…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 <[email protected]>

# 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

- Remove Facebook and Twitter linkage tools

- Reapply protections based on determination settings

* Hotfix v3.1.3 
- Adjusted hotfix merge instructions
- Inventory Management: Bug fix interfering with adding new editors to an inventory project
- Image migration modifications
-- Add option to copy over existing target files
-- Add checks and error handling for non-existent source files and already existing target files
-- Direct log files to be written to /content/logs/
- fix misspelled log directory name, with support still maintained for portals that already have the misspelled directory
- Fix jquery selector to be correct so button is enabled when trait is changed
- Misc language file and wording adjustments

- Add IGNORE to avoid insert failures due to warnings
- Catch and report warnings so that user can resolve issues, if they wish
- Fix final count

Update 3.1 resolution with current master

Update 3.1 merge branch with latest developments pushed into Master branch

- Checklist voucher link bug 
-- Resolves issue where checklist link PK is not passed to link function. 
-- Resolves issue: BioKIC#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: BioKIC#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: BioKIC#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

…e-into-neon

…neon

Update 3.1 review branch with Symbiota 3.1.4 updates

- Add Alternative Identifiers extension (https://rs.gbif.org/extension/gbif/1.0/identifier.xml) to the DwC-Archive export, which includes data backups
- Add support to public download handler
- Add support to DwC-A pub automation handler
- Add support to DwC-A pub webservice handler
- Exclude from CoGe data files
- Mics adjustment to sanitation and language terms
- Tested the DwC-A output file within the GBIF DwC-Archive validation tool: https://www.gbif.org/tools/data-validator

Add Alternative Identifier Ext to DwC-A export

unchecks the include extension when you uncheck the compressed zip file

download checkbox

- Don't display advanced search button, at least until other issues are resolved (see comments added to code)

- Fix bug with function optional input variable defined prior to required variables
- Bug fix interfering with making scientific names actionable links
- Remove warnings when $ACTIVATE_DUPLICATES variable is not defined within symbini file

* Add login form button to prevent circular links
* Bump symfony/process from 5.4.19 to 5.4.46 in /api
* Bump symfony/http-foundation from 5.4.20 to 5.4.46 in /api
* Remove non-template contacts and aboutproject files (BioKIC#1864)
* Add condition for elevation type number in searchform.js, fixed typo for maximum elevation
* Fix typos
* Unify top/northern, bottom/southern usage
* Fix image alignment and button names in flashcards (BioKIC#1881)
* Fix image alignment and button names
* Add stylesheet, removed in-line styling, added flex classes for games in main.css
* Fix over-translated lang tags (BioKIC#1911)
* closes BioKIC#1916 by removing union return type
* Fix parsing issue
* Fix (BioKIC#1920)
* Resolve editor lock bug
* Resolves issue: BioKIC#1923
* Collection Profile issue
* Add form value interpolation for EW NS and units values so sessions is loaded correctly
* Update API Vendor Libraries
* Closes BioKIC#1942 Adjust Language Tags of Cross Portal Results
* Improve Sign-in and Contact Us button layout on <768px wide devices.

---------
Co-authored-by: Edward Gilbert <[email protected]>
Co-authored-by: Katie Pearson <[email protected]>
Co-authored-by: Nikita Salikov <[email protected]>
Co-authored-by: MuchQuak <[email protected]>

* Switch header buttons to use HTML button element for better UX
* Adjust styling to restoring honoring header button text color
* Improve header button layout on <768px display

Setting transparent background for button-tertiary class.

Update 3.1 branch with latest NEON developments

…nflict

Update 3.1 test branch with BioKIC/Symbiota v3.1.5.1