…lict

Hotfix 2024-05-17

- Convert Media POST and PUT data input from parameter values to a data object passed within the body
- Some improvement with response documentation
- Fix duplicate operationId values
- Rebuild Swagger API documentation

* uses leaflet path method to set color so that it will update when group is not re drawn closes 1319

* close BioKIC#1320, addes check for catnum

* adds check for duplicate collectionCode / institutionalCode key when updating collection meta data and gives status msg upon failure closes BioKIC#1311

* changes wording of duplicate error

* link error to new tab

* fixes lang tag error for collmetadata.php title

…oKIC#1338)

* Update searchform.js

Fix sessionStorage.querystring bug.  Javascript was not handling setting db (collections) checkbox array from user sessionStorage.

* Update searchform.js

Correcting variable name

This reverts commit 79e2a1b.

…rms closes BioKIC#1329 (BioKIC#1341)

…oKIC#1343)

* cloFix Occur Editor Nav visiblity with no results closes BioKIC#1333

Shifts conditional hiding search form down a level so it only blocks
tabs that way navigation is still possible when there is no query
results

* shifts formating to correct from one less conditional

The image info was being pushed down to the baseline of the displayed image.  This fix creates a new class that resets the cell alignment to top aligned.

* Update ProfileManager.php
Confirms if 'accessibilityPref' is set in user's dynamic properties and sets AccessibilityPreference to false by default if not.

…KIC#1348)

# Issue 1340
# Summary
This should fit the bottom scroll bar into view when their is few
results.

* remove some font-family references

* remove in-line styling for font-family in all files not .scss, .css, vendor, .js, .less, .html, or .map

* remove <b> from one of the fieldset-likes

* add reference to font-family in reset.css

* remove unecessary font-size restriction on fields-available chips

* fix the page flow bugs but confirm existing collection persistance issues

* display which collections are to be queried in harvest params

* solve the collection selection for the new search page

* clean up and subfunctionalize

* slight refactor to improve readability

* add minor aesthetic improvement

* add styling class

* remove collection display in harvest params

* remove translations that are now cruft

This reverts commit 6580a7a.

- Parse tags and values found within omoccurrences:otherCatalogNumbers field and display within additional identifiers table within the occurrence editor. If form is saved, parsed values are saved within omoccuridentiers table.

othercatalogNumber parsing bug fix

- Fix issue with taxon remapping/merging into another taxon failing due to key violations within taxstatus (relationship already exists). This is another issue with PHP 8.2 throwing fatal error for mysql warnings. Adding an IGNORE to statement solves the issue since already existing relationships don't need to be  transferred, and will be deleted when secondary taxon is deleted.

* Update header.css

Center hamburger menu and flow menu content into body so that menu content is scrollable on small screens.
Remove transitions
Reduce padding around hamburger to unblock 'Home' menu link

Taxonomy remap bug

* Add dialog box with info about merging records

* Remove redundant lang tags

Discovered when finding lang tags corresponding to "more information" via dialog box code that I copied

* Change dialog box to a link to Symbiota Docs

Seems more consistent with where we're going now

$loanType is a string - was being sanitized as a Int.  Variable is not used in any output to client, so should be safe to just use for comparison without filtering.

- Minor adjustment to display of parent taxon to fix issue with lack of space between scientific name and author, with additional minor improvements
- Minor improvement to only italicize taxa at genus rank or above
- Move htmlspecailchars and formatting into class assignment so that rankid can be used to decide formating

php current() expects an array while parse_url with  PHP_URL_PATH paramter should return a string or false.

This changes were also committed to hotfix-2024-05-22

…-issue

Taxonomy Editor format adjustment

* 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 BioKIC#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: BioKIC#1375

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

- Avoid fatal error that are now thrown by PHP v8.1+ instead of the previous warning

3.1-upload-bug

* reroute map result to map search b/c this is fully featured

* closes BioKIC#1345 add add reference marker functionality to map/index so that no funtionality is lost

* inversing switch so logic works out

* default clustering off

* moved cluster switch on by default from needing param and it just defaults to no clustering

# Summary
Only adds lat long data restrictions if something is present in the
`sqlWhere` property. That way if checks to sqlWhere don't fire with
everything searches ever.

