natural">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotRevista+Chilena+de+Historia+Natural&quot
+			</a></p>
 			</td>
+		</tr>
+
+<!-- rhodora -->
+		<tr>
 			<td>
+			<p><a href="http://www.rhodora.org/rhodora/currentissues.html"><img
+				class="journal"
+				src="images/journal_files/image014.gif" alt="Rhodora"/></a></p>
+			</td>
+			<td>
 			<p><a
-				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMuelleria"
-				title="Find records in TreeBASE for articles published in Muelleria">
-			<%=purlBase%>study/find?query=prism.publicationName==Muelleria</a></p>
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DRhodora"
+				title="Find records in TreeBASE for articles published in Rhodora">
+			<%=purlBase%>study/find?query=prism.publicationName==Rhodora</a></p>
 			</td>
 		</tr>
+
 <!-- studies in mycology -->
 		<tr>
 			<td>
@@ -689,9 +954,6 @@
 		title="Proceeding of the National Academy of Sciences of the United States of America">
 	Proceeding of the National Academy of Sciences of the United States of
 	America</a>; <a
-		href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Proceedings+of+the+Royal+Society+B%22"
-		title="Proceedings of the Royal Society B">Proceedings of the Royal
-	Society B</a>; <a
 		href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DTaxon"
 		title="Taxon">Taxon</a>; <a
 		href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DZootaxa"

Added: trunk/treebase-web/src/main/webapp/images/journal_files/ab.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/ab.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/ab.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/ab.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/ab.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/bl.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/bl.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/bl.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/bl.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/bl.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/fe.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/fe.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/fe.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/fe.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/fe.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/iapt.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/iapt.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/iapt.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/iapt.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/iapt.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/je.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/je.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/je.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/je.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/je.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/jn.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/jn.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/jn.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/jn.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/jn.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/jp.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/jp.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/jp.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/jp.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/jp.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/mee.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/mee.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/mee.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/mee.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/mee.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/ob.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/ob.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/ob.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/ob.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/ob.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/prsb.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/prsb.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/prsb.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/prsb.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/prsb.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/pta.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/pta.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/pta.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/pta.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/pta.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/ptb.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/ptb.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/ptb.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/ptb.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/ptb.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/rchn.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/rchn.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/rchn.jpg	2014-04-14 09:41:47 UTC (rev 1109)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/rchn.jpg	2014-04-24 03:31:38 UTC (rev 1110)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/rchn.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[1109] trunk/treebase-web/src/main/webapp/WEB-INF/ pages/home.jsp

From: <sfr...@us...> - 2014-04-14 09:41:50

Revision: 1109
          http://sourceforge.net/p/treebase/code/1109
Author:   sfrgpiel
Date:     2014-04-14 09:41:47 +0000 (Mon, 14 Apr 2014)
Log Message:
-----------
Minor text modification

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp	2014-04-13 18:33:58 UTC (rev 1108)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp	2014-04-14 09:41:47 UTC (rev 1109)
@@ -1,17 +1,20 @@
-<div id="contentRight">
+<div id="contentRight"><div id="contentRight">
 	<div class="gutter">
-		<h1>Welcome to TreeBASE</h1>	
-		<p>
-		TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic 
-		trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., 
+		<h1>Welcome to TreeBASE</h1>
+		<p>TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic 
+		trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., 
 		trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in 
 		TreeBASE are exposed to the public if they are used in a publication that is in press or published 
 		in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in 
-		publications that are in preparation or in review can be submitted to TreeBASE but are only available 
-		to the authors, publication editors, or reviewers using a special access code. TreeBASE is produced and 
-		governed by the <a href="http://www.phylorf.org" title="Phyloinformatics Research Foundation, Inc.">The Phyloinformatics Research Foundation, Inc.</a></p>
-		<p>As of April 2014, TreeBASE contains data for 4,076 publications written by 8,777 different authors. These studies analyzed 8,233 matrices and resulted in 12,817 trees with 761,460 taxon labels that mapped to 104,593 distinct taxa.</p>	</div>
-        <p>Some recent additions:</p>
+		publications that are in preparation or in review can be submitted to TreeBASE but will not be 
+		available to the public until they have passed peer review. Aside from the submitter, such data 
+		are only available to the publication editors or reviewers using a special access URL. TreeBASE 
+		is produced and governed by the <a href="http://www.phylorf.org" title="Phyloinformatics Research 
+		Foundation, Inc.">The Phyloinformatics Research Foundation, Inc.</a></p>
+		<p>As of April 2014, TreeBASE contains data for 4,076 publications written by 8,777 different authors. 
+		These studies analyzed 8,233 matrices and resulted in 12,817 trees with 761,460 taxon labels that mapped 
+		to 104,593 distinct taxa.</p>
+		<p>Some recent additions: 
 		<script language="JavaScript" src="http://peabody.research.yale.edu/treebase-feed/feed2js.php?src=http%3A%2F%2Fpipes.yahoo.com%2Fpipes%2Fpipe.run%3F_id%3D41dc2d1544150c1b8e69367059f26950%26_render%3Drss&amp;num=8&amp;date=y"  type="text/javascript">
 		</script>
 		<noscript>
@@ -23,9 +26,15 @@
 		  <li>A mapping between taxon labels and taxonomic names in uBio and NCBI for improved normalization of names</li>
 		  <li>The ability to visualize and edit trees using Phylowidget</li>
 		  <li>The ability to search on tree topology</li>
-		  <li>Persistent and resolvable URIs for data objects in TreeBASE (i.e. studies, trees, matrices)  serve as both globally unique identification numbers and resource locators.  These  can be included in articles and on researcher's websites, making access to TreeBASE data only a click away</li>
-		  <li>Data are delivered in several  serializations, including <a href="http:/hackathon.nescent.org/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
+		  <li>Persistent and resolvable URIs for data objects in TreeBASE (i.e. studies, trees, matrices)  serve as both globally unique identification numbers and 
+		  resource locators.  These  can be included in articles and on researcher's websites, making access to TreeBASE data only a click away</li>
+		  <li>Data are delivered in several  serializations, including <a href="http:/hackathon.nescent.org/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> 
+		  and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
 		  <li> A special URL  gives journal editors and reviewers anonymous advanced access to data</li>
-		  <li>Programmatic access to the data using the <a href="http://evoinfo.nescent.org/PhyloWS" target="_blank">PhyloWS API</a>.  Queries are expressed in  URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in &quot;Systematic Biology,&quot; or return all trees that include &quot;Homo sapiens,&quot; etc)</li>
+		  <li>Programmatic access to the data using the <a href="http://evoinfo.nescent.org/PhyloWS" target="_blank">PhyloWS API</a>.  Queries are expressed in  
+		  URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite 
+		  RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in &quot;Systematic Biology,&quot; 
+		  or return all trees that include &quot;Homo sapiens,&quot; etc)</li>
 		</ul>
+	</div>
 </div>

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[Treebase-guts] SF.net SVN: treebase:[1108] trunk/treebase-web/src/main/webapp/images/ journal_files

From: <sfr...@us...> - 2014-04-13 18:34:01

Revision: 1108
          http://sourceforge.net/p/treebase/code/1108
Author:   sfrgpiel
Date:     2014-04-13 18:33:58 +0000 (Sun, 13 Apr 2014)
Log Message:
-----------
Updating links to journals

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/images/journal_files/flora.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/ppees.jpg

Modified: trunk/treebase-web/src/main/webapp/images/journal_files/flora.jpg
===================================================================
(Binary files differ)

Modified: trunk/treebase-web/src/main/webapp/images/journal_files/ppees.jpg
===================================================================
(Binary files differ)

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[1107] trunk/treebase-web/src/main/webapp/WEB-INF/ pages

From: <sfr...@us...> - 2014-04-13 15:02:09

Revision: 1107
          http://sourceforge.net/p/treebase/code/1107
Author:   sfrgpiel
Date:     2014-04-13 15:02:06 +0000 (Sun, 13 Apr 2014)
Log Message:
-----------
Updating links to journals

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp	2014-04-13 14:01:53 UTC (rev 1106)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp	2014-04-13 15:02:06 UTC (rev 1107)
@@ -9,7 +9,8 @@
 		in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in 
 		publications that are in preparation or in review can be submitted to TreeBASE but are only available 
 		to the authors, publication editors, or reviewers using a special access code. TreeBASE is produced and 
-		governed by the <a href="http://www.phylofoundation.org" title="Phyloinformatics Research Foundation, Inc.">The Phyloinformatics Research Foundation, Inc.</a></p>
+		governed by the <a href="http://www.phylorf.org" title="Phyloinformatics Research Foundation, Inc.">The Phyloinformatics Research Foundation, Inc.</a></p>
+		<p>As of April 2014, TreeBASE contains data for 4,076 publications written by 8,777 different authors. These studies analyzed 8,233 matrices and resulted in 12,817 trees with 761,460 taxon labels that mapped to 104,593 distinct taxa.</p>	</div>
         <p>Some recent additions:</p>
 		<script language="JavaScript" src="http://peabody.research.yale.edu/treebase-feed/feed2js.php?src=http%3A%2F%2Fpipes.yahoo.com%2Fpipes%2Fpipe.run%3F_id%3D41dc2d1544150c1b8e69367059f26950%26_render%3Drss&amp;num=8&amp;date=y"  type="text/javascript">
 		</script>
@@ -27,5 +28,4 @@
 		  <li> A special URL  gives journal editors and reviewers anonymous advanced access to data</li>
 		  <li>Programmatic access to the data using the <a href="http://evoinfo.nescent.org/PhyloWS" target="_blank">PhyloWS API</a>.  Queries are expressed in  URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in &quot;Systematic Biology,&quot; or return all trees that include &quot;Homo sapiens,&quot; etc)</li>
 		</ul>
-		<p>As of December 2011, TreeBASE contains 2,946 publications written by 6,106 different authors. These studies analyzed 5,717 matrices and resulted in 8,462 trees with 465,762 taxon labels that mapped to 82,043 distinct taxa.</p>	</div>
 </div>

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2014-04-13 14:01:53 UTC (rev 1106)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2014-04-13 15:02:06 UTC (rev 1107)
@@ -29,7 +29,7 @@
 <!-- aliso -->
 		<tr>
 			<td>
-				<p><a href="http://www.rsabg.org/research-department/scientific-publications"
+				<p><a href="http://www.rsabg.org/scientific-publications"
 					title="Aliso"> 
 						<img class="journal"
 						src="images/journal_files/aliso.jpg" alt="Aliso"/> 
@@ -101,7 +101,7 @@
 <!-- the bryologist -->
 		<tr>
 			<td>
-				<p><a href="http://192.104.39.110/bryologist.html"
+				<p><a href="http://www.bioone.org/loi/bryo"
 					title="The Bryologist"> 
 						<img class="journal"
 						src="images/journal_files/bry.jpg" alt="Bryologist"/> 
@@ -211,7 +211,7 @@
 			<td>
 				<p>
 					<a
-						href="http://www3.interscience.wiley.com/journal/119423602/home">
+						href="http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1752-4571">
 						<img class="journal"
 							src="images/journal_files/image002.jpg" alt="Evolutionary Applications"/> 
 					</a>
@@ -526,7 +526,7 @@
 		<tr>
 			<td>
 				<p>
-					<a href="http://apsjournals.apsnet.org/loi/phyto?cookieSet=1"> 
+					<a href="http://apsjournals.apsnet.org/loi/phyto"> 
 						<img 
 							class="journal"
 							src="images/journal_files/image012.jpg" 
@@ -544,7 +544,7 @@
 <!-- plant disease -->
 		<tr>
 			<td>
-			<p><a href="http://www.apsnet.org/pd/">
+			<p><a href="http://apsjournals.apsnet.org/loi/pdis">
 			<img class="journal" src="images/journal_files/image013.jpg" alt="Plant Disease"/>
 			</a></p>
 			</td>
@@ -572,7 +572,7 @@
 <!-- rhodora -->
 		<tr>
 			<td>
-			<p><a href="http://www.rhodora.org/Rhodora.html"><img
+			<p><a href="http://www.rhodora.org/rhodora/currentissues.html"><img
 				class="journal"
 				src="images/journal_files/image014.gif" alt="Rhodora"/></a></p>
 			</td>
@@ -629,7 +629,7 @@
 <!-- systematic botany -->
 		<tr>
 			<td>
-			<p><a href="http://www.sysbot.org/">
+			<p><a href="http://www.bioone.org/loi/sbot">
 			<img class="journal" src="images/journal_files/image018.gif"
 				alt="Systematic Botany"/></a></p>
 			</td>

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[Treebase-guts] SF.net SVN: treebase:[1106] trunk/treebase-web/src/main/webapp

From: <sfr...@us...> - 2014-04-13 14:01:57

Revision: 1106
          http://sourceforge.net/p/treebase/code/1106
Author:   sfrgpiel
Date:     2014-04-13 14:01:53 +0000 (Sun, 13 Apr 2014)
Log Message:
-----------
Updating links to journals

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/images/journal_files/baae.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/flora.jpg
    trunk/treebase-web/src/main/webapp/images/journal_files/ppees.jpg

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2013-08-20 03:02:55 UTC (rev 1105)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2014-04-13 14:01:53 UTC (rev 1106)
@@ -80,6 +80,24 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- basic and applied ecology -->
+		<tr>
+			<td>
+				<p><a href="http://www.elsevier.com/locate/baae"
+					title="Basic and Applied Ecology"> 
+						<img class="journal"
+						src="images/journal_files/baae.jpg" alt="Basic and Applied Ecology"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Basic%20and%20Applied%20Ecology%22"
+				title="Find records in TreeBASE for articles published in Basic and Applied Ecology">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotBasic+and+Applied+Ecology&quot
+			</a></p>
+			</td>
+		</tr>
 <!-- the bryologist -->
 		<tr>
 			<td>
@@ -207,6 +225,24 @@
 			</a></p>
 			</td>
 		</tr>
+<!-- flora -->
+		<tr>
+			<td>
+				<p><a href="http://www.elsevier.com/locate/flora"
+					title="Flora - Morphology, Distribution, Functional Ecology of Plants"> 
+						<img class="journal"
+						src="images/journal_files/flora.jpg" alt="Flora"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Flora%22"
+				title="Find records in TreeBASE for articles published in Flora">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotFlora&quot
+			</a></p>
+			</td>
+		</tr>
 <!-- fungal biology -->
 		<tr>
 			<td>
@@ -468,6 +504,24 @@
 			<%=purlBase%>study/find?query=prism.publicationName==Persoonia</a></p>
 			</td>
 		</tr>
+<!-- perspectives in ecology, evolution and systematics -->
+		<tr>
+			<td>
+				<p><a href="http://www.elsevier.com/locate/ppees"
+					title="Perspectives in Ecology, Evolution and Systematics"> 
+						<img class="journal"
+						src="images/journal_files/ppees.jpg" alt="Perspectives in Ecology, Evolution and Systematics"/> 
+					</a>
+				</p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Perspectives%20in%20Ecology,%20Evolution%20and%20Systematics%22"
+				title="Find records in TreeBASE for articles published in Perspectives in Ecology, Evolution and Systematics">
+			<%=purlBase%>study/find?query=prism.publicationName==&quotPerspectives+in+Ecology,+Evolution+and+Systematics&quot
+			</a></p>
+			</td>
+		</tr>
 <!-- phytopathology -->
 		<tr>
 			<td>

Added: trunk/treebase-web/src/main/webapp/images/journal_files/baae.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/baae.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/baae.jpg	2013-08-20 03:02:55 UTC (rev 1105)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/baae.jpg	2014-04-13 14:01:53 UTC (rev 1106)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/baae.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/flora.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/flora.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/flora.jpg	2013-08-20 03:02:55 UTC (rev 1105)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/flora.jpg	2014-04-13 14:01:53 UTC (rev 1106)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/flora.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/treebase-web/src/main/webapp/images/journal_files/ppees.jpg
===================================================================
(Binary files differ)

Index: trunk/treebase-web/src/main/webapp/images/journal_files/ppees.jpg
===================================================================
--- trunk/treebase-web/src/main/webapp/images/journal_files/ppees.jpg	2013-08-20 03:02:55 UTC (rev 1105)
+++ trunk/treebase-web/src/main/webapp/images/journal_files/ppees.jpg	2014-04-13 14:01:53 UTC (rev 1106)

Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/ppees.jpg
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[1105] trunk/treebase-web/src/main/webapp/WEB-INF/ pages/submitTutorial.jsp

From: <hs...@us...> - 2013-08-20 03:02:59

Revision: 1105
          http://sourceforge.net/p/treebase/code/1105
Author:   hshyket
Date:     2013-08-20 03:02:55 +0000 (Tue, 20 Aug 2013)
Log Message:
-----------
Changing the way submission YouTube videos are embedded.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/submitTutorial.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submitTutorial.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submitTutorial.jsp	2013-07-19 20:03:20 UTC (rev 1104)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submitTutorial.jsp	2013-08-20 03:02:55 UTC (rev 1105)
@@ -67,7 +67,7 @@
 <h3>Instructional Video on Preparing NEXUS Data in Mesquite</h3>
 
 <p>
-<object width="480" height="385"><param name="movie" value="http://www.youtube.com/p/3F38DFE2626A5234?hl=en_US&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/p/3F38DFE2626A5234?hl=en_US&fs=1" type="application/x-shockwave-flash" width="480" height="385" allowscriptaccess="always" allowfullscreen="true"></embed></object>
+<iframe width="560" height="315" src="//www.youtube.com/embed/0bdKW5-Lg7E?list=PL3F38DFE2626A5234" frameborder="0" allowfullscreen></iframe>
 </p>
 
 <h3>Preparation of taxon labels</h3>
@@ -90,7 +90,7 @@
 <p>If you are sufficiently caffeinated, please consider watching this video to understand the process of submitting data to TreeBASE. The video is also available in high-definition if you view in &quot;Full screen&quot;</p>
 
 <p>
-<object width="480" height="385"><param name="movie" value="http://www.youtube.com/p/9AD9904B8782D600?hl=en_US&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/p/9AD9904B8782D600?hl=en_US&fs=1" type="application/x-shockwave-flash" width="480" height="385" allowscriptaccess="always" allowfullscreen="true"></embed></object>
+<iframe width="560" height="315" src="//www.youtube.com/embed/2npvFJX31hs?list=PL9AD9904B8782D600" frameborder="0" allowfullscreen></iframe>
 </p>
 
 </div>
\ No newline at end of file

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[1104] trunk/treebase_feed/.htaccess

From: <hs...@us...> - 2013-07-19 20:03:22

Revision: 1104
          http://sourceforge.net/p/treebase/code/1104
Author:   hshyket
Date:     2013-07-19 20:03:20 +0000 (Fri, 19 Jul 2013)
Log Message:
-----------
Adding a php time zone default for America/New_York in the .htaccess as PHP 5.3 and higher throws an error with date function.

Modified Paths:
--------------
    trunk/treebase_feed/.htaccess

Modified: trunk/treebase_feed/.htaccess
===================================================================
--- trunk/treebase_feed/.htaccess	2013-06-14 00:29:39 UTC (rev 1103)
+++ trunk/treebase_feed/.htaccess	2013-07-19 20:03:20 UTC (rev 1104)
@@ -1,4 +1,5 @@
 Options +FollowSymlinks
 RewriteEngine on
 RewriteCond $1 !^(feed2js\.php)
-RewriteRule ^(.*)$ /treebase-feed/feed2js.php/$1 [L]
\ No newline at end of file
+RewriteRule ^(.*)$ /treebase-feed/feed2js.php/$1 [L]
+php_value date.timezone "America/New_York"
\ No newline at end of file

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[1103] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/ClassificationSearchController.java

From: <hs...@us...> - 2013-06-14 00:29:41

Revision: 1103
          http://sourceforge.net/p/treebase/code/1103
Author:   hshyket
Date:     2013-06-14 00:29:39 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
Adding exception handling for classification search where ncbi identifier is invalid.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ClassificationSearchController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ClassificationSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ClassificationSearchController.java	2013-06-06 19:32:24 UTC (rev 1102)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ClassificationSearchController.java	2013-06-14 00:29:39 UTC (rev 1103)
@@ -41,14 +41,28 @@
 	
 	@SuppressWarnings("unchecked")
 	private Collection<PhyloTree> doSearch(
-			String searchTerm
-		) {
-
+			HttpServletRequest request,
+			HttpServletResponse response,
+			BindException errors,
+			String searchTerm) throws InstantiationException {
+		
 		Collection<PhyloTree> matches = null;
-		PhyloTreeService phyloTreeService = getSearchService().getPhyloTreeService();	
-		matches = phyloTreeService.findTreesByNCBINodes(searchTerm);
+		PhyloTreeService phyloTreeService = getSearchService().getPhyloTreeService();
+		
+		try {
+			matches = phyloTreeService.findTreesByNCBINodes(searchTerm);
+		}
+		catch ( NumberFormatException e ) {
+			addMessage(request, "Malformed NCBI identifier '" + searchTerm );
+			LOGGER.error("Couldn't parse NCBI identifier: "+e.getMessage());
+		}
+		catch ( NullPointerException e) {
+			addMessage(request, "NCBI identifier not found '" + searchTerm );
+			LOGGER.error("Couldn't find NCBI identifier: "+e.getMessage());
+			
+		}
+		
 		return matches;
-
 	}
 	
 	@Override
@@ -59,7 +73,7 @@
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
-		HashSet<PhyloTree> queryResults = doCQLQuery(root, new HashSet<PhyloTree>(),request);
+		HashSet<PhyloTree> queryResults = doCQLQuery(root, new HashSet<PhyloTree>(),request, response, errors);
 		TreeSearchResults tsr = new TreeSearchResults(queryResults);
 		saveSearchResults(request, tsr);
 		
@@ -86,10 +100,16 @@
 		}
 	}
 	
-	protected HashSet<PhyloTree> doCQLQuery(CQLNode node, HashSet<PhyloTree> results, HttpServletRequest request) {
+	protected HashSet<PhyloTree> doCQLQuery(
+			CQLNode node, 
+			HashSet<PhyloTree> results, 
+			HttpServletRequest request, 
+			HttpServletResponse response, 
+			BindException errors
+			) throws InstantiationException {
 		if ( node instanceof CQLBooleanNode ) {
-			HashSet<PhyloTree> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request);
-			HashSet<PhyloTree> resultsRight = doCQLQuery(((CQLBooleanNode)node).right,results, request);
+			HashSet<PhyloTree> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request, response, errors);
+			HashSet<PhyloTree> resultsRight = doCQLQuery(((CQLBooleanNode)node).right,results, request, response, errors);
 			if ( node instanceof CQLNotNode ) {
 				for ( PhyloTree rightTree : resultsRight ) {
 					if ( resultsLeft.contains(rightTree) )
@@ -114,7 +134,10 @@
 				String index = term.getIndex();
 				if ( index.startsWith("tb.identifier") ) {
 					if ( index.endsWith("ncbi") ) {
-						results.addAll(doSearch(term.getTerm()));
+						Collection<PhyloTree> trees = doSearch(request, response, errors, term.getTerm()); 
+						if ( null != trees ) {
+							results.addAll(trees);
+						}
 					}
 					else {
 						// issue warnings

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[1102] trunk/treebase-core/db/cleaning/ 2013-06-04_add_ncbi_tables/ncbi.sql

From: <hs...@us...> - 2013-06-06 19:33:23

Revision: 1102
          http://sourceforge.net/p/treebase/code/1102
Author:   hshyket
Date:     2013-06-06 19:32:24 +0000 (Thu, 06 Jun 2013)
Log Message:
-----------
Updating with ownership changes to NCBI tables.

