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Recent Releases of Symbiota

Symbiota - v3.4.1

What's Changed

New Contributors

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.4...v3.4.1

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 11 days ago

Symbiota - v3.4

What's Changed

New Contributors

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.13...v3.4.0

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 24 days ago

Symbiota - v3.3.13

What's Changed

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.12...v3.3.13

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 2 months ago

Symbiota - v3.3.12

What's Changed

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.11...v3.3.12

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 4 months ago

Symbiota - v3.3.11

What's Changed

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.10...v3.3.11

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 5 months ago

Symbiota - v3.3.10

What's Changed

Hotfix 3.3.10 by @GregoryPost in https://github.com/Symbiota/Symbiota/pull/2980

  • Occurrence Table Display bug
  • Adjustments default footer logos (#2927)
  • Extended Data Import bug
  • Refactor the queries in indexOccurrenceTaxa using the QueryUtil::executeQuery to better handle error behavior
  • Fix image sort bug. Resolves issue: https://github.com/Symbiota/Symbiota/issues/2946
  • Add missing array key check before the for loop in collections/editor/includes/traittab.php
  • Fix syntax error in the getCharList function where countMin was accidentally being included inside the string and was not being explicitly type cast to a float first
  • Checklist bug fix (#2968)
  • Fix register function to only use Bcrypt if enabled (#2976)

Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: atticus29 mark.aaron.fisher@gmail.com
Co-authored-by: Katie Pearson katelin.d.pearson24@gmail.com
Co-authored-by: Samanta Orellana
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.9...v3.3.10

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 5 months ago

Symbiota - v3.3.9

What's Changed

  • Hotfix 3.3.9 by @GregoryPost in https://github.com/Symbiota/Symbiota/pull/2923
    • Closes #2892 Convert deprecated mimes to allow equivalents if able
    • Build collection map search query without html echo for json response
    • Added the speciesName label block (#2898)
    • Fix the submit type order (#2902)
    • Prioritze audio/mpeg for mp3 inference
    • Fix bug where desired processing status is not respected in tesseract OCR pipeline
    • Make the procStatus follow the same pattern of handling the null string as seen in e.g. classes/SpecProcessorManager.php
    • Fix bug in reorderElements where revisedDesired was not being referenced for currentChildIdxInDesiredList.
    • Inventory listing adjustments - Don't display ID key link within inventory listing unless explicitly activated for given key or globally within symbini and not deactivated within key
    • DwC-A publishing adjustments
      • Temporarily remove associatedOccurrences input within the DwC-Simple data concept. Field be re-added in v3.4.
      • Do not override associatedTaxa with data from the associations tables. This will likely return in v3.4
      • Temporarily remove exsiccati data insert into dynamicProperties field

Co-authored-by: atticus29 mark.aaron.fisher@gmail.com
Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: Edward Gilbert egbot@asu.edu

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.8...v3.3.9

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 6 months ago

Symbiota - v3.3.8

What's Changed

  • Readme symbiota icon by @MuchQuak in https://github.com/Symbiota/Symbiota/pull/2864
  • Documentation Improvements by @MuchQuak in https://github.com/Symbiota/Symbiota/pull/2715
  • Fixing Typo in install.md by @MuchQuak in https://github.com/Symbiota/Symbiota/pull/2869
  • Add labels handle for taxa autosuggest (#2856)
  • Bug fixes: Isolate cleaning underscores from search terms to scientific names only, fix bug blocking material sample updates, personal specimen download bugfix (fixes issue blocking non-superAdmin from downloading backups of personal specimen management)
  • Add autofill to Add Occurrence Function (moves getCountry function to geographic thesaurus from OccurrenceSkeletal and add it to OccurrenceEditorManager's addOccurrence function to keep behavior the same)
  • Openid no sid gracefull fail (skip linking sid if none provided)
  • Isolate behavior to old skeletal submit

Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com
Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Greg Post gregory.post@ku.edu
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.7...v3.3.8

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by Atticus29 6 months ago

Symbiota - v3.3.7

What's Changed

  • Hotfix 3.3.7 by @GregoryPost in https://github.com/Symbiota/Symbiota/pull/2854

  • Add host check to rss feed publisher

  • Remove client root from path if it exists to prevent overlap with server root

  • Occurrence Profile Error - string concatenation missing within exsiccati function

  • Remove css elements that were causing 404 & 403 errors (#2833)

