From ad10269e3a6a75276a13e61021821b084d37f852 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sat, 28 Sep 2024 20:30:49 +0000
Subject: [PATCH 01/20] Bump rollup from 2.79.1 to 2.79.2 in /frontend

Bumps [rollup](https://github.com/rollup/rollup) from 2.79.1 to 2.79.2.
- [Release notes](https://github.com/rollup/rollup/releases)
- [Changelog](https://github.com/rollup/rollup/blob/master/CHANGELOG.md)
- [Commits](https://github.com/rollup/rollup/compare/v2.79.1...v2.79.2)

---
updated-dependencies:
- dependency-name: rollup
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 frontend/package-lock.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index edfcafce41..7b4b823ea3 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -16902,9 +16902,9 @@
       }
     },
     "node_modules/rollup": {
-      "version": "2.79.1",
-      "resolved": "https://registry.npmjs.org/rollup/-/rollup-2.79.1.tgz",
-      "integrity": "sha512-uKxbd0IhMZOhjAiD5oAFp7BqvkA4Dv47qpOCtaNvng4HBwdbWtdOh8f5nZNuk2rp51PMGk3bzfWu5oayNEuYnw==",
+      "version": "2.79.2",
+      "resolved": "https://registry.npmjs.org/rollup/-/rollup-2.79.2.tgz",
+      "integrity": "sha512-fS6iqSPZDs3dr/y7Od6y5nha8dW1YnbgtsyotCVvoFGKbERG++CVRFv1meyGDE1SNItQA8BrnCw7ScdAhRJ3XQ==",
       "bin": {
         "rollup": "dist/bin/rollup"
       },
@@ -32043,9 +32043,9 @@
       }
     },
     "rollup": {
-      "version": "2.79.1",
-      "resolved": "https://registry.npmjs.org/rollup/-/rollup-2.79.1.tgz",
-      "integrity": "sha512-uKxbd0IhMZOhjAiD5oAFp7BqvkA4Dv47qpOCtaNvng4HBwdbWtdOh8f5nZNuk2rp51PMGk3bzfWu5oayNEuYnw==",
+      "version": "2.79.2",
+      "resolved": "https://registry.npmjs.org/rollup/-/rollup-2.79.2.tgz",
+      "integrity": "sha512-fS6iqSPZDs3dr/y7Od6y5nha8dW1YnbgtsyotCVvoFGKbERG++CVRFv1meyGDE1SNItQA8BrnCw7ScdAhRJ3XQ==",
       "requires": {
         "fsevents": "~2.3.2"
       }

From 56e22db2db084b66a57321851ba751084940863d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 25 Nov 2024 18:53:09 +0000
Subject: [PATCH 02/20] Bump cross-spawn from 7.0.3 to 7.0.6 in /frontend

Bumps [cross-spawn](https://github.com/moxystudio/node-cross-spawn) from 7.0.3 to 7.0.6.
- [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md)
- [Commits](https://github.com/moxystudio/node-cross-spawn/compare/v7.0.3...v7.0.6)

---
updated-dependencies:
- dependency-name: cross-spawn
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 frontend/package-lock.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 4a01c9476f..840fa891c5 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -7318,9 +7318,9 @@
       }
     },
     "node_modules/cross-spawn": {
-      "version": "7.0.3",
-      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz",
-      "integrity": "sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==",
+      "version": "7.0.6",
+      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz",
+      "integrity": "sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==",
       "dependencies": {
         "path-key": "^3.1.0",
         "shebang-command": "^2.0.0",
@@ -26470,9 +26470,9 @@
       }
     },
     "cross-spawn": {
-      "version": "7.0.3",
-      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz",
-      "integrity": "sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==",
+      "version": "7.0.6",
+      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz",
+      "integrity": "sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==",
       "requires": {
         "path-key": "^3.1.0",
         "shebang-command": "^2.0.0",

From 34a93e6a364550cac5c9cf89c2ee0736e1a9b468 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 15 Dec 2024 01:41:41 +0000
Subject: [PATCH 03/20] Bump nanoid from 3.3.7 to 3.3.8 in /frontend

Bumps [nanoid](https://github.com/ai/nanoid) from 3.3.7 to 3.3.8.
- [Release notes](https://github.com/ai/nanoid/releases)
- [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md)
- [Commits](https://github.com/ai/nanoid/compare/3.3.7...3.3.8)

---
updated-dependencies:
- dependency-name: nanoid
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 frontend/package-lock.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 4a01c9476f..aee7b71a6a 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -14133,9 +14133,9 @@
       }
     },
     "node_modules/nanoid": {
-      "version": "3.3.7",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.7.tgz",
-      "integrity": "sha512-eSRppjcPIatRIMC1U6UngP8XFcz8MQWGQdt1MTBQ7NaAmvXDfvNxbvWV3x2y6CdEUciCSsDHDQZbhYaB8QEo2g==",
+      "version": "3.3.8",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.8.tgz",
+      "integrity": "sha512-WNLf5Sd8oZxOm+TzppcYk8gVOgP+l58xNy58D0nbUnOxOWRWvlcCV4kUF7ltmI6PsrLl/BgKEyS4mqsGChFN0w==",
       "funding": [
         {
           "type": "github",
@@ -31355,9 +31355,9 @@
       }
     },
     "nanoid": {
-      "version": "3.3.7",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.7.tgz",
-      "integrity": "sha512-eSRppjcPIatRIMC1U6UngP8XFcz8MQWGQdt1MTBQ7NaAmvXDfvNxbvWV3x2y6CdEUciCSsDHDQZbhYaB8QEo2g=="
+      "version": "3.3.8",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.8.tgz",
+      "integrity": "sha512-WNLf5Sd8oZxOm+TzppcYk8gVOgP+l58xNy58D0nbUnOxOWRWvlcCV4kUF7ltmI6PsrLl/BgKEyS4mqsGChFN0w=="
     },
     "natural-compare": {
       "version": "1.4.0",

From 0ca27e841c99b849a4c5b096eb7ada41d3a1d6b3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 5 Dec 2024 23:17:36 +0000
Subject: [PATCH 04/20] Bump path-to-regexp and express in /frontend

Bumps [path-to-regexp](https://github.com/pillarjs/path-to-regexp) and [express](https://github.com/expressjs/express). These dependencies needed to be updated together.

Updates `path-to-regexp` from 0.1.7 to 0.1.12
- [Release notes](https://github.com/pillarjs/path-to-regexp/releases)
- [Changelog](https://github.com/pillarjs/path-to-regexp/blob/master/History.md)
- [Commits](https://github.com/pillarjs/path-to-regexp/compare/v0.1.7...v0.1.12)

Updates `express` from 4.19.2 to 4.21.2
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/4.21.2/History.md)
- [Commits](https://github.com/expressjs/express/compare/4.19.2...4.21.2)

---
updated-dependencies:
- dependency-name: path-to-regexp
  dependency-type: indirect
- dependency-name: express
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 frontend/package-lock.json | 196 ++++++++++++++++++++-----------------
 1 file changed, 108 insertions(+), 88 deletions(-)

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 4a01c9476f..2ddee2f4e9 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -6483,9 +6483,9 @@
       "integrity": "sha512-XpNj6GDQzdfW+r2Wnn7xiSAd7TM3jzkxGXBGTtWKuSXv1xUV+azxAm8jdWZN06QTQk+2N2XB9jRDkvbmQmcRtg=="
     },
     "node_modules/body-parser": {
-      "version": "1.20.2",
-      "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.2.tgz",
-      "integrity": "sha512-ml9pReCu3M61kGlqoTm2umSXTlRTuGTx0bfYj+uIUKKYycG5NtSbeetV3faSU6R7ajOPw0g/J1PvK4qNy7s5bA==",
+      "version": "1.20.3",
+      "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.3.tgz",
+      "integrity": "sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g==",
       "dependencies": {
         "bytes": "3.1.2",
         "content-type": "~1.0.5",
@@ -6495,7 +6495,7 @@
         "http-errors": "2.0.0",
         "iconv-lite": "0.4.24",
         "on-finished": "2.4.1",
-        "qs": "6.11.0",
+        "qs": "6.13.0",
         "raw-body": "2.5.2",
         "type-is": "~1.6.18",
         "unpipe": "1.0.0"
@@ -7131,9 +7131,9 @@
       "integrity": "sha512-Kvp459HrV2FEJ1CAsi1Ku+MY3kasH19TFykTz2xWmMeq6bk2NU3XXvfJ+Q61m0xktWwt+1HSYf3JZsTms3aRJg=="
     },
     "node_modules/cookie": {
-      "version": "0.6.0",
-      "resolved": "https://registry.npmjs.org/cookie/-/cookie-0.6.0.tgz",
-      "integrity": "sha512-U71cyTamuh1CRNCfpGY6to28lxvNwPG4Guz/EVjgf3Jmzv0vlDp1atT9eS5dDjMYHucpHbWns6Lwf3BKz6svdw==",
+      "version": "0.7.1",
+      "resolved": "https://registry.npmjs.org/cookie/-/cookie-0.7.1.tgz",
+      "integrity": "sha512-6DnInpx7SJ2AK3+CTUE/ZM0vWTUboZCegxhC2xiIydHR9jNuTAASBrfEpHhiGOZw/nX51bHt6YQl8jsGo4y/0w==",
       "engines": {
         "node": ">= 0.6"
       }
@@ -8303,9 +8303,9 @@
       }
     },
     "node_modules/encodeurl": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-1.0.2.tgz",
-      "integrity": "sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w==",
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-2.0.0.tgz",
+      "integrity": "sha512-Q0n9HRi4m6JuGIV1eFlmvJB7ZEVxu93IrMyiMsGC0lrMJMWzRgx6WGquyfQgZVb31vhGgXnfmPNNXmxnOkRBrg==",
       "engines": {
         "node": ">= 0.8"
       }
@@ -9330,36 +9330,36 @@
       }
     },
     "node_modules/express": {
-      "version": "4.19.2",
-      "resolved": "https://registry.npmjs.org/express/-/express-4.19.2.tgz",
-      "integrity": "sha512-5T6nhjsT+EOMzuck8JjBHARTHfMht0POzlA60WV2pMD3gyXw2LZnZ+ueGdNxG+0calOJcWKbpFcuzLZ91YWq9Q==",
+      "version": "4.21.2",
+      "resolved": "https://registry.npmjs.org/express/-/express-4.21.2.tgz",
+      "integrity": "sha512-28HqgMZAmih1Czt9ny7qr6ek2qddF4FclbMzwhCREB6OFfH+rXAnuNCwo1/wFvrtbgsQDb4kSbX9de9lFbrXnA==",
       "dependencies": {
         "accepts": "~1.3.8",
         "array-flatten": "1.1.1",
-        "body-parser": "1.20.2",
+        "body-parser": "1.20.3",
         "content-disposition": "0.5.4",
         "content-type": "~1.0.4",
-        "cookie": "0.6.0",
+        "cookie": "0.7.1",
         "cookie-signature": "1.0.6",
         "debug": "2.6.9",
         "depd": "2.0.0",
-        "encodeurl": "~1.0.2",
+        "encodeurl": "~2.0.0",
         "escape-html": "~1.0.3",
         "etag": "~1.8.1",
-        "finalhandler": "1.2.0",
+        "finalhandler": "1.3.1",
         "fresh": "0.5.2",
         "http-errors": "2.0.0",
-        "merge-descriptors": "1.0.1",
+        "merge-descriptors": "1.0.3",
         "methods": "~1.1.2",
         "on-finished": "2.4.1",
         "parseurl": "~1.3.3",
-        "path-to-regexp": "0.1.7",
+        "path-to-regexp": "0.1.12",
         "proxy-addr": "~2.0.7",
-        "qs": "6.11.0",
+        "qs": "6.13.0",
         "range-parser": "~1.2.1",
         "safe-buffer": "5.2.1",
-        "send": "0.18.0",
-        "serve-static": "1.15.0",
+        "send": "0.19.0",
+        "serve-static": "1.16.2",
         "setprototypeof": "1.2.0",
         "statuses": "2.0.1",
         "type-is": "~1.6.18",
@@ -9368,6 +9368,10 @@
       },
       "engines": {
         "node": ">= 0.10.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/express"
       }
     },
     "node_modules/express/node_modules/debug": {
@@ -9542,12 +9546,12 @@
       }
     },
     "node_modules/finalhandler": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/finalhandler/-/finalhandler-1.2.0.tgz",
-      "integrity": "sha512-5uXcUVftlQMFnWC9qu/svkWv3GTd2PfUhK/3PLkYNAe7FbqJMt3515HaxE6eRL74GdsriiwujiawdaB1BpEISg==",
+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/finalhandler/-/finalhandler-1.3.1.tgz",
+      "integrity": "sha512-6BN9trH7bp3qvnrRyzsBz+g3lZxTNZTbVO2EV1CS0WIcDbawYVdYvGflME/9QP0h0pYlCDBCTjYa9nZzMDpyxQ==",
       "dependencies": {
         "debug": "2.6.9",
-        "encodeurl": "~1.0.2",
+        "encodeurl": "~2.0.0",
         "escape-html": "~1.0.3",
         "on-finished": "2.4.1",
         "parseurl": "~1.3.3",
@@ -13844,9 +13848,12 @@
       "integrity": "sha512-rkpe71W0N0c0Xz6QD0eJETuWAJGnJ9afsl1srmwPrI+yBCkge5EycXXbYRyvL29zZVUWQCY7InPRCv3GDXuZNw=="
     },
     "node_modules/merge-descriptors": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/merge-descriptors/-/merge-descriptors-1.0.1.tgz",
-      "integrity": "sha512-cCi6g3/Zr1iqQi6ySbseM1Xvooa98N0w31jzUYrXPX2xqObmFGHJ0tQ5u74H3mVh7wLouTseZyYIq39g8cNp1w=="
+      "version": "1.0.3",
+      "resolved": "https://registry.npmjs.org/merge-descriptors/-/merge-descriptors-1.0.3.tgz",
+      "integrity": "sha512-gaNvAS7TZ897/rVaZ0nMtAyxNyi/pdbjbAwUpFQpN70GqnVfOiXpeUUMKRBmzXaSQ8DdTX4/0ms62r2K+hE6mQ==",
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
     },
     "node_modules/merge-stream": {
       "version": "2.0.0",
@@ -14647,9 +14654,9 @@
       }
     },
     "node_modules/path-to-regexp": {
-      "version": "0.1.7",
-      "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.7.tgz",
-      "integrity": "sha512-5DFkuoqlv1uYQKxy8omFBeJPQcdoE07Kv2sferDCrAq1ohOU+MSDswDIbnx3YAM60qIOnYa53wBhXW0EbMonrQ=="
+      "version": "0.1.12",
+      "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.12.tgz",
+      "integrity": "sha512-RA1GjUVMnvYFxuqovrEqZoxxW5NUZqbwKtYz/Tt7nXerk0LbLblQmrsgdeOxV5SFHf0UDggjS/bSeOZwt1pmEQ=="
     },
     "node_modules/path-type": {
       "version": "4.0.0",
@@ -16365,11 +16372,11 @@
       }
     },
     "node_modules/qs": {
-      "version": "6.11.0",
-      "resolved": "https://registry.npmjs.org/qs/-/qs-6.11.0.tgz",
-      "integrity": "sha512-MvjoMCJwEarSbUYk5O+nmoSzSutSsTwF85zcHPQ9OrlFoZOYIjaqBAJIqIXjptyD5vThxGq52Xu/MaJzRkIk4Q==",
+      "version": "6.13.0",
+      "resolved": "https://registry.npmjs.org/qs/-/qs-6.13.0.tgz",
+      "integrity": "sha512-+38qI9SOr8tfZ4QmJNplMUxqjbe7LKvvZgWdExBOmd+egZTtjLB67Gu0HRX3u/XOq7UU2Nx6nsjvS16Z9uwfpg==",
       "dependencies": {
-        "side-channel": "^1.0.4"
+        "side-channel": "^1.0.6"
       },
       "engines": {
         "node": ">=0.6"
@@ -18259,9 +18266,9 @@
       "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A=="
     },
     "node_modules/send": {
-      "version": "0.18.0",
-      "resolved": "https://registry.npmjs.org/send/-/send-0.18.0.tgz",
-      "integrity": "sha512-qqWzuOjSFOuqPjFe4NOsMLafToQQwBSOEpS+FwEt3A2V3vKubTquT3vmLTQpFgMXp8AlFWFuP1qKaJZOtPpVXg==",
+      "version": "0.19.0",
+      "resolved": "https://registry.npmjs.org/send/-/send-0.19.0.tgz",
+      "integrity": "sha512-dW41u5VfLXu8SJh5bwRmyYUbAoSB3c9uQh6L8h/KtsFREPWpbX1lrljJo186Jc4nmci/sGUZ9a0a0J2zgfq2hw==",
       "dependencies": {
         "debug": "2.6.9",
         "depd": "2.0.0",
@@ -18294,6 +18301,14 @@
       "resolved": "https://registry.npmjs.org/ms/-/ms-2.0.0.tgz",
       "integrity": "sha512-Tpp60P6IUJDTuOq/5Z8cdskzJujfwqfOTkrwIwj7IRISpnkJnT6SyJ4PCPnGMoFjC9ddhal5KVIYtAt97ix05A=="
     },
+    "node_modules/send/node_modules/encodeurl": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-1.0.2.tgz",
+      "integrity": "sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w==",
+      "engines": {
+        "node": ">= 0.8"
+      }
+    },
     "node_modules/send/node_modules/ms": {
       "version": "2.1.3",
       "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz",
@@ -18378,14 +18393,14 @@
       }
     },
     "node_modules/serve-static": {
-      "version": "1.15.0",
-      "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.15.0.tgz",
-      "integrity": "sha512-XGuRDNjXUijsUL0vl6nSD7cwURuzEgglbOaFuZM9g3kwDXOWVTck0jLzjPzGD+TazWbboZYu52/9/XPdUgne9g==",
+      "version": "1.16.2",
+      "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.16.2.tgz",
+      "integrity": "sha512-VqpjJZKadQB/PEbEwvFdO43Ax5dFBZ2UECszz8bQ7pi7wt//PWe1P6MN7eCnjsatYtBT6EuiClbjSWP2WrIoTw==",
       "dependencies": {
-        "encodeurl": "~1.0.2",
+        "encodeurl": "~2.0.0",
         "escape-html": "~1.0.3",
         "parseurl": "~1.3.3",
-        "send": "0.18.0"
+        "send": "0.19.0"
       },
       "engines": {
         "node": ">= 0.8.0"
@@ -25861,9 +25876,9 @@
       "integrity": "sha512-XpNj6GDQzdfW+r2Wnn7xiSAd7TM3jzkxGXBGTtWKuSXv1xUV+azxAm8jdWZN06QTQk+2N2XB9jRDkvbmQmcRtg=="
     },
     "body-parser": {
-      "version": "1.20.2",
-      "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.2.tgz",
-      "integrity": "sha512-ml9pReCu3M61kGlqoTm2umSXTlRTuGTx0bfYj+uIUKKYycG5NtSbeetV3faSU6R7ajOPw0g/J1PvK4qNy7s5bA==",
+      "version": "1.20.3",
+      "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.3.tgz",
+      "integrity": "sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g==",
       "requires": {
         "bytes": "3.1.2",
         "content-type": "~1.0.5",
@@ -25873,7 +25888,7 @@
         "http-errors": "2.0.0",
         "iconv-lite": "0.4.24",
         "on-finished": "2.4.1",
-        "qs": "6.11.0",
+        "qs": "6.13.0",
         "raw-body": "2.5.2",
         "type-is": "~1.6.18",
         "unpipe": "1.0.0"
@@ -26344,9 +26359,9 @@
       "integrity": "sha512-Kvp459HrV2FEJ1CAsi1Ku+MY3kasH19TFykTz2xWmMeq6bk2NU3XXvfJ+Q61m0xktWwt+1HSYf3JZsTms3aRJg=="
     },
     "cookie": {
-      "version": "0.6.0",
-      "resolved": "https://registry.npmjs.org/cookie/-/cookie-0.6.0.tgz",
-      "integrity": "sha512-U71cyTamuh1CRNCfpGY6to28lxvNwPG4Guz/EVjgf3Jmzv0vlDp1atT9eS5dDjMYHucpHbWns6Lwf3BKz6svdw=="
+      "version": "0.7.1",
+      "resolved": "https://registry.npmjs.org/cookie/-/cookie-0.7.1.tgz",
+      "integrity": "sha512-6DnInpx7SJ2AK3+CTUE/ZM0vWTUboZCegxhC2xiIydHR9jNuTAASBrfEpHhiGOZw/nX51bHt6YQl8jsGo4y/0w=="
     },
     "cookie-signature": {
       "version": "1.0.6",
@@ -27157,9 +27172,9 @@
       "integrity": "sha512-/kyM18EfinwXZbno9FyUGeFh87KC8HRQBQGildHZbEuRyWFOmv1U10o9BBp8XVZDVNNuQKyIGIu5ZYAAXJ0V2Q=="
     },
     "encodeurl": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-1.0.2.tgz",
-      "integrity": "sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w=="
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-2.0.0.tgz",
+      "integrity": "sha512-Q0n9HRi4m6JuGIV1eFlmvJB7ZEVxu93IrMyiMsGC0lrMJMWzRgx6WGquyfQgZVb31vhGgXnfmPNNXmxnOkRBrg=="
     },
     "enhanced-resolve": {
       "version": "5.17.1",
@@ -27908,36 +27923,36 @@
       }
     },
     "express": {
-      "version": "4.19.2",
-      "resolved": "https://registry.npmjs.org/express/-/express-4.19.2.tgz",
-      "integrity": "sha512-5T6nhjsT+EOMzuck8JjBHARTHfMht0POzlA60WV2pMD3gyXw2LZnZ+ueGdNxG+0calOJcWKbpFcuzLZ91YWq9Q==",
+      "version": "4.21.2",
+      "resolved": "https://registry.npmjs.org/express/-/express-4.21.2.tgz",
+      "integrity": "sha512-28HqgMZAmih1Czt9ny7qr6ek2qddF4FclbMzwhCREB6OFfH+rXAnuNCwo1/wFvrtbgsQDb4kSbX9de9lFbrXnA==",
       "requires": {
         "accepts": "~1.3.8",
         "array-flatten": "1.1.1",
-        "body-parser": "1.20.2",
+        "body-parser": "1.20.3",
         "content-disposition": "0.5.4",
         "content-type": "~1.0.4",
-        "cookie": "0.6.0",
+        "cookie": "0.7.1",
         "cookie-signature": "1.0.6",
         "debug": "2.6.9",
         "depd": "2.0.0",
-        "encodeurl": "~1.0.2",
+        "encodeurl": "~2.0.0",
         "escape-html": "~1.0.3",
         "etag": "~1.8.1",
-        "finalhandler": "1.2.0",
+        "finalhandler": "1.3.1",
         "fresh": "0.5.2",
         "http-errors": "2.0.0",
-        "merge-descriptors": "1.0.1",
+        "merge-descriptors": "1.0.3",
         "methods": "~1.1.2",
         "on-finished": "2.4.1",
         "parseurl": "~1.3.3",
-        "path-to-regexp": "0.1.7",
+        "path-to-regexp": "0.1.12",
         "proxy-addr": "~2.0.7",
-        "qs": "6.11.0",
+        "qs": "6.13.0",
         "range-parser": "~1.2.1",
         "safe-buffer": "5.2.1",
-        "send": "0.18.0",
-        "serve-static": "1.15.0",
+        "send": "0.19.0",
+        "serve-static": "1.16.2",
         "setprototypeof": "1.2.0",
         "statuses": "2.0.1",
         "type-is": "~1.6.18",
@@ -28089,12 +28104,12 @@
       }
     },
     "finalhandler": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/finalhandler/-/finalhandler-1.2.0.tgz",
-      "integrity": "sha512-5uXcUVftlQMFnWC9qu/svkWv3GTd2PfUhK/3PLkYNAe7FbqJMt3515HaxE6eRL74GdsriiwujiawdaB1BpEISg==",
+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/finalhandler/-/finalhandler-1.3.1.tgz",
+      "integrity": "sha512-6BN9trH7bp3qvnrRyzsBz+g3lZxTNZTbVO2EV1CS0WIcDbawYVdYvGflME/9QP0h0pYlCDBCTjYa9nZzMDpyxQ==",
       "requires": {
         "debug": "2.6.9",
-        "encodeurl": "~1.0.2",
+        "encodeurl": "~2.0.0",
         "escape-html": "~1.0.3",
         "on-finished": "2.4.1",
         "parseurl": "~1.3.3",
@@ -31157,9 +31172,9 @@
       "integrity": "sha512-rkpe71W0N0c0Xz6QD0eJETuWAJGnJ9afsl1srmwPrI+yBCkge5EycXXbYRyvL29zZVUWQCY7InPRCv3GDXuZNw=="
     },
     "merge-descriptors": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/merge-descriptors/-/merge-descriptors-1.0.1.tgz",
-      "integrity": "sha512-cCi6g3/Zr1iqQi6ySbseM1Xvooa98N0w31jzUYrXPX2xqObmFGHJ0tQ5u74H3mVh7wLouTseZyYIq39g8cNp1w=="
+      "version": "1.0.3",
+      "resolved": "https://registry.npmjs.org/merge-descriptors/-/merge-descriptors-1.0.3.tgz",
+      "integrity": "sha512-gaNvAS7TZ897/rVaZ0nMtAyxNyi/pdbjbAwUpFQpN70GqnVfOiXpeUUMKRBmzXaSQ8DdTX4/0ms62r2K+hE6mQ=="
     },
     "merge-stream": {
       "version": "2.0.0",
@@ -31715,9 +31730,9 @@
       }
     },
     "path-to-regexp": {
-      "version": "0.1.7",
-      "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.7.tgz",
-      "integrity": "sha512-5DFkuoqlv1uYQKxy8omFBeJPQcdoE07Kv2sferDCrAq1ohOU+MSDswDIbnx3YAM60qIOnYa53wBhXW0EbMonrQ=="
+      "version": "0.1.12",
+      "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.12.tgz",
+      "integrity": "sha512-RA1GjUVMnvYFxuqovrEqZoxxW5NUZqbwKtYz/Tt7nXerk0LbLblQmrsgdeOxV5SFHf0UDggjS/bSeOZwt1pmEQ=="
     },
     "path-type": {
       "version": "4.0.0",
@@ -32737,11 +32752,11 @@
       "integrity": "sha512-kV/CThkXo6xyFEZUugw/+pIOywXcDbFYgSct5cT3gqlbkBE1SJdwy6UQoZvodiWF/ckQLZyDE/Bu1M6gVu5lVw=="
     },
     "qs": {
-      "version": "6.11.0",
-      "resolved": "https://registry.npmjs.org/qs/-/qs-6.11.0.tgz",
-      "integrity": "sha512-MvjoMCJwEarSbUYk5O+nmoSzSutSsTwF85zcHPQ9OrlFoZOYIjaqBAJIqIXjptyD5vThxGq52Xu/MaJzRkIk4Q==",
+      "version": "6.13.0",
+      "resolved": "https://registry.npmjs.org/qs/-/qs-6.13.0.tgz",
+      "integrity": "sha512-+38qI9SOr8tfZ4QmJNplMUxqjbe7LKvvZgWdExBOmd+egZTtjLB67Gu0HRX3u/XOq7UU2Nx6nsjvS16Z9uwfpg==",
       "requires": {
-        "side-channel": "^1.0.4"
+        "side-channel": "^1.0.6"
       }
     },
     "querystringify": {
@@ -34014,9 +34029,9 @@
       }
     },
     "send": {
-      "version": "0.18.0",
-      "resolved": "https://registry.npmjs.org/send/-/send-0.18.0.tgz",
-      "integrity": "sha512-qqWzuOjSFOuqPjFe4NOsMLafToQQwBSOEpS+FwEt3A2V3vKubTquT3vmLTQpFgMXp8AlFWFuP1qKaJZOtPpVXg==",
+      "version": "0.19.0",
+      "resolved": "https://registry.npmjs.org/send/-/send-0.19.0.tgz",
+      "integrity": "sha512-dW41u5VfLXu8SJh5bwRmyYUbAoSB3c9uQh6L8h/KtsFREPWpbX1lrljJo186Jc4nmci/sGUZ9a0a0J2zgfq2hw==",
       "requires": {
         "debug": "2.6.9",
         "depd": "2.0.0",
@@ -34048,6 +34063,11 @@
             }
           }
         },
+        "encodeurl": {
+          "version": "1.0.2",
+          "resolved": "https://registry.npmjs.org/encodeurl/-/encodeurl-1.0.2.tgz",
+          "integrity": "sha512-TPJXq8JqFaVYm2CWmPvnP2Iyo4ZSM7/QKcSmuMLDObfpH5fi7RUGmd/rTDf+rut/saiDiQEeVTNgAmJEdAOx0w=="
+        },
         "ms": {
           "version": "2.1.3",
           "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz",
@@ -34124,14 +34144,14 @@
       }
     },
     "serve-static": {
-      "version": "1.15.0",
-      "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.15.0.tgz",
-      "integrity": "sha512-XGuRDNjXUijsUL0vl6nSD7cwURuzEgglbOaFuZM9g3kwDXOWVTck0jLzjPzGD+TazWbboZYu52/9/XPdUgne9g==",
+      "version": "1.16.2",
+      "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.16.2.tgz",
+      "integrity": "sha512-VqpjJZKadQB/PEbEwvFdO43Ax5dFBZ2UECszz8bQ7pi7wt//PWe1P6MN7eCnjsatYtBT6EuiClbjSWP2WrIoTw==",
       "requires": {
-        "encodeurl": "~1.0.2",
+        "encodeurl": "~2.0.0",
         "escape-html": "~1.0.3",
         "parseurl": "~1.3.3",
-        "send": "0.18.0"
+        "send": "0.19.0"
       }
     },
     "set-function-length": {

