diff --git a/.classpath b/.classpath
index e80e52b1ae1d05764536c4c1d389d9a606f6eecb..e6919ba402a2cbe5f4325777861710882d2442ca 100644
--- a/.classpath
+++ b/.classpath
@@ -1,8 +1,9 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="src"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
- <classpathentry kind="lib" path="json-simple-1.1.1.jar"/>
- <classpathentry kind="output" path="bin"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="src"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+ <classpathentry kind="lib" path="json-simple-1.1.1.jar"/>
+ <classpathentry kind="lib" path="tomcat/lib/servlet-api.jar"/>
+ <classpathentry kind="output" path="bin"/>
+</classpath>
diff --git a/.gitignore b/.gitignore
index df325ba7137bb46cd06ce38e8ed54e02baf9df69..3e44dc3a5fc617ca79a27ecb90884f53a5182d61 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,4 +9,4 @@
*.csv
*.ser
.idea/
-
+*.class
diff --git a/makefile b/makefile
new file mode 100644
index 0000000000000000000000000000000000000000..0c059edb65f32c66ba1f17c281a6a521ab5fa86b
--- /dev/null
+++ b/makefile
@@ -0,0 +1,8 @@
+server:
+ cp -rf bin/* tomcat/webapps/Trawl/WEB-INF/classes
+
+start: server
+ tomcat/bin/startup.sh
+
+stop:
+ tomcat/bin/shutdown.sh
\ No newline at end of file
diff --git a/makefile2 b/makefile2
new file mode 100644
index 0000000000000000000000000000000000000000..28215d0e481bfe2408af690471b82002441d7427
--- /dev/null
+++ b/makefile2
@@ -0,0 +1,69 @@
+TOMCAT_DIR = tomcat/webapps/Trawl
+BIN_DIR = tomcat/webapps/Trawl/bin
+
+server: $(BIN_DIR)/TrawlExpert.class $(BIN_DIR)/../WEB-INF/classes/com/example/web/Director.class
+ javac -d $(TOMCAT_DIR)/WEB-INF/classes/ -classpath tomcat/lib/servlet-api.jar $(TOMCAT_DIR)/src/com/example/listener/StartUpContext.java
+
+
+start:
+ tomcat/bin/startup.sh
+
+stop:
+ tomcat/bin/shutdown.sh
+
+$(BIN_DIR)/TrawlExpert.class: $(BIN_DIR)/data/BioTree.class $(BIN_DIR)/data/DataStore.class $(BIN_DIR)/data/Date.class $(BIN_DIR)/data/FileProcessor.class $(BIN_DIR)/data/Record.class $(BIN_DIR)/data/TaxonNode.class $(BIN_DIR)/data/TaxonType.class $(BIN_DIR)/data/WormsAPI.class $(BIN_DIR)/search/BasicSearch.class $(BIN_DIR)/search/BST.class $(BIN_DIR)/search/Histogram.class $(BIN_DIR)/sort/Bound.class $(BIN_DIR)/sort/GeneralCompare.class $(BIN_DIR)/sort/GeneralRange.class $(BIN_DIR)/sort/KDT.class $(BIN_DIR)/sort/MergeSort.class $(BIN_DIR)/sort/RangeHelper.class
+ javac -d $(TOMCAT_DIR)/WEB-INF/classes/ -classpath $(TOMCAT_DIR)/lib/servlet-api.jar:$(BIN_DIR):bin:json-simple-1.1.1.jar $(TOMCAT_DIR)/src/com/example/model/TrawlExpert.java
+
+$(BIN_DIR)/data/BioTree.class: src/data/BioTree.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/BioTree.java
+
+$(BIN_DIR)/data/DataStore.class: src/data/DataStore.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/DataStore.java
+
+$(BIN_DIR)/data/Date.class: src/Data/date.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/Date.java
+
+$(BIN_DIR)/data/FileProcessor.class: src/data/FileProcessor.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/FileProcessor.java
+
+$(BIN_DIR)/data/Record.class: src/data/Record.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/Record.java
+
+$(BIN_DIR)/data/TaxonNode.class: src/data/TaxonNode.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/TaxonNode.java
+
+$(BIN_DIR)/data/TaxonType.class: src/data/TaxonType.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/TaxonType.java
+
+$(BIN_DIR)/data/WormsAPI.class: src/data/WormsAPI.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/data/WormsAPI.java
+
+$(BIN_DIR)/search/BasicSearch.class: src/search/BasicSearch.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/search/BasicSearch.java
+
+$(BIN_DIR)/search/BST.class: src/search/BST.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/search/BST.java
+
+$(BIN_DIR)/search/Histogram.class: src/search/Histogram.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/search/Histogram.java
+
+$(BIN_DIR)/sort/Bound.class: src/sort/Bound.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/Bound.java
+
+$(BIN_DIR)/sort/GeneralCompare.class: src/sort/GeneralCompare.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/GeneralCompare.java
+
+$(BIN_DIR)/sort/GeneralRange.class: src/sort/GeneralRange.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/GeneralRange.java
+
+$(BIN_DIR)/sort/KDT.class: src/sort/KDT.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/KDT.java
+
+$(BIN_DIR)/sort/MergeSort.class: src/sort/MergeSort.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/MergeSort.java
+
+$(BIN_DIR)/sort/RangeHelper.class: src/sort/RangeHelper.java
+ javac -d $(BIN_DIR) -classpath bin::json-simple-1.1.1.jar src/sort/RangeHelper.java
+
+$(BIN_DIR)/../WEB-INF/classes/com/example/web/Director.class: $(BIN_DIR)/com/example/web/Director.java
+ javac -d $(TOMCAT_DIR)/WEB-INF/classes -classpath src/tomcat/lib/servlet-api.jar:$(BIN_DIR) $(BIN_DIR)/com/example/web/Director.java
\ No newline at end of file
diff --git a/makefile~ b/makefile~
new file mode 100644
index 0000000000000000000000000000000000000000..5bc815d4da2f6aca25833081d6e0572c112575eb
--- /dev/null
+++ b/makefile~
@@ -0,0 +1,2 @@
+server: /TrawlExpert.java
+ javac -classpath
diff --git a/src/TrawlExpert.java b/src/TrawlExpert.java
new file mode 100644
index 0000000000000000000000000000000000000000..1df3aab568a29d82cd075047d428a06f004f0b35
--- /dev/null
+++ b/src/TrawlExpert.java
@@ -0,0 +1,29 @@
+import org.json.simple.parser.ParseException;
+
+import data.BioTree;
+import data.DataStore;
+import data.FileProcessor;
+import data.Record;
+import search.BasicSearch;
+import sort.KDT;
+
+public class TrawlExpert {
+ public TrawlExpert() {
+ //load data
+ try {
+ BioTree.init("data/biotree/");
+ DataStore.records = new KDT<Record>("data/kdt.ser");
+ } catch (Exception e0) {
+ try {
+ BioTree.init();
+ FileProcessor.initProcessing();
+ } catch (NumberFormatException | ParseException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ BioTree.write("data/biotree/");
+ DataStore.records.writeToFile("data/kdt.ser");
+ };
+ BasicSearch.init();
+ }
+}
diff --git a/src/model/TrawlExpert.java b/src/model/TrawlExpert.java
new file mode 100644
index 0000000000000000000000000000000000000000..f6fa8c307b582346668ffd4e7f54ac5909b28020
--- /dev/null
+++ b/src/model/TrawlExpert.java
@@ -0,0 +1,35 @@
+package model;
+
+import org.json.simple.parser.ParseException;
+
+import data.BioTree;
+import data.DataStore;
+import data.FileProcessor;
+import data.Record;
+import search.BasicSearch;
+import sort.KDT;
+
+public class TrawlExpert {
+ public TrawlExpert() {
+ //load data
+ DataStore.records = new KDT<Record>("data/kdt.ser");
+ try {
+ BioTree.init("data/biotree/");
+ DataStore.records = new KDT<Record>("data/kdt.ser");
+ } catch (Exception e0) {
+ try {
+ BioTree.init();
+ FileProcessor.initProcessing();
+ } catch (NumberFormatException | ParseException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ BioTree.write("data/biotree/");
+ DataStore.records.writeToFile("data/kdt.ser");
+ };
+ }
+
+ public Iterable<Integer> listAllSpecies(){
+ return BioTree.getNonEmptyChildren(2);
+ }
+}
diff --git a/src/tomcat/webapps/Trawl/bin/com/example/model/TrawlExpert.java b/src/model/TrawlExpert2.java
old mode 100644
new mode 100755
similarity index 96%
rename from src/tomcat/webapps/Trawl/bin/com/example/model/TrawlExpert.java
rename to src/model/TrawlExpert2.java
index 1a9337aca686cafb15bb67bd3845772c00bb83c7..ab61e04b0ac93590eb01670df06d255726439717
--- a/src/tomcat/webapps/Trawl/bin/com/example/model/TrawlExpert.java
+++ b/src/model/TrawlExpert2.java
@@ -1,23 +1,23 @@
-package com.example.model;
-import java.util.*;
-public class TrawlExpert {
-
-public List getBrands(String phylum) {
- List brands = new ArrayList();
- if (phylum.equals("Arthropoda")) {
- brands.add("Some arthropoda data");
- brands.add("Some more Arthropoda data");
- }
- else {
- brands.add("This aint arthropoda");
- brands.add("Under construction");
- }
- return brands;
- }
-}
-
-// For Testing on Java's Console
-// public static void main(String[]args){
-// String color = "amber";
-// System.out.println(brand.get(0));
+package com.example.model;
+import java.util.*;
+public class TrawlExpert {
+
+public List getBrands(String phylum) {
+ List brands = new ArrayList();
+ if (phylum.equals("Arthropoda")) {
