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@@ -21,9 +21,9 @@ abstract class TripalFieldDownloader {
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static public $default_extension = 'txt';
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/**
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- * The bundle name.
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+ * The data collection assigned to this downloader.
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*/
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- protected $bundle_name = '';
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+ protected $collection = NULL;
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/**
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* The collection ID
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@@ -31,84 +31,119 @@ abstract class TripalFieldDownloader {
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protected $collection_id = NULL;
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/**
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- * The collection bundle IDs
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+ * An array of collection_bundle records for the content types that
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+ * belong to this data collection.
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*/
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- protected $collection_bundles = '';
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-
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- /**
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- * The collection bundle IDs
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- */
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- protected $collection_bundle_ids = array();
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+ protected $collection_bundles = NULL;
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/**
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- * A set of entity IDs.
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+ * The output file URI.
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*/
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- protected $entity_ids = array();
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+ protected $outfile = '';
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/**
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- * The set of fields
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+ * An array of printable fields. Because fields can come from multiple
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+ * bundles and those bundles can be from multiple sites, it is possible that
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+ * 1) two bundles use the same field and we want to conslidate to a
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+ * single printable field; and 2) that a remote site may use the same term
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+ * for a field as a bundle on the local site. The only way to sort out this
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+ * mess is to use the term accession numbers. Therefore, the array contains
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+ * a unique list of printable fields using their accession numbers as keys
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+ * and a field label as the value.
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+ *
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*/
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- protected $fields = array();
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+ protected $printable_fields = array();
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/**
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- * The output file URI.
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+ * The remote site json data returned for the entity
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*/
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- protected $outfile = '';
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+ protected $remote_entity = '';
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/**
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- * An array of the header.
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+ * An array that associates a field ID with a term. The key is the bundle
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+ * name, followed by two subkeys: by_field and by_accession. To lookup
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+ * a field's term you use the 'by_field' subkey with the field_id as the next
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+ * level. To lookup the field ID for a term use the 'by_accession' subkey
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+ * with the accession as the next level. Below is an example of the structure
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+ * of this array.
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+ *
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+ * @code
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+ Array (
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+ [bio_data_7] => Array(
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+ [by_field] => Array(
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+ [56] => data:2091,
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+ [57] => OBI:0100026,
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+ [17] => schema:name,
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+ [58] => data:2044,
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+ [34] => data:0842,
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+ [67] => schema:alternateName,
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+ ),
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+ [by_accession] => Array (
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+ [data:2091] => 56,
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+ [OBI:0100026] => 57,
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+ [schema:name] => 17,
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+ [data:2044] => 58,
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+ [data:0842] => 34,
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+ [schema:alternateName] => 67,
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+ ),
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+ ),
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+ )
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+ * @endcode
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*/
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- protected $header_array = array();
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+ protected $fields2terms = array();
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+
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/**
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- * The remote site json data returned for the entity
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+ * A list of field and instance items, indexed first by bundle_name and
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+ * then by field_id and then by the keys 'field' or 'instance' where the
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+ * value is the field or instance details respectively.
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*/
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- protected $remote_entity = '';
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+ protected $fields = array();
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+
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/**
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* Constructs a new instance of the TripalFieldDownloader class.
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- * @param $bundle_name
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- * The name of the bundle to which the IDs in the $id argument belong.
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- * @param $ids
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- * An array of entity IDs. The order of the IDs will be the order that
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- * output is generated.
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- * @param $fields
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- * An array of numeric field IDs to use when constructing the download. If
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- * no fields are provided then all fields that are appropriate for the
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- * given type will be used.
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+ *
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+ * @param $collection_id
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+ * The ID for the collection.
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* @param $outfile_name
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* The name of the output file to create. The name should not include
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* a path.
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*/
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- public function __construct($bundle_name, $ids, $fields = array(),
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- $outfile_name, $uid, $collection_id) {
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+ public function __construct($collection_id, $outfile_name) {
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- $user = user_load($uid);
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- if (!$user) {
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- throw new Exception(t("The provided user ID does not reference a real user: '@uid'.", array('@uid' => $uid)));
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- }
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if (!$outfile_name) {
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throw new Exception("Please provide an outputfilename");
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}
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+ // Get the collection record and store it.