Modified Paths:
--------------
    trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi.sql

Modified: trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi.sql	2013-06-06 13:29:18 UTC (rev 1101)
+++ trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi.sql	2013-06-06 19:32:24 UTC (rev 1102)
@@ -22,7 +22,7 @@
 --
 -- TOC entry 309 (class 1259 OID 95406)
 -- Dependencies: 3
--- Name: ncbi_names; Type: TABLE; Schema: public; Owner: treebase_app; Tablespace: 
+-- Name: ncbi_names; Type: TABLE; Schema: public; Owner: treebase_owner; Tablespace: 
 --
 
 CREATE TABLE ncbi_names (
@@ -33,8 +33,13 @@
 );
 
 
-ALTER TABLE public.ncbi_names OWNER TO treebase_app;
+ALTER TABLE public.ncbi_names OWNER TO treebase_owner;
+GRANT ALL ON TABLE ncbi_names TO treebase_owner;
+GRANT SELECT, UPDATE, INSERT, DELETE ON TABLE ncbi_names TO treebase_app;
+GRANT SELECT ON TABLE ncbi_names TO treebase_read;
+GRANT ALL ON TABLE ncbi_names TO postgres;
 
+
 --
 -- TOC entry 310 (class 1259 OID 95412)
 -- Dependencies: 2230 3
@@ -60,8 +65,13 @@
 );
 
 
-ALTER TABLE public.ncbi_nodes OWNER TO treebase_app;
+ALTER TABLE public.ncbi_nodes OWNER TO treebase_owner;
+GRANT ALL ON TABLE ncbi_nodes TO treebase_owner;
+GRANT SELECT, UPDATE, INSERT, DELETE ON TABLE ncbi_nodes TO treebase_app;
+GRANT SELECT ON TABLE ncbi_nodes TO treebase_read;
+GRANT ALL ON TABLE ncbi_nodes TO postgres;
 
+
 --
 -- TOC entry 2239 (class 0 OID 95406)
 -- Dependencies: 309
@@ -2178080,361895 +2178090,3 @@
 INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937579, 101273, 'species', 'CS', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1353850, 1353851);
 INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937520, 937477, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538029, 1538030);
 INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937521, 937478, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538033, 1538034);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937526, 937489, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538039, 1538040);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937513, 32374, 'no rank', NULL, 1, 1, 1, 1, 5, 1, 0, 0, NULL, 1538042, 1538059);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937514, 58306, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538119, 1538120);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937519, 58306, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538121, 1538122);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937527, 58306, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538123, 1538124);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937515, 58307, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538149, 1538150);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937516, 58307, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538151, 1538152);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937517, 58307, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538153, 1538154);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937518, 58307, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538155, 1538156);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937523, 58307, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538157, 1538158);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937524, 58307, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538159, 1538160);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937525, 58307, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538161, 1538162);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937495, 48384, 'no rank', NULL, 1, 1, 1, 1, 5, 1, 0, 0, NULL, 1538322, 1538325);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937550, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40410, 40411);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937522, 504575, 'species', 'DN', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538390, 1538391);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937551, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40412, 40413);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937553, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40416, 40417);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937528, 504575, 'species', 'DS', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538392, 1538393);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937554, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40418, 40419);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937555, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40420, 40421);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937501, 504493, 'species group', NULL, 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1538405, 1538408);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937556, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40422, 40423);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937557, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40424, 40425);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937558, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40426, 40427);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937559, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40428, 40429);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937560, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40430, 40431);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937561, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40432, 40433);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937562, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40434, 40435);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937563, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40436, 40437);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937565, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40440, 40441);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937566, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40442, 40443);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937567, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40444, 40445);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937568, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40446, 40447);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937569, 489821, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 40448, 40449);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937546, 490039, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 44148, 44149);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937547, 490039, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 44150, 44151);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937548, 490041, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 44788, 44789);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937570, 499193, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 54178, 54179);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937571, 684605, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 54786, 54787);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937572, 684605, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 54788, 54789);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937574, 684605, 'no rank', NULL, 9, 1, 1, 1, 0, 1, 1, 0, NULL, 54792, 54793);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937530, 469, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 261891, 261892);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937531, 469, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 261893, 261894);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937532, 469, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 261895, 261896);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937533, 469, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 261897, 261898);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937496, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285877, 285878);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937497, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285879, 285880);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937498, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285881, 285882);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937499, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285883, 285884);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937543, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285885, 285886);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937536, 547, 'species', 'ES', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 301397, 301398);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937537, 547, 'species', 'ES', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 301399, 301400);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937538, 547, 'species', 'ES', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 301401, 301402);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937542, 586, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 312077, 312078);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (289808, 23672, 'genus', NULL, 4, 1, 1, 1, 1, 1, 0, 0, NULL, 1099686, 1099717);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (35212, 35211, 'species', 'GE', 1, 1, 1, 1, 1, 1, 1, 0, NULL, 2044514, 2044515);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937604, 139076, 'species', 'OC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1304210, 1304211);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937621, 7490, 'species', 'TS', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1608458, 1608459);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937603, 935900, 'species', 'DG', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1304236, 1304237);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937656, 1663, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 728719, 728720);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937598, 862241, 'genus', NULL, 4, 1, 1, 1, 4, 1, 0, 0, NULL, 1304239, 1304242);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (827707, 156408, 'species', 'HS', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1624358, 1624359);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (289811, 289810, 'species', 'HT', 4, 1, 1, 1, 1, 1, 1, 0, NULL, 1099719, 1099720);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (289810, 23672, 'genus', NULL, 4, 1, 1, 1, 1, 1, 0, 0, NULL, 1099718, 1099721);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937657, 1663, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 728721, 728722);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937643, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399565, 399566);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (289812, 23672, 'genus', NULL, 4, 1, 1, 1, 1, 1, 0, 0, NULL, 1099722, 1099729);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937596, 131324, 'species', 'PS', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1207516, 1207517);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937658, 1663, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 728723, 728724);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937644, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399567, 399568);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937599, 862241, 'genus', NULL, 4, 1, 1, 1, 4, 1, 0, 0, NULL, 1304243, 1304248);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937645, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399569, 399570);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937600, 862241, 'genus', NULL, 4, 1, 1, 1, 4, 1, 0, 0, NULL, 1304249, 1304254);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937669, 1663, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 728725, 728726);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937670, 468922, 'species', 'HS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 737917, 737918);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937655, 2034, 'species', 'CS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 738721, 738722);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937646, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399571, 399572);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937602, 1281901, 'forma', 'MM', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1304260, 1304261);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937647, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399573, 399574);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937668, 110932, 'species', 'LS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 746235, 746236);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937648, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399575, 399576);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937601, 862241, 'genus', NULL, 4, 1, 1, 1, 4, 1, 0, 0, NULL, 1304255, 1304266);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937649, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399577, 399578);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937605, 862241, 'genus', NULL, 4, 1, 1, 1, 4, 1, 0, 0, NULL, 1304267, 1304312);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937625, 6699, 'species', 'PS', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1396966, 1396967);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937592, 1773, 'no rank', NULL, 0, 1, 11, 1, 0, 1, 1, 0, NULL, 750449, 750450);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937637, 1763, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 753989, 753990);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937638, 1763, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 753991, 753992);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937639, 1763, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 753993, 753994);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937640, 1763, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 753995, 753996);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937641, 1763, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 753997, 753998);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937671, 1839, 'species', 'NS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 768371, 768372);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937589, 3174, 'species', 'KC', 4, 1, 1, 1, 1, 1, 1, 0, NULL, 859754, 859755);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937590, 3174, 'species', 'KC', 4, 1, 1, 1, 1, 1, 1, 0, NULL, 859756, 859757);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937591, 3174, 'species', 'KS', 4, 1, 1, 1, 1, 1, 1, 0, NULL, 859758, 859759);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937615, 469, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 261899, 261900);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937650, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399579, 399580);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937616, 469, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 261901, 261902);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937588, 519230, 'species', 'IT', 4, 1, 1, 1, 1, 1, 1, 0, NULL, 859914, 859915);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937617, 469, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 261903, 261904);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937651, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399581, 399582);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937618, 469, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 261905, 261906);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937627, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285887, 285888);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937659, 374, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 399583, 399584);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937630, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285889, 285890);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937631, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285891, 285892);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937660, 186650, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 425301, 425302);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937632, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285893, 285894);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937633, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285895, 285896);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937672, 13687, 'species', 'SS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 453927, 453928);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937634, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285897, 285898);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937635, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285899, 285900);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937636, 286, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 285901, 285902);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937613, 570, 'species', 'KS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 310609, 310610);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937628, 570, 'species', 'KS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 310611, 310612);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937622, 583, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 311657, 311658);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937594, 363568, 'no rank', NULL, 0, 1, 11, 1, 0, 1, 1, 0, NULL, 314306, 314307);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937673, 13687, 'species', 'SS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 453929, 453930);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937626, 507, 'species', 'AS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 465721, 465722);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937663, 174951, 'species', 'RS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 474279, 474280);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937652, 32008, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 479741, 479742);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937653, 48736, 'species', 'RS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 483825, 483826);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937661, 48736, 'species', 'RS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 483827, 483828);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937662, 48736, 'species', 'RS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 483829, 483830);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937610, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537567, 537568);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937629, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537569, 537570);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937664, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537571, 537572);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937593, 1422, 'no rank', NULL, 0, 1, 11, 1, 0, 1, 1, 0, NULL, 551982, 551983);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937654, 44249, 'species', 'PS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 562175, 562176);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937666, 1357, 'species', 'LS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 574137, 574138);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937667, 1357, 'species', 'LS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 574139, 574140);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937612, 1350, 'species', 'ES', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 581343, 581344);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937614, 49928, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 625348, 625349);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937682, 2034, 'species', 'CS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 738723, 738724);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937685, 309349, 'varietas', 'PU', 4, 1, 1, 1, 1, 1, 1, 0, NULL, 1062000, 1062001);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937683, 33882, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 742129, 742130);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937730, 5402, 'species', 'RC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1282398, 1282399);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937684, 33882, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 742131, 742132);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937731, 5402, 'species', 'RC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1282400, 1282401);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937754, 166041, 'species', 'CL', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1812639, 1812640);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937732, 5402, 'species', 'RC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1282402, 1282403);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937721, 34451, 'species', 'CC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1293832, 1293833);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937755, 166041, 'species', 'CM', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1812641, 1812642);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937756, 166041, 'species', 'CS', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1812643, 1812644);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937758, 166041, 'species', 'CH', 1, 1, 1, 1, 5, 1, 1, 0, NULL, 1812645, 1812646);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937746, 13028, 'species', 'CS', 10, 1, 1, 1, 2, 1, 1, 0, NULL, 1883948, 1883949);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937717, 670422, 'species', 'LS', 10, 1, 1, 1, 2, 1, 1, 0, NULL, 1910067, 1910068);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937718, 670422, 'species', 'LS', 10, 1, 1, 1, 2, 1, 1, 0, NULL, 1910069, 1910070);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937719, 670422, 'species', 'LS', 10, 1, 1, 1, 2, 1, 1, 0, NULL, 1910071, 1910072);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937747, 337631, 'species', 'BS', 10, 1, 1, 1, 2, 1, 1, 0, NULL, 1919974, 1919975);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937748, 435127, 'species', 'NS', 10, 1, 1, 1, 2, 1, 1, 0, NULL, 1923186, 1923187);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937760, 164737, 'species', 'AS', 10, 1, 1, 1, 2, 1, 1, 0, NULL, 1937899, 1937900);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937722, 34451, 'species', 'CC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1293834, 1293835);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937674, 149698, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 469167, 469168);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937723, 34451, 'species', 'CC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1293836, 1293837);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937675, 149698, 'species', 'MS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 469169, 469170);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937676, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537573, 537574);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937724, 34451, 'species', 'CC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1293838, 1293839);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937677, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537575, 537576);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937678, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537577, 537578);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937725, 34451, 'species', 'CC', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1293840, 1293841);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937679, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537579, 537580);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937757, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537581, 537582);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937735, 34451, 'species', 'CV', 4, 1, 1, 1, 4, 1, 1, 0, NULL, 1293842, 1293843);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937759, 1386, 'species', 'BS', 0, 1, 11, 1, 0, 1, 1, 0, NULL, 537583, 537584);
-INSERT INTO ncbi_nodes (tax_id, parent_tax_id, rank, embl_code, division_id, inherited_div_flag, genetic_code_id, inherited_gc_flag, mitochondrial_genetic_code_id, inherited_mgc_flag, genbank_hidden_flag, hidden_subtree_root_flag, comments, left_id, right_id) VALUES (937680, 55080, 'species', 'BS', 0, ...
 
[truncated message content]

[Treebase-guts] SF.net SVN: treebase:[1101] trunk/treebase-core/db/cleaning/ 2013-06-04_add_ncbi_tables

From: <hs...@us...> - 2013-06-06 13:29:43

Revision: 1101
          http://sourceforge.net/p/treebase/code/1101
Author:   hshyket
Date:     2013-06-06 13:29:18 +0000 (Thu, 06 Jun 2013)
Log Message:
-----------


Added Paths:
-----------
    trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi.sql

Removed Paths:
-------------
    trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi_nodes.sql