+ brands.add("Some arthropoda data");
+ brands.add("Some more Arthropoda data");
+ }
+ else {
+ brands.add("This aint arthropoda");
+ brands.add("Under construction");
+ }
+ return brands;
+ }
+}
+
+// For Testing on Java's Console
+// public static void main(String[]args){
+// String color = "amber";
+// System.out.println(brand.get(0));
// }
\ No newline at end of file
diff --git a/src/tomcat/webapps/Trawl-Site/WEB-INF/classes/com/example/model/BeerExpert.class b/src/tomcat/webapps/Trawl-Site/WEB-INF/classes/com/example/model/BeerExpert.class
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diff --git a/src/tomcat/webapps/Trawl/bin/com/example/web/Director.class b/src/tomcat/webapps/Trawl/bin/com/example/web/Director.class
deleted file mode 100644
index cec1b7f628df0a3e53cbefd58fcc6e6d29603faa..0000000000000000000000000000000000000000
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diff --git a/src/tomcat/webapps/Trawl/bin/com/example/web/Director.java b/src/tomcat/webapps/Trawl/bin/com/example/web/Director.java
deleted file mode 100644
index e9474b8af604cc4c31828dd7a093249bfe9b99a8..0000000000000000000000000000000000000000
--- a/src/tomcat/webapps/Trawl/bin/com/example/web/Director.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package com.example.web;
-
-import javax.servlet.*;
-import javax.servlet.http.*;
-import java.io.*;
-import java.util.*;
-//import com.example.model.TrawlExpert; // notice this
-import com.example.model.*; // notice this
-
-
-public class Director extends HttpServlet {
- public void doPost(HttpServletRequest request,HttpServletResponse response) throws IOException, ServletException {
- String c = request.getParameter("phylum");
-
- TrawlExpert t = new TrawlExpert();
- List result = t.getBrands(c);
-
- request.setAttribute("styles", result);
- RequestDispatcher view = request.getRequestDispatcher("result.jsp");
- view.forward(request, response);
- }
-}
\ No newline at end of file
diff --git a/src/tomcat/webapps/Trawl/result.jsp b/src/tomcat/webapps/Trawl/result.jsp
deleted file mode 100644
index b6db2621143bd3b60e23259b47e01c318ba5356e..0000000000000000000000000000000000000000
--- a/src/tomcat/webapps/Trawl/result.jsp
+++ /dev/null
@@ -1,15 +0,0 @@
-<%@ page import="java.util.*" %>
-<html>
-<body>
-<h1 align="center">Trawl Results</h1>
-<p>
-
-<%
- List styles = (List)request.getAttribute("styles");
- Iterator it = styles.iterator();
- while (it.hasNext()) {
- out.print("<br>TRY: " + it.next());
- }
-%>
-</body>
-</html>
\ No newline at end of file
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diff --git a/src/web/Director.java b/src/web/Director.java
new file mode 100755
index 0000000000000000000000000000000000000000..6225be3a4d45618d1fd4e4934f380599fcb91a00
--- /dev/null
+++ b/src/web/Director.java
@@ -0,0 +1,55 @@
+package web;
+
+import javax.servlet.*;
+import javax.servlet.http.*;
+import java.io.*;
+import java.util.*;
+//import com.example.model.TrawlExpert; // notice this
+import model.*; // notice this
+
+
+public class Director extends HttpServlet {
+ public void doPost(HttpServletRequest request,HttpServletResponse response) throws IOException, ServletException {
+ String req = getUrlDoPortion(request);
+ //if (req == "doBioLookup.do")
+ //doBioLookup(request, response);
+
+ TrawlExpert te = (TrawlExpert)request.getServletContext().getAttribute("trawl");
+ //very basic example of listing all species
+ Iterable<Integer> result = te.listAllSpecies();
+
+ request.setAttribute("species", result);
+ RequestDispatcher view = request.getRequestDispatcher("result.jsp");
+ view.forward(request, response);
+ }
+
+ private void doBioLookup(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
+ //get answers from form
+ String phylum = request.getParameter("phylum");
+ String bioClass = request.getParameter("class");
+ String order = request.getParameter("order");
+ String family = request.getParameter("family");
+ String genus = request.getParameter("genus");
+ String species = request.getParameter("species");
+
+ TrawlExpert te = (TrawlExpert)request.getServletContext().getAttribute("trawl");
+ //find all applicable things underneath the top most one, need API for this
+
+ //send lists of things to build the dropdowns
+ request.setAttribute("phylum", result);
+ request.setAttribute("bioClass", result);
+ request.setAttribute("order", result);
+ request.setAttribute("family", result);
+ request.setAttribute("genus", result);
+ request.setAttribute("species", result);
+ //send back the index.jsp page
+ RequestDispatcher view = request.getRequestDispatcher("index.jsp");
+ view.forward(request, response);
+ }
+
+ private String getUrlDoPortion(HttpServletRequest request) {
+ String url = (String) request.getRequestURL().toString();
+ String[] s = url.split("/");
+ return s[s.length - 1];
+ }
+}
\ No newline at end of file
diff --git a/src/web/StartUpContext.java b/src/web/StartUpContext.java
new file mode 100644
index 0000000000000000000000000000000000000000..5425dc353926c641baa9dda4a9fa71d971d432e8
--- /dev/null
+++ b/src/web/StartUpContext.java
@@ -0,0 +1,24 @@
+package web;
+
+import javax.servlet.ServletContextEvent;
+import javax.servlet.ServletContextListener;
+import javax.servlet.annotation.WebListener;
+
+import model.TrawlExpert;
+
+//https://www.mkyong.com/servlet/what-is-listener-servletcontextlistener-example/
+@WebListener
+public class StartUpContext implements ServletContextListener{
+ @Override
+ public void contextDestroyed(ServletContextEvent arg0) {
+ System.out.println("ServletContextListener destroyed");
+ }
+
+ //Run this before web application is started
+ @Override
+ public void contextInitialized(ServletContextEvent serverEvent) {
+ System.out.println("Started server.");
+ TrawlExpert te = new TrawlExpert();
+ serverEvent.getServletContext().setAttribute("trawl", te);
+ }
+}
\ No newline at end of file
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rename from src/tomcat/bin/tool-wrapper.bat
rename to tomcat/bin/tool-wrapper.bat
diff --git a/src/tomcat/bin/tool-wrapper.sh b/tomcat/bin/tool-wrapper.sh
similarity index 100%
rename from src/tomcat/bin/tool-wrapper.sh
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diff --git a/src/tomcat/bin/version.bat b/tomcat/bin/version.bat
similarity index 100%
rename from src/tomcat/bin/version.bat
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diff --git a/src/tomcat/bin/version.sh b/tomcat/bin/version.sh
similarity index 100%
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diff --git a/src/tomcat/conf/catalina.policy b/tomcat/conf/catalina.policy
similarity index 100%
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rename to tomcat/conf/catalina.policy
diff --git a/src/tomcat/conf/catalina.properties b/tomcat/conf/catalina.properties
similarity index 100%
rename from src/tomcat/conf/catalina.properties
rename to tomcat/conf/catalina.properties
diff --git a/src/tomcat/conf/context.xml b/tomcat/conf/context.xml
similarity index 100%
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rename to tomcat/conf/context.xml
diff --git a/src/tomcat/conf/jaspic-providers.xml b/tomcat/conf/jaspic-providers.xml
similarity index 100%
rename from src/tomcat/conf/jaspic-providers.xml
rename to tomcat/conf/jaspic-providers.xml
diff --git a/src/tomcat/conf/jaspic-providers.xsd b/tomcat/conf/jaspic-providers.xsd
similarity index 100%
rename from src/tomcat/conf/jaspic-providers.xsd
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diff --git a/src/tomcat/conf/logging.properties b/tomcat/conf/logging.properties
similarity index 100%
rename from src/tomcat/conf/logging.properties
rename to tomcat/conf/logging.properties
diff --git a/src/tomcat/conf/server.xml b/tomcat/conf/server.xml
similarity index 100%
rename from src/tomcat/conf/server.xml
rename to tomcat/conf/server.xml
diff --git a/src/tomcat/conf/tomcat-users.xml b/tomcat/conf/tomcat-users.xml
similarity index 100%
rename from src/tomcat/conf/tomcat-users.xml
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diff --git a/src/tomcat/conf/tomcat-users.xsd b/tomcat/conf/tomcat-users.xsd
similarity index 100%
rename from src/tomcat/conf/tomcat-users.xsd
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diff --git a/src/tomcat/conf/web.xml b/tomcat/conf/web.xml
similarity index 100%
rename from src/tomcat/conf/web.xml
