Merge pull request #584 from tripal/577-tv3-pub_syncing

Syncing of Pubs in Tv3 Legacy Mode
tripal · Aug 31, 2018 · dbdfe0f · dbdfe0f
2 parents 85fa360 + e77f6f0
commit dbdfe0f
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Showing 16 changed files with 539 additions and 532 deletions.
diff --git a/legacy/tripal_contact/tripal_contact.install b/legacy/tripal_contact/tripal_contact.install
@@ -51,14 +51,6 @@ function tripal_contact_requirements($phase) {
  */
 function tripal_contact_install() {
 
-  // Add the contactprop table to Chado.
-  tripal_contact_add_custom_tables();
-
-  // Add loading of the the tripal contact ontology to the job queue.
-  $obo_path = '{tripal_contact}/files/tcontact.obo';
-  $obo_id = tripal_insert_obo('Tripal Contacts', $obo_path);
-  tripal_submit_obo_job(array('obo_id' => $obo_id));
-
   // Add cvterms for relationship types.
   tripal_contact_add_cvs();
   tripal_contact_add_cvterms();
@@ -75,13 +67,7 @@ function tripal_contact_install() {
  * @ingroup tripal_legacy_contact
  */
 function tripal_contact_uninstall() {
-  /*
-  // remove our custom block visibility settings per node type
-  db_delete('block_node_type')
-    ->condition('module', 'chado_contact')
-    ->condition('delta', 'contbase')
-    ->execute();
-    */
+
 }
 
 /**
@@ -166,71 +152,3 @@ function tripal_contact_schema() {
   return $schema;
 }
 
-/**
- * Add any custom tables needed by this module.
- * - Contactprop: keep track of properties of contact
- *
- * @ingroup tripal_legacy_contact
- */
-// This function was moved to tripal_chado/includes/setup/tripal_chado.setup.inc
-/* function tripal_contact_add_custom_tables(){
-  $schema = array (
-    'table' => 'contactprop',
-    'fields' => array (
-      'contactprop_id' => array (
-        'type' => 'serial',
-        'not null' => true,
-      ),
-      'contact_id' => array (
-        'type' => 'int',
-        'not null' => true,
-      ),
-      'type_id' => array (
-        'type' => 'int',
-        'not null' => true,
-      ),
-      'value' => array (
-        'type' => 'text',
-        'not null' => false,
-      ),
-      'rank' => array (
-        'type' => 'int',
-        'not null' => true,
-        'default' => 0,
-      ),
-    ),
-    'primary key' => array (
-      0 => 'contactprop_id',
-    ),
-    'unique keys' => array (
-      'contactprop_c1' => array (
-        0 => 'contact_id',
-        1 => 'type_id',
-        2 => 'rank',
-      ),
-    ),
-    'indexes' => array (
-      'contactprop_idx1' => array (
-        0 => 'contact_id',
-      ),
-      'contactprop_idx2' => array (
-        0 => 'type_id',
-      ),
-    ),
-    'foreign keys' => array (
-      'cvterm' => array (
-        'table' => 'cvterm',
-        'columns' => array (
-          'type_id' => 'cvterm_id',
-        ),
-      ),
-      'contact' => array (
-        'table' => 'contact',
-        'columns' => array (
-          'contact_id' => 'contact_id',
-        ),
-      ),
-    ),
-  );
-  chado_create_custom_table('contactprop', $schema, TRUE);
-} */
diff --git a/legacy/tripal_pub/api/tripal_pub.DEPRECATED.inc b/legacy/tripal_pub/api/tripal_pub.DEPRECATED.inc
@@ -129,11 +129,11 @@ function tripal_pub_import_publications_by_import_id($import_id, $job_id = NULL)
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_pub_import_publications_by_import_id',
-      '%new_function' => 'tripal_execute_pub_importer'
+      '%new_function' => 'chado_execute_pub_importer'
     )
   );
 
-  return tripal_execute_pub_importer($import_id, $job_id);
+  return chado_execute_pub_importer($import_id, TRUE, FALSE, $job_id);
 }
 
 /**

diff --git a/legacy/tripal_pub/tripal_pub.install b/legacy/tripal_pub/tripal_pub.install
@@ -49,17 +49,6 @@ function tripal_pub_requirements($phase) {
 function tripal_pub_install() {
   global $base_path;
 
-  // add loading of the the tripal pub ontology to the job queue
-  $obo_path = '{tripal_pub}/files/tpub.obo';
-  $obo_id = tripal_insert_obo('Tripal Publication', $obo_path);
-  tripal_submit_obo_job(array('obo_id' => $obo_id));
-
-  tripal_pub_add_cvs();
-  tripal_pub_add_cvterms();
-
-  // add the custom tables
-  tripal_pub_add_custom_tables();
-
   // set the default vocabularies
   tripal_set_default_cv('pub', 'type_id', 'tripal_pub');
   tripal_set_default_cv('pubprop', 'type_id', 'tripal_pub');
@@ -126,95 +115,9 @@ function tripal_pub_schema() {
     'primary key' => array('nid'),
   );
 