* add important to screen reader only class

* fixing contrast adding styling class for the insert border labels

* collection search uses body color instead of grey for better contrast

* updating screen-reader-only for base.css

* fixing use of data-labels with content to just normal spans

* focus now uses medium color for contrast

…C#1391)

* adds guard to do either 'AND' or 'WHERE' if $sqlWhere is empty

* fix accidental populating of sqlWhere in setGeoSqlWhere

---------

Co-authored-by: Mark <mark.aaron.fisher@gmail.com>

* swaps all the merge record queries to be prepared statements (mostly) and puts them in a try catch so blank errors don't occur on the user side

* Add $collId as arg for dupManager merge Records since collId would be undefined otherwise and fixed control flow to only navigate you when error occurs

* Adds Ignores to mergeRecord and Error Control Flow to deleteOccurrence

* Add forgotten lang tags for dupManager

* saving determinations work

* determination history priortizes source records current determinations

…se over xss (BioKIC#1380)

…to make burpsuite happy (BioKIC#1394)

…d in collections/datasets/emlhandler… (BioKIC#1398)

* adds is_numeric checker for collid in collections/datasets/emlhandler.php

* respond to code review feedback. If it does not pass the is_numeric check off the bat, it probably should not be treated as valid

* select collections from the url if present

* DRY up sanitizedCollectionSource section, which has the same pattern as occurs elsewhere

* fix typo

* change default to empty array

* add better type checking to collIdsFromUrl

Update ImInventories.php

)

* attempt to fix the injection issues

* change setSciNamesByVerns to use prepared statement

* remove extra htmlspecialchars call now that prepared statement is in place

* removed extra spaces

---------

Co-authored-by: Mark <mark.aaron.fisher@gmail.com>

# Issue BioKIC#1396
# Summary
Adds Parameter to let rpc call reduce output to distict results
Fixes parent dependent search detection so that initial id is used
forever even after the parent param changes

Issue came up when `calif` would show `Baja California` before
`California` because it was sorted by alphabetical but it really should
be the more exact match ie the smaller one usually first

* pointaid only autoselects tool if point not present and click to edit is now possible with leaflet draw

* fixes deletion problem with marker and circle present. Also fixes drag not being possible when click editing

* change checklist point aid to just use collection point aid to reduce duplicated effort

* fixed problem that occured while in edit mode and changing the error radius

* more form enhancements so that circle and marker move with each other during position edits

* add display format radio button and handle case where user navigates back from table display to list display and then clicks breadcrumbs

* handle logic flow of list->table->list

* add translation and respond to self code review

* fix bug where breadcrumbs in collections/listtabledisplay.php were not respecting whether user was coming from new search page

…KIC#1419)

…ring kml download attempt (BioKIC#1421)

…ioKIC#1378 (BioKIC#1423)

# Issues BioKIC#1378

# Summary
Default css in reset.css removed default table vertical alignment which
skewed the inputs in the table

BioKIC#1426)

* fix types for taxa id-related prepared statements to match sqls expectation of integer types as well as make some cosmetic fixes to spacing for code readbility

* change result to statement for close

Schema patch adjustments based on running patch through a new portal 3.0 install and a 1.x => 3.0 => 3.1 portal update. Install/update tests were run both through command line and using the schema manager tool.
- Remove omoccurrences index keys that are never set within previous schema updates
- Temporarily turn off foreign key checks to allow renaming of omoccurrences collid index

Schema Manager adjustments 
- Adjust code to accept and run the 3.1 patch
- Add try-catch and other db checks to avoid PHP 8.1 throwing fatal errors when SQL statements fail, where the previous action only involved a return of a NULL result set

* address xss vulnerability for taxa in imagelib/search.php

* fix sql injection bug for cntperpage in imagelib/search.php

* address sql injection of taxa parameter in checklists/checklist.php and, indirectly, /collections/list.php

* hopefully resolves sql injection issue with db/searchvar in /collections/map/kmlhandler.php

* hopefully address sql injection for downloadhandler.php

…s as disabled until [3.2] part 2 is done) (BioKIC#1429)

All requested changes made by @MuchQuak have been incorporated into the Part 2 of the ticket.

* establish minimal_header_template.php

* remove defaults

* freeze of current work to address burpsuite stuff

* continue making aesthetics improvements at both small and large screen sizes for the minimal header

* makes the map header configurable and handles some styling that has to be dynamic depending on presence or absence of map header

* adds minimal header optionally to collections/tools/mappointaid.php

* adds minimal header optionally to CHECKLISTS/tools/mappointaid.php

* move the z-index styling to the css file so that it can be overwritten more easily in collections/georef/georefclone.php. Implements the minimal header in collections/georef/georefclone.php

* fix bug where clicking advanced search from coll profile had a parsing error from the db query param in the url

* implement minimal header in collections/individual/index.php

* remove cruft

* handle cass where [db] is not set

* make progress on /checklists/checklistmap.php?clid=78&thesfilter=0&taxonfilter= and on http://localhost/Symbiota/checklists/clgmap.php?pid=7 but both are currently buggy but commented out

* add default  = false; value to symbini_template

* change defaults to false

* remove absolute and top styling

Media API development

The hardcoded import of the variables.css breaks portals customized using a css/custom folder. (issues presented in /collections/misc/collprofiles.php )

The import also appeared to be unnecessary / redundant as both the customized and v202209 folder version were being brought in.