From 1ebfd9f8710a6e7943c31a61572dc9a67ca51f4c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 13 Sep 2024 16:32:27 +0000
Subject: [PATCH 05/20] Bump body-parser and express in /frontend

Bumps [body-parser](https://github.com/expressjs/body-parser) and [express](https://github.com/expressjs/express). These dependencies needed to be updated together.

Updates `body-parser` from 1.20.2 to 1.20.3
- [Release notes](https://github.com/expressjs/body-parser/releases)
- [Changelog](https://github.com/expressjs/body-parser/blob/master/HISTORY.md)
- [Commits](https://github.com/expressjs/body-parser/compare/1.20.2...1.20.3)

Updates `express` from 4.19.2 to 4.21.0
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/4.21.0/History.md)
- [Commits](https://github.com/expressjs/express/compare/4.19.2...4.21.0)

---
updated-dependencies:
- dependency-name: body-parser
  dependency-type: indirect
- dependency-name: express
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 frontend/package-lock.json | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 2ddee2f4e9..66d23579f5 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -6483,6 +6483,9 @@
       "integrity": "sha512-XpNj6GDQzdfW+r2Wnn7xiSAd7TM3jzkxGXBGTtWKuSXv1xUV+azxAm8jdWZN06QTQk+2N2XB9jRDkvbmQmcRtg=="
     },
     "node_modules/body-parser": {
+      "version": "1.20.3",
+      "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.3.tgz",
+      "integrity": "sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g==",
       "version": "1.20.3",
       "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.3.tgz",
       "integrity": "sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g==",

From 3ef7ee2eba510ec382942eeb78c7df70c6c7f3b0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 13 Sep 2024 16:32:27 +0000
Subject: [PATCH 06/20] Bump send and express in /frontend

Bumps [send](https://github.com/pillarjs/send) and [express](https://github.com/expressjs/express). These dependencies needed to be updated together.

Updates `send` from 0.18.0 to 0.19.0
- [Release notes](https://github.com/pillarjs/send/releases)
- [Changelog](https://github.com/pillarjs/send/blob/master/HISTORY.md)
- [Commits](https://github.com/pillarjs/send/compare/0.18.0...0.19.0)

Updates `express` from 4.19.2 to 4.21.0
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/4.21.0/History.md)
- [Commits](https://github.com/expressjs/express/compare/4.19.2...4.21.0)

---
updated-dependencies:
- dependency-name: send
  dependency-type: indirect
- dependency-name: express
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 frontend/package-lock.json | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 66d23579f5..2ddee2f4e9 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -6483,9 +6483,6 @@
       "integrity": "sha512-XpNj6GDQzdfW+r2Wnn7xiSAd7TM3jzkxGXBGTtWKuSXv1xUV+azxAm8jdWZN06QTQk+2N2XB9jRDkvbmQmcRtg=="
     },
     "node_modules/body-parser": {
-      "version": "1.20.3",
-      "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.3.tgz",
-      "integrity": "sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g==",
       "version": "1.20.3",
       "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.3.tgz",
       "integrity": "sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g==",

From 6c824e29c16d03c0c3cf48d48017002ad6ad67da Mon Sep 17 00:00:00 2001
From: erinz2020 <erinz2020@gmail.com>
Date: Thu, 19 Dec 2024 15:52:31 +0000
Subject: [PATCH 07/20] fix react favIcon inconsistency issue

---
 frontend/src/FrontDesk.jsx | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/frontend/src/FrontDesk.jsx b/frontend/src/FrontDesk.jsx
index 828b832dd9..b08fefd8bc 100644
--- a/frontend/src/FrontDesk.jsx
+++ b/frontend/src/FrontDesk.jsx
@@ -15,8 +15,10 @@ import {
   sessionCountdownTime,
 } from "./constants/sessionWarning";
 import useGetSiteSettings from "./models/useGetSiteSettings";
+import useDocumentTitle from "./hooks/useDocumentTitle";
 
 export default function FrontDesk() {
+  useDocumentTitle();
   const [isLoggedIn, setIsLoggedIn] = useState(false);
   const [collaborationTitle, setCollaborationTitle] = useState();
   const [collaborationData, setCollaborationData] = useState([]);

From 3b4dd9f89483e1fe670b04bd55e98e47ddd50cc0 Mon Sep 17 00:00:00 2001
From: holmbergius <holmbergius@gmail.com>
Date: Wed, 25 Dec 2024 15:29:54 -0800
Subject: [PATCH 08/20] LOCAL: temporarily unblock users while OpenSearch syncs

---
 src/main/webapp/encounters/encounterSearch.jsp | 2 +-
 src/main/webapp/encounters/searchResults.jsp   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/webapp/encounters/encounterSearch.jsp b/src/main/webapp/encounters/encounterSearch.jsp
index 07294ff9a1..d9812d77cd 100755
--- a/src/main/webapp/encounters/encounterSearch.jsp
+++ b/src/main/webapp/encounters/encounterSearch.jsp
@@ -250,7 +250,7 @@ $(".search-collapse-header a").click(function(){
 <p><em><%=encprops.getProperty("instructions")%>
 </em></p>
 
-<form action="/react/login" method="get" name="encounterSearch" id="search">
+<form action="searchResults.jsp" method="get" name="encounterSearch" id="search">
 
   <%
 		if(request.getParameter("referenceImageName")!=null){
diff --git a/src/main/webapp/encounters/searchResults.jsp b/src/main/webapp/encounters/searchResults.jsp
index 19cbacdecd..d2548e3b6d 100755
--- a/src/main/webapp/encounters/searchResults.jsp
+++ b/src/main/webapp/encounters/searchResults.jsp
@@ -35,7 +35,7 @@ context=ServletUtilities.getContext(request);
 
 
   Shepherd myShepherd = new Shepherd(context);
-  myShepherd.setAction("/react/login");
+  myShepherd.setAction("searchResults.jsp");
   String[] projectIds = null;
   int projectIdCount = 0;
   if(Util.isUUID(request.getParameter("projectId"))){

From c61cd57e4abc0e6d356676ee24dc93eb3d9a35d0 Mon Sep 17 00:00:00 2001
From: holmbergius <holmbergius@gmail.com>
Date: Fri, 27 Dec 2024 18:57:25 -0800
Subject: [PATCH 09/20] removes redundant database close that will otherwise
 happy anyway in the finaly{} block, even if the return is called.

---
 src/main/java/org/ecocean/MarkedIndividual.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/ecocean/MarkedIndividual.java b/src/main/java/org/ecocean/MarkedIndividual.java
index 3eaa80005c..82428c55e4 100644
--- a/src/main/java/org/ecocean/MarkedIndividual.java
+++ b/src/main/java/org/ecocean/MarkedIndividual.java
@@ -2609,7 +2609,7 @@ public void run() {
                 try {
                     MarkedIndividual indiv = bgShepherd.getMarkedIndividual(indivId);
                     if ((indiv == null) || (indiv.getEncounters() == null)) {
-                        bgShepherd.rollbackAndClose();
+                        //bgShepherd.rollbackAndClose();
                         executor.shutdown();
                         return;
                     }

From 625eb88adcae727fd2f0b153f5d0b56827a0c0a3 Mon Sep 17 00:00:00 2001
From: holmbergius <holmbergius@gmail.com>
Date: Sun, 29 Dec 2024 22:00:14 -0800
Subject: [PATCH 10/20] Remove an unnecessary and functional blocker indexing
 line

---
 .../java/org/ecocean/servlet/IndividualRemoveEncounter.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/ecocean/servlet/IndividualRemoveEncounter.java b/src/main/java/org/ecocean/servlet/IndividualRemoveEncounter.java
index d3a1cd8167..b9a8630b1a 100644
--- a/src/main/java/org/ecocean/servlet/IndividualRemoveEncounter.java
+++ b/src/main/java/org/ecocean/servlet/IndividualRemoveEncounter.java
@@ -107,7 +107,7 @@ public void doPost(HttpServletRequest request, HttpServletResponse response)
                 }
                 if (!locked) {
                     myShepherd.commitDBTransaction();
-                    if (enc2remove != null) enc2remove.opensearchIndexDeep();
+                    //if (enc2remove != null) enc2remove.opensearchIndexDeep();
                     out.println(ServletUtilities.getHeader(request));
                     response.setStatus(HttpServletResponse.SC_OK);
                     out.println("<strong>Success:</strong> Encounter #" +

From 411f5a736b78c690f196d8d0a0ab7ae88e947d2c Mon Sep 17 00:00:00 2001
From: holmbergius <holmbergius@gmail.com>
Date: Tue, 31 Dec 2024 10:26:20 -0800
Subject: [PATCH 11/20] Remove unneeded Encounter indexing from occurrence

---
 .../java/org/ecocean/servlet/OccurrenceRemoveEncounter.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/ecocean/servlet/OccurrenceRemoveEncounter.java b/src/main/java/org/ecocean/servlet/OccurrenceRemoveEncounter.java
index b6dc7c135e..97d8c18853 100644
--- a/src/main/java/org/ecocean/servlet/OccurrenceRemoveEncounter.java
+++ b/src/main/java/org/ecocean/servlet/OccurrenceRemoveEncounter.java
@@ -83,7 +83,7 @@ public void doPost(HttpServletRequest request, HttpServletResponse response)
                 if (!locked) {
                     myShepherd.commitDBTransaction();
                     // out.println(ServletUtilities.getHeader(request));
-                    if (enc2remove != null) enc2remove.opensearchIndexDeep();
+                    //if (enc2remove != null) enc2remove.opensearchIndexDeep();
                     out.println("<strong>Success:</strong> Encounter " +
                         request.getParameter("number") +
                         " was successfully removed from occurrence " + old_name + ".");

From 57fa4d4a32b58120ba8f10edbeb0596a01fe87de Mon Sep 17 00:00:00 2001
From: erinz2020 <erinz2020@gmail.com>
Date: Thu, 19 Dec 2024 22:35:55 +0000
Subject: [PATCH 12/20] add meta description, author, keywords to react pages

---
 frontend/src/hooks/useDocumentTitle.js | 34 ++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/frontend/src/hooks/useDocumentTitle.js b/frontend/src/hooks/useDocumentTitle.js
index b1a2192f8c..5008470e01 100644
--- a/frontend/src/hooks/useDocumentTitle.js
+++ b/frontend/src/hooks/useDocumentTitle.js
@@ -3,10 +3,44 @@ import useGetSiteSettings from "../models/useGetSiteSettings";
 
 export default function useDocumentTitle() {
   const { data: siteSettings } = useGetSiteSettings();
+
+  console.log("siteSettings", siteSettings);
   document.title = siteSettings?.siteName || "wildbook";
   useEffect(() => {
+    if (!siteSettings) return;
     let iconURL = siteSettings?.siteFavicon;
     let link = document.querySelector("link[rel*='icon']");
+    const metaDescription = document.querySelector("meta[name='description']");
+    const metaKeywords = document.querySelector("meta[name='keywords']");
+    const metaAuthor = document.querySelector("meta[name='author']");
+
+    if (!metaDescription) {
+      const meta = document.createElement("meta");
+      meta.name = "description";
+      meta.content = siteSettings?.siteDescription;
+      document.getElementsByTagName("head")[0].appendChild(meta);
+    }
+
+    if (!metaKeywords) {
+      const meta = document.createElement("meta");
+      meta.name = "keywords";
+      meta.content = siteSettings?.siteKeywords;
+      document.getElementsByTagName("head")[0].appendChild(meta);
+    }
+
+    if (!metaAuthor) {
+      const meta = document.createElement("meta");
+      meta.name = "author";
+      meta.content = siteSettings?.siteAuthor;
+      document.getElementsByTagName("head")[0].appendChild(meta);
+    }
+
+    console.log(
+      "++++++++++++",
+      siteSettings.siteDescription,
+      siteSettings.siteKeywords,
+      siteSettings.siteAuthor,
+    );
 
     if (link) {
       link.href = iconURL;

From df0ba8b026aba49b8d3b3247d9c9b9833d405853 Mon Sep 17 00:00:00 2001
From: erinz2020 <erinz2020@gmail.com>
Date: Fri, 20 Dec 2024 15:11:20 +0000
Subject: [PATCH 13/20] get properties from commonConfiguration

---
 frontend/src/hooks/useDocumentTitle.js          | 8 --------
 src/main/java/org/ecocean/api/SiteSettings.java | 3 +++
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/frontend/src/hooks/useDocumentTitle.js b/frontend/src/hooks/useDocumentTitle.js
index 5008470e01..a11c8e8053 100644
--- a/frontend/src/hooks/useDocumentTitle.js
+++ b/frontend/src/hooks/useDocumentTitle.js
@@ -4,7 +4,6 @@ import useGetSiteSettings from "../models/useGetSiteSettings";
 export default function useDocumentTitle() {
   const { data: siteSettings } = useGetSiteSettings();
 
-  console.log("siteSettings", siteSettings);
   document.title = siteSettings?.siteName || "wildbook";
   useEffect(() => {
     if (!siteSettings) return;
@@ -35,13 +34,6 @@ export default function useDocumentTitle() {
       document.getElementsByTagName("head")[0].appendChild(meta);
     }
 
-    console.log(
-      "++++++++++++",
-      siteSettings.siteDescription,
-      siteSettings.siteKeywords,
-      siteSettings.siteAuthor,
-    );
-
     if (link) {
       link.href = iconURL;
     } else {
diff --git a/src/main/java/org/ecocean/api/SiteSettings.java b/src/main/java/org/ecocean/api/SiteSettings.java
index 898e612eb5..696208dac2 100644
--- a/src/main/java/org/ecocean/api/SiteSettings.java
+++ b/src/main/java/org/ecocean/api/SiteSettings.java
@@ -47,6 +47,9 @@ protected void doGet(HttpServletRequest request, HttpServletResponse response)
         // note: there is a CommonConfiguration property: htmlShortcutIcon=images/favicon.ico?v=2
         settings.put("siteFavicon", "/images/favicon.ico");
         settings.put("siteName", CommonConfiguration.getHTMLTitle(context));
+        settings.put("siteDescription", CommonConfiguration.getHTMLDescription(context));
+        settings.put("siteKeywords", CommonConfiguration.getHTMLKeywords(context));
+        settings.put("siteAuthor", CommonConfiguration.getHTMLAuthor(context));
         settings.put("locationData", LocationID.getLocationIDStructure());
 
         settings.put("mapCenterLat", CommonConfiguration.getCenterLat(context));

From 31c77556f737dde3265c7f12fdbe7b671a7371cd Mon Sep 17 00:00:00 2001
From: Jon Van Oast <jon@wildme.org>
Date: Fri, 3 Jan 2025 10:31:53 -0700
Subject: [PATCH 14/20] close shepherd

---
 src/main/java/org/ecocean/EncounterQueryProcessor.java | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/main/java/org/ecocean/EncounterQueryProcessor.java b/src/main/java/org/ecocean/EncounterQueryProcessor.java
index 5b020bd3b2..dd0a038833 100644
--- a/src/main/java/org/ecocean/EncounterQueryProcessor.java
+++ b/src/main/java/org/ecocean/EncounterQueryProcessor.java
@@ -112,11 +112,14 @@ public static String queryStringBuilder(HttpServletRequest request, StringBuffer
             } catch (Exception ex) {
                 ex.printStackTrace();
                 return failed;
+            } finally {
+                myShepherd.rollbackAndClose();
             }
             filter += " (catalogNumber == \"" + String.join("\") || (catalogNumber == \"",
                 encIds) + "\")";
             System.out.println("queryStringBuilder: searchQueryId=" + searchQueryId + " yielded " +
                 encIds.size() + " matching encounters");
+            myShepherd.rollbackAndClose();
             return filter;
         }
         // filter for location------------------------------------------

From 035b33e2c8dbfc7c8cd68ab5ea889664f959e93e Mon Sep 17 00:00:00 2001
From: Jon Van Oast <jon@wildme.org>
Date: Fri, 3 Jan 2025 10:42:28 -0700
Subject: [PATCH 15/20] think we dont need this

---
 src/main/java/org/ecocean/EncounterQueryProcessor.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/main/java/org/ecocean/EncounterQueryProcessor.java b/src/main/java/org/ecocean/EncounterQueryProcessor.java
index dd0a038833..011265a174 100644
--- a/src/main/java/org/ecocean/EncounterQueryProcessor.java
+++ b/src/main/java/org/ecocean/EncounterQueryProcessor.java
@@ -119,7 +119,6 @@ public static String queryStringBuilder(HttpServletRequest request, StringBuffer
                 encIds) + "\")";
             System.out.println("queryStringBuilder: searchQueryId=" + searchQueryId + " yielded " +
                 encIds.size() + " matching encounters");
-            myShepherd.rollbackAndClose();
             return filter;
         }
         // filter for location------------------------------------------

From 73cd9dd15234837046d7d180d2e4dc6f52aab453 Mon Sep 17 00:00:00 2001
From: Jon Van Oast <jon@wildme.org>
Date: Fri, 3 Jan 2025 11:01:18 -0700
Subject: [PATCH 16/20] begin transaction

---
 src/main/java/org/ecocean/EncounterQueryProcessor.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/org/ecocean/EncounterQueryProcessor.java b/src/main/java/org/ecocean/EncounterQueryProcessor.java
index 011265a174..0e0653b338 100644
--- a/src/main/java/org/ecocean/EncounterQueryProcessor.java
+++ b/src/main/java/org/ecocean/EncounterQueryProcessor.java
@@ -48,6 +48,7 @@ public static String queryStringBuilder(HttpServletRequest request, StringBuffer
         context = ServletUtilities.getContext(request);
         Shepherd myShepherd = new Shepherd(context);
         myShepherd.setAction("EncounterQueryProcessor.class");
+        myShepherd.beginDBTransaction();
 
         String searchQueryId = request.getParameter("searchQueryId");
         // hack to build a ridiculous query string from an OpenSearch query

From 4fb3a149777c4832ffca8112638544413acef60a Mon Sep 17 00:00:00 2001
From: Jon Van Oast <jon@wildme.org>
Date: Fri, 3 Jan 2025 11:57:45 -0700
Subject: [PATCH 17/20] one big try/catch wrap

