Simplified taxonomy traversal, added tests for incomplete records.

myfossil · Oct 19, 2014 · 3c23ff4 · 3c23ff4
1 parent 773221d
commit 3c23ff4
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Showing 6 changed files with 204 additions and 32 deletions.
diff --git a/src/API/Object.php b/src/API/Object.php
@@ -53,6 +53,10 @@ public function __get( $key ) {
                 && !is_null( $this->_cache->{ $key } ) )
             return $this->_cache->$key;
 
+        // Special case for the PBDB ID
+        if ( $key == 'pbdbid' )
+            return $this->parameters->id;
+
         // If not a local property, try loading from PBDB
         if ( is_null( $this->properties->{ $key } ) )
             $this->load( $this->properties->block( $key ) );

diff --git a/src/FossilOccurence.php b/src/FossilOccurence.php
@@ -40,8 +40,8 @@ public function __construct() {
      */
     public function __get( $key ) {
         $p = parent::__get( $key );
-        if ( !in_array( $key, array( 'taxon', 'genus', 'kingdom', 'phylum',
-                        'class', 'order', 'family' ) ) ) {
+        if ( !in_array( $key, array( 'taxon', 'species', 'genus', 'kingdom',
+                        'phylum', 'class', 'order', 'family' ) ) ) {
             if ( !is_null( $p ) ) {
                 return $p;
             }
@@ -54,26 +54,19 @@ public function __get( $key ) {
             case 'reidentification':
                 return self::factory( $this->properties->reid_no );
                 break;
-            case 'species':
-                return $this->properties->species_name;
-                break;
             case 'taxon':
+                if ( property_exists( $this->_cache, 'taxon' ) )
+                    return $this->_cache->taxon;
+                $this->_cache->taxon = Taxon::factory( $this->taxon_no );
+                return $this->_cache->taxon;
+            case 'species':
             case 'genus':
-                $_key = !isset( $_key ) ? 'taxon_no' : $_key;
             case 'kingdom':
-                $_key = !isset( $_key ) ? 'kingdom_no' : $_key;
             case 'phylum':
-                $_key = !isset( $_key ) ? 'phylum_no' : $_key;
             case 'class':
-                $_key = !isset( $_key ) ? 'class_no' : $_key;
             case 'order':
-                $_key = !isset( $_key ) ? 'order_no' : $_key;
             case 'family':
-                $_key = !isset( $_key ) ? 'family_no' : $_key;
-                return Taxon::factory( $this->properties->$_key );
-                break;
-            default:
-                throw new \DomainException( 'Invalid property ' . $key );
+                return $this->taxon->{ $key };
         }
 
         return null;

diff --git a/src/Taxon.php b/src/Taxon.php
@@ -41,8 +41,8 @@ public function __construct() {
      */
     public function __get( $key ) {
         $p = parent::__get( $key );
-        if ( !in_array( $key, array( 'taxon', 'genus', 'kingdom', 'phylum',
-                        'class', 'order', 'family' ) ) ) {
+        if ( !in_array( $key, array( 'taxon', 'species', 'genus', 'kingdom',
+                        'phylum', 'class', 'order', 'family' ) ) ) {
             if ( !is_null( $p ) ) {
                 return $p;
             }
@@ -74,7 +74,10 @@ public function __get( $key ) {
             case 'genus':
                 if ( $this->rank == 'species' )
                     return $this->parent;
-                return $this;
+                elseif ( $this->rank == 'genus' )
+                    return $this;
+                else
+                    return null;
             case 'order':
                 $_key = !isset( $_key ) ? 'order_no' : $_key;
             case 'kingdom':
@@ -94,20 +97,14 @@ public function __get( $key ) {
                  * returned a cached object if we had one to offer, so we're
                  * making a new one and returning it.
                  */
-                if ( !property_exists( $this->_cache, $key ) ) {
-                    $this->_cache->{ $key } = self::factory( $this->{ $_key }
-                            );
-                    return $this->_cache->{ $key };
-                } else {
-                    return $this->_cache->{ $key };
-                }
+                if ( !$this->{ $_key } ) return null;
 
