[TM-1400] Tree Species taxonomic schema

app/Console/Commands/OneOff/PopulateTreeSpeciesResearch.php

@@ -0,0 +1,87 @@
+<?php
+
+namespace App\Console\Commands\OneOff;
+
+use App\Console\Commands\Traits\Abortable;
+use App\Console\Commands\Traits\AbortException;
+use App\Models\V2\TreeSpecies\TreeSpeciesResearch;
+use Illuminate\Console\Command;
+
+class PopulateTreeSpeciesResearch extends Command
+{
+    use Abortable;
+
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'one-off:populate-tree-species-research {file}';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Given an input file, populates the tree_species_research table';
+
+    // The names of the columns we require for inserting into the DB. Key is column name in the header row of the CSV,
+    // value is the column name in the DB definition
+    protected const COLUMN_MAPPING = [
+        'taxonID' => 'taxon_id',
+        'scientificName' => 'scientific_name',
+        'family' => 'family',
+        'genus' => 'genus',
+        'specificEpithet' => 'specific_epithet',
+    ];
+
+    // Populated by parseHeaders(), a mapping of DB colum name to the index in each row where that data is expected to
+    // exist
+    protected $columns = [];
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $this->executeAbortableScript(function () {
+            $fileHandle = fopen($this->argument('file'), 'r');
+            $this->parseHeaders(fgetcsv($fileHandle, separator: "\t"));
+
+            // The input file at the time of this writing has 1618549 rows of data
+            $this->withProgressBar(1618549, function ($progressBar) use ($fileHandle) {
+                while ($csvRow = fgetcsv($fileHandle, separator: "\t")) {
+                    $data = [];
+                    foreach ($this->columns as $column => $index) {
+                        $data[$column] = $csvRow[$index];
+                    }
+                    TreeSpeciesResearch::create($data);
+                    $progressBar->advance();
+                }
+
+                $progressBar->finish();
+            });
+
+            fclose($fileHandle);
+        });
+    }
+
+    /**
+     * @throws AbortException
+     */
+    protected function parseHeaders(array $headerRow): void
+    {
+        foreach ($headerRow as $index => $header) {
+            $header = trim($header);
+
+            if (array_key_exists($header, self::COLUMN_MAPPING)) {
+                $this->columns[self::COLUMN_MAPPING[$header]] = $index;
+            }
+        }
+
+        $this->assert(
+            count(self::COLUMN_MAPPING) === count($this->columns),
+            'Not all required columns were found'
+        );
+    }
+}

app/Console/Commands/OneOff/UpdateTreeCollections.php

@@ -0,0 +1,66 @@
+<?php
+
+namespace App\Console\Commands\OneOff;
+
+use App\Models\V2\Organisation;
+use App\Models\V2\ProjectPitch;
+use App\Models\V2\Projects\Project;
+use App\Models\V2\Sites\SiteReport;
+use App\Models\V2\TreeSpecies\TreeSpecies;
+use App\Models\V2\UpdateRequests\UpdateRequest;
+use Illuminate\Console\Command;
+
+class UpdateTreeCollections extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'one-off:update-tree-collections';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Removes old / missing collection names and updates to a correct value.';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $this->info('Updating collections in v2_tree_species');
+        TreeSpecies::withoutTimestamps(function () {
+            TreeSpecies::withTrashed()->where('speciesable_type', ProjectPitch::class)
+                ->update(['collection' => TreeSpecies::COLLECTION_PLANTED]);
+            TreeSpecies::withTrashed()->where('speciesable_type', Project::class)->where('collection', 'primary')
+                ->update(['collection' => TreeSpecies::COLLECTION_PLANTED]);
+            TreeSpecies::withTrashed()->where('speciesable_type', Organisation::class)
+                ->update(['collection' => TreeSpecies::COLLECTION_HISTORICAL]);
+            TreeSpecies::withTrashed()->where('speciesable_type', SiteReport::class)->where('collection', null)
+                ->update(['collection' => TreeSpecies::COLLECTION_NON_TREE]);
+        });
+
+        $this->info('Updating collections in v2_update_requests content');
+        // This is kind of a hassle; fortunately, the only model type above that has bad data embedded in update requests
+        // is Project
+        UpdateRequest::withoutTimestamps(function () {
+            $updateRequests = UpdateRequest::where('updaterequestable_type', Project::class)
+                ->where('content', 'LIKE', '%"collection":"primary"%')
+                ->get();
+            foreach ($updateRequests as $updateRequest) {
+                $content = $updateRequest->content;
+                foreach (array_keys($content) as $key) {
+                    $collections = data_get($content, "$key.*.collection");
+                    if (is_array($collections) && in_array('primary', $collections)) {
+                        data_set($content, "$key.*.collection", TreeSpecies::COLLECTION_PLANTED);
+                    }
+                }
+
+                $updateRequest->update(['content' => $content]);
+            }
+        });
+    }
+}