---
 .../org/ecocean/EncounterQueryProcessor.java  | 2643 +++++++++--------
 1 file changed, 1336 insertions(+), 1307 deletions(-)

diff --git a/src/main/java/org/ecocean/EncounterQueryProcessor.java b/src/main/java/org/ecocean/EncounterQueryProcessor.java
index 0e0653b338..a1ed1a38ba 100644
--- a/src/main/java/org/ecocean/EncounterQueryProcessor.java
+++ b/src/main/java/org/ecocean/EncounterQueryProcessor.java
@@ -49,220 +49,152 @@ public static String queryStringBuilder(HttpServletRequest request, StringBuffer
         Shepherd myShepherd = new Shepherd(context);
         myShepherd.setAction("EncounterQueryProcessor.class");
         myShepherd.beginDBTransaction();
-
-        String searchQueryId = request.getParameter("searchQueryId");
-        // hack to build a ridiculous query string from an OpenSearch query
-        if (searchQueryId != null) {
-            String failed = filter + " 1 == 0";
-            List<String> encIds = new ArrayList<String>();
-            User user = myShepherd.getUser(request);
-            if (user == null) return failed;
-            JSONObject searchQuery = OpenSearch.queryLoad(searchQueryId);
-            if (searchQuery == null) return failed;
-            String indexName = searchQuery.optString("indexName", null);
-            if (indexName == null) return failed;
-            searchQuery = OpenSearch.queryScrubStored(searchQuery);
-            JSONObject sanitized = null;
-            try {
-                sanitized = OpenSearch.querySanitize(searchQuery, user, myShepherd);
-            } catch (IOException ex) {
-                ex.printStackTrace();
-                // this should be unlikely, so fail hard
-                throw new RuntimeException("query failed");
-            }
-            OpenSearch os = new OpenSearch();
-            String sort = request.getParameter("sort");
-            String sortOrder = request.getParameter("sortOrder");
-            int numFrom = 0;
-            // for historical code reasons, this needs to be "all" encounters,
-            // so we hope this does the job if background indexing set correctly
-            int pageSize = 10000;
-            try {
-                pageSize = os.getSettings(indexName).optInt("max_result_window", 10000);
-            } catch (Exception ex) {}
-            try {
-                os.deletePit(indexName);
-                JSONObject queryRes = os.queryPit(indexName, sanitized, numFrom, pageSize, sort,
-                    sortOrder);
-                JSONObject outerHits = queryRes.optJSONObject("hits");
-                if (outerHits == null) {
-                    System.out.println("could not find (outer) hits");
-                    return failed;
-                }
-                JSONArray hits = outerHits.optJSONArray("hits");
-                if (hits == null) {
-                    System.out.println("could not find hits");
-                    return failed;
+        // wrap all myShepherd use in try/catch block
+        try {
+            String searchQueryId = request.getParameter("searchQueryId");
+            // hack to build a ridiculous query string from an OpenSearch query
+            if (searchQueryId != null) {
+                String failed = filter + " 1 == 0";
+                List<String> encIds = new ArrayList<String>();
+                User user = myShepherd.getUser(request);
+                if (user == null) return failed;
+                JSONObject searchQuery = OpenSearch.queryLoad(searchQueryId);
+                if (searchQuery == null) return failed;
+                String indexName = searchQuery.optString("indexName", null);
+                if (indexName == null) return failed;
+                searchQuery = OpenSearch.queryScrubStored(searchQuery);
+                JSONObject sanitized = null;
+                try {
+                    sanitized = OpenSearch.querySanitize(searchQuery, user, myShepherd);
+                } catch (IOException ex) {
+                    ex.printStackTrace();
+                    // this should be unlikely, so fail hard
+                    throw new RuntimeException("query failed");
                 }
-                for (int i = 0; i < hits.length(); i++) {
-                    JSONObject h = hits.optJSONObject(i);
-                    if (h == null) {
-                        System.out.println("failed to parse hits[" + i + "]");
+                OpenSearch os = new OpenSearch();
+                String sort = request.getParameter("sort");
+                String sortOrder = request.getParameter("sortOrder");
+                int numFrom = 0;
+                // for historical code reasons, this needs to be "all" encounters,
+                // so we hope this does the job if background indexing set correctly
+                int pageSize = 10000;
+                try {
+                    pageSize = os.getSettings(indexName).optInt("max_result_window", 10000);
+                } catch (Exception ex) {}
+                try {
+                    os.deletePit(indexName);
+                    JSONObject queryRes = os.queryPit(indexName, sanitized, numFrom, pageSize, sort,
+                        sortOrder);
+                    JSONObject outerHits = queryRes.optJSONObject("hits");
+                    if (outerHits == null) {
+                        System.out.println("could not find (outer) hits");
                         return failed;
                     }
-                    String hId = h.optString("_id", null);
-                    if (hId == null) {
-                        System.out.println("failed to parse _id from hits[" + i + "]");
+                    JSONArray hits = outerHits.optJSONArray("hits");
+                    if (hits == null) {
+                        System.out.println("could not find hits");
                         return failed;
                     }
-                    // Encounter enc = myShepherd.getEncounter(hId);
-                    boolean hasAccess = Encounter.opensearchAccess(h.optJSONObject("_source"), user,
-                        myShepherd);
-                    if (hasAccess) encIds.add(hId);
-                }
-            } catch (Exception ex) {
-                ex.printStackTrace();
-                return failed;
-            } finally {
-                myShepherd.rollbackAndClose();
-            }
-            filter += " (catalogNumber == \"" + String.join("\") || (catalogNumber == \"",
-                encIds) + "\")";
-            System.out.println("queryStringBuilder: searchQueryId=" + searchQueryId + " yielded " +
-                encIds.size() + " matching encounters");
-            return filter;
-        }
-        // filter for location------------------------------------------
-        if ((request.getParameter("locationField") != null) &&
-            (!request.getParameter("locationField").equals(""))) {
-            String locString = request.getParameter("locationField").toLowerCase().replaceAll("%20",
-                " ").trim();
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "(verbatimLocality.toLowerCase().indexOf('" + locString + "') != -1)";
-            } else {
-                filter += " && (verbatimLocality.toLowerCase().indexOf('" + locString + "') != -1)";
-            }
-            prettyPrint.append("locationField contains \"" + locString + "\".<br />");
-        }
-        // end location filter--------------------------------------------------------------------------------------
-        // filter for organization-------------------
-        if ((request.getParameter("organizationId") != null) &&
-            (!request.getParameter("organizationId").equals("")) &&
-            Util.isUUID(request.getParameter("organizationId"))) {
-            String orgId = request.getParameter("organizationId");
-            filter =
-                "SELECT FROM org.ecocean.Encounter WHERE user.username == this.submitterID && org.members.contains(user) && org.id == '"
-                + orgId + "'";
-            String variables_statement =
-                " VARIABLES org.ecocean.User user; org.ecocean.Organization org";
-            jdoqlVariableDeclaration = addOrgVars(variables_statement, filter);
-        } else {}
-        // end filter for organization------------------
-        // filter for projectName-------------------
-        if (Util.isUUID(request.getParameter("projectId"))) {
-            filter = SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE +
-                " proj.encounters.contains(this) && ";
-            String[] projectIds = request.getParameterValues("projectId");
-            if ((projectIds != null) && (!projectIds[0].equals("None"))) {
-                prettyPrint.append("Assigned to one of the following projects: ");
-                int numProjIds = projectIds.length;
-                String projIdFilter = "(";
-                for (int i = 0; i < numProjIds; i++) {
-                    String currentProjId = projectIds[i].toLowerCase().replaceAll("%20",
-                        " ").trim();
-                    if (!currentProjId.equals("")) {
-                        if (projIdFilter.equals("(")) {
-                            projIdFilter += " proj.id == \"" + currentProjId + "\"";
-                        } else {
-                            projIdFilter += " || proj.id == \"" + currentProjId + "\"";
+                    for (int i = 0; i < hits.length(); i++) {
+                        JSONObject h = hits.optJSONObject(i);
+                        if (h == null) {
+                            System.out.println("failed to parse hits[" + i + "]");
+                            return failed;
+                        }
+                        String hId = h.optString("_id", null);
+                        if (hId == null) {
+                            System.out.println("failed to parse _id from hits[" + i + "]");
+                            return failed;
                         }
+                        // Encounter enc = myShepherd.getEncounter(hId);
+                        boolean hasAccess = Encounter.opensearchAccess(h.optJSONObject("_source"),
+                            user, myShepherd);
+                        if (hasAccess) encIds.add(hId);
                     }
+                } catch (Exception ex) {
+                    ex.printStackTrace();
+                    return failed;
                 }
-                projIdFilter += " )";
-                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE +
-                    " proj.encounters.contains(this) && ")) {
-                    filter += projIdFilter;
+                filter += " (catalogNumber == \"" + String.join("\") || (catalogNumber == \"",
+                    encIds) + "\")";
+                System.out.println("queryStringBuilder: searchQueryId=" + searchQueryId +
+                    " yielded " + encIds.size() + " matching encounters");
+                return filter;
+            }
+            // filter for location------------------------------------------
+            if ((request.getParameter("locationField") != null) &&
+                (!request.getParameter("locationField").equals(""))) {
+                String locString = request.getParameter("locationField").toLowerCase().replaceAll(
+                    "%20", " ").trim();
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += "(verbatimLocality.toLowerCase().indexOf('" + locString + "') != -1)";
                 } else {
-                    filter += (" && " + projIdFilter);
+                    filter += " && (verbatimLocality.toLowerCase().indexOf('" + locString +
+                        "') != -1)";
                 }
-                prettyPrint.append(filter);
-                prettyPrint.append("<br/>");
-            }
-            String variables_statement = " VARIABLES org.ecocean.Project proj";
-            jdoqlVariableDeclaration = addOrgVars(variables_statement, filter);
-        } else {}
-        // end filter for projectName------------------
-        // username filters-------------------------------------------------
-        String[] usernames = request.getParameterValues("username");
-        if ((usernames != null) && (!usernames[0].equals("None"))) {
-            prettyPrint.append("Assigned to one of the following usernames: ");
-            int kwLength = usernames.length;
-            String locIDFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = usernames[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (locIDFilter.equals("(")) {
-                        locIDFilter += " submitterID == \"" + kwParam + "\"";
-                    } else {
-                        locIDFilter += " || submitterID == \"" + kwParam + "\"";
+                prettyPrint.append("locationField contains \"" + locString + "\".<br />");
+            }
+            // end location filter--------------------------------------------------------------------------------------
+            // filter for organization-------------------
+            if ((request.getParameter("organizationId") != null) &&
+                (!request.getParameter("organizationId").equals("")) &&
+                Util.isUUID(request.getParameter("organizationId"))) {
+                String orgId = request.getParameter("organizationId");
+                filter =
+                    "SELECT FROM org.ecocean.Encounter WHERE user.username == this.submitterID && org.members.contains(user) && org.id == '"
+                    + orgId + "'";
+                String variables_statement =
+                    " VARIABLES org.ecocean.User user; org.ecocean.Organization org";
+                jdoqlVariableDeclaration = addOrgVars(variables_statement, filter);
+            } else {}
+            // end filter for organization------------------
+            // filter for projectName-------------------
+            if (Util.isUUID(request.getParameter("projectId"))) {
+                filter = SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE +
+                    " proj.encounters.contains(this) && ";
+                String[] projectIds = request.getParameterValues("projectId");
+                if ((projectIds != null) && (!projectIds[0].equals("None"))) {
+                    prettyPrint.append("Assigned to one of the following projects: ");
+                    int numProjIds = projectIds.length;
+                    String projIdFilter = "(";
+                    for (int i = 0; i < numProjIds; i++) {
+                        String currentProjId = projectIds[i].toLowerCase().replaceAll("%20",
+                            " ").trim();
+                        if (!currentProjId.equals("")) {
+                            if (projIdFilter.equals("(")) {
+                                projIdFilter += " proj.id == \"" + currentProjId + "\"";
+                            } else {
+                                projIdFilter += " || proj.id == \"" + currentProjId + "\"";
+                            }
+                        }
                     }
-                    prettyPrint.append(kwParam + " ");
-                }
-            }
-            locIDFilter += " )";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += locIDFilter;
-            } else { filter += (" && " + locIDFilter); }
-            prettyPrint.append("<br/>");
-        }
-        // end username filters-----------------------------------------------
-        // filter for resighted encounter------------------------------------------
-        if (request.getParameter("resightOnly") != null) {
-            // String locString=request.getParameter("locationField").toLowerCase().replaceAll("%20", " ").trim();
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "(individual != null)";
-            } else { filter += " && (individual != null)"; }
-            prettyPrint.append("Identified and resighted.<br />");
-        }
-        // end resighted filter--------------------------------------------------------------------------------------
-        // filter for unassigned encounters------------------------------------------
-        if (request.getParameter("unassigned") != null) {
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "(individual == null)";
-            } else { filter += " && (individual == null)"; }
-            prettyPrint.append("Unidentified.<br />");
-        }
-        // end unassigned filter--------------------------------------------------------------------------------------
-        // locationID filters-------------------------------------------------
-        String[] locCodes = request.getParameterValues("locationCodeField");
-        if ((locCodes != null) && (!locCodes[0].equals(""))) {
-            prettyPrint.append("locationCodeField is one of the following: ");
-            int kwLength = locCodes.length;
-            String locIDFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = locCodes[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (locIDFilter.equals("(")) {
-                        locIDFilter += " locationID == \"" + kwParam + "\"";
+                    projIdFilter += " )";
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE +
+                        " proj.encounters.contains(this) && ")) {
+                        filter += projIdFilter;
                     } else {
-                        locIDFilter += " || locationID == \"" + kwParam + "\"";
+                        filter += (" && " + projIdFilter);
                     }
-                    prettyPrint.append(kwParam + " ");
+                    prettyPrint.append(filter);
+                    prettyPrint.append("<br/>");
                 }
-            }
-            locIDFilter += " )";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += locIDFilter;
-            } else { filter += (" && " + locIDFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end locationID filters-----------------------------------------------
-        // annotation viewpoint and class filters-------------------------------------------------
-        String[] hasViewpoint = request.getParameterValues("hasViewpoint");
-        String[] hasIAClass = request.getParameterValues("hasIAClass");
-        if (((hasViewpoint != null) && (!hasViewpoint[0].equals(""))) ||
-            ((hasIAClass != null) && (!hasIAClass[0].equals("")))) {
-            if ((hasViewpoint != null) && (!hasViewpoint[0].equals(""))) {
-                prettyPrint.append("Viewpoint is one of the following: ");
-                int kwLength = hasViewpoint.length;
+                String variables_statement = " VARIABLES org.ecocean.Project proj";
+                jdoqlVariableDeclaration = addOrgVars(variables_statement, filter);
+            } else {}
+            // end filter for projectName------------------
+            // username filters-------------------------------------------------
+            String[] usernames = request.getParameterValues("username");
+            if ((usernames != null) && (!usernames[0].equals("None"))) {
+                prettyPrint.append("Assigned to one of the following usernames: ");
+                int kwLength = usernames.length;
                 String locIDFilter = "(";
                 for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                    String kwParam = hasViewpoint[kwIter].trim();
+                    String kwParam = usernames[kwIter].replaceAll("%20", " ").trim();
                     if (!kwParam.equals("")) {
                         if (locIDFilter.equals("(")) {
-                            locIDFilter += " annot46.viewpoint == \"" + kwParam + "\"";
+                            locIDFilter += " submitterID == \"" + kwParam + "\"";
                         } else {
-                            locIDFilter += " || annot46.viewpoint == \"" + kwParam + "\"";
+                            locIDFilter += " || submitterID == \"" + kwParam + "\"";
                         }
                         prettyPrint.append(kwParam + " ");
                     }
@@ -271,19 +203,39 @@ public static String queryStringBuilder(HttpServletRequest request, StringBuffer
                 if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
                     filter += locIDFilter;
                 } else { filter += (" && " + locIDFilter); }
-                prettyPrint.append("<br />");
+                prettyPrint.append("<br/>");
+            }
+            // end username filters-----------------------------------------------
+            // filter for resighted encounter------------------------------------------
+            if (request.getParameter("resightOnly") != null) {
+                // String locString=request.getParameter("locationField").toLowerCase().replaceAll("%20", " ").trim();
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += "(individual != null)";
+                } else { filter += " && (individual != null)"; }
+                prettyPrint.append("Identified and resighted.<br />");
             }
-            if ((hasIAClass != null) && (!hasIAClass[0].equals(""))) {
-                prettyPrint.append("IA class is one of the following: ");
-                int kwLength = hasIAClass.length;
+            // end resighted filter--------------------------------------------------------------------------------------
+            // filter for unassigned encounters------------------------------------------
+            if (request.getParameter("unassigned") != null) {
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += "(individual == null)";
+                } else { filter += " && (individual == null)"; }
+                prettyPrint.append("Unidentified.<br />");
+            }
+            // end unassigned filter--------------------------------------------------------------------------------------
+            // locationID filters-------------------------------------------------
+            String[] locCodes = request.getParameterValues("locationCodeField");
+            if ((locCodes != null) && (!locCodes[0].equals(""))) {
+                prettyPrint.append("locationCodeField is one of the following: ");
+                int kwLength = locCodes.length;
                 String locIDFilter = "(";
                 for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                    String kwParam = hasIAClass[kwIter].trim();
+                    String kwParam = locCodes[kwIter].replaceAll("%20", " ").trim();
                     if (!kwParam.equals("")) {
                         if (locIDFilter.equals("(")) {
-                            locIDFilter += " annot46.iaClass == \"" + kwParam + "\"";
+                            locIDFilter += " locationID == \"" + kwParam + "\"";
                         } else {
-                            locIDFilter += " || annot46.iaClass == \"" + kwParam + "\"";
+                            locIDFilter += " || locationID == \"" + kwParam + "\"";
                         }
                         prettyPrint.append(kwParam + " ");
                     }
@@ -294,1240 +246,1317 @@ public static String queryStringBuilder(HttpServletRequest request, StringBuffer
                 } else { filter += (" && " + locIDFilter); }
                 prettyPrint.append("<br />");
             }
-            // set the jdoql variable used by both
-            filter += (" && annotations.contains(annot46)");
-            if (jdoqlVariableDeclaration.length() > 0) {
-                jdoqlVariableDeclaration += ";org.ecocean.Annotation annot46;";
-            } else {
-                jdoqlVariableDeclaration = " VARIABLES org.ecocean.Annotation annot46";
-            }
-        }
-        // end viewpoint and class filters-----------------------------------------------
-        // state filters-------------------------------------------------
-        String[] states = request.getParameterValues("state");
-        if ((states != null) && (!states[0].equals("None"))) {
-            prettyPrint.append("State is one of the following: ");
-            int kwLength = states.length;
-            String locIDFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = states[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (locIDFilter.equals("(")) {
-                        locIDFilter += " state == \"" + kwParam + "\"";
-                    } else {
-                        locIDFilter += " || state == \"" + kwParam + "\"";
+            // end locationID filters-----------------------------------------------
+            // annotation viewpoint and class filters-------------------------------------------------
+            String[] hasViewpoint = request.getParameterValues("hasViewpoint");
+            String[] hasIAClass = request.getParameterValues("hasIAClass");
+            if (((hasViewpoint != null) && (!hasViewpoint[0].equals(""))) ||
+                ((hasIAClass != null) && (!hasIAClass[0].equals("")))) {
+                if ((hasViewpoint != null) && (!hasViewpoint[0].equals(""))) {
+                    prettyPrint.append("Viewpoint is one of the following: ");
+                    int kwLength = hasViewpoint.length;
+                    String locIDFilter = "(";
+                    for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                        String kwParam = hasViewpoint[kwIter].trim();
+                        if (!kwParam.equals("")) {
+                            if (locIDFilter.equals("(")) {
+                                locIDFilter += " annot46.viewpoint == \"" + kwParam + "\"";
+                            } else {
+                                locIDFilter += " || annot46.viewpoint == \"" + kwParam + "\"";
+                            }
+                            prettyPrint.append(kwParam + " ");
+                        }
                     }
-                    prettyPrint.append(kwParam + " ");
+                    locIDFilter += " )";
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += locIDFilter;
+                    } else { filter += (" && " + locIDFilter); }
+                    prettyPrint.append("<br />");
                 }
-            }
-            locIDFilter += " )";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += locIDFilter;
-            } else { filter += (" && " + locIDFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end state filters-----------------------------------------------
-        // individualID filters-------------------------------------------------
-        // supports multiple individualID parameters as well as comma-separated lists of individualIDs within them
-        String individualID = request.getParameter("individualID");
-        if ((individualID != null) && (!individualID.equals("None")) &&
-            (!individualID.trim().equals(""))) {
-            prettyPrint.append("Individual ID contains the following: ");
-
-            String locIDFilter = " (individual.individualID == \"" + individualID +
-                "\" || individual.names.valuesAsString.toLowerCase().indexOf(\"" +
-                individualID.toLowerCase() + "\") != -1) ";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += locIDFilter;
-            } else { filter += (" && " + locIDFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end individualID filters-----------------------------------------------
-        // occurrenceID filters-------------------------------------------------
-        String occurrenceID = request.getParameter("occurrenceID");
-        if ((occurrenceID != null) && (!occurrenceID.equals("None")) &&
-            (!occurrenceID.trim().equals(""))) {
-            prettyPrint.append("occurrence ID contains the following: ");
-
-            String locIDFilter = " occurrenceID == \"" + occurrenceID + "\"";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += locIDFilter;
-            } else { filter += (" && " + locIDFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end occurrenceID filters-----------------------------------------------
-        // individualIDExact filters-------------------------------------------------
-        // supports one individualID parameter as well as comma-separated lists of individualIDs within them
-        String individualIDExact = request.getParameter("individualIDExact");
-        if ((individualIDExact != null) && (!individualIDExact.trim().equals(""))) {
-            prettyPrint.append("Individual ID is exactly the following: ");
-
-            String locIDFilter = " individual.individualID == \"" + individualIDExact.trim() +
-                "\" ";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += locIDFilter;
-            } else { filter += (" && " + locIDFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end individualID filters-----------------------------------------------
-        // socialunit filters------------------------------------------------------------------
-        // community search
-        /*
-         * to filter Encounnter based on community firstly we need to get the social units associated with the communities and get the individualIDs
-         * from the social units and then use these individualIDs to filter the Encounters
-         */
-        if (request.getParameterValues("community") != null) {
-            String[] communities = request.getParameterValues("community");
-            int numCommunities = communities.length;
-            prettyPrint.append("Social unit is one of the following: ");
-
-            Set<String> individualsIdsSet = new HashSet<String>();
-            for (int i = 0; i < numCommunities; i++) {
-                prettyPrint.append(communities[i] + " ");
-
-                SocialUnit su = myShepherd.getSocialUnit(communities[i]);
-                if (su == null) continue;
-                for (Membership member : su.getAllMembers()) {
-                    if (member.getMarkedIndividual() != null) {
-                        individualsIdsSet.add(member.getMarkedIndividual().getId());
+                if ((hasIAClass != null) && (!hasIAClass[0].equals(""))) {
+                    prettyPrint.append("IA class is one of the following: ");
+                    int kwLength = hasIAClass.length;
+                    String locIDFilter = "(";
+                    for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                        String kwParam = hasIAClass[kwIter].trim();
+                        if (!kwParam.equals("")) {
+                            if (locIDFilter.equals("(")) {
+                                locIDFilter += " annot46.iaClass == \"" + kwParam + "\"";
+                            } else {
+                                locIDFilter += " || annot46.iaClass == \"" + kwParam + "\"";
+                            }
+                            prettyPrint.append(kwParam + " ");
+                        }
                     }
+                    locIDFilter += " )";
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += locIDFilter;
+                    } else { filter += (" && " + locIDFilter); }
+                    prettyPrint.append("<br />");
+                }
+                // set the jdoql variable used by both
+                filter += (" && annotations.contains(annot46)");
+                if (jdoqlVariableDeclaration.length() > 0) {
+                    jdoqlVariableDeclaration += ";org.ecocean.Annotation annot46;";
+                } else {
+                    jdoqlVariableDeclaration = " VARIABLES org.ecocean.Annotation annot46";
                 }
             }
-            List<String> individualsIds = new ArrayList<String>(individualsIdsSet);
-            if (individualsIds.size() > 0) {
-                String locIDFilter = " ( individual.individualID == \"" + individualsIds.get(0) +
-                    "\" ";
-                for (int j = 1; j < individualsIds.size(); j++) {
-                    locIDFilter += " || individual.individualID == \"" + individualsIds.get(j) +
-                        "\" ";
+            // end viewpoint and class filters-----------------------------------------------
+            // state filters-------------------------------------------------
+            String[] states = request.getParameterValues("state");
+            if ((states != null) && (!states[0].equals("None"))) {
+                prettyPrint.append("State is one of the following: ");
+                int kwLength = states.length;
+                String locIDFilter = "(";
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String kwParam = states[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (locIDFilter.equals("(")) {
+                            locIDFilter += " state == \"" + kwParam + "\"";
+                        } else {
+                            locIDFilter += " || state == \"" + kwParam + "\"";
+                        }
+                        prettyPrint.append(kwParam + " ");
+                    }
                 }
-                locIDFilter = locIDFilter + " ) ";
+                locIDFilter += " )";
                 if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
                     filter += locIDFilter;
                 } else { filter += (" && " + locIDFilter); }
+                prettyPrint.append("<br />");
             }
-            prettyPrint.append("<br />");
-        }
-        // role search
-        /*