  • Closes #2826 Add tidinterpreted to submit

  • Deprecate OccurrenceSkeletal in favor of using OccurrenceEditorManager - elated to #2826

  • Fix broken Symbiota docs links on search page (#2832)

  • Fix issue with old function name reference not being cleaned up

  • Closes #2840 fix password auth failure on password resets

  • Add Dynamic Memory Adjustment for Image Derivative Creation - Issue https://help.symbiota.org/scp/tickets.php?id=6261

  • Fix personal occurrence backup tool

  • Revert back end to verbatimAttributes, recordnumber, and recordedby (#2844)

  • Change extension check to cross reference for synonyms if not equal - # Issue #2846

  • Add octal to mkdir for windows support

  • Fix issue where null family does not save images

  • Various bug and issues with loan specimen check-in

  • Fix form rest to also change form layout to match Checkboxs

  • Occurrence editor bug - Bug fix that avoids conversion of recordsecurity value of 0 to save as null

  • Seperate layout from form reset

  • Upload fix - Convert NULL localitysecurity values to 0 within the Occurrence utility cleaning function, which fixes null localitysecurity imports.

  • Add function removeThirdPartySid - Needed to remove stale 3rd party sessions from DB

Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Katie Pearson katelin.d.pearson24@gmail.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: Mark mark.aaron.fisher@gmail.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.6...v3.3.7

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 7 months ago

Symbiota - v3.3.6

Hotfix 3.3.6 (https://github.com/Symbiota/Symbiota/pull/2807)

Security improvements

  • Add bcyrpt password hashing and check functions
  • Add new hashing for registering users
  • Add slash to password reset email body (https://github.com/Symbiota/Symbiota/pull/2767)
  • Remove Option to run portal with http, session is http secure always
  • Set SymbiotaCrumb to be secure and httpOnly
  • Add Toggle for https only
  • Move to using bcyrpt for hashing
  • remove manual server salt because wouldn't help plus lib already does this
  • Swap over to use new hashing and add rehashing rollover
  • Fix logout errors when refurl is missing and logout redirect target
  • Save MS Word label files to TEMP_DIR_ROOT
  • Remap downloads that explicitly point to /temp/download to point to TEMP_DIR_ROOT
  • Remove code that sets exports to /temp/download if TEMP_DIR_ROOT is not defined within symbini file
  • Remap report generation to official temp dir
  • labeldefault.json is used to define the default label format for a new installation, or an old installation that doesn't have a custom labeljson.php file defined, which would need to be manually converted to label.json

Misc issues addressed

  • When create a directory use 764 instead of 744 so that if ownership commands change the owner away from apache then it is still writable.
  • Handle unwritable media delete and add
  • Adds is_writable check to upload on target path
  • Adds new exception to handle filepaths not be writable with translations
  • Closes https://github.com/Symbiota/Symbiota/issues/2777 Lower case extensions before comparision
  • added bold fonts to required in obs submit, fixed typos in dwca publishing (https://github.com/Symbiota/Symbiota/pull/2776)
  • Add tryExectueQuery Function
  • Add conditional to executeQuery to prevent error if bind did not work
  • get rid of unused function and param that had backwards compatability issues
  • Add fixed width to glossary image instead of getimagesize
  • added onerror default image for collection icons (https://github.com/Symbiota/Symbiota/pull/2791)
  • Revert mysqli error reporting behavior to match php prior to 8.1 - This is a temporary fix that should be resolved in a future release.
  • Make Execute Query always throw exception regardless of mysqli reporting to keep behavior consistent
  • Adds a str_replace to get_ocdcurrence_upload_path function to fix issue with collections or institutions that have spaces in them
  • Voucher search by country fix (https://github.com/Symbiota/Symbiota/pull/2800)
  • added country check for vouchers
  • Add more prepared statements to ProfileManager.php (https://github.com/Symbiota/Symbiota/pull/2782)
  • refactor deleteUserTaxonomy to leverage prepared statements
  • fix issue where I forgot to comment the store_result call back in (https://github.com/Symbiota/Symbiota/pull/2801)
  • Added check that requires temp directory to be set for DwC-A download with error message displayed if temp path is not set or doesn't exist
  • Add improved error handling for download, but this can be improved and extended

Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Greg Post gregory.post@ku.edu
Co-authored-by: Edward Gilbert egilbert@ku.edu
Co-authored-by: Mark mark.aaron.fisher@gmail.com
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by egbot 7 months ago