rename to tomcat/conf/web.xml
diff --git a/src/tomcat/lib/annotations-api.jar b/tomcat/lib/annotations-api.jar
similarity index 100%
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diff --git a/src/tomcat/lib/catalina-ant.jar b/tomcat/lib/catalina-ant.jar
similarity index 100%
rename from src/tomcat/lib/catalina-ant.jar
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diff --git a/src/tomcat/lib/catalina-ha.jar b/tomcat/lib/catalina-ha.jar
similarity index 100%
rename from src/tomcat/lib/catalina-ha.jar
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diff --git a/src/tomcat/lib/catalina-storeconfig.jar b/tomcat/lib/catalina-storeconfig.jar
similarity index 100%
rename from src/tomcat/lib/catalina-storeconfig.jar
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diff --git a/src/tomcat/lib/catalina-tribes.jar b/tomcat/lib/catalina-tribes.jar
similarity index 100%
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diff --git a/src/tomcat/lib/catalina.jar b/tomcat/lib/catalina.jar
similarity index 100%
rename from src/tomcat/lib/catalina.jar
rename to tomcat/lib/catalina.jar
diff --git a/src/tomcat/lib/ecj-4.6.3.jar b/tomcat/lib/ecj-4.6.3.jar
similarity index 100%
rename from src/tomcat/lib/ecj-4.6.3.jar
rename to tomcat/lib/ecj-4.6.3.jar
diff --git a/src/tomcat/lib/el-api.jar b/tomcat/lib/el-api.jar
similarity index 100%
rename from src/tomcat/lib/el-api.jar
rename to tomcat/lib/el-api.jar
diff --git a/src/tomcat/lib/jasper-el.jar b/tomcat/lib/jasper-el.jar
similarity index 100%
rename from src/tomcat/lib/jasper-el.jar
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diff --git a/src/tomcat/lib/jasper.jar b/tomcat/lib/jasper.jar
similarity index 100%
rename from src/tomcat/lib/jasper.jar
rename to tomcat/lib/jasper.jar
diff --git a/src/tomcat/lib/jaspic-api.jar b/tomcat/lib/jaspic-api.jar
similarity index 100%
rename from src/tomcat/lib/jaspic-api.jar
rename to tomcat/lib/jaspic-api.jar
diff --git a/src/tomcat/lib/jsp-api.jar b/tomcat/lib/jsp-api.jar
similarity index 100%
rename from src/tomcat/lib/jsp-api.jar
rename to tomcat/lib/jsp-api.jar
diff --git a/src/tomcat/lib/servlet-api.jar b/tomcat/lib/servlet-api.jar
similarity index 100%
rename from src/tomcat/lib/servlet-api.jar
rename to tomcat/lib/servlet-api.jar
diff --git a/src/tomcat/lib/tomcat-api.jar b/tomcat/lib/tomcat-api.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-api.jar
rename to tomcat/lib/tomcat-api.jar
diff --git a/src/tomcat/lib/tomcat-coyote.jar b/tomcat/lib/tomcat-coyote.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-coyote.jar
rename to tomcat/lib/tomcat-coyote.jar
diff --git a/src/tomcat/lib/tomcat-dbcp.jar b/tomcat/lib/tomcat-dbcp.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-dbcp.jar
rename to tomcat/lib/tomcat-dbcp.jar
diff --git a/src/tomcat/lib/tomcat-i18n-es.jar b/tomcat/lib/tomcat-i18n-es.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-i18n-es.jar
rename to tomcat/lib/tomcat-i18n-es.jar
diff --git a/src/tomcat/lib/tomcat-i18n-fr.jar b/tomcat/lib/tomcat-i18n-fr.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-i18n-fr.jar
rename to tomcat/lib/tomcat-i18n-fr.jar
diff --git a/src/tomcat/lib/tomcat-i18n-ja.jar b/tomcat/lib/tomcat-i18n-ja.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-i18n-ja.jar
rename to tomcat/lib/tomcat-i18n-ja.jar
diff --git a/src/tomcat/lib/tomcat-jdbc.jar b/tomcat/lib/tomcat-jdbc.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-jdbc.jar
rename to tomcat/lib/tomcat-jdbc.jar
diff --git a/src/tomcat/lib/tomcat-jni.jar b/tomcat/lib/tomcat-jni.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-jni.jar
rename to tomcat/lib/tomcat-jni.jar
diff --git a/src/tomcat/lib/tomcat-util-scan.jar b/tomcat/lib/tomcat-util-scan.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-util-scan.jar
rename to tomcat/lib/tomcat-util-scan.jar
diff --git a/src/tomcat/lib/tomcat-util.jar b/tomcat/lib/tomcat-util.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-util.jar
rename to tomcat/lib/tomcat-util.jar
diff --git a/src/tomcat/lib/tomcat-websocket.jar b/tomcat/lib/tomcat-websocket.jar
similarity index 100%
rename from src/tomcat/lib/tomcat-websocket.jar
rename to tomcat/lib/tomcat-websocket.jar
diff --git a/src/tomcat/lib/websocket-api.jar b/tomcat/lib/websocket-api.jar
similarity index 100%
rename from src/tomcat/lib/websocket-api.jar
rename to tomcat/lib/websocket-api.jar
diff --git a/src/tomcat/logs/localhost_access_log.2018-03-12.txt b/tomcat/logs/localhost_access_log.2018-03-12.txt
similarity index 100%
rename from src/tomcat/logs/localhost_access_log.2018-03-12.txt
rename to tomcat/logs/localhost_access_log.2018-03-12.txt
diff --git a/src/tomcat/logs/localhost_access_log.2018-03-13.txt b/tomcat/logs/localhost_access_log.2018-03-13.txt
similarity index 100%
rename from src/tomcat/logs/localhost_access_log.2018-03-13.txt
rename to tomcat/logs/localhost_access_log.2018-03-13.txt
diff --git a/src/tomcat/logs/localhost_access_log.2018-03-21.txt b/tomcat/logs/localhost_access_log.2018-03-21.txt
similarity index 100%
rename from src/tomcat/logs/localhost_access_log.2018-03-21.txt
rename to tomcat/logs/localhost_access_log.2018-03-21.txt
diff --git a/tomcat/logs/localhost_access_log.2018-03-22.txt b/tomcat/logs/localhost_access_log.2018-03-22.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4bc48db81c0fe8375bba47c563835a72503f3e3
--- /dev/null
+++ b/tomcat/logs/localhost_access_log.2018-03-22.txt
@@ -0,0 +1,247 @@
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:41:54 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:46:22 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:53:58 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:53:59 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:55:39 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:57:50 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:57:51 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:58:07 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:58:08 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:58:10 -0400] "GET /Trawl/ HTTP/1.1" 200 3755
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:17:58:11 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:00:16 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2335
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:00:16 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:00:19 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 1757
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:02:07 -0400] "GET /Trawl/ HTTP/1.1" 304 -
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:02:07 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:02:08 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2335
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:03:58 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:03:59 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:04:08 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:15:25 -0400] "GET /Trawl/index.html HTTP/1.1" 304 -
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:15:26 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:15:27 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:15:31 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:15:31 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:16:18 -0400] "GET /Trawl/index.html HTTP/1.1" 304 -
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:16:18 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:16:19 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:17:38 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 2271
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:18:48 -0400] "GET /Trawl/index.html HTTP/1.1" 304 -
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:18:49 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:18:49 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 3145
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:19:47 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 6112
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:19:47 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:20:12 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 88
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:20:12 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:23:36 -0400] "GET /Trawl/index.html HTTP/1.1" 304 -
