Tags: Symbiota/Symbiota
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Hotfix 2024 01 29 (#921) - 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 22 (#815) * Hotfix 2023-12-22 - Mysql schema compatibility updates - Password encryption updates - Make collector and identifier ORCID actionable (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 08 (#762) Hotfix 2023 12 08 (#760) * hotfix-2023-12-08 - 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 --------- Co-authored-by: Greg Post <[email protected]>
Hotfix 2023-11-05 (#735) * 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 (#648) - Occurrence and Image Search tool functions -- Improve taxon query algorithm 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 - Mics fixes -- Add eventID to csv output that is streamed to GeoLocate CoGe -- Identification Matrix Editor: Avoid SQL error when taxon select doesn't include child linked taxon relevant characters -- Variable cleaning and styling adjustments
Hotfix 2023 09 25 (#636) * add wording changes to the pr template * make other small changes to the PR template * respond to code review feedback * add link to the pull request template to docs/CONTRIBUTING.md per suggestion by James in slack: https://symbiota-support.slack.com/archives/C01T76H9UCB/p1695673343797719
Hotfix 2023 08 08 (#606) * 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 (#564) 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