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@egbot egbot released this 28 Apr 19:06
· 772 commits to master since this release
v3.0.35
a2f8e8b
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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 [email protected]

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

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 deprecated utf8_decode and utf8_encode
    -- Block null values being used within string functions (now deprecated)

Hotfix 2023-12-22 (7a6b002)

  • MySQL schema compatibility updates
  • Password encryption updates
  • Make collector and identifier ORCIDs actionable out-links (NEON Biorepo portal requirement)
  • Identification key: difficultyRank interfering with proper display and sort of characters/states
    Co-authored-by: MuchQuak [email protected]

Hotfix 2023-12-12 (6899bb7)
-Checklist Display
-- Fix subgeneric sorting within checklist list display when display subgenera option is turned on. The taxa identifiers (tid) were being reset within the return arrange.

  • Occurrence Downloads
    -- Both the Determination and Dataset aliases being set to "d" was causing the determination file to fail when a query included a datasetID search variable.
    -Taxonomy Display and Management
    -- Update dojo JS library used within taxonomic tree module (security issue)
    -- Support hybrid matching with proper formatting of name import
    -- Fix syntax of published hybrid taxonomic names
    -- Fix issue within taxon profile editor with ability to link image to an occurrence record (#796)

Hotfix 2023-12-11 (#770)

  • Checklist Management
    -- Apply special sorting only when display subgenera option is tagged as the default
    -- Allow display of embedded subgenera to be saved as an option
    -- Ensure that all options are carried forward via links and form submissions
  • Misc input variable sanitation and other security issues

Hotfix 2023-12-08 (#760)

  • Checklist display
    -- Adjust checklist sort method to include subgeneric notations
  • Occurrence Download
    -- Fix bug interfering Georeference download tool
  • Taxon Loader
    -- Modify taxon parser in to catch and properly format non-standardized subgeneric name formats.
  • Taxonomy Harvester and Management
    -- Fix bug that blocked harvest of infraSpecificEpithet unit
    -- SQL adjustments to enable taxon matching using kingdom name as a search variable

Hotfix 2023-11-30 (#755)

  • Checklist Module
    -- allow addition of taxa that have been entered into the thesaurus with subgenus embedded within name
    -- Display subgenus as part of the output when a taxon is linked to a subgeneric parent, but subgenus is not directly defined within name
  • Occurrence Download module
    -- But fix interfering with DwC-A downloads
  • Occurrence Upload module
    -- Throw an exception when json_encode() encounters an error and catches error to report to UI. functionality added to material sample and paleo data imports.
    -- Specimen Upload: suspend removal of staging directories during post upload cleaning.
    -- Support Occurrence Attribute DwC export throughout all DwC-A output options
  • OmCollection data prep function adjustment to avoid warning when updating a collection profile
  • Taxonomy tools
    -- Refactor Taxonomy Harvesting tool to harvest Catalog of Life (COL) data from ChecklistBank API rather than COL API, which was taken offline

Hotfix 2023-11-05

  • Checklist Management
    -- Protect against cases where a parent-child relationship is accidentally created with ones self, which shouldn't happen, but could
    -- In order to resolve confusion with checklists with "private" access still being sharable to non-editors, we added a "Strict Private" option that full restricts access to all non-editors
  • CrowdSource management
    -- Adjust project stats function so that is reports distinct count of specimens when multiple images are linked to each specimen (#650)
  • Glossary issues
    -- Fix issue interfering with deletion of images
    -- Fix sort issue caused by imbedded html tags
    -- Resolve issue of returning term details based term text
    -- Variable sanitation improvements
    -- Avoid warnings when improper term or term id is supplied
    -- Convert some SQL INSERT statements to prepared statements for improved protection against SQL Injection attacks
  • Batch Image Processor
    -- Fix issue that was adding double forward slashes to image URLs (issue: #668)
  • Occurrence Determinations:
    -- Focus current occurrence determination SQL into a single shared function to standardize action
    -- Apply function whenever a determination is updated
  • Occurrence Download tool
    -- Images failed to download when a dataset is included in the searched parameters
  • Profile manager: Return status of success when password is attempted to be update to current password, rather than reporting that update failed (issue: #730)
  • Taxonomy Harvesting tool
    -- Catch issues when WoRMS returns -999
    -- Fix issue when tautonym is automatically added without infraspecific rank name included
  • Misc cross function fixes
    -- Convert occurrence to collection table LEFT JOINs to INNER JOIN to make statements more efficient, especially within large datasets.
    -- Add .tab and .dat extensions to data file cleaning function

Hotfix 2023-09-21

  • Occurrence and Image Search
    -- Improve taxon query algorithm and put in-sync with basic occurrence search
    -- Fix common name search within public occurrence and image search tools. Additional improvements include adding Scientific Name to auto-complete display
  • Occurrence editor bug
    -- Elevation conversion failed to convert elevation containing decimal values
  • Checklist management
    -- Fix issue with multiple vouchers failing to link to new taxa, and non-accepted occurrence taxa failing to link to accepted checklist taxa
    -- Improved efficiency of clTaxaID lookup via tid-clTaxaID caching
    -- Fix incomplete list display: Extend list for adding additional vouchers to existing data so that it includes non-accepted checklist taxa linked to other non-accepted occurrence taxa
    -- Resolve issue with reset of checklist sort order anytime metadata is modified
  • Authentication
    -- Upon successful authentication (i.e. login), reset session variable login name to login value stored within database. Login standardization particularly necessary when user logs in using email address

Hotfix 2023-09-07

  • Loan management
    -- Fix issue with catalog number display within loan module specimen listings
  • Management of files temporarily placed within temp directory
    -- Added function to remove all files in temp directory that are older than 2 days. This is to ensure that old file are removed, even when an upload is abandoned prematurely before upload files cleaning step
    -- Upload files are staged within a sub-directory named after collid. This directory is cleared at each load, thus ensuring that failed uploads attempted multiple times won't negatively affect disk space.
  • Checklist Management
    -- Strip "NO-BREAK SPACE codepoint" multibyte characters from scientific name within the checklist batch upload tool. This character, which looks like a space, interferes with matching the input name with the taxonomic thesaurus

Hotfix 2023-08-31

  • Variable sanitation and other security patch issues

Hotfix 2023-08-08

  • 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 (#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 [email protected]

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