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:23:37 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:23:38 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 88
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:26:29 -0400] "GET / HTTP/1.1" 200 11450
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:26:35 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 88
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:30:52 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 1430
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:45 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 113
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:46 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:48 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 113
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:50 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 113
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:50 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:51 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 113
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:51 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:52 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 113
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:52 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:52 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 113
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:32:53 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:35:22 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 113
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:35:25 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 113
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:35:25 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:41:15 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 500 1430
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:46:42 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 404 1097
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:46:43 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:46:49 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 404 1097
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:18 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 404 1097
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:18 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:20 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 404 1097
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:22 -0400] "GET /Trawl/index.html HTTP/1.1" 404 1093
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:23 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:25 -0400] "GET /Trawl/index.html HTTP/1.1" 404 1093
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:25 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:26 -0400] "GET /Trawl/index.html HTTP/1.1" 404 1093
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:47:26 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:55:46 -0400] "GET /Trawl/index.html HTTP/1.1" 200 3755
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:55:46 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:55:48 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 2513
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:55:52 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 2513
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:55:52 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:57:08 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 2513
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:57:08 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:57:14 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 2513
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:59:01 -0400] "GET /Trawl/index.html HTTP/1.1" 404 1093
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:59:01 -0400] "GET / HTTP/1.1" 200 11450
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:59:02 -0400] "GET /Trawl/ HTTP/1.1" 200 3755
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:59:05 -0400] "GET /Trawl/index.html HTTP/1.1" 404 1093
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:59:08 -0400] "GET /Trawl/index.jsp HTTP/1.1" 200 3755
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:18:59:22 -0400] "GET /Trawl/ HTTP/1.1" 200 3755
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:02:07 -0400] "GET /Trawl/ HTTP/1.1" 200 3756
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:02:08 -0400] "GET / HTTP/1.1" 200 11450
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:04:44 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 2513
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:04:59 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:05:00 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 2513
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:05:05 -0400] "POST /Trawl/callServlet.do HTTP/1.1" 200 2513
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:05:05 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:06:46 -0400] "GET /Trawl/? HTTP/1.1" 200 3548
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:06:46 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:10:18 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:10:19 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:10:22 -0400] "POST /Trawl/doBioLookup.do HTTP/1.1" 404 1097
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:10:59 -0400] "GET /Trawl/ HTTP/1.1" 200 3551
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:11:00 -0400] "GET /favicon.ico HTTP/1.1" 200 21630
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:11:02 -0400] "POST /Trawl/doBioLookup.do HTTP/1.1" 200 2517
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:17:06 -0400] "POST /Trawl/doBioLookup.do HTTP/1.1" 200 2555
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:22:53 -0400] "POST /Trawl/doBioLookup.do HTTP/1.1" 500 1722
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+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:35:43 -0400] "GET /Trawl/style.css HTTP/1.1" 200 821
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:35:43 -0400] "GET /Trawl/script.js HTTP/1.1" 200 425
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:35:45 -0400] "GET /Trawl/? HTTP/1.1" 200 3551
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:35:45 -0400] "GET /Trawl/style.css HTTP/1.1" 200 821
+0:0:0:0:0:0:0:1 - - [22/Mar/2018:19:35:45 -0400] "GET /Trawl/script.js HTTP/1.1" 200 425
diff --git a/src/tomcat/temp/safeToDelete.tmp b/tomcat/temp/safeToDelete.tmp
similarity index 100%
rename from src/tomcat/temp/safeToDelete.tmp
rename to tomcat/temp/safeToDelete.tmp
diff --git a/src/tomcat/webapps/ROOT/RELEASE-NOTES.txt b/tomcat/webapps/ROOT/RELEASE-NOTES.txt
similarity index 100%
rename from src/tomcat/webapps/ROOT/RELEASE-NOTES.txt
rename to tomcat/webapps/ROOT/RELEASE-NOTES.txt
diff --git a/src/tomcat/webapps/ROOT/WEB-INF/web.xml b/tomcat/webapps/ROOT/WEB-INF/web.xml
similarity index 100%
rename from src/tomcat/webapps/ROOT/WEB-INF/web.xml
rename to tomcat/webapps/ROOT/WEB-INF/web.xml
diff --git a/src/tomcat/webapps/ROOT/asf-logo-wide.svg b/tomcat/webapps/ROOT/asf-logo-wide.svg
similarity index 100%
rename from src/tomcat/webapps/ROOT/asf-logo-wide.svg
rename to tomcat/webapps/ROOT/asf-logo-wide.svg
diff --git a/src/tomcat/webapps/ROOT/bg-button.png b/tomcat/webapps/ROOT/bg-button.png
similarity index 100%
rename from src/tomcat/webapps/ROOT/bg-button.png
rename to tomcat/webapps/ROOT/bg-button.png
diff --git a/src/tomcat/webapps/ROOT/bg-middle.png b/tomcat/webapps/ROOT/bg-middle.png
similarity index 100%
rename from src/tomcat/webapps/ROOT/bg-middle.png
rename to tomcat/webapps/ROOT/bg-middle.png
diff --git a/src/tomcat/webapps/ROOT/bg-nav.png b/tomcat/webapps/ROOT/bg-nav.png
similarity index 100%
rename from src/tomcat/webapps/ROOT/bg-nav.png
rename to tomcat/webapps/ROOT/bg-nav.png
diff --git a/src/tomcat/webapps/ROOT/bg-upper.png b/tomcat/webapps/ROOT/bg-upper.png
similarity index 100%
rename from src/tomcat/webapps/ROOT/bg-upper.png
rename to tomcat/webapps/ROOT/bg-upper.png
diff --git a/src/tomcat/webapps/ROOT/favicon.ico b/tomcat/webapps/ROOT/favicon.ico
similarity index 100%
rename from src/tomcat/webapps/ROOT/favicon.ico