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+ $this->collection = db_select('tripal_collection', 'tc')
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+ ->fields('tc')
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+ ->condition('collection_id', $collection_id, '=')
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+ ->execute()
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+ ->fetchObject();
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+
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+ // Make sure the user directory exists
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+ $user = user_load($this->collection->uid);
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+ $user_dir = 'public://tripal/users/' . $user->uid;
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+
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+ // Set the collection ID of the collection that this downloader will use.
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+ $this->collection_id = $collection_id;
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+ $this->outfile = $user_dir . '/' . $outfile_name;
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+ $this->selected_fields = $selected_fields;
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+
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+ // A data collection may have multiple bundles. We'll need to get
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+ // them all and store them.
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$this->collection_bundles = db_select('tripal_collection_bundle')
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->fields('tripal_collection_bundle')
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->condition('collection_id', $collection_id, '=')
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->execute()
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->fetchAll();
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-
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foreach ($this->collection_bundles as $collection_bundle) {
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- $collection_id = $collection_bundle->collection_bundle_id;
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- $this->collection_bundle_ids[] = $collection_id;
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- $this->bundle_name_ . $collection_id = $collection_bundle->bundle_name;
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- $this->entity_ids_ . $collection_id = unserialize($collection_bundle->ids);
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- $this->fields_ . $collection_id = unserialize($collection_bundle->fields);
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- $this->site_id_ . $collection_id = $collection_bundle->site_id;
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+ $collection_bundle->ids = unserialize($collection_bundle->ids);
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+ $collection_bundle->fields = unserialize($collection_bundle->fields);
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+ $this->collection_bundles[] = $collection_bundle;
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}
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- $this->collection_id = $collection_id;
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-
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- // Make sure the user directory exists
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- $user_dir = 'public://tripal/users/' . $user->uid;
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if (!file_prepare_directory($user_dir, FILE_CREATE_DIRECTORY)) {
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$message = 'Could not access the directory on the server for storing this file.';
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@@ -121,7 +156,36 @@ abstract class TripalFieldDownloader {
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return;
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}
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- $this->outfile = $user_dir . '/' . $outfile_name;
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+ // Map the fields to their term accessions.
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+ $this->setFields();
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+ $this->setFields2Terms();
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+ $this->setPrintableFields();
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+ }
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+
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+ /**
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+ * Inidcates if a given field is supported by this Downloader class.
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+ *
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+ * @param $field
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+ * A field info array.
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+ */
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+ public function isFieldSupported($field, $instance) {
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+ $field_name = $field['field_name'];
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+ $field_type = $field['type'];
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+
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+ // If a field is a TripalField then check its supported downloaders.
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+ if (tripal_load_include_field_class($field_type)) {
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+ $formatters = $field_type::$download_formatters;
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+ if (in_array($formatter, $settings['download_formatters'])) {
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+ return TRUE;
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+ }
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+ }
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+
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+ $is_remote = $field['field']['storage']['type'] == 'tripal_remote_field' ? TRUE : FALSE;
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+ if ($is_remote) {
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+ if (in_array($formatter, $instance['formatters'])) {
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+ return TRUE;
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+ }
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+ }
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}
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/**
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@@ -151,7 +215,8 @@ abstract class TripalFieldDownloader {
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* Creates the downloadable file.
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*/
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public function write() {
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- global $user;
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+ $user = user_load($this->collection->uid);
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+
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$fh = fopen(drupal_realpath($this->outfile), "w");
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if (!$fh) {
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@@ -169,40 +234,33 @@ abstract class TripalFieldDownloader {
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foreach ($bundle_collections as $bundle_collection) {
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$collection_bundle_id = $bundle_collection->collection_bundle_id;
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$bundle_name = $bundle_collection->bundle_name;
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- $fields = unserialize($bundle_collection->fields);
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- $entity_ids = unserialize($bundle_collection->ids);
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+ $entity_ids = $bundle_collection->ids;
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+ $fields = $bundle_collection->fields;
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$site_id = $bundle_collection->site_id;
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- // Determine if the entity is remote or local.
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- if (strpos($bundle_name, 'bio_data_') !== 0) {
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- $external = TRUE;
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- }
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- else {
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- $external = FALSE;
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- }
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+ foreach ($entity_ids as $entity_id) {
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+
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- // Now handle the external bundles.
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- if ($external) {
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- // Now we have the remote site info we need to check against the
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- // passed field and entity ids.
