tripal_file.install

<?php
/**
 * @file
 *
 * Installation of the file module
 */


/**
 * Implements hook_requirements().
 */
function tripal_file_requirements($phase) {
  $requirements = [];
  if ($phase == 'install') {
    if (!module_exists('tripal_core') and !module_exists('tripal')) {
      $requirements['tripal_file'] = [
        'title' => "tripal_file",
        'value' => "ERROR: You must have Tripal v2 or v3 installed to use this module.",
        'severity' => REQUIREMENT_ERROR,
      ];
    }
  }
  return $requirements;
}

/**
 * Implements hook_install().
 *
 * Performs actions when the modules is first installed.
 *
 * @ingroup tripal_file
 */
function tripal_file_install() {
  // Add the custom tables needed to associate Chado content with files.
  tripal_file_add_file_table();
  tripal_file_add_license_table();
  tripal_file_add_file_contact_table();
  tripal_file_add_fileloc_table();
  tripal_file_add_fileprop_table();
  tripal_file_add_file_relationship_table();
  tripal_file_add_file_license_table();
  tripal_file_add_file_pub_table();
  tripal_file_add_linker_tables();

  // Add the terms and content types.
  tripal_file_add_terms();
  tripal_file_add_ctypes();

  tripal_file_add_EDAM_obo();

  // Associate terms with the linker tables.
  tripal_file_add_linker_tables_terms();

  tripal_file_add_default_licenses();
}

/**
 *
 */
function tripal_file_add_EDAM_obo() {
  // Add the EDAM ontology
  $obo_id = tripal_insert_obo('EDAM', 'http://edamontology.org/EDAM.obo');
  drupal_set_message('NOTICE: Added the EDAM ontology. Please navigate to Tripal >> Data Loaders >> Chado Vocabularies >> OBO Vocabulary Loader and submit a job to import the EDAM vocabulary.');
}

/**
 *
 */
function tripal_file_add_terms() {
  // The SIO cv does not need to be added because it is
  // automatically added by the base Tripal setup.

  //
  // Content type terms
  //
  $term = chado_insert_cvterm([
    'id' => 'SIO:000396',
    'name' => 'file',
    'cv_name' => 'SIO',
    'definition' => 'A file is an information-bearing object that contains a physical embodiment of some information using a particular character encoding',
  ], ['update_existing' => false]);
  chado_associate_semweb_term(NULL, 'file_id', $term);

  $term = chado_insert_cvterm([
    'id' => 'schema:license',
    'name' => 'license',
    'cv_name' => 'schema',
    'definition' => 'A license document that applies to this content, typically indicated by URL.',
  ], ['update_existing' => false]);
  chado_associate_semweb_term(NULL, 'license_id', $term);

  //
  // Terms for the File table.
  //
  $term = chado_get_cvterm(['id' => 'schema:name']);
  chado_associate_semweb_term('file', 'name', $term);

  $term = chado_get_cvterm(['id' => 'schema:description']);
  chado_associate_semweb_term('file', 'description', $term);

  $term = chado_insert_cvterm([
    'id' => 'format:1915',
    'name' => 'Format',
    'cv_name' => 'EDAM',
    'definition' => 'A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.',
  ], ['update_existing' => false]);
  chado_associate_semweb_term('file', 'type_id', $term);

  //
  // Terms for the file_contact table
  //
  $term = chado_get_cvterm(['id' => 'local:contact']);
  chado_associate_semweb_term('file_contact', 'contact_id', $term);

  //
  // Terms for the fileloc table
  //
  $term = chado_get_cvterm(['id' => 'data:1047']);
  chado_associate_semweb_term('fileloc', 'uri', $term);

  $term = chado_get_cvterm(['id' => 'OBCS:0000117']);
  chado_associate_semweb_term('fileloc', 'rank', $term);

  $term = chado_get_cvterm(['id' => 'data:2190']);
  chado_associate_semweb_term('fileloc', 'md5checksum', $term);