rename to tomcat/webapps/ROOT/favicon.ico
diff --git a/src/tomcat/webapps/ROOT/index.jsp b/tomcat/webapps/ROOT/index.jsp
similarity index 100%
rename from src/tomcat/webapps/ROOT/index.jsp
rename to tomcat/webapps/ROOT/index.jsp
diff --git a/src/tomcat/webapps/ROOT/tomcat-power.gif b/tomcat/webapps/ROOT/tomcat-power.gif
similarity index 100%
rename from src/tomcat/webapps/ROOT/tomcat-power.gif
rename to tomcat/webapps/ROOT/tomcat-power.gif
diff --git a/src/tomcat/webapps/ROOT/tomcat.css b/tomcat/webapps/ROOT/tomcat.css
similarity index 100%
rename from src/tomcat/webapps/ROOT/tomcat.css
rename to tomcat/webapps/ROOT/tomcat.css
diff --git a/src/tomcat/webapps/ROOT/tomcat.gif b/tomcat/webapps/ROOT/tomcat.gif
similarity index 100%
rename from src/tomcat/webapps/ROOT/tomcat.gif
rename to tomcat/webapps/ROOT/tomcat.gif
diff --git a/src/tomcat/webapps/ROOT/tomcat.png b/tomcat/webapps/ROOT/tomcat.png
similarity index 100%
rename from src/tomcat/webapps/ROOT/tomcat.png
rename to tomcat/webapps/ROOT/tomcat.png
diff --git a/src/tomcat/webapps/ROOT/tomcat.svg b/tomcat/webapps/ROOT/tomcat.svg
similarity index 100%
rename from src/tomcat/webapps/ROOT/tomcat.svg
rename to tomcat/webapps/ROOT/tomcat.svg
diff --git a/src/tomcat/webapps/Trawl-Site/bin/com/example/model/BeerExpert.java b/tomcat/webapps/Trawl-Site/bin/com/example/model/BeerExpert.java
similarity index 100%
rename from src/tomcat/webapps/Trawl-Site/bin/com/example/model/BeerExpert.java
rename to tomcat/webapps/Trawl-Site/bin/com/example/model/BeerExpert.java
diff --git a/src/tomcat/webapps/Trawl-Site/bin/com/example/web/BeerSelect.java b/tomcat/webapps/Trawl-Site/bin/com/example/web/BeerSelect.java
similarity index 100%
rename from src/tomcat/webapps/Trawl-Site/bin/com/example/web/BeerSelect.java
rename to tomcat/webapps/Trawl-Site/bin/com/example/web/BeerSelect.java
diff --git a/src/tomcat/webapps/Trawl-Site/index.html b/tomcat/webapps/Trawl-Site/index.html
similarity index 100%
rename from src/tomcat/webapps/Trawl-Site/index.html
rename to tomcat/webapps/Trawl-Site/index.html
diff --git a/src/tomcat/webapps/Trawl-Site/result.jsp b/tomcat/webapps/Trawl-Site/result.jsp
similarity index 100%
rename from src/tomcat/webapps/Trawl-Site/result.jsp
rename to tomcat/webapps/Trawl-Site/result.jsp
diff --git a/tomcat/webapps/Trawl/WEB-INF/lib/json-simple-1.1.1.jar b/tomcat/webapps/Trawl/WEB-INF/lib/json-simple-1.1.1.jar
new file mode 100644
index 0000000000000000000000000000000000000000..66347a6c86b7d6442358ca7643e4dc484fb01866
Binary files /dev/null and b/tomcat/webapps/Trawl/WEB-INF/lib/json-simple-1.1.1.jar differ
diff --git a/tomcat/webapps/Trawl/WEB-INF/web.xml b/tomcat/webapps/Trawl/WEB-INF/web.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e647d8ddd9521866f2300eef991dbf82d5b6b4eb
--- /dev/null
+++ b/tomcat/webapps/Trawl/WEB-INF/web.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<web-app xmlns="http://java.sun.com/xml/ns/j2ee"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
+ version="2.4">
+
+ <servlet>
+ <servlet-name>Trawl</servlet-name>
+ <servlet-class>web.Director</servlet-class>
+ </servlet>
+
+ <servlet-mapping>
+ <servlet-name>Trawl</servlet-name>
+ <url-pattern>/doBioLookup.do</url-pattern>
+ </servlet-mapping>
+</web-app>
\ No newline at end of file
diff --git a/src/tomcat/webapps/Trawl/index.html b/tomcat/webapps/Trawl/index.jsp
similarity index 85%
rename from src/tomcat/webapps/Trawl/index.html
rename to tomcat/webapps/Trawl/index.jsp
index c3cac77bb3bc87e0edf2a777cc9a70a7cf1612ef..f61cde953864f929452d5d1f75d01763dd93746e 100644
--- a/src/tomcat/webapps/Trawl/index.html
+++ b/tomcat/webapps/Trawl/index.jsp
@@ -1,3 +1,4 @@
+<%@ page import="java.util.*" %>
<!--
Double Handle Slider Modified from: http://jqueryui.com/slider/#range
@@ -41,7 +42,7 @@ Double Handle Slider Modified from: http://jqueryui.com/slider/#range
<section id="options">
<section id="nameDropdownIn">
- <form method="POST" action="callServlet.do"> <!--.do extension is not necessary. This field is the servlet's url in web.xml-->
+ <form method="POST" action="doBioLookup.do"> <!--.do extension is not necessary. This field is the servlet's url in web.xml-->
Phylum:
<select name="phylum" size="1">
<option>Arthropoda</option>
@@ -49,39 +50,29 @@ Double Handle Slider Modified from: http://jqueryui.com/slider/#range
<option>Mollusca</option>
</select>
<input type="SUBMIT">
- </form>
- <form>
Class:
- <select name="phylum" size="1">
+ <select name="class" size="1">
</select>
<!--<input type="SUBMIT">-->
- </form>
- <form>
Order:
- <select name="phylum" size="1">
+ <select name="order" size="1">
</select>
<!--<input type="SUBMIT">-->
- </form>
- <form>
Family:
- <select name="phylum" size="1">
+ <select name="family" size="1">
</select>
<!--<input type="SUBMIT">-->
- </form>
- <form>
Genus:
- <select name="phylum" size="1">
+ <select name="genus" size="1">
</select>
<!--<input type="SUBMIT">-->
- </form>
- <form>
- Scientific Name:
- <select name="phylum" size="1">
+ Species:
+ <select name="species" size="1">
</select>
<!--<input type="SUBMIT">-->
@@ -104,7 +95,7 @@ Double Handle Slider Modified from: http://jqueryui.com/slider/#range
<input type="radio" name="gender" value="female"> Histogram
<input type="submit">
</form>
- <form>
+ <form method="POST" action=">
<input type="submit" value="Individual Records"> <!--To records.html-->
</form>
</section>
diff --git a/src/tomcat/webapps/Trawl/jquery-3.3.1.slim.min.js b/tomcat/webapps/Trawl/jquery-3.3.1.slim.min.js
similarity index 100%
rename from src/tomcat/webapps/Trawl/jquery-3.3.1.slim.min.js
rename to tomcat/webapps/Trawl/jquery-3.3.1.slim.min.js
diff --git a/src/tomcat/webapps/Trawl/records.html b/tomcat/webapps/Trawl/records.html
similarity index 100%
rename from src/tomcat/webapps/Trawl/records.html
rename to tomcat/webapps/Trawl/records.html
diff --git a/tomcat/webapps/Trawl/result.jsp b/tomcat/webapps/Trawl/result.jsp
new file mode 100644
index 0000000000000000000000000000000000000000..9ebd56779f74fb31e1f6871ce11c8470d54770fd
--- /dev/null
+++ b/tomcat/webapps/Trawl/result.jsp
@@ -0,0 +1,14 @@
+<%@ page import="java.util.*" %>
+<html>
+<body>
+<h1 align="center">Trawl Results</h1>
+<p>
+
+<%
+ Iterable<Integer> species = (Iterable<Integer>)request.getAttribute("species");
+ for (Integer s: species)
+ out.print("SpeciesID: " + s + "<br>");
+ out.print((String) request.getAttribute("url"));
+%>
+</body>
+</html>
\ No newline at end of file
diff --git a/src/tomcat/webapps/Trawl/script.js b/tomcat/webapps/Trawl/script.js
similarity index 100%
rename from src/tomcat/webapps/Trawl/script.js
rename to tomcat/webapps/Trawl/script.js
diff --git a/src/tomcat/webapps/Trawl/style-records.css b/tomcat/webapps/Trawl/style-records.css
similarity index 100%
rename from src/tomcat/webapps/Trawl/style-records.css
rename to tomcat/webapps/Trawl/style-records.css
diff --git a/src/tomcat/webapps/Trawl/style.css b/tomcat/webapps/Trawl/style.css
similarity index 100%
rename from src/tomcat/webapps/Trawl/style.css
rename to tomcat/webapps/Trawl/style.css
diff --git a/src/tomcat/webapps/docs/BUILDING.txt b/tomcat/webapps/docs/BUILDING.txt
similarity index 100%
rename from src/tomcat/webapps/docs/BUILDING.txt
rename to tomcat/webapps/docs/BUILDING.txt
diff --git a/src/tomcat/webapps/docs/RELEASE-NOTES.txt b/tomcat/webapps/docs/RELEASE-NOTES.txt
similarity index 100%
rename from src/tomcat/webapps/docs/RELEASE-NOTES.txt
rename to tomcat/webapps/docs/RELEASE-NOTES.txt
diff --git a/src/tomcat/webapps/docs/RUNNING.txt b/tomcat/webapps/docs/RUNNING.txt
similarity index 100%
rename from src/tomcat/webapps/docs/RUNNING.txt
rename to tomcat/webapps/docs/RUNNING.txt
diff --git a/src/tomcat/webapps/docs/WEB-INF/web.xml b/tomcat/webapps/docs/WEB-INF/web.xml
similarity index 100%
rename from src/tomcat/webapps/docs/WEB-INF/web.xml
rename to tomcat/webapps/docs/WEB-INF/web.xml
diff --git a/src/tomcat/webapps/docs/aio.html b/tomcat/webapps/docs/aio.html
similarity index 100%
rename from src/tomcat/webapps/docs/aio.html
rename to tomcat/webapps/docs/aio.html
diff --git a/src/tomcat/webapps/docs/api/index.html b/tomcat/webapps/docs/api/index.html
similarity index 100%
rename from src/tomcat/webapps/docs/api/index.html
rename to tomcat/webapps/docs/api/index.html
diff --git a/src/tomcat/webapps/docs/appdev/build.xml.txt b/tomcat/webapps/docs/appdev/build.xml.txt