Symbiota - v3.3.5

Hotfix 3.3.5 (https://github.com/Symbiota/Symbiota/pull/2763)

  • Restore functionality of https://github.com/Symbiota/Symbiota/pull/2619/files (https://github.com/Symbiota/Symbiota/pull/2747)
  • Seperate media classes into own files for modular usage
  • Add UploadUtil with some generalized classes from media
  • Replace parseFileName with path info
  • Add decompose_url static function to replace parseFileName
  • Rename checkFileUpload to be camel case
  • Replace size2Bytes
  • Add download from remote function
  • Save work for media refactor
  • Add comments to new insert and insertAndUpload Functions
  • Remove old media::add function
  • Add accept to imageoccur submit
  • Update Occurrence Image Submit to use media class
  • Move getRemoteFileInfo to util class
  • Remove mime2ext from media class, fix usage to point at uploadUtil
  • Add empty catalogNumber option for get_occurrence_upload_path
  • Refactor uploadAndInsert to take post array instead of direct access
  • Get Basic Observation submit working with media and occurrence editor classes
  • Fix tidInterpreted not being populated in observation submit
  • Add media error status message to observation submit
  • Depercate Observation Submit Manager
  • Add upload check for iconFile
  • Add upload file check to loans
  • Add loan, image, audio, mimes for easier/more-finegrain usage than symbbase global value
  • Add mime type enforcement before download and improve docs for downloadFromRemote
  • Forces checkFileUpload to check mimes defaulint to imageMimes and removes size check because file is already uploaded so no point
  • Add extension data get remote file info
  • Add file checks to glossary for remote and file upload
  • Fix geothesaurus options for mapcoord aid
  • Remove lang tool that got added accidently
  • Authentication improvements
  • Increase length of password to 10 characters or more
  • Check new password against old password to ensure doesn't reset to the old password
  • Add file checks to glossary for remote and file upload
  • Add taxonomy upload
  • Add Taxonomy Upload Check
  • Quote styles
  • Handle some dev warnings and errors (https://github.com/Symbiota/Symbiota/pull/2758)
  • Handle case where fetching contact fetches null
  • Add missing loanIdOwn
  • Fix csv uploads not being included taxonomy upload
  • Fix error handling for media errors upload taxa
  • Move imageProcessor temp folders to use tempDir util to get them out of the docroot
  • Comment out unused and insecure functions
  • Change spec upload base to use temp dir
  • Give temp dir hardcoded fallback
  • Change temp path function to use getTempDir utility
  • Change Image import to use getTempDir
  • Add Upload util file check to thumbnail upload
  • Add gif back into allowed types
  • Add tiny mce upload check
  • Comment out unused functions with security issues
  • Fix UtilitiesFileImport to use getTempDir to avoid server root file placement
  • Deprecate remapImage because not used

Co-authored-by: Mark mark.aaron.fisher@gmail.com
Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: Edward Gilbert egbot@asu.edu

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 8 months ago

Symbiota - V3.3.4

What's Changed

  • Hotfix 3.3.4 by @GregoryPost in https://github.com/Symbiota/Symbiota/pull/2745

  • Closes #2702 Fix Improper Data Passing Georefclone. Fixes issue with lat data being passed as lng data.

  • Added onerror for damaged links (#2709)

  • Change header of download pop-up (#2714)

  • Add function for fetching recordId, assign recordId value to occurrenceid if empty, gray out if recordID is used

  • Fix typo in sql query

  • Avoid fatal error within Plugin Manager

  • Initial setup file for selinux configurations

  • Update setup.bash

  • Add protections against mismatching types and extensions

  • Fix bug in verifyIconImage where it was getting the element by the wrong ID (#2727)

  • Fix import issue with database

  • Trim file path if already including in path them when checking if file exists

  • Add file type rename checks

  • Only upload after imagesize check and separate audio upload so it could do its own checks

  • Enforce allowed mimes in add media

  • Rename suspicious mime to suspicious file

  • Temp dir path recommendations

  • Update symbini_template with recommended temp path.

  • Add .htaccess file to content folder.

