Merge branch 'subspecies-search-support' into africancarnivorewildboo…

…k-acw

# Conflicts:
#	archive/fixSomeFields.jsp
#	archive/individualGalleryPanel.jsp
#	src/main/java/org/ecocean/Annotation.java
#	src/main/java/org/ecocean/CommonConfiguration.java
#	src/main/java/org/ecocean/Encounter.java
#	src/main/java/org/ecocean/EncounterQueryProcessor.java
#	src/main/java/org/ecocean/LocationID.java
#	src/main/java/org/ecocean/MetricsBot.java
#	src/main/java/org/ecocean/Occurrence.java
#	src/main/java/org/ecocean/Shepherd.java
#	src/main/java/org/ecocean/StartupWildbook.java
#	src/main/java/org/ecocean/Util.java
#	src/main/java/org/ecocean/identity/IBEISIA.java
#	src/main/java/org/ecocean/security/HiddenDataReporter.java
#	src/main/java/org/ecocean/servlet/SessionExtend.java
#	src/main/java/org/ecocean/servlet/export/EncounterAnnotationExportExcelFile.java
#	src/main/java/org/ecocean/servlet/export/EncounterSearchExportMetadataExcel.java
#	src/main/java/org/ecocean/servlet/export/EncounterSearchExportShapefile.java
#	src/main/java/org/ecocean/servlet/export/ExportColumn.java
#	src/main/java/org/ecocean/servlet/export/OccurrenceSearchExportMetadataExcel.java
#	src/main/resources/bundles/contexts.properties
#	src/main/resources/bundles/en/header.properties
#	src/main/resources/bundles/en/index.properties
#	src/main/resources/bundles/en/pictureBook.properties
#	src/main/resources/bundles/es/header.properties
#	src/main/resources/bundles/fr/header.properties
#	src/main/resources/bundles/fr/index.properties
#	src/main/resources/bundles/fr/submit.properties
#	src/main/resources/bundles/fr/users.properties
#	src/main/resources/bundles/googleKeys.properties
#	src/main/resources/bundles/it/header.properties
#	src/main/resources/bundles/it/submit.properties
#	src/main/resources/bundles/locationID.json
#	src/main/resources/bundles/submitActionClass.properties
#	src/main/resources/emails/en/adoptionSpotting.html
#	src/main/resources/emails/en/individualAddEncounter.html
#	src/main/resources/emails/en/individualCreate.html
#	src/main/resources/emails/en/individualUpdate.html
#	src/main/resources/emails/en/oneTimeDonation.html
#	src/main/webapp/appadmin/iaBreakdownBySpecies.jsp
#	src/main/webapp/contactus.jsp
#	src/main/webapp/cust/mantamatcher/styles/_bootstrap-overrides.less
#	src/main/webapp/encounters/manualAnnotation.jsp
#	src/main/webapp/header.jsp
#	src/main/webapp/javascript/bubbleDiagram/encounter-calls.js
#	src/main/webapp/match.jsp
#	src/main/webapp/privacyPolicy.jsp
#	src/main/webapp/termsOfUse.jsp

.factorypath

@@ -232,4 +232,4 @@
     <factorypathentry kind="VARJAR" id="M2_REPO/org/glassfish/javax.json/1.0.4/javax.json-1.0.4.jar" enabled="true" runInBatchMode="false"/>
     <factorypathentry kind="VARJAR" id="M2_REPO/sutime-stanford-corenlp-models/sutime-stanford-corenlp-models/3.6.0/sutime-stanford-corenlp-models-3.6.0.jar" enabled="true" runInBatchMode="false"/>
     <factorypathentry kind="VARJAR" id="M2_REPO/edu/stanford/nlp/stanford-parser/3.7.0/stanford-parser-3.7.0.jar" enabled="true" runInBatchMode="false"/>
-</factorypath>
+</factorypath>

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,19 @@
+---
+name: Bug report
+about: A problem you find in Wildbook. Can be technical or user-facing
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Expected Behavior**
+If a user-facing issue, provide step-by-step instructions in a numbered list for test purposes
+If a technical issue, provide a general description of what the code should be doing and expected effects of the change.
+
+**Current Behavior**
+If a user-facing issue, provide step-by-step instructions for reproducibility and, at a minimum, the page on which the issue is occurring. If the issue is not consistently reproducible, add the `question` label
+If a technical issue, provide a general description of the problem, where in the code the issue was found.
+
+**Testing Notes**
+If there's any additional considerations for testing, such a secondary confirmation paths, failure or success states, etc, include here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/wild-me-feature.md

@@ -0,0 +1,21 @@
+---
+name: Wild Me feature
+about: Features generated by Wild Me team
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+## Feature description and context
+Why this feature? Why now?
+
+## Feature sign-off requirements
+Provide a list of tasks that, once complete, the feature will be done
+
+## Design
+- Figma link (static or prototype; specify)
+- Component list/reference
+- Navigation sitemap
+- Product theme references and any known in-line customization that may be needed
+- Are there images needed for design? (attach below in zip)

