Merge branch '7.x-3.x' into 7.x-3.x-remotedata

legacy/tripal_analysis/tripal_analysis.info

@@ -3,7 +3,7 @@ description = Supports the companalyses tables of Chado by providing pages for v
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 configure = admin/tripal/legacy/tripal_analysis/configuration
 
 dependencies[] = tripal_core

legacy/tripal_contact/tripal_contact.info

@@ -3,7 +3,7 @@ description = Supports the contact tables of Chado by providing pages for viewin
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal_core
 dependencies[] = tripal_chado_views

legacy/tripal_core/tripal_core.info

@@ -3,7 +3,7 @@ description = Provides support for all Tripal modules and includes the Tripal AP
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 configure = admin/tripal
 
 stylesheets[all][] = theme/css/tripal_core.css

legacy/tripal_cv/tripal_cv.info

@@ -3,7 +3,7 @@ description = Supports the Controlled Vocabulary (CV) tables of Chado by providi
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 configure = admin/tripal/vocab
 
 dependencies[] = tripal_core

legacy/tripal_db/tripal_db.info

@@ -3,7 +3,7 @@ description = Supports the database cross-reference tables of Chado by providing
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 configure = admin/tripal/legacy/tripal_db
 
 dependencies[] = tripal_core

legacy/tripal_feature/tripal_feature.info

@@ -3,7 +3,7 @@ description = Supports the sequence (feature) tables of Chado by providing pages
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 stylesheets[all][] = theme/css/tripal_feature.css
 scripts[]          = theme/js/tripal_feature.js

legacy/tripal_featuremap/tripal_featuremap.info

@@ -3,7 +3,7 @@ description = Supports the map tables of Chado by providing pages for viewing an
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal_core
 dependencies[] = tripal_chado_views

legacy/tripal_genetic/tripal_genetic.info

@@ -3,7 +3,7 @@ description = Supports the genetic tables of Chado by providing pages for viewin
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal_core
 dependencies[] = tripal_chado_views

legacy/tripal_library/tripal_library.info

@@ -3,7 +3,7 @@ description = Supports the library tables of Chado by providing pages for viewin
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal_core
 dependencies[] = tripal_chado_views

legacy/tripal_natural_diversity/tripal_natural_diversity.info

@@ -3,7 +3,7 @@ description = Supports the natural diversity (ND) tables of Chado by providing p
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal_core
 dependencies[] = tripal_chado_views

legacy/tripal_organism/tripal_organism.info

@@ -3,7 +3,7 @@ description = Supports the organism tables of Chado by providing pages for viewi
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 configure = admin/tripal/legacy/tripal_organism
 
 stylesheets[all][] = theme/css/tripal_organism.css

legacy/tripal_phenotype/tripal_phenotype.info

@@ -3,7 +3,7 @@ description = Supports the phenotype tables of Chado by providing pages for view
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal_core
 dependencies[] = tripal_chado_views

legacy/tripal_phylogeny/tripal_phylogeny.info

@@ -3,7 +3,7 @@ description = Supports the phylogeny tables of Chado by providing pages for view
 core = 7.x
 project = tripal_phylogeny
 package = Tripal Extensions
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 dependencies[] = tripal_core
 dependencies[] = tripal_cv
 dependencies[] = tripal_db

legacy/tripal_project/tripal_project.info

@@ -3,7 +3,7 @@ description = Supports the project tables of Chado by providing pages for viewin
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 configure = admin/tripal/legacy/tripal_project
 
 dependencies[] = tripal_core

legacy/tripal_pub/tripal_pub.info

@@ -3,7 +3,7 @@ description = Supports the pub (publication) tables of Chado by providing pages
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 stylesheets[all][] = theme/css/tripal_pub.css
 

legacy/tripal_stock/tripal_stock.info

@@ -3,7 +3,7 @@ description = Supports the stock tables of Chado by providing pages for viewing,
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal_core
 dependencies[] = tripal_chado_views

legacy/tripal_views/tripal_views.info

@@ -3,4 +3,4 @@ description = Deprecated-- no longer provides any functionality. See Tripal Chad
 core = 7.x
 project = tripal
 package = Tripal v2 Legacy
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2

tripal/includes/TripalFieldDownloader/TripalFASTADownloader.inc

@@ -0,0 +1,5 @@
+<?php
+
+class TripalFASTADownloader extends TripalFieldDownloader {
+
+}