-                // We couldn't find what we were looking for, exit.
-                return null;
+                if ( !property_exists( $this->_cache, $key ) )
+                    $this->_cache->{ $key } = self::factory( $this->{ $_key } );
+
+                if ( property_exists( $this->_cache, $key ) )
+                    return $this->_cache->{ $key };
 
-                break;
-            default:
-                throw new \DomainException( 'Invalid property ' . $key );
                 break;
         }
 

diff --git a/tests/FossilOccurenceTest.php b/tests/FossilOccurenceTest.php
@@ -39,6 +39,63 @@ public function testAbstractedRetrieveData() {
         $this->assertContains( "Brachiopoda", $fossil->phylum->name );
         $this->assertContains( "Wellerella", $fossil->genus->name );
         $this->assertContains( "Wellerella", $fossil->taxon->name );
+
+        $data = array(
+                'taxon' => "Pinocetus polonicus",
+                'species' => "Pinocetus polonicus",
+                'genus' => "Pinocetus",
+                'family' => "Aglaocetidae",
+                'order' => "Cetacea",
+                'class' => "Mammalia",
+                'phylum' => "Chordata",
+                'kingdom' => "Metazoa",
+            );
+
+        $fossil = FossilOccurence::factory( 147937 );
+
+        foreach ( $data as $lvl => $taxon_name ) {
+            $expected = $taxon_name;
+            $observed = $fossil->{ $lvl }->name;
+            $this->assertEquals( $expected, $observed );
+        }
+    }
+
+    public function testIncompleteTaxa() {
+        $fossil_data_json = file_get_contents( 'tests/data/fossils-incomplete-taxa.json' );
+        $fossil_data = json_decode( $fossil_data_json );
+
+        $valid_ranks = array( 'species', 'genus', 'family', 'order', 'class',
+                'phylum', 'kingdom' );
+
+        // These are occurrence_no's that should probably be pointed out to
+        // PBDB as being anomalous in how their taxonomy is being calculated.
+        $exclude_ids = array( 461074, 462836 );
+
+        foreach ( $fossil_data as $fossil_datum ) {
+            $rank        = $fossil_datum->taxon_rank;
+            $rank_no     = array_search( $rank, $valid_ranks );
+            $fossil_no   = (int) $fossil_datum->occurrence_no;
+
+            // Skip taxon ranks that we do not support
+            if ( !in_array( $rank, $valid_ranks ) 
+                    || in_array( $fossil_no, $exclude_ids )
+                    || $rank == 'species' 
+                    || $rank == 'kingdom' )
+                continue;
+
+            $rank_child  = $valid_ranks[ ( $rank_no - 1 ) ];
+            $rank_parent = $valid_ranks[ ( $rank_no + 1 ) ];
+            $taxon_no    = (int) $fossil_datum->taxon_no;
+
+
+            $f = FossilOccurence::factory( $fossil_no );
+            $this->assertEquals( $rank, $f->taxon->rank );
+            $this->assertEquals( $taxon_no, $f->taxon_no );
+            $this->assertEquals( $taxon_no, $f->taxon->pbdbid );
+            $this->assertNull( $f->taxon->{ $rank_child } );
+            $this->assertNotNull( $f->taxon->{ $rank_parent } );
+        }
+
     }
 
 }
diff --git a/tests/TaxonTest.php b/tests/TaxonTest.php
@@ -61,8 +61,6 @@ public function testFactory() {
         $this->assertEquals( $taxon->name, "Pinocetus polonicus" );
     }
 
-    /**
-     */
     public function testHierarchy() {
         // from {@link http://paleobiodb.org/data1.1/taxa/single.json?id=53140}
         $data = array(
@@ -84,4 +82,5 @@ public function testHierarchy() {
         }
 