-  $schema['tripal_pub_import'] = array(
-    'fields' => array(
-      'pub_import_id' => array(
-        'type' => 'serial',
-        'not null' => TRUE
-      ),
-      'name' => array(
-        'type' => 'varchar',
-        'length' => 255,
-        'not null' => TRUE
-      ),
-      'criteria' => array(
-        'type' => 'text',
-        'size' => 'normal',
-        'not null' => TRUE,
-        'description' => 'Contains a serialized PHP array containing the search criteria'
-      ),
-      'disabled'  => array(
-        'type' => 'int',
-        'unsigned' => TRUE,
-        'not NULL' => TRUE,
-        'default' => 0
-      ),
-      'do_contact'  => array(
-        'type' => 'int',
-        'unsigned' => TRUE,
-        'not NULL' => TRUE,
-        'default' => 0
-      ),
-    ),
-    'primary key' => array('pub_import_id'),
-    'indexes' => array(
-      'name' => array('name')
-    ),
-  );
-
   return $schema;
 }
 
-/**
- * Add custom table related to publications
- *  - pubauthor_contact
- *
- * @ingroup tripal_legacy_pub
- */
-// This function was moved to tripal_chado/includes/setup/tripal_chado.setup.inc
-/* function tripal_pub_add_custom_tables() {
-  $schema = array (
-    'table' => 'pubauthor_contact',
-    'fields' => array (
-      'pubauthor_contact_id' => array (
-        'type' => 'serial',
-        'not null' => true,
-      ),
-      'contact_id' => array (
-        'type' => 'int',
-        'not null' => true,
-      ),
-      'pubauthor_id' => array (
-        'type' => 'int',
-        'not null' => true,
-      ),
-    ),
-    'primary key' => array (
-      0 => 'pubauthor_contact_id',
-    ),
-    'unique keys' => array (
-      'pubauthor_contact_c1' => array (
-        0 => 'contact_id',
-        1 => 'pubauthor_id',
-      ),
-    ),
-    'foreign keys' => array (
-      'contact' => array (
-        'table' => 'contact',
-        'columns' => array (
-          'contact_id' => 'contact_id',
-        ),
-      ),
-      'pubauthor' => array (
-        'table' => 'pubauthor',
-        'columns' => array (
-          'pubauthor_id' => 'pubauthor_id',
-        ),
-      ),
-    ),
-  );
-  chado_create_custom_table('pubauthor_contact', $schema, TRUE);
-} */
 
 /**
  * This is the required update for tripal_pub when upgrading from Drupal core API 6.x.

diff --git a/legacy/tripal_pub/tripal_pub.module b/legacy/tripal_pub/tripal_pub.module
@@ -338,7 +338,7 @@ function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
 function tripal_pub_job_describe_args($callback, $args) {
 
   $new_args = array();
-  if ($callback == 'tripal_execute_pub_importer') {
+  if ($callback == 'chado_execute_pub_importer') {
     // get all of the loaders
     $qargs = array(':import_id' => $args[0]);
     $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :import_id ";

diff --git a/tripal/api/tripal.jobs.api.inc b/tripal/api/tripal.jobs.api.inc
@@ -567,4 +567,4 @@ function tripal_execute_job($job_id, $redirect = TRUE) {
   if ($redirect) {
     drupal_goto("admin/tripal/tripal_jobs/view/$job_id");
   }
-}
+}
diff --git a/tripal/api/tripal.notice.api.inc b/tripal/api/tripal.notice.api.inc
@@ -31,8 +31,13 @@ define('TRIPAL_DEBUG',7);
 /**
  * Provide better error notice for Tripal.
  *
+ * Please be sure to set the $options array as desired. For example, by default
+ * this function sends all messages to the Drupal watchdog. If a long running
+ * job uses this function and prints status messages you may not want to have
+ * those go to the watchdog as it can dramatically affect performance. 
+ * 
  * If the environment variable 'TRIPAL_DEBUG' is set to 1 then this function
- * will add backtrace information to the message.
+ * will add backtrace information to the message.  
  *
  * @param $type
  *   The catagory to which this message belongs. Can be any string, but the
@@ -60,6 +65,12 @@ define('TRIPAL_DEBUG',7);
  *       display is the command-line
  *     - drupal_set_message: set to TRUE to call drupal_set_message with the 
  *       same error.
+ *     - drupal_set_message:  set to TRUE then send the message to the
+ *       drupal_set_message function.
+ *     - watchdog:  set to FALSE to disable logging to Drupal's watchdog.
+ *     - job: The jobs management object for the job if this function is run 
+ *       as a job. Adding the job object here ensures that any status or error
+ *       messages are also logged with the job.
  *
  * @ingroup tripal_notify_api
  */
@@ -110,13 +121,15 @@ function tripal_report_error($type, $severity, $message, $variables = array(), $
     }
   }
 