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- foreach ($entity_ids as $remote_id) {
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- $fake_tripal_entity = $this->getRemoteEntity($remote_id, $site_id, $fields, $bundle_name);
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- $lines = $this->formatEntity($fake_tripal_entity);
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- foreach ($lines as $line) {
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- fwrite($fh, $line . "\r\n");
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+ // if we have a site_id then we need to get the entity from the
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+ // remote service. Otherwise create the entity from the local system.
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+ if ($site_id) {
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+ $entity = $this->loadRemoteEntity($entity_id, $site_id, $bundle_name);
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+ if (!$entity) {
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+ continue;
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}
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}
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- }
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- else {
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- // Now handle the local bundles.
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- foreach ($entity_ids as $entity) {
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- // If the field is from a remote entity then we need to load the info through web services.
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- $result = tripal_load_entity('TripalEntity', array($entity), FALSE, $fields);
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- $entity_info = $result[$entity];
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- $lines = $this->formatEntity($entity_info);
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- foreach ($lines as $line) {
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- fwrite($fh, $line . "\r\n");
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- }
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+ else {
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+ $result = tripal_load_entity('TripalEntity', array($entity_id), FALSE, $fields);
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+ $entity = $result[$entity_id];
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+ }
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+
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+ if (!$entity) {
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+ continue;
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+ }
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+
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+ $lines = $this->formatEntity($entity);
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+ foreach ($lines as $line) {
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+ fwrite($fh, $line . "\r\n");
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}
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}
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}
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@@ -214,12 +272,34 @@ abstract class TripalFieldDownloader {
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$file->filemime = file_get_mimetype($this->outfile);
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$file->uid = $user->uid;
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$file->status = FILE_STATUS_PERMANENT;
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- $file = file_save($file);
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- $fid = $file->fid;
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- $file = file_load($fid);
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+
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+ // Check if this file already exists. If it does then just update
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+ // the stats.
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+ $fid = db_select('file_managed', 'fm')
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+ ->fields('fm', array('fid'))
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+ ->condition('uri', $this->outfile)
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+ ->execute()
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+ ->fetchField();
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+ if ($fid) {
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+ $file->fid = $fid;
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+ $file = file_save($file);
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+ }
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+ else {
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+ $file = file_save($file);
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+ $fid = $file->fid;
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+ $file = file_load($fid);
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+ }
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+
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+
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// We use the fid for the last argument because these files
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- // aren't really associated with any entity, but we need a value.
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- file_usage_add($file, 'tripal', 'data-collection', $fid);
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+ // aren't really associated with any entity, but we need a value./
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+ // But, only add the usage if it doens't already exists.
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+ $usage = file_usage_list($file);
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+ if (array_key_exists('tripal', $usage)) {
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+ if (!array_key_exists('data-collection', $usage['tripal'])) {
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+ file_usage_add($file, 'tripal', 'data-collection', $fid);
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+ }
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+ }
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}
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/**
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@@ -229,286 +309,267 @@ abstract class TripalFieldDownloader {
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}
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- /**
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- * Recursive function to walk down the array looking for the passed value.
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- *
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- * @param $haystack
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- * The array of vocab returned from the remote site.
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- * @param $needle
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- * The field which is trying to be matched to.
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- * @param $current_array
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- * Holder for the last array identified.
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- *
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- * @return
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- * The array of the field with title included.
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- */
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- public function vocabSearch($haystack, $needle, &$current_array) {
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- static $_return_array = array();
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- // If the $current_array has a value and the $item is not an array
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- // then we are at the single item section of the nested vocab array
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- // and we can start to check for the $needle.
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- if ($current_array['property'] == $needle) {
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- $_return_array = $current_array;
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- return $_return_array;
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- }
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- elseif (is_array($haystack) && count($haystack) > 0) {
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- foreach ($haystack as $item) {
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- if (is_array($item)) {
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- // Clear out the previous array.
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- $current_array = [];
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- $current_array = $item;
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- $this->vocabSearch($item, $needle, $current_array);
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- }
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- }
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- }
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- return $_return_array;
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- }
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-
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/**
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* Build and return a fake entity from a remote site using
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* tripal web services calls.
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*
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* @param $remote_ids
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* Array of the remote ids.
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- *
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+ *
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* @param $site_id
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* Unique site id assigned in the tripal_sites table when
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* a new site is created via the web services interface.
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- *
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+ *
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* @param $remote_fields
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* Array of the remote fields.
