Merge pull request #17 from statonlab/add-db-checks

Add db checks

src/CLIPrompt.php

@@ -26,7 +26,7 @@ class CLIPrompt {
   /**
    * CLIPrompt constructor.
    *
-   * @param $file string [optional] Input file path.
+   * @param string $file [optional] Input file path.
    *
    * @return void
    */
@@ -38,18 +38,88 @@ public function __construct($file = 'php://stdin') {
   /**
    * Prompts the user for an answer to the provided question.
    *
-   * @param $question string Question to prompt the user.
+   * @param string $question Question to prompt the user.
    *
    * @return string
    */
-  public function ask($question) {
-    while (empty($response = readline($question))) {
+  public function ask($question, $style = NULL) {
+    if ($style) {
+      $question = $this->applyStyle($question, $style);
+    }
+
+   echo $question;
+    while (empty($response = readline())) {
       $this->error('Please provide a response');
+      echo $question;
     }
 
     return $response;
   }
 
+  protected function applyStyle($str, $style) {
+    switch ($style) {
+      case 'warning':
+        $str = $this->colored->str($str, 'yellow');
+        break;
+      case 'danger':
+      case 'error':
+        $str = $this->colored->str($str, 'red');
+        break;
+      case 'info':
+        $str = $this->colored->str($str, 'blue');
+        break;
+    }
+
+    return $str;
+  }
+
+  /**
+   * Ask a yes or no question.
+   *
+   * @param string $question the question.
+   *
+   * @return bool
+   */
+  public function askBool($question, $style = NULL) {
+    $answer = strtolower($this->ask($question . ' [Y/n]:', $style));
+    while (!in_array($answer, ['y', 'n', 'yes', 'no'])) {
+      $this->error('Please answer with "yes", "no", "y" or "n"');
+    }
+
+    if (substr($answer, 0, 1) === 'y') {
+      return TRUE;
+    }
+
+    return FALSE;
+  }
+
+  /**
+   * Ask multiple choice questions.
+   *
+   * @param string $question The question.
+   * @param array $options A list of options.
+   *
+   * @return int The index of the selected option.
+   */
+  public function askMultipleChoice($question, $options, $style = NULL) {
+    if($style) {
+      $question = $this->applyStyle($question, $style);
+    }
+
+    $this->line($question);
+    $len = count($options);
+
+    for ($i = 1; $i <= $len; $i++) {
+      $this->line("[$i] {$options[$i - 1]}");
+    }
+
+    do {
+      $answer = $this->ask('Please enter an option number: ');
+    } while ($answer < 1 || $answer > $len);
+
+    return intval($answer) - 1;
+  }
+
   /**
    * Prints a line to the file.
    *
@@ -62,7 +132,7 @@ public function line($message) {
   /**
    * Prints a line with a blue background.
    *
-   * @param $message
+   * @param string $message
    */
   public function info($message) {
     echo $this->colored->str($message, 'blue') . PHP_EOL;
@@ -71,7 +141,7 @@ public function info($message) {
   /**
    * Prints a line with a red background.
    *
-   * @param $message
+   * @param string $message
    */
   public function error($message) {
     echo $this->colored->str($message, 'red') . PHP_EOL;
@@ -80,7 +150,7 @@ public function error($message) {
   /**
    * Prints a line with yellow background.
    *
-   * @param $message
+   * @param string $message
    */
   public function warn($message) {
     echo $this->colored->str($message, 'yellow') . PHP_EOL;
@@ -89,7 +159,7 @@ public function warn($message) {
   /**
    * Prints a line with a green background.
    *
-   * @param $message
+   * @param string $message
    */
   public function success($message) {
     echo $this->colored->str($message, 'black', 'green') . PHP_EOL;

src/Colors.php

@@ -60,7 +60,7 @@ public function __construct() {
   public function str($string, $foreground_color = NULL, $background_color = NULL) {
     $colored_string = '';
     $colored_padding = '';
-    $string = ' ' . $string . ' ';
+    //$string = ' ' . $string . ' ';
     $padding = str_pad('', strlen($string), ' ');;
 
     // Check if given foreground color found
@@ -77,9 +77,9 @@ public function str($string, $foreground_color = NULL, $background_color = NULL)
       // Add string and end coloring
       $colored_string .= $string . "\033[0m";
 
-      $full_string = '  ' . $colored_padding . PHP_EOL;
-      $full_string .= '  ' . $colored_string . PHP_EOL;
-      $full_string .= '  ' . $colored_padding;
+      //$full_string = $colored_padding . PHP_EOL;
+      $full_string =  $colored_string;// . PHP_EOL;
+      //$full_string .=  $colored_padding;
     }
     else {
       $full_string = $colored_string;

src/DB.php

@@ -28,6 +28,7 @@ class DB {
 
   /**
    * P
+   *
    * @var array
    */
   protected $parameters;
@@ -134,11 +135,20 @@ public function query($sql, $parameters = []) {
   public function get() {
     $execute = $this->prepared->execute($this->parameters);
 
-    if(!$execute) {
+    if (!$execute) {
       $error = $this->prepared->errorInfo();
-      throw new Exception("Couldn't execute query. $this->sql. " . $error[2]);
+      throw new Exception("Couldn't execute query. $this->sql. " . PHP_EOL . implode(' ', $error));
     }
 
     return $this->prepared->fetchAll();
   }
+
+  /**
+   * Get the count directly.
+   *
+   * @return mixed
+   */
+  public function count() {
+    return intval($this->get()[0]['count']);
+  }
 }

src/Generator.php

@@ -107,6 +107,11 @@ class Generator {
    */
   protected $options;
 
+  /**
+   * Database connection.
+   *
+   * @var null|\StatonLab\FieldGenerator\DB
+   */
   protected $db = NULL;
 