tripal/includes/TripalFieldDownloader/TripalFieldDownloader.inc

@@ -0,0 +1,114 @@
+<?php
+
+
+class TripalFieldDownloader {
+
+  /**
+   * The bundle name.
+   * @var string
+   */
+  protected $bundle_name = '';
+
+  /**
+   * A set of entity IDs. The entities must all be of the same bundle type.
+   */
+  protected $entity_ids = array();
+
+  /**
+   * The set of fields
+   */
+  protected $fields = array();
+
+  /**
+   * The output file URI.
+   */
+  protected $outfile = '';
+
+  /**
+   * Constructs a new instance of the TripalFieldDownloader class.
+   * @param $bundle_name
+   *   The name of the bundle to which the IDs in the $id argument belong.
+   * @param $ids
+   *   An array of entity IDs
+   * @param $fields
+   *   An array of numeric field IDs to use when constructing the download. If
+   *   no fields are provided then all fields that are appropriate for the
+   *   given type will be used.
+   * @param $outfile_name
+   *   The name of the output file to create (minus any extension).
+   * @param $extension
+   *   The extension to add to the end of the output file.
+   */
+  public function __construct($bundle_name, $ids, $fields = array(),
+      $outfile_name = '', $extension = 'txt') {
+    global $user;
+
+    $this->entity_ids = $ids;
+    $this->fields = $fields;
+
+    // Make sure the user directory exists
+    $user_dir = 'public://tripal/users/' . $user->uid;
+    if (!file_prepare_directory($user_dir, FILE_CREATE_DIRECTORY)) {
+      $message = 'Could not access the directory on the server for storing this file.';
+      watchdog('tripal', $message, array(), WATCHDOG_ERROR);
+      drupal_json_output(array(
+        'status'  => 'failed',
+        'message' => $message,
+        'file_id' => '',
+      ));
+      return;
+    }
+
+    if (!$outfile_name) {
+      $outfile_name = unqiueid();
+    }
+
+    $this->outfile = $user_dir. '/' . $outfile_name . '.' . $outfile_ext;
+  }
+
+  /**
+   * Retrieves the URL for the downloadable file.
+   */
+  public function getURL() {
+     return $this0>outfile;
+  }
+
+  /**
+   * Creates the download able file.
+   */
+  public function create() {
+    $fh = fopen($this->outfile, "w");
+    foreach ($this->entity_ids as $entity_id) {
+      $entity = tripal_load_entity('TripalEntity', array($entity_id), FALSE, $this->fields);
+      $content = $this->format($entity, $this->fields);
+      fwrite($fh, $content);
+    }
+    fclose($fh);
+  }
+
+  /**
+   * Setups a download stream for the file.
+   */
+  public function download() {
+
+  }
+
+  /**
+   * Formats the output for a given entity.
+   *
+   * This function should be implemented by a child class. It should iterate
+   * over the fields for the entity and return the appropriate format.
+   *
+   * @param $entity
+   *   The entity object.  The fields that should be formatted are already
+   *   loaded.
+   * @param $fields
+   *   A list of field names that should be formatted.
+   *
+   * @return
+   *   A string containing the formatted output.
+   */
+  protected function format($entity, $fields) {
+
+  }
+}

tripal/includes/TripalFieldDownloader/TripalGFFDownloader.inc

@@ -0,0 +1,5 @@
+<?php
+
+class TripalGFFDownloader extends TripalFieldDownloader {
+
+}

tripal/includes/TripalFieldDownloader/TripalTabCSVDownloader.inc

@@ -0,0 +1,5 @@
+<?php
+
+class TripalCSVDownloader extends TripalFieldDownloader {
+
+}

tripal/includes/TripalFieldDownloader/TripalTabDownloader.inc

@@ -0,0 +1,5 @@
+<?php
+
+class TripalTabDownloader extends TripalFieldDownloader {
+
+}

tripal/includes/TripalFields/TripalFieldFormatter.inc

@@ -1,15 +1,27 @@
 <?php
 
 class TripalFieldFormatter {
-  // The default lable for this field.
+  /**
+   * The default lable for this field.
+   */
   public static $default_label = 'Tripal Field.';
 
-  // The list of field types for which this formatter is appropriate.
+  /**
+   * The list of field types for which this formatter is appropriate.
+   */
   public static $field_types = array();
 
-  // The list of default settings for this formatter.
+  /**
+   *  The list of default settings for this formatter.
+   */
   public static $default_settings = array();
 
+  /**
+   * An array of formatter classes supported by the field.
+   */
+  public static $download_formats = array();
+
+
   /**
    * Instantiates a new TripalFieldFormatter object.
    *

tripal/includes/tripal.fields.inc

@@ -252,6 +252,11 @@ function tripal_field_no_delete() {
  */
 function tripal_form_field_ui_field_overview_form_alter(&$form, &$form_state, $form_id) {
 