similarity index 100%
rename from src/tomcat/webapps/docs/appdev/build.xml.txt
rename to tomcat/webapps/docs/appdev/build.xml.txt
diff --git a/src/tomcat/webapps/docs/appdev/deployment.html b/tomcat/webapps/docs/appdev/deployment.html
similarity index 100%
rename from src/tomcat/webapps/docs/appdev/deployment.html
rename to tomcat/webapps/docs/appdev/deployment.html
diff --git a/src/tomcat/webapps/docs/appdev/index.html b/tomcat/webapps/docs/appdev/index.html
similarity index 100%
rename from src/tomcat/webapps/docs/appdev/index.html
rename to tomcat/webapps/docs/appdev/index.html
diff --git a/src/tomcat/webapps/docs/appdev/installation.html b/tomcat/webapps/docs/appdev/installation.html
similarity index 100%
rename from src/tomcat/webapps/docs/appdev/installation.html
rename to tomcat/webapps/docs/appdev/installation.html
diff --git a/src/tomcat/webapps/docs/appdev/introduction.html b/tomcat/webapps/docs/appdev/introduction.html
similarity index 100%
rename from src/tomcat/webapps/docs/appdev/introduction.html
rename to tomcat/webapps/docs/appdev/introduction.html
diff --git a/src/tomcat/webapps/docs/appdev/processes.html b/tomcat/webapps/docs/appdev/processes.html
similarity index 100%
rename from src/tomcat/webapps/docs/appdev/processes.html
rename to tomcat/webapps/docs/appdev/processes.html
diff --git a/src/tomcat/webapps/docs/appdev/sample/build.xml b/tomcat/webapps/docs/appdev/sample/build.xml
similarity index 100%
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rename to tomcat/webapps/docs/appdev/sample/build.xml
diff --git a/src/tomcat/webapps/docs/appdev/sample/docs/README.txt b/tomcat/webapps/docs/appdev/sample/docs/README.txt
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similarity index 100%
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rename to tomcat/webapps/docs/appdev/sample/sample.war
diff --git a/src/tomcat/webapps/docs/appdev/sample/src/mypackage/Hello.java b/tomcat/webapps/docs/appdev/sample/src/mypackage/Hello.java
similarity index 100%
rename from src/tomcat/webapps/docs/appdev/sample/src/mypackage/Hello.java
rename to tomcat/webapps/docs/appdev/sample/src/mypackage/Hello.java
diff --git a/src/tomcat/webapps/docs/appdev/sample/web/WEB-INF/web.xml b/tomcat/webapps/docs/appdev/sample/web/WEB-INF/web.xml
similarity index 100%
rename from src/tomcat/webapps/docs/appdev/sample/web/WEB-INF/web.xml
rename to tomcat/webapps/docs/appdev/sample/web/WEB-INF/web.xml
diff --git a/src/tomcat/webapps/docs/appdev/sample/web/hello.jsp b/tomcat/webapps/docs/appdev/sample/web/hello.jsp
similarity index 100%
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rename to tomcat/webapps/docs/appdev/sample/web/hello.jsp
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diff --git a/src/tomcat/webapps/examples/WEB-INF/classes/jsp2/examples/simpletag/TileSimpleTag.java b/tomcat/webapps/examples/WEB-INF/classes/jsp2/examples/simpletag/TileSimpleTag.java
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rename from src/tomcat/webapps/manager/WEB-INF/jsp/401.jsp
rename to tomcat/webapps/manager/WEB-INF/jsp/401.jsp
diff --git a/src/tomcat/webapps/manager/WEB-INF/jsp/403.jsp b/tomcat/webapps/manager/WEB-INF/jsp/403.jsp
similarity index 100%
rename from src/tomcat/webapps/manager/WEB-INF/jsp/403.jsp
rename to tomcat/webapps/manager/WEB-INF/jsp/403.jsp
diff --git a/src/tomcat/webapps/manager/WEB-INF/jsp/404.jsp b/tomcat/webapps/manager/WEB-INF/jsp/404.jsp
similarity index 100%
rename from src/tomcat/webapps/manager/WEB-INF/jsp/404.jsp
rename to tomcat/webapps/manager/WEB-INF/jsp/404.jsp
diff --git a/src/tomcat/webapps/manager/WEB-INF/jsp/connectorCerts.jsp b/tomcat/webapps/manager/WEB-INF/jsp/connectorCerts.jsp
similarity index 100%
rename from src/tomcat/webapps/manager/WEB-INF/jsp/connectorCerts.jsp
rename to tomcat/webapps/manager/WEB-INF/jsp/connectorCerts.jsp
diff --git a/src/tomcat/webapps/manager/WEB-INF/jsp/connectorCiphers.jsp b/tomcat/webapps/manager/WEB-INF/jsp/connectorCiphers.jsp
similarity index 100%
rename from src/tomcat/webapps/manager/WEB-INF/jsp/connectorCiphers.jsp
rename to tomcat/webapps/manager/WEB-INF/jsp/connectorCiphers.jsp
diff --git a/src/tomcat/webapps/manager/WEB-INF/jsp/connectorTrustedCerts.jsp b/tomcat/webapps/manager/WEB-INF/jsp/connectorTrustedCerts.jsp
similarity index 100%
rename from src/tomcat/webapps/manager/WEB-INF/jsp/connectorTrustedCerts.jsp
rename to tomcat/webapps/manager/WEB-INF/jsp/connectorTrustedCerts.jsp
diff --git a/src/tomcat/webapps/manager/WEB-INF/jsp/sessionDetail.jsp b/tomcat/webapps/manager/WEB-INF/jsp/sessionDetail.jsp
similarity index 100%
rename from src/tomcat/webapps/manager/WEB-INF/jsp/sessionDetail.jsp
rename to tomcat/webapps/manager/WEB-INF/jsp/sessionDetail.jsp
diff --git a/src/tomcat/webapps/manager/WEB-INF/jsp/sessionsList.jsp b/tomcat/webapps/manager/WEB-INF/jsp/sessionsList.jsp
similarity index 100%
rename from src/tomcat/webapps/manager/WEB-INF/jsp/sessionsList.jsp
rename to tomcat/webapps/manager/WEB-INF/jsp/sessionsList.jsp
diff --git a/src/tomcat/webapps/manager/WEB-INF/web.xml b/tomcat/webapps/manager/WEB-INF/web.xml
similarity index 100%
rename from src/tomcat/webapps/manager/WEB-INF/web.xml
rename to tomcat/webapps/manager/WEB-INF/web.xml
diff --git a/src/tomcat/webapps/manager/images/asf-logo.svg b/tomcat/webapps/manager/images/asf-logo.svg
similarity index 100%
rename from src/tomcat/webapps/manager/images/asf-logo.svg
rename to tomcat/webapps/manager/images/asf-logo.svg
diff --git a/src/tomcat/webapps/manager/images/tomcat.gif b/tomcat/webapps/manager/images/tomcat.gif
similarity index 100%
rename from src/tomcat/webapps/manager/images/tomcat.gif
rename to tomcat/webapps/manager/images/tomcat.gif
diff --git a/src/tomcat/webapps/manager/index.jsp b/tomcat/webapps/manager/index.jsp
similarity index 100%
rename from src/tomcat/webapps/manager/index.jsp
rename to tomcat/webapps/manager/index.jsp
diff --git a/src/tomcat/webapps/manager/status.xsd b/tomcat/webapps/manager/status.xsd
similarity index 100%
rename from src/tomcat/webapps/manager/status.xsd
rename to tomcat/webapps/manager/status.xsd
diff --git a/src/tomcat/webapps/manager/xform.xsl b/tomcat/webapps/manager/xform.xsl
similarity index 100%
rename from src/tomcat/webapps/manager/xform.xsl
rename to tomcat/webapps/manager/xform.xsl
diff --git a/src/tomcat/windows-script.py b/tomcat/windows-script.py
similarity index 91%
rename from src/tomcat/windows-script.py
rename to tomcat/windows-script.py
index 3cfa0a9cab06219d72c0dfcfdc128b3f63203592..f19d8f69ccd091aedd03a2abda6303925acd5592 100644
--- a/src/tomcat/windows-script.py
+++ b/tomcat/windows-script.py
@@ -1,6 +1,6 @@
import subprocess
-pathToTomcat = "C:\\Users\\liang\\Documents\\Git\\Trawl\\tomcat" # REPLACE ME - CUSTOM
+pathToTomcat = "C:\\Users\\liang\\Documents\\Git\\Trawl\\src\\tomcat" # REPLACE ME - CUSTOM
pathToSrc = "\\webapps\\Trawl\\bin\\com\\example\\"
pathToFin = "\\webapps\\Trawl\\WEB-INF\\classes\\com\\example\\"
diff --git a/src/tomcat/work/Catalina/localhost/ROOT/org/apache/jsp/index_jsp.java b/tomcat/work/Catalina/localhost/ROOT/org/apache/jsp/index_jsp.java
similarity index 100%
rename from src/tomcat/work/Catalina/localhost/ROOT/org/apache/jsp/index_jsp.java
rename to tomcat/work/Catalina/localhost/ROOT/org/apache/jsp/index_jsp.java
diff --git a/src/tomcat/work/Catalina/localhost/Trawl-Site/org/apache/jsp/result_jsp.java b/tomcat/work/Catalina/localhost/Trawl-Site/org/apache/jsp/result_jsp.java
similarity index 100%
rename from src/tomcat/work/Catalina/localhost/Trawl-Site/org/apache/jsp/result_jsp.java
rename to tomcat/work/Catalina/localhost/Trawl-Site/org/apache/jsp/result_jsp.java
diff --git a/tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/index_jsp.java b/tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/index_jsp.java
new file mode 100644
index 0000000000000000000000000000000000000000..aab6c18a470b964a5035124d685af1c0cd268d1b
--- /dev/null
+++ b/tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/index_jsp.java
@@ -0,0 +1,248 @@
+/*
+ * Generated by the Jasper component of Apache Tomcat
+ * Version: Apache Tomcat/9.0.6
+ * Generated at: 2018-03-22 23:33:57 UTC
+ * Note: The last modified time of this file was set to
+ * the last modified time of the source file after
+ * generation to assist with modification tracking.