Added: trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi.sql	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi.sql	2013-06-06 13:29:18 UTC (rev 1101)
@@ -0,0 +1,2539974 @@
+--
+-- PostgreSQL database dump
+--
+
+-- Dumped from database version 8.4.0
+-- Dumped by pg_dump version 9.1.3
+-- Started on 2013-05-31 14:03:07
+
+SET statement_timeout = 0;
+SET client_encoding = 'UTF8';
+SET standard_conforming_strings = off;
+SET check_function_bodies = false;
+SET client_min_messages = warning;
+SET escape_string_warning = off;
+
+SET search_path = public, pg_catalog;
+
+SET default_tablespace = '';
+
+SET default_with_oids = false;
+
+--
+-- TOC entry 309 (class 1259 OID 95406)
+-- Dependencies: 3
+-- Name: ncbi_names; Type: TABLE; Schema: public; Owner: treebase_app; Tablespace: 
+--
+
+CREATE TABLE ncbi_names (
+    tax_id integer NOT NULL,
+    name_txt character varying(255) NOT NULL,
+    unique_name character varying(255),
+    name_class character varying(32)
+);
+
+
+ALTER TABLE public.ncbi_names OWNER TO treebase_app;
+
+--
+-- TOC entry 310 (class 1259 OID 95412)
+-- Dependencies: 2230 3
+-- Name: ncbi_nodes; Type: TABLE; Schema: public; Owner: treebase_app; Tablespace: 
+--
+
+CREATE TABLE ncbi_nodes (
+    tax_id integer NOT NULL,
+    parent_tax_id integer NOT NULL,
+    rank character varying(32),
+    embl_code character varying(16),
+    division_id integer NOT NULL,
+    inherited_div_flag integer NOT NULL,
+    genetic_code_id integer NOT NULL,
+    inherited_gc_flag integer NOT NULL,
+    mitochondrial_genetic_code_id integer NOT NULL,
+    inherited_mgc_flag integer NOT NULL,
+    genbank_hidden_flag integer NOT NULL,
+    hidden_subtree_root_flag integer NOT NULL,
+    comments character varying(255) DEFAULT NULL::character varying,
+    left_id integer NOT NULL,
+    right_id integer NOT NULL
+);
+
+
+ALTER TABLE public.ncbi_nodes OWNER TO treebase_app;
+
+--
+-- TOC entry 2239 (class 0 OID 95406)
+-- Dependencies: 309
+-- Data for Name: ncbi_names; Type: TABLE DATA; Schema: public; Owner: treebase_app
+--
+
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (1, 'all', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (1, 'root', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'Bacteria', 'Bacteria <prokaryote>', 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'Monera', 'Monera <Bacteria>', 'in-part');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'Procaryotae', 'Procaryotae <Bacteria>', 'in-part');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'Prokaryota', 'Prokaryota <Bacteria>', 'in-part');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'Prokaryotae', 'Prokaryotae <Bacteria>', 'in-part');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'bacteria', 'bacteria <blast2>', 'blast name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'eubacteria', NULL, 'genbank common name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'not Bacteria Haeckel 1894', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'prokaryote', 'prokaryote <Bacteria>', 'in-part');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (2, 'prokaryotes', 'prokaryotes <Bacteria>', 'in-part');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (6, 'Azorhizobium', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (6, 'Azorhizobium Dreyfus et al. 1988', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (6, 'Azotirhizobium', NULL, 'equivalent name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'ATCC 43989', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'Azorhizobium caulinodans', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'Azorhizobium caulinodans Dreyfus et al. 1988', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'Azotirhizobium caulinodans', NULL, 'equivalent name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'CCUG 26647', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'DSM 5975', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'IFO 14845', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'JCM 20966', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'LMG 6465', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'NBRC 14845', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (7, 'ORS 571', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (9, 'Acyrthosiphon pisum symbiont P', NULL, 'includes');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (9, 'Buchnera aphidicola', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (9, 'Buchnera aphidicola Munson et al. 1991', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (10, '"Cellvibrio" Winogradsky 1929', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (10, 'Cellvibrio', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (10, 'Cellvibrio (ex Winogradsky 1929) Blackall et al. 1986 emend. Humphry et al. 2003', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (11, '"Cellvibrio gilvus" Hulcher and King 1958', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (11, 'Cellvibrio gilvus', NULL, 'equivalent name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (11, '[Cellvibrio] gilvus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (13, 'Dictyoglomus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (13, 'Dictyoglomus Saiki et al. 1985', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (14, 'ATCC 35947', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (14, 'DSM 3960', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (14, 'Dictyoglomus thermophilum', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (14, 'Dictyoglomus thermophilum Saiki et al. 1985', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (14, 'strain H-6-12', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (16, 'Methyliphilus', NULL, 'equivalent name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (16, 'Methylophilus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (16, 'Methylophilus Jenkins et al. 1987', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (16, 'Methylotrophus', NULL, 'misspelling');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'ATCC 53528', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'DSM 46235', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'LMG 6787', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'Methyliphilus methylitrophus', NULL, 'equivalent name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'Methyliphilus methylotrophus', NULL, 'equivalent name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'Methylophilus methylitrophus', NULL, 'equivalent name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'Methylophilus methylotrophus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'Methylophilus methylotrophus Jenkins et al. 1987', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'Methylophilus sp. CBMB147', NULL, 'includes');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'Methylotrophus methylophilus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'NCIB 10515', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'NCIMB 10515', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (17, 'VKM B-1623', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (18, 'Pelobacter', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (18, 'Pelobacter Schink and Pfennig 1983', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (19, 'DSM 2380', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (19, 'NBRC 103641', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (19, 'Pelobacter carbinolicus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (19, 'Pelobacter carbinolicus Schink 1984', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (19, 'strain Gra Bd 1', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (20, 'Phenylobacterium', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (20, 'Phenylobacterium Lingens et al. 1985 emend. Abraham et al. 2008', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (20, 'Phenylobacterium Lingens et al. 1985 emend. Kanso and Patel 2004', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (20, 'Phenylobacterium Lingens et al. 1985 emend. Oh and Roh 2012', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (20, 'Phenylobacterium Lingens et al. 1985 emend. Tiago et al. 2005', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (21, 'ATCC 35973', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (21, 'CIP 103305', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (21, 'DSM 1986', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (21, 'LMG 6165', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (21, 'Phenylobacterium immobile', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (21, 'Phenylobacterium immobile Lingens et al. 1985', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (22, 'Shewanella', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (22, 'Shewanella MacDonell and Colwell 1986', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (23, 'ATCC 39565', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (23, 'Alteromonas colwelliana', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (23, 'Alteromonas colwelliana Weiner et al. 1988', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (23, 'Shewanella affinis', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (23, 'Shewanella affinis Ivanova et al. 2004', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (23, 'Shewanella colwelliana', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (23, 'Shewanella colwelliana (Weiner et al. 1988) Coyne et al. 1990', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (23, 'strain LST-W', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, '"Pseudomonas putrefaciens" (Derby and Hammer) Long and Hammer 1941', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'ATCC 8071', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'Alteromonas putrefaciens', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'Alteromonas putrefaciens (ex Derby and Hammer) Lee et al. 1981', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'Alteromonas putrifaciens', NULL, 'misspelling');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'CCUG 13452 D', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'CFBP 3033', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'CFBP 3034', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'CIP 80.40', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'DSM 6067', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'IFO 3908', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'JCM 20190', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'JCM 9294', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'LMG 2268', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'NBRC 3908', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'NCIB 10471', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'NCIMB 10471', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'NCTC 12960', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'Pseudomonas putrefaciens', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'Shewanella putrefaciens', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'Shewanella putrefaciens (Lee et al. 1981) MacDonell and Colwell 1986', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'Shewanella putrifaciens', NULL, 'misspelling');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (24, 'strain Hammer 95', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'ATCC 33224', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'Alteromonas hanedai', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'Alteromonas hanedai Jensen et al. 1981', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'CCUG 16097', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'CIP 103207', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'DSM 6066', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'JCM 20706', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'LMG 19004', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'NBRC 102223', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'Shewanella hanedai', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'Shewanella hanedai (Jensen et al. 1981) MacDonell and Colwell 1986', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (25, 'strain 281', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (27, 'halophilic eubacterium (NRCC 41227)', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (27, 'halophilic eubacterium NRCC 41227', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (27, 'halophilic eubacterium NRCC41227', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (28, 'halophilic eubacterium', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (29, 'Myxobacteria', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (29, 'Myxococcales', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (29, 'Myxococcales Tchan et al. 1948', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (29, 'The Myxobacteria', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (29, 'fruiting gliding bacteria', NULL, 'genbank common name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (31, 'Myxococcaceae', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (31, 'Myxococcaceae Jahn 1924', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (32, 'Myxococcus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (32, 'Myxococcus Thaxter 1892', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (33, '"Micrococcus fulvus" Cohn 1875', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (33, 'ATCC 25199', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (33, 'Micrococcus fulvus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (33, 'Myxococcus fulvus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (33, 'Myxococcus fulvus (Cohn 1875) Jahn 1911', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (33, 'NBRC 100333', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (33, 'NCIMB 13349', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'ATCC 25232', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'CCUG 2079', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'CIP 107069', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'IFO 13542', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'Myxococcus xanthus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'Myxococcus xanthus Beebe 1941', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'Myxococcus xanthus retron Mx162', NULL, 'includes');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'Myxococcus xanthus retron Mx65', NULL, 'includes');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (34, 'NBRC 13542', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, '"Chondrococcus macrosporus" Krzemieniewska and Krzemieniewski 1926', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'CIP 109128', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'Chondrococcus macrosporus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'Corallococcus macrosporus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'Corallococcus macrosporus Reichenbach 2007', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'DSM 14697', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'JCM 12621', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'Myxococcus macrosporus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'Myxococcus macrosporus (Krzemieniewska and Krzemieniewski 1926) Zahler and McCurdy 1974 (Approved Lists 1980)', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'not "Myxococcus macrosporus" Zukal 1897', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (35, 'strain Cc m8', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (38, '"Angiococcus disciformis" (Thaxter 1904) Jahn 1924', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (38, '"Cystobacter disciformis" (Thaxter 1904) Brockman and McCurdy 1989', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (38, 'Angiococcus disciformis', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (38, 'Angiococcus disciformis (Thaxter 1904) Hook et al. 1980', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (38, 'Cystobacter disciformis', NULL, 'genbank synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (38, 'Myxococcus disciformis', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (38, 'Myxococcus disciformis Thaxter 1904 (Approved Lists 1980)', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (39, 'Archangiaceae', NULL, 'includes');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (39, 'Archangiaceae Jahn 1924', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (39, 'Cystobacteraceae', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (39, 'Cystobacteraceae McCurdy 1970', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (40, 'Stigmatella', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (40, 'Stigmatella Berkeley and Curtis 1875', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (41, '"Chondromyces aurantiacus" (Berkeley and Curtis) Thaxter 1892', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (41, 'ATCC 25190', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (41, 'Chondromyces aurantiacus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (41, 'Stigmatella aurantiaca', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (41, 'Stigmatella aurantiaca Berkeley and Curtis 1875', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (42, '"Angiococcus" Jahn 1924', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (42, 'Angiococcus', NULL, 'includes');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (42, 'Angiococcus (ex Jahn 1924) Hook et al. 1980', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (42, 'Cystobacter', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (42, 'Cystobacter Schroeter 1886', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (43, '"Polyangium fuscum" (Schroeter 1886) Thaxter 1904', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (43, 'ATCC 25194', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (43, 'Cystobacter fuscus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (43, 'Cystobacter fuscus Schroeter 1886', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (43, 'DSM 2262', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (43, 'Polyangium fuscum', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (44, 'Melittangium', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (44, 'Melittangium Jahn 1924', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, '"Chondromyces gracilipes" Thaxter 1897', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, '"Chondromyces lichenicolus" Thaxter 1892', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, '"Chondromyces minor" Krzemieniewska and Krzemieniewski 1930', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, '"Podangium gracilipes" (Thaxter 1897) Jahn 1924', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, '"Podangium lichenicolum" (Thaxter 1892) Jahn 1924', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, 'ATCC 25944', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, 'Chondromyces gracilipes', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, 'Chondromyces lichenicolus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, 'Chondromyces minor', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, 'Melittangium lichenicola', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, 'Melittangium lichenicola (Thaxter 1892) McCurdy 1971', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, 'Podangium gracilipes', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (45, 'Podangium lichenicolum', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (47, 'Archangium', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (47, 'Archangium Jahn 1924', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, '"Chondrococcus cerebriformis" (Kofler) Jahn 1924', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, '"Chondromyces serpens" Quehl 1906', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, '"Myxococcus cerebriformis" Kofler 1913', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, 'ATCC 25201', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, 'Archangium gephyra', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, 'Archangium gephyra Jahn 1924', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, 'Chondrococcus cerebriformis', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, 'Chondromyces serpens', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, 'DSM 2261', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (48, 'Myxococcus cerebriformis', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (49, '"Sorangiaceae" Jahn 1924', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (49, 'Polyangiaceae', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (49, 'Polyangiaceae Jahn 1924', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (49, 'Sorangiaceae', NULL, 'includes');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (50, '"Myxobotrys" Zukal 1896', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (50, '"Polycephalum" Kalchbrenner and Cooke 1880', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (50, 'Chondromyces', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (50, 'Chondromyces Berkeley and Curtis 1874', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (50, 'Chrondromyces', NULL, 'misspelling');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (50, 'Myxobotrys', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (50, 'Polycephalum', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (51, 'Chondromyces apiculatus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (51, 'Chondromyces apiculatus Thaxter 1897', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (51, 'Chrondromyces apiculatus', NULL, 'misspelling');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (51, 'TC 4481', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (52, '"Myxobotrys variabilis" Zukal 1896 (putative synonym)', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (52, 'Chondromyces crocatus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (52, 'Chondromyces crocatus Berkeley and Curtis 1874', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (52, 'Chrondromyces crocatus', NULL, 'misspelling');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (52, 'Myxobotrys variabilis', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (52, 'TC 601', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (53, 'Nannocystis', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (53, 'Nannocystis Reichenbach 1970', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (54, 'ATCC 25963', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (54, 'DSM 71', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (54, 'Nannocystis exedens', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (54, 'Nannocystis exedens Reichenbach 1970', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (55, 'Polyangium', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (55, 'Polyangium Link 1809', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, '"Polyangium compositum" Thaxter 1904', '"Polyangium compositum" Thaxter 1904 <Sorangium cellulosum>', 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, '"Sorangium cellulosum" (Imshenetski and Solntseva 1936) Imshenetski and Solntseva 1937', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, '"Sorangium compositum" Jahn 1924', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, '"Sorangium compositum" Krzemieniewska and Krzemieniewski 1937', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, '"Sorangium nigrescens" Krzemieniewska and Krzemieniewski 1937', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, '"Sorangium nigrum" Krzemieniewska and Krzemieniewski 1937', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'CIP 109122', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'DSM 14627', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'JCM 12707', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'Polyangium cellulosum', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'Polyangium cellulosum (ex Imshenetski and Solntseva 1936) Brockman 1989', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'Polyangium compositum', 'Polyangium compositum <Sorangium cellulosum>', 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'Sorangium cellulosum', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'Sorangium cellulosum (Brockman 1989) Reichenbach 2007', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'Sorangium compositum', 'Sorangium compositum <Sorangium cellulosum>', 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'Sorangium nigrescens', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'Sorangium nigrum', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (56, 'strain So ce1871', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (57, 'Polyangium sp.', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (59, 'Vitreoscilla', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (59, 'Vitreoscilla Pringsheim 1949', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (60, 'Vitreoscilla sp.', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (61, 'ATCC 15218', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (61, 'DSM 513', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (61, 'LMG 7756', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (61, 'Vitreoscilla stercoraria', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (61, 'Vitreoscilla stercoraria Pringsheim 1951 (Approved Lists 1980) emend. Strohl et al. 1986', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (62, 'ATCC 43189', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (62, 'Vitreoscilla beggiatoides', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (62, 'Vitreoscilla beggiatoides Pringsheim 1949 (Approved Lists 1980) emend. Strohl et al. 1986', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (62, 'strain B23SS', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (63, '"Vitreoscilla filiformis" Pringsheim 1951', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (63, 'ATCC 43190', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (63, 'Vitreoscilla filiformis', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (63, 'Vitreoscilla filiformis (ex Pringsheim 1951) Strohl et al. 1986', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (63, 'strain L1401-2', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (64, 'Herpetosiphon', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (64, 'Herpetosiphon Holt and Lewin 1968', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (65, 'ATCC 23779', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (65, 'CCUG 48726', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (65, 'DSM 785', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (65, 'HAMBI 1968', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (65, 'Herpetosiphon aurantiacus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (65, 'Herpetosiphon aurantiacus Holt and Lewin 1968', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (65, 'Herpetosiphon giganteus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (68, 'Lysobacter', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (68, 'Lysobacter Christensen and Cook 1978 (Approved Lists 1980) emend. Park et al. 2008', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (69, 'ATCC 29487', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (69, 'DSM 2043', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (69, 'LMG 8762', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (69, 'Lysobacter enzymogenes', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (69, 'Lysobacter enzymogenes Christensen and Cook 1978', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (69, 'UASM 495', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (71, 'Simonsiella', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (71, 'Simonsiella Schmid 1922', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, '"Caryophanon muelleri" (Schmid 1922) Peshkoff 1948', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'ATCC 29453', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'CCUG 30554', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'CIP 103436', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'Caryophanon muelleri', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'DSM 2579', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'LMG 7828', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'Scheibenbakterien', NULL, 'common name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'Scheibenbakterien Muller 1911', NULL, 'common name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'Simonsiella muelleri', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (72, 'Simonsiella muelleri Schmid 1922', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (75, 'Caulobacter', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (75, 'Caulobacter Henrici and Johnson 1935 (Approved Lists 1980) emend. Abraham et al. 1999', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (78, 'Caulobacter sp.', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (81, 'Hyphomicrobium', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (81, 'Hyphomicrobium Stutzer and Hartleb 1898', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (81, 'Hyphomicrobium Stutzer and Hartleb 1899 (sic)', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (82, 'Hyphomicrobium sp.', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (83, 'ATCC 33404', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (83, 'Hyphomicrobium vulgare', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (83, 'Hyphomicrobium vulgare Stutzer and Hartleb 1898', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (83, 'Hyphomicrobium vulgare Stutzer and Hartleb 1899 (sic)', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (83, 'JCM 6889', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (83, 'NCIB 9698', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (84, 'ATCC 35216', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (84, 'DSM 5458', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (84, 'Hyphomicrobium methylovorum', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (84, 'Hyphomicrobium methylovorum Izumi et al. 1983', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (84, 'IFO 14180', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (84, 'JCM 6890', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (84, 'NBRC 14180', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (84, 'strain KM 146', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (85, 'Hyphomonas', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (85, 'Hyphomonas (ex Pongratz 1957) Moore et al. 1984 emend. Weiner et al. 2000', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (86, 'ATCC 33883', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (86, 'DSM 5153', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (86, 'Hyphomonas jannaschiana', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (86, 'Hyphomonas jannaschiana Weiner et al. 1985', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (86, 'strain VP2', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (87, 'Hyphomonas sp.', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (88, '"Chlamydothrix" Migula 1900', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (88, '"Detoniella" Trevisan in de Toni and Trevisan 1889', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (88, 'Chlamydothrix', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (88, 'Detoniella', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (88, 'Leptothrix', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (88, 'Leptothrix Kutzing 1843', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, '"Leptothrix crassa" Cholodny 1924', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, '"Leptothrix discophora" (Schwers 1912) Dorff 1934', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, '"Megalothrix discophora" Schwers 1912', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, 'ATCC 43182', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, 'LMG 8141', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, 'Leptothrix crassa', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, 'Leptothrix discophora', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, 'Leptothrix discophora (ex Schwers 1912) Spring et al. 1997', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, 'Megalothrix discophora', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (89, 'strain SS-1', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (93, 'Stella', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (93, 'Stella Vasilyeva 1985', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (94, 'ATCC 43930', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (94, 'AUCM B-1137', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (94, 'DSM 5900', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (94, 'Stella humosa', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (94, 'Stella humosa Vasilyeva 1985', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (94, 'VKM B-1137', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (96, 'Gallionella', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (96, 'Gallionella Ehrenberg 1838', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (97, '"Chlamydothrix ferruginea" (Ehrenberg 1838) Migula 1900', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (97, '"Spirillum ferrugineum" (Ehrenberg 1838) de Toni and Trevisan 1889', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (97, '"Spirophyllum ferrugineum" (Ehrenberg 1838) Ellis 1907', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (97, 'Chlamydothrix ferruginea', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (97, 'Gallionella ferruginea', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (97, 'Gallionella ferruginea Ehrenberg 1838', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (97, 'Spirillum ferrugineum', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (97, 'Spirophyllum ferrugineum', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (99, '"Renobacter" Nikitin 1971', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (99, 'Ancylobacter', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (99, 'Ancylobacter Raj 1983', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (99, 'Microcyclus', 'Microcyclus <bacteria>', 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (99, 'Microcyclus Orskov 1928 (Approved Lists 1980)', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (99, 'Renobacter', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'ATCC 25396', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'Ancylobacter aquaticus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'Ancylobacter aquaticus (Orskov 1928) Raj 1983', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'CCUG 1820', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'CCUG 30551', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'DSM 101', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'JCM 20518', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'LMG 4052', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'Microcyclus aquaticus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'Microcyclus aquaticus Orskov 1928 (Approved Lists 1980)', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'NBRC 102453', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'VKM B-1287', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (100, 'strain rskov', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (101, 'Flectobacillus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (101, 'Flectobacillus Larkin et al. 1977 (Approved Lists 1980) emend. Raj and Maloy 1990', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'ACAM 171', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'ATCC 43844', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'CIP 103112', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'Flectobacillus glomeratus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'Flectobacillus glomeratus McGuire et al. 1988', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'LMG 13858', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'Polaribacter glomeratus', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'Polaribacter glomeratus (McGuire et al. 1988) Gosink et al. 1998', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (102, 'UQM 3055', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (103, '"Microcyclus major" Gromov 1963', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (103, 'ATCC 29496', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (103, 'DSM 103', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (103, 'Flectobacillus major', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (103, 'Flectobacillus major (Gromov 1963) Larkin et al. 1977', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (103, 'LMG 13163', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (103, 'Microcyclus major', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (103, 'VKM B-859', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, '"Microcyclus marinus" Raj 1976', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'ATCC 25205', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'Cyclibacterium marinum', NULL, 'misspelling');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'Cyclobacterium marinum', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'Cyclobacterium marinum corrig. (Raj 1976) Raj and Maloy 1990', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'Cyclobacterium marinus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'DSM 745', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'Flectobacillus marinus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'Flectobacillus marinus (Raj 1976) Borrall and Larkin 1978 (Approved Lists 1980)', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'LMG 13164', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'Microcyclus marinus', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (104, 'strain Raj', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (105, 'Runella', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (105, 'Runella Larkin and Williams 1978', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (106, 'ATCC 29530', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (106, 'DSM 19594', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (106, 'LMG 11500', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (106, 'Runella slithyformis', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (106, 'Runella slithyformis Larkin and Williams 1978', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (107, 'Spirosoma', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (107, 'Spirosoma Migula 1894 (Approved Lists 1980) emend. Finster et al. 2009', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (108, 'ATCC 33905', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (108, 'DSM 74', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (108, 'LMG 10896', NULL, 'type material');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (108, 'Spirosoma linguale', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (108, 'Spirosoma linguale Migula 1894', NULL, 'authority');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (109, 'Blastobacter', NULL, 'scientific name');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (109, 'Blastobacter Zavarzin 1961 (Approved Lists 1980) emend. Sly 1985', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (110, '"Blastobacter viscosus" Loginova and Trotensko 1979', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, name_class) VALUES (110, '"Blastobacter viscosus" Loginova and Trotsenok 1979', NULL, 'synonym');
+INSERT INTO ncbi_names (tax_id, name_txt, unique_name, ...
 
[truncated message content]

[Treebase-guts] SF.net SVN: treebase:[1100] trunk

From: <hs...@us...> - 2013-06-04 17:44:51

Revision: 1100
          http://sourceforge.net/p/treebase/code/1100
Author:   hshyket
Date:     2013-06-04 17:44:39 +0000 (Tue, 04 Jun 2013)
Log Message:
-----------
Adding classification search functionality. Adding NCBI tables.  Updating POM files to point to new JBoss repository.

Modified Paths:
--------------
    trunk/pom.xml
    trunk/treebase-core/pom.xml
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeHome.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeService.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/tree/PhyloTreeServiceImpl.java
    trunk/treebase-web/pom.xml
    trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml

Added Paths:
-----------
    trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/
    trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi_nodes.sql
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ClassificationSearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSClassificationController.java
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/classificationSearch.jsp

Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml	2013-02-22 22:37:40 UTC (rev 1099)
+++ trunk/pom.xml	2013-06-04 17:44:39 UTC (rev 1100)
@@ -184,7 +184,7 @@
     <repository>
       <id>repository.jboss.org</id>
       <name>JBoss Maven Repository</name>
-      <url>http://repository.jboss.org/maven2</url>
+      <url>https://repository.jboss.org/nexus/content/groups/public/maven2</url>
       <layout>default</layout>
     </repository>
 

