v3.1.4

• Checklist voucher link bug
  -- Resolves issue where checklist link PK is not passed to link function.
  -- Resolves issue: #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: #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: #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: v3.1.3...BioKIC:Symbiota:v3.1.4

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

Symbiota 3.0.35

Hotfix 2024-08-22

• Minor bug fix that was interfering with saving of locationRemarks when a new record is saved (resolves #1445)

Hotfix 2024-08-07

• Taxonomy Editor
  -- Add taxamaps table to data remapping functions when taxon is deleted or remapped. Resolves issue https://github.com/BioKIC/Symbiota/issues/1598
• Glossary Management
  -- Fix issue associated within new sources failing to save when displaying all terms without a taxon group selected. Resolves issue https://github.com/BioKIC/Symbiota/issues/1584
  -- Display all source definitions when taxon group is not selected
• Occurrence Cleaner - duplicate merge tool
  -- Replace catalog numbers as the unique identifier for duplicate cluster with numeric key, thus avoiding interference of target form element due to existence of space or period within catalog number. Resolves issue https://github.com/BioKIC/Symbiota/issues/1471
  -- Add header and footer to cleaning page
• Specimen Upload
  -- Remove display of Data Versioning Checkbox option for snapshot datasets. Batch import data versioning is only available for live managed collections.

Hotfix 2024-07-25

• Inventory and Project Management
  -- Display all checklists that have at least one linked taxon OR is a parent checklist inheriting taxa from a child checklist (Issue #1532)
  -- Removed limit that required checklist to have at least 10 linked taxa
  -- Order checklists by project and checklists names
  -- Only display Global symbol within map display option when one or more checklists within a group have lat/long centroids
  -- Make project title an active link that opens the project within the project details page
• DwC-A Publishing
  -- Fix fatal error when DwC-A path fails to return a data file

Hotfix 2024-06-24

• Image tools
  -- Return false when file size cannot be determined within getImgDim1 function
• Glossary (resolves issue: #1526)
  -- SQL error causing term list display to fail when a taxon group was included in the search
  -- Change table linkages associated with taxon group condition to LEFT JOINs so that all terms are displayed, including those without linkages to synonyms

Hotfix 2024-05-22

• Checklist management:
  -- Adjust taxon merge function to accommodate PHP v8.1 fatal exceptions during foreign key conflicts within SQL update statements, which previously simply returned false value with a warning
• Image processing:
  -- Bug resolution to avoid fatal error where an array function is incorrectly used on a string. Resolves issue #1366
• Occurrence Mapping:
  -- Fix bug interfering with the exclusion of protected occurrences within the mapping tools when user is not approved to view these records. Associated with issue: #1375
  Co-authored-by: Greg Post gregory.post@asu.edu

Hotfix 2024-05-17
DwC-A Publishing

• Fix issue with file handler being closed prematurely (re-addresses issue: #1306)

Hotfix 2024-05-15

• DwC-A Publisher
  -- Fix fatal error caused by fclose function being called on NULL value (addresses issue #1306)
  -- Fix warning and failed data output within citation template block due to mismatch variable call within different code positions where the code is imported via an include call
• Occurrence Editor
  -- Adjust function that removes duplicate catalog numbers when comparing otherCatalogNumbers verbatim values against omoccuridentifiers tag/value combinations to improve ability to match and remove compound tag/value combinations (addresses issue #1146)

Hotfix 2024-05-09

• Checklist Management
  -- Bug fix: non-superadmin users were being logged out after creating a new checklist due to error in resetting permissions to include new checklist

Hotfix 2024-04-29

• DWC-A publushing
  -- Close and destroy file handlers and class instances, thus ensuring full output of buffers. Integrates Dev bug fix https://github.com/BioKIC/Symbiota/pull/1223 into master.
• Occurrence Search:
  -- URL encode search variables to ensure "copy link" function and map links work when spaces or special characters are included within terms. Addresses issue: #1212
• Occurrence Editor:
  -- Ensure that image tids are updated to make occurrence identifications. Integrates Dev bug fix https://github.com/BioKIC/Symbiota/pull/1239 into master.