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "maven"
+    directory: "/" # Location of pom.xml
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "github-actions"
+    directory: "/"  #actions are all over the build, need to clean up before can get specific
+    schedule:
+      interval: "weekly"

.github/workflows/maven-publish.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up JDK 1.8
       uses: actions/setup-java@v1

.github/workflows/nightly.yml

@@ -1,6 +1,7 @@
 name: Nightly
 
 on:
+  workflow_dispatch:
   push:
     branches:
       - master
@@ -9,12 +10,6 @@ on:
       - 'v**'
   release:
     types: [created]
-  schedule:
-    - cron: '0 0 * * *' # Every day at midnight
-  pull_request:
-    paths:
-      - '.github/workflows/nightly.yml'
-      - 'devops/**'
 
 jobs:
   devops:
@@ -23,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       # Build containers
       - name: Build containers
@@ -40,6 +35,3 @@ jobs:
       - name: Push to GitHub Packages
         run: bash devops/publish.sh -t nightly -r docker.pkg.github.com
 
-      - name: Push to Docker Hub
-        if: github.event_name == 'schedule'
-        run: bash devops/publish.sh -t nightly

.gitignore

@@ -1,4 +1,5 @@
-.settings
+.settings/
+.project
 .factorypath
 *.DS_Store
 target
@@ -24,6 +25,7 @@ src/main/webapp/encounters/*20*
 src/main/caribwhale_data_dir
 /webapps
 /src/main/webapp/javascript/git-info.json
+/src/main/webapp/react/
 /node_modules
 .vscode/
 *.swp
@@ -32,3 +34,9 @@ src/main/caribwhale_data_dir
 .classpath
 
 catalina.base_IS_UNDEFINED
+
+/frontend/node_modules
+/frontend/dist
+/frontend/.env
+/frontend/build
+/frontend/.env

.husky/java/canonicalize_filename.sh

@@ -0,0 +1,48 @@
+#!/bin/sh
+
+# Provide the canonicalize filename (physical filename with out any symlinks)
+# like the GNU version readlink with the -f option regardless of the version of
+# readlink (GNU or BSD).
+
+# This file is part of a set of unofficial pre-commit hooks available
+# at github.
+# Link:    https://github.com/ddddavidmartin/Pre-commit-hooks
+# Contact: David Martin, [email protected]
+
+###########################################################
+# There should be no need to change anything below this line.
+
+# Canonicalize by recursively following every symlink in every component of the
+# specified filename.  This should reproduce the results of the GNU version of
+# readlink with the -f option.
+#
+# Reference: http://stackoverflow.com/questions/1055671/how-can-i-get-the-behavior-of-gnus-readlink-f-on-a-mac
+canonicalize_filename () {
+    local target_file="$1"
+    local physical_directory=""
+    local result=""
+
+    # Need to restore the working directory after work.
+    local working_dir="`pwd`"
+
+    cd -- "$(dirname -- "$target_file")"
+    target_file="$(basename -- "$target_file")"
+
+    # Iterate down a (possible) chain of symlinks
+    while [ -L "$target_file" ]
+    do
+        target_file="$(readlink -- "$target_file")"
+        cd -- "$(dirname -- "$target_file")"
+        target_file="$(basename -- "$target_file")"
+    done
+
+    # Compute the canonicalized name by finding the physical path
+    # for the directory we're in and appending the target file.
+    physical_directory="`pwd -P`"
+    result="$physical_directory/$target_file"
+
+    # restore the working directory after work.
+    cd -- "$working_dir"
+
+    echo "$result"
+}