Added: trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi_nodes.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi_nodes.sql	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2013-06-04_add_ncbi_tables/ncbi_nodes.sql	2013-06-04 17:44:39 UTC (rev 1100)
@@ -0,0 +1,1496333 @@
+--
+-- PostgreSQL database dump
+--
+
+-- Dumped from database version 9.1.3
+-- Dumped by pg_dump version 9.1.3
+-- Started on 2013-05-31 13:56:07
+
+SET statement_timeout = 0;
+SET client_encoding = 'UTF8';
+SET standard_conforming_strings = on;
+SET check_function_bodies = false;
+SET client_min_messages = warning;
+
+SET search_path = public, pg_catalog;
+
+SET default_tablespace = '';
+
+SET default_with_oids = false;
+
+--
+-- TOC entry 161 (class 1259 OID 83891)
+-- Dependencies: 5
+-- Name: ncbi_names; Type: TABLE; Schema: public; Owner: piel; Tablespace: 
+--
+
+CREATE TABLE ncbi_names (
+    tax_id integer NOT NULL,
+    name_txt character varying(255) NOT NULL,
+    unique_name character varying(255),
+    name_class character varying(32)
+);
+
+
+ALTER TABLE public.ncbi_names OWNER TO piel;
+
+--
+-- TOC entry 1877 (class 0 OID 83891)
+-- Dependencies: 161
+-- Data for Name: ncbi_names; Type: TABLE DATA; Schema: public; Owner: piel
+--
+
+COPY ncbi_names (tax_id, name_txt, unique_name, name_class) FROM stdin;
+1	all	\N	synonym
+1	root	\N	scientific name
+2	Bacteria	Bacteria <prokaryote>	scientific name
+2	Monera	Monera <Bacteria>	in-part
+2	Procaryotae	Procaryotae <Bacteria>	in-part
+2	Prokaryota	Prokaryota <Bacteria>	in-part
+2	Prokaryotae	Prokaryotae <Bacteria>	in-part
+2	bacteria	bacteria <blast2>	blast name
+2	eubacteria	\N	genbank common name
+2	not Bacteria Haeckel 1894	\N	synonym
+2	prokaryote	prokaryote <Bacteria>	in-part
+2	prokaryotes	prokaryotes <Bacteria>	in-part
+6	Azorhizobium	\N	scientific name
+6	Azorhizobium Dreyfus et al. 1988	\N	synonym
+6	Azotirhizobium	\N	equivalent name
+7	ATCC 43989	\N	type material
+7	Azorhizobium caulinodans	\N	scientific name
+7	Azorhizobium caulinodans Dreyfus et al. 1988	\N	synonym
+7	Azotirhizobium caulinodans	\N	equivalent name
+7	CCUG 26647	\N	type material
+7	DSM 5975	\N	type material
+7	IFO 14845	\N	type material
+7	JCM 20966	\N	type material
+7	LMG 6465	\N	type material
+7	NBRC 14845	\N	type material
+7	ORS 571	\N	type material
+9	Acyrthosiphon pisum symbiont P	\N	includes
+9	Buchnera aphidicola	\N	scientific name
+9	Buchnera aphidicola Munson et al. 1991	\N	synonym
+10	"Cellvibrio" Winogradsky 1929	\N	synonym
+10	Cellvibrio	\N	scientific name
+10	Cellvibrio (ex Winogradsky 1929) Blackall et al. 1986 emend. Humphry et al. 2003	\N	synonym
+11	"Cellvibrio gilvus" Hulcher and King 1958	\N	authority
+11	Cellvibrio gilvus	\N	equivalent name
+11	[Cellvibrio] gilvus	\N	scientific name
+13	Dictyoglomus	\N	scientific name
+13	Dictyoglomus Saiki et al. 1985	\N	authority
+14	ATCC 35947	\N	type material
+14	DSM 3960	\N	type material
+14	Dictyoglomus thermophilum	\N	scientific name
+14	Dictyoglomus thermophilum Saiki et al. 1985	\N	authority
+14	strain H-6-12	\N	type material
+16	Methyliphilus	\N	equivalent name
+16	Methylophilus	\N	scientific name
+16	Methylophilus Jenkins et al. 1987	\N	synonym
+16	Methylotrophus	\N	misspelling
+17	ATCC 53528	\N	type material
+17	DSM 46235	\N	type material
+17	LMG 6787	\N	type material
+17	Methyliphilus methylitrophus	\N	equivalent name
+17	Methyliphilus methylotrophus	\N	equivalent name
+17	Methylophilus methylitrophus	\N	equivalent name
+17	Methylophilus methylotrophus	\N	scientific name
+17	Methylophilus methylotrophus Jenkins et al. 1987	\N	authority
+17	Methylophilus sp. CBMB147	\N	includes
+17	Methylotrophus methylophilus	\N	synonym
+17	NCIB 10515	\N	type material
+17	NCIMB 10515	\N	type material
+17	VKM B-1623	\N	type material
+18	Pelobacter	\N	scientific name
+18	Pelobacter Schink and Pfennig 1983	\N	authority
+19	DSM 2380	\N	type material
+19	NBRC 103641	\N	type material
+19	Pelobacter carbinolicus	\N	scientific name
+19	Pelobacter carbinolicus Schink 1984	\N	authority
+19	strain Gra Bd 1	\N	type material
+20	Phenylobacterium	\N	scientific name
+20	Phenylobacterium Lingens et al. 1985 emend. Abraham et al. 2008	\N	authority
+20	Phenylobacterium Lingens et al. 1985 emend. Kanso and Patel 2004	\N	authority
+20	Phenylobacterium Lingens et al. 1985 emend. Oh and Roh 2012	\N	authority
+20	Phenylobacterium Lingens et al. 1985 emend. Tiago et al. 2005	\N	authority
+21	ATCC 35973	\N	type material
+21	CIP 103305	\N	type material
+21	DSM 1986	\N	type material
+21	LMG 6165	\N	type material
+21	Phenylobacterium immobile	\N	scientific name
+21	Phenylobacterium immobile Lingens et al. 1985	\N	authority
+22	Shewanella	\N	scientific name
+22	Shewanella MacDonell and Colwell 1986	\N	synonym
+23	ATCC 39565	\N	type material
+23	Alteromonas colwelliana	\N	synonym
+23	Alteromonas colwelliana Weiner et al. 1988	\N	authority
+23	Shewanella affinis	\N	synonym
+23	Shewanella affinis Ivanova et al. 2004	\N	authority
+23	Shewanella colwelliana	\N	scientific name
+23	Shewanella colwelliana (Weiner et al. 1988) Coyne et al. 1990	\N	authority
+23	strain LST-W	\N	type material
+24	"Pseudomonas putrefaciens" (Derby and Hammer) Long and Hammer 1941	\N	authority
+24	ATCC 8071	\N	type material
+24	Alteromonas putrefaciens	\N	synonym
+24	Alteromonas putrefaciens (ex Derby and Hammer) Lee et al. 1981	\N	authority
+24	Alteromonas putrifaciens	\N	misspelling
+24	CCUG 13452 D	\N	type material
+24	CFBP 3033	\N	type material
+24	CFBP 3034	\N	type material
+24	CIP 80.40	\N	type material
+24	DSM 6067	\N	type material
+24	IFO 3908	\N	type material
+24	JCM 20190	\N	type material
+24	JCM 9294	\N	type material
+24	LMG 2268	\N	type material
+24	NBRC 3908	\N	type material
+24	NCIB 10471	\N	type material
+24	NCIMB 10471	\N	type material
+24	NCTC 12960	\N	type material
+24	Pseudomonas putrefaciens	\N	synonym
+24	Shewanella putrefaciens	\N	scientific name
+24	Shewanella putrefaciens (Lee et al. 1981) MacDonell and Colwell 1986	\N	authority
+24	Shewanella putrifaciens	\N	misspelling
+24	strain Hammer 95	\N	type material
+25	ATCC 33224	\N	type material
+25	Alteromonas hanedai	\N	synonym
+25	Alteromonas hanedai Jensen et al. 1981	\N	synonym
+25	CCUG 16097	\N	type material
+25	CIP 103207	\N	type material
+25	DSM 6066	\N	type material
+25	JCM 20706	\N	type material
+25	LMG 19004	\N	type material
+25	NBRC 102223	\N	type material
+25	Shewanella hanedai	\N	scientific name
+25	Shewanella hanedai (Jensen et al. 1981) MacDonell and Colwell 1986	\N	synonym
+25	strain 281	\N	type material
+27	halophilic eubacterium (NRCC 41227)	\N	synonym
+27	halophilic eubacterium NRCC 41227	\N	scientific name
+27	halophilic eubacterium NRCC41227	\N	synonym
+28	halophilic eubacterium	\N	scientific name
+29	Myxobacteria	\N	synonym
+29	Myxococcales	\N	scientific name
+29	Myxococcales Tchan et al. 1948	\N	authority
+29	The Myxobacteria	\N	synonym
+29	fruiting gliding bacteria	\N	genbank common name
+31	Myxococcaceae	\N	scientific name
+31	Myxococcaceae Jahn 1924	\N	synonym
+32	Myxococcus	\N	scientific name
+32	Myxococcus Thaxter 1892	\N	synonym
+33	"Micrococcus fulvus" Cohn 1875	\N	authority
+33	ATCC 25199	\N	type material
+33	Micrococcus fulvus	\N	synonym
+33	Myxococcus fulvus	\N	scientific name
+33	Myxococcus fulvus (Cohn 1875) Jahn 1911	\N	authority
+33	NBRC 100333	\N	type material
+33	NCIMB 13349	\N	type material
+34	ATCC 25232	\N	type material
+34	CCUG 2079	\N	type material
+34	CIP 107069	\N	type material
+34	IFO 13542	\N	type material
+34	Myxococcus xanthus	\N	scientific name
+34	Myxococcus xanthus Beebe 1941	\N	authority
+34	Myxococcus xanthus retron Mx162	\N	includes
+34	Myxococcus xanthus retron Mx65	\N	includes
+34	NBRC 13542	\N	type material
+35	"Chondrococcus macrosporus" Krzemieniewska and Krzemieniewski 1926	\N	authority
+35	CIP 109128	\N	type material
+35	Chondrococcus macrosporus	\N	synonym
+35	Corallococcus macrosporus	\N	scientific name
+35	Corallococcus macrosporus Reichenbach 2007	\N	authority
+35	DSM 14697	\N	type material
+35	JCM 12621	\N	type material
+35	Myxococcus macrosporus	\N	synonym
+35	Myxococcus macrosporus (Krzemieniewska and Krzemieniewski 1926) Zahler and McCurdy 1974 (Approved Lists 1980)	\N	authority
+35	not "Myxococcus macrosporus" Zukal 1897	\N	authority
+35	strain Cc m8	\N	type material
+38	"Angiococcus disciformis" (Thaxter 1904) Jahn 1924	\N	authority
+38	"Cystobacter disciformis" (Thaxter 1904) Brockman and McCurdy 1989	\N	authority
+38	Angiococcus disciformis	\N	scientific name
+38	Angiococcus disciformis (Thaxter 1904) Hook et al. 1980	\N	authority
+38	Cystobacter disciformis	\N	genbank synonym
+38	Myxococcus disciformis	\N	synonym
+38	Myxococcus disciformis Thaxter 1904 (Approved Lists 1980)	\N	authority
+39	Archangiaceae	\N	includes
+39	Archangiaceae Jahn 1924	\N	authority
+39	Cystobacteraceae	\N	scientific name
+39	Cystobacteraceae McCurdy 1970	\N	authority
+40	Stigmatella	\N	scientific name
+40	Stigmatella Berkeley and Curtis 1875	\N	synonym
+41	"Chondromyces aurantiacus" (Berkeley and Curtis) Thaxter 1892	\N	authority
+41	ATCC 25190	\N	type material
+41	Chondromyces aurantiacus	\N	synonym
+41	Stigmatella aurantiaca	\N	scientific name
+41	Stigmatella aurantiaca Berkeley and Curtis 1875	\N	authority
+42	"Angiococcus" Jahn 1924	\N	authority
+42	Angiococcus	\N	includes
+42	Angiococcus (ex Jahn 1924) Hook et al. 1980	\N	authority
+42	Cystobacter	\N	scientific name
+42	Cystobacter Schroeter 1886	\N	authority
+43	"Polyangium fuscum" (Schroeter 1886) Thaxter 1904	\N	authority
+43	ATCC 25194	\N	type material
+43	Cystobacter fuscus	\N	scientific name
+43	Cystobacter fuscus Schroeter 1886	\N	authority
+43	DSM 2262	\N	type material
+43	Polyangium fuscum	\N	synonym
+44	Melittangium	\N	scientific name
+44	Melittangium Jahn 1924	\N	synonym
+45	"Chondromyces gracilipes" Thaxter 1897	\N	authority
+45	"Chondromyces lichenicolus" Thaxter 1892	\N	authority
+45	"Chondromyces minor" Krzemieniewska and Krzemieniewski 1930	\N	authority
+45	"Podangium gracilipes" (Thaxter 1897) Jahn 1924	\N	authority
+45	"Podangium lichenicolum" (Thaxter 1892) Jahn 1924	\N	authority
+45	ATCC 25944	\N	type material
+45	Chondromyces gracilipes	\N	synonym
+45	Chondromyces lichenicolus	\N	synonym
+45	Chondromyces minor	\N	synonym
+45	Melittangium lichenicola	\N	scientific name
+45	Melittangium lichenicola (Thaxter 1892) McCurdy 1971	\N	authority
+45	Podangium gracilipes	\N	synonym
+45	Podangium lichenicolum	\N	synonym
+47	Archangium	\N	scientific name
+47	Archangium Jahn 1924	\N	synonym
+48	"Chondrococcus cerebriformis" (Kofler) Jahn 1924	\N	synonym
+48	"Chondromyces serpens" Quehl 1906	\N	synonym
+48	"Myxococcus cerebriformis" Kofler 1913	\N	synonym
+48	ATCC 25201	\N	type material
+48	Archangium gephyra	\N	scientific name
+48	Archangium gephyra Jahn 1924	\N	synonym
+48	Chondrococcus cerebriformis	\N	synonym
+48	Chondromyces serpens	\N	synonym
+48	DSM 2261	\N	type material
+48	Myxococcus cerebriformis	\N	synonym
+49	"Sorangiaceae" Jahn 1924	\N	authority
+49	Polyangiaceae	\N	scientific name
+49	Polyangiaceae Jahn 1924	\N	authority
+49	Sorangiaceae	\N	includes
+50	"Myxobotrys" Zukal 1896	\N	authority
+50	"Polycephalum" Kalchbrenner and Cooke 1880	\N	authority
+50	Chondromyces	\N	scientific name
+50	Chondromyces Berkeley and Curtis 1874	\N	authority
+50	Chrondromyces	\N	misspelling
+50	Myxobotrys	\N	synonym
+50	Polycephalum	\N	synonym
+51	Chondromyces apiculatus	\N	scientific name
+51	Chondromyces apiculatus Thaxter 1897	\N	authority
+51	Chrondromyces apiculatus	\N	misspelling
+51	TC 4481	\N	type material
+52	"Myxobotrys variabilis" Zukal 1896 (putative synonym)	\N	synonym
+52	Chondromyces crocatus	\N	scientific name
+52	Chondromyces crocatus Berkeley and Curtis 1874	\N	synonym
+52	Chrondromyces crocatus	\N	misspelling
+52	Myxobotrys variabilis	\N	synonym
+52	TC 601	\N	type material
+53	Nannocystis	\N	scientific name
+53	Nannocystis Reichenbach 1970	\N	authority
+54	ATCC 25963	\N	type material
+54	DSM 71	\N	type material
+54	Nannocystis exedens	\N	scientific name
+54	Nannocystis exedens Reichenbach 1970	\N	synonym
+55	Polyangium	\N	scientific name
+55	Polyangium Link 1809	\N	authority
+56	"Polyangium compositum" Thaxter 1904	"Polyangium compositum" Thaxter 1904 <Sorangium cellulosum>	authority
+56	"Sorangium cellulosum" (Imshenetski and Solntseva 1936) Imshenetski and Solntseva 1937	\N	authority
+56	"Sorangium compositum" Jahn 1924	\N	authority
+56	"Sorangium compositum" Krzemieniewska and Krzemieniewski 1937	\N	authority
+56	"Sorangium nigrescens" Krzemieniewska and Krzemieniewski 1937	\N	authority
+56	"Sorangium nigrum" Krzemieniewska and Krzemieniewski 1937	\N	authority
+56	CIP 109122	\N	type material
+56	DSM 14627	\N	type material
+56	JCM 12707	\N	type material
+56	Polyangium cellulosum	\N	synonym
+56	Polyangium cellulosum (ex Imshenetski and Solntseva 1936) Brockman 1989	\N	authority
+56	Polyangium compositum	Polyangium compositum <Sorangium cellulosum>	synonym
+56	Sorangium cellulosum	\N	scientific name
+56	Sorangium cellulosum (Brockman 1989) Reichenbach 2007	\N	authority
+56	Sorangium compositum	Sorangium compositum <Sorangium cellulosum>	synonym
+56	Sorangium nigrescens	\N	synonym
+56	Sorangium nigrum	\N	synonym
+56	strain So ce1871	\N	type material
+57	Polyangium sp.	\N	scientific name
+59	Vitreoscilla	\N	scientific name
+59	Vitreoscilla Pringsheim 1949	\N	synonym
+60	Vitreoscilla sp.	\N	scientific name
+61	ATCC 15218	\N	type material
+61	DSM 513	\N	type material
+61	LMG 7756	\N	type material
+61	Vitreoscilla stercoraria	\N	scientific name
+61	Vitreoscilla stercoraria Pringsheim 1951 (Approved Lists 1980) emend. Strohl et al. 1986	\N	synonym
+62	ATCC 43189	\N	type material
+62	Vitreoscilla beggiatoides	\N	scientific name
+62	Vitreoscilla beggiatoides Pringsheim 1949 (Approved Lists 1980) emend. Strohl et al. 1986	\N	synonym
+62	strain B23SS	\N	type material
+63	"Vitreoscilla filiformis" Pringsheim 1951	\N	synonym
+63	ATCC 43190	\N	type material
+63	Vitreoscilla filiformis	\N	scientific name
+63	Vitreoscilla filiformis (ex Pringsheim 1951) Strohl et al. 1986	\N	synonym
+63	strain L1401-2	\N	type material
+64	Herpetosiphon	\N	scientific name
+64	Herpetosiphon Holt and Lewin 1968	\N	synonym
+65	ATCC 23779	\N	type material
+65	CCUG 48726	\N	type material
+65	DSM 785	\N	type material
+65	HAMBI 1968	\N	type material
+65	Herpetosiphon aurantiacus	\N	scientific name
+65	Herpetosiphon aurantiacus Holt and Lewin 1968	\N	authority
+65	Herpetosiphon giganteus	\N	synonym
+68	Lysobacter	\N	scientific name
+68	Lysobacter Christensen and Cook 1978 (Approved Lists 1980) emend. Park et al. 2008	\N	authority
+69	ATCC 29487	\N	type material
+69	DSM 2043	\N	type material
+69	LMG 8762	\N	type material
+69	Lysobacter enzymogenes	\N	scientific name
+69	Lysobacter enzymogenes Christensen and Cook 1978	\N	authority
+69	UASM 495	\N	type material
+71	Simonsiella	\N	scientific name
+71	Simonsiella Schmid 1922	\N	synonym
+72	"Caryophanon muelleri" (Schmid 1922) Peshkoff 1948	\N	authority
+72	ATCC 29453	\N	type material
+72	CCUG 30554	\N	type material
+72	CIP 103436	\N	type material
+72	Caryophanon muelleri	\N	synonym
+72	DSM 2579	\N	type material
+72	LMG 7828	\N	type material
+72	Scheibenbakterien	\N	common name
+72	Scheibenbakterien Muller 1911	\N	common name
+72	Simonsiella muelleri	\N	scientific name
+72	Simonsiella muelleri Schmid 1922	\N	authority
+75	Caulobacter	\N	scientific name
+75	Caulobacter Henrici and Johnson 1935 (Approved Lists 1980) emend. Abraham et al. 1999	\N	synonym
+78	Caulobacter sp.	\N	scientific name
+80	'Caulobacter spinosum'	\N	synonym
+80	Caulobacter spinosum	\N	scientific name
+81	Hyphomicrobium	\N	scientific name
+81	Hyphomicrobium Stutzer and Hartleb 1898	\N	authority
+81	Hyphomicrobium Stutzer and Hartleb 1899 (sic)	\N	authority
+82	Hyphomicrobium sp.	\N	scientific name
+83	ATCC 33404	\N	type material
+83	Hyphomicrobium vulgare	\N	scientific name
+83	Hyphomicrobium vulgare Stutzer and Hartleb 1898	\N	synonym
+83	Hyphomicrobium vulgare Stutzer and Hartleb 1899 (sic)	\N	synonym
+83	JCM 6889	\N	type material
+83	NCIB 9698	\N	type material
+84	ATCC 35216	\N	type material
+84	DSM 5458	\N	type material
+84	Hyphomicrobium methylovorum	\N	scientific name
+139	ATCC 35210	\N	type material
+84	Hyphomicrobium methylovorum Izumi et al. 1983	\N	synonym
+84	IFO 14180	\N	type material
+84	JCM 6890	\N	type material
+84	NBRC 14180	\N	type material
+84	strain KM 146	\N	type material
+85	Hyphomonas	\N	scientific name
+85	Hyphomonas (ex Pongratz 1957) Moore et al. 1984 emend. Weiner et al. 2000	\N	authority
+86	ATCC 33883	\N	type material
+86	DSM 5153	\N	type material
+86	Hyphomonas jannaschiana	\N	scientific name
+86	Hyphomonas jannaschiana Weiner et al. 1985	\N	authority
+86	strain VP2	\N	type material
+87	Hyphomonas sp.	\N	scientific name
+88	"Chlamydothrix" Migula 1900	\N	synonym
+88	"Detoniella" Trevisan in de Toni and Trevisan 1889	\N	synonym
+88	Chlamydothrix	\N	synonym
+88	Detoniella	\N	synonym
+88	Leptothrix	\N	scientific name
+88	Leptothrix Kutzing 1843	\N	synonym
+89	"Leptothrix crassa" Cholodny 1924	\N	synonym
+89	"Leptothrix discophora" (Schwers 1912) Dorff 1934	\N	synonym
+89	"Megalothrix discophora" Schwers 1912	\N	synonym
+89	ATCC 43182	\N	type material
+89	LMG 8141	\N	type material
+89	Leptothrix crassa	\N	synonym
+89	Leptothrix discophora	\N	scientific name
+89	Leptothrix discophora (ex Schwers 1912) Spring et al. 1997	\N	synonym
+89	Megalothrix discophora	\N	synonym
+89	strain SS-1	\N	type material
+93	Stella	\N	scientific name
+93	Stella Vasilyeva 1985	\N	synonym
+94	ATCC 43930	\N	type material
+94	AUCM B-1137	\N	type material
+94	DSM 5900	\N	type material
+94	Stella humosa	\N	scientific name
+94	Stella humosa Vasilyeva 1985	\N	synonym
+94	VKM B-1137	\N	type material
+96	Gallionella	\N	scientific name
+96	Gallionella Ehrenberg 1838	\N	authority
+97	"Chlamydothrix ferruginea" (Ehrenberg 1838) Migula 1900	\N	authority
+97	"Spirillum ferrugineum" (Ehrenberg 1838) de Toni and Trevisan 1889	\N	authority
+97	"Spirophyllum ferrugineum" (Ehrenberg 1838) Ellis 1907	\N	authority
+97	Chlamydothrix ferruginea	\N	synonym
+97	Gallionella ferruginea	\N	scientific name
+97	Gallionella ferruginea Ehrenberg 1838	\N	authority
+97	Spirillum ferrugineum	\N	synonym
+97	Spirophyllum ferrugineum	\N	synonym
+99	"Renobacter" Nikitin 1971	\N	authority
+99	Ancylobacter	\N	scientific name
+99	Ancylobacter Raj 1983	\N	authority
+99	Microcyclus	Microcyclus <bacteria>	synonym
+99	Microcyclus Orskov 1928 (Approved Lists 1980)	\N	authority
+99	Renobacter	\N	synonym
+100	ATCC 25396	\N	type material
+100	Ancylobacter aquaticus	\N	scientific name
+100	Ancylobacter aquaticus (Orskov 1928) Raj 1983	\N	synonym
+100	CCUG 1820	\N	type material
+100	CCUG 30551	\N	type material
+100	DSM 101	\N	type material
+100	JCM 20518	\N	type material
+100	LMG 4052	\N	type material
+100	Microcyclus aquaticus	\N	synonym
+100	Microcyclus aquaticus Orskov 1928 (Approved Lists 1980)	\N	synonym
+100	NBRC 102453	\N	type material
+100	VKM B-1287	\N	type material
+100	strain rskov	\N	type material
+101	Flectobacillus	\N	scientific name
+101	Flectobacillus Larkin et al. 1977 (Approved Lists 1980) emend. Raj and Maloy 1990	\N	authority
+102	ACAM 171	\N	type material
+102	ATCC 43844	\N	type material
+102	CIP 103112	\N	type material
+102	Flectobacillus glomeratus	\N	synonym
+102	Flectobacillus glomeratus McGuire et al. 1988	\N	authority
+102	LMG 13858	\N	type material
+102	Polaribacter glomeratus	\N	scientific name
+102	Polaribacter glomeratus (McGuire et al. 1988) Gosink et al. 1998	\N	authority
+102	UQM 3055	\N	type material
+103	"Microcyclus major" Gromov 1963	\N	authority
