Base/3.4.1

.github/ISSUE_TEMPLATE/bug.md

@@ -0,0 +1,58 @@
+---
+name: Bug Ticket
+about: Follow this template when reporting a new bug
+title: "[BUG] "
+labels: ["bug"]
+assignees: []
+---
+
+# Required
+
+## Summary
+
+## Github Issue/Projects Fields
+
+- [ ] Populate label(s) (e.g., bug, etc.)
+- [ ] Populate the GitHub Projects fields (e.g., status, priority, affected branch, etc.)
+- [ ] If relevant, add reference to original osTicket: 
+
+# Optional
+
+## Environment Details
+
+**Symbiota Portal URL:**
+
+**Browser:**
+
+**Operating System:** <!-- e.g., Windows 11, macOS 14, Ubuntu 22.04 -->
+
+**Device:** <!-- e.g., Desktop, Mobile, Tablet -->
+
+## Current Behavior
+
+<!-- Describe what is currently happening -->
+
+## Expected Behavior
+
+<!-- Describe what you expected to happen -->
+
+## Steps to Reproduce
+
+<!-- If reporting a problem, provide detailed steps to reproduce the issue -->
+
+1. Go to '...'
+2. Click on '...'
+3. Enter '...'
+4. See error
+
+## Screenshots/Attachments
+
+<!-- If applicable, add screenshots, error logs, or other files to help explain your problem -->
+
+## Error Messages
+
+<!-- If you're seeing any error messages, please copy and paste them here -->
+
+```
+Paste error message here
+```

.github/ISSUE_TEMPLATE/newfeature.md

@@ -0,0 +1,54 @@
+---
+name: New Feature Ticket
+about: Follow this template when requesting a new feature
+title: "[FEATURE] "
+labels: ["feature", "feature description"]
+assignees: []
+---
+
+# Required
+
+## Summary
+
+## Github Issue/Projects Fields
+
+- [ ] Populate label (e.g., enhancement, etc.)
+- [ ] Populate the github projects fields (e.g., status, feature description, priority, affected branch)
+- [ ] For any new pages that will be generated by this feature, add those pages to the [Symbiota-Laravel github issues](https://github.com/Symbiota/Symbiota-Laravel/issues) with a "Page porting" tag. Link it to this issue.
+- [ ] If relevant, add reference to original osTicket:
+
+# Ideal
+
+## User Stories/Detailed Outline of All of the Specs
+
+Avoid specific implementation details here. This section is for what needs to be done, not how it should be done.
+
+- As a super admin, I want to be able to ...
+- As a collection admin, I want to be able to ...
+- As a signed in user with no admin authorizations, I want to be able to ...
+- As an anonymous user, I want to be able to ...
+- Etc.
+
+## Implementation Details
+
+If any specifics have been ironed out during the feature planning, add them here.
+
+## Acceptance Criteria
+
+- [ ] Criterion 1
+- [ ] Criterion 2
+- [ ] ...
+
+## Dependencies
+
+- [ ] List any dependencies, blockers, or prerequisites
+- [ ] Related issues or PRs that need to be completed first
+
+## Documentation
+
+- [ ] API documentation updates needed
+
+## Additional Context
+
+Add any other context, screenshots, mockups, or examples that would be helpful.
+

.github/PULL_REQUEST_TEMPLATE/feature_or_bugfix.md

@@ -0,0 +1,26 @@
+# Pull Request Checklist:
+
+## Pre-Approval
+
+- [ ] Does the PR have a **release-notes-friendly title**?
+- [ ] There is a **description section** in the pull request that details what the proposed changes do. It can be very brief if need be, but it ought to exist.
+- [ ] Features and backlog bugs should be merged into the `Development` branch, **NOT** `master`
+
+- [ ] All new **text** is preferably **internationalized** (i.e., no end-user-visible text is hard-coded on the PHP pages), and the [spreadsheet tracking internationalizations](https://docs.google.com/spreadsheets/d/133fps9w2pUCEjUA6IGCcQotk7dn9KvepMXJ2IWUZsE8/edit?usp=sharing) has been updated either with a new row or with checkmarks to existing rows.
+- [ ] There are **no linter errors**
+- [ ] New features have **responsive design** (i.e., look aesthetically pleasing both full screen and with small or mobile screens)
+- [ ] [**Symbiota coding standards**](https://docs.google.com/document/d/1-FwCZP5Zu4f-bPwsKeVVsZErytALOJyA2szjbfSUjmc/edit?usp=sharing) have been followed
+- [ ] If any files have been reformatted (e.g., by an **autoformatter**), the reformat is its own, **separate commit** in the PR
+- [ ] Comment which **GitHub issue(s)**, if any does this PR address
+- [ ] If this PR makes any changes that would require **additional configuration** of any Symbiota portals outside of the files tracked in this repository, make sure that those changes are **detailed in [this document]**(https://docs.google.com/document/d/1T7xbXEf2bjjm-PMrlXpUBa69aTMAIROPXVqJqa2ow_I/edit?usp=sharing)
+- [ ] If this **feature** has not been **documented** in [https://docs.symbiota.org/](https://docs.symbiota.org/) OR if changes are needed to the documentation, create a new github issue in [https://github.com/Symbiota/Symbiota/issues](https://github.com/Symbiota/Symbiota/issues) **labeled as documentation** and **add a link** to it herein.
+- [ ] If there are **merge conflicts** with this PR's **parent branch, resolve** them before marking the PR as ready for review.
+
+## Post-Approval
+
+- [ ] It is the code author's responsibility to **merge** their own pull request after it has been approved
+- [ ] Remember to use the **squash & merge** option when merging into the Development branch.
+- [ ] Don't forget to **delete** your feature **branch** upon merge. Ignore this step as required.
+- [ ] **Close** relevant github **issues** as warranted
+
+Thanks for contributing and keeping it clean!