-         * to filter Encounnter based on role fetch all the MarkedIndividuals for each MarkedIndividuals gets all roles then check if requested role
-         * is not present remove that MarkedIndividuals finally use these individualIDs to filter the Encounters
-         */
-        if (request.getParameterValues("role") != null) {
-            boolean orRoles = true;
-            Iterator<MarkedIndividual> allSharks = myShepherd.getAllMarkedIndividuals();
-            Vector<MarkedIndividual> rIndividuals = new Vector<MarkedIndividual>();
-            if (allSharks != null) {
-                while (allSharks.hasNext()) {
-                    MarkedIndividual temp_shark = allSharks.next();
-                    rIndividuals.add(temp_shark);
-                }
-            }
-            if (request.getParameter("andRoles") != null) { orRoles = false; }
-            String[] roles = request.getParameterValues("role");
-            int numRoles = roles.length;
-            if (!orRoles) {
-                prettyPrint.append("Social roles include all of the following: ");
-            } else {
-                prettyPrint.append("Social roles is one of the following: ");
-            }
-            for (int h = 0; h < numRoles; h++) {
-                prettyPrint.append(roles[h] + "&nbsp;");
+            // end state filters-----------------------------------------------
+            // individualID filters-------------------------------------------------
+            // supports multiple individualID parameters as well as comma-separated lists of individualIDs within them
+            String individualID = request.getParameter("individualID");
+            if ((individualID != null) && (!individualID.equals("None")) &&
+                (!individualID.trim().equals(""))) {
+                prettyPrint.append("Individual ID contains the following: ");
+
+                String locIDFilter = " (individual.individualID == \"" + individualID +
+                    "\" || individual.names.valuesAsString.toLowerCase().indexOf(\"" +
+                    individualID.toLowerCase() + "\") != -1) ";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += locIDFilter;
+                } else { filter += (" && " + locIDFilter); }
+                prettyPrint.append("<br />");
             }
-            // logical OR the roles
-            for (int q = 0; q < rIndividuals.size(); q++) {
-                MarkedIndividual tShark = (MarkedIndividual)rIndividuals.get(q);
-                List<String> myRoles = myShepherd.getAllRoleNamesForMarkedIndividual(
-                    tShark.getIndividualID());
-                if (orRoles) {
-                    // logical OR the role
-                    boolean hasRole = false;
-                    int f = 0;
-                    while (!hasRole && (f < numRoles)) {
-                        if (myRoles.contains(roles[f])) { hasRole = true; }
-                        f++;
-                    }
-                    if (!hasRole) {
-                        rIndividuals.remove(q);
-                        q--;
-                    }
-                } else {
-                    // logical AND the roles
-                    boolean hasRole = true;
-                    int f = 0;
-                    while (hasRole && (f < numRoles)) {
-                        if (!myRoles.contains(roles[f])) { hasRole = false; }
-                        f++;
-                    }
-                    if (!hasRole) {
-                        rIndividuals.remove(q);
-                        q--;
-                    }
-                }
+            // end individualID filters-----------------------------------------------
+            // occurrenceID filters-------------------------------------------------
+            String occurrenceID = request.getParameter("occurrenceID");
+            if ((occurrenceID != null) && (!occurrenceID.equals("None")) &&
+                (!occurrenceID.trim().equals(""))) {
+                prettyPrint.append("occurrence ID contains the following: ");
+
+                String locIDFilter = " occurrenceID == \"" + occurrenceID + "\"";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += locIDFilter;
+                } else { filter += (" && " + locIDFilter); }
+                prettyPrint.append("<br />");
             }
-            if (rIndividuals.size() > 0) {
-                String locIDFilter = " ( individual.individualID == \"" +
-                    rIndividuals.get(0).getId() + "\"  ";
-                for (int j = 1; j < rIndividuals.size(); j++) {
-                    locIDFilter += " || individual.individualID == \"" +
-                        rIndividuals.get(j).getId() + "\"  ";
-                }
-                locIDFilter = locIDFilter + " ) ";
+            // end occurrenceID filters-----------------------------------------------
+            // individualIDExact filters-------------------------------------------------
+            // supports one individualID parameter as well as comma-separated lists of individualIDs within them
+            String individualIDExact = request.getParameter("individualIDExact");
+            if ((individualIDExact != null) && (!individualIDExact.trim().equals(""))) {
+                prettyPrint.append("Individual ID is exactly the following: ");
+
+                String locIDFilter = " individual.individualID == \"" + individualIDExact.trim() +
+                    "\" ";
                 if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
                     filter += locIDFilter;
                 } else { filter += (" && " + locIDFilter); }
+                prettyPrint.append("<br />");
             }
-            prettyPrint.append("<br />");
-        }
-        // patterningCode filters-------------------------------------------------
-        String[] patterningCodes = request.getParameterValues("patterningCodeField");
-        if ((patterningCodes != null) && (!patterningCodes[0].equals("None"))) {
-            prettyPrint.append("Patterning code is one of the following: ");
-            int kwLength = patterningCodes.length;
-            String patterningCodeFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = patterningCodes[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (patterningCodeFilter.equals("(")) {
-                        patterningCodeFilter += " patterningCode == \"" + kwParam + "\"";
-                    } else {
-                        patterningCodeFilter += " || patterningCode == \"" + kwParam + "\"";
+            // end individualID filters-----------------------------------------------
+            // socialunit filters------------------------------------------------------------------
+            // community search
+            /*
+             * to filter Encounnter based on community firstly we need to get the social units associated with the communities and get the individualIDs
+             * from the social units and then use these individualIDs to filter the Encounters
+             */
+            if (request.getParameterValues("community") != null) {
+                String[] communities = request.getParameterValues("community");
+                int numCommunities = communities.length;
+                prettyPrint.append("Social unit is one of the following: ");
+
+                Set<String> individualsIdsSet = new HashSet<String>();
+                for (int i = 0; i < numCommunities; i++) {
+                    prettyPrint.append(communities[i] + " ");
+
+                    SocialUnit su = myShepherd.getSocialUnit(communities[i]);
+                    if (su == null) continue;
+                    for (Membership member : su.getAllMembers()) {
+                        if (member.getMarkedIndividual() != null) {
+                            individualsIdsSet.add(member.getMarkedIndividual().getId());
+                        }
                     }
-                    prettyPrint.append(kwParam + " ");
                 }
-            }
-            patterningCodeFilter += " )";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += patterningCodeFilter;
-            } else { filter += (" && " + patterningCodeFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end patterningCode filters-----------------------------------------------
-        // behavior filters-------------------------------------------------
-        String[] behaviors = request.getParameterValues("behaviorField");
-        if ((behaviors != null) && (!behaviors[0].equals("None"))) {
-            prettyPrint.append("behaviorField is one of the following: ");
-            int kwLength = behaviors.length;
-            String locIDFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = behaviors[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (locIDFilter.equals("(")) {
-                        locIDFilter += " behavior == \"" + kwParam + "\"";
-                    } else {
-                        locIDFilter += " || behavior == \"" + kwParam + "\"";
+                List<String> individualsIds = new ArrayList<String>(individualsIdsSet);
+                if (individualsIds.size() > 0) {
+                    String locIDFilter = " ( individual.individualID == \"" +
+                        individualsIds.get(0) + "\" ";
+                    for (int j = 1; j < individualsIds.size(); j++) {
+                        locIDFilter += " || individual.individualID == \"" + individualsIds.get(j) +
+                            "\" ";
                     }
-                    prettyPrint.append(kwParam + " ");
+                    locIDFilter = locIDFilter + " ) ";
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += locIDFilter;
+                    } else { filter += (" && " + locIDFilter); }
                 }
+                prettyPrint.append("<br />");
             }
-            locIDFilter += " )";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += locIDFilter;
-            } else { filter += (" && " + locIDFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end behavior filters-----------------------------------------------
-        // begin observation filters -----------------------------------------
-        boolean hasValue = false;
-        if (request.getParameter("numSearchedObs") != null) {
-            if (request.getParameter("observationKey1") != null &&
-                !request.getParameter("observationKey1").equals("")) {
-                hasValue = true;
-            }
-        }
-        Enumeration<String> allParams = request.getParameterNames();
-        if (allParams != null && hasValue) {
-            String keyID = "observationKey";
-            String valID = "observationValue";
-            HashMap<String, String> obKeys = new HashMap<>();
-            HashMap<String, String> obVals = new HashMap<>();
-            StringBuilder obQuery = new StringBuilder();
-            int numObsSearched = 0;
-            while (allParams.hasMoreElements()) {
-                String thisParam = allParams.nextElement();
-                if (thisParam != null && thisParam.startsWith(keyID)) {
-                    numObsSearched++;
-                    System.out.println("Num Obs Searched? " + numObsSearched);
-                    String keyParam = request.getParameter(thisParam);
-                    String keyNum = thisParam.replace(keyID, "");
-                    if (keyParam != null && !keyParam.equals("")) {
-                        obKeys.put(keyNum, keyParam);
+            // role search
+            /*
+             * to filter Encounnter based on role fetch all the MarkedIndividuals for each MarkedIndividuals gets all roles then check if requested role
+             * is not present remove that MarkedIndividuals finally use these individualIDs to filter the Encounters
+             */
+            if (request.getParameterValues("role") != null) {
+                boolean orRoles = true;
+                Iterator<MarkedIndividual> allSharks = myShepherd.getAllMarkedIndividuals();
+                Vector<MarkedIndividual> rIndividuals = new Vector<MarkedIndividual>();
+                if (allSharks != null) {
+                    while (allSharks.hasNext()) {
+                        MarkedIndividual temp_shark = allSharks.next();
+                        rIndividuals.add(temp_shark);
                     }
                 }
-                if (thisParam != null && thisParam.startsWith(valID)) {
-                    String valParam = request.getParameter(thisParam);
-                    String valNum = thisParam.replace(valID, "");
-                    if (valParam != null && !valParam.equals("")) {
-                        obVals.put(valNum, valParam);
-                    }
+                if (request.getParameter("andRoles") != null) { orRoles = false; }
+                String[] roles = request.getParameterValues("role");
+                int numRoles = roles.length;
+                if (!orRoles) {
+                    prettyPrint.append("Social roles include all of the following: ");
+                } else {
+                    prettyPrint.append("Social roles is one of the following: ");
                 }
-            }
-            for (int i = 1; i <= numObsSearched; i++) {
-                String num = String.valueOf(i);
-                if (Util.basicSanitize(obKeys.get(num)) != null) {
-                    String thisKey = Util.basicSanitize(obKeys.get(num));
-                    prettyPrint.append("observation ");
-                    prettyPrint.append(thisKey);
-                    prettyPrint.append("<br/>");
-                    String qAsString = obQuery.toString().trim();
-                    System.out.println("Query As String" + qAsString);
-                    if (qAsString.length() >= 2 &&
-                        !qAsString.substring(qAsString.length() - 2).equals("&&")) {
-                        obQuery.append("&&");
-                    }
-                    obQuery.append("(observations.contains(observation" + num + ") && ");
-                    obQuery.append("observation" + num + ".name == " + Util.quote(thisKey.trim()));
-                    if (obVals.get(num) != null && !obVals.get(num).trim().equals("")) {
-                        String thisVal = Util.basicSanitize(obVals.get(num));
-                        prettyPrint.append(" is ");
-                        prettyPrint.append(thisVal);
-                        obQuery.append(" && observation" + num + ".value == " +
-                            Util.quote(thisVal.trim()));
-                    }
-                    obQuery.append(")");
+                for (int h = 0; h < numRoles; h++) {
+                    prettyPrint.append(roles[h] + "&nbsp;");
                 }
-                if (obQuery.length() > 0) {
-                    if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                        filter += " && ";
+                // logical OR the roles
+                for (int q = 0; q < rIndividuals.size(); q++) {
+                    MarkedIndividual tShark = (MarkedIndividual)rIndividuals.get(q);
+                    List<String> myRoles = myShepherd.getAllRoleNamesForMarkedIndividual(
+                        tShark.getIndividualID());
+                    if (orRoles) {
+                        // logical OR the role
+                        boolean hasRole = false;
+                        int f = 0;
+                        while (!hasRole && (f < numRoles)) {
+                            if (myRoles.contains(roles[f])) { hasRole = true; }
+                            f++;
+                        }
+                        if (!hasRole) {
+                            rIndividuals.remove(q);
+                            q--;
+                        }
+                    } else {
+                        // logical AND the roles
+                        boolean hasRole = true;
+                        int f = 0;
+                        while (hasRole && (f < numRoles)) {
+                            if (!myRoles.contains(roles[f])) { hasRole = false; }
+                            f++;
+                        }
+                        if (!hasRole) {
+                            rIndividuals.remove(q);
+                            q--;
+                        }
                     }
-                    filter += obQuery.toString();
-                    for (int j = 0; j < numObsSearched; j++) {
-                        QueryProcessor.updateJdoqlVariableDeclaration(jdoqlVariableDeclaration,
-                            "org.ecocean.Observation observation" + j);
+                }
+                if (rIndividuals.size() > 0) {
+                    String locIDFilter = " ( individual.individualID == \"" +
+                        rIndividuals.get(0).getId() + "\"  ";
+                    for (int j = 1; j < rIndividuals.size(); j++) {
+                        locIDFilter += " || individual.individualID == \"" +
+                            rIndividuals.get(j).getId() + "\"  ";
                     }
-                    System.out.println("ObQuery: " + obQuery);
-                    System.out.println("Filter? " + filter);
+                    locIDFilter = locIDFilter + " ) ";
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += locIDFilter;
+                    } else { filter += (" && " + locIDFilter); }
                 }
+                prettyPrint.append("<br />");
             }
-        }
-        // Tag Filters--------------------------------------------------------
-
-        StringBuilder metalTagFilter = new StringBuilder();
-        Enumeration<String> parameterNames = request.getParameterNames();
-        int metalTagsInQuery = 0;
-        while (parameterNames.hasMoreElements()) {
-            String parameterName = parameterNames.nextElement();
-            final String metalTagPrefix = "metalTag(";
-            if (parameterName.startsWith(metalTagPrefix)) {
-                String metalTagLocation = parameterName.substring(metalTagPrefix.length(),
-                    parameterName.lastIndexOf(')'));
-                String value = request.getParameter(parameterName);
-                if (value != null && value.trim().length() > 0) {
-                    prettyPrint.append("metal tag ");
-                    prettyPrint.append(metalTagLocation);
-                    prettyPrint.append(" is ");
-                    prettyPrint.append(value);
-                    prettyPrint.append("<br/>");
-                    String metalTagVar = "metalTag" + metalTagsInQuery++;
-                    metalTagFilter.append("(metalTags.contains(" + metalTagVar + ") && ");
-                    metalTagFilter.append(metalTagVar + ".location == " +
-                        Util.quote(metalTagLocation));
-                    String jdoParam = "tagNumber" + metalTagsInQuery;
-                    metalTagFilter.append(" && " + metalTagVar + ".tagNumber == " + jdoParam + ")");
-                    paramMap.put(jdoParam, value);
-                    parameterDeclaration = updateParametersDeclaration(parameterDeclaration,
-                        "String " + jdoParam);
+            // patterningCode filters-------------------------------------------------
+            String[] patterningCodes = request.getParameterValues("patterningCodeField");
+            if ((patterningCodes != null) && (!patterningCodes[0].equals("None"))) {
+                prettyPrint.append("Patterning code is one of the following: ");
+                int kwLength = patterningCodes.length;
+                String patterningCodeFilter = "(";
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String kwParam = patterningCodes[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (patterningCodeFilter.equals("(")) {
+                            patterningCodeFilter += " patterningCode == \"" + kwParam + "\"";
+                        } else {
+                            patterningCodeFilter += " || patterningCode == \"" + kwParam + "\"";
+                        }
+                        prettyPrint.append(kwParam + " ");
+                    }
                 }
+                patterningCodeFilter += " )";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += patterningCodeFilter;
+                } else { filter += (" && " + patterningCodeFilter); }
+                prettyPrint.append("<br />");
             }
-        }
-        if (metalTagFilter.length() > 0) {
-            if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += " && ";
-            }
-            filter += metalTagFilter.toString();
-            for (int i = 0; i < metalTagsInQuery; i++) {
-                QueryProcessor.updateJdoqlVariableDeclaration(jdoqlVariableDeclaration,
-                    "org.ecocean.tag.MetalTag metalTag" + i);
-            }
-        }
-        // We don't do metal tags (above) in processTagFilters because of the dependency on jdoqlVariableDeclaration
-        String tagFilters = processTagFilters(request, prettyPrint);
-        if (tagFilters.length() > 0) {
-            if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += " && ";
-            }
-            filter += tagFilters.toString();
-        }
-        // end tag filters----------------------------------------------------
-        // lifeStage filters-------------------------------------------------
-        String[] stages = request.getParameterValues("lifeStageField");
-        if ((stages != null) && (!stages[0].equals("None")) && (!stages[0].equals(""))) {
-            prettyPrint.append("lifeStage is one of the following: ");
-            int kwLength = stages.length;
-            String stageFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = stages[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (stageFilter.equals("(")) {
-                        stageFilter += " lifeStage == \"" + kwParam + "\"";
-                    } else {
-                        stageFilter += " || lifeStage == \"" + kwParam + "\"";
+            // end patterningCode filters-----------------------------------------------
+            // behavior filters-------------------------------------------------
+            String[] behaviors = request.getParameterValues("behaviorField");
+            if ((behaviors != null) && (!behaviors[0].equals("None"))) {
+                prettyPrint.append("behaviorField is one of the following: ");
+                int kwLength = behaviors.length;
+                String locIDFilter = "(";
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String kwParam = behaviors[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (locIDFilter.equals("(")) {
+                            locIDFilter += " behavior == \"" + kwParam + "\"";
+                        } else {
+                            locIDFilter += " || behavior == \"" + kwParam + "\"";
+                        }
+                        prettyPrint.append(kwParam + " ");
                     }
-                    prettyPrint.append(kwParam + " ");
                 }
+                locIDFilter += " )";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += locIDFilter;
+                } else { filter += (" && " + locIDFilter); }
+                prettyPrint.append("<br />");
             }
-            stageFilter += " ) ";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += stageFilter;
-            } else { filter += (" && " + stageFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end lifeStage filters
-        // country filters-------------------------------------------------
-        String[] countries = request.getParameterValues("country");
-        if ((countries != null) && (!countries[0].equals("None")) && (!countries[0].equals(""))) {
-            prettyPrint.append("Country is one of the following: ");
-            int kwLength = countries.length;
-            String stageFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = countries[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (stageFilter.equals("(")) {
-                        stageFilter += " country == \"" + kwParam + "\"";
-                    } else {
-                        stageFilter += " || country == \"" + kwParam + "\"";
-                    }
-                    prettyPrint.append(kwParam + " ");
+            // end behavior filters-----------------------------------------------
+            // begin observation filters -----------------------------------------
+            boolean hasValue = false;
+            if (request.getParameter("numSearchedObs") != null) {
+                if (request.getParameter("observationKey1") != null &&
+                    !request.getParameter("observationKey1").equals("")) {
+                    hasValue = true;
                 }
             }
-            stageFilter += " ) ";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += stageFilter;
-            } else { filter += (" && " + stageFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end country filters
-        // Measurement filters-----------------------------------------------
-        List<MeasurementDesc> measurementDescs = Util.findMeasurementDescs("en", context);
-        String measurementPrefix = "measurement";
-        StringBuilder measurementFilter = new StringBuilder(); // "( collectedData.contains(measurement) && (");
-        boolean atLeastOneMeasurement = false;
-        int measurementsInQuery = 0;
-        for (MeasurementDesc measurementDesc : measurementDescs) {
-            String valueParamName = measurementPrefix + measurementDesc.getType() + "(value)";
-            String value = request.getParameter(valueParamName);
-            if (value != null) {
-                value = value.trim();
-                if (value.length() > 0) {
-                    String operatorParamName = measurementPrefix + measurementDesc.getType() +
-                        "(operator)";
-                    String operatorParamValue = request.getParameter(operatorParamName);
-                    if (operatorParamValue == null) {
-                        operatorParamValue = "";
+            Enumeration<String> allParams = request.getParameterNames();
+            if (allParams != null && hasValue) {
+                String keyID = "observationKey";
+                String valID = "observationValue";
+                HashMap<String, String> obKeys = new HashMap<>();
+                HashMap<String, String> obVals = new HashMap<>();
+                StringBuilder obQuery = new StringBuilder();
+                int numObsSearched = 0;
+                while (allParams.hasMoreElements()) {
+                    String thisParam = allParams.nextElement();
+                    if (thisParam != null && thisParam.startsWith(keyID)) {
+                        numObsSearched++;
+                        System.out.println("Num Obs Searched? " + numObsSearched);
+                        String keyParam = request.getParameter(thisParam);
+                        String keyNum = thisParam.replace(keyID, "");
+                        if (keyParam != null && !keyParam.equals("")) {
+                            obKeys.put(keyNum, keyParam);
+                        }
                     }
-                    String operator = null;
-                    if ("gt".equals(operatorParamValue)) {
-                        operator = ">";
-                    } else if ("lt".equals(operatorParamValue)) {
-                        operator = "<";
-                    } else if ("eq".equals(operatorParamValue)) {
-                        operator = "==";
-                    } else if ("gteq".equals(operatorParamValue)) {
-                        operator = ">=";
-                    } else if ("lteq".equals(operatorParamValue)) {
-                        operator = "<=";
+                    if (thisParam != null && thisParam.startsWith(valID)) {
+                        String valParam = request.getParameter(thisParam);
+                        String valNum = thisParam.replace(valID, "");
+                        if (valParam != null && !valParam.equals("")) {
+                            obVals.put(valNum, valParam);
+                        }
                     }
-                    if (operator != null) {
-                        prettyPrint.append(measurementDesc.getUnitsLabel());
-                        prettyPrint.append(" is ");
-                        prettyPrint.append(operator);
-                        prettyPrint.append(value);
+                }
+                for (int i = 1; i <= numObsSearched; i++) {
+                    String num = String.valueOf(i);
+                    if (Util.basicSanitize(obKeys.get(num)) != null) {
+                        String thisKey = Util.basicSanitize(obKeys.get(num));
+                        prettyPrint.append("observation ");
+                        prettyPrint.append(thisKey);
                         prettyPrint.append("<br/>");
-                        if (atLeastOneMeasurement) {
-                            measurementFilter.append("&&");
+                        String qAsString = obQuery.toString().trim();
+                        System.out.println("Query As String" + qAsString);
+                        if (qAsString.length() >= 2 &&
+                            !qAsString.substring(qAsString.length() - 2).equals("&&")) {
+                            obQuery.append("&&");
+                        }
+                        obQuery.append("(observations.contains(observation" + num + ") && ");
+                        obQuery.append("observation" + num + ".name == " +
+                            Util.quote(thisKey.trim()));
+                        if (obVals.get(num) != null && !obVals.get(num).trim().equals("")) {
+                            String thisVal = Util.basicSanitize(obVals.get(num));
+                            prettyPrint.append(" is ");
+                            prettyPrint.append(thisVal);
+                            obQuery.append(" && observation" + num + ".value == " +
+                                Util.quote(thisVal.trim()));
                         }
-                        String measurementVar = "measurement" + measurementsInQuery++;
-                        measurementFilter.append("measurements.contains(" + measurementVar +
-                            ") && ");
-                        measurementFilter.append("(" + measurementVar + ".value " + operator + " " +
-                            value + ")");
-                        measurementFilter.append(" && (" + measurementVar + ".type == ");
-                        measurementFilter.append("\"" + measurementDesc.getType() + "\")");
-                        atLeastOneMeasurement = true;
+                        obQuery.append(")");
+                    }
+                    if (obQuery.length() > 0) {
+                        if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                            filter += " && ";
+                        }
+                        filter += obQuery.toString();
+                        for (int j = 0; j < numObsSearched; j++) {
+                            QueryProcessor.updateJdoqlVariableDeclaration(jdoqlVariableDeclaration,
+                                "org.ecocean.Observation observation" + j);
+                        }
+                        System.out.println("ObQuery: " + obQuery);
+                        System.out.println("Filter? " + filter);
                     }
                 }
             }
-        }
-        if (atLeastOneMeasurement) {
-            if (jdoqlVariableDeclaration.length() > 0) {
-                jdoqlVariableDeclaration += ";";
-            } else {
-                jdoqlVariableDeclaration = " VARIABLES ";
-            }
-            for (int i = 0; i < measurementsInQuery; i++) {
-                if (i > 0) {
-                    jdoqlVariableDeclaration += "; ";
-                }
-                jdoqlVariableDeclaration += " org.ecocean.Measurement measurement" + i;
-            }
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += measurementFilter.toString();
-            } else {
-                filter += (" && " + measurementFilter.toString());
-            }
-        }
-        // end measurement filters
-        // BiologicalMeasurement filters-----------------------------------------------
-        List<MeasurementDesc> bioMeasurementDescs = Util.findBiologicalMeasurementDescs("en",
-            context);
-        String bioMeasurementPrefix = "biomeasurement";
-        StringBuilder bioMeasurementFilter = new StringBuilder();
-        bioMeasurementFilter.append("tissueSamples.contains(dce322) ");
-        boolean bioAtLeastOneMeasurement = false;
-        int bioMeasurementsInQuery = 0;
-        for (MeasurementDesc measurementDesc : bioMeasurementDescs) {
-            String valueParamName = bioMeasurementPrefix + measurementDesc.getType() + "(value)";
-            String value = request.getParameter(valueParamName);
-            if (value != null) {
-                value = value.trim();
-                if (value.length() > 0) {
-                    String operatorParamName = bioMeasurementPrefix + measurementDesc.getType() +
-                        "(operator)";
-                    String operatorParamValue = request.getParameter(operatorParamName);
-                    if (operatorParamValue == null) {
-                        operatorParamValue = "";