+103	ATCC 29496	\N	type material
+103	DSM 103	\N	type material
+103	Flectobacillus major	\N	scientific name
+103	Flectobacillus major (Gromov 1963) Larkin et al. 1977	\N	authority
+103	LMG 13163	\N	type material
+103	Microcyclus major	\N	synonym
+103	VKM B-859	\N	type material
+104	"Microcyclus marinus" Raj 1976	\N	authority
+104	ATCC 25205	\N	type material
+104	Cyclibacterium marinum	\N	misspelling
+104	Cyclobacterium marinum	\N	scientific name
+104	Cyclobacterium marinum corrig. (Raj 1976) Raj and Maloy 1990	\N	authority
+104	Cyclobacterium marinus	\N	synonym
+104	DSM 745	\N	type material
+104	Flectobacillus marinus	\N	synonym
+104	Flectobacillus marinus (Raj 1976) Borrall and Larkin 1978 (Approved Lists 1980)	\N	authority
+104	LMG 13164	\N	type material
+104	Microcyclus marinus	\N	synonym
+104	strain Raj	\N	type material
+105	Runella	\N	scientific name
+105	Runella Larkin and Williams 1978	\N	authority
+106	ATCC 29530	\N	type material
+106	DSM 19594	\N	type material
+106	LMG 11500	\N	type material
+106	Runella slithyformis	\N	scientific name
+106	Runella slithyformis Larkin and Williams 1978	\N	authority
+107	Spirosoma	\N	scientific name
+107	Spirosoma Migula 1894 (Approved Lists 1980) emend. Finster et al. 2009	\N	authority
+108	ATCC 33905	\N	type material
+108	DSM 74	\N	type material
+108	LMG 10896	\N	type material
+108	Spirosoma linguale	\N	scientific name
+108	Spirosoma linguale Migula 1894	\N	authority
+109	Blastobacter	\N	scientific name
+109	Blastobacter Zavarzin 1961 (Approved Lists 1980) emend. Sly 1985	\N	synonym
+110	"Blastobacter viscosus" Loginova and Trotensko 1979	\N	synonym
+110	"Blastobacter viscosus" Loginova and Trotsenok 1979	\N	synonym
+110	ATCC BAA-298	\N	type material
+110	Blastobacter viscosus	\N	synonym
+110	Blastobacter viscosus 7d	\N	includes
+110	VKM B-2253	\N	type material
+110	Xanthobacter viscosus	\N	scientific name
+110	Xanthobacter viscosus Doronina and Trotsenko 2003	\N	synonym
+110	strain 7d	\N	type material
+112	"Planctomycetales" Schlesner and Stackebrandt 1987 emend. Ward 2011	\N	authority
+112	Planctomycetales	\N	scientific name
+112	Planctomycetales Schlesner and Stackebrandt 1987	\N	authority
+112	planctomycetes	planctomycetes<blast112>	blast name
+113	Gemmata	\N	scientific name
+113	Gemmata Franzmann and Skerman 1985	\N	authority
+114	DSM 5831	\N	type material
+114	Gemmata obscuriglobus	\N	scientific name
+114	Gemmata obscuriglobus Franzmann and Skerman 1985	\N	authority
+114	UQM 2246	\N	type material
+117	Pirella sp.	\N	misspelling
+117	Pirellula sp.	\N	scientific name
+118	"Acinothrix" Novacek 1938	\N	authority
+118	"Blastocaulis" Henrici and Johnson 1935	\N	authority
+118	Acinothrix	\N	synonym
+118	Blastocaulis	\N	synonym
+118	Planctomyces	\N	scientific name
+118	Planctomyces Gimesi 1924	\N	authority
+119	ATCC 49424	\N	type material
+119	DSM 5305	\N	type material
+119	IFAM 1448	\N	type material
+119	JCM 21570	\N	type material
+119	NBRC 103401	\N	type material
+119	Planctomyces brasiliensis	\N	scientific name
+119	Planctomyces brasiliensis Schlesner 1990	\N	authority
+120	ATCC 43296	\N	type material
+120	DSM 3776	\N	type material
+120	IFAM 1008	\N	type material
+120	Planctomyces limnophilus	\N	scientific name
+120	Planctomyces limnophilus Hirsch and Muller 1986	\N	authority
+120	strain M 290	\N	type material
+122	"Planctomyces maris" Bauld and Staley 1976	\N	authority
+122	ATCC 29201	\N	type material
+122	DSM 8797	\N	type material
+122	Planctomyces maris	\N	scientific name
+122	Planctomyces maris (ex Bauld and Staley 1976) Bauld and Staley 1980	\N	authority
+122	strain 534-30	\N	type material
+123	Pirella	Pirella <bacterial misnomer>	misnomer
+123	Pirella Schlesner and Hirsch 1984	\N	authority
+123	Pirellula	\N	scientific name
+123	Pirellula Schlesner and Hirsch 1987 emend. Schlesner et al. 2004	\N	authority
+123	Pivellula	\N	misspelling
+124	ATCC 49069	\N	type material
+124	Blastopirellula marina	\N	scientific name
+124	Blastopirellula marina (Schlesner 1987) Schlesner et al. 2004	\N	authority
+124	DSM 3645	\N	type material
+124	IFAM 1313	\N	type material
+124	Pirella marina	\N	misnomer
+124	Pirella marina Schlesner 1987	\N	authority
+124	Pirellula marina	\N	synonym
+124	Pirellula marina (Schlesner 1987) Schlesner and Hirsch 1987	\N	authority
+124	Pivellula marina	\N	misspelling
+124	strain SH 106	\N	type material
+125	ATCC 27377	\N	type material
+125	DSM 6068	\N	type material
+125	Pasteuria ramosa ATCC 27377	\N	includes
+125	Pirella staleyi	\N	misnomer
+125	Pirella staleyi Schlesner and Hirsch 1984	\N	authority
+125	Pirellula staleyi	\N	scientific name
+125	Pirellula staleyi (Schlesner and Hirsch 1984) Schlesner and Hirsch 1987	\N	authority
+125	Planctomyces staleyi	\N	misnomer
+126	"Planctomycetaceae" Schlesner and Stackebrandt 1987 emend. Ward 2011	\N	authority
+126	Planctomycetaceae	\N	scientific name
+126	Planctomycetaceae Schlesner and Stackebrandt 1987	\N	authority
+127	Isosphaera	\N	scientific name
+127	Isosphaera Giovannoni et al. 1995	\N	authority
+128	"Isocystis pallida" Woronichin 1927 (as cyanobacterium)	\N	authority
+128	"Torulopsidosira pallida" (Woronichin 1927) Geitler 1963 (as a yeast)	\N	authority
+128	ATCC 43644	\N	type material
+128	DSM 9630	\N	type material
+128	Isocystis pallida	\N	synonym
+128	Isosphaera pallida	\N	scientific name
+128	Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995	\N	authority
+128	Torulopsidosira pallida	\N	synonym
+128	strain IS1B	\N	type material
+131	Tuberoidobacter	\N	scientific name
+132	'Tuberoidobacter mutans'	\N	synonym
+132	Tuberoidobacter mutans	\N	scientific name
+133	Methylocystis	\N	scientific name
+133	Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993 emend. Dedysh et al. 2007	\N	authority
+134	ACM 3309	\N	type material
+134	ATCC 35066	\N	type material
+134	IMET 10483	\N	type material
+134	Methylocystis parva	\N	misspelling
+134	Methylocystis parvus	\N	scientific name
+134	Methylocystis parvus Bowman et al. 1993	\N	authority
+134	NCIMB 11129	\N	type material
+134	UNIQEM 38	\N	type material
+134	VKM B-2129	\N	type material
+134	strain OBBP	\N	type material
+136	Spirochaetales	\N	scientific name
+136	Spirochaetales Buchanan 1917	\N	authority
+136	spirochetes	spirochetes<blast136>	blast name
+137	"Spirochaetaceae" Swellengrebel 1907 emend. Abt et al. 2012	\N	authority
+137	Spirochaetaceae	\N	scientific name
+137	Spirochaetaceae Swellengrebel 1907	\N	authority
+137	Treponemataceae	Treponemataceae <Spirochaetaceae>	in-part
+137	Treponemataceae Robinson 1948 (Approved Lists 1980)	Treponemataceae Robinson 1948 (Approved Lists 1980) <Spirochaetaceae>	authority
+138	Borrelia	\N	scientific name
+138	Borrelia Swellengrebel 1907	\N	authority
+139	Borrelia burdorferi	\N	misspelling
+139	Borrelia burgdorferi	\N	scientific name
+139	Borrelia burgdorferi Johnson et al. 1984 emend. Baranton et al. 1992	\N	authority
+139	Borrelia burgdorferi sensu stricto	\N	equivalent name
+139	Borrelia burgdorffragment	\N	misspelling
+139	CIP 102532	\N	type material
+139	DSM 4680	\N	type material
+139	Lyme disease spirochete	\N	genbank common name
+139	strain B31	strain B31 <Borrelia burgdorferi>	type material
+140	"Spirochaeta hermsi" (sic) Davis 1942	\N	authority
+140	Borrelia hermsii	\N	scientific name
+140	Borrelia hermsii (Davis 1942) Steinhaus 1946	\N	authority
+140	Spirochaeta hermsi	\N	synonym
+141	"Spirochaeta parkeri" Davis 1942	\N	synonym
+141	Borrelia parkeri	\N	scientific name
+141	Borrelia parkeri (Davis 1942) Steinhaus 1946	\N	synonym
+141	Spirochaeta parkeri	\N	synonym
+142	"Spirochaeta turicatae" Brumpt 1933	\N	synonym
+142	Borrelia turicatae	\N	scientific name
+142	Borrelia turicatae (Brumpt 1933) Steinhaus 1946	\N	synonym
+142	Spirochaeta turicatae	\N	synonym
+143	"Spirochaeta anserina" Sakharoff 1891	\N	authority
+143	"Spirochaete gallinarum" (sic) Stephens and Christophers 1904	\N	authority
+143	"Spiroschaudinnia anserina" (Sakharoff 1891) Sambon 1907	\N	authority
+143	Borrelia anserina	\N	scientific name
+143	Borrelia anserina (Sakharoff 1891) Bergey et al. 1925	\N	authority
+143	Spirochaeta anserina	\N	synonym
+143	Spirochaete gallinarum	\N	synonym
+143	Spiroschaudinnia anserina	\N	synonym
+144	ATCC 43381	\N	type material
+144	Borrelia coriaceae	\N	scientific name
+144	Borrelia coriaceae Johnson et al. 1987	\N	synonym
+144	CIP 104208	\N	type material
+144	strain Co53	\N	type material
+145	Borrelia sp.	\N	scientific name
+146	"Ehrenbergia" Gieszczykiewiez 1939	\N	authority
+146	"Spirochaete" Cohn 1872 (orthographic variant of Spirochaeta)	\N	authority
+146	"Spirochoeta" Dujardin 1841 (orthographic variant of Spirochaeta)	\N	authority
+146	Ehrenbergia	\N	synonym
+146	Spirochaeta	\N	scientific name
+146	Spirochaeta Ehrenberg 1835 (Approved Lists 1980) emend. Pikuta et al. 2009	\N	authority
+146	Spirochaete	\N	synonym
+146	Spirochoeta	\N	synonym
+147	"Spirochaeta aurantia" Vinzent 1926	\N	synonym
+147	ATCC 25082	\N	type material
+147	DSM 1902	\N	type material
+147	Spirochaeta aurantia	\N	scientific name
+147	Spirochaeta aurantia (ex Vinzent 1926) Canale-Parola 1980	\N	synonym
+148	ATCC 35968	\N	type material
+148	DSM 16054	\N	type material
+148	Spirochaeta bajacaliforniensis	\N	scientific name
+148	Spirochaeta bajacaliforniensis Fracek and Stolz 2004	\N	synonym
+148	strain BA-2	\N	type material
+149	ATCC 29478	\N	type material
+149	DSM 10522	\N	type material
+149	Spirochaeta halophila	\N	scientific name
+149	Spirochaeta halophila Greenberg and Canale-Parola 1977	\N	synonym
+150	ATCC 33939	\N	type material
+150	DSM 2461	\N	type material
+150	Spirochaeta isovalerica	\N	scientific name
+150	Spirochaeta isovalerica Harwood and Canale-Parola 1983	\N	synonym
+150	strain MA-2	strain MA-2 <Spirochaeta isovalerica>	type material
+151	"Spirochaeta litoralis" Hespell and Canale-Parola 1970	\N	synonym
+151	ATCC 27000	\N	type material
+151	DSM 2029	\N	type material
+151	Spirochaeta litoralis	\N	scientific name
+151	Spirochaeta litoralis (ex Hespell and Canale-Parola 1970) Canale-Parola 1980	\N	synonym
+151	strain R1	strain R1 <Spirochaeta litoralis>	type material
+152	ATCC 25083	\N	type material
+152	DSM 2028	\N	type material
+152	JCM 16534	\N	type material
+152	Spirochaeta stenostrepta	\N	scientific name
+152	Spirochaeta stenostrepta Zuelzer 1912	\N	authority
+154	ATCC 700085	\N	type material
+154	DSM 6578	\N	type material
+154	Spirochaeta thermophila	\N	scientific name
+154	Spirochaeta thermophila Aksenova et al. 1992	\N	authority
+154	strain Z-1203	\N	type material
+156	"Spirochaeta zuelzerae" (Veldkamp 1960) Canale-Parola, Udris and Mandel 1968	\N	synonym
+156	"Treponema zuelzerae" Veldkamp 1960	\N	synonym
+156	ATCC 19044	\N	type material
+156	DSM 1903	\N	type material
+156	Spirochaeta zuelzerae	\N	scientific name
+156	Spirochaeta zuelzerae (ex Veldkamp 1960) Canale-Parola 1980	\N	synonym
+156	Spirochaeta zuelzeri	\N	misspelling
+156	Treponema zuelzerae	\N	synonym
+157	"Microspironema" Stiles and Pfender 1905	\N	authority
+157	"Spironema" Vuillemin 1905	\N	authority
+157	Microspironema	\N	synonym
+157	Treponema	\N	scientific name
+157	Treponema Schaudinn 1905	\N	authority
+158	"Spirillum dentium" (Miller 1889) Sternberg 1892	\N	authority
+158	"Spirochaeta ambigua" Seguin and Vinzent 1936	\N	authority
+158	"Spirochaeta comandonii" Seguin and Vinzent 1936	\N	authority
+158	"Spirochaeta dentium" (Miller 1889) Migula 1895	\N	authority
+158	"Spirochaeta microdentium" (Noguchi 1912) Heim 1922	\N	authority
+158	"Spirochaeta orthodonta" Hoffmann 1920	\N	authority
+158	"Spirochaete denticola" Flugge 1886	\N	authority
+158	"Spirochaete dentium" Miller 1889	\N	authority
+158	"Spironema dentium" (Miller 1889) Gross 1912	\N	authority
+158	"Treponema ambiguum" (Seguin and Vinzent 1936) Prevot 1940	\N	authority
+158	"Treponema comandonii" (Seguin and Vinzent 1936) Prevot 1940	\N	authority
+158	"Treponema dentium" (Miller 1889) Dobell 1912	\N	authority
+158	"Treponema dentium-stenogyratum" Pettit 1928	\N	authority
+158	"Treponema microdentium" Noguchi 1912	\N	authority
+158	"Treponema orthodontum" (Hoffmann 1920) Noguchi 1928	\N	authority
+158	ATCC 35405	\N	type material
+158	CIP 103919	\N	type material
+158	DSM 14222	\N	type material
+158	JCM 8153	\N	type material
+158	Spirillum dentium	\N	synonym
+158	Spirochaeta ambigua	\N	synonym
+158	Spirochaeta comandonii	\N	synonym
+158	Spirochaeta dentium	\N	synonym
+158	Spirochaeta microdentium	\N	synonym
+158	Spirochaeta orthodonta	\N	synonym
+158	Spirochaete denticola	\N	synonym
+158	Spirochaete dentium	\N	synonym
+158	Spironema dentium	\N	synonym
+158	Treponema ambiguum	\N	synonym
+158	Treponema comandonii	\N	synonym
+158	Treponema denticola	\N	scientific name
+158	Treponema denticola (ex Brumpt 1925) Chan et al. 1993	\N	authority
+158	Treponema denticola (ex Flugge 1886) Chan et al. 1993	\N	authority
+158	Treponema dentium	\N	synonym
+158	Treponema dentium-stenogyratum	\N	synonym
+158	Treponema microdentium	\N	synonym
+158	Treponema orthodontum	\N	synonym
+159	ATCC 27164	\N	type material
+159	Brachyspira hyodysenteriae	\N	scientific name
+159	Brachyspira hyodysenteriae (Harris et al. 1972) Ochiai et al. 1998	\N	authority
+159	CCUG 46668	\N	type material
+159	NCTC 13041	\N	type material
+159	Serpula hyodysenteriae	\N	misnomer
+159	Serpula hyodysenteriae (Harris et al. 1972) Stanton et al. 1991	\N	authority
+159	Serpulina hyodysenteriae	\N	synonym
+159	Serpulina hyodysenteriae (Harris et al. 1972) Stanton 1992	\N	authority
+159	Treponema hyodysenteriae	\N	synonym
+159	Treponema hyodysenteriae Harris et al. 1972 (Approved Lists 1980)	\N	authority
+159	strain B78	\N	type material
+160	"Microspironema pallidum" (Schaudinn and Hoffmann 1905) Stiles and Pfender 1905	\N	authority
+160	"Spirillum pallidum" (Schaudinn and Hoffmann 1905) Mace 1913	\N	authority
+160	"Spirochaeta pallida" Schaudinn and Hoffmann 1905	\N	authority
+160	"Spironema pallidum" (Schaudinn and Hoffmann 1905) Vuillemin 1905	\N	authority
+160	Microspironema pallidum	\N	synonym
+160	Spirillum pallidum	\N	synonym
+160	Spirochaeta pallida	\N	synonym
+160	Spironema pallidum	\N	synonym
+160	Treponema pallidum	\N	scientific name
+160	Treponema pallidum (Schaudinn and Hoffmann 1905) Schaudinn 1905	\N	authority
+161	"Treponema pallidum subsp. pallidum" (Schaudinn and Hoffmann 1905) Schaudinn 1905	\N	authority
+161	Treponema pallidum pallidum	\N	equivalent name
+161	Treponema pallidum subsp. pallidum	\N	scientific name
+161	syphilis treponeme	\N	genbank common name
+162	"Treponema phagedenis" (Noguchi 1912) Brumpt	\N	authority
+162	Treponema phagedenis	\N	scientific name
+163	ATCC 33254	\N	type material
+163	DSM 1788	\N	type material
+163	Treponema bryantii	\N	scientific name
+163	Treponema bryantii Stanton and Canale-Parola 1980	\N	authority
+163	strain RUS-1	\N	type material
+164	ATCC 33768	\N	type material
+164	Treponema pectinivorum	\N	equivalent name
+164	Treponema pectinovorum	\N	scientific name
+164	Treponema pectinovorum Smibert and Burmeister 1983	\N	authority
+164	VPI D-36DR-2	\N	type material
+165	ATCC 43261	\N	type material
+165	DSM 2985	\N	type material
+165	Treponema saccharophilum	\N	scientific name
+165	Treponema saccharophilum Paster and Canale-Parola 1986	\N	authority
+165	Treponema sacchrophilum	\N	misspelling
+166	Treponema sp.	\N	scientific name
+167	ATCC 33096	\N	type material
+167	DSM 2489	\N	type material
+167	Treponema succinifaciens	\N	scientific name
+167	Treponema succinifaciens Cwyk and Canale-Parola 1981	\N	authority
+167	strain 6091	\N	type material
+168	"Treponema pallidum subsp. pertenue" Smibert 1984	\N	authority
+168	Treponema pallidium subsp. pertenue	\N	misspelling
+168	Treponema pallidum pertenue	\N	equivalent name
+168	Treponema pallidum subsp. pertenue	\N	scientific name
+168	Treponema pertenue	\N	synonym
+168	yaws treponeme	\N	genbank common name
+170	Leptospiraceae	\N	scientific name
+170	Leptospiraceae Hovind-Hougen 1979 (Approved Lists 1980) emend. Levett et al. 2005	\N	authority
+170	Leptospiraceae Hovind-Houger (sic) 1978 (sic)	\N	authority
+170	Treponemataceae	Treponemataceae <Leptospiraceae>	in-part
+170	Treponemataceae Robinson 1948 (Approved Lists 1980)	Treponemataceae Robinson 1948 (Approved Lists 1980) <Leptospiraceae>	authority
+171	Ancona	\N	misnomer
+171	Canela	\N	misnomer
+171	Jequitaia	\N	misnomer
+171	Leptospira	\N	scientific name
+171	Leptospira Noguchi 1917 (Approved Lists 1980) emend. Faine and Stallman 1982	\N	authority
+172	"Spirochaeta biflexa" Wolbach and Binger 1914	"Spirochaeta biflexa" Wolbach and Binger 1914 <Leptospira biflexa>	authority
+172	ATCC 23582	\N	type material
+172	Leptospira biflexa	\N	scientific name
+172	Leptospira biflexa (Wolbach and Binger 1914) Noguchi 1918 (Approved Lists 1980) emend. Faine and Stallman 1982	\N	authority
+172	Spirochaeta biflexa	Spirochaeta biflexa <Leptospira biflexa>	in-part
+172	strain Patoc I	\N	type material
+173	"Leptospira icteroides" Noguchi 1919	\N	authority
+173	"Spirochaeta biflexa" Wolbach and Binger 1914	"Spirochaeta biflexa" Wolbach and Binger 1914 <Leptospira interrogans>	authority
+173	"Spirochaeta icterogenes" Uhlenhuth and Fromme 1916	\N	authority
+173	"Spirochaeta icterohaemorrhagiae" Inada et al. 1916	\N	authority
+173	"Spirochaeta interrogans" Stimson 1907	\N	authority
+173	"Spirochaeta nodosa" Hubener and Reiter 1916	\N	authority
+173	ATCC 23581	\N	type material
+173	Leptospira icteroides	\N	synonym
+173	Leptospira interrogans	\N	scientific name
+173	Leptospira interrogans (Stimson 1907) Wenyon 1926 (Approved Lists 1980) emend. Faine and Stallman 1982	\N	authority
+173	Spirochaeta biflexa	Spirochaeta biflexa <Leptospira interrogans>	in-part
+173	Spirochaeta icterogenes	\N	synonym
+173	Spirochaeta icterohaemorrhagiae	\N	synonym
+173	Spirochaeta interrogans	\N	synonym
+173	Spirochaeta nodosa	\N	synonym
+173	strain RGA	\N	type material
+174	ATCC 43292	\N	type material
+174	DSM 21538	\N	type material
+174	Leptospira borgpeterseni	\N	misspelling
+174	Leptospira borgpetersenii	\N	scientific name
+174	Leptospira borgpetersenii Yasuda et al. 1987	\N	authority
+174	strain Veldrat Bataviae 46	\N	type material
+176	Leptospira hardjo	\N	synonym
+176	Leptospira interrogans serovar Hardjo	\N	scientific name
+178	Leptospira sp.	\N	scientific name
+179	"Leptospirillum" Markosyan 1972	\N	synonym
+179	Leptospirillum	\N	scientific name
+179	Leptospirillum (ex Markosyan 1972) Hippe 2000	\N	synonym
+180	"Leptospirillum ferrooxidans" Markosyan 1972	\N	authority
+180	ATCC 29047	\N	type material
+180	DSM 2705	\N	type material
+180	Leptospirillum ferrooxidans	\N	scientific name
+180	Leptospirillum ferrooxidans (ex Markosyan 1972) Hippe 2000	\N	authority
+180	Leptospirillum ferroxidans	\N	misspelling
+180	VKM B-1339	\N	type material
+181	Leptospirillum sp.	\N	scientific name
+183	"Leptospira illini" Hanson et al. 1974	\N	authority
+183	Leptonema illini	\N	scientific name
+183	Leptonema illini Hovind-Hougen 1983	\N	authority
+183	Leptonema illinoisense	\N	misspelling
+183	Leptospira illini	\N	synonym
+183	NCTC 11301	\N	type material
+183	strain 3055	\N	type material
+185	Wall less Spirochaeta sp.	\N	synonym
+185	wall-less Spirochaeta sp.	\N	synonym
+185	wall-less spirochete	\N	scientific name
+187	Aquaspirillum	\N	scientific name
+187	Aquaspirillum Hylemon et al. 1973	\N	synonym
+188	ATCC 31632	\N	type material
+188	Aquaspirillum magnetotacticum	\N	synonym
+188	Aquaspirillum magnetotacticum Maratea and Blakemore 1981	\N	synonym
+188	DSM 3856	\N	type material
+188	IFO 15272	\N	type material
+188	JCM 21281	\N	type material
+188	LMG 10894	\N	type material
+188	Magnetospirillum magnetotacticum	\N	scientific name