  • Deactivate Glossary Upload function

  • Fixed the path to occurrenceeditor definitions in Symb Doc (#2728)

  • Add es, fr and pt translations

  • Fix Symbiota Docs links with recent changes

  • Escape the SERVER address and port

  • Confirm successful transferFromPhpToDynamicProperties and fetchGlobalLabelJson methods

  • Implement deletion of a profile

  • Security Patch KeyCharAdmin

  • Change the code to not consume the php label file at all

  • Add more return statements to indicate whether form validation worked or not in order to prevent or allow default form submission (#2739)

  • Fix rename issue

  • Taxonomy Loader: Check extension of input file on server side. Make sure file check happens on files submitted within a zip file.

  • Taxonomy Loader: Add error messages when input file is an unexpected format

  • Game and slideshow adjustments

  • Move Organism of the Day control file location from "temp" directory to "content"

  • Move Slideshow plugin control file location from "temp" directory to "content". These adjustments are done to database and portal created content into the "content" directory.

  • Remove temp directory permissions settings from setup scripts

  • Replace labeljson.php with labeldefault.json

Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com
Co-authored-by: Katie Pearson katelin.d.pearson24@gmail.com
Co-authored-by: Nikita Salikov nsalikov@asu.edu
Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: Mark mark.aaron.fisher@gmail.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.3...v3.3.4

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 8 months ago

Symbiota - v3.3.3

What's Changed

Hotfix 3.3.3 (https://github.com/Symbiota/Symbiota/pull/2697)

Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com
Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: Mark mark.aaron.fisher@gmail.com
Co-authored-by: Katie Pearson katelin.d.pearson24@gmail.com
Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.2...v3.3.3

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 8 months ago

Symbiota - v3.3.2

What's Changed

  • Optimize identifier update
  • Increase button spacing in loans/ (duplicate to new Hotfix) (#2608)
  • Increase space between buttons in loans
  • Removed extra class
  • Hotfix html link display image processor (#2626)
  • Added option to not escape string in logOrEcho function
  • Fixed link in warning
  • Closes #2623 Fixes Map Taxa links when Client root exists
  • Link to occurrence button fix (#2609)
  • Added the editorImages manager
  • Returned to occManager, moved the image function, moved translations
  • Change collector name verbiage in search (#2642)
  • Label queue hotfix (#2648)
  • Change symbiota-docs links to new docusaurus links (#2612)
  • Fix link to "security" (no longer locality security)

Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com
Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: Katie Pearson katelin.d.pearson24@gmail.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.1...v3.3.2

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 9 months ago

Symbiota - v.3.3.1

What's Changed

Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: Katie Pearson katelin.d.pearson24@gmail.com
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com
Co-authored-by: Mark mark.aaron.fisher@gmail.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.3.0...v3.3.1

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 10 months ago

Symbiota - v3.3.0

New Features

  • Support exporting associations as Resource Relationship file #1924
  • Support importing additional identifiers using the Extended Data Importer
  • Added additional occurrence record security level
  • Support configurable gated content

What's Changed

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.2.4...v3.3.0

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 10 months ago

Symbiota - v3.2.4

What's Changed

  • Closes #2465 Fixes Issue with Map not searching on navigation
  • Fixes Image search bug
  • Minor adjustment to countryCode updater
  • Removes redundant main.css link, fixed width for selector in occurrence editor admin tab

Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: Nikita Salikov nsalikov@asu.edu
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.2.3...v3.2.4

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 11 months ago

Symbiota - v3.2.3

  • Fixes Sql Typo that was breaking Duplicate Clustering
  • Fixes spec processor not generating MediaType for mapped images
  • Closes #2417 Fixes media update issue with sourceUrl field
  • PHP 8.1 compatibility issues
  • GBIF publishing bug fix
  • Resolves issue #2431
  • Closes #2408 Fixes Thumbnail Gen Bounding Box Issue
  • Checklists: Only display link to dynamic occurrence search if user is logged in.
  • SQL bugfixes and performance improvements
  • Add sort option to image search
  • Closes #2437 Fixes Media Tags not saving

Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: Mark mark.aaron.fisher@gmail.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.2.2...v3.2.3

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 11 months ago

Symbiota - v.3.2.2

What's Changed

Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com
Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com

Full Changelog: https://github.com/Symbiota/Symbiota/compare/V.3.2.1...v3.2.2

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 12 months ago

Symbiota - V.3.2.1

What's Changed

Hotfix 3.2.1 (https://github.com/Symbiota/Symbiota/pull/2349)