app/Exports/V2/OrganisationsExport.php

@@ -181,9 +181,9 @@ private function addFileCollectionHeadings(array $headings): array
     private function buildTreeSpecies(Organisation $organisation): string
     {
         $list = [];
-        $treeSpecies = $organisation->treeSpecies()->select('name', 'amount')->get();
-        foreach ($treeSpecies as $treeSpecies) {
-            $list[] = $treeSpecies->name . '(' . $treeSpecies->amount . ')';
+        $treeSpecies = $organisation->treeSpeciesHistorical()->select('name', 'amount')->get();
+        foreach ($treeSpecies as $instance) {
+            $list[] = $instance->name . '(' . $instance->amount . ')';
         }
 
         return '[ ' . implode(',', $list) . ' ]';

app/Http/Controllers/V2/Projects/CreateProjectWithFormController.php

@@ -101,7 +101,7 @@ public function __invoke(Request $request): EntityWithSchemaResource
 
         foreach ($projectPitch->treeSpecies()->get() as $treeSpecies) {
             $project->treeSpecies()->create([
-                'collection' => $treeSpecies->collection ?? TreeSpecies::COLLECTION_PRIMARY,
+                'collection' => $treeSpecies->collection ?? TreeSpecies::COLLECTION_PLANTED,
                 'name' => $treeSpecies->name,
                 'amount' => $treeSpecies->amount,
             ]);

app/Http/Resources/V2/Organisation/MonitoringOrganisationResource.php

@@ -40,7 +40,7 @@ public function toArray($request)
             'founding_date' => $this->founding_date,
             'description' => $this->description,
 
-            'tree_species' => TreeSpeciesResource::collection($this->treeSpecies),
+            'tree_species' => TreeSpeciesResource::collection($this->treeSpeciesHistorical),
 
             'web_url' => $this->web_url,
             'facebook_url' => $this->facebook_url,

app/Http/Resources/V2/Organisation/OrganisationResource.php

@@ -39,8 +39,7 @@ public function toArray($request)
             'founding_date' => $this->founding_date,
             'description' => $this->description,
 
-            'tree_species' => TreeSpeciesResource::collection($this->treeSpecies),
-            'tree_species_restored' => TreeSpeciesResource::collection($this->treeSpeciesRestored),
+            'tree_species_historical' => TreeSpeciesResource::collection($this->treeSpeciesHistorical),
             'project_pitches' => ProjectPitchResource::collection($this->projectPitches),
             'leadership_team' => LeadershipTeamResource::collection($this->leadershipTeam),
             'core_team_leaders' => CoreTeamLeaderResource::collection($this->coreTeamLeaders),

app/Models/V2/Organisation.php

@@ -225,16 +225,10 @@ public static function search($query)
             ->where('organisations.name', 'like', "%$query%");
     }
 
-    public function treeSpecies(): MorphMany
+    public function treeSpeciesHistorical(): MorphMany
     {
         return $this->morphMany(TreeSpecies::class, 'speciesable')
-            ->whereNull('collection');
-    }
-
-    public function treeSpeciesRestored(): MorphMany
-    {
-        return $this->morphMany(TreeSpecies::class, 'speciesable')
-            ->where('collection', TreeSpecies::COLLECTION_RESTORED);
+            ->where('collection', TreeSpecies::COLLECTION_HISTORICAL);
     }
 
     public function owners(): HasMany

app/Models/V2/TreeSpecies/TreeSpecies.php

@@ -47,16 +47,14 @@ class TreeSpecies extends Model implements EntityRelationModel
     public const COLLECTION_PLANTED = 'tree-planted';
     public const COLLECTION_NON_TREE = 'non-tree';
     public const COLLECTION_NURSERY = 'nursery-seedling';
-    public const COLLECTION_RESTORED = 'restored';
-    public const COLLECTION_PRIMARY = 'primary';
+    public const COLLECTION_HISTORICAL = 'historical-tree-species';
 
     public static $collections = [
         self::COLLECTION_DIRECT_SEEDING => 'Direct Seeding',
         self::COLLECTION_PLANTED => 'Planted',
         self::COLLECTION_NON_TREE => 'Non Tree',
         self::COLLECTION_NURSERY => 'Nursery Seedling',
-        self::COLLECTION_RESTORED => 'Restored',
-        self::COLLECTION_PRIMARY => 'Primary',
+        self::COLLECTION_HISTORICAL => 'Historical Tree Species',
     ];
 
     public static function createResourceCollection(EntityModel $entity): JsonResource