+188	Magnetospirillum magnetotacticum (Maratea and Blakemore 1981) Schleifer et al. 1992	\N	synonym
+188	NBRC 15272	\N	type material
+189	"Spirillum itersonii" Giesberger 1936	\N	authority
+189	Aquaspirillum itersoni	\N	misspelling
+189	Aquaspirillum itersonii	\N	synonym
+189	Aquaspirillum itersonii (Giesberger 1936) Hylemon et al. 1973	\N	authority
+189	Novispirillum itersonii	\N	scientific name
+189	Novispirillum itersonii (Giesberger 1936) Yoon et al. 2007	\N	authority
+189	Novospirillum itersonii	\N	misspelling
+189	Spirillum itersoni	\N	misspelling
+189	Spirillum itersonii	\N	synonym
+190	"Spirillum serpens" (Muller 1786) Winter 1884	\N	synonym
+190	"Vibrio serpens" Muller 1786	\N	synonym
+190	ATCC 12638	\N	type material
+190	Aquaspirillum bengal	\N	synonym
+190	Aquaspirillum bengal Kumar et al. 1974 (Approved Lists 1980)	\N	synonym
+190	Aquaspirillum serpens	\N	scientific name
+190	Aquaspirillum serpens (Muller 1786) Hylemon et al. 1973 (AL 1980) emend. Boivin et al. 1985	\N	synonym
+190	CCUG 2092	\N	type material
+190	CIP 63.19	\N	type material
+190	DSM 68	\N	type material
+190	IFO 14924	\N	type material
+190	JCM 20995	\N	type material
+190	LMG 3734	\N	type material
+190	NBRC 14924	\N	type material
+190	NCTC 10593	\N	type material
+190	Spirillum serpens	\N	synonym
+190	Vibrio serpens	\N	synonym
+191	Azospirillum	\N	scientific name
+191	Azospirillum Tarrand et al. 1979 (Approved Lists 1980) emend. Falk et al. 1985	\N	authority
+192	ATCC 29145	\N	type material
+192	Azospirillum brasilense	\N	scientific name
+192	Azospirillum brasilense corrig. Tarrand et al. 1979	\N	authority
+192	Azospirillum brasiliense	\N	synonym
+192	DSM 1690	\N	type material
+192	JCM 1224	\N	type material
+192	LMG 13127	\N	type material
+192	NBRC 102289	\N	type material
+192	NRRL B-14647	\N	type material
+192	Roseomonas fauriae	\N	synonym
+192	Roseomonas fauriae Rihs et al. 1998	\N	authority
+192	Spirillum lipoferum	\N	synonym
+192	VKM B-1547	\N	type material
+192	bacterium ASAZOES-148	\N	includes
+192	strain sp. 7	\N	type material
+193	"Spirillum lipoferum" Beijerinck 1925	\N	authority
+193	ATCC 29707	\N	type material
+193	Azospirillum lipoferum	\N	scientific name
+193	Azospirillum lipoferum (Beijerinck 1925) Tarrand et al. 1979	\N	authority
+193	CIP 106280	\N	type material
+193	DSM 1691	\N	type material
+193	JCM 1247	\N	type material
+193	LMG 13128	\N	type material
+193	NBRC 102290	\N	type material
+193	NCAIM B.01801	\N	type material
+193	NRRL B-14654	\N	type material
+193	VKM B-1519	\N	type material
+193	strain sp. 59b	\N	type material
+194	Ampylobacter	\N	misspelling
+194	Campylobacter	\N	scientific name
+194	Campylobacter Sebald and Veron 1963 (Approved Lists 1980) emend. Tanner et al. 1981	\N	authority
+206	ATCC 35980	\N	type material
+194	Campylobacter Sebald and Veron 1963 (Approved Lists 1980) emend. Vandamme et al. 1991	\N	authority
+194	Campylobacter Sebald and Veron 1963 (Approved Lists 1980) emend. Vandamme et al. 2010	\N	authority
+195	"Vibrio coli" Doyle 1948	\N	authority
+195	ATCC 33559	\N	type material
+195	CCUG 11283	\N	type material
+195	CCUG 14540	\N	type material
+195	CIP 70.80	\N	type material
+195	Campylobacter coli	\N	scientific name
+195	Campylobacter coli (Doyle 1948) Veron and Chatelain 1973	\N	authority
+195	Campylobacter hyoilei	\N	genbank synonym
+195	Campylobacter hyoilei Alderton et al. 1995	\N	authority
+195	DSM 4689	\N	type material
+195	JCM 2529	\N	type material
+195	LMG 6440	\N	type material
+195	NCTC 11366	\N	type material
+195	Vibrio coli	\N	synonym
+196	"Spirillum fetus" Lehmann and Neumann 1927	\N	synonym
+196	"Vibrio fetus" Smith and Taylor 1919	\N	synonym
+196	ATCC 27374	\N	type material
+196	CCUG 6823 A	\N	type material
+196	CIP 53.96	\N	type material
+196	Campylobacter fetus	\N	scientific name
+196	Campylobacter fetus (Smith and Taylor 1919) Sebald and Veron 1963	\N	synonym
+196	DSM 5361	\N	type material
+196	JCM 2527	\N	type material
+196	LMG 6442	\N	type material
+196	NCTC 10842	\N	type material
+196	Spirillum fetus	\N	synonym
+196	Vibrio fetus	\N	synonym
+197	"Campylobacter fetus subsp. jejuni" Smibert 1974	\N	authority
+197	"Vibrio hepaticus" Mathey and Rissberger 1964	\N	authority
+197	"Vibrio jejuni" Jones et al. 1931	\N	authority
+197	ATCC 33560	\N	type material
+197	Ampylobacter jejuni	\N	misspelling
+197	CCUG 11284	\N	type material
+197	CIP 70.2	\N	type material
+197	Campylobacter fetus subsp. jejuni	\N	synonym
+197	Campylobacter jejuni	\N	scientific name
+197	Campylobacter jejuni (Jones et al. 1931) Veron and Chatelain 1973	\N	authority
+197	DSM 4688	\N	type material
+197	LMG 8841	\N	type material
+197	NCTC 11351	\N	type material
+197	Vibrio hepaticus	\N	synonym
+197	Vibrio jejuni	\N	synonym
+198	ATCC 35217	\N	type material
+198	CCUG 14169	\N	type material
+198	CIP 103746	\N	type material
+198	Campylobacter hyointestinalis	\N	scientific name
+198	Campylobacter hyointestinalis Gebhart et al. 1985 emend. On et al. 1995	\N	authority
+198	DSM 19053	\N	type material
+198	LMG 7817	\N	type material
+198	NCTC 11608	\N	type material
+198	strain 80-4577-4	\N	type material
+199	ATCC 33237	\N	type material
+199	CCUG 13144	\N	type material
+199	CIP 103757	\N	type material
+199	Campylobacter concisus	\N	scientific name
+199	Campylobacter concisus Tanner et al. 1981	\N	authority
+199	DSM 9716	\N	type material
+199	FDC 484	\N	type material
+199	LMG 7788	\N	type material
+199	NCTC 11485	\N	type material
+200	ATCC 35224	\N	type material
+200	CCUG 13146	\N	type material
+200	CIP 103747	\N	type material
+200	Campylobacter curvus	\N	scientific name
+200	Campylobacter curvus (Tanner et al. 1984) Vandamme et al. 1991	\N	synonym
+200	DSM 6644	\N	type material
+200	LMG 7609	\N	type material
+200	NCTC 11649	\N	type material
+200	VPI 9584	\N	type material
+200	Wolinella curva	\N	synonym
+200	Wolinella curva Tanner et al. 1984	\N	synonym
+201	ATCC 35221	\N	type material
+201	CCUG 23947	\N	type material
+201	CIP 102722	\N	type material
+201	Campylobacter lari	\N	scientific name
+201	Campylobacter lari corrig. Benjamin et al. 1984 emend. Debruyne et al. 2009	\N	authority
+201	Campylobacter laridis	\N	synonym
+201	DSM 11375	\N	type material
+201	JCM 2530	\N	type material
+201	LMG 8846	\N	type material
+201	NCTC 11352	\N	type material
+201	WRI 3034/77	\N	type material
+202	ATCC 43264	\N	type material
+202	CCUG 6822	\N	type material
+202	CIP 103750	\N	type material
+202	Campylobacter mucosalis	\N	scientific name
+202	Campylobacter mucosalis (Lawson et al. 1981) Roop et al. 1985	\N	authority
+202	Campylobacter sputorum mucosalis	\N	synonym
+202	Campylobacter sputorum subsp. mucosalis (ex Lawson and Rowland 1974) Lawson et al. 1981	\N	authority
+202	Campylobacter sputorum supsp. mucosalis	\N	synonym
+202	DSM 21682	\N	type material
+202	NCTC 11000	\N	type material
+202	strain FS253/72	\N	type material
+203	ATCC 33238	\N	type material
+203	CCUG 20446 B	\N	type material
+203	CIP 103748	\N	type material
+203	Campylobacter rectus	\N	scientific name
+203	Campylobacter rectus (Tanner et al. 1981) Vandamme et al. 1991	\N	synonym
+203	DSM 3260	\N	type material
+203	FDC 371	\N	type material
+203	JCM 6301	\N	type material
+203	NCTC 11489	\N	type material
+203	Wolinella recta	\N	synonym
+203	Wolinella recta Tanner et al. 1981	\N	synonym
+204	ATCC 51146	\N	type material
+204	CCUG 30254	\N	type material
+204	CIP 103970	\N	type material
+204	Campylobacter showae	\N	scientific name
+204	Campylobacter showae Etoh et al. 1993	\N	authority
+204	JCM 12989	\N	type material
+204	LMG 12635	\N	type material
+204	strain SU A4	\N	type material
+205	Campylobacter sp.	\N	scientific name
+206	"Vibrio sputorum" Prevot 1940	\N	authority
+206	ATCC 33562	\N	type material
+206	CCUG 9728	\N	type material
+206	CIP 103749	\N	type material
+206	Campylobacter sputorum	\N	scientific name
+206	Campylobacter sputorum (Prevot 1940) Veron and Chatelain 1973 (Approved Lists 1980) emend. On et al. 1998	\N	authority
+206	Campylobacter sputorum (Prevot 1940) Veron and Chatelain 1973 (Aproved Lists 1980) emend. Roop et al. 1986	\N	authority
+206	LMG 7795	\N	type material
+206	NCTC 11528	\N	type material
+206	VPI S-17	\N	type material
+206	Vibrio sputorum	\N	synonym
+206	strain Forsyth ER33	\N	type material
+207	Campylobacter jejuni-like bacterium	\N	scientific name
+209	Gastrospirillum	\N	includes
+209	Helicobacter	\N	scientific name
+209	Helicobacter Goodwin et al. 1989 emend. Vandamme et al. 1991	\N	authority
+210	ATCC 43504	\N	type material
+210	CCUG 15815 B	\N	type material
+210	CCUG 17874	\N	type material
+210	CCUG 39500	\N	type material
+210	CIP 103995	\N	type material
+210	Campylobacter pylori	\N	synonym
+210	Campylobacter pylori Marshall et al. 1985 corrig. Marshall and Goodwin 1987	\N	authority
+210	Campylobacter pylori corrig. Marshall et al. 1985 emend. Fox et al. 1988	\N	authority
+210	Campylobacter pylori corrig. Marshall et al. 1985 emend. Fox et al. 1989	\N	authority
+210	Campylobacter pylori subsp. pylori	\N	synonym
+210	Campylobacter pylori subsp. pylori Marshall et al. 1985	\N	authority
+210	Campylobacter pyloridis	\N	synonym
+210	Campylobacter pyloridis Marshall et al.1985	\N	authority
+210	DSM 21031	\N	type material
+210	DSM 4867	\N	type material
+210	Helicobacter nemestrinae	\N	synonym
+210	Helicobacter nemestrinae Bronsdon et al. 1991	\N	authority
+210	Helicobacter pylori	\N	scientific name
+210	Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989	\N	authority
+210	JCM 12093	\N	type material
+210	LMG 18041	\N	type material
+210	LMG 19449	\N	type material
+210	NCTC 11637	\N	type material
+210	strain Royal Perth Hospital 13487	\N	type material
+211	Helicobacter CLO3	\N	synonym
+211	Helicobacter sp. (strain CLO3)	\N	synonym
+211	Helicobacter sp. CLO-3	\N	scientific name
+211	Helicobacter sp. CLO3	\N	synonym
+212	ATCC 51101	\N	type material
+212	CCUG 29263	\N	type material
+212	CIP 104247	\N	type material
+212	Helicobacter acinonychis	\N	scientific name
+212	Helicobacter acinonychis corrig. Eaton et al. 1993	\N	synonym
+212	Helicobacter acinonyx	\N	synonym
+212	NCTC 12686	\N	type material
+212	strain 90-119	\N	type material
+213	"Helicobacter westmeadii" Trivett-Moore et al. 1997	\N	authority
+213	CCUG 18818	\N	type material
+213	CIP 103752	\N	type material
+213	Campylobacter cinaedi	\N	synonym
+213	Campylobacter cinaedi Totten et al. 1988	\N	authority
+213	DSM 5359	\N	type material
+213	Helicobacter cinaedi	\N	scientific name
+213	Helicobacter cinaedi (Totten et al. 1988) Vandamme et al. 1991	\N	authority
+213	Helicobacter westmeadii	\N	synonym
+213	LMG 7543	\N	type material
+213	NCTC 12423	\N	type material
+213	strain Fennell 165	\N	type material
+214	ATCC 49179	\N	type material
+214	CIP 104382	\N	type material
+214	Helicobacter felis	\N	scientific name
+214	Helicobacter felis Paster et al. 1991	\N	authority
+214	NCTC 12436	\N	type material
+215	ATCC 35684	\N	type material
+215	CCUG 18820	\N	type material
+215	CIP 103758	\N	type material
+215	Campylobacter fennelliae	\N	synonym
+215	Campylobacter fennelliae Totten et al. 1988	\N	authority
+215	DSM 7491	\N	type material
+215	Helicobacter fennelliae	\N	scientific name
+215	Helicobacter fennelliae (Totten et al. 1988) Vandamme et al. 1991	\N	authority
+215	NCTC 11612	\N	type material
+215	strain Fennell 231	\N	type material
+216	ATCC 49282	\N	type material
+216	CCUG 29262	\N	type material
+216	CIP 104248	\N	type material
+216	DSM 22221	\N	type material
+216	Helicobacter muridarum	\N	scientific name
+216	Helicobacter muridarum Lee et al. 1992	\N	synonym
+216	LMG 13646	\N	type material
+216	NCTC 12714	\N	type material
+216	strain ST1	\N	type material
+217	ATCC 43772	\N	type material
+217	CCUG 25715	\N	type material
+217	CIP 103759	\N	type material
+217	Campylobacter mustelae	\N	synonym
+217	Campylobacter mustelae (Fox et al. 1988) Fox et al. 1989	\N	synonym
+217	Campylobacter pylori mustelae	\N	synonym
+217	Campylobacter pylori subsp. mustelae	\N	synonym
+217	Campylobacter pylori subsp. mustelae Fox et al. 1988	\N	synonym
+217	Helicobacter mustelae	\N	scientific name
+217	Helicobacter mustelae (Fox et al. 1988) Goodwin et al. 1989	\N	synonym
+217	NCTC 12198	\N	type material
+217	strain R85-13-6	\N	type material
+218	Helicobacter sp.	\N	scientific name
+222	Achromobacter	\N	scientific name
+222	Achromobacter Yabuuchi and Yano 1981 emend. Yabuuchi et al. 1998	\N	synonym
+223	"Achromobacter cycloclastes" (Gray and Thornton) Bergey et al.	\N	synonym
+223	'Achromobacter cycloclastes'	\N	synonym
+223	Achromobacter cycloclastes	\N	scientific name
+223	Achromobacter cycolclastes	\N	misspelling
+224	"Achromobacter lyticus" Isono et al. 1972	\N	synonym
+224	'Achromobacter lyticus'	\N	synonym
+224	Achromobacter lyticus	\N	scientific name
+226	Alteromonas	\N	scientific name
+244	IFO 12536	\N	type material
+226	Alteromonas Baumann et al. 1972 (Approved Lists 1980) emend. Gauthier et al. 1995	\N	synonym
+226	Alteromonas Baumann et al. 1972 (Approved Lists 1980) emend. Novick and Tyler 1985	\N	synonym
+226	Alteromonas Baumann et al. 1972 (Approved Lists 1980) emend. Van Trappen et al. 2004	\N	synonym
+227	ATCC 43555	\N	type material
+227	Alteromonas carrageenovora	\N	synonym
+227	CIP 103674	\N	type material
+227	DSM 6820	\N	type material
+227	IAM 12662	\N	type material
+227	IFO 12985	\N	type material
+227	JCM 8851	\N	type material
+227	NBRC 12985	\N	type material
+227	NCIMB 302	\N	type material
+227	Pseudoalteromonas carrageenovora	\N	scientific name
+227	Pseudoalteromonas carrageenovora (Akagawa-Matsushita et al. 1992) Gauthier et al. 1995	\N	synonym
+228	"Alteromonas marinopraesens" (ZoBell and Upham 1944) Baumann et al. 1972	\N	authority
+228	"Vibrio haloplanktis" ZoBell and Upham 1944	\N	authority
+228	"Vibrio marinopraesens" ZoBell and Upham 1944	\N	authority
+228	ATCC 14393	\N	type material
+228	Alteromonas haloplanctis	\N	misspelling
+228	Alteromonas haloplanktis	\N	synonym
+228	Alteromonas haloplanktis (ZoBell and Upham 1944) Reichelt and Baumann 1973 (Approved Lists 1980)	\N	authority
+228	Alteromonas marinopraesens	\N	synonym
+228	CIP 103197	\N	type material
+228	DSM 6060	\N	type material
+228	IAM 12915	\N	type material
+228	JCM 20767	\N	type material
+228	LMG 2852	\N	type material
+228	Moraxella sp. TAC 125	\N	includes
+228	NBRC 102225	\N	type material
+228	NCCB 71020	\N	type material
+228	Pseudoalteromonas haloplanktis	\N	scientific name
+228	Pseudoalteromonas haloplanktis (ZoBell and Upham 1944) Gauthier et al. 1995	\N	authority
+228	Psychrophilic bacterium (strain TAE 79)	\N	includes
+228	Vibrio haloplanktis	\N	synonym
+228	Vibrio marinopraesens	\N	synonym
+228	psychrophilic bacterium TAE 79	\N	includes
+232	Alteromonas sp	\N	misspelling
+232	Alteromonas sp.	\N	scientific name
+234	Brucella	\N	scientific name
+234	Brucella Meyer and Shaw 1920	\N	synonym
+235	"Bacillus of abortion" Bang 1897	\N	authority
+235	"Bacterium abortus" Schmidt in Schmidt and Weis 1901	\N	authority
+235	ATCC 23448	\N	type material
+235	Bacterium abortus	\N	synonym
+235	Brucella abortus	\N	scientific name
+235	Brucella abortus (Schmidt 1901) Meyer and Shaw 1920 (Approved Lists 1980)	\N	authority
+235	Brucella melitensis (Hughes 1893) Meyer and Shaw 1920 (Approved Lists 1980) emend. Verger et al. 1985, biovar Abortus	\N	authority
+235	Brucella melitensis biovar Abortus	\N	genbank synonym
+235	Brucella melitensis bv. Abortus	\N	equivalent name
+235	NCTC 10093	\N	type material
+235	strain 544	\N	type material
+236	ATCC 25840	\N	type material
+236	Brucella melitensis (Hughes 1893) Meyer and Shaw 1920 (Approved Lists 1980) emend. Verger et al. 1985, biovar Ovis	\N	authority
+236	Brucella melitensis biovar Ovis	\N	genbank synonym
+236	Brucella melitensis bv. Ovis	\N	equivalent name
+236	Brucella ovis	\N	scientific name
+236	Brucella ovis Buddle 1956 (Approved Lists 1980)	\N	authority
+236	Brucella ovis.	\N	misspelling
+236	NCTC 10512	\N	type material
+236	not "Brucella ovis" van Drimmelen 1953	\N	authority
+236	strain 63/290	\N	type material
+237	Flavibacterium	\N	misspelling
+237	Flavobacterium	\N	scientific name
+237	Flavobacterium Bergey et al. 1923 (Approved Lists 1980) emend. Bernardet et al. 1996	\N	authority
+238	ATCC 13253	\N	type material
+238	CCUG 214	\N	type material
+238	CIP 60.57	\N	type material
+238	Chryseobacterium (Flavobacterium) meningosepticum	\N	synonym
+238	Chryseobacterium meningosepticum	\N	synonym
+238	Chryseobacterium meningosepticum (King 1959) Vandamme et al. 1994	\N	authority
+238	DSM 2800	\N	type material
+238	Elizabethkingia meningoseptica	\N	scientific name
+238	Elizabethkingia meningoseptica (King 1959) Kim et al. 2005	\N	authority
+238	Flavobacterium menginosepticum	\N	misspelling
+238	Flavobacterium meningosepticum	\N	synonym
+238	Flavobacterium meningosepticum King 1959 (Approved Lists 1980)	\N	authority
+238	JCM 21065	\N	type material
+238	LMG 12279	\N	type material
+238	NBRC 12535	\N	type material
+238	NCTC 10016	\N	type material
+239	Flavibacterium sp.	\N	equivalent name
+239	Flavobacterium sp.	\N	scientific name
+240	Flavibacterium sp. 141-8	\N	equivalent name
+240	Flavobacterium 141-8	\N	synonym
+240	Flavobacterium sp. (strain 141-8)	\N	synonym
+240	Flavobacterium sp. 141-8	\N	scientific name
+240	Flavobacterium sp. strain 141-8	\N	synonym
+241	Flavibacterium sp. SC12154	\N	equivalent name
+241	Flavobacterium SC12154	\N	synonym
+241	Flavobacterium sp. (strain SC 12,154)	\N	synonym
+241	Flavobacterium sp. SC12154	\N	scientific name
+241	Flavobacterium sp. strain SC 12154	\N	synonym
+242	Flavibacterium sp. U-188	\N	equivalent name
+242	Flavobacterium U-188	\N	synonym
+242	Flavobacterium sp. (strain U-188)	\N	synonym
+242	Flavobacterium sp. U-188	\N	scientific name
+244	ATCC 33414	\N	type material
+244	CCM 320	\N	type material
+244	CIP 105082	\N	type material
+244	Flavobacterium okeanokoites	\N	synonym
+244	Flavobacterium okeanokoites (IFO 12536)	\N	includes
+244	Flavobacterium okeanokoites IFO12536	\N	includes
+244	Flavobacterium okeanokoites ZoBell and Upham 1944 (Approved Lists 1980)	\N	authority
+244	Flavobacterium okeanoloites (IFO 12536)	\N	misspelling
+244	LMG 4030	\N	type material
+244	NBRC 12536	\N	type material
+244	NCIMB 561	\N	type material
+244	Planococcus okeanokoites	\N	synonym
+244	Planococcus okeanokoites (ZoBell and Upham 1944) Nakagawa et al. 1996	\N	authority
+244	Planococcus okeanokoites IFO 12536	\N	includes
+244	Planococcus okeanokoites IFO12536	\N	includes
+244	Planococcus okeanokoites Nakagawa et al. 1996 (sic)	\N	authority
+244	Planomicrobium okeanokoites	\N	scientific name
+244	Planomicrobium okeanokoites (Nakagawa et al. 1996) Yoon et al. 2001 (sic)	\N	authority
+244	Planomicrobium okeanokoites (ZoBell and Upham 1944) Yoon et al. 2001	\N	authority
+244	Planomicrobium sp. K3B3a	\N	includes
+244	VKM B-1175	\N	type material
+245	"Bacillus aquatilis" Frankland and Frankland 1889	\N	authority
+245	"Bacterium aquatilis" (sic) (Frankland and Frankland 1889) Chester 1897	\N	authority
+245	"Chromobacterium aquatilis" (sic) (Frankland and Frankland 1889) Topley and Wilson 1929	\N	authority
+245	"Empedobacter aquatile" (sic) (Frankland and Frankland 1889) Brisou et al. 1960	\N	authority
+245	"Flavobacterium aquatilis" (sic) (Frankland and Frankland 1889) Bergey et al. 1923	\N	authority
+245	ATCC 11947	\N	type material
+245	Bacillus aquatilis	\N	synonym
+245	Bacterium aquatilis	\N	synonym
+245	CCUG 29304	\N	type material
+245	CIP 103744	\N	type material
+245	CIP 55.141	\N	type material
+245	Chromobacterium aquatilis	\N	synonym
+245	DSM 1132	\N	type material
+245	Empedobacter aquatile	\N	synonym
+245	Flavibacterium aquatile	\N	equivalent name
+245	Flavobacterium aquatile	\N	scientific name
+245	Flavobacterium aquatile (...
 