  • Limit vernacular name search to only when user is searching common names. Previously was being included in all searches.
  • Taxon voucher search bug
  • Fixes issue that was failing to display taxa of given rank within taxon voucher search. Previously only showed child taxa.
    *Misc. media bugs
  • Fixes Image Library Browser
  • Taxa media add and display fix in taxon editor (https://github.com/Symbiota/Symbiota/pull/2336)
  • Fixes the URL upload, fixed the media display, added warnings, added translations
  • Fixes the sort media display

Co-authored-by: MuchQuak loganpwilt@gmail.com
Co-authored-by: Logan Wilt 91149982+MuchQuak@users.noreply.github.com
Co-authored-by: Edward Gilbert egbot@asu.edu
Co-authored-by: NikitaSalikov 86389284+NikitaSalikov@users.noreply.github.com
Co-authored-by: Katie Pearson katelin.d.pearson24@gmail.com
Co-authored-by: Nikita Salikov nsalikov@asu.edu

What's Changed

Full Changelog: https://github.com/Symbiota/Symbiota/compare/v3.2...V.3.2.1

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost 12 months ago

Symbiota - v3.2

New Features

  • Support attaching audio files to occurrence records
  • Ability to parse "other catalog numbers" on file import
  • Ability to search by associated resource
  • Support export of image tags to Darwin Core Archives
  • Support alternativeIdentifiers extension in Darwin Core Archive exports
  • Support cultivar epithet and tradename fields on taxonomy

What's Changed

New Contributors

Full Changelog: https://github.com/BioKIC/Symbiota/compare/v3.1.8...v3.2

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost about 1 year ago

Symbiota - v3.1.8

What's Changed

  • API developments
    ** Fix bug associated with displaying all media. Previous output was limited to first 200 records only
    ** Add limit and offset variables to display all media
    ** Add filters to display all media endpoint: tid filter, includeSynonyms, includeChildren
  • Out of bounds hyperlink within occurrence editor. Resolves https://github.com/BioKIC/Symbiota/issues/2099

Full Changelog: https://github.com/BioKIC/Symbiota/compare/v3.1.7...v3.1.8

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost about 1 year ago

Symbiota - v3.1.6.1

What's Changed

Resolve image rendering issue on individual occurrence view

Full Changelog: https://github.com/BioKIC/Symbiota/compare/V3.1.6...v3.1.6.1

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost about 1 year ago

Symbiota - Hotfix Version 3.1.6

What's Changed

Full Changelog: https://github.com/BioKIC/Symbiota/compare/v3.1.5.1...V3.1.6

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost about 1 year ago

Symbiota - v3.1.5.1

What's Changed

  • Switch header buttons to use HTML button element for better UX
  • Adjust styling to restoring honoring header button text color
  • Improve header button layout on <768px display

Full Changelog: https://github.com/BioKIC/Symbiota/compare/v3.1.5...v3.1.5.1

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost over 1 year ago

Symbiota - v3.1.5

What's Changed

Full Changelog: https://github.com/BioKIC/Symbiota/compare/v3.1.4...v3.1.5

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost over 1 year ago

Symbiota - v3.1.4

  • Checklist voucher link bug
    -- Resolves issue where checklist link PK is not passed to link function.
    -- Resolves issue: https://github.com/BioKIC/Symbiota/issues/1828
  • Specimen upload bug
    -- Add IGNORE to avoid complete failure of insert statement
    -- Capture and display warnings to user
    -- Fix display of final record process count
  • Occurrence Search breadcrumb bug fix
    -- Add comingFrom variable to pagination links within the list and tablelist pages
    -- If comingFrom variable is not set, or set to anything other than "newsearch" or "harvestparams", set the variable to what is defined as the default within the symbini file. If default action is not defined within symbini, default to new search form.
    -- Add comingFrom variable to harvestparams.php form
    -- Resolves issue: https://github.com/BioKIC/Symbiota/issues/1840
  • Occurrence Association Form Validation bug
    -- Fix issue with internal association form validation failing and allowing for creation of an association without an internal occurrence being defined
    -- Add form validation for external resource and general observation
    -- Addresses issue: https://github.com/BioKIC/Symbiota/issues/1852
    -- Add guid omoassociations RecordID on insert within occurrence editor
  • Vendor library updates via composer
    -- update phpoffice/phpspreadsheet to v3.3.0
    -- updated phpseclib/phpseclib explicitly to v3.0.42
    -- update phpoffice/phpword to v1.3.0
  • Fix data binding bug associated with searching occurrence via GUID within Occurrence Profile pages
  • Misc language translation issues

