Merge pull request #1410 from tripal/tv4g0-issue1404-improveMaintaina…

…bility Improve Maintainability as suggested by CodeClimate
tripal · Feb 10, 2023 · c786dbf · c786dbf
2 parents 1b6bec1 + 773f55e
commit c786dbf
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Showing 3 changed files with 51 additions and 25 deletions.
diff --git a/.codeclimate.yml b/.codeclimate.yml
@@ -4,7 +4,7 @@ checks:
   argument-count:
     enabled: false
     config:
-      threshold: 4
+      threshold: 8
   complex-logic:
     enabled: true
     config:
@@ -16,7 +16,7 @@ checks:
   method-complexity:
     enabled: true
     config:
-      threshold: 7
+      threshold: 25
   method-count:
     enabled: false
     config:
@@ -38,7 +38,7 @@ checks:
     config:
       threshold: #language-specific defaults. overrides affect all languages.
   identical-code:
-    enabled: true
+    enabled: false
     config:
       threshold: #language-specific defaults. overrides affect all languages.
 

diff --git a/tripal_chado/src/Database/ChadoSchema.php b/tripal_chado/src/Database/ChadoSchema.php
@@ -110,18 +110,31 @@ public function getMainTables() {
     if (isset($schema['referring_tables'])) {
       foreach ($schema['referring_tables'] as $tablename) {
 
-        // Ignore the cvterm tables, relationships, chadoprop tables.
-        if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
-          $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
-          $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
-          preg_match('/_cvterm$/', $tablename) ||
-          // Ignore prop tables
-          preg_match('/prop$/', $tablename) || preg_match('/prop_.+$/', $tablename) ||
-          // Ignore nd_tables
-          preg_match('/^nd_/', $tablename)) {
-          continue;
+        $is_base_table = TRUE;
+
+        // Ignore the cvterm tables + chadoprop tables.
+        if (in_array($tablename, ['cvterm_dbxref', 'cvterm_relationship', 'cvtermpath', 'cvtermprop', 'chadoprop', 'cvtermsynonym'])) {
+          $is_base_table = FALSE;
+        }
+        // Ignore relationship linked tables.
+        elseif (preg_match('/_relationship$/', $tablename)) {
+          $is_base_table = FALSE;
+        }
+        // Ignore cvterm annotation linking tables.
+        elseif (preg_match('/_cvterm$/', $tablename)) {
+          $is_base_table = FALSE;
         }
-        else {
+        // Ignore property tables.
+        elseif (preg_match('/prop$/', $tablename) || preg_match('/prop_.+$/', $tablename)) {
+          $is_base_table = FALSE;
+        }
+        // Ignore natural diversity tables.
+        elseif (preg_match('/^nd_/', $tablename)) {
+          $is_base_table = FALSE;
+        }
+
+        // If it's not any of the above then add it to the list.
+        if ($is_base_table === TRUE) {
           array_push($base_tables, $tablename);
         }
       }

diff --git a/tripal_chado/src/api/ChadoSchema.php b/tripal_chado/src/api/ChadoSchema.php
@@ -352,18 +352,31 @@ function getBaseTables() {
     if (isset($schema['referring_tables'])) {
       foreach ($schema['referring_tables'] as $tablename) {
 
-        // Ignore the cvterm tables, relationships, chadoprop tables.
-        if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
-          $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
-          $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
-          preg_match('/_cvterm$/', $tablename) ||
-          // Ignore prop tables
-          preg_match('/prop$/', $tablename) || preg_match('/prop_.+$/', $tablename) ||
-          // Ignore nd_tables
-          preg_match('/^nd_/', $tablename)) {
-          continue;
+        $is_base_table = TRUE;
+
+        // Ignore the cvterm tables + chadoprop tables.
+        if (in_array($tablename, ['cvterm_dbxref', 'cvterm_relationship', 'cvtermpath', 'cvtermprop', 'chadoprop', 'cvtermsynonym'])) {
+          $is_base_table = FALSE;
+        }
+        // Ignore relationship linked tables.
+        elseif (preg_match('/_relationship$/', $tablename)) {
+          $is_base_table = FALSE;
+        }
+        // Ignore cvterm annotation linking tables.
+        elseif (preg_match('/_cvterm$/', $tablename)) {
+          $is_base_table = FALSE;
         }
-        else {
+        // Ignore property tables.
+        elseif (preg_match('/prop$/', $tablename) || preg_match('/prop_.+$/', $tablename)) {
+          $is_base_table = FALSE;
+        }
+        // Ignore natural diversity tables.
+        elseif (preg_match('/^nd_/', $tablename)) {
+          $is_base_table = FALSE;
+        }
+
+        // If it's not any of the above then add it to the list.
+        if ($is_base_table === TRUE) {
           array_push($base_tables, $tablename);
         }
       }