From 8fb4ca5b828ed765147fdec06a9e76620e974aae Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Tue, 16 Jul 2024 17:51:00 -0400
Subject: [PATCH 1/2] Add taxon code

- Create a model for NeonTaxonomy table
- Add taxonCode to Taxonomy model
- Add taxon code to Taxonomy Controlled targeting output for single taxon API
---
 .../Http/Controllers/TaxonomyController.php   |  2 ++
 api/app/Models/NeonTaxonomy.php               | 27 +++++++++++++++++++
 api/app/Models/Taxonomy.php                   |  4 +++
 3 files changed, 33 insertions(+)
 create mode 100644 api/app/Models/NeonTaxonomy.php

diff --git a/api/app/Http/Controllers/TaxonomyController.php b/api/app/Http/Controllers/TaxonomyController.php
index 6556c9b8f2..be45749c0a 100644
--- a/api/app/Http/Controllers/TaxonomyController.php
+++ b/api/app/Http/Controllers/TaxonomyController.php
@@ -228,6 +228,8 @@ public function showOneTaxon($id, Request $request){
 		$parStatusResult = $parStatus->get();
 		$taxonObj->classification = $parStatusResult;
 
+		$taxonObj->taxonCodes;
+
 		if(!$taxonObj->count()) $taxonObj = ['status' =>false, 'error' => 'Unable to locate inventory based on identifier'];
 		return response()->json($taxonObj);
 	}
diff --git a/api/app/Models/NeonTaxonomy.php b/api/app/Models/NeonTaxonomy.php
new file mode 100644
index 0000000000..188871e97c
--- /dev/null
+++ b/api/app/Models/NeonTaxonomy.php
@@ -0,0 +1,27 @@
+<?php
+
+namespace App\Models;
+
+use Illuminate\Auth\Authenticatable;
+use Illuminate\Contracts\Auth\Access\Authorizable as AuthorizableContract;
+use Illuminate\Contracts\Auth\Authenticatable as AuthenticatableContract;
+use Illuminate\Database\Eloquent\Factories\HasFactory;
+use Illuminate\Database\Eloquent\Model;
+use Laravel\Lumen\Auth\Authorizable;
+
+class NeonTaxonomy extends Model implements AuthenticatableContract, AuthorizableContract{
+	use Authenticatable, Authorizable, HasFactory;
+
+	protected $table = 'neon_taxonomy';
+	protected $primaryKey = 'taxonPK';
+	public $timestamps = false;
+
+	protected $fillable = [  ];
+
+	protected $hidden = [ 'taxonPK', 'verbatimScientificName', 'tid', 'sciname', 'scientificNameAuthorship', 'family', 'acceptedTaxonCode', 'taxonProtocolCategory',
+		'vernacular', 'source', 'sourceReference', 'notes', 'initialTimestamp' ];
+
+	public function taxa() {
+		return $this->belongsTo(Taxonomy::class, 'tid', 'tid');
+	}
+}
diff --git a/api/app/Models/Taxonomy.php b/api/app/Models/Taxonomy.php
index f743e6d7d2..8ee7857d88 100644
--- a/api/app/Models/Taxonomy.php
+++ b/api/app/Models/Taxonomy.php
@@ -23,4 +23,8 @@ public function descriptions(){
 	public function media(){
 		return $this->hasMany(media::class, 'tid', 'tid');
 	}
+
+	public function taxonCodes(){
+		return $this->hasMany(NeonTaxonomy::class, 'tid', 'tid');
+	}
 }

From 1435351bef170a7fb686ddb3e5d62ee35576563f Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Wed, 17 Jul 2024 13:02:59 -0400
Subject: [PATCH 2/2] Taxonomy API development

- Add taxonCodes to output
- Reduce complexity of taxonomy search endpoint
---
 .../Http/Controllers/TaxonomyController.php   | 26 +++++++------------
 1 file changed, 10 insertions(+), 16 deletions(-)

diff --git a/api/app/Http/Controllers/TaxonomyController.php b/api/app/Http/Controllers/TaxonomyController.php
index be45749c0a..5ea02d3481 100644
--- a/api/app/Http/Controllers/TaxonomyController.php
+++ b/api/app/Http/Controllers/TaxonomyController.php
@@ -55,7 +55,7 @@ public function showAllTaxa(Request $request){
 		$offset = $request->input('offset',0);
 
 		$fullCnt = Taxonomy::count();
-		$result = Taxonomy::skip($offset)->take($limit)->get();
+		$result = Taxonomy::with('taxonCodes')->skip($offset)->take($limit)->get();
 
 		$eor = false;
 		$retObj = [
@@ -134,32 +134,26 @@ public function showAllTaxaSearch(Request $request){
 
 		$type = $request->input('type', 'EXACT');
 
-		$fullCnt = 0;
-		$result = [];
+		$taxaModel = Taxonomy::with('taxonCodes');
 		if($type == 'START'){
-			$fullCnt = Taxonomy::where('sciname', 'like', $request->taxon . '%')->count();
-			$result = Taxonomy::where('sciname', 'like', $request->taxon . '%')->skip($offset)->take($limit)->get();
+			$taxaModel->where('sciname', 'like', $request->taxon . '%');
 		}
 		elseif($type == 'WILD'){
-			$fullCnt = Taxonomy::where('sciname', 'like', '%' . $request->taxon . '%')->count();
-			$result = Taxonomy::where('sciname', 'like', '%' . $request->taxon . '%')->skip($offset)->take($limit)->get();
+			$taxaModel->where('sciname', 'like', '%' . $request->taxon . '%');
 		}
 		elseif($type == 'WHOLEWORD'){
-			$fullCnt = Taxonomy::where('unitname1', $request->taxon)
+			$taxaModel->where('unitname1', $request->taxon)
 				->orWhere('unitname2', $request->taxon)
-				->orWhere('unitname3', $request->taxon)
-				->count();
-			$result = Taxonomy::where('unitname1', $request->taxon)
-				->orWhere('unitname2', $request->taxon)
-				->orWhere('unitname3', $request->taxon)
-				->skip($offset)->take($limit)->get();
+				->orWhere('unitname3', $request->taxon);
 		}
 		else{
 			//Exact match
-			$fullCnt = Taxonomy::where('sciname', $request->taxon)->count();
-			$result = Taxonomy::where('sciname', $request->taxon)->skip($offset)->take($limit)->get();
+			$taxaModel->where('sciname', $request->taxon);
 		}
 
+		$fullCnt = $taxaModel->count();
+		$result = $taxaModel->skip($offset)->take($limit)->get();
+
 		$eor = false;
 		$retObj = [
 			'offset' => (int)$offset,