+  // If this isn't a TripalEntity content type then skip this form.
+  if ($form['#entity_type'] != 'TripalEntity') {
+    return;
+  }
+
   // Add the 'Storage Location' to the table header.
   $form['fields']['#header'][] = 'Term';
   $form['fields']['#header'][] = 'Supported By * ';

tripal/tripal.info

@@ -3,7 +3,7 @@ description = Tripal is an toolkit to facilitate construction of online genomic,
 core = 7.x
 project = tripal
 package = Tripal
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 configure = admin/tripal
 
 stylesheets[all][] = theme/css/tripal.css

tripal/tripal.module

@@ -893,7 +893,7 @@ function tripal_block_save($delta = '', $edit = array()) {
 /**
  * Implements hook_block_configure().
  */
-function tripal_block_configure ($delta = '') {
+function tripal_block_configure($delta = '') {
   $form = array();
 
   switch ($delta) {

tripal_bulk_loader/tripal_bulk_loader.info

@@ -3,7 +3,7 @@ description = Supports the construction of templates for customizable uploading
 core = 7.x
 project = tripal
 package = Tripal
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal_core
 dependencies[] = tripal_chado_views

tripal_chado/api/tripal_chado.api.inc

@@ -174,7 +174,6 @@ function tripal_chado_publish_records($values, $job_id = NULL) {
   // Perform the query.
   $sql = $select . $from . $where;
   $records = chado_query($sql, $args);
-
   $transaction = db_transaction();
 
   print "\nNOTE: publishing records is performed using a database transaction. \n" .

tripal_chado/includes/TripalFields/chado_linker__prop/chado_linker__prop_widget.inc

@@ -74,7 +74,9 @@ class chado_linker__prop_widget extends ChadoFieldWidget {
           'accession' => $accession,
         ),
       ));
-      $type_id = $cvterm->cvterm_id;
+      if ($cvterm) {
+        $type_id = $cvterm->cvterm_id;
+      }
     }
 
     $widget['value'] = array(

tripal_chado/includes/TripalImporter/OBOImporter.inc

@@ -661,7 +661,6 @@ class OBOImporter extends TripalImporter {
    *   The name of the default database.
    */
   private function processTerms($defaultcv, &$newcvs, $default_db) {
-
     $i = 0;
 
     // Iterate through each term from the OBO file and add it.
@@ -1117,6 +1116,7 @@ class OBOImporter extends TripalImporter {
     $default_db = '';
     $line_num = 0;
     $num_read = 0;
+    $type = '';
 
     $filesize = filesize($obo_file);
     $this->setTotalItems($filesize);
@@ -1145,7 +1145,6 @@ class OBOImporter extends TripalImporter {
 
       //remove comments from end of lines
       $line = preg_replace('/^(.*?)\!.*$/', '\1', $line);  // TODO: if the explamation is escaped
-      $type = '';
 
       // at the first stanza we're out of header
       if (preg_match('/^\s*\[/', $line)) {
@@ -1172,6 +1171,7 @@ class OBOImporter extends TripalImporter {
         $stanza = array();
         continue;
       }
+
       // break apart the line into the tag and value but ignore any escaped colons
       preg_replace("/\\:/", "|-|-|", $line); // temporarily replace escaped colons
       $pair = explode(":", $line, 2);

tripal_chado/includes/tripal_chado.cv.inc

@@ -3,11 +3,14 @@
 /**
  * Loads an OBO File using the new TripalImporter. Expected to be run by a Tripal Job.
  */
-function tripal_cv_load_obo($obo_id) {
+function tripal_cv_load_obo($obo_id, $job = NULL) {
 
   module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/OBOImporter');
   $obo_importer = new OBOImporter();
   $obo_importer->create(array('obo_id' => $obo_id));
+  if ($job) {
+    $obo_importer->setJob($job);
+  }
   $obo_importer->run();
 
 }

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -107,7 +107,7 @@ function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {
  * @return
  *   The unique record ID.
  */
-function tripal_chado_field_storage_write_table($table_name, $values, $base_table, $base_pkey = NULL, $base_record_id= NULL) {
+function tripal_chado_field_storage_write_table($table_name, $values, $base_table, $base_pkey = NULL, $base_record_id = NULL) {
   $schema = chado_get_schema($table_name);
   $fkeys = $schema['foreign keys'];
   $pkey = $schema['primary key'][0];

