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Update branch with Development #2288

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egbot and others added 30 commits September 26, 2024 09:12
* 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

---------

Co-authored-by: Katie Pearson <[email protected]>
Co-authored-by: Mark <[email protected]>
Co-authored-by: MuchQuak <[email protected]>
Co-authored-by: Logan Wilt <[email protected]>
* 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

---------

Co-authored-by: Katie Pearson <[email protected]>
Co-authored-by: Mark <[email protected]>
Co-authored-by: MuchQuak <[email protected]>
Co-authored-by: Logan Wilt <[email protected]>
# Summary
Removed fixed hieght of selects in occurrence editor so it fits to the
body text size appropriately
…lic record (#1762)

* separated determiner and date determined

* changed the text
- Replace deprecated utf8_encode with mb_detect_encoding
3.1.2 Release: Merge Master Branch into Development after Hotfix release
Fix issue with Chrome autocomplete. See BioKIC/symbiota-docs#633.
- the $this->encodeArr() function receives input array by reference, which means it returns nothing (null)
* Utility Class Refactor

- Move OccurrenceUtility and UuidFactory into new utilities directory
- Remap class import to new location
- Remove non-static functions from UuidFactory into new GuidManager class
- Remap GUID manager functions to new class
- Convert UtilityFunctions class to GeneralUtilities placed within utilities directory
- Remove getDomain from Manager class
- Remap Manager->getDomain() to GeneralUtilities::getDomain()
- Move TaxonomyUtilities into utilities directory and remap all function calls to new location
- Rename SymbUtil to QueryUtil and move into /classes/utilties/ directory
- Move and remap Encoding class into /classes/utilities/ directory
- Move and remap Encryption class into /classes/utilities/ directory
- Move and remap RdfUtilities class into /classes/utilities/ directory
- Move and remap SpecProcNlpUtilities class into /classes/utilities/ directory
-Standardize utility file naming
- DwC-A Publishing: $this->encodeArr() function receives input array by reference, which means it returns nothing (null)
- Minor error in Glossary and Media tools
add prepared statement to getOccurrenceArr
Styling correction to map index top  menu
* Add lang files for exsiccati batch import

* Add lang files for exsiccati/index

* Add es and fr exsiccatae pages

* Adjustments

* add pt to batch import exsiccati

* add pt translation to exisccati/index

* Update batchimport.pt.php

* Update index.pt.php

---------

Co-authored-by: MuchQuak <[email protected]>
* Finish lang tags for editor/rpc

- Combined all the lang tags in this folder into a single lang tag file (short)

* Add lang tags to editor/tools
Issue is so solve when their is over lapping markers of different
groups, ie would not get clustered.
* Inventory Project updates

- Update sanitation of input and output variables
- Complete internalization
-- Update import of language terms
-- Add missing LANG tags and remove tags not referenced
-- Translate French that were entered in English
- Remove deprecated code
Atticus29 and others added 30 commits February 11, 2025 13:48
* only add star in edit mode

* respond to QA feedback

* remove cruft
- Add functions that evaluates index and constraint statement fragments and compares them against database to ensure statements will not fail. Otherwise, they are pruned out and logged.
- Fix errors testing column existence within ALTER TABLE statements
- Improve error handling
- Re-add statements that got pruned out
Print errors from buildHierarchyEnumTree during taxonomy upload
add missing table name.
Resolves #2219
- Maps to new location for query utility static function
- Resolves issue #2229
- use of old images table within SQL statement
…written by empty form value (#2233)

* Closes #2231 Fixes sort sequence being overwritten default being overritten by empty form value

* Fix undefined variable issue

* Fix undefined array key being used after access issue
* fix bug where points array was null

* begin to implement exsiccati endpoint

* fix bug from PR 2198 and update api docs

* auto-format TaxonomyController.php

* remove this change that should not be here

* Update symbbase.php

Update version

* change exsiccati -> exsiccata

* Update api-docs.json

Trim out taxonomy description out of the documentation since they currently are not working

---------

Co-authored-by: Edward Gilbert <[email protected]>
- Schema installer can't handle the modification of an index when it is both dropped and added within the same ALTER TABLE statement. Thus, I separated the lines into two different statements.
- Explicitly define new tables using the INNODB db engine
Add logic to handle presence of ds.datasetid in setSqlJoins function

Co-authored-by: Mark <[email protected]>
* add thumbnail code back in for media

* remove commented-out code
* Swap openMapPopup function on taxon profile page to open to taxon search

* Open with menu closed by default when coming from taxon profile page

* Remove deprecated map files

* remove associated lang files with deprecated map files
#2260)

# Issue Closes #2251
# Summary
Full text syntax got messed up at some point when changing over the full
text indexes to the omoccurrence table. This is a simple fix by putting
the parens in the right place.
* Closes #2258 Shink Marker size by half

# Issue Closes #2258

# Summary
Reduces Marker size on map search to be about half of what it was before

* bump size a bit
Fixes errant UTF character and restores variable reference
- Remove sort from update statements
* fixed the field names for media query

* set the empty values to NULL for media query
Add indexes to media table for following columns that are commonly used within SQL conditions: sortSequence, sortOccurrence, thumbnailUrl, mediaType
- Adjust position of new fields
* add pagination to datasetmanager.php

* add translations

* remove cruft

* checkout Development versions of checklists/checklist.php and collections/listtabledisplay.php

* remove more cruft and simplify

* begin to implement jump to page in large paginators

* move the start of the form

* add styling to make one line and handle logic for which pages to display a little better

* combine sliding window with ensuring end and beginning always show

* add media queries and other styling changes

* add responsive design

* clean up cruft

* make slight logic improvement

* add intermediate number of page links by getting rid of even page number links

* handle first and last page links and extra | symbols

* change sql queries such that they use QueryUtil::executeQuery

* autoformat classes/OccurrenceDataset.php because it is unlikely to have been touched
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