-                    }
-                    String operator = null;
-                    if ("gt".equals(operatorParamValue)) {
-                        operator = ">";
-                    } else if ("lt".equals(operatorParamValue)) {
-                        operator = "<";
-                    } else if ("eq".equals(operatorParamValue)) {
-                        operator = "==";
-                    } else if ("gteq".equals(operatorParamValue)) {
-                        operator = ">=";
-                    } else if ("lteq".equals(operatorParamValue)) {
-                        operator = "<=";
-                    }
-                    if (operator != null) {
-                        prettyPrint.append("Biological/chemical measurement " +
-                            measurementDesc.getType());
+            // Tag Filters--------------------------------------------------------
+
+            StringBuilder metalTagFilter = new StringBuilder();
+            Enumeration<String> parameterNames = request.getParameterNames();
+            int metalTagsInQuery = 0;
+            while (parameterNames.hasMoreElements()) {
+                String parameterName = parameterNames.nextElement();
+                final String metalTagPrefix = "metalTag(";
+                if (parameterName.startsWith(metalTagPrefix)) {
+                    String metalTagLocation = parameterName.substring(metalTagPrefix.length(),
+                        parameterName.lastIndexOf(')'));
+                    String value = request.getParameter(parameterName);
+                    if (value != null && value.trim().length() > 0) {
+                        prettyPrint.append("metal tag ");
+                        prettyPrint.append(metalTagLocation);
                         prettyPrint.append(" is ");
-                        prettyPrint.append(operator);
                         prettyPrint.append(value);
                         prettyPrint.append("<br/>");
-                        if (bioAtLeastOneMeasurement) {
-                            bioMeasurementFilter.append("&&");
-                        }
-                        String measurementVar = "biomeasurement" + bioMeasurementsInQuery++;
-                        bioMeasurementFilter.append(" & dce322.analyses.contains(" +
-                            measurementVar + ")  ");
-                        bioMeasurementFilter.append(" && ( " + measurementVar + ".value " +
-                            operator + " " + value + " )");
-                        bioMeasurementFilter.append(" && ( " + measurementVar +
-                            ".measurementType == ");
-                        bioMeasurementFilter.append("\"" + measurementDesc.getType() + "\" )");
-                        bioAtLeastOneMeasurement = true;
+                        String metalTagVar = "metalTag" + metalTagsInQuery++;
+                        metalTagFilter.append("(metalTags.contains(" + metalTagVar + ") && ");
+                        metalTagFilter.append(metalTagVar + ".location == " +
+                            Util.quote(metalTagLocation));
+                        String jdoParam = "tagNumber" + metalTagsInQuery;
+                        metalTagFilter.append(" && " + metalTagVar + ".tagNumber == " + jdoParam +
+                            ")");
+                        paramMap.put(jdoParam, value);
+                        parameterDeclaration = updateParametersDeclaration(parameterDeclaration,
+                            "String " + jdoParam);
                     }
                 }
             }
-        }
-        if (bioAtLeastOneMeasurement) {
-            if (jdoqlVariableDeclaration.length() > 0) {
-                jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce322;";
-            } else {
-                jdoqlVariableDeclaration = " VARIABLES org.ecocean.genetics.TissueSample dce322;";
-            }
-            for (int i = 0; i < bioMeasurementsInQuery; i++) {
-                if (i > 0) {
-                    jdoqlVariableDeclaration += "; ";
+            if (metalTagFilter.length() > 0) {
+                if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += " && ";
+                }
+                filter += metalTagFilter.toString();
+                for (int i = 0; i < metalTagsInQuery; i++) {
+                    QueryProcessor.updateJdoqlVariableDeclaration(jdoqlVariableDeclaration,
+                        "org.ecocean.tag.MetalTag metalTag" + i);
                 }
-                jdoqlVariableDeclaration +=
-                    "org.ecocean.genetics.BiologicalMeasurement biomeasurement" + i;
-            }
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += bioMeasurementFilter.toString();
-            } else {
-                filter += (" && " + bioMeasurementFilter.toString());
             }
-        }
-        // end BiologicalMeasurement filters
-        // verbatimEventDate filters-------------------------------------------------
-        String[] verbatimEventDates = request.getParameterValues("verbatimEventDateField");
-        if ((verbatimEventDates != null) && (!verbatimEventDates[0].equals("None"))) {
-            prettyPrint.append("verbatimEventDateField is one of the following: ");
-            int kwLength = verbatimEventDates.length;
-            String locIDFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = verbatimEventDates[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (locIDFilter.equals("(")) {
-                        locIDFilter += " verbatimEventDate == \"" + kwParam + "\"";
-                    } else {
-                        locIDFilter += " || verbatimEventDate == \"" + kwParam + "\"";
+            // We don't do metal tags (above) in processTagFilters because of the dependency on jdoqlVariableDeclaration
+            String tagFilters = processTagFilters(request, prettyPrint);
+            if (tagFilters.length() > 0) {
+                if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += " && ";
+                }
+                filter += tagFilters.toString();
+            }
+            // end tag filters----------------------------------------------------
+            // lifeStage filters-------------------------------------------------
+            String[] stages = request.getParameterValues("lifeStageField");
+            if ((stages != null) && (!stages[0].equals("None")) && (!stages[0].equals(""))) {
+                prettyPrint.append("lifeStage is one of the following: ");
+                int kwLength = stages.length;
+                String stageFilter = "(";
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String kwParam = stages[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (stageFilter.equals("(")) {
+                            stageFilter += " lifeStage == \"" + kwParam + "\"";
+                        } else {
+                            stageFilter += " || lifeStage == \"" + kwParam + "\"";
+                        }
+                        prettyPrint.append(kwParam + " ");
                     }
-                    prettyPrint.append(kwParam + " ");
                 }
+                stageFilter += " ) ";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += stageFilter;
+                } else { filter += (" && " + stageFilter); }
+                prettyPrint.append("<br />");
             }
-            locIDFilter += " )";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += locIDFilter;
-            } else { filter += (" && " + locIDFilter); }
-            prettyPrint.append("<br />");
-        }
-        // end verbatimEventDate filters-----------------------------------------------
-        // hasTissueSample filters-------------------------------------------------
-        if (request.getParameter("hasTissueSample") != null) {
-            prettyPrint.append("Has tissue sample.");
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "tissueSamples.contains(dce)";
-            } else if (filter.indexOf("tissueSamples.contains(dce)") == -1) {
-                filter += (" && tissueSamples.contains(dce) ");
+            // end lifeStage filters
+            // country filters-------------------------------------------------
+            String[] countries = request.getParameterValues("country");
+            if ((countries != null) && (!countries[0].equals("None")) &&
+                (!countries[0].equals(""))) {
+                prettyPrint.append("Country is one of the following: ");
+                int kwLength = countries.length;
+                String stageFilter = "(";
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String kwParam = countries[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (stageFilter.equals("(")) {
+                            stageFilter += " country == \"" + kwParam + "\"";
+                        } else {
+                            stageFilter += " || country == \"" + kwParam + "\"";
+                        }
+                        prettyPrint.append(kwParam + " ");
+                    }
+                }
+                stageFilter += " ) ";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += stageFilter;
+                } else { filter += (" && " + stageFilter); }
+                prettyPrint.append("<br />");
             }
-            prettyPrint.append("<br />");
-            if (jdoqlVariableDeclaration.equals("")) {
-                jdoqlVariableDeclaration = " VARIABLES org.ecocean.genetics.TissueSample dce";
-            } else if (!jdoqlVariableDeclaration.contains(
-                "org.ecocean.genetics.TissueSample dce")) {
-                jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce";
+            // end country filters
+            // Measurement filters-----------------------------------------------
+            List<MeasurementDesc> measurementDescs = Util.findMeasurementDescs("en", context);
+            String measurementPrefix = "measurement";
+            StringBuilder measurementFilter = new StringBuilder(); // "( collectedData.contains(measurement) && (");
+            boolean atLeastOneMeasurement = false;
+            int measurementsInQuery = 0;
+            for (MeasurementDesc measurementDesc : measurementDescs) {
+                String valueParamName = measurementPrefix + measurementDesc.getType() + "(value)";
+                String value = request.getParameter(valueParamName);
+                if (value != null) {
+                    value = value.trim();
+                    if (value.length() > 0) {
+                        String operatorParamName = measurementPrefix + measurementDesc.getType() +
+                            "(operator)";
+                        String operatorParamValue = request.getParameter(operatorParamName);
+                        if (operatorParamValue == null) {
+                            operatorParamValue = "";
+                        }
+                        String operator = null;
+                        if ("gt".equals(operatorParamValue)) {
+                            operator = ">";
+                        } else if ("lt".equals(operatorParamValue)) {
+                            operator = "<";
+                        } else if ("eq".equals(operatorParamValue)) {
+                            operator = "==";
+                        } else if ("gteq".equals(operatorParamValue)) {
+                            operator = ">=";
+                        } else if ("lteq".equals(operatorParamValue)) {
+                            operator = "<=";
+                        }
+                        if (operator != null) {
+                            prettyPrint.append(measurementDesc.getUnitsLabel());
+                            prettyPrint.append(" is ");
+                            prettyPrint.append(operator);
+                            prettyPrint.append(value);
+                            prettyPrint.append("<br/>");
+                            if (atLeastOneMeasurement) {
+                                measurementFilter.append("&&");
+                            }
+                            String measurementVar = "measurement" + measurementsInQuery++;
+                            measurementFilter.append("measurements.contains(" + measurementVar +
+                                ") && ");
+                            measurementFilter.append("(" + measurementVar + ".value " + operator +
+                                " " + value + ")");
+                            measurementFilter.append(" && (" + measurementVar + ".type == ");
+                            measurementFilter.append("\"" + measurementDesc.getType() + "\")");
+                            atLeastOneMeasurement = true;
+                        }
+                    }
+                }
             }
-        }
-        // end hasTissueSample filters-----------------------------------------------
-        // TissueSample sampleID filters-------------------------------------------------
-        if ((request.getParameter("tissueSampleID") != null) &&
-            (!request.getParameter("tissueSampleID").trim().equals(""))) {
-            prettyPrint.append("Has biological sample with ID: " +
-                request.getParameter("tissueSampleID"));
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter +=
-                    "tissueSamples.contains(dce123) && (dce123.sampleID.toLowerCase().indexOf('" +
-                    request.getParameter("tissueSampleID").trim().toLowerCase() + "') != -1)";
-            } else if (filter.indexOf("tissueSamples.contains(dce)") == -1) {
-                filter +=
-                    (
-                    " && tissueSamples.contains(dce123) && (dce123.sampleID.toLowerCase().indexOf('"
-                    + request.getParameter("tissueSampleID").trim().toLowerCase() + "') != -1) ");
-            }
-            prettyPrint.append("<br />");
-            if (jdoqlVariableDeclaration.equals("")) {
-                jdoqlVariableDeclaration = " VARIABLES org.ecocean.genetics.TissueSample dce123";
-            } else if (!jdoqlVariableDeclaration.contains(
-                "org.ecocean.genetics.TissueSample dce123")) {
-                jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce123";
-            }
-        }
-        // end hasTissueSample filters-----------------------------------------------
-        // hasPhoto filters-------------------------------------------------
-        if (request.getParameter("hasPhoto") != null) {
-            prettyPrint.append("Has at least one MediaAsset.");
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter +=
-                    "annotations.contains(dce15) && dce15.features.contains(feat15) && feat15.asset != null";
-            } else if (filter.indexOf("annotations.contains(dce15)") == -1) {
-                filter +=
-                    (
-                    " && annotations.contains(dce15) && dce15.features.contains(feat15) && feat15.asset != null");
-            }
-            prettyPrint.append("<br />");
-            if (jdoqlVariableDeclaration.equals("")) {
-                jdoqlVariableDeclaration = " VARIABLES org.ecocean.Annotation dce15";
-            } else if (!jdoqlVariableDeclaration.contains("org.ecocean.Annotation dce15")) {
-                jdoqlVariableDeclaration += ";org.ecocean.Annotation dce15";
-            }
-            if (jdoqlVariableDeclaration.equals("")) {
-                jdoqlVariableDeclaration = " VARIABLES org.ecocean.media.Feature feat15";
-            } else if (!jdoqlVariableDeclaration.contains("org.ecocean.media.Feature feat15")) {
-                jdoqlVariableDeclaration += ";org.ecocean.media.Feature feat15";
+            if (atLeastOneMeasurement) {
+                if (jdoqlVariableDeclaration.length() > 0) {
+                    jdoqlVariableDeclaration += ";";
+                } else {
+                    jdoqlVariableDeclaration = " VARIABLES ";
+                }
+                for (int i = 0; i < measurementsInQuery; i++) {
+                    if (i > 0) {
+                        jdoqlVariableDeclaration += "; ";
+                    }
+                    jdoqlVariableDeclaration += " org.ecocean.Measurement measurement" + i;
+                }
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += measurementFilter.toString();
+                } else {
+                    filter += (" && " + measurementFilter.toString());
+                }
             }
-        }
-        // end hasPhoto filters-----------------------------------------------
-        // hasSpots filters-------------------------------------------------
-        if (request.getParameter("hasSpots") != null) {
-            prettyPrint.append("Has patterning points.");
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "spots != null ";
-            } else if (filter.indexOf("spots != null") == -1) { filter += (" && spots !=null "); }
-            prettyPrint.append("<br />");
-        }
-        // end hasSpots filters-----------------------------------------------
-        // has no Spots filters-------------------------------------------------
-        if (request.getParameter("hasNoSpots") != null) {
-            prettyPrint.append("Has no patterning points.");
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "spots == null ";
-            } else if (filter.indexOf("spots == null") == -1) { filter += (" && spots == null "); }
-            prettyPrint.append("<br />");
-        }
-        // end has no Spots filters-----------------------------------------------
-        // filter for encounters of MarkedIndividuals that have been resighted------------------------------------------
-        if ((request.getParameter("resightOnly") != null) &&
-            (request.getParameter("numResights") != null)) {
-            int numResights = 1;
-
-            try {
-                numResights = (new Integer(request.getParameter("numResights"))).intValue();
-                prettyPrint.append("numResights for related Marked Individual is >= " +
-                    numResights + ".<br />");
-            } catch (NumberFormatException nfe) { nfe.printStackTrace(); }
-            String localFilter =
-                "markedindy.encounters.contains(this) && markedindy.encounters.size() >= " +
-                numResights + " ";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += localFilter;
-            } else { filter += (" && " + localFilter); }
-            if (jdoqlVariableDeclaration.equals("")) {
-                jdoqlVariableDeclaration = " VARIABLES org.ecocean.MarkedIndividual markedindy";
-            } else { jdoqlVariableDeclaration += ";org.ecocean.MarkedIndividual markedindy"; }
-        }
-        // end if resightOnly--------------------------------------------------------------------------------------
-        // keyword filters-------------------------------------------------
-
-        // shared var between keywords and labeledKeywords
-        int nUnlabeledKeywords = 0;
-
-        myShepherd.beginDBTransaction();
-        String[] keywords = request.getParameterValues("keyword");
-        String photoKeywordOperator = "&&";
-        if ((request.getParameter("photoKeywordOperator") != null) &&
-            (request.getParameter("photoKeywordOperator").equals("_OR_"))) {
-            photoKeywordOperator = "||";
-        }
-        if ((keywords != null) && (!keywords[0].equals("None"))) {
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) { filter += "("; } else {
-                filter += " && (";
+            // end measurement filters
+            // BiologicalMeasurement filters-----------------------------------------------
+            List<MeasurementDesc> bioMeasurementDescs = Util.findBiologicalMeasurementDescs("en",
+                context);
+            String bioMeasurementPrefix = "biomeasurement";
+            StringBuilder bioMeasurementFilter = new StringBuilder();
+            bioMeasurementFilter.append("tissueSamples.contains(dce322) ");
+            boolean bioAtLeastOneMeasurement = false;
+            int bioMeasurementsInQuery = 0;
+            for (MeasurementDesc measurementDesc : bioMeasurementDescs) {
+                String valueParamName = bioMeasurementPrefix + measurementDesc.getType() +
+                    "(value)";
+                String value = request.getParameter(valueParamName);
+                if (value != null) {
+                    value = value.trim();
+                    if (value.length() > 0) {
+                        String operatorParamName = bioMeasurementPrefix +
+                            measurementDesc.getType() + "(operator)";
+                        String operatorParamValue = request.getParameter(operatorParamName);
+                        if (operatorParamValue == null) {
+                            operatorParamValue = "";
+                        }
+                        String operator = null;
+                        if ("gt".equals(operatorParamValue)) {
+                            operator = ">";
+                        } else if ("lt".equals(operatorParamValue)) {
+                            operator = "<";
+                        } else if ("eq".equals(operatorParamValue)) {
+                            operator = "==";
+                        } else if ("gteq".equals(operatorParamValue)) {
+                            operator = ">=";
+                        } else if ("lteq".equals(operatorParamValue)) {
+                            operator = "<=";
+                        }
+                        if (operator != null) {
+                            prettyPrint.append("Biological/chemical measurement " +
+                                measurementDesc.getType());
+                            prettyPrint.append(" is ");
+                            prettyPrint.append(operator);
+                            prettyPrint.append(value);
+                            prettyPrint.append("<br/>");
+                            if (bioAtLeastOneMeasurement) {
+                                bioMeasurementFilter.append("&&");
+                            }
+                            String measurementVar = "biomeasurement" + bioMeasurementsInQuery++;
+                            bioMeasurementFilter.append(" & dce322.analyses.contains(" +
+                                measurementVar + ")  ");
+                            bioMeasurementFilter.append(" && ( " + measurementVar + ".value " +
+                                operator + " " + value + " )");
+                            bioMeasurementFilter.append(" && ( " + measurementVar +
+                                ".measurementType == ");
+                            bioMeasurementFilter.append("\"" + measurementDesc.getType() + "\" )");
+                            bioAtLeastOneMeasurement = true;
+                        }
+                    }
+                }
             }
-            if ((request.getParameter("photoKeywordOperator") != null) &&
-                (request.getParameter("photoKeywordOperator").equals("_OR_"))) {
-                prettyPrint.append("MediaAsset keyword is any one of the following: ");
-            } else {
-                prettyPrint.append("All of these MediaAsset keywords are applied: ");
+            if (bioAtLeastOneMeasurement) {
+                if (jdoqlVariableDeclaration.length() > 0) {
+                    jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce322;";
+                } else {
+                    jdoqlVariableDeclaration =
+                        " VARIABLES org.ecocean.genetics.TissueSample dce322;";
+                }
+                for (int i = 0; i < bioMeasurementsInQuery; i++) {
+                    if (i > 0) {
+                        jdoqlVariableDeclaration += "; ";
+                    }
+                    jdoqlVariableDeclaration +=
+                        "org.ecocean.genetics.BiologicalMeasurement biomeasurement" + i;
+                }
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += bioMeasurementFilter.toString();
+                } else {
+                    filter += (" && " + bioMeasurementFilter.toString());
+                }
             }
-            int kwLength = keywords.length;
-            nUnlabeledKeywords += kwLength;
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+            // end BiologicalMeasurement filters
+            // verbatimEventDate filters-------------------------------------------------
+            String[] verbatimEventDates = request.getParameterValues("verbatimEventDateField");
+            if ((verbatimEventDates != null) && (!verbatimEventDates[0].equals("None"))) {
+                prettyPrint.append("verbatimEventDateField is one of the following: ");
+                int kwLength = verbatimEventDates.length;
                 String locIDFilter = "(";
-                String kwParam = keywords[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (locIDFilter.equals("(")) {
-                        locIDFilter += " word" + kwIter + ".indexname == \"" + kwParam + "\" ";
-                    } else {
-                        locIDFilter += " " + photoKeywordOperator + " word" + kwIter +
-                            ".indexname == \"" + kwParam + "\" ";
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String kwParam = verbatimEventDates[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (locIDFilter.equals("(")) {
+                            locIDFilter += " verbatimEventDate == \"" + kwParam + "\"";
+                        } else {
+                            locIDFilter += " || verbatimEventDate == \"" + kwParam + "\"";
+                        }
+                        prettyPrint.append(kwParam + " ");
                     }
-                    Keyword kw = myShepherd.getKeyword(kwParam.trim());
-                    prettyPrint.append("\"" + kw.getReadableName() + "\" ");
                 }
                 locIDFilter += " )";
-                if (filter.indexOf("annotations.contains(photo" + kwIter + ")") == -1) {
-                    if (kwIter > 0) { filter += " " + photoKeywordOperator + " "; }
-                    filter += " ( annotations.contains(photo" + kwIter + ")";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += locIDFilter;
+                } else { filter += (" && " + locIDFilter); }
+                prettyPrint.append("<br />");
+            }
+            // end verbatimEventDate filters-----------------------------------------------
+            // hasTissueSample filters-------------------------------------------------
+            if (request.getParameter("hasTissueSample") != null) {
+                prettyPrint.append("Has tissue sample.");
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += "tissueSamples.contains(dce)";
+                } else if (filter.indexOf("tissueSamples.contains(dce)") == -1) {
+                    filter += (" && tissueSamples.contains(dce) ");
                 }
-                if (filter.indexOf("photo" + kwIter + ".features.contains(feat" + kwIter + ")") ==
-                    -1) {
-                    filter += " && photo" + kwIter + ".features.contains(feat" + kwIter + ")";
+                prettyPrint.append("<br />");
+                if (jdoqlVariableDeclaration.equals("")) {
+                    jdoqlVariableDeclaration = " VARIABLES org.ecocean.genetics.TissueSample dce";
+                } else if (!jdoqlVariableDeclaration.contains(
+                    "org.ecocean.genetics.TissueSample dce")) {
+                    jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce";
                 }
-                if (filter.indexOf("feat" + kwIter + ".asset.keywords.contains(word" + kwIter +
-                    ")") == -1) {
-                    filter += " && feat" + kwIter + ".asset.keywords.contains(word" + kwIter + ")";
+            }
+            // end hasTissueSample filters-----------------------------------------------
+            // TissueSample sampleID filters-------------------------------------------------
+            if ((request.getParameter("tissueSampleID") != null) &&
+                (!request.getParameter("tissueSampleID").trim().equals(""))) {
+                prettyPrint.append("Has biological sample with ID: " +
+                    request.getParameter("tissueSampleID"));
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter +=
+                        "tissueSamples.contains(dce123) && (dce123.sampleID.toLowerCase().indexOf('"
+                        + request.getParameter("tissueSampleID").trim().toLowerCase() + "') != -1)";
+                } else if (filter.indexOf("tissueSamples.contains(dce)") == -1) {
+                    filter +=
+                        (
+                        " && tissueSamples.contains(dce123) && (dce123.sampleID.toLowerCase().indexOf('"
+                        + request.getParameter("tissueSampleID").trim().toLowerCase() +
+                        "') != -1) ");
                 }
-                filter += (" && " + locIDFilter + ")");
-                if ((kwIter == 0) && (jdoqlVariableDeclaration.equals(""))) {
-                    jdoqlVariableDeclaration = " VARIABLES ";
+                prettyPrint.append("<br />");
+                if (jdoqlVariableDeclaration.equals("")) {
+                    jdoqlVariableDeclaration =
+                        " VARIABLES org.ecocean.genetics.TissueSample dce123";
+                } else if (!jdoqlVariableDeclaration.contains(
+                    "org.ecocean.genetics.TissueSample dce123")) {
+                    jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce123";
                 }
-                if (kwIter > 0) { jdoqlVariableDeclaration += ";"; }
-                if (!jdoqlVariableDeclaration.contains("org.ecocean.Annotation photo" + kwIter)) {
-                    jdoqlVariableDeclaration += "org.ecocean.Annotation photo" + kwIter;
+            }
+            // end hasTissueSample filters-----------------------------------------------
+            // hasPhoto filters-------------------------------------------------
+            if (request.getParameter("hasPhoto") != null) {
+                prettyPrint.append("Has at least one MediaAsset.");
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter +=
+                        "annotations.contains(dce15) && dce15.features.contains(feat15) && feat15.asset != null";
+                } else if (filter.indexOf("annotations.contains(dce15)") == -1) {
+                    filter +=
+                        (
+                        " && annotations.contains(dce15) && dce15.features.contains(feat15) && feat15.asset != null");
                 }
-                if (!jdoqlVariableDeclaration.contains("org.ecocean.Keyword word" + kwIter)) {
-                    jdoqlVariableDeclaration += ";org.ecocean.Keyword word" + kwIter;
+                prettyPrint.append("<br />");
+                if (jdoqlVariableDeclaration.equals("")) {
+                    jdoqlVariableDeclaration = " VARIABLES org.ecocean.Annotation dce15";
+                } else if (!jdoqlVariableDeclaration.contains("org.ecocean.Annotation dce15")) {
+                    jdoqlVariableDeclaration += ";org.ecocean.Annotation dce15";
                 }
-                if (!jdoqlVariableDeclaration.contains("org.ecocean.media.Feature feat" + kwIter)) {
-                    jdoqlVariableDeclaration += ";org.ecocean.media.Feature feat" + kwIter;
+                if (jdoqlVariableDeclaration.equals("")) {
+                    jdoqlVariableDeclaration = " VARIABLES org.ecocean.media.Feature feat15";
+                } else if (!jdoqlVariableDeclaration.contains("org.ecocean.media.Feature feat15")) {
+                    jdoqlVariableDeclaration += ";org.ecocean.media.Feature feat15";
                 }
             }
-            filter += " ) ";
+            // end hasPhoto filters-----------------------------------------------
+            // hasSpots filters-------------------------------------------------
+            if (request.getParameter("hasSpots") != null) {
+                prettyPrint.append("Has patterning points.");
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += "spots != null ";
+                } else if (filter.indexOf("spots != null") == -1) {
+                    filter += (" && spots !=null ");
+                }
+                prettyPrint.append("<br />");
+            }
+            // end hasSpots filters-----------------------------------------------
+            // has no Spots filters-------------------------------------------------
+            if (request.getParameter("hasNoSpots") != null) {
+                prettyPrint.append("Has no patterning points.");
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += "spots == null ";
+                } else if (filter.indexOf("spots == null") == -1) {
+                    filter += (" && spots == null ");
+                }
+                prettyPrint.append("<br />");
+            }
+            // end has no Spots filters-----------------------------------------------
+            // filter for encounters of MarkedIndividuals that have been resighted------------------------------------------
+            if ((request.getParameter("resightOnly") != null) &&
+                (request.getParameter("numResights") != null)) {
+                int numResights = 1;
 
