periodic checkin

tripal/includes/TripalImporter.inc

@@ -634,37 +634,36 @@ class TripalImporter {
 
     if ($total_handled == 0) {
       $memory = number_format(memory_get_usage());
-      print "Percent complete: 0%. Memory: " . $memory . " bytes.\r";
+      print t("Percent complete: 0%. Memory: !memory  bytes.", ['!memory' => $memory]) . "\r";
       return;
     }
 
     // Now see if we need to report to the user the percent done.  A message
     // will be printed on the command-line if the job is run there.
-    $percent = sprintf("%.2f", ($this->num_handled / $this->total_items) * 100);
-    $diff = $percent - $this->prev_update;
-
-    if ($diff >= $this->interval) {
-
+    $percent = ($this->num_handled / $this->total_items) * 100;
+    $ipercent  = (int) $percent;
+    
+    // If we've reached our interval then print update info.
+    if ($ipercent > 0 and $ipercent % $this->interval == 0) {
       $memory = number_format(memory_get_usage());
-      print "Percent complete: " . $percent . "%. Memory: " . $memory . " bytes.\r";
+      $spercent = sprintf("%.2f", $percent);
+      print t("Percent complete: !percent %. Memory: !memory bytes.", 
+        ['!percent' => $spercent, '!memory' => $memory]) . "\r";
 
       // If we have a job the update the job progress too.
       if ($this->job) {
         $this->job->setProgress($percent);
       }
-
-      $this->prev_update = $diff;
     }
   }
 
   /**
    * Updates the percent interval when the job progress is updated.
    *
-   * Updating the job
-   * progress incurrs a database write which takes time and if it occurs to
-   * frequently can slow down the loader.  This should be a value between
-   * 0 and 100 to indicate a percent interval (e.g. 1 means update the
-   * progress every time the num_handled increases by 1%).
+   * Updating the job progress incurrs a database write which takes time 
+   * and if it occurs to frequently can slow down the loader.  This should 
+   * be a value between 0 and 100 to indicate a percent interval (e.g. 1 
+   * means update the progress every time the num_handled increases by 1%).
    *
    * @param $interval
    *   A number between 0 and 100.