  $term = chado_insert_cvterm([
    'id' => 'schema:fileSize',
    'name' => 'fileSize',
    'cv_name' => 'schema',
    'definition' => 'Size of the application / package (e.g. 18MB). In the absence of a unit (MB, KB etc.), KB will be assumed.',
  ], ['update_existing' => false]);
  chado_associate_semweb_term('fileloc', 'size', $term);

  $term = chado_insert_cvterm([
    'id' => 'data:1050',
    'name' => 'File name',
    'cv_name' => 'EDAM',
    'definition' => 'The name (or part of a name) of a file (of any type).',
  ], ['update_existing' => false]);
  chado_associate_semweb_term('fileloc', 'filename', $term);

  //
  // Terms for the fileprop table
  //
  $term = chado_get_cvterm(['id' => 'OBCS:0000117']);
  chado_associate_semweb_term('fileprop', 'rank', $term);

  $term = chado_get_cvterm(['id' => 'NCIT:C25712']);
  chado_associate_semweb_term('fileprop', 'value', $term);

  $term = chado_get_cvterm(['id' => 'schema:additionalType']);
  chado_associate_semweb_term('fileprop', 'type_id', $term);

  //
  // Terms for the license table
  //

  $term = chado_get_cvterm(['id' => 'schema:name']);
  chado_associate_semweb_term('license', 'name', $term);

  $term = chado_get_cvterm(['id' => 'data:1047']);
  chado_associate_semweb_term('license', 'uri', $term);

  $term = chado_insert_cvterm([
    'id' => 'schema:disambiguatingDescription',
    'name' => 'disambiguatingDescription',
    'cv_name' => 'schema',
    'definition' => 'A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.',
  ], ['update_existing' => false]);
  chado_associate_semweb_term('license', 'summary', $term);


  //
  // Terms for the file_license table
  //
  // No terms needed, just linking fields.


  //
  // Field types
  //
  $term = chado_insert_cvterm([
    'id' => 'schema:itemLocation',
    'name' => 'itemLocation',
    'cv_name' => 'schema',
    'definition' => 'Current location of the item.',
  ], ['update_existing' => false]);
}

/**
 * Adds Tripal v3 content types.
 */
function tripal_file_add_ctypes() {

  // Add the File content type
  $bundle = tripal_load_bundle_entity(['accession' => 'SIO:000396']);
  if (!$bundle) {
    $args = [
      'vocabulary' => 'SIO',
      'accession' => '000396',
      'term_name' => 'file',
      'label' => "File",
      'storage_args' => [
        'data_table' => 'file',
      ],
      'category' => 'Other',
    ];
    if (!tripal_create_bundle($args, $job)) {
      $msg = t('Error encountered creating !type Content Type.', ['!type' => $args['term_name']]);
      throw new Exception($msg);
    }
  }

  // Add the License content type
  $bundle = tripal_load_bundle_entity(['accession' => 'schema:license']);
  if (!$bundle) {
    $args = [
      'vocabulary' => 'schema',
      'accession' => 'license',
      'term_name' => 'license',
      'label' => "License",
      'storage_args' => [
        'data_table' => 'license',
      ],
      'category' => 'Other',
    ];
    if (!tripal_create_bundle($args, $job)) {
      $msg = t('Error encountered creating !type Content Type.', ['!type' => $args['term_name']]);
      throw new Exception($msg);
    }
  }
}

/**
 * Adds the 'file' custom table to Chado.
 *
 * @ingroup tripal_file
 */
function tripal_file_add_file_table() {
  $schema = [
    'table' => 'file',
    'fields' => [
      'file_id' => [
        'size' => 'big',
        'type' => 'serial',
        'not null' => TRUE,
      ],
      'name' => [
        'type' => 'text',
        'not null' => TRUE,
      ],
      'type_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
      'description' => [
        'type' => 'text',
      ],
    ],
    'primary key' => ['file_id'],
    'unique keys' => [
      'file_c1' => ['name'],
    ],
    'indexes' => [
      'file_idx1' => ['name'],
      'file_idx2' => ['type_id'],
    ],
    'foreign keys' => [
      'cvterm' => [
        'table' => 'cvterm',
        'columns' => [
          'type_id' => 'cvterm_id',
        ],
      ],
    ],
  ];
  chado_create_custom_table('file', $schema, TRUE, NULL, FALSE);
}

