GBIF support refinements

Author: remarq

WEB-INF/web.xml

@@ -220,4 +220,11 @@
     <tracking-mode>COOKIE</tracking-mode>
   </session-config>
 
+  <resource-ref>
+    <description>DB Connection</description>
+    <res-ref-name>jdbc/AntSource</res-ref-name>
+    <res-type>javax.sql.DataSource</res-type>
+    <res-link>jdbc/AntSource</res-link>
+  </resource-ref>
+
 </web-app>

doc/release.txt

@@ -1,3 +1,6 @@
+Release 8.111
+  GBIF support refinements.
+
 Release 8.110
   GBIF support for date types and long values for type_status and habitat.
 

src/org/calacademy/antweb/home/TaxonDb.java

@@ -39,6 +39,10 @@ public Genus getGenus(String subfamily, String genus) throws SQLException, Antwe
         String taxonName = getTaxonName(subfamily, genus, null, null, "genus");
         return (Genus) getTaxon(taxonName);
     }
+    public Genus getGenus(String genus) throws SQLException, AntwebException {
+        String taxonName = getTaxonName(null, genus, null, null, "genus");
+        return (Genus) getTaxon(taxonName);
+    }
     public Species getSpecies(String subfamily, String genus, String species) throws SQLException, AntwebException {
         String taxonName = getTaxonName(subfamily, genus, species, null, "species");
         return (Species) getTaxon(taxonName);
@@ -72,7 +76,7 @@ public Taxon getTaxon(String taxonName) throws SQLException { //, tring tableNam
 
         String theQuery = "";
 
-        boolean log = true && "myrmicinaetetramorium vernicosum".equals(taxonName);
+        boolean log = false && AntwebProps.isDevMode() && "formicinaecamponotus".equals(taxonName); // && "myrmicinaetetramorium vernicosum".equals(taxonName);
         ResultSet rset = null;
         PreparedStatement stmt = null;
         try {
@@ -95,7 +99,7 @@ public Taxon getTaxon(String taxonName) throws SQLException { //, tring tableNam
 
             int count = 0;
             while (rset.next()) {
-                if (log) s_log.debug("getTaxon() IN query:" + theQuery);
+                //if (log) A.log("getTaxon() IN query:" + theQuery);
 
                 ++count; // Only one record expected
 
@@ -206,12 +210,13 @@ public Taxon getTaxon(String taxonName) throws SQLException { //, tring tableNam
           //It may not be found during Worldants, for instance amblyoponinae, but after the cleanup process it will...
           String warning = " taxon not found taxonName:" + taxonName;
           //if (AntwebProps.isDevMode()) warning += " theQuery:" + theQuery;
-          s_log.debug("getTaxon() " + warning + " query:" + theQuery + " taxonFromMgr:" + TaxonMgr.getTaxon(taxonName) + " antcatCount:" + getAntcatCount());
+          //A.log("getTaxon() " + warning + " query:" + theQuery + " taxonFromMgr:" + TaxonMgr.getTaxon(taxonName) + " antcatCount:" + getAntcatCount());
           return null;
         }
 
-        if (AntwebProps.isDevMode() && "myrmicinaestrumigenys emmae".equals("taxonName")) {
-            s_log.warn("getTaxon() name:" + taxonName + " taxon:" + taxon.getTaxonName() + " query:" + theQuery);
+        if (log) {
+            A.log("getTaxon() name:" + taxonName + " taxon:" + taxon.getTaxonName() + " query:" + theQuery);
+            //AntwebUtil.logShortStackTrace(10);
         }
         return taxon;
     }

src/org/calacademy/antweb/home/UploadDb.java

@@ -684,7 +684,7 @@ public String getAntwebSubfamily(String genus)
               debugSubfamilyList += ", " + subfamily;
             }
           }
-          if (AntwebProps.isDevMode() && count == 0) s_log.error("getAntwebSubfamily() Problem? Not sure.  No subfamily for genus:" + genus + " subfamilySet:" + debugSubfamilyList);
+          if (AntwebProps.isDevMode() && count == 0) A.iLog("getAntwebSubfamily() Problem? Not sure.  No subfamily for genus:" + genus + " subfamilySet:" + debugSubfamilyList);
           if (count > 1) s_log.error("getAntwebSubfamily() more than one subfamily for genus:" + genus + " subfamilySet:" + debugSubfamilyList);
         } finally {
           DBUtil.close(stmt, rset, "UploadDb.getAntwebSubfamily()");