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- *
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+ *
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* @param $bundle_name
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- * Bundle name of the remote field, in this instance it will be
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+ * Bundle name of the remote field, in this instance it will be
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* the accession of the field.
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*
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* @return $fake_tripal_entity
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* This is a fake entity structured to allow the format
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* entity function to process and return the info.
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*/
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- public function getRemoteEntity($remote_ids, $site_id, $remote_fields, $bundle_name) {
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- // Before a request can be made we need to get the entity type
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- // '@id' contains the bundle_name, so look for that.
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- if (!empty($site_id)) {
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- $cache_name = 'tripal_web_services_vocab_' . $site_id;
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- if ($cache = cache_get($cache_name)) {
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- $site_vocab = $cache->data;
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+ protected function loadRemoteEntity($remote_id, $site_id, $bundle_name) {
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+
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+ // Get the site documentation
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+ $site_doc = $this->retrieveRemoteAPIDoc($site_id);
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+
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+ // Get the remote entity and create the fake entity.
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+ $query = $bundle_name . '/' . $remote_id;
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+ $remote_entity = tripal_query_remote_site($site_id, $query);
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+ if (!$remote_entity) {
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+ return FALSE;
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+ }
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+
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+ // Start building the fake id.
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|
+ $entity = new stdClass();
|
|
|
+ $entity->entityType = 'TripalEntity';
|
|
|
+ $entity->entityInfo = [];
|
|
|
+ $entity->id = $remote_id;
|
|
|
+ $entity->type = 'TripalEntity';
|
|
|
+ $entity->bundle = $bundle_name;
|
|
|
+
|
|
|
+ // Get the context JSON for this remote entity, we'll use it to map
|
|
|
+ // the properties to the correct fields.
|
|
|
+ $context = drupal_http_request($remote_entity['@context']);
|
|
|
+ $context = drupal_json_decode($context->data);
|
|
|
+ $context = $context['@context'];
|
|
|
+
|
|
|
+ // Iterate through the fields that are printable and get those values
|
|
|
+ // from the results.
|
|
|
+ foreach ($this->printable_fields as $accession => $label) {
|
|
|
+ $field_id = $this->fields2terms[$bundle_name]['by_accession'][$accession];
|
|
|
+
|
|
|
+ // If the field isn't part of this bundle then skip it.
|
|
|
+ if (!$field_id) {
|
|
|
+ continue;
|
|
|
}
|
|
|
- else {
|
|
|
- $site_vocab = tripal_web_services_vocab_request($site_id);
|
|
|
- if (!empty($site_vocab)) {
|
|
|
- cache_set('tripal_web_services_vocab', $site_vocab);
|
|
|
+
|
|
|
+ $field = $this->fields[$bundle_name][$field_id]['field'];
|
|
|
+ $instance = $this->fields[$bundle_name][$field_id]['instance'];
|
|
|
+ $field_name = $field['field_name'];
|
|
|
+ $accession = $instance['settings']['term_vocabulary'] . ':' . $instance['settings']['term_accession'];
|
|
|
+
|
|
|
+ // Get the key for this field from the context.
|
|
|
+ $field_key = $accession;
|
|
|
+ foreach ($context as $k => $v) {
|
|
|
+ if (!is_array($v)) {
|
|
|
}
|
|
|
- }
|
|
|
- // Now we have the vocab we can look for the bundle_name in the @id field.
|
|
|
- foreach ($site_vocab as $item) {
|
|
|
- if (is_array($item)) {
|
|
|
- foreach ($item as $vocab_term) {
|
|
|
- if (!empty($vocab_term['@id'])) {
|
|
|
- if (strpos($vocab_term['@id'], $bundle_name) !== FALSE) {
|
|
|
- $entity_type = $vocab_term['hydra:title'];
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
+ if (!is_array($v) and $v == $accession) {
|
|
|
+ $field_key = $k;
|
|
|
}
|
|
|
}
|
|
|
- if (is_array($remote_ids)) {
|
|
|
- foreach ($remote_ids as $remote_id) {
|
|
|
- // This entity needs to be pulled down and data grabbed.
|
|
|
- $query = $entity_type . '/' . $remote_id;
|
|
|
- $this->remote_entity = tripal_web_services_remote_request($site_id, $query);
|
|
|
- }
|
|
|
+
|
|
|
+ // If the field is not in this remote bundle then add an empty value for
|
|
|
+ // it.
