Merge pull request #601 from wri/feat/TM-1401-cleaned-tree-species

[TM-1401] Import cleaned tree species associations.

.github/workflows/pull-request.yml

@@ -1,7 +1,6 @@
 name: pull-request
 on:
   pull_request:
-    branches: [main, staging, release/**]
 jobs:
   lintTest:
     runs-on: ubuntu-latest

app/Console/Commands/ImportTreeSpeciesAssociations.php

@@ -0,0 +1,80 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Console\Commands\Traits\Abortable;
+use App\Models\V2\TreeSpecies\TreeSpecies;
+use Illuminate\Console\Command;
+use Symfony\Component\Process\Process;
+
+class ImportTreeSpeciesAssociations extends Command
+{
+    use Abortable;
+
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'import-tree-species-associations {file}';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Imports a CSV that links UUIDs from v2_tree_species to taxon_ids from tree_species_research';
+
+    protected int $treeSpeciesUuidColumn;
+
+    protected int $taxonIdColumn;
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $this->executeAbortableScript(function () {
+            $process = new Process(['wc', '-l', $this->argument('file')]);
+            $process->run();
+            $this->assert($process->isSuccessful(), "WC failed {$process->getErrorOutput()}");
+
+            $lines = ((int)explode(' ', $process->getOutput())[0]) - 1;
+
+            $fileHandle = fopen($this->argument('file'), 'r');
+            $this->parseHeaders(fgetcsv($fileHandle));
+
+            $this->withProgressBar($lines, function ($progressBar) use ($fileHandle) {
+                while ($csvRow = fgetcsv($fileHandle)) {
+                    $treeSpeciesUuid = $csvRow[$this->treeSpeciesUuidColumn];
+                    $taxonId = $csvRow[$this->taxonIdColumn];
+
+                    if ($taxonId != 'NA') {
+                        TreeSpecies::isUuid($treeSpeciesUuid)->update(['taxon_id' => $taxonId]);
+                    }
+                    $progressBar->advance();
+                }
+
+                $progressBar->finish();
+            });
+
+            fclose($fileHandle);
+        });
+    }
+
+    protected function parseHeaders(array $headerRow): void
+    {
+        foreach ($headerRow as $index => $header) {
+            if ($header == 'tree_species_uuid') {
+                $this->treeSpeciesUuidColumn = $index;
+            } elseif ($header == 'taxon_id') {
+                $this->taxonIdColumn = $index;
+            }
+        }
+
+        $this->assert(
+            $this->treeSpeciesUuidColumn != null && $this->taxonIdColumn != null,
+            'Not all required columns were found'
+        );
+    }
+}

app/Models/V2/TreeSpecies/TreeSpecies.php

@@ -38,9 +38,7 @@ class TreeSpecies extends Model implements EntityRelationModel
         'speciesable_id',
         'collection',
         'hidden',
-
-        'old_id',
-        'old_model',
+        'taxon_id',
     ];
 
     public const COLLECTION_DIRECT_SEEDING = 'direct-seeding';
@@ -82,6 +80,11 @@ public function speciesable()
         return $this->morphTo();
     }
 
+    public function taxonomicSpecies()
+    {
+        return $this->belongsTo(TreeSpeciesResearch::class, 'taxon_id');
+    }
+
     public function getRouteKeyName()
     {
         return 'uuid';