migrate tripal 2 node fields to chado properties for tripal 3 compatibility and best FAIR practices

README.md

The Tripal 3 migration process will not convert custom Drupal fields that were attached to your nodes when content is migrated from nodes to entities.

To circumvent this, this PHP class is designed to loop through a field's storage table, and create Chado properties for each entry. You must supply a CVterm for each field.

To adapt for your site, simply fill out the array of field and term mappings in convert_all to match what you need.

We dont provide an interface etc, but you can use the devel module to run the code:

http://yoursite/devel/php

testing

I've tested this converter for base mappings only, ie, that organism props are created for organism attached fields. I haven't yet tested that a linker field workup works.

Migrate_node_fields.php

<?php
//if we made this into a module, we would use the tripal jobs... but we dont so its commented out for now.
//
//global $user;
//tripal_add_job(
//  "Convert fields to properties", 'no_module',
//  'snippet_tripal_job_callback',
//  'chado_update_existing_node_urls',
//  [],
//  $user->uid
//);
//
//function snippet_tripal_job_callback(){
//
//  $obj = new ConvertFieldsToChadoProps();
//
//  $obj->convert_all();
//}
$obj = new ConvertFieldsToChadoProps();
$obj->convert_all();
class ConvertFieldsToChadoProps {
  public function convert_all() {
    $contig_n50_term = chado_insert_cvterm([
      'id' => 'local:contig_n50',
      'name' => 'contig n50',
      'definition' => 'The size of the n50 contig.',
      'cv_name' => 'local',
    ])->cvterm_id;
    $gc_term = chado_insert_cvterm([
      'id' => 'local:gc_content',
      'name' => 'GC Content',
      'definition' => '% GC',
      'cv_name' => 'local',
    ])->cvterm_id;
    $community_contact_term = chado_insert_cvterm([
      'id' => 'local:community_contact',
      'name' => 'Community Contact',
      'definition' => '',
      'cv_name' => 'local',
    ])->cvterm_id;
    $n_genes_term = chado_insert_cvterm([
      'id' => 'n_genes',
      'name' => 'Number of Genes',
      'definition' => '',
      'cv_name' => 'local',
    ])->cvterm_id;
    $scaffold_n50_term = chado_insert_cvterm([
      'id' => 'scaffold_n50',
      'name' => 'Scaffold n50',
      'definition' => '',
      'cv_name' => 'local',
    ])->cvterm_id;
    $field_photographer_term = chado_insert_cvterm([
      'id' => 'field_photographer',
      'name' => 'Field Photographer',
      'definition' => '',
      'cv_name' => 'local',
    ])->cvterm_id;
    $image_credit_term  = chado_insert_cvterm([
      'id' => 'image_credit',
      'name' => 'Image Credit',
      'definition' => '',
      'cv_name' => 'local',
    ])->cvterm_id;
    $identifying_info_term = chado_insert_cvterm([
      'id' => 'identify_info',
      'name' => 'Other Identifying Info',
      'definition' => '',
      'cv_name' => 'local',
    ])->cvterm_id;
    $sets = [
      ['field' => 'field_contig_n50', 'term' => $contig_n50_term],
      ['field' => 'field_gc_content', 'term' => $gc_term],
      ['field' => 'field_community_contact', 'term' => $community_contact_term],
      ['field' => 'field_number_of_genes', 'term' => $n_genes_term],
      ['field' => 'field_scaffold_n50', 'term' => $scaffold_n50_term],
      ['field' => 'field_photographer', 'term' => $field_photographer_term],
      ['field' => 'field_image_credit', 'term' => $image_credit_term],
      ['field' => 'field_other_identifying_informat', 'term' => $identifying_info_term],
    ];
    $source_base = 'organism';
    //$linker = 'organism_analysis';
    $linker = NULL;
    $target_base = NULL;
    $linker = NULL;
    foreach ($sets as $set) {
      $field = $set['field'];
      $cvterm_id = $set['term'];

      $field_table = 'field_data_' . $field;

      if (!db_table_exists($field_table)){

        print(t("Warning: !field  not present on this website.  Skipping.\n", ['!field' => $field]));
        continue;
      };

      print(t("Converting field: !field .\n", ['!field' => $field]));

      $this->convert_all_instances_for_field($field, $cvterm_id, $source_base, $target_base, $linker);
    }
  }
  /**
   * This function would run after a user submits a form, where they have
   * chosen a bundle, a linker table and target content type (optional), a
   * field, and a cvterm for the new field.
   *
   * @param $field The field machine name.
   */
  public function convert_all_instances_for_field($field, $cvterm_id, $source_base, $target_base = NULL, $linker = NULL) {
    $field_table = 'field_data_' . $field;
    $field_value_field = $field . '_value';
    $source_column = $source_base . '_id';
    if ($linker) {
      $target_column = $target_base . '_id';
    }
    $query = db_select($field_table, 'ft');
    $query->fields('ft', [$field_value_field, 'entity_id']);
    $query->join('chado_' . $source_base, 'c', 'c.nid = ft.entity_id');
    $query->fields('c', [$source_column]);
    $entries = $query->execute();
    foreach ($entries as $entry) {
      $value = $entry->$field_value_field;
      $record_id = $entry->$source_column;
      $target_record_id = $record_id;
      if ($linker && $target_base) {
        $targets = db_select('chado.' . $linker, 'lt')
          ->fields('lt', [$target_column])
          ->condition('lt.' . $source_column, $record_id)
          ->execute()
          ->fetchAll();
        if (count($targets) > 1) {
          print(t("Error!  More than one target for !base record: !record in !linker", [
            '!record',
            $record_id,
            !'base' => $source_base,
            '!linker',
            $linker,
          ]));
          return;
        }
        if (count($targets) == 0) {
          print(t("Error!  No targets for !base record: !record in !linker", [
            '!record',
            $record_id,
            !'base' => $source_base,
            '!linker',
            $linker,
          ]));
          return;
        }
        $target_record_id = $targets[0]->$target_column;
      }
      else {
        $target_base = $source_base;
      }
      $record = [
        'table' => $target_base,
        'id' => $target_record_id,
      ];
      $property = [
        'type_id' => $cvterm_id,
        'value' => $value,
      ];
      //allow for multiple values.
      $options = ['update_if_present' => FALSE];
      //tripal_chado API.
      $result = chado_insert_property($record, $property, $options);
      if (!$result) {
        print("error!  couldnt insert property.");
        return;
      }
      //delete the field instance?  for now we keep it.
    }
  }
}