|
|
|
+ if (!$field_key) {
|
|
|
+ $entity->{$field_name}['und'][0]['value'] = '';
|
|
|
+ continue;
|
|
|
}
|
|
|
- else {
|
|
|
- $query = $entity_type . '/' . $remote_ids;
|
|
|
- $this->remote_entity = tripal_web_services_remote_request($site_id, $query);
|
|
|
+
|
|
|
+ // If the key is for a field that is not "auto attached' then we need
|
|
|
+ // to get that field through a separate call.
|
|
|
+ $needs_query = FALSE;
|
|
|
+ if (array_key_exists($field_name, $context) and is_array($context[$field_name]) and
|
|
|
+ array_key_exists('@type', $context[$field_name]) and $context[$field_name]['@type'] == '@id'){
|
|
|
+ $needs_query = TRUE;
|
|
|
}
|
|
|
- /**
|
|
|
- * remote_entity looks like this:
|
|
|
- * [@context] => http://demo.tripal.info/3.x/sites/default/files/tripal/ws/context/content.v0_1.gene.296.json
|
|
|
- * [@id] => http://demo.tripal.info/3.x/web-services/content/v0.1/Gene/296
|
|
|
- * [@type] => gene
|
|
|
- * [label] => td01_000348m.g
|
|
|
- * [ItemPage] => http://demo.tripal.info/3.x/bio_data/296
|
|
|
- * [type] => Gene
|
|
|
- * [organism] => Array
|
|
|
- * (
|
|
|
- * [label] => <i>Tripalus databasica</i>
|
|
|
- * [genus] => Tripalus
|
|
|
- * [species] => databasica
|
|
|
- * )
|
|
|
- *
|
|
|
- * [name] => td01_000348m.g
|
|
|
- * [identifier] => td01_000348m.g
|
|
|
- * [sequence_checksum] => d41d8cd98f00b204e9800998ecf8427e
|
|
|
- * [time_accessioned] => 2011-06-30 17:00:58.050856
|
|
|
- * [time_last_modified] => 2011-06-30 17:00:58.050856
|
|
|
- * [sequence_coordinates] => http://demo.tripal.info/3.x/web-services/content/v0.1/Gene/296/Sequence+coordinates
|
|
|
- * [relationship] => http://demo.tripal.info/3.x/web-services/content/v0.1/Gene/296/relationship
|
|
|
- */
|
|
|
-
|
|
|
- // Build the fields for the fake entity.
|
|
|
- /**
|
|
|
- * $site_vocab will look like this:
|
|
|
- * [3] => Array(
|
|
|
- * [property] => data:0842
|
|
|
- * [hydra:title] => Identifier
|
|
|
- * [hydra:description] =>
|
|
|
- * [required] => 1
|
|
|
- * [readable] =>
|
|
|
- * [writeable] => 1
|
|
|
- * [tripal_formatters] => Array
|
|
|
- * (
|
|
|
- * [0] => TripalTabDownloader
|
|
|
- * [1] => TripalCSVDownloader
|
|
|
- * )
|
|
|
- * )
|
|
|
- */
|
|
|
- // If only one field was passed then it needs to be handled differently.
|
|
|
- if (!is_array($remote_fields)) {
|
|
|
- $field_entity = array();
|
|
|
- $returned_array = $this->vocabSearch($site_vocab, $remote_fields, $field_entity);
|
|
|
- if ($returned_array['hydra:title']) {
|
|
|
- $fields[$remote_fields]['field_name'] = $returned_array['hydra:title'];
|
|
|
- // Turn the hydra:title into the machine name to get the label.
|
|
|
- $machine_name = (str_replace(' ', '-', strtolower($fields[$remote_fields]['field_name'])));
|
|
|
- $fields[$remote_fields]['label'] = $machine_name;
|
|
|
- // Get the value from the previously created entity.
|
|
|
- $fields[$remote_fields]['value'] = $this->remote_entity[$machine_name];
|
|
|
- // Add the accession information.