-            prettyPrint.append("<br />");
-        }
-        myShepherd.rollbackDBTransaction();
-        myShepherd.closeDBTransaction();
+                try {
+                    numResights = (new Integer(request.getParameter("numResights"))).intValue();
+                    prettyPrint.append("numResights for related Marked Individual is >= " +
+                        numResights + ".<br />");
+                } catch (NumberFormatException nfe) { nfe.printStackTrace(); }
+                String localFilter =
+                    "markedindy.encounters.contains(this) && markedindy.encounters.size() >= " +
+                    numResights + " ";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += localFilter;
+                } else { filter += (" && " + localFilter); }
+                if (jdoqlVariableDeclaration.equals("")) {
+                    jdoqlVariableDeclaration = " VARIABLES org.ecocean.MarkedIndividual markedindy";
+                } else { jdoqlVariableDeclaration += ";org.ecocean.MarkedIndividual markedindy"; }
+            }
+            // end if resightOnly--------------------------------------------------------------------------------------
+            // keyword filters-------------------------------------------------
 
-        // end photo keyword filters-----------------------------------------------
-        // labeled keyword filters-------------------------------------------------
-        List<String> labels = ServletUtilities.getIndexedParameters("label", request);
-        System.out.println("LKW filter got labels " + labels);
-        int index = 0;
-        boolean multipleLabels = labels.size() > 1;
-        String lkwFilter = "(";
-        for (int labelN = 0; labelN < labels.size(); labelN++) {
-            int kwNum = labelN + nUnlabeledKeywords;
-            int annotNum = nUnlabeledKeywords; // this way all labeledKeyword queries apply to the same annotation
-            String label = labels.get(labelN);
-            if (labelN == 0) {
-                prettyPrint.append("Encounter has a photo with the LabeledKeyword label \"" +
-                    label + "\"");
-            } else {
-                prettyPrint.append(",<br>\t AND that photo has LabeledKeyword label \"" + label +
-                    "\"");
-                lkwFilter += " && ";
+            // shared var between keywords and labeledKeywords
+            int nUnlabeledKeywords = 0;
+            String[] keywords = request.getParameterValues("keyword");
+            String photoKeywordOperator = "&&";
+            if ((request.getParameter("photoKeywordOperator") != null) &&
+                (request.getParameter("photoKeywordOperator").equals("_OR_"))) {
+                photoKeywordOperator = "||";
             }
-            // ------ start variables and declarations for this LKW
-            String annotVar = "photo" + annotNum;
-            // we only add the annotation the first time, so all subsequent keywords still apply to that first annotation
-            // bc if we search for "fluke photo, of quality 3-5" we are talking about one photo with two keywords, not two photos
-            if (labelN == 0) {
-                lkwFilter += "annotations.contains(" + annotVar + ")";
-                jdoqlVariableDeclaration = QueryProcessor.updateJdoqlVariableDeclaration(
-                    jdoqlVariableDeclaration, "org.ecocean.Annotation " + annotVar);
+            if ((keywords != null) && (!keywords[0].equals("None"))) {
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += "(";
+                } else {
+                    filter += " && (";
+                }
+                if ((request.getParameter("photoKeywordOperator") != null) &&
+                    (request.getParameter("photoKeywordOperator").equals("_OR_"))) {
+                    prettyPrint.append("MediaAsset keyword is any one of the following: ");
+                } else {
+                    prettyPrint.append("All of these MediaAsset keywords are applied: ");
+                }
+                int kwLength = keywords.length;
+                nUnlabeledKeywords += kwLength;
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String locIDFilter = "(";
+                    String kwParam = keywords[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (locIDFilter.equals("(")) {
+                            locIDFilter += " word" + kwIter + ".indexname == \"" + kwParam + "\" ";
+                        } else {
+                            locIDFilter += " " + photoKeywordOperator + " word" + kwIter +
+                                ".indexname == \"" + kwParam + "\" ";
+                        }
+                        Keyword kw = myShepherd.getKeyword(kwParam.trim());
+                        prettyPrint.append("\"" + kw.getReadableName() + "\" ");
+                    }
+                    locIDFilter += " )";
+                    if (filter.indexOf("annotations.contains(photo" + kwIter + ")") == -1) {
+                        if (kwIter > 0) { filter += " " + photoKeywordOperator + " "; }
+                        filter += " ( annotations.contains(photo" + kwIter + ")";
+                    }
+                    if (filter.indexOf("photo" + kwIter + ".features.contains(feat" + kwIter +
+                        ")") == -1) {
+                        filter += " && photo" + kwIter + ".features.contains(feat" + kwIter + ")";
+                    }
+                    if (filter.indexOf("feat" + kwIter + ".asset.keywords.contains(word" + kwIter +
+                        ")") == -1) {
+                        filter += " && feat" + kwIter + ".asset.keywords.contains(word" + kwIter +
+                            ")";
+                    }
+                    filter += (" && " + locIDFilter + ")");
+                    if ((kwIter == 0) && (jdoqlVariableDeclaration.equals(""))) {
+                        jdoqlVariableDeclaration = " VARIABLES ";
+                    }
+                    if (kwIter > 0) { jdoqlVariableDeclaration += ";"; }
+                    if (!jdoqlVariableDeclaration.contains("org.ecocean.Annotation photo" +
+                        kwIter)) {
+                        jdoqlVariableDeclaration += "org.ecocean.Annotation photo" + kwIter;
+                    }
+                    if (!jdoqlVariableDeclaration.contains("org.ecocean.Keyword word" + kwIter)) {
+                        jdoqlVariableDeclaration += ";org.ecocean.Keyword word" + kwIter;
+                    }
+                    if (!jdoqlVariableDeclaration.contains("org.ecocean.media.Feature feat" +
+                        kwIter)) {
+                        jdoqlVariableDeclaration += ";org.ecocean.media.Feature feat" + kwIter;
+                    }
+                }
+                filter += " ) ";
+
+                prettyPrint.append("<br />");
             }
-            // only one feature per annotation, so only one feature for all keywords
-            String featVar = "feat" + annotNum;
-            if (labelN == 0) {
-                lkwFilter += " && ";
-                lkwFilter += annotVar + ".features.contains(" + featVar + ")";
+            // myShepherd.rollbackDBTransaction();
+            // myShepherd.closeDBTransaction();
+
+            // end photo keyword filters-----------------------------------------------
+            // labeled keyword filters-------------------------------------------------
+            List<String> labels = ServletUtilities.getIndexedParameters("label", request);
+            System.out.println("LKW filter got labels " + labels);
+            int index = 0;
+            boolean multipleLabels = labels.size() > 1;
+            String lkwFilter = "(";
+            for (int labelN = 0; labelN < labels.size(); labelN++) {
+                int kwNum = labelN + nUnlabeledKeywords;
+                int annotNum = nUnlabeledKeywords; // this way all labeledKeyword queries apply to the same annotation
+                String label = labels.get(labelN);
+                if (labelN == 0) {
+                    prettyPrint.append("Encounter has a photo with the LabeledKeyword label \"" +
+                        label + "\"");
+                } else {
+                    prettyPrint.append(",<br>\t AND that photo has LabeledKeyword label \"" +
+                        label + "\"");
+                    lkwFilter += " && ";
+                }
+                // ------ start variables and declarations for this LKW
+                String annotVar = "photo" + annotNum;
+                // we only add the annotation the first time, so all subsequent keywords still apply to that first annotation
+                // bc if we search for "fluke photo, of quality 3-5" we are talking about one photo with two keywords, not two photos
+                if (labelN == 0) {
+                    lkwFilter += "annotations.contains(" + annotVar + ")";
+                    jdoqlVariableDeclaration = QueryProcessor.updateJdoqlVariableDeclaration(
+                        jdoqlVariableDeclaration, "org.ecocean.Annotation " + annotVar);
+                }
+                // only one feature per annotation, so only one feature for all keywords
+                String featVar = "feat" + annotNum;
+                if (labelN == 0) {
+                    lkwFilter += " && ";
+                    lkwFilter += annotVar + ".features.contains(" + featVar + ")";
+                    jdoqlVariableDeclaration = QueryProcessor.updateJdoqlVariableDeclaration(
+                        jdoqlVariableDeclaration, "org.ecocean.media.Feature " + featVar);
+                }
+                String wordVar = "word" + kwNum;
+                if (labelN == 0) lkwFilter += " && ";
+                lkwFilter += featVar + ".asset.keywords.contains(" + wordVar + ")";
                 jdoqlVariableDeclaration = QueryProcessor.updateJdoqlVariableDeclaration(
-                    jdoqlVariableDeclaration, "org.ecocean.media.Feature " + featVar);
-            }
-            String wordVar = "word" + kwNum;
-            if (labelN == 0) lkwFilter += " && ";
-            lkwFilter += featVar + ".asset.keywords.contains(" + wordVar + ")";
-            jdoqlVariableDeclaration = QueryProcessor.updateJdoqlVariableDeclaration(
-                jdoqlVariableDeclaration, "org.ecocean.LabeledKeyword " + wordVar);
-            // ------ done with variables and declarations for this LKW
+                    jdoqlVariableDeclaration, "org.ecocean.LabeledKeyword " + wordVar);
+                // ------ done with variables and declarations for this LKW
 
-            lkwFilter += " && " + wordVar + ".label == " + Util.quote(label);
-            // the filter is now done if we don't have any values defined --- so we're querying for an enc with this label on a keyword.
+                lkwFilter += " && " + wordVar + ".label == " + Util.quote(label);
+                // the filter is now done if we don't have any values defined --- so we're querying for an enc with this label on a keyword.
 
-            String valueKey = "label" + labelN + ".values";
-            String[] values = request.getParameterValues(valueKey);
-            if (values != null) {
-                System.out.println("EQP got valueKey " + valueKey + " and values " +
-                    String.join(", ", values));
-                String valueFilter = "(";
-                for (int valueN = 0; valueN < values.length; valueN++) {
-                    if (valueN > 0) valueFilter += " || ";
-                    valueFilter += wordVar + ".readableName == " + Util.quote(values[valueN]);
-                }
-                valueFilter += ")";
-                if (!valueFilter.equals("()")) lkwFilter += " && " + valueFilter;
-                if (values.length == 1) {
-                    prettyPrint.append(" with value \"" + values[0] + "\"");
-                } else if (values.length > 1) {
-                    String allVals = String.join("\", OR \"", values);
-                    allVals = "\"" + allVals + "\"";
-                    prettyPrint.append(" with value (" + allVals + ")");
-                }
-            } else {
-                System.out.println("EQP got null values for valueKey " + valueKey);
+                String valueKey = "label" + labelN + ".values";
+                String[] values = request.getParameterValues(valueKey);
+                if (values != null) {
+                    System.out.println("EQP got valueKey " + valueKey + " and values " +
+                        String.join(", ", values));
+                    String valueFilter = "(";
+                    for (int valueN = 0; valueN < values.length; valueN++) {
+                        if (valueN > 0) valueFilter += " || ";
+                        valueFilter += wordVar + ".readableName == " + Util.quote(values[valueN]);
+                    }
+                    valueFilter += ")";
+                    if (!valueFilter.equals("()")) lkwFilter += " && " + valueFilter;
+                    if (values.length == 1) {
+                        prettyPrint.append(" with value \"" + values[0] + "\"");
+                    } else if (values.length > 1) {
+                        String allVals = String.join("\", OR \"", values);
+                        allVals = "\"" + allVals + "\"";
+                        prettyPrint.append(" with value (" + allVals + ")");
+                    }
+                } else {
+                    System.out.println("EQP got null values for valueKey " + valueKey);
+                }
             }
-        }
-        lkwFilter += ")";
+            lkwFilter += ")";
 
-        System.out.println("EQP got lkwFilter " + lkwFilter);
-        if (!lkwFilter.equals("()")) {
-            filter = filterWithCondition(filter, lkwFilter);
-            prettyPrint.append("<br>");
-        }
-        // end labeled keyword filters
-        // ms markers filters-------------------------------------------------
-        myShepherd.beginDBTransaction();
-        List<String> markers = myShepherd.getAllLoci();
-        int numMarkers = markers.size();
-        String theseMarkers = "";
-        boolean hasMarkers = false;
-        for (int h = 0; h < numMarkers; h++) {
-            String marker = markers.get(h);
-            if (request.getParameter(marker) != null) {
-                hasMarkers = true;
-                String locIDFilter = "(";
-                locIDFilter += " " + marker.replaceAll("-", "") + ".name == \"" + marker + "\" ";
-                locIDFilter += " )";
+            System.out.println("EQP got lkwFilter " + lkwFilter);
+            if (!lkwFilter.equals("()")) {
+                filter = filterWithCondition(filter, lkwFilter);
+                prettyPrint.append("<br>");
+            }
+            // end labeled keyword filters
+            // ms markers filters-------------------------------------------------
+            // myShepherd.beginDBTransaction();
+            List<String> markers = myShepherd.getAllLoci();
+            int numMarkers = markers.size();
+            String theseMarkers = "";
+            boolean hasMarkers = false;
+            for (int h = 0; h < numMarkers; h++) {
+                String marker = markers.get(h);
+                if (request.getParameter(marker) != null) {
+                    hasMarkers = true;
+                    String locIDFilter = "(";
+                    locIDFilter += " " + marker.replaceAll("-",
+                        "") + ".name == \"" + marker + "\" ";
+                    locIDFilter += " )";
 