Change log: https://github.com/BioKIC/Symbiota/compare/v3.1.3...BioKIC:Symbiota:v3.1.4

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by GregoryPost over 1 year ago

Symbiota - Symbiota 3.1.1

3.1.1 - Hotfix 2024-09-26

  • Occurrence Mapping: Adjust SQL to relax enforcement of link to taxon thesaurus, thus to include records with coordinates but lacking thesaurus relationship
  • Styling: Various styling, spacing, and display adjustments
  • Occurrence search: add type attribute to buttons to avoid defaulting as submit buttons
  • Occurrence Profile: Fix error triggered when otherCatalogNumbers are used to create backlink to original snapshot record within external institution web resource
  • Occurrence editing functions
    -- Fix fatal error triggered by cloning an occurrence record with the create association option selected
    -- Fix fatal error triggered when quick association feature is activated within occurrence editor
    -- Fix fatal error when deleting an occurrence when the occurrence was previously deleted (e.g. record already in omoccurarchive)
    -- Adjust occurrence restore option to dynamically determine associationType when restoring a record that was deleted prior to this field being added as a required input
    -- If resource association does not have an objectID, use url as the display text
  • Taxonomy editor: bug fix triggered by adding a child directly to the root node of the thesaurus (e.g. kingdom)
  • Scientific name parsing utility functions: Integrate cleanInfra function directly into code. It served no purpose being separate, and was also causing a bug where parent authors were being incorrectly merged with insfraspecific authors

[3.1] - 2024-08-29

New Feature

  • 508 Accessibility features
  • Extended occurrence data upload module. Supports import and linking occurrence to: associated occurrences, identifications/annotations, image links, material samples, and reference links
  • LeafLet JavaScript added as an open source mapping option
  • MediaWiki parser for mapping and integration of Flora of North American descriptions into taxon profile pages
  • Occurrence associations management tools
  • Occurrence distribution static map thumbnail generator
  • Public occurrence search form - new streamline version (via NEON support)
  • Responsive design framework
  • Specimen image batch tagging tool

Changed

  • Bionomia badges and GBIF citation counts/links added to collection profile pages
  • Glossary improvements including ability to link terms into identification keys
  • Identification Key user interface improved to including display of taxa as thumbnails
  • Significant extension of Spanish and French translation files, including refactor of how header, footer, and index language are integrated
  • Support for new Occurrence fields: waterBody, continent, islandGroup, island, countryCode, locationID, eventID, vitality, eventDateEnd
  • Restructure css files, including removal of deprecated and redundant stylings
  • Taxon harvesting tool reconfigured to import directly from ChecklistBank API rather than Catalog of Life
  • Security patches
    ** Update TinyMCE JS library
    ** Update jQuery JS libraries
    ** Cross-site scripting (XSS) protections - Improve sanitation of input variables to protect against
    ** SQL Injection protections - Improved prepared statements support

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by egbot over 1 year ago

Symbiota - Symbiota 3.0.13

hotfix 2023-07-31

  • Occurrence Voucher bugs
    -- Resolve error associated adding an occurrence as a checklist voucher from the occurrence details page
    -- Ensure that editing permissions are verified, to ensure that edit additions can't be applied by none authorized used.
  • Identification Key
    -- Avoid warning when there are no terms set within the Glossary
  • Occurrence Upload
    -- Expand back-mapping snapshot dbpk value capabilities to make use of occurrenceID identifiers, as well as catalogNumber
  • Styling
    -- Minor working adjustment to header translation file template
    -- Resolve styling issues with button-icons and quick search default setup
  • Documentation and Language translations
    -- Add documentation for installation a robots.txt file
    -- Fix issues with language translation terms interfering with submit button functions
  • Security fixes reported by Qualys:
    -- Resolve issue with sanitation of occurrence search variables held within session storage
    -- Various variable sanitation updates
    -- Remove deprecated sanitation methods such as filter_var/FILTER_SANITIZE_STRING
    -- Improve integer sanitation methods
    -- Add index redirects to avoid directory content viewing when this is not configured within web server