|
|
|
- $fields[$remote_fields]['accession'] = $remote_fields;
|
|
|
- }
|
|
|
+
|
|
|
+ $value = '';
|
|
|
+ if (!$needs_query) {
|
|
|
+ $value = $remote_entity[$field_key];
|
|
|
}
|
|
|
- else {
|
|
|
- foreach ($remote_fields as $field) {
|
|
|
- $field_entity = array();
|
|
|
- $returned_array = $this->vocabSearch($site_vocab, $field, $field_entity);
|
|
|
- if (!empty($returned_array)) {
|
|
|
- if ($returned_array['hydra:title']) {
|
|
|
- $fields[$field]['field_name'] = $returned_array['hydra:title'];
|
|
|
- // Turn the hydra:title into the machine name to get the label.
|
|
|
- $machine_name = (str_replace(' ', '-', strtolower($fields[$field]['field_name'])));
|
|
|
- $fields[$field]['label'] = $machine_name;
|
|
|
- // Get the value from the previously created entity.
|
|
|
- $fields[$field]['value'] = $this->remote_entity[$machine_name];
|
|
|
- // Add the accession information.
|
|
|
- $fields[$field]['accession'] = $field;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
+ $entity->{$field_name}['und'][0]['value'] = $value;
|
|
|
+ }
|
|
|
+
|
|
|
+ return $entity;
|
|
|
+ }
|
|
|
+
|
|
|
+ /**
|
|
|
+ * Retrieves the vocabulary for a remote Tripal web service.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * The vocabulary of a remote Tripal web service.
|
|
|
+ */
|
|
|
+ protected function retrieveRemoteAPIDoc($site_id) {
|
|
|
+ $cache_name = 'tripal_web_services_doc_' . $site_id;
|
|
|
+ if ($cache = cache_get($cache_name)) {
|
|
|
+ $site_doc = $cache->data;
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $site_doc = tripal_get_remote_site_doc($site_id);
|
|
|
+ if (!$site_doc) {
|
|
|
+ cache_set('tripal_web_services_doc_' . $site_id, $site_doc);
|
|
|
}
|
|
|
- // Because this is a remote field we need to construct a fake entity.
|
|
|
- $fake_tripal_entity = new stdClass();
|
|
|
- $fake_tripal_entity->entityType = 'TripalEntity';
|
|
|
- $fake_tripal_entity->entityInfo = [];
|
|
|
- $fake_tripal_entity->id = $entity_id;
|
|
|
- $fake_tripal_entity->type = 'TripalEntity';
|
|
|
- $fake_tripal_entity->bundle = $bundle_name;
|
|
|
- if (is_array($fields)) {
|
|
|
- foreach ($fields as $name => $field) {
|
|
|
- $fake_tripal_entity->$name = [
|
|
|
- 'und' => [
|
|
|
- '0' => [
|
|
|
- 'field_name' => $field['field_name'],
|
|
|
- 'label' => $field['label'],
|
|
|
- 'value' => $field['value'],
|
|
|
- 'accession' => $field['accession'],
|
|
|
- ],
|
|
|
- ],
|
|
|
- ];
|
|
|
- };
|
|
|
+ }
|
|
|
+ return $site_doc;
|
|
|
+ }
|
|
|
+
|
|
|
+ /**
|
|
|
+ * A helper function for the setFields() function.
|
|
|
+ *
|
|
|
+ * Adds local fields to the list of fields.
|
|
|
+ */
|
|
|
+ private function setLocalFields() {
|
|
|
+ foreach ($this->collection_bundles as $collection_bundle) {
|
|
|
+ $bundle_name = $collection_bundle->bundle_name;
|
|
|
+ // Skip remote fields.
|
|
|
+ if ($collection_bundle->site_id) {
|
|
|
+ continue;
|
|
|
}
|
|
|
- else {
|
|
|
- $fake_tripal_entity->$name = [
|
|
|
- 'und' => [
|
|
|
- '0' => [
|
|
|
- 'field_name' => $fields[$remote_fields]['field_name'],
|
|
|
- 'label' => $fields[$remote_fields]['label'],
|
|
|
- 'value' => $fields[$remote_fields]['value'],
|
|
|
- 'accession' => $fields[$remote_fields]['accession'],
|
|
|
- ],
|
|
|
- ],
|
|
|
- ];
|
|
|
+ foreach ($collection_bundle->fields as $field_id) {
|
|
|
+ $field = field_info_field_by_id($field_id);
|
|
|
+ $instance = field_info_instance('TripalEntity', $field['field_name'], $bundle_name);
|
|
|
+ $this->fields[$bundle_name][$field_id]['field'] = $field;
|
|
|
+ $this->fields[$bundle_name][$field_id]['instance'] = $instance;
|
|
|
}
|
|
|
}
|
|
|
- return $fake_tripal_entity;
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
- * Process and return a header for tab delimited file formats.