     }
+
 }
diff --git a/tests/data/fossils-incomplete-taxa.json b/tests/data/fossils-incomplete-taxa.json
@@ -0,0 +1,122 @@
+[
+  {
+    "occurrence_no": 187702,
+    "taxon_rank": "genus",
+    "taxon_name": "Pomatodelphis cf. sp.",
+    "taxon_no": 36819
+  },
+  {
+    "occurrence_no": 289579,
+    "taxon_rank": "genus",
+    "taxon_name": "Squalodon ? sp.",
+    "taxon_no": 36852
+  },
+  {
+    "occurrence_no": 371205,
+    "taxon_rank": "family",
+    "taxon_name": "Delphinidae indet.",
+    "taxon_no": 42953
+  },
+  {
+    "occurrence_no": 395326,
+    "taxon_rank": "family",
+    "taxon_name": "Cetotheriidae indet.",
+    "taxon_no": 42973
+  },
+  {
+    "occurrence_no": 460978,
+    "taxon_rank": "subfamily",
+    "taxon_name": "Physeterinae indet.",
+    "taxon_no": 62911
+  },
+  {
+    "occurrence_no": 460984,
+    "taxon_rank": "family",
+    "taxon_name": "Kentriodontidae indet.",
+    "taxon_no": 42938
+  },
+  {
+    "occurrence_no": 460985,
+    "taxon_rank": "family",
+    "taxon_name": "Physeteridae indet.",
+    "taxon_no": 42967
+  },
+  {
+    "occurrence_no": 460989,
+    "taxon_rank": "suborder",
+    "taxon_name": "Odontoceti indet.",
+    "taxon_no": 42937
+  },
+  {
+    "occurrence_no": 460991,
+    "taxon_rank": "family",
+    "taxon_name": "Ziphiidae indet.",
+    "taxon_no": 42951
+  },
+  {
+    "occurrence_no": 460993,
+    "taxon_rank": "family",
+    "taxon_name": "Pontoporiidae indet.",
+    "taxon_no": 42965
+  },
+  {
+    "occurrence_no": 460994,
+    "taxon_rank": "family",
+    "taxon_name": "Delphinidae indet.",
+    "taxon_no": 42953
+  },
+  {
+    "occurrence_no": 461048,
+    "taxon_rank": "genus",
+    "taxon_name": "Scaldicetus sp.",
+    "taxon_no": 36728
+  },
+  {
+    "occurrence_no": 461074,
+    "taxon_rank": "genus",
+    "taxon_name": "Scaldicetus sp.",
+    "taxon_no": 36900
+  },
+  {
+    "occurrence_no": 462836,
+    "taxon_rank": "family",
+    "taxon_name": "Eurhinodelphinidae indet.",
+    "taxon_no": 53264
+  },
+  {
+    "occurrence_no": 462855,
+    "taxon_rank": "family",
+    "taxon_name": "Delphinidae indet.",
+    "taxon_no": 42953
+  },
+  {
+    "occurrence_no": 463341,
+    "taxon_rank": "order",
+    "taxon_name": "Cetacea indet.",
+    "taxon_no": 36652
+  },
+  {
+    "occurrence_no": 464110,
+    "taxon_rank": "subfamily",
+    "taxon_name": "Pomatodelphininae indet.",
+    "taxon_no": 63630
+  },
+  {
+    "occurrence_no": 464111,
+    "taxon_rank": "subfamily",
+    "taxon_name": "Platanistinae indet.",
+    "taxon_no": 63585
+  },
+  {
+    "occurrence_no": 464112,
+    "taxon_rank": "family",
+    "taxon_name": "Platanistidae indet.",
+    "taxon_no": 42941
+  },
+  {
+    "occurrence_no": 464113,
+    "taxon_rank": "suborder",
+    "taxon_name": "Odontoceti indet.",
+    "taxon_no": 42937
+  }
+]