hotfix 2023-07-31

  • Glossary issues
    -- Allow terms search to do a double wildcard search to expand functionality and resolve issue with zero return when html tags (e.g. italic) are included with the terms
    -- Remove restrictions and unnecessary default actions associated with unset language and taxon terms so that thesaurus better functions as a single language glossaries
    -- Fix various issues with export of report when there is a single language glossary and/or terms are not linked to specific taxa
    -- Fix issue report export not including full list when terms have complex language relationships
    -- Improve file naming and content/layout of Word report export
    -- Resolve issues with inclusion of all Spanish language translation files
    -- Include translations for some missed terms
  • Occurrence editor
    -- Fix bug with year, month, day field failing to null when eventDate is nulled out
    -- allow tidInterpreted value to be transferred when scientific name is added to form via duplicate tool
  • Occurrence Search
    -- Fix issue with autocomplete failing to return names that contain single or double quotes
    -- Fix issue taxon name search failing to return correct data when name contains single or double quotes
    -- Map Search: resolved issue where map recenters in the middle of the ocean when a search returns no coordinates
  • Taxonomy issues and bugs
    -- Taxonomy Utilities: Fix issue interfering import of taxa with hybrid symbol when there is not a space between symbol and name units
    -- Taxonomy Harvesting: Resolve 'Unranked" taxonRank designations when taxon is a non-accepted genus
    -- Taxonomy Upload: Minor adjustments needed to support processing of taxa immediately adjacent to kingdom rank

Hotfix - 2023-07-22

  • DwcArchivePublishing: Material Sample publishing bug
  • DwC-A upload: Scientific name failed to be built when taxonomic data is supplied by by individual components
  • Taxonomic autocomplete: Allow autocomplete handle apostrophes
  • Checklist Display: Bug fix that interfered with display of linked voucher images
  • Checklist Manager: Checklist taxon search autocomplete failed to include higher taxa (parent data)
  • Taxonomy Harvester bug: F-dex harvest failed to grab parents when source was not "Index Fungorum"
  • Specimen Upload: Set version data changes as the default action only when a collection is live managed
  • Occurrence Search Harvest: Reworked search form validation to be more efficient; Fix bug with occurrence attribute checkbox/radio failing to be recognized as a selected component

Hotfix 2023-06-19 (https://github.com/BioKIC/Symbiota/pull/518)

  • Taxonomy Harvesting: Don't check following taxonomic resource on a positive match and input; synchronize display text
  • Refactor ImageLocalProcessor:
    -- Provide support for input file to include medium and thumbnail image derivatives
    -- Expand Image Map processing to allow mapping file to include any images table field name
    -- Expand images insert function to handle any valid field found within images table
    -- MD5 hash large version of image input file, but don't overwrite hash if supplied by source
    -- Handle BOM characters at start of csv file.
    -- Trim header elements for testing column names.
    -- Enforce default action of accepting derivative urls supplied within a csv image map file
    -- Make sure to remove staging images
  • Occurrence Public Display: Allow occurrence archive (deleted occurrences) to be searchable by GUID (occurrenceID, recordID), thus reporting when a record is deleted
  • Checklist multi-polygon Map: resolve Multipolygons failing to map within both simple and dynamic maps
  • Occurrence Reviewer: Fix for field name and start and end date filter variables failing to be carried forward when advancing to pages beyond 1000 records
  • Collection metadata editor: Reset contact array to ensure that JSON string is standardized as a non-associated array

Co-authored-by: Greg Post gregory.post@asu.edu

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by egbot almost 3 years ago

Symbiota - Symbiota 1.2.1

Final code updates prior to 3.0 schema release

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by egbot almost 3 years ago

Symbiota - Symbiota 1.2.0

What's Changed

  • Occurrence dataset management toolkits (available via My Profile => Occurrence Management) (2020-12-23)
  • New module for creating custom Specimen Labels formats linked to portal, collection, or user
  • Option to link multiple ResponsibleParty associations to a collection (e.g. collection contacts) (2020-12-21)
  • Option to associate multiple reference links to a collection (2020-12-21)
  • Support tables for defining Controlled Vocabularies
  • Paleo data management module including support for: editor, import, export, public display
  • Establishing and managing relationships between occurrences (e.g. parasite/host)
  • Occurrence Traits management tool development

New Contributors

  • @arbolitoloco
  • @cdtyrrell
  • @themerekat
  • @mickley
  • @mandrewj

Full Changelog: https://github.com/BioKIC/Symbiota/compare/v1.0...v1.2.0

Biosphere - Biodiversity Data Access and Management - JavaScript
Published by egbot about 4 years ago