app/Models/V2/TreeSpecies/TreeSpeciesResearch.php

@@ -0,0 +1,27 @@
+<?php
+
+namespace App\Models\V2\TreeSpecies;
+
+use Illuminate\Database\Eloquent\Model;
+use Illuminate\Database\Eloquent\SoftDeletes;
+
+class TreeSpeciesResearch extends Model
+{
+    use SoftDeletes;
+
+    public $table = 'tree_species_research';
+
+    public $primaryKey = 'taxon_id';
+
+    public $keyType = 'string';
+
+    public $incrementing = false;
+
+    protected $fillable = [
+        'taxon_id',
+        'scientific_name',
+        'family',
+        'genus',
+        'specific_epithet',
+    ];
+}

config/wri/linked-fields.php

@@ -165,11 +165,11 @@
                     'input_type' => 'coreTeamLeaders',
                 ],
                 'org-tree-species-restored' => [
-                    'property' => 'treeSpeciesRestored',
+                    'property' => 'treeSpeciesHistorical',
                     'label' => 'Tree species restored in landscape',
                     'resource' => 'App\Http\Resources\V2\TreeSpecies\TreeSpeciesResource',
                     'input_type' => 'treeSpecies',
-                    'collection' => 'restored'
+                    'collection' => 'historical-tree-species'
                 ],
                 'org-ownership-stake' => [
                     'property' => 'ownershipStake',
@@ -277,7 +277,7 @@
                     'label' => 'Tree Species',
                     'resource' => App\Http\Resources\V2\TreeSpecies\TreeSpeciesResource::class,
                     'input_type' => 'treeSpecies',
-                    'collection' => 'primary',
+                    'collection' => 'tree-planted',
                 ],
             ],
         ],
@@ -364,7 +364,7 @@
                     'label' => 'Tree Species',
                     'resource' => 'App\Http\Resources\V2\TreeSpecies\TreeSpeciesResource',
                     'input_type' => 'treeSpecies',
-                    'collection' => 'primary',
+                    'collection' => 'tree-planted',
                 ],
             ],
         ],

database/factories/V2/TreeSpecies/TreeSpeciesFactory.php

@@ -18,7 +18,6 @@ public function definition()
             'speciesable_id' => Project::factory()->create(),
             'name' => $this->faker->word(),
             'amount' => $this->faker->numberBetween(0, 2147483647),
-            'type' => 'tree',
             'collection' => $this->faker->randomElement(TreeSpecies::$collections),
         ];
     }

database/migrations/2024_11_23_005836_create_tree_species_research.php

@@ -0,0 +1,34 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+
+return new class extends Migration {
+    /**
+     * Run the migrations.
+     */
+    public function up(): void
+    {
+        Schema::create('tree_species_research', function (Blueprint $table) {
+            // This table intentionally avoids having an auto increment int ID PK.
+            $table->string('taxon_id')->primary();
+
+            $table->string('scientific_name');
+            $table->string('family');
+            $table->string('genus');
+            $table->string('specific_epithet');
+
+            $table->timestamps();
+            $table->softDeletes();
+        });
+    }
+
+    /**
+     * Reverse the migrations.
+     */
+    public function down(): void
+    {
+        Schema::dropIfExists('tree_species_research');
+    }
+};

database/migrations/2024_11_25_212923_connect_v2_tree_species_research.php

@@ -0,0 +1,53 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+
+return new class extends Migration {
+    /**
+     * Run the migrations.
+     */
+    public function up(): void
+    {
+        Schema::table('v2_tree_species', function (Blueprint $table): void {
+            if (Schema::hasColumn('v2_tree_species', 'old_model')) {
+                $table->dropColumn('old_model');
+            }
+            if (Schema::hasColumn('v2_tree_species', 'old_id')) {
+                $table->dropColumn('old_id');
+            }
+            if (Schema::hasColumn('v2_tree_species', 'type')) {
+                $table->dropColumn('type');
+            }
+
+            $table->string('taxon_id')->nullable();
+            $table->index('taxon_id');
+        });
+
+        Schema::table('v2_seedings', function (Blueprint $table): void {
+            if (Schema::hasColumn('v2_seedings', 'old_model')) {
+                $table->dropColumn('old_model');
+            }
+            if (Schema::hasColumn('v2_seedings', 'old_id')) {
+                $table->dropColumn('old_id');
+            }
+
+            $table->string('taxon_id')->nullable();
+            $table->index('taxon_id');
+        });
+    }
+
+    /**
+     * Reverse the migrations.
+     */
+    public function down(): void
+    {
+        Schema::table('v2_tree_species', function (Blueprint $table): void {
+            $table->dropColumn('taxon_id');
+        });
+        Schema::table('v2_seedings', function (Blueprint $table): void {
+            $table->dropColumn('taxon_id');
+        });
+    }
+};