tripal_chado/includes/tripal_chado.semweb.inc

@@ -33,6 +33,7 @@ function tripal_chado_populate_chado_semweb_table() {
   tripal_chado_populate_vocab_RDFS();
   tripal_chado_populate_vocab_SBO();
   tripal_chado_populate_vocab_SCHEMA();
+  tripal_chado_populate_vocab_SEP();
   tripal_chado_populate_vocab_SIO();
   tripal_chado_populate_vocab_SO();
   tripal_chado_populate_vocab_SWO();

tripal_chado/tripal_chado.info

@@ -3,7 +3,7 @@ description = Provides a set of Chado-based fields for the Tripal Entities.
 core = 7.x
 project = tripal
 package = Tripal
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 files[] = views_handlers/chado_views_handler_field.inc
 files[] = views_handlers/chado_views_handler_filter.inc

tripal_chado/tripal_chado.module

@@ -164,7 +164,20 @@ function tripal_chado_menu() {
 
   // Adds a +Publish Chado Content link on the 'Tripal Content Types' page.
   $items['admin/structure/bio_data/publish'] = array(
-    'title' => 'Publish Chado Content',
+    'title' => 'Publish Tripal Content',
+    'description' => t('Publish data that is present in Chado but which does
+        not yet have a page on this site for viewing. In Tripal v2.0 or
+        earlier this was refered to as "syncing".'),
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_chado_publish_form'),
+    'access arguments' => array('administer tripal'),
+    'file' => 'includes/tripal_chado.publish.inc',
+    'file path' => drupal_get_path('module', 'tripal_chado'),
+    'type' => MENU_LOCAL_ACTION,
+    'weight' => 2
+  );
+  $items['admin/content/bio_data/publish'] = array(
+    'title' => 'Publish Tripal Content',
     'description' => t('Publish data that is present in Chado but which does
         not yet have a page on this site for viewing. In Tripal v2.0 or
         earlier this was refered to as "syncing".'),

tripal_chado_views/tripal_chado_views.info

@@ -3,7 +3,7 @@ description = Integrates all Chado tables with Drupal Views and provides basic s
 core = 7.x
 project = tripal
 package = Tripal
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 configure = admin/tripal/storage/chado/views-integration
 
 files[] = views/handlers/tripal_views_handler_filter_textarea.inc

tripal_ds/includes/tripal_ds.field_group.inc

@@ -164,14 +164,14 @@ function _data_sequence_field_group_info($bundle_name, $fields){
   $field_group_tripalpane->mode = 'default';
   $field_group_tripalpane->parent_name = '';
   $field_group_tripalpane->data = array(
-    'label' => 'Data Sequences',
+    'label' => 'Sequences',
     'weight' => '1',
     'children' => array(
         0 => 'group_sequence_table',
     ),
     'format_type' => 'tripalpane',
     'format_settings' => array(
-      'label' => 'Data Sequences',
+      'label' => 'Sequences',
       'instance_settings' => array(
         'id' => 'tripal_ds-fieldset-group_sequence_tripalpane',
         'classes' => 'group-sequence-tripalpane field-group-tripalpane ',
@@ -195,12 +195,12 @@ function _data_sequence_field_group_info($bundle_name, $fields){
   $field_group->mode = 'default';
   $field_group->parent_name = 'group_sequence_tripalpane';
   $field_group->data = array(
-    'label' => 'Data Sequences Table',
+    'label' => 'Sequences Table',
     'weight' => '1',
     'children' => $fields,
     'format_type' => 'table',
     'format_settings' => array(
-      'label' => 'Data Sequences Table',
+      'label' => 'Sequences Table',
       'instance_settings' => array(
         'label_visibility' => '1',
         'desc' => '',

tripal_ds/includes/views/tripal_ds.views.inc

@@ -58,7 +58,7 @@ function tripal_ds_views_data() {
 
   $data['tripal_ds']['tripal_ds_field_label'] = array(
    'title' => t('Field Label'),
-   'help' => t('The human readable name of the field, like "Data Sequences".'),
+   'help' => t('The human readable name of the field, like "Sequences".'),
    'field' => array(
         'handler' => 'views_handler_field',
         'click sortable' => TRUE, // This is use by the table display plugin.

tripal_ds/tripal_ds.info

@@ -3,7 +3,7 @@ description = Provides display options for Tripal Entities through extending Dis
 core = 7.x
 project = tripal
 package = Tripal
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 stylesheets[all][] = theme/css/tripal_ds.css
 

tripal_ws/tripal_ws.info

@@ -3,6 +3,6 @@ description = Exposes Tripal Entites as RESTful web services.
 core = 7.x
 project = tripal
 package = Tripal
-version = 7.x-3.0-rc1
+version = 7.x-3.0-rc2
 
 dependencies[] = tripal