[truncated message content]

[Treebase-guts] SF.net SVN: treebase:[1099] trunk/treebase-web/src/main/webapp

From: <sfr...@us...> - 2013-02-22 22:37:48

Revision: 1099
          http://treebase.svn.sourceforge.net/treebase/?rev=1099&view=rev
Author:   sfrgpiel
Date:     2013-02-22 22:37:40 +0000 (Fri, 22 Feb 2013)
Log Message:
-----------
Testing whether I can commit okay... and also adding the logo for the Thomson Reuters Data Citation Index, seeing as they are indexing TreeBASE and this can only have a positive appeal for our submitters. 

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/images/DCI_button.png

Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp	2013-01-22 13:03:18 UTC (rev 1098)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp	2013-02-22 22:37:40 UTC (rev 1099)
@@ -26,6 +26,8 @@
 			<a href="http://www.mendeley.com/groups/734351/treebase/" title="All publications in TreeBASE on Mendeley"><img src="<c:url value="images/mendeley-logo.png"/>" alt="All publications in TreeBASE on Mendeley" /></a>
 			<br /><br />
 			<a href="http://twitter.com/treebase" title="Follow @TreeBASE on Twitter"><img src="<c:url value="images/twitter-logo.png"/>" alt="Follow @TreeBASE on twitter" /></a>			
+			<br /><br />
+			<a href="http://wokinfo.com//products_tools/multidisciplinary/dci/" title="Covered by Data Citation Index"><img src="<c:url value="images/DCI_button.png"/>" alt="Covered by Data Citation Index" /></a>			
 		</center>
 	</div>
 	<img src="<c:url value="images/footer_bg.gif"/>" style="width:100%" alt="" />

Added: trunk/treebase-web/src/main/webapp/images/DCI_button.png
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/DCI_button.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] [ treebase-Bugs-3604529 ] searches return no results unless prev. results discarded

From: SourceForge.net <no...@so...> - 2013-02-14 01:00:11

Bugs item #3604529, was opened at 2013-02-13 08:09
Message generated for change (Comment added) made by sfrgpiel
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604529&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Rick Ree ()
Assigned to: Nobody/Anonymous (nobody)
Summary: searches return no results unless prev. results discarded

Initial Comment:
I am finding that searches return no results unless I clear the results of the previous search. This is quite confusing.

----------------------------------------------------------------------

>Comment By: William Piel (sfrgpiel)
Date: 2013-02-13 17:00

Message:
Providing a toggle switch so that new queries are not applied to the result
set of the previous query is on our to-do list. 

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604529&group_id=248804

[Treebase-guts] [ treebase-Bugs-3604527 ] Legacy study S912

From: SourceForge.net <no...@so...> - 2013-02-14 00:58:26

Bugs item #3604527, was opened at 2013-02-13 08:02
Message generated for change (Comment added) made by sfrgpiel
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604527&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Rick Ree ()
Assigned to: William Piel (sfrgpiel)
Summary: Legacy study S912

Initial Comment:
When I search for '912' using the Legacy study id field, I get back Yang & Yoder 2003 (S1021). I do not get study S912, Kretzer et al 2003, which is the study I was looking for.

----------------------------------------------------------------------

>Comment By: William Piel (sfrgpiel)
Date: 2013-02-13 16:58

Message:
Hi Rick. How did you get hold of the ID 912? Had the author quoted an ID
number in his or her paper, it would have been S787, not S912. The data
migration from old TreeBASE to the new one generated new IDs (sorry!), but
anything added subsequently (>3000) doesn't have this problem. 

----------------------------------------------------------------------

Comment By: Rick Ree ()
Date: 2013-02-13 08:07

Message:
Searching for '912' using the 'study id' field correctly returns Kretzer et
al 2003. This seems to conflict with the instructions to use the legacy id
field if the number is less than 3000.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604527&group_id=248804

[Treebase-guts] [ treebase-Bugs-3604529 ] searches return no results unless prev. results discarded

From: SourceForge.net <no...@so...> - 2013-02-13 16:09:08

Bugs item #3604529, was opened at 2013-02-13 08:09
Message generated for change (Tracker Item Submitted) made by 
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604529&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Rick Ree ()
Assigned to: Nobody/Anonymous (nobody)
Summary: searches return no results unless prev. results discarded

Initial Comment:
I am finding that searches return no results unless I clear the results of the previous search. This is quite confusing.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604529&group_id=248804

[Treebase-guts] [ treebase-Bugs-3604527 ] Legacy study S912

From: SourceForge.net <no...@so...> - 2013-02-13 16:07:14

Bugs item #3604527, was opened at 2013-02-13 08:02
Message generated for change (Comment added) made by 
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604527&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Rick Ree ()
Assigned to: William Piel (sfrgpiel)
Summary: Legacy study S912

Initial Comment:
When I search for '912' using the Legacy study id field, I get back Yang & Yoder 2003 (S1021). I do not get study S912, Kretzer et al 2003, which is the study I was looking for.

----------------------------------------------------------------------

>Comment By: Rick Ree ()
Date: 2013-02-13 08:07

Message:
Searching for '912' using the 'study id' field correctly returns Kretzer et
al 2003. This seems to conflict with the instructions to use the legacy id
field if the number is less than 3000.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604527&group_id=248804

[Treebase-guts] [ treebase-Bugs-3604527 ] Legacy study S912

From: SourceForge.net <no...@so...> - 2013-02-13 16:02:33

Bugs item #3604527, was opened at 2013-02-13 08:02
Message generated for change (Tracker Item Submitted) made by 
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604527&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Rick Ree ()
Assigned to: William Piel (sfrgpiel)
Summary: Legacy study S912

Initial Comment:
When I search for '912' using the Legacy study id field, I get back Yang & Yoder 2003 (S1021). I do not get study S912, Kretzer et al 2003, which is the study I was looking for.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3604527&group_id=248804

[Treebase-guts] SF.net SVN: treebase:[1098] trunk/treebase-web/src/main

From: <hl...@us...> - 2013-01-22 13:03:29

Revision: 1098
          http://treebase.svn.sourceforge.net/treebase/?rev=1098&view=rev
Author:   hlapp
Date:     2013-01-22 13:03:18 +0000 (Tue, 22 Jan 2013)
Log Message:
-----------
Rolling back revisions 1084 through 1091 on the main trunk. These revisions are now on the simple-search-UI branch.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSearch.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/simpleSearchForm.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studySearch.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearch.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSearch.jsp

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java	2013-01-22 13:03:18 UTC (rev 1098)
@@ -14,7 +14,6 @@
 import org.apache.log4j.Logger;
 import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.RangeExpression.MalformedRangeExpression;
-import org.cipres.treebase.domain.TBPersistable;
 import org.cipres.treebase.domain.matrix.CharacterMatrix;
 import org.cipres.treebase.domain.matrix.Matrix;
 import org.cipres.treebase.domain.matrix.MatrixService;
@@ -22,6 +21,8 @@
 import org.cipres.treebase.domain.search.SearchResults;
 import org.cipres.treebase.domain.search.SearchResultsType;
 import org.cipres.treebase.web.Constants;
+import org.cipres.treebase.web.util.RequestMessageSetter;
+import org.cipres.treebase.web.util.SearchMessageSetter;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 import org.z3950.zing.cql.CQLAndNode;
@@ -56,16 +57,65 @@
 		byTB1ID
 	}
 	
-	protected ModelAndView onSubmit(HttpServletRequest req,HttpServletResponse res,Object comm,BindException err) throws Exception {
+	protected ModelAndView onSubmit(
+			HttpServletRequest request,
+			HttpServletResponse response,
+			Object command,
+			BindException errors) throws Exception {
+
 		LOGGER.info("in matrixSearchController.onSubmit");
-		clearMessages(req);
-		String query = req.getParameter("query");
+
+		clearMessages(request);
+		String formName = request.getParameter("formName");
+		String query = request.getParameter("query");
+		
+		LOGGER.info("formName is '" + formName + "'");
+		
 		if ( ! TreebaseUtil.isEmpty(query) ) {
-			return handleQueryRequest(req, res, err, query);
+			return this.handleQueryRequest(request, response, errors, query);
+		}		
+		
+		if (formName.equals("matrixSimple")) {
+			String buttonName = request.getParameter("searchButton");
+			Set<Matrix> matches = new HashSet<Matrix>();
+			String searchTerm = convertStars(request.getParameter("searchTerm"));
+		 	SearchMessageSetter mSetter = new RequestMessageSetter(request);
+			MatrixSearchResults oldRes;	
+			{
+				SearchResults<?> sr = searchResults(request);
+				if (sr != null) {
+					oldRes = (MatrixSearchResults) sr.convertToMatrices();
+				} else {
+					oldRes = new MatrixSearchResults ();   // TODO: Convert existing search results to new type	
+				}
+			}			
+			if (buttonName.equals("matrixID")) {
+				matches.addAll(doSearch(request, response, SearchType.byID, errors,searchTerm));
+			} else if  (buttonName.equals("matrixTitle")) {
+				matches.addAll(doSearch(request, response, SearchType.byTitle, errors,searchTerm));
+			} else if  (buttonName.equals("matrixType")) {
+				matches.addAll(doSearch(request, response, SearchType.byType, errors,searchTerm));
+			} else if  (buttonName.equals("matrixNTAX")) {
+				matches.addAll(doSearch(request, response, SearchType.byNTAX, errors,searchTerm));	
+			} else if  (buttonName.equals("matrixNCHAR")) {
+				matches.addAll(doSearch(request, response, SearchType.byNCHAR, errors,searchTerm));
+			} else {
+				throw new Error("Unknown search button name '" + buttonName + "'");
+			}
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+				SearchResults<Matrix> newRes = intersectSearchResults(oldRes, 
+						new MatrixSearchResults(matches), mSetter, "No matching matrices found");
+				saveSearchResults(request, newRes);	
+				return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, newRes); 
+			}
+			else {
+				return this.searchResultsAsRDF(new MatrixSearchResults(matches), request, null, "matrix", "matrix");
+			}			
+		} 
+		
+		else { 
+			return super.onSubmit(request, response, command, errors);
 		}
-		else {
-			return super.onSubmit(req, res, comm, err);
-		}
 	}
 	
 	protected Set<Matrix> doCQLQuery(
@@ -111,7 +161,7 @@
 			} else if ( index.startsWith("tb.ntax") ) {
 				results.addAll(doSearch(request, response, SearchType.byNTAX, errors, term.getTerm()));
 			} else if ( index.startsWith("tb.nchar") ) {
-				results.addAll(doSearch(request, response, SearchType.byNCHAR, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byNTAX, errors, term.getTerm()));
 			} else {
 				// issue warnings
 				addMessage(request, "Unsupported index: " + index);
@@ -121,6 +171,7 @@
 		return results;		
 	}
 	
+	@SuppressWarnings("unchecked")
 	private Collection<Matrix> doSearch(
 			HttpServletRequest request,
 			HttpServletResponse response,
@@ -128,68 +179,62 @@
 			BindException errors,
 			String searchTerm) throws InstantiationException {
 
-		Collection<Matrix> results = new HashSet<Matrix>();
+		Collection<Matrix> matches = null;
 		MatrixService matrixService = getSearchService().getMatrixService();	
 
 		switch(searchType) {
-			case byID: {
-				addMatchesToResults(doSearchByIDString(request, matrixService, Matrix.class, searchTerm), results);
-				break;
+		case byID:
+			matches = (Collection<Matrix>) doSearchByIDString(request, matrixService, Matrix.class, searchTerm);
+			break;
+		
+		case byTB1ID:
+			matches = new HashSet<Matrix>();
+			matches.add(matrixService.findByTB1StudyID(searchTerm));
+			break;
+			
+		case byTitle:
+			matches = matrixService
+	  		.findSomethingBySubstring(Matrix.class, "title", searchTerm);
+			break;
+
+		case byType:
+			matches = matrixService
+	  		.findSomethingByItsDescription(Matrix.class, "matrixKind", searchTerm, false);
+			break;
+
+		case byNCHAR:
+			try {
+				matches = matrixService
+				.findSomethingByRangeExpression(CharacterMatrix.class, "nChar", searchTerm);
+			} catch (MalformedRangeExpression e) {
+				addMessage(request, "Malformed range expression: " + e.getMessage());
 			}
-			case byTB1ID: {
-				Matrix match = matrixService.findByTB1StudyID(searchTerm);
-				if ( null != match ) {
-					results.add(match);
-				}
-				break;
+			break;
+
+
+		case byNTAX:
+			try {
+				matches = matrixService
+				.findSomethingByRangeExpression(CharacterMatrix.class, "nTax", searchTerm);
+			} catch (MalformedRangeExpression e) {
+				addMessage(request, "Malformed range expression: " + e.getMessage());
 			}
-			case byTitle: {
-				addMatchesToResults(matrixService.findSomethingBySubstring(Matrix.class, "title", searchTerm), results);
-				break;
-			}
-			case byType: {
-				addMatchesToResults(matrixService.findSomethingByItsDescription(Matrix.class, "matrixKind", searchTerm, false),results);
-				break;
-			}
-			case byNCHAR: {
-				try {
-					addMatchesToResults(matrixService.findSomethingByRangeExpression(CharacterMatrix.class, "nChar", searchTerm),results);
-				} catch (MalformedRangeExpression e) {
-					addMessage(request, "Malformed range expression: " + e.getMessage());
-				}
-				break;	
-			}
-			case byNTAX: {
-				try {
-					addMatchesToResults(matrixService.findSomethingByRangeExpression(CharacterMatrix.class, "nTax", searchTerm),results);
-				} catch (MalformedRangeExpression e) {
-					addMessage(request, "Malformed range expression: " + e.getMessage());
-				}
-				break;
-			}
+			break;
 
 		}
 		
 		// XXX need to filter out orphaned matrices or matrices whose studies are unpublished
 		Collection<Matrix> orphanedMatrices = new HashSet<Matrix>();
-		for ( Matrix m : results ) {
-			if ( m.getStudy() == null || m.getStudy().isPublished() == false ) {
+		for ( Matrix m : matches ) {
+			if ( m.getStudy() == null || (m.getStudy().isPublished() == false)  ) {
 				orphanedMatrices.add(m);
-			}	
+			}		
 		}
-		results.removeAll(orphanedMatrices);
-		return results;
+		matches.removeAll(orphanedMatrices);
+		return matches;
 
 	}
 
-	@SuppressWarnings("unchecked")
-	private void addMatchesToResults(Collection<? extends TBPersistable> matches,
-			Collection<Matrix> results) {
-		if ( null != matches && ! matches.isEmpty() ) {
-			results.addAll((Collection<? extends Matrix>) matches);
-		}
-	}
-
 	SearchResultsType currentSearchType() {
 		return SearchResultsType.MATRIX;
 	}
@@ -201,6 +246,7 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors, String query) throws CQLParseException, IOException, InstantiationException {
+		//String query = request.getParameter("query");				
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java	2013-01-22 13:03:18 UTC (rev 1098)
@@ -26,6 +26,7 @@
 import org.cipres.treebase.domain.study.SubmissionService;
 import org.cipres.treebase.web.Constants;
 import org.cipres.treebase.web.model.Identify;
+import org.cipres.treebase.web.util.RequestMessageSetter;
 import org.cipres.treebase.web.util.IdentifyUtil;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
@@ -39,6 +40,8 @@
 import org.z3950.zing.cql.CQLRelation;
 import org.z3950.zing.cql.CQLTermNode;
 
+import java.text.DateFormat;
+
 /**
  * StudySearchController.java
  * 
@@ -93,15 +96,73 @@
 		byDOI
 	}
 
-	protected ModelAndView onSubmit(HttpServletRequest req,HttpServletResponse res,Object comm,BindException err) throws Exception {
+	protected ModelAndView onSubmit(
+			HttpServletRequest request,
+			HttpServletResponse response,
+			Object command,
+			BindException errors) throws Exception {
+
 		LOGGER.info("in StudySearchController.onSubmit");
-		clearMessages(req);
-		String query = req.getParameter("query");
-		if ( ! TreebaseUtil.isEmpty(query) ) {
-			return handleQueryRequest(req, res, err, query);
-		}
+
+		clearMessages(request);
+		String formName = request.getParameter("formName");
+		String query = request.getParameter("query");
+		
+		LOGGER.info("formName is '" + formName + "'");
+		
+		if ( ! TreebaseUtil.isEmpty(query) && ! query.equals("")) {
+			LOGGER.info("query is '" + query + "'");
+			return this.handleQueryRequest(request, response, errors, query);
+		}		
+		
+		if (formName.equals("searchKeyword")) {
+			SearchType searchType;
+			String buttonName = request.getParameter("searchButton");
+			String searchTerm = convertStars(request.getParameter("searchTerm"));
+			StudySearchResults oldRes;
+			{
+				SearchResults<?> sr = searchResults(request);
+				if (sr != null) {
+					oldRes = (StudySearchResults) sr.convertToStudies();
+				} else {
+					oldRes = new StudySearchResults ();   // TODO: Convert existing search results to new type	
+				}
+			}			
+			if (buttonName.equals("authorKeyword")) {
+				searchType = SearchType.byAuthorName;
+			} else if (buttonName.equals("studyID")) {
+				searchType = SearchType.byID;
+			} else if (buttonName.equals("legacyStudyID")) {
+				searchType = SearchType.byLegacyID;
+			} else if (buttonName.equals("titleKeyword")) {
+				searchType = SearchType.byTitle;
+			} else if (buttonName.equals("textKeyword")) {
+				searchType = SearchType.byKeyword;
+			} else if (buttonName.equals("citationKeyword")) {
+				searchType = SearchType.inCitation;
+			} else if (buttonName.equals("abstractKeyword")) {
+				searchType = SearchType.inAbstract;
+			} else if (buttonName.equals("doiKeyword")) {
+				searchType = SearchType.byDOI;
+			}
+			else {
+				throw new Error("Unknown search button name '" + buttonName + "'");
+			}
+			// XXX we now never do an exact match with terms provided through the web app. We can change
+			// this, e.g. by adding a check box whose value is the boolean argument of doSearch()
+			Collection<Study> matches = doSearch(request, response, searchType, errors,searchTerm,false,null);	
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {				
+				SearchResults<Study> newRes = intersectSearchResults(oldRes, new StudySearchResults(matches), 
+				new RequestMessageSetter(request), "No matching studies found");	
+				saveSearchResults(request, newRes);
+				return new ModelAndView("search/studySearch", Constants.RESULT_SET, newRes); 		
+			}
+			else {
+				return this.searchResultsAsRDF(new StudySearchResults(matches), request, null,"study","study");
+			}
+		} 
 		else {
-			return super.onSubmit(req, res, comm, err);
+			return super.onSubmit(request, response, command, errors);
 		}
 	}
 	

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java	2013-01-22 13:03:18 UTC (rev 1098)
@@ -47,14 +47,51 @@
 	private enum NamingAuthority { TREEBASE, UBIO, NCBI };
 	
 	@Override
-	protected ModelAndView onSubmit(HttpServletRequest req, HttpServletResponse res, Object comm, BindException err) throws Exception {
-		clearMessages(req);
-		String query = req.getParameter("query");
+	protected ModelAndView onSubmit(HttpServletRequest request,
+			HttpServletResponse response, Object searchCommand, BindException errors)
+	throws Exception {
+		clearMessages(request);
+		String formName = request.getParameter("formName");
+		String query = request.getParameter("query");
 		if ( ! TreebaseUtil.isEmpty(query) ) {
-			return handleQueryRequest(req, res, err, query);
+			return this.handleQueryRequest(request, response, errors, query);
 		}
-		else {
-			return super.onSubmit(req, res, comm, err);
+		if (formName.equals("searchByTaxonLabel")) {
+			SearchCommand newSearchCommand = (SearchCommand)searchCommand;
+			String searchOn = request.getParameter("searchOn");
+			String searchTerm = convertStars(request.getParameter("searchTerm"));
+			String[] searchTerms = searchTerm.split("\\r\\n");	
+			Collection<Taxon> taxa = new HashSet<Taxon>();
+			for ( int i = 0; i < searchTerms.length; i++ ) {
+				if ( searchOn.equals("TextSearch") ) {
+					taxa.addAll(doTaxonSearch(request, newSearchCommand, searchTerms[i], SearchIndex.LABEL, null));
+				}
+				else if ( searchOn.equals("Identifiers") ) {
+					String objectIdentifier = request.getParameter("objectIdentifier");
+					if ( objectIdentifier.equals("TreeBASE") ) {
+						taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.TREEBASE));
+					}
+					else if ( objectIdentifier.equals("NCBI") ) {
+						taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.NCBI));
+					}
+					else if ( objectIdentifier.equals("uBio") ) {
+						taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.UBIO));
+					}								
+				}	
+			}
+			TaxonSearchResults tsr = new TaxonSearchResults(taxa);
+			saveSearchResults(request, tsr);
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+				return samePage(request);
+			}
+			else {
+				return this.searchResultsAsRDF(tsr, request, null,"taxon","taxon");
+			}			
+			
+		} else if (formName.equals("taxonResultsAction")) {
+			return modifySearchResults(request, response, errors);
+		} else {
+			return super.onSubmit(request, response, (SearchCommand) searchCommand, errors);
 		}
 	}
 	
@@ -129,6 +166,31 @@
 		logger.debug(node);
 		return results;		
 	}
+	
+	private ModelAndView modifySearchResults(HttpServletRequest request,
+			HttpServletResponse response, BindException errors) throws InstantiationException {
+		TaxonSearchResults results = searchResults(request).convertToTaxa();
+		
+		String buttonName = request.getParameter("taxonResultsaction");
+		if (buttonName.equals("addCheckedToResults")) {
+//			Map<String,String> parameterMap = request.getParameterMap();
+			Collection<Taxon> newTaxa = new HashSet<Taxon> ();
+			for (String taxonIdString : request.getParameterValues("selection")) {
+				Taxon tx;
+				try {
+					tx = getTaxonLabelService().findTaxonByIDString(taxonIdString);
+				} catch (MalformedTreebaseIDString e) {
+					// This can only occur if the ID numbers in our web form are
+					// malformed, so it represents a programming error.  20090312 MJD
+					throw new Error(e);
+				}
+				if (tx != null) newTaxa.add(tx);
+			}
+			results.union(newTaxa);
+			saveSearchResults(request, results);
+		}
+		return samePage(request);
+	}
 
 	protected Collection<Taxon> doTaxonSearch(HttpServletRequest request,
 			SearchCommand searchCommand, String searchTerm, SearchIndex searchIndex, NamingAuthority namingAuthority) throws Exception {
@@ -161,6 +223,9 @@
 		getTaxonLabelService().resurrectAll(taxa);
 		LOGGER.debug("Found " + taxa.size() + " taxa");
 		return taxa;
+//		TaxonSearchResults tsr = new TaxonSearchResults(taxa);
+//		saveSearchResults(request, tsr);
+//		return samePage(request);	
 	}
 	
 	/**
@@ -198,20 +263,16 @@
 					}
 					if ( null != tb1LegacyId && null != index && index.matches(".*taxonVariant.*") ) {
 						TaxonVariant tv = getTaxonHome().findVariantByTB1LegacyId(tb1LegacyId);
-						if ( null != tv ) {
-							LOGGER.debug("Found taxon variant: " + tv.getId());
-							if ( null != tv.getTaxon() ) {
-								taxaFound.add(tv.getTaxon());
-							}
+						LOGGER.debug("Found taxon variant: " + tv.getId());
+						if ( null != tv.getTaxon() ) {
+							taxaFound.add(tv.getTaxon());
 						}
 					}
 					else if ( null != tb1LegacyId ){
 						Taxon taxon = getTaxonHome().findByTB1LegacyId(tb1LegacyId);
+						LOGGER.debug("Found taxon: " + taxon.getId());
 						if ( null != taxon ) {
-							LOGGER.debug("Found taxon: " + taxon.getId());
-							if ( null != taxon ) {
-								taxaFound.add(taxon);
-							}
+							taxaFound.add(taxon);
 						}
 					}					
 				}

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java	2013-01-22 13:03:18 UTC (rev 1098)
@@ -14,12 +14,14 @@
 import org.apache.log4j.Logger;
 import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.RangeExpression.MalformedRangeExpression;
+import org.cipres.treebase.domain.matrix.Matrix;
 import org.cipres.treebase.domain.search.SearchResults;
 import org.cipres.treebase.domain.search.SearchResultsType;
 import org.cipres.treebase.domain.search.TreeSearchResults;
 import org.cipres.treebase.domain.tree.PhyloTree;
 import org.cipres.treebase.domain.tree.PhyloTreeService;
 import org.cipres.treebase.web.Constants;
+import org.cipres.treebase.web.util.RequestMessageSetter;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 import org.z3950.zing.cql.CQLAndNode;
@@ -54,15 +56,73 @@
 		byNTAX
 	}
 	