/**
 *
 */
function tripal_file_add_file_contact_table(){
  $schema = [
    'table' => 'file_contact',
    'fields' => [
      'file_contact_id' => [
        'size' => 'big',
        'type' => 'serial',
        'not null' => TRUE
      ],
      'file_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
      'contact_id' => [
        'type' => 'int'
      ],
    ],
    'primary key' => ['file_contact_id'],
    'unique keys' => [
      'file_contact_c1' => ['file_id', 'contact_id'],
    ],
    'indexes' => [
      'file_contact_idx1' => ['file_id'],
      'file_contact_idx2' => ['contact_id'],
    ],
    'foreign keys' => [
      'file' => [
        'table' => 'file',
        'columns' => [
          'file_id' => 'file_id',
        ],
      ],
      'contact' => [
        'table' => 'contact',
        'columns' => [
          'contact_id' => 'contact_id',
        ],
      ],
    ],
  ];
  chado_create_custom_table('file_contact', $schema, TRUE, NULL, FALSE);
}

/**
 *
 */
function tripal_file_add_file_pub_table() {
  
  $schema = [
    'table' => 'file_pub',
    'fields' => [
      'file_pub_id' => [
        'size' => 'big',
        'type' => 'serial',
        'not null' => TRUE,
      ],
      'file_id' => [
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ],
      'pub_id' => [
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ],
    ],
    'primary key' => [
      0 => 'file_pub_id',
    ],
    'unique keys' => [
      'file_pub_c1' => [
        0 => 'file_id',
        1 => 'pub_id',
      ],
    ],
    'indexes' => [
      'file_pub_idx1' => [
        0 => 'file_id',
      ],
      'file_pub_idx2' => [
        0 => 'pub_id',
      ],
    ],
    'foreign keys' => [
      'pub' => [
        'table' => 'pub',
        'columns' => [
          'pub_id' => 'pub_id',
        ],
      ],
      'file' => [
        'table' => 'file',
        'columns' => [
          'file_id' => 'file_id',
        ],
      ],
    ],
  ];
  chado_create_custom_table('file_pub', $schema, TRUE, NULL, FALSE);
}

/**
 *
 */
function tripal_file_add_fileloc_table(){
  $schema = [
    'table' => 'fileloc',
    'fields' => [
      'fileloc_id' => [
        'size' => 'big',
        'type' => 'serial',
        'not null' => TRUE
      ],
      'file_id' => [
        'type' => 'int',
        'not null' => TRUE,
      ],
      'uri' => [
        'type' => 'text',
        'not null' => TRUE,
        'description' => t('Can be one of the following 1) A relative URL which can be concatenated to the http://[domain]. 2) A Drupal scheme (e.g. public://[path]) 3) A full URL to a remote site.')
      ],
      'rank' => [
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0
      ],
      'md5checksum' => [
        'size' => 'normal',
        'type' => 'char',
        'length' => '32',
        'not null' => FALSE
      ],
      'size' => [
        'type' => 'varchar',
        'length' => 1024,
        'not null' => FALSE
      ],
      'filename' => [
        'type' => 'text',
        'not null' => FALSE,
        'description' => t('The short name of the uri as displayed to the user.'),
      ],
    ],
    'primary key' => ['fileloc_id'],
    'unique keys' => [
      'fileloc_c1' => ['file_id', 'uri'],
    ],
    'indexes' => [
      'fileloc_idx1' => ['file_id'],
    ],
    'foreign keys' => [
      'file' => [
        'table' => 'file',
        'columns' => [
          'file_id' => 'file_id',
        ],
      ],
    ],
  ];
  chado_create_custom_table('fileloc', $schema, TRUE, NULL, FALSE);
}