   /**
@@ -140,7 +145,7 @@ public function run() {
     $this->printIntro();
 
     foreach ($this->questions as $question => $field) {
-      $this->{$field} = $this->prompt->ask($question);
+      $this->{$field} = trim($this->prompt->ask($question));
     }
 
     // Auto construct field name
@@ -151,7 +156,7 @@ public function run() {
 
     $files = $this->generate();
 
-    // TODO: CHECK TERMS AGAINST DB HERE
+    $this->validateTerms();
 
     try {
       return $this->make($files);
@@ -174,6 +179,146 @@ protected function validateOptions() {
     }
   }
 
+  /**
+   * Validate provided terms in DB.
+   */
+  protected function validateTerms() {
+    $this->prompt->info('Performing DB checks to validate entries ...');
+    $failed = FALSE;
+
+    // Validate DB
+    $count = $this->count('chado.db', 'name', $this->db_name);
+    if ($count <= 0) {
+      $failed = TRUE;
+      $answer = $this->prompt->askBool("The DB \"{$this->db_name}\" does not exist in the chado.db table. Using this value will create a new DB. Are you sure?");
+      if (!$answer) {
+        $this->terminate();
+      }
+    }
+
+    // Validate CV
+    $count = $this->count('chado.cv', 'name', $this->cv_name);
+    if ($count <= 0) {
+      $failed = TRUE;
+      $answer = $this->prompt->askBool("The CV \"{$this->cv_name}\" does not exist in the chado.cv table. Using this value will create a new CV. Are you sure?");
+      if (!$answer) {
+        $this->terminate();
+      }
+    }
+
+    // Validate CV Term
+    $count = $this->count('chado.cvterm', 'name', $this->cv_term);
+    if ($count <= 0) {
+      $failed = TRUE;
+      $answer = $this->prompt->askBool("The CV term \"{$this->cv_term}\" does not exist in the chado.cvterm table. Using this value will create a new CV. Are you sure?");
+      if (!$answer) {
+        $this->terminate();
+      }
+    }
+
+    if (!$failed) {
+      $results = $this->db->query('SELECT CV.name AS cv_name, DB.name AS db_name, DBX.accession AS accession
+                        FROM chado.cvterm AS CVTERM
+                        JOIN  chado.cv AS CV ON CVTERM.cv_id  = CV.cv_id
+                        JOIN  chado.dbxref AS DBX ON CVTERM.dbxref_id = DBX.dbxref_id
+                        JOIN  chado.db AS DB ON DBX.db_id = DB.db_id
+                        WHERE CVTERM.name = :cv_term', [':cv_term' => $this->cv_term])
+                          ->get();
+      $count = count($results);
+      switch ($count) {
+        case 0:
+          $this->prompt->askBool('Warning: the CV, DB, and CVterm are not properly linked through the chado.dbxref table. If this term was manually inserted into the db, remove it before adding the new term.', 'warning');
+          break;
+        case 1:
+          $this->verifyAccession($results[0]);
+          break;
+        default:
+          $this->handleMultiDBXRef($results);
+          break;
+      }
+    }
+
+    $this->prompt->info("Chosen CV Term ID {$this->db_name}:{$this->field_accession} and CV {$this->cv_name}");
+    $this->prompt->info('DB checks succeeded');
+  }
+
+  /**
+   * Verify that the entered accession is equivalent to the one in the DB.
+   *
+   * @param array $result
+   */
+  protected function verifyAccession($result) {
+    if (!$this->checkAccessionInDB($result)) {
+      $answer = $this->prompt->askBool("The accession in chado is {$result['accession']}, which does not match the provided the accession ({$this->field_accession}). Would you like to use {$result['accession']} instead?", 'warning');
+      if ($answer) {
+        $this->field_accession = $result['accession'];
+      }
+    }
+  }
+
+  /**
+   * Handle multiple results from DB.
+   *
+   * @param array $results 2d array of db results.
+   */
+  protected function handleMultiDBXRef($results) {
+    // Create options array.
+    $options = [];
+    $len = count($results);
+    foreach ($results as $result) {
+      $options[] = "ID {$result['db_name']}:{$results['accesion']} and controlled vocabulary {$results['cv_name']}";
+    }
+    $options[] = "None of the above. I'd like to keep my settings.";
+
+    $index = $this->prompt->askMultipleChoice('Multiple links were found to the same CV term. Please select the most accurate CV term from the list below.', $options, 'warning');
+
+    if ($index === $len) {
+      return;
+    }
+
+    $selected = $results[$index];
+
+    $this->field_accession = $selected['accession'];
+    $this->db_name = $selected['db_name'];
+    $this->cv_name = $selected['cv_name'];
+  }
+
+  /**
+   * Checks the accession validity against the DB result.
+   *
+   * @param array $result A single DB result.
+   *
+   * @return bool
+   */
+  protected function checkAccessionInDB($result) {
+    // Wrapped in quotes to make sure both are evaluated as strings
+    return "$this->field_accession" === trim("{$result['accession']}");
+  }
+
+  /**
+   * Get the total count to a query.
+   *
+   * @param $table
+   * @param $condition_column
+   * @param $condition_value
+   *
+   * @return mixed
+   */
+  protected function count($table, $condition_column, $condition_value) {
+    $sql = "SELECT COUNT(*) AS count FROM $table AS DB WHERE DB.{$condition_column} = :condition_column";
+    return $this->db->query($sql, [':condition_column' => $condition_value])
+                    ->count();
+  }
+
+  /**
+   * Terminate the generator.
+   *
+   * @throws \Exception
+   */
+  protected function terminate() {
+    throw new Exception('User Terminated.');
+  }
+
   /**
    * Prints introduction message.
    */