tripal_chado/api/ChadoRecord.inc

@@ -0,0 +1,457 @@
+<?php
+
+class ChadoRecord {
+  /**
+   * @var string
+   *   Holds the name of the table that this record belogns to.
+   */
+  protected $table_name = '';
+  /**
+   * @var array
+   *   Holds the Drupal schema definition for this table.
+   */
+  protected $schema = [];
+  /**
+   * @var array
+   *   Holds the values for the columns of the record
+   */
+  protected $values = [];
+  
+  /**
+   * @var array
+   *   An array of required columns.
+   */
+  protected $required_cols = [];
+  
+  /**
+   * @var integer
+   *   The numeric Id for this record.
+   */
+  protected $record_id = NULL;
+  
+  
+  /**
+   * @var string
+   *   The column name for the primary key.
+   */
+  protected $pkey = '';
+  
+  
+  /**
+   * The list of column names in the table.
+   * @var array
+   */
+  protected $column_names = [];
+  
+  
+  /**
+   * The ChadoRecord constructor
+   * 
+   * @param string $table_name
+   *   The name of the table that the record belongs to.
+   */
+  public function __construct($table_name, $record_id = NULL) {
+    
+    if (!$table_name) {
+      $message = t('ChadoRecord::_construct(). The $table_name argument is required for a ChadoRecord instance.');
+      throw new Exception($message);
+    }
+    
+    // Set the table name and schema.
+    $this->table_name = $table_name;
+    $this->schema = chado_get_schema($this->table_name);
+    if (!$this->schema) {
+      $message = t('ChadoRecord::_construct(). Could not find a matching table schema in Chado for the table: !table.',
+        ['!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    // Chado tables never have more than one column as a primary key so
+    // we are good just getting the first element.
+    $this->pkey = $this->schema['primary key'][0];
+    
+    // Save the column names.
+    foreach ($this->schema['fields'] as $column_name => $col_details) {
+      $this->column_names[] = $column_name;
+    }
+    
+    // Get the required columns.
+    foreach ($this->schema['fields'] as $column => $col_schema) {
+      foreach ($col_schema as $param => $val) {
+        if (preg_match('/not null/i', $param) and $col_schema[$param]) {
+          $this->required_cols[] = $column;
+        }
+      }
+    }
+    
+    // If a record_id was provided then lookup the record and set the values.
+    if ($record_id) {
+      try {
+        $sql = 'SELECT * FROM {' . $this->table_name . '} WHERE ' . $this->pkey . ' = :record_id';
+        $result = chado_query($sql, [':record_id' => $record_id]);
+        $values = $result->fetchAssoc();
+        if (empty($values)) {
+          $message = t('ChadoRecord::_construct(). Could not find a record in table, !table, with the given !pkey: !record_id.',
+            ['!pkey' => $this->pkey, '!record_id' => $record_id, '!table' => $this->table_name]);
+          throw new Exception($message);
+        }
+        $this->record_id = $record_id;
+        $this->values = $values;
+      }
+      catch (Exception $e) {
+        $message = t('ChadoRecord::_construct(). Could not find a record in table, !table, with the given !pkey: !record_id. ERROR: !error',
+          ['!pkey' => $this->pkey, '!record_id' => $record_id, '!table' => $this->table_name, '!error' => $e->getMessage()]);
+        throw new Exception($message);
+      }
+    }
+  }
+  
+  /**
+   * Retrieves the record ID.
+   * 
+   * @return number
+   */
+  public function getID() {
+    return $this->record_id;
+  }
+  
+  /**
+   * Retrieves the table name.
+   * 
+   * @return string
+   *   The name of the table that the record belongs to.
+   */
+  public function getTable() {
+    return $this->table;
+  }
+  
+  /**
+   * Retrieves the table schema.
+   * 
+   * @return array
+   *   The Drupal schema array for the table.
+   */
+  public function getSchema() {
+    return $this->schema;
+  }
+  
+  /**
+   * Creates a clone of this record, but without the record ID.
+   * 
+   * @return ChadoRecord
+   *   Returns a new ChadoRecord but with all of the same values but
+   *   without the record ID.
+   */
+  public function clone() {
+    $clone = new ChadoRecord($this->table_name);
+    $clone_values = $this->values;
+    unset($clone_values[$this->pkey]);
+    $clone->setValues($clone_values);
+    
+    return $clone;
+  }
+  
+  /**
+   * Performs either an update or insert into the table using the values.
+   * 
+   * If the record already exists it will be updated. If the record does not
+   * exist it will be inserted.  This function adds a bit more overhead by
+   * checking for the existance of the record and performing the appropriate
+   * action. You can save time by using the insert or update functions directly
+   * if you only need to do one of those actions specifically.
+   * 
+   * @throws Exception
+   */
+  public function save() {
+    
+    // Determine if we need to perform an update or an insert.
+    $num_matches = $this->find();
+    if ($num_matches == 1) {
+      $this->update();
+    }
+    if ($num_matches == 0) {
+      $this->insert();
+    }
+    if ($num_matches > 1) {