.github/PULL_REQUEST_TEMPLATE/general_release.md

@@ -0,0 +1,12 @@
+# Pull Request Checklist:
+
+## Pre-Approval
+- [ ] **increment** the Symbiota **version** number in the symbase.php file and commit to the `Development` branch
+
+## Post-Approval
+
+- [ ] It is the code author's responsibility to **merge** their own pull request after it has been approved
+- [ ] **Close** relevant github **issues** as warranted
+- [ ] If this PR represents a merge from the `_rc` branch into the master branch, remember to use the **merge** option
+
+Thanks for contributing and keeping it clean!

.github/PULL_REQUEST_TEMPLATE/hotfix.md

@@ -0,0 +1,28 @@
+# Pull Request Checklist:
+
+## Pre-Approval
+
+- [ ] Does the PR have a **release-notes-friendly title**?
+- [ ] There is a **description section** in the pull request that details what the proposed changes do. It can be very brief if need be, but it ought to exist.
+- [ ] Hotfixes should be branched off of the `master` branch and PR'd using the **squash & merge** option into the `Hotfix-x.x.x` branch.
+
+- [ ] All new **text** is preferably **internationalized** (i.e., no end-user-visible text is hard-coded on the PHP pages), and the [spreadsheet tracking internationalizations](https://docs.google.com/spreadsheets/d/133fps9w2pUCEjUA6IGCcQotk7dn9KvepMXJ2IWUZsE8/edit?usp=sharing) has been updated either with a new row or with checkmarks to existing rows.
+- [ ] There are **no linter errors**
+- [ ] New features have **responsive design** (i.e., look aesthetically pleasing both full screen and with small or mobile screens)
+- [ ] [**Symbiota coding standards**](https://docs.google.com/document/d/1-FwCZP5Zu4f-bPwsKeVVsZErytALOJyA2szjbfSUjmc/edit?usp=sharing) have been followed
+- [ ] If any files have been reformatted (e.g., by an **autoformatter**), the reformat is its own, **separate commit** in the PR
+- [ ] Comment which **GitHub issue(s)**, if any does this PR address
+- [ ] If this PR makes any changes that would require **additional configuration** of any Symbiota portals outside of the files tracked in this repository, make sure that those changes are **detailed in [this document]**(https://docs.google.com/document/d/1T7xbXEf2bjjm-PMrlXpUBa69aTMAIROPXVqJqa2ow_I/edit?usp=sharing)
+- [ ] If this **feature** has not been **documented** in [https://docs.symbiota.org/](https://docs.symbiota.org/) OR if changes are needed to the documentation, create a new github issue in [https://github.com/Symbiota/Symbiota/issues](https://github.com/Symbiota/Symbiota/issues) **labeled as documentation** and **add a link** to it herein.
+- [ ] If there are **merge conflicts** with this PR's **parent branch, resolve** them before marking the PR as ready for review.
+
+## Post-Approval
+
+- [ ] It is the code author's responsibility to **merge** their own pull request after it has been approved
+- [ ] Remember to use the **squash & merge** option for a merge into the `hotfix` branch
+- [ ] Use the **merge** option (not squashed) for merges from the `hotfix` branch into the `master` branch.
+  - [ ] a **subsequent PR from `master`** into `Development` should be made with the **merge** option (i.e., no squash)
+  - [ ] **Immediately** **delete the `hotfix` branch** and create a new `hotfix` branch
+  - [ ] **increment** the Symbiota **version** number in the symbase.php file and commit to the `hotfix` branch
+
+Thanks for contributing and keeping it clean!

.github/pull_request_template.md

@@ -0,0 +1,5 @@
+Please go to the `Preview` tab and select the appropriate sub-template:
+
+* [Feature or Bugfix](?expand=1&template=feature_or_bugfix.md)
+* [Hotfix](?expand=1&template=hotfix.md)
+* [General Release](?expand=1&template=general_release.md)

.gitignore

@@ -6,6 +6,7 @@
 /leftmenu.php
 /index.php
 includes/header.php
+includes/minimalheader.php
 includes/footer.php
 includes/head.php
 includes/leftmenu.php
@@ -15,3 +16,5 @@ includes/citationgbif.php
 includes/citationcollection.php
 includes/citationdataset.php
 includes/citationportal.php
+includes/donationButton.php
+temp/cap_storage.json