-                int alleleNum = 0;
-                boolean hasMoreAlleles = true;
-                while (hasMoreAlleles) {
-                    if (request.getParameter((marker + "_alleleValue" + alleleNum)) != null) {
-                        try {
-                            Integer thisInt = new Integer(request.getParameter((marker +
-                                "_alleleValue" + alleleNum)));
-                            Integer relaxValue = new Integer(request.getParameter(
-                                "alleleRelaxValue"));
-                            Integer upperValue = thisInt + relaxValue;
-                            Integer lowerValue = thisInt - relaxValue;
-                            locIDFilter += (" && (" + marker.replaceAll("-",
-                                "") + ".allele" + alleleNum + " >= " + lowerValue + ")" + " && (" +
-                                marker.replaceAll("-",
-                                "") + ".allele" + alleleNum + " <= " + upperValue + ")");
-                        } catch (Exception e) {
+                    int alleleNum = 0;
+                    boolean hasMoreAlleles = true;
+                    while (hasMoreAlleles) {
+                        if (request.getParameter((marker + "_alleleValue" + alleleNum)) != null) {
+                            try {
+                                Integer thisInt = new Integer(request.getParameter((marker +
+                                    "_alleleValue" + alleleNum)));
+                                Integer relaxValue = new Integer(request.getParameter(
+                                    "alleleRelaxValue"));
+                                Integer upperValue = thisInt + relaxValue;
+                                Integer lowerValue = thisInt - relaxValue;
+                                locIDFilter += (" && (" + marker.replaceAll("-",
+                                    "") + ".allele" + alleleNum + " >= " + lowerValue + ")" +
+                                    " && (" + marker.replaceAll("-",
+                                    "") + ".allele" + alleleNum + " <= " + upperValue + ")");
+                            } catch (Exception e) {
+                                hasMoreAlleles = false;
+                            }
+                        } else {
                             hasMoreAlleles = false;
                         }
+                        alleleNum++;
+                    }
+                    theseMarkers += (marker + " ");
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter +=
+                            "tissueSamples.contains(dce) && dce.analyses.contains(msanalysis) && msanalysis.loci.contains("
+                            + marker.replaceAll("-", "") + ") && " + locIDFilter;
+                    } else {
+                        if (filter.indexOf("tissueSamples.contains(dce)") == -1) {
+                            filter += " && tissueSamples.contains(dce)";
+                        }
+                        if (filter.indexOf("dce.analyses.contains(msanalysis)") == -1) {
+                            filter += " && dce.analyses.contains(msanalysis)";
+                        }
+                        if (filter.indexOf("msanalysis.loci.contains(" + marker.replaceAll("-",
+                            "") + ")") == -1) {
+                            filter += " && msanalysis.loci.contains(" + marker.replaceAll("-",
+                                "") + ")";
+                        }
+                        filter += (" && " + locIDFilter);
+                    }
+                    if (jdoqlVariableDeclaration.equals("")) {
+                        jdoqlVariableDeclaration =
+                            " VARIABLES org.ecocean.genetics.TissueSample dce;org.ecocean.genetics.MicrosatelliteMarkersAnalysis msanalysis;org.ecocean.genetics.Locus "
+                            + marker.replaceAll("-", "");
                     } else {
-                        hasMoreAlleles = false;
+                        if (!jdoqlVariableDeclaration.contains(
+                            "org.ecocean.genetics.TissueSample dce")) {
+                            jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce";
+                        }
+                        if (!jdoqlVariableDeclaration.contains(
+                            "org.ecocean.genetics.MicrosatelliteMarkersAnalysis msanalysis")) {
+                            jdoqlVariableDeclaration +=
+                                ";org.ecocean.genetics.MicrosatelliteMarkersAnalysis msanalysis";
+                        }
+                        if (!jdoqlVariableDeclaration.contains("org.ecocean.genetics.Locus " +
+                            marker.replaceAll("-", ""))) {
+                            jdoqlVariableDeclaration += ";org.ecocean.genetics.Locus " +
+                                marker.replaceAll("-", "");
+                        }
                     }
-                    alleleNum++;
                 }
-                theseMarkers += (marker + " ");
+            }
+            if (hasMarkers) {
+                prettyPrint.append("Microsatellite marker is one of the following: ");
+                theseMarkers += "<br />";
+                prettyPrint.append(theseMarkers);
+            }
+            // myShepherd.rollbackDBTransaction();
+            // myShepherd.closeDBTransaction();
+            // end ms markers filters-----------------------------------------------
+            // filter for alternate ID------------------------------------------
+            if ((request.getParameter("alternateIDField") != null) &&
+                (!request.getParameter("alternateIDField").equals(""))) {
+                String altID = request.getParameter("alternateIDField").replaceAll("%20",
+                    " ").trim().toLowerCase();
                 if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                    filter +=
-                        "tissueSamples.contains(dce) && dce.analyses.contains(msanalysis) && msanalysis.loci.contains("
-                        + marker.replaceAll("-", "") + ") && " + locIDFilter;
+                    filter += "otherCatalogNumbers.toLowerCase().indexOf('" + altID + "') != -1";
+                } else {
+                    filter += " && otherCatalogNumbers.toLowerCase().indexOf('" + altID +
+                        "') != -1";
+                }
+                prettyPrint.append("alternateID field contains \"" + altID + "\".<br />");
+            }
+            // haplotype filters-------------------------------------------------
+            String[] haplotypes = request.getParameterValues("haplotypeField");
+            if ((haplotypes != null) && (!haplotypes[0].equals("None"))) {
+                prettyPrint.append("Haplotype is one of the following: ");
+                int kwLength = haplotypes.length;
+                String locIDFilter = "(";
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String kwParam = haplotypes[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (locIDFilter.equals("(")) {
+                            locIDFilter += " analysis.haplotype == \"" + kwParam + "\" ";
+                        } else {
+                            locIDFilter += " || analysis.haplotype == \"" + kwParam + "\" ";
+                        }
+                        prettyPrint.append(kwParam + " ");
+                    }
+                }
+                locIDFilter += " )";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += "tissueSamples.contains(dce) && dce.analyses.contains(analysis) && " +
+                        locIDFilter;
                 } else {
                     if (filter.indexOf("tissueSamples.contains(dce)") == -1) {
                         filter += " && tissueSamples.contains(dce)";
                     }
-                    if (filter.indexOf("dce.analyses.contains(msanalysis)") == -1) {
-                        filter += " && dce.analyses.contains(msanalysis)";
-                    }
-                    if (filter.indexOf("msanalysis.loci.contains(" + marker.replaceAll("-",
-                        "") + ")") == -1) {
-                        filter += " && msanalysis.loci.contains(" + marker.replaceAll("-",
-                            "") + ")";
+                    if (filter.indexOf("dce.analyses.contains(analysis)") == -1) {
+                        filter += " && dce.analyses.contains(analysis)";
                     }
                     filter += (" && " + locIDFilter);
                 }
+                prettyPrint.append("<br />");
                 if (jdoqlVariableDeclaration.equals("")) {
                     jdoqlVariableDeclaration =
-                        " VARIABLES org.ecocean.genetics.TissueSample dce;org.ecocean.genetics.MicrosatelliteMarkersAnalysis msanalysis;org.ecocean.genetics.Locus "
-                        + marker.replaceAll("-", "");
+                        " VARIABLES org.ecocean.genetics.TissueSample dce;org.ecocean.genetics.MitochondrialDNAAnalysis analysis";
                 } else {
                     if (!jdoqlVariableDeclaration.contains(
                         "org.ecocean.genetics.TissueSample dce")) {
                         jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce";
                     }
                     if (!jdoqlVariableDeclaration.contains(
-                        "org.ecocean.genetics.MicrosatelliteMarkersAnalysis msanalysis")) {
+                        "org.ecocean.genetics.MitochondrialDNAAnalysis analysis")) {
                         jdoqlVariableDeclaration +=
-                            ";org.ecocean.genetics.MicrosatelliteMarkersAnalysis msanalysis";
-                    }
-                    if (!jdoqlVariableDeclaration.contains("org.ecocean.genetics.Locus " +
-                        marker.replaceAll("-", ""))) {
-                        jdoqlVariableDeclaration += ";org.ecocean.genetics.Locus " +
-                            marker.replaceAll("-", "");
+                            ";org.ecocean.genetics.MitochondrialDNAAnalysis analysis";
                     }
                 }
             }
-        }
-        if (hasMarkers) {
-            prettyPrint.append("Microsatellite marker is one of the following: ");
-            theseMarkers += "<br />";
-            prettyPrint.append(theseMarkers);
-        }
-        myShepherd.rollbackDBTransaction();
-        myShepherd.closeDBTransaction();
-        // end ms markers filters-----------------------------------------------
-        // filter for alternate ID------------------------------------------
-        if ((request.getParameter("alternateIDField") != null) &&
-            (!request.getParameter("alternateIDField").equals(""))) {
-            String altID = request.getParameter("alternateIDField").replaceAll("%20",
-                " ").trim().toLowerCase();
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "otherCatalogNumbers.toLowerCase().indexOf('" + altID + "') != -1";
-            } else {
-                filter += " && otherCatalogNumbers.toLowerCase().indexOf('" + altID + "') != -1";
-            }
-            prettyPrint.append("alternateID field contains \"" + altID + "\".<br />");
-        }
-        // haplotype filters-------------------------------------------------
-        String[] haplotypes = request.getParameterValues("haplotypeField");
-        if ((haplotypes != null) && (!haplotypes[0].equals("None"))) {
-            prettyPrint.append("Haplotype is one of the following: ");
-            int kwLength = haplotypes.length;
-            String locIDFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = haplotypes[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (locIDFilter.equals("(")) {
-                        locIDFilter += " analysis.haplotype == \"" + kwParam + "\" ";
-                    } else {
-                        locIDFilter += " || analysis.haplotype == \"" + kwParam + "\" ";
+            // end haplotype filters-----------------------------------------------
+            // genetic sex filters-------------------------------------------------
+            String[] genSexes = request.getParameterValues("geneticSexField");
+            if ((genSexes != null) && (!genSexes[0].equals("None"))) {
+                prettyPrint.append("Genetic determination of sex is one of the following: ");
+                int kwLength = genSexes.length;
+                String locIDFilter = "(";
+                for (int kwIter = 0; kwIter < kwLength; kwIter++) {
+                    String kwParam = genSexes[kwIter].replaceAll("%20", " ").trim();
+                    if (!kwParam.equals("")) {
+                        if (locIDFilter.equals("(")) {
+                            locIDFilter += " sexanalysis.sex == \"" + kwParam + "\" ";
+                        } else {
+                            locIDFilter += " || sexanalysis.sex == \"" + kwParam + "\" ";
+                        }
+                        prettyPrint.append(kwParam + " ");
                     }
-                    prettyPrint.append(kwParam + " ");
-                }
-            }
-            locIDFilter += " )";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "tissueSamples.contains(dce) && dce.analyses.contains(analysis) && " +
-                    locIDFilter;
-            } else {
-                if (filter.indexOf("tissueSamples.contains(dce)") == -1) {
-                    filter += " && tissueSamples.contains(dce)";
-                }
-                if (filter.indexOf("dce.analyses.contains(analysis)") == -1) {
-                    filter += " && dce.analyses.contains(analysis)";
-                }
-                filter += (" && " + locIDFilter);
-            }
-            prettyPrint.append("<br />");
-            if (jdoqlVariableDeclaration.equals("")) {
-                jdoqlVariableDeclaration =
-                    " VARIABLES org.ecocean.genetics.TissueSample dce;org.ecocean.genetics.MitochondrialDNAAnalysis analysis";
-            } else {
-                if (!jdoqlVariableDeclaration.contains("org.ecocean.genetics.TissueSample dce")) {
-                    jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce";
                 }
-                if (!jdoqlVariableDeclaration.contains(
-                    "org.ecocean.genetics.MitochondrialDNAAnalysis analysis")) {
-                    jdoqlVariableDeclaration +=
-                        ";org.ecocean.genetics.MitochondrialDNAAnalysis analysis";
-                }
-            }
-        }
-        // end haplotype filters-----------------------------------------------
-        // genetic sex filters-------------------------------------------------
-        String[] genSexes = request.getParameterValues("geneticSexField");
-        if ((genSexes != null) && (!genSexes[0].equals("None"))) {
-            prettyPrint.append("Genetic determination of sex is one of the following: ");
-            int kwLength = genSexes.length;
-            String locIDFilter = "(";
-            for (int kwIter = 0; kwIter < kwLength; kwIter++) {
-                String kwParam = genSexes[kwIter].replaceAll("%20", " ").trim();
-                if (!kwParam.equals("")) {
-                    if (locIDFilter.equals("(")) {
-                        locIDFilter += " sexanalysis.sex == \"" + kwParam + "\" ";
-                    } else {
-                        locIDFilter += " || sexanalysis.sex == \"" + kwParam + "\" ";
+                locIDFilter += " )";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter +=
+                        "tissueSamples.contains(dce9) && dce9.analyses.contains(sexanalysis) && " +
+                        locIDFilter;
+                } else {
+                    if (filter.indexOf("tissueSamples.contains(dce9)") == -1) {
+                        filter += " && tissueSamples.contains(dce9)";
                     }
-                    prettyPrint.append(kwParam + " ");
-                }
-            }
-            locIDFilter += " )";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter +=
-                    "tissueSamples.contains(dce9) && dce9.analyses.contains(sexanalysis) && " +
-                    locIDFilter;
-            } else {
-                if (filter.indexOf("tissueSamples.contains(dce9)") == -1) {
-                    filter += " && tissueSamples.contains(dce9)";
-                }
-                if (filter.indexOf("dce9.analyses.contains(sexanalysis)") == -1) {
-                    filter += " && dce9.analyses.contains(sexanalysis)";
+                    if (filter.indexOf("dce9.analyses.contains(sexanalysis)") == -1) {
+                        filter += " && dce9.analyses.contains(sexanalysis)";
+                    }
+                    filter += (" && " + locIDFilter);
                 }
-                filter += (" && " + locIDFilter);
-            }
-            prettyPrint.append("<br />");
-            if (jdoqlVariableDeclaration.equals("")) {
-                jdoqlVariableDeclaration =
-                    " VARIABLES org.ecocean.genetics.TissueSample dce9;org.ecocean.genetics.SexAnalysis sexanalysis";
-            } else {
-                if (!jdoqlVariableDeclaration.contains("org.ecocean.genetics.TissueSample dce9")) {
-                    jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce9";
-                }
-                if (!jdoqlVariableDeclaration.contains(
-                    "org.ecocean.genetics.SexAnalysis sexanalysis")) {
-                    jdoqlVariableDeclaration += ";org.ecocean.genetics.SexAnalysis sexanalysis";
+                prettyPrint.append("<br />");
+                if (jdoqlVariableDeclaration.equals("")) {
+                    jdoqlVariableDeclaration =
+                        " VARIABLES org.ecocean.genetics.TissueSample dce9;org.ecocean.genetics.SexAnalysis sexanalysis";
+                } else {
+                    if (!jdoqlVariableDeclaration.contains(
+                        "org.ecocean.genetics.TissueSample dce9")) {
+                        jdoqlVariableDeclaration += ";org.ecocean.genetics.TissueSample dce9";
+                    }
+                    if (!jdoqlVariableDeclaration.contains(
+                        "org.ecocean.genetics.SexAnalysis sexanalysis")) {
+                        jdoqlVariableDeclaration += ";org.ecocean.genetics.SexAnalysis sexanalysis";
+                    }
                 }
             }
-        }
-        // end genetic sex filters-----------------------------------------------
+            // end genetic sex filters-----------------------------------------------
 // end photo filename filtering
-        // filter for genus------------------------------------------
-        if ((request.getParameter("genusField") != null) &&
-            (!request.getParameter("genusField").equals(""))) {
-            String genusSpecies = request.getParameter("genusField").replaceAll("%20", " ").trim();
-            String genus = "";
-            String specificEpithet = "";
+            // filter for genus------------------------------------------
+            if ((request.getParameter("genusField") != null) &&
+                (!request.getParameter("genusField").equals(""))) {
+                String genusSpecies = request.getParameter("genusField").replaceAll("%20",
+                    " ").trim();
+                String genus = "";
+                String specificEpithet = "";
 
-            // now we have to break apart genus species
-            StringTokenizer tokenizer = new StringTokenizer(genusSpecies, " ");
-            if (tokenizer.countTokens() == 2) {
-                genus = tokenizer.nextToken();
-                specificEpithet = tokenizer.nextToken();
-                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                    filter += "genus == '" + genus + "' ";
-                } else { filter += " && genus == '" + genus + "' "; }
-                filter += " && specificEpithet == '" + specificEpithet + "' ";
+                // now we have to break apart genus species
+                StringTokenizer tokenizer = new StringTokenizer(genusSpecies, " ");
+                if (tokenizer.countTokens() == 2) {
+                    genus = tokenizer.nextToken();
+                    specificEpithet = tokenizer.nextToken();
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += "genus == '" + genus + "' ";
+                    } else { filter += " && genus == '" + genus + "' "; }
+                    filter += " && specificEpithet == '" + specificEpithet + "' ";
 
-                prettyPrint.append("genus and species are \"" + genusSpecies + "\".<br />");
-            }
-        }
-        // filter for identificationRemarks------------------------------------------
-        if ((request.getParameter("identificationRemarksField") != null) &&
-            (!request.getParameter("identificationRemarksField").equals(""))) {
-            String idRemarks = request.getParameter("identificationRemarksField").trim();
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += "identificationRemarks.startsWith('" + idRemarks + "')";
-            } else { filter += " && identificationRemarks.startsWith('" + idRemarks + "')"; }
-            prettyPrint.append("identificationRemarks starts with \"" + idRemarks + "\".<br />");
-        }
-        // end identification remarks filter
-        // filter gpsOnly - return only Encounters with a defined location. This is mostly used for mapping JSP pages
-        if (request.getAttribute("gpsOnly") != null) {
-            filter = filterWithGpsBox("decimalLatitude", "decimalLongitude", filter, request);
-        }
-        // end filter gpsOnly
-        // filter by alive/dead status------------------------------------------
-        if ((request.getParameter("alive") != null) || (request.getParameter("dead") != null)) {
-            if (request.getParameter("alive") == null) {
-                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                    filter += "!livingStatus.startsWith('alive')";
-                } else { filter += " && !livingStatus.startsWith('alive')"; }
-                prettyPrint.append("Not alive.<br />");
+                    prettyPrint.append("genus and species are \"" + genusSpecies + "\".<br />");
+                }
             }
-            if (request.getParameter("dead") == null) {
+            // filter for identificationRemarks------------------------------------------
+            if ((request.getParameter("identificationRemarksField") != null) &&
+                (!request.getParameter("identificationRemarksField").equals(""))) {
+                String idRemarks = request.getParameter("identificationRemarksField").trim();
                 if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                    filter += "!livingStatus.startsWith('dead')";
-                } else { filter += " && !livingStatus.startsWith('dead')"; }
-                prettyPrint.append("Not dead.<br />");
-            }
-        }
-        // filter by alive/dead status--------------------------------------------------------------------------------------
-        // submitter or photographer name filter------------------------------------------
-        if ((request.getParameter("nameField") != null) &&
-            (!request.getParameter("nameField").equals(""))) {
-            String nameString = request.getParameter("nameField").replaceAll("%20",
-                " ").toLowerCase().trim();
-            String filterString = "" + "(" +
-                "(submitters.contains(submitter) && ((submitter.fullName.toLowerCase().indexOf('" +
-                nameString + "') != -1)||(submitter.emailAddress.toLowerCase().indexOf('" +
-                nameString + "') != -1))) || " +
-                "(photographers.contains(photographer) && ((photographer.fullName.toLowerCase().indexOf('"
-                + nameString + "') != -1)||(photographer.emailAddress.toLowerCase().indexOf('" +
-                nameString + "') != -1))) " +
-                "||(informOthers.contains(other) && ((other.fullName.toLowerCase().indexOf('" +
-                nameString + "') != -1)||(other.emailAddress.toLowerCase().indexOf('" + nameString +
-                "') != -1)))" + ")";
-            if (jdoqlVariableDeclaration.equals("")) {
-                jdoqlVariableDeclaration =
-                    " VARIABLES org.ecocean.User submitter;org.ecocean.User photographer;org.ecocean.User other";
-            } else {
-                if (!jdoqlVariableDeclaration.contains("org.ecocean.User submitter")) {
-                    jdoqlVariableDeclaration += ";org.ecocean.User submitter";
-                }
-                if (!jdoqlVariableDeclaration.contains("org.ecocean.User photographer")) {
-                    jdoqlVariableDeclaration += ";org.ecocean.User photographer";
-                }
-                if (!jdoqlVariableDeclaration.contains("org.ecocean.User other")) {
-                    jdoqlVariableDeclaration += ";org.ecocean.User other";
+                    filter += "identificationRemarks.startsWith('" + idRemarks + "')";
+                } else { filter += " && identificationRemarks.startsWith('" + idRemarks + "')"; }
+                prettyPrint.append("identificationRemarks starts with \"" + idRemarks +
+                    "\".<br />");
+            }
+            // end identification remarks filter
+            // filter gpsOnly - return only Encounters with a defined location. This is mostly used for mapping JSP pages
+            if (request.getAttribute("gpsOnly") != null) {
+                filter = filterWithGpsBox("decimalLatitude", "decimalLongitude", filter, request);
+            }
+            // end filter gpsOnly
+            // filter by alive/dead status------------------------------------------
+            if ((request.getParameter("alive") != null) || (request.getParameter("dead") != null)) {
+                if (request.getParameter("alive") == null) {
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += "!livingStatus.startsWith('alive')";
+                    } else { filter += " && !livingStatus.startsWith('alive')"; }
+                    prettyPrint.append("Not alive.<br />");
+                }
+                if (request.getParameter("dead") == null) {
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += "!livingStatus.startsWith('dead')";
+                    } else { filter += " && !livingStatus.startsWith('dead')"; }
+                    prettyPrint.append("Not dead.<br />");
                 }
             }
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += filterString;
-            } else { filter += (" && " + filterString); }
-            prettyPrint.append("Related fullName or emailAddress contains: \"" + nameString +
-                "\"<br />");
-        }
-        // end name and email filter--------------------------------------------------------------------------------------
-        // additional comments filter------------------------------------------
-        if ((request.getParameter("additionalCommentsField") != null) &&
-            (!request.getParameter("additionalCommentsField").equals(""))) {
-            String nameString = request.getParameter("additionalCommentsField").replaceAll("%20",
-                " ").toLowerCase().trim();
-            String filterString = "(occurrenceRemarks.toLowerCase().indexOf('" + nameString +
-                "') != -1)";
-            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                filter += filterString;
-            } else { filter += (" && " + filterString); }
-            prettyPrint.append("Remarks contains: \"" + nameString + "\"<br />");
-        }
-        // end additional comments filter--------------------------------------------------------------------------------------
-        // start date filter----------------------------
-        if ((request.getParameter("datepicker1") != null) &&
-            (!request.getParameter("datepicker1").trim().equals("")) &&
-            (request.getParameter("datepicker2") != null) &&
-            (!request.getParameter("datepicker2").trim().equals(""))) {
-            try {
-                DateTimeFormatter parser = ISODateTimeFormat.dateTimeParser();
-                DateTime date1 = parser.parseDateTime(request.getParameter("datepicker1"));
-                DateTime date2 = parser.parseDateTime(request.getParameter("datepicker2"));
-                long date1Millis = date1.getMillis();
-                long date2Millis = date2.getMillis();
-                // if same dateTime is set by both pickers, then add a full day of milliseconds to picker2 to cover the entire day
-                date2Millis += (24 * 60 * 60 * 1000 - 1);
-
-                prettyPrint.append("Dates between: " + date1.toString(ISODateTimeFormat.date()) +
-                    " and " + date2.toString(ISODateTimeFormat.date()) + "<br />");
-                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                    filter += "((dateInMilliseconds >= " + date1Millis +
-                        ") && (dateInMilliseconds <= " + date2Millis + "))";
+            // filter by alive/dead status--------------------------------------------------------------------------------------
+            // submitter or photographer name filter------------------------------------------
+            if ((request.getParameter("nameField") != null) &&
+                (!request.getParameter("nameField").equals(""))) {
+                String nameString = request.getParameter("nameField").replaceAll("%20",
+                    " ").toLowerCase().trim();
+                String filterString = "" + "(" +
+                    "(submitters.contains(submitter) && ((submitter.fullName.toLowerCase().indexOf('"
+                    + nameString + "') != -1)||(submitter.emailAddress.toLowerCase().indexOf('" +
+                    nameString + "') != -1))) || " +
+                    "(photographers.contains(photographer) && ((photographer.fullName.toLowerCase().indexOf('"
+                    + nameString + "') != -1)||(photographer.emailAddress.toLowerCase().indexOf('" +
+                    nameString + "') != -1))) " +
+                    "||(informOthers.contains(other) && ((other.fullName.toLowerCase().indexOf('" +
+                    nameString + "') != -1)||(other.emailAddress.toLowerCase().indexOf('" +
+                    nameString + "') != -1)))" + ")";
+                if (jdoqlVariableDeclaration.equals("")) {
+                    jdoqlVariableDeclaration =
+                        " VARIABLES org.ecocean.User submitter;org.ecocean.User photographer;org.ecocean.User other";
                 } else {
-                    filter += " && ((dateInMilliseconds >= " + date1Millis +
-                        ") && (dateInMilliseconds <= " + date2Millis + "))";
+                    if (!jdoqlVariableDeclaration.contains("org.ecocean.User submitter")) {
+                        jdoqlVariableDeclaration += ";org.ecocean.User submitter";
+                    }
+                    if (!jdoqlVariableDeclaration.contains("org.ecocean.User photographer")) {
+                        jdoqlVariableDeclaration += ";org.ecocean.User photographer";
+                    }
+                    if (!jdoqlVariableDeclaration.contains("org.ecocean.User other")) {
+                        jdoqlVariableDeclaration += ";org.ecocean.User other";
+                    }
                 }
-            } catch (Exception e) { e.printStackTrace(); }
-        }
-        // end date filter------------------------------------------
-        // start date added filter----------------------------
-        if ((request.getParameter("dateaddedpicker1") != null) &&
-            (!request.getParameter("dateaddedpicker1").trim().equals("")) &&
-            (request.getParameter("dateaddedpicker2") != null) &&
-            (!request.getParameter("dateaddedpicker2").trim().equals(""))) {
-            try {
-                DateTimeFormatter parser = ISODateTimeFormat.dateTimeParser();
-                DateTime date1 = parser.parseDateTime(request.getParameter("dateaddedpicker1"));
-                DateTime date2 = parser.parseDateTime(request.getParameter("dateaddedpicker2"));
-
-                prettyPrint.append("Encounter creation dates between: " +
-                    date1.toString(ISODateTimeFormat.date()) + " and " +
-                    date2.toString(ISODateTimeFormat.date()) + "<br />");
                 if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                    filter += "((dwcDateAddedLong >= " + date1.getMillis() +
-                        ") && (dwcDateAddedLong <= " + date2.getMillis() + "))";
-                } else {
-                    filter += " && ((dwcDateAddedLong >= " + date1.getMillis() +
-                        ") && (dwcDateAddedLong <= " + date2.getMillis() + "))";
+                    filter += filterString;
+                } else { filter += (" && " + filterString); }
+                prettyPrint.append("Related fullName or emailAddress contains: \"" + nameString +
+                    "\"<br />");
+            }
+            // end name and email filter--------------------------------------------------------------------------------------
+            // additional comments filter------------------------------------------
+            if ((request.getParameter("additionalCommentsField") != null) &&
+                (!request.getParameter("additionalCommentsField").equals(""))) {
+                String nameString = request.getParameter("additionalCommentsField").replaceAll(
+                    "%20", " ").toLowerCase().trim();
+                String filterString = "(occurrenceRemarks.toLowerCase().indexOf('" + nameString +
+                    "') != -1)";
+                if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                    filter += filterString;
+                } else { filter += (" && " + filterString); }
+                prettyPrint.append("Remarks contains: \"" + nameString + "\"<br />");
+            }
+            // end additional comments filter--------------------------------------------------------------------------------------
+            // start date filter----------------------------
+            if ((request.getParameter("datepicker1") != null) &&
+                (!request.getParameter("datepicker1").trim().equals("")) &&
+                (request.getParameter("datepicker2") != null) &&
+                (!request.getParameter("datepicker2").trim().equals(""))) {
+                try {
+                    DateTimeFormatter parser = ISODateTimeFormat.dateTimeParser();
+                    DateTime date1 = parser.parseDateTime(request.getParameter("datepicker1"));
+                    DateTime date2 = parser.parseDateTime(request.getParameter("datepicker2"));
+                    long date1Millis = date1.getMillis();
+                    long date2Millis = date2.getMillis();
+                    // if same dateTime is set by both pickers, then add a full day of milliseconds to picker2 to cover the entire day
+                    date2Millis += (24 * 60 * 60 * 1000 - 1);
+
+                    prettyPrint.append("Dates between: " +
+                        date1.toString(ISODateTimeFormat.date()) + " and " +
+                        date2.toString(ISODateTimeFormat.date()) + "<br />");
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += "((dateInMilliseconds >= " + date1Millis +
+                            ") && (dateInMilliseconds <= " + date2Millis + "))";
+                    } else {
+                        filter += " && ((dateInMilliseconds >= " + date1Millis +
+                            ") && (dateInMilliseconds <= " + date2Millis + "))";
+                    }
+                } catch (Exception e) { e.printStackTrace(); }
+            }
+            // end date filter------------------------------------------
+            // start date added filter----------------------------
+            if ((request.getParameter("dateaddedpicker1") != null) &&
+                (!request.getParameter("dateaddedpicker1").trim().equals("")) &&
+                (request.getParameter("dateaddedpicker2") != null) &&
+                (!request.getParameter("dateaddedpicker2").trim().equals(""))) {
+                try {
+                    DateTimeFormatter parser = ISODateTimeFormat.dateTimeParser();
+                    DateTime date1 = parser.parseDateTime(request.getParameter("dateaddedpicker1"));
+                    DateTime date2 = parser.parseDateTime(request.getParameter("dateaddedpicker2"));
+
+                    prettyPrint.append("Encounter creation dates between: " +
+                        date1.toString(ISODateTimeFormat.date()) + " and " +
+                        date2.toString(ISODateTimeFormat.date()) + "<br />");
+                    if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += "((dwcDateAddedLong >= " + date1.getMillis() +
+                            ") && (dwcDateAddedLong <= " + date2.getMillis() + "))";
+                    } else {
+                        filter += " && ((dwcDateAddedLong >= " + date1.getMillis() +
+                            ") && (dwcDateAddedLong <= " + date2.getMillis() + "))";
+                    }
+                } catch (NumberFormatException nfe) {
+                    // do nothing, just skip on
+                    nfe.printStackTrace();
                 }
-            } catch (NumberFormatException nfe) {
-                // do nothing, just skip on
-                nfe.printStackTrace();
-            }
-        }
-        // end date added filter------------------------------------------
-        // filter for sex------------------------------------------
-        if ((request.getParameter("male") != null) || (request.getParameter("female") != null) ||
-            (request.getParameter("unknown") != null)) {
-            System.out.println("Filter at beginning of sex filtering: " + filter);
-            if (request.getParameter("male") == null) {
-                filter = filterWithCondition(filter, "!sex.startsWith('male')");
-                prettyPrint.append("Sex is not male.<br />");
             }
-            if (request.getParameter("female") == null) {
-                filter = filterWithCondition(filter, "!sex.startsWith('female')");
-                prettyPrint.append("Sex is not female.<br />");
-            }
-            if (request.getParameter("unknown") == null) {
-                filter = filterWithCondition(filter, "!sex.startsWith('unknown') && sex != null");
-                prettyPrint.append("Sex is not unknown.<br />");
-            }
-            System.out.println("Filter at end of sex filtering: " + filter);
-        }
-        // filter by sex--------------------------------------------------------------------------------------
-        String releaseDateFromStr = request.getParameter("releaseDateFrom");
-        String releaseDateToStr = request.getParameter("releaseDateTo");
-        String pattern = CommonConfiguration.getProperty("releaseDateFormat", context);
-        SimpleDateFormat simpleDateFormat = new SimpleDateFormat(pattern);
-        if (releaseDateFromStr != null && releaseDateFromStr.trim().length() > 0) {
-            try {
-                Date releaseDateFrom = simpleDateFormat.parse(releaseDateFromStr);
-                if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                    filter += " && ";
+            // end date added filter------------------------------------------
+            // filter for sex------------------------------------------
+            if ((request.getParameter("male") != null) ||
+                (request.getParameter("female") != null) ||
+                (request.getParameter("unknown") != null)) {
+                System.out.println("Filter at beginning of sex filtering: " + filter);
+                if (request.getParameter("male") == null) {
+                    filter = filterWithCondition(filter, "!sex.startsWith('male')");
+                    prettyPrint.append("Sex is not male.<br />");
+                }
+                if (request.getParameter("female") == null) {
+                    filter = filterWithCondition(filter, "!sex.startsWith('female')");
+                    prettyPrint.append("Sex is not female.<br />");
+                }
+                if (request.getParameter("unknown") == null) {
+                    filter = filterWithCondition(filter,
+                        "!sex.startsWith('unknown') && sex != null");
+                    prettyPrint.append("Sex is not unknown.<br />");
+                }
+                System.out.println("Filter at end of sex filtering: " + filter);
+            }
+            // filter by sex--------------------------------------------------------------------------------------
+            String releaseDateFromStr = request.getParameter("releaseDateFrom");
+            String releaseDateToStr = request.getParameter("releaseDateTo");
+            String pattern = CommonConfiguration.getProperty("releaseDateFormat", context);
+            SimpleDateFormat simpleDateFormat = new SimpleDateFormat(pattern);
+            if (releaseDateFromStr != null && releaseDateFromStr.trim().length() > 0) {
+                try {
+                    Date releaseDateFrom = simpleDateFormat.parse(releaseDateFromStr);
+                    if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += " && ";
+                    }
+                    filter += "(releaseDate >= releaseDateFrom)";
+                    parameterDeclaration = updateParametersDeclaration(parameterDeclaration,
+                        "java.util.Date releaseDateFrom");
+                    paramMap.put("releaseDateFrom", releaseDateFrom);
+                    prettyPrint.append("release date >= " +
+                        simpleDateFormat.format(releaseDateFrom));
+                } catch (Exception e) {
+                    e.printStackTrace();
                 }
-                filter += "(releaseDate >= releaseDateFrom)";
-                parameterDeclaration = updateParametersDeclaration(parameterDeclaration,
-                    "java.util.Date releaseDateFrom");
-                paramMap.put("releaseDateFrom", releaseDateFrom);
-                prettyPrint.append("release date >= " + simpleDateFormat.format(releaseDateFrom));
-            } catch (Exception e) {
-                e.printStackTrace();
             }
-        }
-        if (releaseDateToStr != null && releaseDateToStr.trim().length() > 0) {
-            try {
-                Date releaseDateTo = simpleDateFormat.parse(releaseDateToStr);
-                if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-                    filter += " && ";
+            if (releaseDateToStr != null && releaseDateToStr.trim().length() > 0) {
+                try {
+                    Date releaseDateTo = simpleDateFormat.parse(releaseDateToStr);
+                    if (!filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                        filter += " && ";
+                    }
+                    filter += "(releaseDate <= releaseDateTo)";
+                    parameterDeclaration = updateParametersDeclaration(parameterDeclaration,
+                        "java.util.Date releaseDateTo");
+                    paramMap.put("releaseDateTo", releaseDateTo);
+                    prettyPrint.append("releaseDate <= " + simpleDateFormat.format(releaseDateTo));
+                } catch (Exception e) {
+                    e.printStackTrace();
                 }
-                filter += "(releaseDate <= releaseDateTo)";
-                parameterDeclaration = updateParametersDeclaration(parameterDeclaration,
-                    "java.util.Date releaseDateTo");
-                paramMap.put("releaseDateTo", releaseDateTo);
-                prettyPrint.append("releaseDate <= " + simpleDateFormat.format(releaseDateTo));
-            } catch (Exception e) {
-                e.printStackTrace();
             }
-        }
-        for (String fieldName : SIMPLE_STRING_FIELDS)
-            filter = QueryProcessor.filterWithBasicStringField(filter, fieldName, request,
-                prettyPrint);
-        filter = filterWithGpsBox("decimalLatitude", "decimalLongitude", filter, request);
-        // end GPS filters-----------------------------------------------
-        if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
-            filter = "SELECT FROM org.ecocean.Encounter WHERE catalogNumber != null";
-        }
-        filter += jdoqlVariableDeclaration;
-
-        filter += parameterDeclaration;
-        System.out.println("EncounterQueryProcessor filter: " + filter);
+            for (String fieldName : SIMPLE_STRING_FIELDS)
+                filter = QueryProcessor.filterWithBasicStringField(filter, fieldName, request,
+                    prettyPrint);
+            filter = filterWithGpsBox("decimalLatitude", "decimalLongitude", filter, request);
+            // end GPS filters-----------------------------------------------
+            if (filter.equals(SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE)) {
+                filter = "SELECT FROM org.ecocean.Encounter WHERE catalogNumber != null";
+            }
+            filter += jdoqlVariableDeclaration;
 