-  // Send to watchdog.
-  try {
-    watchdog($type, $message, $variables, $severity);
-  }
-  catch (Exception $e) {
-    print "CRITICAL (TRIPAL): Unable to add error message with watchdog: " . $e->getMessage(). "\n.";
-    $options['print'] = TRUE;
+  // Send to watchdog if the user wants.
+  if (array_key_exists('watchdog', $options) and $options['watchdog'] !== FALSE) {   
+    try {
+      watchdog($type, $message, $variables, $severity);
+    }
+    catch (Exception $e) {
+      print "CRITICAL (TRIPAL): Unable to add error message with watchdog: " . $e->getMessage(). "\n.";
+      $options['print'] = TRUE;
+    }
   }
 
   // Format the message for printing (either to the screen, log or both).
@@ -149,7 +162,10 @@ function tripal_report_error($type, $severity, $message, $variables = array(), $
   if (($severity != TRIPAL_INFO)) {
     tripal_log('[' . strtoupper($type) . '] ' . $print_message . "\n", $severity_string);
   }
-
+
+  if (array_key_exists('job', $options) and is_a($options['job'], 'TripalJob')) {   
+    $options['job']->logMessage($message, $variables, $severity);
+  }
 }
 
 /**
@@ -231,16 +247,20 @@ function tripal_set_message($message, $importance = TRIPAL_INFO, $options = arra
 }
 
 /**
- * File-based logging for Tripal.
- *
+ * File-based error logging for Tripal.
+ * 
+ * Consider using the tripal_report_error function rather than
+ * calling this function directly, as that function calls this one for non
+ * INFO messages and has greater functionality. 
+ * 
  * @param $message
  *   The message to be logged. Need not contain date/time information.
  * @param $log_type
  *   The type of log. Should be one of 'error' or 'job' although other types
  *   are supported.
  * @param $options
  *   An array of options where the following keys are supported:
- *     - first_progress_bar: this sohuld be used for the first log call for a
+ *     - first_progress_bar: this should be used for the first log call for a
  *       progress bar.
  *     - is_progress_bar: this option should be used for all but the first print
  *       of a progress bar to allow it all to be printed on the same line

diff --git a/tripal/includes/TripalJob.inc b/tripal/includes/TripalJob.inc
@@ -595,6 +595,15 @@ class TripalJob {
    * Logging works regardless if the job uses a transaction. If the
    * transaction must be rolled back to to an error the error messages will
    * persist.
+   * 
+   * If a function can be executed by the Tripal job system (and hence the
+   * job object is passed in) then you can directly use this function to
+   * log messages. However, if the function can be run via drush on the 
+   * command-line, consider using the tripal_report_error() function which can
+   * accept a job object as an $option and will print to both the terminal
+   * and to the job object.  If you use the tripal_report_error() be sure
+   * to set the 'watchdog' option only if you need log messages also going 
+   * to the watchdog.
    *
    * @param $message
    *   The message to store in the log. Keep $message translatable by not

diff --git a/tripal/includes/tripal.jobs.inc b/tripal/includes/tripal.jobs.inc
@@ -279,12 +279,21 @@ function tripal_jobs_view($job_id) {
   }
 
   // build the links
-  $links  = l('Return to jobs list', "admin/tripal/tripal_jobs/") . ' | ';
-  $links .= l('Re-run this job', "admin/tripal/tripal_jobs/rerun/" . $job->job_id) . ' | ';
+  $items = [];
+  $items[] = l('Return to jobs list', "admin/tripal/tripal_jobs/");
+  $items[] = l('Re-run this job', "admin/tripal/tripal_jobs/rerun/" . $job->job_id);
   if ($job->start_time == 0 and $job->end_time == 0) {
-    $links .= l('Cancel this job', "admin/tripal/tripal_jobs/cancel/" . $job->job_id) . ' | ';
-    $links .= l('Execute this job', "admin/tripal/tripal_jobs/execute/".$job->job_id);
+    $items[] = l('Cancel this job', "admin/tripal/tripal_jobs/cancel/" . $job->job_id);
+    $items[] = l('Execute this job', "admin/tripal/tripal_jobs/execute/".$job->job_id);
   }
+  $links = theme_item_list([    
+    'items' => $items,
+    'title' => '',
+    'type' => 'ul',
+    'attributes' => [
+      'class' => ['action-links'],
+    ],
+  ]);
 
   // make our start and end times more legible
   $job->submit_date = tripal_get_job_submit_date($job);
@@ -320,7 +329,7 @@ function tripal_jobs_view($job_id) {
 
   $content['links'] = array(
     '#type' => 'markup',
-    '#markup' => '<p>' . substr($links, 0, -2) . '</p>',
+    '#markup' => $links,
   );
   $content['job_title'] = array(
     '#type' => 'item',
@@ -362,7 +371,7 @@ function tripal_jobs_view($job_id) {
   );
   $content['log_fset']['job_logs'] = array(
     '#type' => 'markup',
-    '#markup' => '<pre>' . $job->error_msg . '</pre>',
+    '#markup' => '<pre class="tripal-job-logs">' . $job->error_msg . '</pre>',
   );
   return $content;
 }