README.md

@@ -1,3 +1,13 @@
+<p align="center">
+    <a href="https://symbiota.org/" target="_blank">
+        <picture>
+		    <source width="500" media="(prefers-color-scheme: dark)" srcset="https://github.com/user-attachments/assets/94a3507e-675f-4fe8-8504-12a567f268e9">
+   		    <source width="500" media="(prefers-color-scheme: light)" srcset="https://github.com/user-attachments/assets/a3897966-7240-4345-ae27-af095adfdde0">
+            <img width="500px" src="https://github.com/user-attachments/assets/94a3507e-675f-4fe8-8504-12a567f268e9" />
+		</picture>
+    </a>
+</p>
+
 This fork of the Symbiota code is actively being developed by the Symbiota Support Hub (SSH, https://symbiota.org/about-us) development team at the University of Kansas Biodiversity Institute.
 Even though SSH code developments are regularly pushed back to this repository, we recommend that you download/fork code directly from the
 Symbiota/Symbiota repository (https://github.com/Symbiota/Symbiota) to ensure that you obtain the most recently code changes.
@@ -10,7 +20,7 @@ The Symbiota Software Project is building a library of webtools to aid biologist
 
 More information about this project can be accessed through [https://symbiota.org](https://symbiota.org).
 
-For documentation and user guides please visit [Symbiota Docs](https://symbiota.org/docs).
+For documentation and user guides please visit [Symbiota Docs](https://docs.symbiota.org/).
 
 ## ACKNOWLEDGEMENTS
 

accessibility/module.php

@@ -1,7 +1,8 @@
 <?php
-if($LANG_TAG == 'en' || !file_exists($SERVER_ROOT.'/content/lang/templates/accessibility.' . $LANG_TAG . '.php'))
-	include_once($SERVER_ROOT . '/content/lang/templates/accessibility.en.php');
-else include_once($SERVER_ROOT . '/content/lang/templates/accessibility.' . $LANG_TAG . '.php');
+include_once($SERVER_ROOT . '/classes/utilities/Language.php');
+
+Language::load('templates/accessibility');
+
 ?>
 <dialog id="accessibility-modal" class="accessibility-dialog" aria-label="<?= $LANG['A_ACCESSIBILITY_OPTIONS']; ?>">
 	<h1><?= $LANG['A_ACCESSIBILITY_OPTIONS']; ?></h1>

admin/othercatalog.php

@@ -0,0 +1,63 @@
+<?php
+include_once('../config/symbini.php');
+//Manual Permission Check
+if($LANG_TAG != 'en' && file_exists($SERVER_ROOT . '/content/lang/prohibit.' . $LANG_TAG . '.php')) include_once($SERVER_ROOT.'/content/lang/prohibit.' . $LANG_TAG . '.php');
+else include_once($SERVER_ROOT . '/content/lang/prohibit.en.php');
+
+if (!$IS_ADMIN) {
+    echo '<h1>' . $LANG['FORBIDDEN'] . '</h1>';
+    echo $LANG['NO_PERMISSION'];
+    exit;
+}
+include_once($SERVER_ROOT . '/classes/OtherCatalog.php');
+ini_set('max_execution_time', 300);
+
+//allow partial bufferring, real-time updates on progress
+@apache_setenv('no-gzip', 1);
+@ini_set('zlib.output_compression', 0);
+@ini_set('implicit_flush', 1);
+ob_implicit_flush(1);
+while (ob_get_level() > 0) ob_end_flush();
+$message = '';
+
+if ($_SERVER['REQUEST_METHOD'] === 'POST' && isset($_POST['run_copy'])) {
+    $conn = MySQLiConnectionFactory::getCon("write");
+
+    if (!$conn) {
+        $message = "Failed to connect to the database.";
+    } else {
+        $catalogCopier = new OtherCatalog($conn, $GLOBALS['SYMB_UID']);
+        $result = $catalogCopier->copyOtherCatalogNumbers();
+
+        $message = "Processed {$result['processed']} records. Inserted {$result['inserted']} new row(s) into omoccuridentifiers.<br>{$result['time']}";
+        $conn->close();
+    }
+}
+?>
+
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>Copy Other Catalog Numbers</title>
+    <?php include_once($SERVER_ROOT.'/includes/head.php'); ?>
+</head>
+<body>
+<?php include($SERVER_ROOT.'/includes/header.php'); ?>
+
+<div class="container" id="innertext">
+    <h2>Copy Other Catalog Numbers to Identifier Table</h2>
+    <p>This tool copies all non-empty otherCatalogNumbers from the omoccurrences table to the omoccuridentifiers table, unless values in omoccuridentifiers already exist. Each value is inserted as a new row using the current user ID as modifiedUID.</p>
+
+    <?php if (!empty($message)): ?>
+        <div class="successbox"><?= $message ?></div>
+    <?php endif; ?>
+
+    <form method="post">
+        <button type="submit" name="run_copy" class="button">Run Copy Process</button>
+    </form>
+</div>
+
+<?php include($SERVER_ROOT.'/includes/footer.php'); ?>
+</body>
+</html>