|
|
|
- *
|
|
|
- * @param $bundle_collections
|
|
|
- * The accession which is stored as the field id.
|
|
|
+ * A helper function for the setFields() function.
|
|
|
*
|
|
|
- * @return array
|
|
|
- * The impoded array for the header.
|
|
|
+ * Adds remote fields to the list of fields.
|
|
|
*/
|
|
|
- public function processTabHeader($bundle_collections) {
|
|
|
- $row = array();
|
|
|
- $accession_ids = array();
|
|
|
+ private function setRemoteFields() {
|
|
|
+ foreach ($this->collection_bundles as $collection_bundle) {
|
|
|
+ $bundle_name = $collection_bundle->bundle_name;
|
|
|
+ // Skip local fields.
|
|
|
+ if (!$collection_bundle->site_id) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
|
|
|
- foreach ($bundle_collections as $bundle_collection) {
|
|
|
- $collection_id = $bundle_collection->collection_bundle_id;
|
|
|
- $bundle_name = $bundle_collection->bundle_name;
|
|
|
- $fields = unserialize($bundle_collection->fields);
|
|
|
- $entity_ids = unserialize($bundle_collection->ids);
|
|
|
- $site_id = $bundle_collection->site_id;
|
|
|
+ $site_doc = $this->retrieveRemoteAPIDoc($collection_bundle->site_id);
|
|
|
+
|
|
|
+ // Get the class that matches this bundle.
|
|
|
+ $class = $this->getRemoteClass($bundle_name, $site_doc);
|
|
|
+
|
|
|
+ // Iterate through the fields of this collection and get the
|
|
|
+ // info for each one from the class. We will create "fake" field and
|
|
|
+ // instance info arrays.
|
|
|
+ foreach ($collection_bundle->fields as $field_id) {
|
|
|
+
|
|
|
+ // Get the property from the document for this field.
|
|
|
+ $property = $this->getRemoteClassProperty($class, $field_id, $site_doc);
|
|
|
+
|
|
|
+ // Now create the fake field and instance.
|
|
|
+ list($vocab, $accession) = explode(':', $field_id);
|
|
|
+ $field_name = 'tripal_remote_site_' . $collection_bundle->site_id . '_' . $field_id;
|
|
|
+ $field = array(
|
|
|
+ 'field_name' => $field_name,
|
|
|
+ 'type' => $field_name,
|
|
|
+ 'storage' => array(
|
|
|
+ 'type' => 'tripal_remote_site'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $instance = array(
|
|
|
+ 'label' => $property['hydra:title'],
|
|
|
+ 'description' => $property['hydra:description'],
|
|
|
+ 'formatters' => $property['tripal_formatters'],
|
|
|
+ 'settings' => array(
|
|
|
+ 'term_vocabulary' => $vocab,
|
|
|
+ 'term_accession' => $accession
|
|
|
+ ),
|
|
|
+ 'field_name' => $field_name,
|
|
|
+ 'entity_type' => 'TripalEntity',
|
|
|
+ 'bundle_name' => $bundle_name,
|
|
|
+ );
|
|
|
+ $this->fields[$bundle_name][$field_id]['field'] = $field;
|
|
|
+ $this->fields[$bundle_name][$field_id]['instance'] = $instance;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ private function getRemoteClass($class_id, $site_doc){
|
|
|
+ // Get the class that matches this bundle.
|
|
|
+ $classes = $site_doc['supportedClass'];
|
|
|
+ $class = NULL;
|
|
|
+ foreach ($classes as $item) {
|
|
|
+ if ($item['@id'] == $class_id) {
|
|
|
+ $class = $item;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ return $class;
|
|
|
+ }
|
|
|
|
|
|
- // Determine if the entity is remote or local.