+ */
+package org.apache.jsp;
+
+import javax.servlet.*;
+import javax.servlet.http.*;
+import javax.servlet.jsp.*;
+import java.util.*;
+
+public final class index_jsp extends org.apache.jasper.runtime.HttpJspBase
+ implements org.apache.jasper.runtime.JspSourceDependent,
+ org.apache.jasper.runtime.JspSourceImports {
+
+ private static final javax.servlet.jsp.JspFactory _jspxFactory =
+ javax.servlet.jsp.JspFactory.getDefaultFactory();
+
+ private static java.util.Map<java.lang.String,java.lang.Long> _jspx_dependants;
+
+ private static final java.util.Set<java.lang.String> _jspx_imports_packages;
+
+ private static final java.util.Set<java.lang.String> _jspx_imports_classes;
+
+ static {
+ _jspx_imports_packages = new java.util.HashSet<>();
+ _jspx_imports_packages.add("javax.servlet");
+ _jspx_imports_packages.add("java.util");
+ _jspx_imports_packages.add("javax.servlet.http");
+ _jspx_imports_packages.add("javax.servlet.jsp");
+ _jspx_imports_classes = null;
+ }
+
+ private volatile javax.el.ExpressionFactory _el_expressionfactory;
+ private volatile org.apache.tomcat.InstanceManager _jsp_instancemanager;
+
+ public java.util.Map<java.lang.String,java.lang.Long> getDependants() {
+ return _jspx_dependants;
+ }
+
+ public java.util.Set<java.lang.String> getPackageImports() {
+ return _jspx_imports_packages;
+ }
+
+ public java.util.Set<java.lang.String> getClassImports() {
+ return _jspx_imports_classes;
+ }
+
+ public javax.el.ExpressionFactory _jsp_getExpressionFactory() {
+ if (_el_expressionfactory == null) {
+ synchronized (this) {
+ if (_el_expressionfactory == null) {
+ _el_expressionfactory = _jspxFactory.getJspApplicationContext(getServletConfig().getServletContext()).getExpressionFactory();
+ }
+ }
+ }
+ return _el_expressionfactory;
+ }
+
+ public org.apache.tomcat.InstanceManager _jsp_getInstanceManager() {
+ if (_jsp_instancemanager == null) {
+ synchronized (this) {
+ if (_jsp_instancemanager == null) {
+ _jsp_instancemanager = org.apache.jasper.runtime.InstanceManagerFactory.getInstanceManager(getServletConfig());
+ }
+ }
+ }
+ return _jsp_instancemanager;
+ }
+
+ public void _jspInit() {
+ }
+
+ public void _jspDestroy() {
+ }
+
+ public void _jspService(final javax.servlet.http.HttpServletRequest request, final javax.servlet.http.HttpServletResponse response)
+ throws java.io.IOException, javax.servlet.ServletException {
+
+ if (!javax.servlet.DispatcherType.ERROR.equals(request.getDispatcherType())) {
+ final java.lang.String _jspx_method = request.getMethod();
+ if ("OPTIONS".equals(_jspx_method)) {
+ response.setHeader("Allow","GET, HEAD, POST, OPTIONS");
+ return;
+ }
+ if (!"GET".equals(_jspx_method) && !"POST".equals(_jspx_method) && !"HEAD".equals(_jspx_method)) {
+ response.setHeader("Allow","GET, HEAD, POST, OPTIONS");
+ response.sendError(HttpServletResponse.SC_METHOD_NOT_ALLOWED, "JSPs only permit GET, POST or HEAD. Jasper also permits OPTIONS");
+ return;
+ }
+ }
+
+ final javax.servlet.jsp.PageContext pageContext;
+ javax.servlet.http.HttpSession session = null;
+ final javax.servlet.ServletContext application;
+ final javax.servlet.ServletConfig config;
+ javax.servlet.jsp.JspWriter out = null;
+ final java.lang.Object page = this;
+ javax.servlet.jsp.JspWriter _jspx_out = null;
+ javax.servlet.jsp.PageContext _jspx_page_context = null;
+
+
+ try {
+ response.setContentType("text/html");
+ pageContext = _jspxFactory.getPageContext(this, request, response,
+ null, true, 8192, true);
+ _jspx_page_context = pageContext;
+ application = pageContext.getServletContext();
+ config = pageContext.getServletConfig();
+ session = pageContext.getSession();
+ out = pageContext.getOut();
+ _jspx_out = out;
+
+ out.write("\n");
+ out.write("<!--\n");
+ out.write("\n");
+ out.write("Double Handle Slider Modified from: http://jqueryui.com/slider/#range\n");
+ out.write("\n");
+ out.write("-->\n");
+ out.write("\n");
+ out.write("<!DOCTYPE html>\n");
+ out.write("<html lang=\"en\">\n");
+ out.write("<head>\n");
+ out.write(" <meta charset=\"UTF-8\">\n");
+ out.write(" <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">\n");
+ out.write(" <meta name=\"keywords\" content=\"insert, some, keywords\"> <!--TODO-->\n");
+ out.write(" <meta name=\"description\" content=\"insert a description\"> <!--TODO-->\n");
+ out.write(" <title>TrawlTool</title>\n");
+ out.write(" <link rel=\"stylesheet\" type=\"text/css\" href=\"style.css\">\n");
+ out.write("\n");
+ out.write("\n");
+ out.write(" <!--JQuery-->\n");
+ out.write(" <script src=\"https://code.jquery.com/jquery-1.12.4.js\"></script>\n");
+ out.write(" <script src=\"https://code.jquery.com/ui/1.12.1/jquery-ui.js\"></script>\n");
+ out.write(" <link rel=\"stylesheet\" href=\"//code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css\">\n");
+ out.write("\n");
+ out.write(" <!-- MUST load JQuery Library before loading this-->\n");
+ out.write(" <script src=\"script.js\"></script>\n");
+ out.write(" <!--Fonts-->\n");
+ out.write(" <!--Open Sans Rg-400/Semi-600/Bd-700-->\n");
+ out.write(" <link href=\"https://fonts.googleapis.com/css?family=Open+Sans:300,400,600,700\" rel=\"stylesheet\">\n");
+ out.write("\n");
+ out.write(" <!--Plugins-->\n");
+ out.write("</head>\n");
+ out.write("\n");
+ out.write("<body>\n");
+ out.write(" <header>\n");
+ out.write(" <a href=\"index.html\" >TrawlTool</a>\n");
+ out.write(" </header>\n");
+ out.write("\n");
+ out.write(" <span id=\"menu-bar\">\n");
+ out.write(" <a href=\"index.html\">Non functional Menu Item 1</a> |\n");
+ out.write(" <a href=\"index.html\" target=\"_blank\">Item 2</a>\n");
+ out.write(" </span>\n");
+ out.write("\n");
+ out.write(" <section id=\"options\">\n");
+ out.write(" <section id=\"nameDropdownIn\">\n");
+ out.write(" <form method=\"POST\" action=\"doBioLookup.do\"> <!--.do extension is not necessary. This field is the servlet's url in web.xml-->\n");
+ out.write(" Phylum:\n");
+ out.write(" <select name=\"phylum\" size=\"1\">\n");
+ out.write(" <option>Arthropoda</option>\n");
+ out.write(" <option>Chordata</option>\n");
+ out.write(" <option>Mollusca</option>\n");
+ out.write(" </select>\n");
+ out.write(" <input type=\"SUBMIT\">\n");
+ out.write("\n");
+ out.write(" Class:\n");
+ out.write(" <select name=\"class\" size=\"1\">\n");
+ out.write(" </select>\n");
+ out.write(" <!--<input type=\"SUBMIT\">-->\n");
+ out.write("\n");
+ out.write(" Order:\n");
+ out.write(" <select name=\"order\" size=\"1\">\n");
+ out.write(" </select>\n");
+ out.write(" <!--<input type=\"SUBMIT\">-->\n");
+ out.write("\n");
+ out.write(" Family:\n");
+ out.write(" <select name=\"family\" size=\"1\">\n");