.husky/java/pre-commit-uncrustify

@@ -0,0 +1,154 @@
+#!/bin/sh
+
+# git pre-commit hook that runs an Uncrustify stylecheck.
+# Features:
+#  - abort commit when commit does not comply with the style guidelines
+#  - create a patch of the proposed style changes
+#
+# More info on Uncrustify: http://uncrustify.sourceforge.net/
+
+# This file is part of a set of unofficial pre-commit hooks available
+# at github.
+# Link:    https://github.com/ddddavidmartin/Pre-commit-hooks
+# Contact: David Martin, [email protected]
+
+##################################################################
+# There should be no need to change anything below this line.
+# For configuration see pre-commit-uncrustify.cfg and
+# pre-commit-uncrustify.example.cfg.
+
+. "$(dirname -- "$0")/java/canonicalize_filename.sh"
+
+# exit on error
+set -e
+
+# Absolute path to this script, e.g. /home/user/bin/foo.sh
+SCRIPT="$(canonicalize_filename "$0")"
+# Absolute path this script is in, e.g. /home/user/bin/
+SCRIPTPATH="$(dirname -- "$SCRIPT")/java"
+CONFIG="$SCRIPTPATH/pre-commit-uncrustify.cfg"
+
+
+if [ ! -f "$CONFIG" ] ; then
+    echo "Missing config file $CONFIG."
+    exit 1
+else
+    . "$CONFIG"
+fi
+
+# NOTE: just hard-coding this rather than using $CONFIG, cuz it was
+#   not working with relative path
+UNCRUST_CONFIG="$SCRIPTPATH/uncrustify-style.cfg"
+UNCRUSTIFY="$SCRIPTPATH/uncrustify"
+
+# check whether the given file matches any of the set extensions
+matches_extension() {
+    local filename="$(basename -- "$1")"
+    local extension=".${filename##*.}"
+    local ext
+
+    for ext in $FILE_EXTS; do [ "$ext" = "$extension" ] && return 0; done
+
+    return 1
+}
+
+# necessary check for initial commit
+if git rev-parse --verify HEAD >/dev/null 2>&1 ; then
+    against=HEAD
+else
+    # Initial commit: diff against an empty tree object
+    against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
+fi
+
+# make sure the config file and executable are correctly set
+if [ ! -f "$UNCRUST_CONFIG" ] ; then
+    printf "Error: uncrustify config file not found.\n"
+    printf "Set the correct path in $CONFIG.\n"
+    exit 1
+fi
+
+if ! command -v "$UNCRUSTIFY" > /dev/null ; then
+    printf "Error: uncrustify executable not found.\n"
+    printf "Set the correct path in $CONFIG.\n"
+    exit 1
+fi
+
+# create a filename to store our generated patch
+prefix="pre-commit-uncrustify"
+suffix="$(date +%C%y-%m-%d_%Hh%Mm%Ss)"
+patch="/tmp/$prefix-$suffix.patch"
+
+# clean up any older uncrustify patches
+$DELETE_OLD_PATCHES && rm -f /tmp/$prefix*.patch
+
+# create one patch containing all changes to the files
+# sed to remove quotes around the filename, if inserted by the system
+# (done sometimes, if the filename contains special characters, like the quote itself)
+git diff-index --cached --diff-filter=ACMR --name-only $against -- | \
+sed -e 's/^"\(.*\)"$/\1/' | \
+while read file
+do
+    # ignore file if we do check for file extensions and the file
+    # does not match any of the extensions specified in $FILE_EXTS
+    if $PARSE_EXTS && ! matches_extension "$file"; then
+        continue;
+    fi
+
+    # escape special characters in the source filename:
+    # - '\': backslash needs to be escaped
+    # - '*': used as matching string => '*' would mean expansion
+    #        (curiously, '?' must not be escaped)
+    # - '[': used as matching string => '[' would mean start of set
+    # - '|': used as sed split char instead of '/', so it needs to be escaped
+    #        in the filename
+    # printf %s particularly important if the filename contains the % character
+    file_escaped_source=$(printf "%s" "$file" | sed -e 's/[\*[|]/\\&/g')
+
+    # escape special characters in the target filename:
+    # phase 1 (characters escaped in the output diff):
+    #     - '\': backslash needs to be escaped in the output diff
+    #     - '"': quote needs to be escaped in the output diff if present inside
+    #            of the filename, as it used to bracket the entire filename part
+    # phase 2 (characters escaped in the match replacement):
+    #     - '\': backslash needs to be escaped again for sed itself
+    #            (i.e. double escaping after phase 1)
+    #     - '&': would expand to matched string
+    #     - '|': used as sed split char instead of '/'
+    # printf %s particularly important if the filename contains the % character
+    file_escaped_target=$(printf "%s" "$file" | sed -e 's/[\"]/\\&/g' -e 's/[\&|]/\\&/g')
+
+    # Uncrustify detects the language automatically if it is not specified
+    language_option=""
+    if [ "$SOURCE_LANGUAGE" != "AUTO" ] ; then
+        language_option="-l $SOURCE_LANGUAGE"
+    fi
+
+    # uncrustify our sourcefile, create a patch with diff and append it to our $patch
+    # The sed call is necessary to transform the patch from
+    #    --- $file timestamp
+    #    +++ - timestamp
+    # to both lines working on the same file and having a a/ and b/ prefix.
+    # Else it can not be applied with 'git apply'.
+    "$UNCRUSTIFY" -c "$UNCRUST_CONFIG" -f "$file" $language_option | \
+        diff -u -- "$file" - | \
+        sed -e "1s|--- $file_escaped_source|--- \"a/$file_escaped_target\"|" -e "2s|+++ -|+++ \"b/$file_escaped_target\"|" >> "$patch"
+done
+
+# if no patch has been generated all is ok, clean up the file stub and exit
+if [ ! -s "$patch" ] ; then
+    printf "Files in this commit comply with the uncrustify rules.\n"
+    rm -f "$patch"
+    exit 0
+fi
+
+# a patch has been created, notify the user and exit
+printf "\nThe following differences were found between the code to commit "
+printf "and the uncrustify rules:\n\n"
+cat "$patch"
+
+printf "\nYou can apply these changes with:\n git apply $patch\n"
+printf "(may need to be called from the root directory of your repository)\n"
+printf "Aborting commit. Apply changes and commit again or skip checking with"
+printf " --no-verify (not recommended).\n"
+
+exit 1