-	protected ModelAndView onSubmit(HttpServletRequest req,HttpServletResponse res,Object comm,BindException err) throws Exception {
+	protected ModelAndView onSubmit(
+			HttpServletRequest request,
+			HttpServletResponse response,
+			Object command,
+			BindException errors) throws Exception {
+
 		LOGGER.info("in TreeSearchController.onSubmit");
-		clearMessages(req);
-		String query = req.getParameter("query");
+
+		clearMessages(request);
+		String formName = request.getParameter("formName");
+		String query = request.getParameter("query");
+		
+		LOGGER.info("formName is '" + formName + "'");
+		
 		if ( ! TreebaseUtil.isEmpty(query) ) {
-			return handleQueryRequest(req, res, err, query);
+			return this.handleQueryRequest(request, response, errors, query);
 		}
-		else {
-			return super.onSubmit(req, res, comm, err);
+		
+		if (formName.equals("treeSimple")) {
+			String buttonName = request.getParameter("searchButton");
+			String searchTerm = convertStars(request.getParameter("searchTerm"));
+			Collection<PhyloTree> matches = null;
+			TreeSearchResults oldRes;	
+			{
+				SearchResults<?> sr = searchResults(request);
+				if (sr != null) {
+					oldRes = (TreeSearchResults) sr.convertToTrees();
+				} else {
+					oldRes = new TreeSearchResults ();   // TODO: Convert existing search results to new type	
+				}
+			}			
+			if (buttonName.equals("treeID")) {
+				matches = doSearch(request, response, SearchType.byID, errors, searchTerm);
+			} else if  (buttonName.equals("treeTitle")) {
+				matches =  doSearch(request, response, SearchType.byTitle, errors, searchTerm);
+			} else if  (buttonName.equals("treeType")) {
+				matches = doSearch(request, response, SearchType.byType, errors, searchTerm);
+			} else if  (buttonName.equals("treeKind")) {
+				matches = doSearch(request, response, SearchType.byKind, errors, searchTerm);
+			} else if  (buttonName.equals("treeQuality")) {
+				matches = doSearch(request, response, SearchType.byQuality, errors, searchTerm);
+			} else if  (buttonName.equals("treeNTAX")) {
+				matches = doSearch(request, response, SearchType.byNTAX, errors, searchTerm);
+			} else {
+				throw new Error("Unknown search button name '" + buttonName + "'");
+			}
+			
+			// XXX need to filter out orphaned matrices or matrices whose studies are unpublished
+			Collection<PhyloTree> orphanedTrees = new HashSet<PhyloTree>();
+			for ( PhyloTree t : matches ) {
+				if (t.getStudy() == null || (t.getStudy().isPublished() == false)){
+					orphanedTrees.add(t);
+				}		
+			}
+			matches.removeAll(orphanedTrees);
+
+			SearchResults<PhyloTree> newRes = intersectSearchResults(oldRes, new TreeSearchResults(matches), 
+			new RequestMessageSetter(request), "No matching trees found");	
+			saveSearchResults(request, newRes);	
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {			
+				return new ModelAndView("search/treeSearch", Constants.RESULT_SET, newRes); 			
+			}
+			else {
+				return this.searchResultsAsRDF(newRes, request, null,"tree","tree");
+			}
+		} else { 
+			return super.onSubmit(request, response, command, errors);
 		}
 	}
 
@@ -188,6 +248,7 @@
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
 			HttpServletResponse response, BindException errors, String query)
 			throws CQLParseException, IOException, InstantiationException {
+		//String query = request.getParameter("query");
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSearch.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSearch.jsp	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSearch.jsp	2013-01-22 13:03:18 UTC (rev 1098)
@@ -15,25 +15,16 @@
       'integer' : [ 'tb.identifier.matrix', 'tb.identifier.matrix.tb1', 'tb.ntax.matrix', 'tb.nchar.matrix' ],
       'id' : [ 'tb.identifier.matrix', 'tb.identifier.matrix.tb1' ],
       'word' : [ 'tb.title.matrix', 'tb.type.matrix' ],
+      'doi' : [ 'prism.doi' ] // this doesn't work yet, we have no search on doi
     };
     
-    // purlBase is assigned in /common/search-nav.jsp
+ 	// purlBase is assigned in /common/search-nav.jsp
     var phyloWSURI = purlBase + 'matrix/find?query=';
   //]]>
 </script>
 
-<%-- jsp:include page="matrixSimpleSearchForm.jsp"/ --%>
+<jsp:include page="matrixSimpleSearchForm.jsp"/>
 
-<fieldset>
-	<legend>
-	  	Matrix search
-		<a href="#" class="openHelp" onclick="openHelp('matrixSimpleSearchForm')">
-			<img class="iconButton" src="<fmt:message key="icons.help"/>" />
-		</a>	  		
-	</legend>
-<jsp:include page="simpleSearchForm.jsp"/>
-</fieldset>
-
 <c:set var="searchType" value="matrix" scope="request"/>
 
 <div id="s-clear"></div>

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/simpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/simpleSearchForm.jsp	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/simpleSearchForm.jsp	2013-01-22 13:03:18 UTC (rev 1098)
@@ -5,7 +5,7 @@
 		<input type="radio" name="join" onclick="TreeBASE.expandQuery(); return true;" id="all" value="and"/> All
 		<input type="radio" name="join" onclick="TreeBASE.expandQuery(); return true;" value="or" checked="checked"/> Any<br/>
 		<a onclick="TreeBASE.collapseExpand('expanded','block',this)" id="expander">
-			<img src="/treebase-web/images/plus.gif"/>
+			<img src="http://www.treebase.org/treebase-web/images/plus.gif"/>
 		  	<small style="color:silver">Advanced search</small>
 		</a>
 		<textarea id="expanded" style="display:none;width:500px;height:300px"></textarea><br/>

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studySearch.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studySearch.jsp	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studySearch.jsp	2013-01-22 13:03:18 UTC (rev 1098)
@@ -20,25 +20,15 @@
       'doi' : [ 'prism.doi' ]
     };
     
-    // purlBase is assigned in /common/search-nav.jsp
+ 	// purlBase is assigned in /common/search-nav.jsp
     var phyloWSURI = purlBase + 'study/find?query=';
   //]]>
 </script>
 
 <c:set var="searchType" value="study" scope="request"/>
 
-<%-- jsp:include page="studyKeywordSearchForm.jsp"/ --%>
+<jsp:include page="studyKeywordSearchForm.jsp"/>
 
-<fieldset>
-	<legend>
-	  	Study search
-		<a href="#" class="openHelp" onclick="openHelp('studyKeywordSearchForm')">
-			<img class="iconButton" src="<fmt:message key="icons.help"/>" />
-		</a>	  		
-	</legend>
-<jsp:include page="simpleSearchForm.jsp"/>
-</fieldset>
-
 <div id="s-clear"></div>
 
 <jsp:include page="searchMessages.jsp"/>

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearch.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearch.jsp	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearch.jsp	2013-01-22 13:03:18 UTC (rev 1098)
@@ -15,9 +15,10 @@
       'integer' : [ 'tb.identifier.ncbi', 'tb.identifier.ubio', 'tb.identifier.taxon', 'tb.identifier.taxon.tb1' ],
       'id' : [ 'tb.identifier.taxon', 'tb.identifier.taxon.tb1' ],
       'word' : [ 'tb.title.taxon', 'tb.title.taxonLabel', 'tb.title.taxonVariant' ],
+      'doi' : [ 'prism.doi' ] // this doesn't work yet, we have no search on doi
     };
     
-    // purlBase is assigned in /common/search-nav.jsp
+ 	// purlBase is assigned in /common/search-nav.jsp
     var phyloWSURI = purlBase + 'taxon/find?query=';
   //]]>
 </script>

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSearch.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSearch.jsp	2013-01-22 13:00:20 UTC (rev 1097)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSearch.jsp	2013-01-22 13:03:18 UTC (rev 1098)
@@ -19,23 +19,13 @@
       'word' : [ 'tb.title.tree', 'tb.type.tree', 'tb.kind.tree', 'tb.quality.tree' ],
     };
     
-    // purlBase is assigned in /common/search-nav.jsp
+ 	// purlBase is assigned in /common/search-nav.jsp
     var phyloWSURI = purlBase + 'tree/find?query=';
   //]]>
 </script>
 
-<%-- jsp:include page="treeSimpleSearchForm.jsp"/ --%>
+<jsp:include page="treeSimpleSearchForm.jsp"/>
 
-<fieldset>
-	<legend>
-	  	Tree search
-		<a href="#" class="openHelp" onclick="openHelp('treeSimpleSearchForm')">
-			<img class="iconButton" src="<fmt:message key="icons.help"/>" />
-		</a>	  		
-	</legend>
-<jsp:include page="simpleSearchForm.jsp"/>
-</fieldset>
-
 <c:set var="searchType" value="tree" scope="request"/>
 
 <div id="s-clear"></div>

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[Treebase-guts] SF.net SVN: treebase:[1097] branches/simple-search-UI

From: <hl...@us...> - 2013-01-22 13:00:32

Revision: 1097
          http://treebase.svn.sourceforge.net/treebase/?rev=1097&view=rev
Author:   hlapp
Date:     2013-01-22 13:00:20 +0000 (Tue, 22 Jan 2013)
Log Message:
-----------
Rolling back revisions 1092 through 1095 on the simple-search-UI branch so that from its branching point onward it doesn't have changes that are also on the main trunk.

Modified Paths:
--------------
    branches/simple-search-UI/treebase-core/pom.xml
    branches/simple-search-UI/treebase-web/pom.xml
    branches/simple-search-UI/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java
    branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
    branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/web.xml

Removed Paths:
-------------
    branches/simple-search-UI/treebase-web/src/main/webapp/images/paypalsub.jpg

Modified: branches/simple-search-UI/treebase-core/pom.xml
===================================================================
--- branches/simple-search-UI/treebase-core/pom.xml	2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-core/pom.xml	2013-01-22 13:00:20 UTC (rev 1097)
@@ -127,7 +127,7 @@
 		<dependency>
 			<groupId>postgresql</groupId>
 			<artifactId>postgresql</artifactId>
-			<version>8.4-702.jdbc3</version>
+			<version>8.3-603.jdbc3</version>
 		</dependency>
 		
 		<dependency>
@@ -171,8 +171,6 @@
 					<groupId>org.slf4j</groupId>
 					<artifactId>slf4j-jdk14</artifactId>
 				</exclusion>
-				
-					
 			</exclusions>
 		</dependency>
 		<dependency>
@@ -188,10 +186,6 @@
 					<groupId>org.slf4j</groupId>
 					<artifactId>slf4j-jdk14</artifactId>
 				</exclusion>
-				<exclusion>
-					<groupId>org.apache.geronimo.specs</groupId>
-					<artifactId>geronimo-servlet_2.5_spec</artifactId>
-				</exclusion>
 			</exclusions>
 		</dependency>
 		<dependency>

Modified: branches/simple-search-UI/treebase-web/pom.xml
===================================================================
--- branches/simple-search-UI/treebase-web/pom.xml	2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-web/pom.xml	2013-01-22 13:00:20 UTC (rev 1097)
@@ -115,6 +115,12 @@
 
 		<dependency>
 			<groupId>javax.servlet</groupId>
+			<artifactId>servlet-api</artifactId>
+			<version>2.4</version>
+		</dependency>
+
+		<dependency>
+			<groupId>javax.servlet</groupId>
 			<artifactId>jstl</artifactId>
 			<version>1.1.2</version>
 		</dependency>
@@ -413,6 +419,13 @@
                         </exclusion>
                 </exclusions>
         </dependency>
+        
+		<dependency>
+    		<groupId>opensymphony</groupId>
+    		<artifactId>oscache</artifactId>
+    		<version>2.4.1</version>
+		</dependency>
+
 </dependencies>
 		
 </project>

Modified: branches/simple-search-UI/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java
===================================================================
--- branches/simple-search-UI/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java	2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java	2013-01-22 13:00:20 UTC (rev 1097)
@@ -248,7 +248,7 @@
 				errors.add(label.getTaxonLabel() + " has not been linked to the external taxonomy");
 			}
 			else if ( label.getAttemptedLinking() && label.getNcbiTaxID() == null ) {
-				errors.add(label.getTaxonLabel() + " - an unsuccessful attempt has been made to link this to the external taxonomy");
+				errors.add(label.getTaxonLabel() + " - an unsuccesful attempt has been made to link this to the external taxonomy");
 			}
 		}
 		

Modified: branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
===================================================================
--- branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp	2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp	2013-01-22 13:00:20 UTC (rev 1097)
@@ -18,8 +18,8 @@
 <p>TreeBASE provides an advanced access URL for anonymous reviewers and referees to provide additional quality control before the data are made public. Although additional NSF requirements relating to provenance and how data were generated are not normally required or scrutinized by TreeBASE staff, submitters who flag their submission (in the submission notes section) as NSF-sponsored data will receive special attention by our staff. In these cases, TreeBASE staff will check to make sure that provenance and analysis metadata are adequately provided, and, as needed, communicate with the submitter and assist in properly formatting and ingesting these data. </p>
 <h2>Data Standards and Dissemination</h2>
 <p>TreeBASE plans to remain in compliance with the emerging, but still evolving, standard of Minimal Information for a Phylogenetic Analysis (<a href="http://www.nescent.org/sites/evoio/MIAPA" target="_blank">MIAPA</a>). In addition, TreeBASE publishes persistant and resolvable globally unique identifiers (GUIDs) for all major data objects and disseminates data and metadata using commonly accepted standards. A Restful <a href="http://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS" target="_blank">PhyloWS</a>  API exposes metadata using RSS feeds in RDF; a <a href="http://www.nexml.org/" target="_blank">NeXML</a>  serialization exposes data marked up with metadata using published vocabularies and fully qualified URIs in compliance with <a href="http://linkeddata.org/" target="_blank">Linked Data</a>  standards. Basic record metadata are published through an OIA-PMH service, and TreeBASE records are mirrored by Dryad, which provides a secondary Dryad <a href="http://www.datacite.org" target="_blank">DataCite DOI</a>. However, for most people in the scientific community, data will be retrieved using the web user interface and downloaded in the NEXUS format, while metadata can be downloaded separately in a tab-separated text format. </p>
-<h2>Data Persistence</h2>
-<p>Although no data service can guarantee indefinite persistence, TreeBASE will make every effort to preserve its services as long as possible. Additionally, the Articles of Incorporation of the <a href="http://www.phylofoundation.org" target="_blank">Phyloinformatics Research Foundation</a>, which oversees TreeBASE activities, specify that if dissolution is ever required the assets will be transferred to a similar entity with a comparable mission. </p>
+<h2>Data Persistance</h2>
+<p>Although no data service can guarantee indefinite persistance, TreeBASE will make every effort to preserve its services as long as possible. Additionally, the Articles of Incorporation of the <a href="http://www.phylofoundation.org" target="_blank">Phyloinformatics Research Foundation</a>, which oversees TreeBASE activities, specify that if dissolution is ever required the assets will be transferred to a similar entity with a comparable mission. </p>
 <h2>Preparing a Data Management Plan for NSF</h2>
 <p>Scientists are welcome to designate TreeBASE as their selected repository and dissemination service for phylogenetic data generated by sponsored research. In their Data Management Plan, we suggest that the following  be mentioned:</p>
 <ul>
@@ -43,7 +43,7 @@
 <table>
 <tr><td><input type="hidden" name="on0" value="TreeBASE Study URI:">TreeBASE Study URI:</td></tr><tr><td><input type="text" name="os0" maxlength="60"></td></tr>
 </table>
-<input type="image" src="images/paypalsub.jpg" border="0" name="submit" alt="PayPal - The safer, easier way to pay online!">
+<input type="image" src="http://www.phylofoundation.org/icns/sub.jpg" border="0" name="submit" alt="PayPal - The safer, easier way to pay online!">
 <img alt="" border="0" src="https://www.paypalobjects.com/WEBSCR-640-20110401-1/en_US/i/scr/pixel.gif" width="1" height="1">
 </form></td>
     <td><form action="https://www.paypal.com/cgi-bin/webscr" method="post">

Modified: branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/web.xml	2013-01-22 01:17:59 UTC (rev 1096)
+++ branches/simple-search-UI/treebase-web/src/main/webapp/WEB-INF/web.xml	2013-01-22 13:00:20 UTC (rev 1097)
@@ -58,7 +58,47 @@
 	<listener>
   		<listener-class>net.bull.javamelody.SessionListener</listener-class>
 	</listener>
+	
+	<filter>
+    	<filter-name>CacheFilter</filter-name>
+    	<filter-class>com.opensymphony.oscache.web.filter.CacheFilter</filter-class>
+    	<init-param>
+        	<param-name>expires</param-name>
+        	<param-value>time</param-value>
+    	</init-param>
+    	<init-param>
+        	<param-name>time</param-name>
+        	<param-value>2592000</param-value> <!-- one month -->
+    	</init-param>
+	</filter>
 
+	<filter-mapping>
+    	<filter-name>CacheFilter</filter-name>
+    	<url-pattern>/search/downloadAStudy.html</url-pattern>
+	</filter-mapping>
+	
+	<filter-mapping>
+    	<filter-name>CacheFilter</filter-name>
+    	<url-pattern>/search/study/anyObjectAsRDF.rdf</url-pattern>
+	</filter-mapping>
+	
+	<filter-mapping>
+    	<filter-name>CacheFilter</filter-name>
+    	<url-pattern>/search/downloadANexusFile.html</url-pattern>
+	</filter-mapping>
+	
+	<filter-mapping>
+    	<filter-name>CacheFilter</filter-name>
+    	<url-pattern>/search/downloadAMatrix.html</url-pattern>
+	</filter-mapping>
+	
+	<filter-mapping>
+    	<filter-name>CacheFilter</filter-name>
+    	<url-pattern>/search/downloadATree.html</url-pattern>
+	</filter-mapping>
+	
+
+
 	<!-- =================================================================== -->
 	<!-- Declarations of JNDI Resources expected from the Tomcat container   -->
 	<!-- =================================================================== -->

Deleted: branches/simple-search-UI/treebase-web/src/main/webapp/images/paypalsub.jpg
===================================================================
(Binary files differ)

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[Treebase-guts] SF.net SVN: treebase:[1096] branches/simple-search-UI/

From: <hl...@us...> - 2013-01-22 01:18:06

Revision: 1096
          http://treebase.svn.sourceforge.net/treebase/?rev=1096&view=rev
Author:   hlapp
Date:     2013-01-22 01:17:59 +0000 (Tue, 22 Jan 2013)
Log Message:
-----------
Branching off rvos' changes r1084-r1091, for which the ideas was "to make the search interfaces a lot simpler". However, this currently fails to build on production.

Revision Links:
--------------
    http://treebase.svn.sourceforge.net/treebase/?rev=1084&view=rev
    http://treebase.svn.sourceforge.net/treebase/?rev=1091&view=rev

Added Paths:
-----------
    branches/simple-search-UI/

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[Treebase-guts] [ treebase-Bugs-3556175 ] Switching between "Book Section" and "Book"

From: SourceForge.net <no...@so...> - 2012-08-10 20:26:20

Bugs item #3556175, was opened at 2012-08-10 13:26
Message generated for change (Tracker Item Submitted) made by jonesmcc
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3556175&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Michael Jones (jonesmcc)
Assigned to: Nobody/Anonymous (nobody)
Summary: Switching between "Book Section" and "Book"

Initial Comment:
On the "Citation" pane, for any given submission, if you set the publication type as "Book Section", click the "Update" button, and then set the publication type as "Book" and click the "Update" button, TreeBASE will give you a "Data Access Failure" error message with the description below.

Object with id: null was not of the specified subclass: org.cipres.treebase.domain.study.BookCitation (class of the given object did not match class of persistent copy); nested exception is org.hibernate.WrongClassException: Object with id: null was not of the specified subclass: org.cipres.treebase.domain.study.BookCitation (class of the given object did not match class of persistent copy)

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3556175&group_id=248804

[Treebase-guts] [ treebase-Bugs-3544738 ] Author email address whitespace

From: SourceForge.net <no...@so...> - 2012-07-16 19:26:51

Bugs item #3544738, was opened at 2012-07-16 12:26
Message generated for change (Tracker Item Submitted) made by jonesmcc
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3544738&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Michael Jones (jonesmcc)
Assigned to: Nobody/Anonymous (nobody)
Summary: Author email address whitespace

Initial Comment:
I often paste emails into the "authoremailstring" field on the Author pane. I've found that TreeBASE doesn't parse out whitespace characters (spaces) before it tries to validate emails, consequently causing the checks to fail. This isn't readily apparent (especially if the whitespace is at the end of the string) and can lead to confusion.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3544738&group_id=248804

[Treebase-guts] SF.net SVN: treebase:[1095] trunk

From: <hs...@us...> - 2012-06-15 15:19:22

Revision: 1095
          http://treebase.svn.sourceforge.net/treebase/?rev=1095&view=rev
Author:   hshyket
Date:     2012-06-15 15:19:11 +0000 (Fri, 15 Jun 2012)
Log Message:
-----------
Updating PostgreSQL dependency to 8.4.  Excluding geronimo-servlet and servlet-api from dependecies.

Modified Paths:
--------------
    trunk/treebase-core/pom.xml
    trunk/treebase-web/pom.xml

Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml	2012-06-11 18:10:38 UTC (rev 1094)
+++ trunk/treebase-core/pom.xml	2012-06-15 15:19:11 UTC (rev 1095)
@@ -127,7 +127,7 @@
 		<dependency>
 			<groupId>postgresql</groupId>
 			<artifactId>postgresql</artifactId>
-			<version>8.3-603.jdbc3</version>
+			<version>8.4-702.jdbc3</version>
 		</dependency>
 		
 		<dependency>
@@ -171,6 +171,8 @@
 					<groupId>org.slf4j</groupId>
 					<artifactId>slf4j-jdk14</artifactId>
 				</exclusion>
+				
+					
 			</exclusions>
 		</dependency>
 		<dependency>
@@ -186,6 +188,10 @@
 					<groupId>org.slf4j</groupId>
 					<artifactId>slf4j-jdk14</artifactId>
 				</exclusion>
+				<exclusion>
+					<groupId>org.apache.geronimo.specs</groupId>
+					<artifactId>geronimo-servlet_2.5_spec</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 		<dependency>

Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml	2012-06-11 18:10:38 UTC (rev 1094)
+++ trunk/treebase-web/pom.xml	2012-06-15 15:19:11 UTC (rev 1095)
@@ -115,12 +115,6 @@
 
 		<dependency>
 			<groupId>javax.servlet</groupId>
-			<artifactId>servlet-api</artifactId>
-			<version>2.4</version>
-		</dependency>
-
-		<dependency>
-			<groupId>javax.servlet</groupId>
 			<artifactId>jstl</artifactId>
 			<version>1.1.2</version>
 		</dependency>

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