* added checks for sciname, date, identifiedBy, added try catch to skip errors instead of stopping

* replaced ERROR with SKIPPED

* unified styling for error/skip displaying

* fixed the sql errors displaying

* go back to original error display

* added note at the end and translations

- Change sciName to scientificName alias
- Make Taxa searchable by taxon search variable
- Support exact, starts with, wildcard, and wholeword search types
- Standardize taxa table indexes
- Update Swagger documentation with new functionality

- Fix bug associated with Swagger documentation
- Update API title output

Modifies logic to display available boundary tool when no active geographic thesaurus exist in the DB

* CSS drop-down menus

Add styling to header.css that enables top drop-down menus

Errant line of code short circuiting collection meta data update.

- Add formatting for eventDate2
- Adjust exsicati
- Remove from display: additional identifiers, behavior, vitality

- Add vertical-align to crowdsource css to override value set within reset.css
- Force refresh of crowdsource.css within client's browsers

BioKIC#1458)

- resolve vertical-align issue, which persisted when opening in crowdsourcing mode and then switching between long and short forms
- Fix fieldset padding issue within image popout

Occurrence editor crowdsource adjustments

- Fix route bug interfering with POST write calls
- Add recordID UUID to POST call
- Improve error output media object isn't found (400 error)
- Improve standardization of all response output
- Add sort fields to api documentation
- Add function that attempts to determine mime type via file header. Has added benefit of ensuring input file exists.
- Update swagger documentation

- Add ability to match images based on recordID UUID within PATCH call

Media API

…C#1454)

…haracters or quotes (BioKIC#1436)

* do not add taxa to query if there are special characters or quotes

* cherry pick fix in 6250abd where getTaxonWhereFrag was getting un-cleaned taxon string

* respond to code review feedback

- searchvar term is being sanitized prior to being set as a session variable, which is converting & to &, thus interfering with parsing of all terms after the first term. Translating & to & fixes the issue.
- The cleanOutStr function santizes output using htmlspecialchars. The htmlspecialchars on line 638 will double sanitize output, thus converting "east & west" to "east & west".
- Variable is getting sanitized within index.php with htmlspecialchars twice. Once on line 12 and again on line 205

Addresses GH issue: BioKIC#1470

* increase font size globally to 14 instead of 12, and then make improvements to other parts that looked a little weird in light of this change and addressed them as well

* Update header_template.php

* swap fonts to 1rem so it always matches html font size, 1rem = font-size of html

* header and footer font fixing

* removing footer font styling

* overhauling base/main/variable css files font sizing

* fixing head template font-size usage

* fixing sitemap fonts

* fixing leafletmap fonts

* removing fonts from occur editor and adding reactive styles to button element

* reactive fonts for occurrencelist from map search page

* jquery-ui-icons-fix

* map search font fixes

* checklist/index.php font fixes

* fixing fonts on collections/list

* font fixes taxa profile and taxa editor

* fixing missing span

* fix merge issues on map search

* fixing sitemap badges to scale with font via height based on rem

* adjusting font styles and solving conflicts with contrast change on col search

* saving col profile layout fixes

* move quicksearch to side and make sticky

* collections/list/spacing

* spacing fix for maps

* making checklist.php layout reactive so it works with different font sizes

* font and layout fixes for checklistadmin

* #tabs font size uses body variable

* Reactive quicksearch colprofile

* layout and font fixes for query form

* fieldset-like alteration

* updating header template

* standardize some spacing in checklists/checklistadminmeta.php

* cleanup on unecessary fonts specs

* fixing collectiontitle layout

* fixing collection group layout with new font size

* fixing error from merge

* more clean up of unused font-size declarations

* add font-size-normalization on tabs ui

* fixing checklist "games" font

* modify jquery ui classes to normalize font

* adjusting searchStyles inner to use rem

* cleanup on some old map inlines that are uneeded

* removing redundant font-size3

* removing uneeded font-family

---------

Co-authored-by: MuchQuak <loganpwilt@gmail.com>
Co-authored-by: Logan Wilt <91149982+MuchQuak@users.noreply.github.com>

* make random color function produce a color above 40 luminence so that very dark colors are never produced

* add custom clustering strategy so for map/index so that clusters fit in with other points better and also don't cluster far less aggressively

* init slider for clustering aggressiveness

* fix random color gen create rgb values larger than 255

* add cluster to google maps and point oms.js to cdn so it is up to date

* cleaning old gen clusters from leaflet section of map/index

- Resolve issue interfering with activation of paleo tools

* Audit collmetadata lang tags

* Minor fix

* Fix popup issue

* Shorten Select Language

* Change Contact Us

* Change sample search language

* Search page fix

* Change html characters

* Fix lang tags

* Spacing fix

* Es translation fixes

* Audit lang tags for guidmapper.php

* Fix guidmapper buttons

* Fix inputs for different actions

* Translation edits to collprofiles

* List and listtabledisplay translations

* Fix table display translations

* Add basic translation files for usagepolicy

- Remove no longer needed code fragments that ensure that old configuration variable formats are supported after a minor update

Update Development branch

- Add activate material sample to collection metadata array

Material Sample minor style adjust