+      $message = t('ChadoRecord::save(). Could not save the record into the table, !table. '. 
+        'Multiple records already exist that match the values: !values. '. 
+        'Please provide a set of values that can uniquely identify a record.',
+        ['!table' => $this->table_name, '!values' => print_r($this->values, TRUE), '!error' => $e->getMessage()]);
+      throw new Exception($message);
+    }
+  }
+  /**
+   * Inserts the values of this object as a new record.
+   * 
+   * @throws Exception 
+   */
+  public function insert() {
+    
+    // Make sure we have values for this record before inserting.
+    if (empty($this->values)) {
+      $message = t('ChadoRecord::insert(). Could not insert a record into the table, !table, without any values.',
+        ['!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    // Build the SQL statement for insertion.
+    $insert_cols = [];
+    $insert_vals = [];
+    $insert_args = [];
+    foreach ($this->values as $column => $value) {
+      $insert_cols[] = $column;
+      $insert_vals[] = ':' . $column;
+      $insert_args[':' . $column] = $value;
+    }
+    $sql = 'INSERT INTO {' . $this->table_name . '} (' . 
+      implode(", ", $insert_cols) . ') VALUES (' . 
+      implode(", ", $insert_vals) . ')';
+    try {
+      chado_query($sql, $insert_args);
+      $this->find();
+    }
+    catch (Exception $e) {
+      $message = t('ChadoRecord::insert(). Could not insert a record into the table, !table, with the following values: !values. ERROR: !error',
+        ['!table' => $this->table_name, '!values' => print_r($this->values, TRUE), '!error' => $e->getMessage()]);
+      throw new Exception($message);
+    }
+  }
+  
+  /**
+   * Updates the values of this object as a new record.
+   * 
+   * @throws Exception
+   */
+  public function update() {
+    
+    // Make sure we have values for this record before updating.
+    if (empty($this->values)) {
+      $message = t('ChadoRecord::update(). Could not update a record into the table, !table, without any values.',
+        ['!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    // We have to have a record ID for the record to update.
+    if (!$this->record_id) {
+      $message = t('ChadoRecord::update(). Could not update a record in the table, !table, without a record ID.',
+        ['!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    // Build the SQL statement for updating.
+    $update_args = [];
+    $sql = 'UPDATE {' . $this->table_name . '}  SET ';
+    foreach ($this->values as $column => $value) {
+      // We're not updating the primary key so skip that if it's in the values.
+      if ($column == $this->pkey) {
+        continue;
+      }
+      $sql .= $column . ' = :' . $column . ', '; 
+      $update_args[':' . $column] = $value;
+    }
+    // Remove the trailing comma and space.
+    $sql = substr($sql, 0, -2);
+    $sql .= ' WHERE ' . $this->pkey . ' = :record_id';
+    $update_args[':record_id'] = $this->record_id;
+    
+    // Now try the update.
+    try {
+      chado_query($sql, $update_args);
+    }
+    catch (Exception $e) {
+      $message = t('ChadoRecord::update(). Could not update a record in the table, !table, with !record_id as the record ID and the following values: !values. ERROR: !error',
+        ['!table' => $this->table_name, 
+         '!record_id' => $this->record_id, 
+         '!values' => print_r($this->values, TRUE), 
+         '!error' => $e->getMessage()]);
+      throw new Exception($message);
+    }
+  }
+  
+  /**
+   * Deletes the record that matches the given values.
+   * 
+   * A record ID must be part of the current values.
+   * 
+   * @throws Exception
+   */
+  public function delete() {
+    
+    // We have to have a record ID for the record to be deleted.
+    if (!$this->record_id) {
+      $message = t('ChadoRecord::delete(). Could not delete a record in the table, !table, without a record ID.',
+        ['!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    try {
+      $sql = 'DELETE FROM {' . $this->table_name . '} WHERE ' . $this->pkey . ' = :record_id';
+      chado_query($sql, [':record_id' => $this->record_id]);
+    }
+    catch (Exception $e) {
+      $message = t('ChadoRecord::delete(). Could not delete a record in the table, !table, with !record_id as the record ID. ERROR: !error',
+        ['!table' => $this->table_name,
+         '!record_id' => $this->record_id,
+         '!error' => $e->getMessage()]);
+        throw new Exception($message);
+    }
+  }
+  /**
+   * A general-purpose setter function to set the column values for the record.
+   * 
+   * This function should be used prior to insert or update of a record. For
+   * an update, be sure to include the record ID in the list of values passed
+   * to the function.
+   * 
+   * @param array $values
+   *    An associative array where the keys are the table column names and
+   *    the values are the record values for each column.
+   *    
+   * @throws Exception
+   */
+  public function setValues($values) {
+    
+    // Intiailze the values array.
