Merge resolution branch into biorepo master #559
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- Avoid fatal error that are now thrown by PHP v8.1+ instead of the previous warning
* 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 <[email protected]>
* 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
…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
…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.
- Archive NEON styles to conserve in case needed later - Adjust head to accommodate biorepo CSS reorganizations - misc customizations required for the Biorepo portal
* 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]>
Update branch with latest developments
- Misc styling adjustments: -- Transferring styles from old base.css into main-neon.css -- Zero out 2 normalize css file which appear to no longer be needed, but keep in case we need to transfer later -- Mics styling adjustments - Reapply some NEON specific modifications
- 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
…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)
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