Hotfix 2024-04-08

• Inventory Management
  -- Ensure that checklist parent-child relationships exclude the ability to define a checklist as its own child, and avoid the use of ill-defined relationships within data output.
• Occurrence Profile
  -- Ensure that rights set within image table take precedence over rights defined as the general default for the collection
• Taxon Description
  -- Fix bug interfering with editing taxon description caption. Addresses the following issues:
  --- #1142
  --- BioKIC/symbiota-docs#492
• Taxonomy Import Managers
  -- Fix bug causing taxonomy harvester to fail during import of certain subgeneric taxa from Checklist Bank / Catalog of Life
  -- Debug Taxonomic Node import tool resolving issues introduced when ChecklistBank replaced Catalog of Life API, including clarification of awkward points of the general workflow

Hotfix 2024-03-25

• Occurrence export
  -- Activate sampleProtocol within occurrence export tools
• Institution manger
  -- Fix error due to data entered into $retArr both as an object (line 190) and an associate array (line 186)
• Checklist Management
  -- SQL bug fix with voucher transfer module
  -- Add html tags that should be retained with html input

Hotfix 2024-03-18

• Batch Georeferencer bug
  -- Fix for FATAL error when user has editor permissions for more than one collections, but not admin permissions
• Occurrence Editor bugs
  -- Adjust occurrence editor to support filtering dynamic fields using 0 (zero) - resolves issue #1038
  -- Don't trim % off of search terms to allow for % type search to match only on % - resolves issue #1039
• Checklist Management
  -- Only sanitize output data once it is in the view. Fixes issue where cloning a checklist corrupts embedded html

Hotfix 2024-02-12

• Occurrence editor:
  -- Fix bug associated with locality security failing to auto-set when a globally protected taxon is entered
  -- Fix issue where occurrence image input was being double escaped when a new image was added within the editor
• Occurrence import:
  -- Fix current determination update failure when one of required determination fields are null
  -- Increase efficiency of SQL statements used to generate import report counts
• DwC-A publishing and export:
  -- Fix bug that was failing to exclude extension file output upon request
  -- Rework batch DwC-A generation to trigger rebuild of RSS feed and trigger of GBIF crawl after each DwC-A build event, which avoids the issue of these steps failing upon page timeouts.
• Occurrence Attribute coder bug:
  -- Ensure that country/state filter attribute is persistent after an attribute is coded. Github issue: #1012

Hotfix 2024-01-29

• Fix Occurrence Profile display of institutionCode and collectionCode override values set within the omoccurrences table
• Adjust for omoccurdetermination sourceIdentifier being renamed to identificationID within schema 3.0
• Avoid SQL statements that query deprecated geographic lookup tables (only an issue with v3.0 installs)
• Adjust install docs to include file permission adjustments needed for API

Hotfix 2023-12-28 (1aa64b4)

• Checklist and Identification key Management
  -- Identification Key: remove unnecessary input variable sanitation that was causing issues with display of characters within key
  -- Remove connection sharing to avoid read-only connections being shared with ChecklistVoucherAdmin needing a writable connection
• OccurrenceAccessStats: Ensure that all SQL statements are set within a condition that checks that STORE_STATISTICS is set and true
• Occurrence Listing and Editor functions
  -- Add try-catch blocks for SQL insert statements that produce a fatal exception within PHP >v8.1 (#824, #825)
  -- Avoid >8.1+ deprecated warnings associated with passing null variables to string functions
  -- Bug interfering with Coordinate download option listed within map tab of occurrence listing page
• Taxonomy and Taxon Profile Editor
  -- Adjust TinyMCE description editor to not convert reference link URLs to relative paths (#794)
  -- Fix SQL errors within taxonomy editor and loader that are now producing permanent error since 8.2 update (#823, #826)
• General code adjustments
  -- Replace deprecated use of FILTER_SANITIZE_STRING option within filter_var function
  -- Sanitize integer input using filter_var and the FILTER_SANITIZE_NUMBER_INT option
  -- Ensure that NULLs and undefined values are not evaluated by PHP string functions
  -- Remove deprecated auto_detect_line_endings
  -- Avoid >8.1 SQL fatal errors
  -- Update UTF-8 and ISO-8859-1 encoding to remove deprecate...

Symbiota 1.2.1

Final code updates prior to 3.0 schema release

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: v1.0...v1.2.0