+    $this->values = [];
+    
+    // Add the values provided into the values property.
+    foreach ($values as $column => $value) {
+      if (in_array($column, $this->column_names)) {
+        $this->values[$column] = $value;
+      }
+      else {
+        $message = t('ChadoRecord::setValues(). The column named, "!column", does not exist in table: "!table".', 
+          ['!column' => $column, '!table' => $this->table_name]);
+        throw new Exception($message);
+      }
+    }
+  
+    // Make sure that the user did not miss any required columns or has
+    // set a column to be NULL when it doesn't allow NULLs.
+    foreach ($this->required_cols as $rcol) {
+      // It's okay if the primary key is missing, esepecially if the user
+      // wants to use the find() or insert() functions.
+      if ($rcol == $this->pkey) {
+        continue;
+      }
+      
+      if (in_array($rcol, array_keys($this->values)) and $this->values[$rcol] === '__NULL__') {
+        $message = t('ChadoRecord::setValues(). The column named, "!column", requires a value for the table: "!table".',
+          ['!column' => $rcol, '!table' => $this->table_name]);
+        throw new Exception($message);
+      }
+    }
+    
+    // Check to see if the user provided the primary key (record_id).
+    if (in_array($this->pkey, array_keys($values))) {
+      $this->record_id = $values[$this->pkey];
+    }
+  }
+  
+  /**
+   * Returns all values for the record.
+   * 
+   * @return array
+   */
+  public function getValues() {
+    return $this->values;
+  }
+  
+  /**
+   * Sets the value for a specific column.
+   * 
+   * @param string $column_name
+   *   The name of the column to which the value should be set.
+   * @param $value
+   *   The value to set.
+   */
+  public function setValue($column_name, $value) {
+    
+    // Make sure the column is valid.
+    if (!in_array($column_name, $this->column_names)) {
+      $message = t('ChadoRecord::setValue(). The column named, "!column", does not exist in table: "!table".',
+        ['!column' => $column, '!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    // Make sure that the value is not NULL if this is a required field.
+    if (!in_array($column_name, $this->required_cols) and $value == '__NULL__') {
+      $message = t('ChadoRecord::setValue(). The column named, "!column", requires a value for the table: "!table".',
+        ['!column' => $rcol, '!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    $this->values[$column_name] = $value;
+  }
+  /**
+   * Returns the value of a specific column.
+   * 
+   * @param string $column_name
+   *   The name of a column from the table from which to retrieve the value.
+   */
+  public function getValue($column_name) {
+    
+    // Make sure the column is valid.
+    if (!in_array($column_name, $this->column_names)) {
+      $message = t('ChadoRecord::getValue(). The column named, "!column", does not exist in table: "!table".',
+        ['!column' => $column, '!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    return $this->values[$column_name];
+  }
+
+  /**
+   * Uses the current values given to this object to find a record.
+   *
+   * Use the setValues function first to set values for searching, then call
+   * this function to find matching record.  The values provided to the
+   * setValues function must uniquely identify a record.
+   * 
+   * @return
+   *   The number of matches found.  If 1 is returned then the query
+   *   successfully found a match. If 0 then no matching records were found.
+   *   
+   * @throws Exception
+   */
+  public function find() {
+    
+    // Make sure we have values for this record before searching.
+    if (empty($this->values)) {
+      $message = t('ChadoRecord::find(). Could not find a record from the table, !table, without any values.',
+        ['!table' => $this->table_name]);
+      throw new Exception($message);
+    }
+    
+    // Build the SQL statement for searching.
+    $select_args = [];
+    $sql = 'SELECT * FROM {' . $this->table_name . '} WHERE 1=1 ';
+    foreach ($this->values as $column => $value) {
+      $sql .= ' AND ' . $column . ' = :' . $column;
+      $select_args[':' . $column] = $value;
+    }
+    try {
+      $results = chado_query($sql, $select_args);
+    }
+    catch (Exception $e) {
+      $message = t('ChadoRecord::find(). Could not find a record in the table, !table, with the following values: !values. ERROR: !error',
+        ['!table' => $this->table_name, '!values' => print_r($this->values, TRUE), '!error' => $e->getMessage()]);
+      throw new Exception($message);
+    }
+    
+    // If we only have a single match then we're good and we can update the
+    // values for this object.
+    $num_matches = $results->rowCount();
+    if ($num_matches == 1) {
+      $record = $results->fetchAssoc();
+      $this->values = [];
+      foreach ($record as $column => $value) {
+        $this->values[$column] = $value;
+      }
+      $this->record_id = $record[$this->pkey];
+    }
+    
+    // Return the number of matches.
+    return $num_matches;
+  }
+}