+ out.write(" </select>\n");
+ out.write(" <!--<input type=\"SUBMIT\">-->\n");
+ out.write("\n");
+ out.write(" Genus:\n");
+ out.write(" <select name=\"genus\" size=\"1\">\n");
+ out.write(" </select>\n");
+ out.write(" <!--<input type=\"SUBMIT\">-->\n");
+ out.write("\n");
+ out.write(" Species:\n");
+ out.write(" <select name=\"species\" size=\"1\">\n");
+ out.write("\n");
+ out.write(" </select>\n");
+ out.write(" <!--<input type=\"SUBMIT\">-->\n");
+ out.write(" </form>\n");
+ out.write(" </section>\n");
+ out.write("\n");
+ out.write(" <section id=\"yearIn\">\n");
+ out.write(" Year Range:\n");
+ out.write(" <span id=\"fromtoYear\">InnerHtml</span>\n");
+ out.write(" <form>\n");
+ out.write(" <!--<input type=\"number\" id=\"fromYear\" class=\"yearN\" value=\"2000\" min=\"1960\" max=\"2016\" oninput=\"brightN()\">-->\n");
+ out.write(" <div id=\"slider-range\"></div>\n");
+ out.write(" </form>\n");
+ out.write(" </section>\n");
+ out.write("\n");
+ out.write(" <section id=\"outputIn\">\n");
+ out.write(" <form>\n");
+ out.write(" <!--TODO: Set Default button entered-->\n");
+ out.write(" <input type=\"radio\" name=\"gender\" value=\"male\"> Map\n");
+ out.write(" <input type=\"radio\" name=\"gender\" value=\"female\"> Histogram\n");
+ out.write(" <input type=\"submit\">\n");
+ out.write(" </form>\n");
+ out.write(" <form>\n");
+ out.write(" <input type=\"submit\" value=\"Individual Records\"> <!--To records.html-->\n");
+ out.write(" </form>\n");
+ out.write(" </section>\n");
+ out.write(" </section>\n");
+ out.write("\n");
+ out.write(" <section id=\"outputWrapper\">\n");
+ out.write(" <section id=\"outputDetails\">Stuff like population count, entries found, etc. go here</section>\n");
+ out.write(" <section id=\"outputBox\">Map, Histogram Box</section>\n");
+ out.write(" </section>\n");
+ out.write(" <footer>\n");
+ out.write(" Footer\n");
+ out.write(" </footer>\n");
+ out.write("</body>\n");
+ out.write("</html>\n");
+ } catch (java.lang.Throwable t) {
+ if (!(t instanceof javax.servlet.jsp.SkipPageException)){
+ out = _jspx_out;
+ if (out != null && out.getBufferSize() != 0)
+ try {
+ if (response.isCommitted()) {
+ out.flush();
+ } else {
+ out.clearBuffer();
+ }
+ } catch (java.io.IOException e) {}
+ if (_jspx_page_context != null) _jspx_page_context.handlePageException(t);
+ else throw new ServletException(t);
+ }
+ } finally {
+ _jspxFactory.releasePageContext(_jspx_page_context);
+ }
+ }
+}
diff --git a/src/tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/result_jsp.java b/tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/result_jsp.java
similarity index 90%
rename from src/tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/result_jsp.java
rename to tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/result_jsp.java
index da1966168ecab8c04c3c080771c67ade39182c21..6a8a4c5aaf32297ae2ab7b85b11147c8f9406383 100644
--- a/src/tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/result_jsp.java
+++ b/tomcat/work/Catalina/localhost/Trawl/org/apache/jsp/result_jsp.java
@@ -1,7 +1,7 @@
/*
* Generated by the Jasper component of Apache Tomcat
* Version: Apache Tomcat/9.0.6
- * Generated at: 2018-03-13 21:29:18 UTC
+ * Generated at: 2018-03-22 23:11:01 UTC
* Note: The last modified time of this file was set to
* the last modified time of the source file after
* generation to assist with modification tracking.
@@ -115,21 +115,20 @@ public final class result_jsp extends org.apache.jasper.runtime.HttpJspBase
out = pageContext.getOut();
_jspx_out = out;
- out.write("\r\n");
- out.write("<html>\r\n");
- out.write("<body>\r\n");
- out.write("<h1 align=\"center\">Trawl Results</h1>\r\n");
- out.write("<p>\r\n");
- out.write("\r\n");
-
- List styles = (List)request.getAttribute("styles");
- Iterator it = styles.iterator();
- while (it.hasNext()) {
- out.print("<br>TRY: " + it.next());
- }
-
- out.write("\r\n");
- out.write("</body>\r\n");
+ out.write("\n");
+ out.write("<html>\n");
+ out.write("<body>\n");
+ out.write("<h1 align=\"center\">Trawl Results</h1>\n");
+ out.write("<p>\n");
+ out.write("\n");
+
+ Iterable<Integer> species = (Iterable<Integer>)request.getAttribute("species");
+ for (Integer s: species)
+ out.print("SpeciesID: " + s + "<br>");
+ out.print((String) request.getAttribute("url"));
+
+ out.write("\n");
+ out.write("</body>\n");
out.write("</html>");
} catch (java.lang.Throwable t) {
if (!(t instanceof javax.servlet.jsp.SkipPageException)){
diff --git a/src/tomcat/work/Catalina/localhost/examples/org/apache/jsp/jsp/dates/date_jsp.java b/tomcat/work/Catalina/localhost/examples/org/apache/jsp/jsp/dates/date_jsp.java
similarity index 100%
rename from src/tomcat/work/Catalina/localhost/examples/org/apache/jsp/jsp/dates/date_jsp.java
rename to tomcat/work/Catalina/localhost/examples/org/apache/jsp/jsp/dates/date_jsp.java
diff --git a/src/tomcat/work/Catalina/localhost/examples/org/apache/jsp/jsp/jsp2/el/basic_002darithmetic_jsp.java b/tomcat/work/Catalina/localhost/examples/org/apache/jsp/jsp/jsp2/el/basic_002darithmetic_jsp.java
similarity index 100%
rename from src/tomcat/work/Catalina/localhost/examples/org/apache/jsp/jsp/jsp2/el/basic_002darithmetic_jsp.java
rename to tomcat/work/Catalina/localhost/examples/org/apache/jsp/jsp/jsp2/el/basic_002darithmetic_jsp.java
diff --git a/src/tomcat/work/Catalina/localhost/host-manager/org/apache/jsp/WEB_002dINF/jsp/_401_jsp.java b/tomcat/work/Catalina/localhost/host-manager/org/apache/jsp/WEB_002dINF/jsp/_401_jsp.java
similarity index 100%
rename from src/tomcat/work/Catalina/localhost/host-manager/org/apache/jsp/WEB_002dINF/jsp/_401_jsp.java
rename to tomcat/work/Catalina/localhost/host-manager/org/apache/jsp/WEB_002dINF/jsp/_401_jsp.java
diff --git a/src/tomcat/work/Catalina/localhost/manager/org/apache/jsp/WEB_002dINF/jsp/_401_jsp.java b/tomcat/work/Catalina/localhost/manager/org/apache/jsp/WEB_002dINF/jsp/_401_jsp.java
similarity index 100%
rename from src/tomcat/work/Catalina/localhost/manager/org/apache/jsp/WEB_002dINF/jsp/_401_jsp.java
rename to tomcat/work/Catalina/localhost/manager/org/apache/jsp/WEB_002dINF/jsp/_401_jsp.java
diff --git a/src/tomcat/webapps/Trawl/WEB-INF/web.xml b/web.xml
similarity index 84%
rename from src/tomcat/webapps/Trawl/WEB-INF/web.xml
rename to web.xml
index 3c0e13219f2a069b4cee7c7bd9d22bd501ac1fb7..4787168bfd934462099c56ad14916b7b8533fefe 100644
--- a/src/tomcat/webapps/Trawl/WEB-INF/web.xml
+++ b/web.xml
@@ -6,9 +6,7 @@
<servlet>
<servlet-name>Trawl</servlet-name>
- <servlet-class>
- com.example.web.Director
- </servlet-class>
+ <servlet-class>web.Director</servlet-class>
</servlet>
<servlet-mapping>