|
|
|
- if (strpos($bundle_name, 'bio_data_') !== 0) {
|
|
|
- $external = TRUE;
|
|
|
+ private function getRemoteClassProperty($class, $prop_id, $site_doc){
|
|
|
+ $properties = $class['supportedProperty'];
|
|
|
+ foreach ($properties as $item) {
|
|
|
+ if ($item['property'] == $prop_id) {
|
|
|
+ return $item;
|
|
|
}
|
|
|
- else {
|
|
|
- $external = FALSE;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ /**
|
|
|
+ * Sets the fields array
|
|
|
+ */
|
|
|
+ protected function setFields() {
|
|
|
+ $this->setLocalFields();
|
|
|
+ $this->setRemoteFields();
|
|
|
+ }
|
|
|
+
|
|
|
+ /**
|
|
|
+ * Sets the fields2term array.
|
|
|
+ *
|
|
|
+ * The fields2term array provides an easy lookup for mapping a term
|
|
|
+ * to it's accession number.
|
|
|
+ **/
|
|
|
+ protected function setFields2Terms() {
|
|
|
+ foreach ($this->fields as $bundle_name => $bundle_fields) {
|
|
|
+ foreach ($bundle_fields as $field_id => $info) {
|
|
|
+ $instance = $info['instance'];
|
|
|
+ $accession = $instance['settings']['term_vocabulary'] . ':' . $instance['settings']['term_accession'];
|
|
|
+ $this->fields2terms[$bundle_name]['by_field'][$field_id] = $accession;
|
|
|
+ $this->fields2terms[$bundle_name]['by_accession'][$accession] = $field_id;
|
|
|
}
|
|
|
+ }
|
|
|
+ }
|
|
|
|
|
|
- foreach ($fields as $field) {
|
|
|
- if ($external) {
|
|
|
- $fake_tripal_entity = $this->getRemoteEntity($entity_ids, $site_id, $field, $bundle_name);
|
|
|
- $field_name = $fake_tripal_entity->$field['und'][0]['field_name'];
|
|
|
- $accession = $fake_tripal_entity->$field['und'][0]['accession'];
|
|
|
- if (!empty($accession_ids) && !empty($row)) {
|
|
|
- // If the accession is already in the accession_ids list skip.
|
|
|
- if (array_search($accession, $accession_ids)) {
|
|
|
- continue;
|
|
|
- }
|
|
|
- else {
|
|
|
- $row[] = $field_name;
|
|
|
- $accession_ids[] = $accession;
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $row[] = $field_name;
|
|
|
- $accession_ids[] = $accession;
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $field_info = field_info_field_by_id($field);
|
|
|
- //$field_name is the accession info.
|
|
|
- $field_name = $field_info['field_name'];
|
|
|
- $instance = field_info_instance('TripalEntity', $field_name, $bundle_name);
|
|
|
-
|
|
|
- // Build the accession incase someone renames a cord field name.
|
|
|
- $accession = $instance['settings']['term_vocabulary'] . $instance['settings']['term_accession'];
|
|
|
- if (!empty($accession_ids) && !empty($row)) {
|
|
|
- // If the accession is already in the accession_ids list skip.
|
|
|
- if (array_search($accession, $accession_ids)) {
|
|
|
- continue;
|
|
|
- }
|
|
|
- else {
|
|
|
- $accession_ids[] = $accession;
|
|
|
- $row[] = $instance['label'];
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $accession_ids[] = $accession;
|
|
|
- $row[] = $instance['label'];
|
|
|
+ /**
|
|
|
+ * Conslidates all the fields into a single list of accession numbers.
|
|
|
+ *
|
|
|
+ * The array of printable fields will contain an array containing the
|
|
|
+ * accession number and the label. The title used is from the first
|
|
|
+ * occurance of an accession.
|
|
|
+ */
|
|
|
+ protected function setPrintableFields() {
|
|
|
+
|
|
|
+ foreach ($this->fields as $bundle_name => $bundle_fields) {
|
|
|
+ foreach ($bundle_fields as $field_id => $info) {
|
|
|
+ $instance = $info['instance'];
|
|
|
+ $accession = $instance['settings']['term_vocabulary'] . ':' . $instance['settings']['term_accession'];
|
|
|
+ if (!array_key_exists($accession, $this->printable_fields)) {
|
|
|
+ // Only include fields that support this downloader type in
|
|
|
+ // or list of printable fields.
|
|
|
+ if ($this->isFieldSupported($field, $instance)) {
|
|
|
+ $this->printable_fields[$accession] = $instance['label'];
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
- $this->header_array = $accession_ids;
|
|
|
- return array(implode("\t", $row));
|
|
|
}
|
|
|
|
|
|
/**
|
Stephen Ficklin