tripal_chado/api/modules/tripal_chado.cv.api.inc

@@ -924,7 +924,7 @@ function chado_insert_cv($name, $definition) {
  *      automatically updated.
  *
  * @return
- *   A cvterm object
+ *   A cvterm object.
  *
  * @ingroup tripal_chado_cv_api
  */
@@ -1043,7 +1043,7 @@ function chado_insert_cvterm($term, $options = array()) {
   $db->setValues(['name' => $dbname]);
   if (!$db->find()) {
     $db->insert();
-  }  
+  }
 
   // The cvterm table has two unique dependencies:
   //

tripal_chado/includes/tripal_chado.semweb.inc

@@ -1995,6 +1995,14 @@ function tripal_chado_populate_vocab_NCIT() {
     'cv_name' => 'ncit',
     'definition' => 'Any formal business entity for profit, which may be a corporation, a partnership, association or individual proprietorship. [ NCI http://dictionary.law.com ]',
   ));
+  
+  $term = chado_insert_cvterm(array(
+    'id' => 'NCIT:C25693',
+    'name' => 'Subgroup',
+    'cv_name' => 'ncit',
+    'definition' => 'A subdivision of a larger group with members often exhibiting similar characteristics. [ NCI ]',
+  ));
+  
 }
 
 /**

tripal_chado/tripal_chado.install

@@ -1620,3 +1620,34 @@ function tripal_chado_update_7331() {
     throw new DrupalUpdateException('Could not perform update: '. $error);
   }
 }
+
+/**
+ * Adds the NCIT subgroup term for use by the OBO loader when setting vocabulary subsets.
+ */
+function tripal_chado_update_7332() {
+  try {
+    // We have to add the db and cv in case the user hasn't yet prepared Chado.
+    // If they have prepared Chado then no harm done.
+    chado_insert_db([
+      'name' => 'NCI Thesaurus OBO Edition',
+      'description' => 'NCI Thesaurus OBO Edition.',
+      'url' => 'http://purl.obolibrary.org/obo/ncit.owl',
+      'urlprefix' => ' http://purl.obolibrary.org/obo/{db}_{accession}',
+    ]);
+    chado_insert_cv(
+      'ncit',
+      'The NCIt OBO Edition project aims to increase integration of the NCIt with OBO Library ontologies. NCIt is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. NCIt OBO Edition releases should be considered experimental.'
+    );
+    
+    $term = chado_insert_cvterm([
+      'id' => 'NCIT:C25693',
+      'name' => 'Subgroup',
+      'cv_name' => 'ncit',
+      'definition' => 'A subdivision of a larger group with members often exhibiting similar characteristics. [ NCI ]',
+    ]);
+  }
+  catch (\PDOException $e) {
+    $error = $e->getMessage();
+    throw new DrupalUpdateException('Could not perform update: '. $error);
+  }
+}