+            filter += parameterDeclaration;
+            System.out.println("EncounterQueryProcessor filter: " + filter);
+        } catch (Exception ex) {
+            System.out.println("Shepherd usage caught: " + ex);
+            ex.printStackTrace();
+        } finally {
+            myShepherd.rollbackAndClose();
+        }
         return filter;
     }
 

From af4409e655484039b0a1e4bc3a49b55e5beb9ec8 Mon Sep 17 00:00:00 2001
From: holmbergius <holmbergius@gmail.com>
Date: Fri, 3 Jan 2025 16:51:04 -0800
Subject: [PATCH 18/20] Simple commit to more elegantly handle Shepherd closure
 after observing some issues with this servlet in the wild

---
 .../ecocean/servlet/SubmitSpotsAndImage.java  | 245 +++++++++---------
 1 file changed, 123 insertions(+), 122 deletions(-)

diff --git a/src/main/java/org/ecocean/servlet/SubmitSpotsAndImage.java b/src/main/java/org/ecocean/servlet/SubmitSpotsAndImage.java
index 2965eafea8..c83dc2d505 100644
--- a/src/main/java/org/ecocean/servlet/SubmitSpotsAndImage.java
+++ b/src/main/java/org/ecocean/servlet/SubmitSpotsAndImage.java
@@ -50,132 +50,133 @@ public void doPost(HttpServletRequest request, HttpServletResponse response)
         myShepherd.setAction("SubmitSpotsAndImage.class");
 
         myShepherd.beginDBTransaction();
-        JSONObject json = ServletUtilities.jsonFromHttpServletRequest(request);
-        int maId = json.optInt("mediaAssetId", -1);
-        if (maId < 0) {
-            myShepherd.rollbackDBTransaction();
-            myShepherd.closeDBTransaction();
-            throw new IOException("invalid mediaAssetId");
-        }
-        String encId = json.optString("encId", null);
-        if (encId == null) {
-            myShepherd.rollbackDBTransaction();
-            myShepherd.closeDBTransaction();
-            throw new IOException("invalid encId");
-        }
-        Encounter enc = myShepherd.getEncounter(encId);
-        if (enc == null) {
-            myShepherd.rollbackDBTransaction();
-            myShepherd.closeDBTransaction();
-            throw new IOException("invalid encId");
-        }
-        boolean rightSide = json.optBoolean("rightSide", false);
-        ArrayList<SuperSpot> spots = parseSpots(json.optJSONArray("spots"));
-        if (spots == null) {
-            myShepherd.rollbackDBTransaction();
-            myShepherd.closeDBTransaction();
-            throw new IOException("invalid spots");
-        }
-        ArrayList<SuperSpot> refSpots = parseSpots(json.optJSONArray("refSpots"));
-        if (refSpots == null) {
-            myShepherd.rollbackDBTransaction();
-            myShepherd.closeDBTransaction();
-            throw new IOException("invalid refSpots");
-        }
-        AssetStore store = AssetStore.getDefault(myShepherd);
-        // this should put it in the same old (pre-MediaAsset) location to maintain url pattern
-
-        // setup data dir
-        String rootWebappPath = getServletContext().getRealPath("/");
-        File webappsDir = new File(rootWebappPath).getParentFile();
-        File shepherdDataDir = new File(webappsDir,
-            CommonConfiguration.getDataDirectoryName(context));
-        // if(!shepherdDataDir.exists()){shepherdDataDir.mkdirs();}
-        // File encountersDir=new File(shepherdDataDir.getAbsolutePath()+"/encounters");
-        // if(!encountersDir.exists()){encountersDir.mkdirs();}
-        String thisEncDirString = Encounter.dir(shepherdDataDir, encId);
-        File thisEncounterDir = new File(thisEncDirString);
-        if (!thisEncounterDir.exists()) {
-            thisEncounterDir.mkdirs();
-            System.out.println("I am making the encDir: " + thisEncDirString);
-        }
-        // now persist
-        JSONObject params = store.createParameters(new File("encounters/" +
-            Encounter.subdir(encId) + "/extract" + (rightSide ? "Right" : "") + encId + ".jpg"));
-        System.out.println("====> params = " + params);
-        MediaAsset crMa = store.create(params);
-        crMa.copyInBase64(json.optString("imageData", null));
-        crMa.addLabel("_spot" + (rightSide ? "Right" : "")); // we are sticking with "legacy" '_spot' for left
-        // crMa.setParentId(maId);
-        crMa.addDerivationMethod("spotTool", json.optJSONObject("imageToolValues"));
-        // ma.updateMinimalMetadata();
+        
+        try{
+	        JSONObject json = ServletUtilities.jsonFromHttpServletRequest(request);
+	        int maId = json.optInt("mediaAssetId", -1);
+	        if (maId < 0) {
+	            throw new IOException("invalid mediaAssetId");
+	        }
+	        String encId = json.optString("encId", null);
+	        if (encId == null) {
+	            throw new IOException("invalid encId");
+	        }
+	        Encounter enc = myShepherd.getEncounter(encId);
+	        if (enc == null) {
+	            throw new IOException("invalid encId");
+	        }
+	        boolean rightSide = json.optBoolean("rightSide", false);
+	        ArrayList<SuperSpot> spots = parseSpots(json.optJSONArray("spots"));
+	        if (spots == null) {
+	            throw new IOException("invalid spots");
+	        }
+	        ArrayList<SuperSpot> refSpots = parseSpots(json.optJSONArray("refSpots"));
+	        if (refSpots == null) {
+	            throw new IOException("invalid refSpots");
+	        }
+	        AssetStore store = AssetStore.getDefault(myShepherd);
+	        // this should put it in the same old (pre-MediaAsset) location to maintain url pattern
+	
+	        // setup data dir
+	        String rootWebappPath = getServletContext().getRealPath("/");
+	        File webappsDir = new File(rootWebappPath).getParentFile();
+	        File shepherdDataDir = new File(webappsDir,
+	            CommonConfiguration.getDataDirectoryName(context));
+	        // if(!shepherdDataDir.exists()){shepherdDataDir.mkdirs();}
+	        // File encountersDir=new File(shepherdDataDir.getAbsolutePath()+"/encounters");
+	        // if(!encountersDir.exists()){encountersDir.mkdirs();}
+	        String thisEncDirString = Encounter.dir(shepherdDataDir, encId);
+	        File thisEncounterDir = new File(thisEncDirString);
+	        if (!thisEncounterDir.exists()) {
+	            thisEncounterDir.mkdirs();
+	            System.out.println("I am making the encDir: " + thisEncDirString);
+	        }
+	        // now persist
+	        JSONObject params = store.createParameters(new File("encounters/" +
+	            Encounter.subdir(encId) + "/extract" + (rightSide ? "Right" : "") + encId + ".jpg"));
+	        System.out.println("====> params = " + params);
+	        MediaAsset crMa = store.create(params);
+	        crMa.copyInBase64(json.optString("imageData", null));
+	        crMa.addLabel("_spot" + (rightSide ? "Right" : "")); // we are sticking with "legacy" '_spot' for left
+	        // crMa.setParentId(maId);
+	        crMa.addDerivationMethod("spotTool", json.optJSONObject("imageToolValues"));
+	        // ma.updateMinimalMetadata();
+	
+	        Keyword crKeyword = myShepherd.getOrCreateKeyword("CR Image");
+	        String crParentId = request.getParameter("dataCollectionEventID");
+	        // crMa.addDerivationMethod("crParentId", crParentId);
+	        // crMa.addLabel("CR");
+	        crMa.addKeyword(crKeyword);
+	        crMa.updateMinimalMetadata();
+	        crMa.setDetectionStatus("complete");
+	        System.out.println("    + updated made media asset");
+	        MediaAssetFactory.save(crMa, myShepherd);
+	        System.out.println("    + saved media asset " + crMa.toString());
+	        myShepherd.updateDBTransaction();
+	        System.out.println("    + updated transaction, about to make children");
+	        crMa.updateStandardChildren(myShepherd);
+	        crMa.updateMetadata();
+	        System.out.println("    + updated children for asset " + crMa.toString() +
+	            "; hasFamily = " + crMa.hasFamily(myShepherd));
+	        String speciesString = enc.getTaxonomyString();
+	        Annotation ann = new Annotation(speciesString, crMa);
+	        ann.setMatchAgainst(true);
+	        String iaClass = "whalesharkCR"; // should we change this?
+	        ann.setIAClass(iaClass);
+	        if (rightSide) { ann.setViewpoint("right"); } else { ann.setViewpoint("left"); }
+	        enc.addAnnotation(ann);
+	        System.out.println("    + made annotation " + ann.toString());
 
-        Keyword crKeyword = myShepherd.getOrCreateKeyword("CR Image");
-        String crParentId = request.getParameter("dataCollectionEventID");
-        // crMa.addDerivationMethod("crParentId", crParentId);
-        // crMa.addLabel("CR");
-        crMa.addKeyword(crKeyword);
-        crMa.updateMinimalMetadata();
-        crMa.setDetectionStatus("complete");
-        System.out.println("    + updated made media asset");
-        MediaAssetFactory.save(crMa, myShepherd);
-        System.out.println("    + saved media asset " + crMa.toString());
-        myShepherd.updateDBTransaction();
-        System.out.println("    + updated transaction, about to make children");
-        crMa.updateStandardChildren(myShepherd);
-        crMa.updateMetadata();
-        System.out.println("    + updated children for asset " + crMa.toString() +
-            "; hasFamily = " + crMa.hasFamily(myShepherd));
-        String speciesString = enc.getTaxonomyString();
-        Annotation ann = new Annotation(speciesString, crMa);
-        ann.setMatchAgainst(true);
-        String iaClass = "whalesharkCR"; // should we change this?
-        ann.setIAClass(iaClass);
-        if (rightSide) { ann.setViewpoint("right"); } else { ann.setViewpoint("left"); }
-        enc.addAnnotation(ann);
-        System.out.println("    + made annotation " + ann.toString());
-        myShepherd.getPM().makePersistent(ann);
-        System.out.println("    + saved annotation");
 
-        // we need to intake mediaassets so they get acmIds and are matchable
-        ArrayList<MediaAsset> maList = new ArrayList<MediaAsset>();
-        maList.add(crMa);
-        ArrayList<Annotation> annList = new ArrayList<Annotation>();
-        annList.add(ann);
-        try {
-            System.out.println("    + sending asset to IA");
-            IBEISIA.sendMediaAssetsNew(maList, context);
-            myShepherd.updateDBTransaction();
-            System.out.println("    + asset sent, sending annot");
-            IBEISIA.sendAnnotationsNew(annList, context, myShepherd);
-            myShepherd.updateDBTransaction();
-            System.out.println("    + annot sent.");
-        } catch (Exception e) {
-            e.printStackTrace();
-            System.out.println("hit above exception while trying to send CR ma & annot to IA");
+	        myShepherd.getPM().makePersistent(ann);
+	        System.out.println("    + saved annotation");
+	
+	        // we need to intake mediaassets so they get acmIds and are matchable
+	        ArrayList<MediaAsset> maList = new ArrayList<MediaAsset>();
+	        maList.add(crMa);
+	        ArrayList<Annotation> annList = new ArrayList<Annotation>();
+	        annList.add(ann);
+	        try {
+	            System.out.println("    + sending asset to IA");
+	            IBEISIA.sendMediaAssetsNew(maList, context);
+	            myShepherd.updateDBTransaction();
+	            System.out.println("    + asset sent, sending annot");
+	            IBEISIA.sendAnnotationsNew(annList, context, myShepherd);
+	            myShepherd.updateDBTransaction();
+	            System.out.println("    + annot sent.");
+	        } catch (Exception e) {
+	            e.printStackTrace();
+	            System.out.println("hit above exception while trying to send CR ma & annot to IA");
+	        }
+	        System.out.println("    + done processing new CR annot");
+	        if (rightSide) {
+	            enc.setRightSpots(spots);
+	            enc.setRightReferenceSpots(refSpots);
+	        } else {
+	            enc.setSpots(spots);
+	            enc.setLeftReferenceSpots(refSpots);
+	        }
+	        // reset the entry in the GridManager graph
+	        GridManager gm = GridManagerFactory.getGridManager();
+	        gm.addMatchGraphEntry(encId, new EncounterLite(enc));
+	
+	        myShepherd.commitDBTransaction();
+	        myShepherd.closeDBTransaction();
+	
+	        JSONObject rtn = new JSONObject("{\"success\": true}");
+	        rtn.put("spotAssetId", crMa.getId());
+	        rtn.put("spotAssetUrl", crMa.webURL());
+	        response.setContentType("text/plain");
+	        PrintWriter out = response.getWriter();
+	        out.println(rtn.toString());
+	        out.close();
         }
-        System.out.println("    + done processing new CR annot");
-        if (rightSide) {
-            enc.setRightSpots(spots);
-            enc.setRightReferenceSpots(refSpots);
-        } else {
-            enc.setSpots(spots);
-            enc.setLeftReferenceSpots(refSpots);
+        catch(Exception e) {
+        	e.printStackTrace();
+        }
+        finally {
+        	myShepherd.rollbackAndClose();
         }
-        // reset the entry in the GridManager graph
-        GridManager gm = GridManagerFactory.getGridManager();
-        gm.addMatchGraphEntry(encId, new EncounterLite(enc));
-
-        myShepherd.commitDBTransaction();
-        myShepherd.closeDBTransaction();
-
-        JSONObject rtn = new JSONObject("{\"success\": true}");
-        rtn.put("spotAssetId", crMa.getId());
-        rtn.put("spotAssetUrl", crMa.webURL());
-        response.setContentType("text/plain");
-        PrintWriter out = response.getWriter();
-        out.println(rtn.toString());
-        out.close();
     }
 
     private ArrayList<SuperSpot> parseSpots(JSONArray arr) {

From cfa23fdc23e8699c1e1903f9918c5a57a64f3f94 Mon Sep 17 00:00:00 2001
From: Jon Van Oast <jon@wildme.org>
Date: Tue, 7 Jan 2025 18:20:08 -0700
Subject: [PATCH 19/20] no longer background encounter indexing itself; fix a
 duplicate rollback/close; timing/debugging on indexing (semi-temporary)

---
 src/main/java/org/ecocean/Base.java       |  3 +++
 src/main/java/org/ecocean/Encounter.java  | 31 -----------------------
 src/main/java/org/ecocean/Occurrence.java |  2 +-
 3 files changed, 4 insertions(+), 32 deletions(-)

diff --git a/src/main/java/org/ecocean/Base.java b/src/main/java/org/ecocean/Base.java
index ff94170d5d..8313503d1c 100644
--- a/src/main/java/org/ecocean/Base.java
+++ b/src/main/java/org/ecocean/Base.java
@@ -106,9 +106,12 @@ public JSONObject opensearchMapping() {
 
     public void opensearchIndex()
     throws IOException {
+        long startT = System.currentTimeMillis();
         OpenSearch opensearch = new OpenSearch();
 
         opensearch.index(this.opensearchIndexName(), this);
+        long endT = System.currentTimeMillis();
+        System.out.println("opensearchIndex(): " + (endT - startT) + "ms indexing " + this);
     }
 
     // this will index "related" objects as needed
diff --git a/src/main/java/org/ecocean/Encounter.java b/src/main/java/org/ecocean/Encounter.java
index 584e9d70cf..16a2aa8b45 100644
--- a/src/main/java/org/ecocean/Encounter.java
+++ b/src/main/java/org/ecocean/Encounter.java
@@ -4705,35 +4705,4 @@ public void sendCreationEmails(Shepherd myShepherd, String langCode) {
         }
     }
 
-    public void opensearchIndexDeep()
-    throws IOException {
-        final String encId = this.getId();
-        final Encounter origEnc = this;
-        ExecutorService executor = Executors.newFixedThreadPool(4);
-        Runnable rn = new Runnable() {
-            public void run() {
-                Shepherd bgShepherd = new Shepherd("context0");
-                bgShepherd.setAction("Encounter.opensearchIndexDeep_" + encId);
-                bgShepherd.beginDBTransaction();
-                try {
-                    Encounter enc = bgShepherd.getEncounter(encId);
-                    if (enc == null) {
-                        // we use origEnc if we can (especially necessary on initial creation of Encounter)
-                        if (origEnc != null) origEnc.opensearchIndex();
-                        bgShepherd.rollbackAndClose();
-                        executor.shutdown();
-                        return;
-                    }
-                    enc.opensearchIndex();
-                } catch (Exception e) {
-                    e.printStackTrace();
-                } finally {
-                    bgShepherd.rollbackAndClose();
-                }
-                executor.shutdown();
-            }
-        };
-
-        executor.execute(rn);
-    }
 }
diff --git a/src/main/java/org/ecocean/Occurrence.java b/src/main/java/org/ecocean/Occurrence.java
index 1f4cce4a65..f267d6cb54 100644
--- a/src/main/java/org/ecocean/Occurrence.java
+++ b/src/main/java/org/ecocean/Occurrence.java
@@ -1370,7 +1370,7 @@ public void run() {
                 try {
                     Occurrence occur = bgShepherd.getOccurrence(occurId);
                     if ((occur == null) || (occur.getEncounters() == null)) {
-                        bgShepherd.rollbackAndClose();
+                        // rollbackAndClose handled by finally
                         executor.shutdown();
                         return;
                     }

From ae7cf1f13d1527b5d031c9162a80bc44497b00ba Mon Sep 17 00:00:00 2001
From: holmbergius <holmbergius@gmail.com>
Date: Sat, 11 Jan 2025 11:52:22 -0800
Subject: [PATCH 20/20] Setting version to 10.5.3

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 0b38baacda..b25fdff89a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.ecocean</groupId>
   <artifactId>wildbook</artifactId>
-  <version>10.5.2</version>
+  <version>10.5.3</version>
   <packaging>war</packaging>
 
   <properties>