/**
 *
 */
function tripal_file_add_fileprop_table(){
  $schema = [
    'table' => 'fileprop',
    'fields' => [
      'fileprop_id' => [
        'type' => 'serial',
        'not null' => TRUE
      ],
      'file_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
      'type_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
      'value' => [
        'type' => 'text'
      ],
      'rank' => [
        'type' => 'int',
        'not null' => TRUE,
        'default' => 0
      ],
    ],
    'primary key' => ['fileprop_id'],
    'unique keys' => [
      'fileprop_c1' => ['file_id', 'type_id', 'rank'],
    ],
    'indexes' => [
      'fileprop_idx1' => ['file_id'],
      'fileprop_idx2' => ['type_id'],
    ],
    'foreign keys' => [
      'file' => [
        'table' => 'file',
        'columns' => [
          'file_id' => 'file_id',
        ],
      ],
      'cvterm' => [
        'table' => 'cvterm',
        'columns' => [
          'type_id' => 'cvterm_id',
        ],
      ],
    ],
  ];
  chado_create_custom_table('fileprop', $schema, TRUE, NULL, FALSE);
}

/**
 *
 */
function tripal_file_add_file_relationship_table(){
  $schema = [
    'table' => 'file_relationship',
    'fields' => [
      'file_relationship_id' => [
        'type' => 'serial',
        'not null' => TRUE
      ],
      'subject_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
      'object_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
      'type_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
    ],
    'primary key' => ['file_relationship_id'],
    'unique keys' => [
      'file_relationship_c1' => ['subject_id', 'object_id', 'type_id'],
    ],
    'indexes' => [
      'file_relationship_idx1' => ['subject_id'],
      'file_relationship_idx2' => ['object_id'],
      'file_relationship_idx3' => ['type_id'],
    ],
    'foreign keys' => [
      'file' => [
        'table' => 'file',
        'columns' => [
          'subject_id' => 'file_id',
          'object_id' => 'file_id',
        ],
      ],
      'cvterm' => [
        'table' => 'cvterm',
        'columns' => [
          'type_id' => 'cvterm_id',
        ],
      ],
    ],
  ];
  chado_create_custom_table('file_relationship', $schema, TRUE, NULL, FALSE);
}

/**
 *
 */
function tripal_file_add_license_table(){
  $schema = [
    'table' => 'license',
    'fields' => [
      'license_id' => [
        'type' => 'serial',
        'not null' => TRUE
      ],
      'name' => [
        'type' => 'varchar',
        'length' => 1024,
        'not null' => TRUE
      ],
      'summary' => [
        'type' => 'text',
      ],
      'uri' => [
        'type' => 'text',
      ],
    ],
    'primary key' => ['license_id'],
    'unique keys' => [
      'license_c1' => ['name'],
      'license_c2' => ['uri'],
    ],
    'indexes' => [
      'license_idx1' => ['name'],
    ],
  ];
  chado_create_custom_table('license', $schema, TRUE, NULL, FALSE);
}

/**
 *
 */
function tripal_file_add_file_license_table() {
  $schema = [
    'table' => 'file_license',
    'fields' => [
      'file_license_id' => [
        'type' => 'serial',
        'not null' => TRUE
      ],
      'file_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
      'license_id' => [
        'type' => 'int',
        'not null' => TRUE
      ],
    ],
    'primary key' => ['file_license_id'],
    'unique keys' => [
      'file_license_c1' => ['file_id', 'license_id'],
    ],
    'indexes' => [
      'file_license_idx1' => ['file_id'],
      'file_license_idx2' => ['license_id'],
    ],
    'foreign keys' => [
      'file' => [
        'table' => 'file',
        'columns' => [
          'file_id' => 'file_id',
        ],
      ],
      'license' => [
        'table' => 'license',
        'columns' => [
          'license_id' => 'license_id',
        ],
      ],
    ],
  ];
  chado_create_custom_table('file_license', $schema, TRUE, NULL, FALSE);
}

/**
 * A simple function that lists supported base tables.
 *
 * We want to be specific about what these supported tables
 * are because we don't want to accidentaly support any custom table
 * that might have a _file suffix.
 */
function tripal_file_get_linked_tables() {
  return [
    'analysis', 'assay', 'biomaterial', 'cv', 'eimage',
    'feature', 'featuremap', 'library', 'nd_protocol', 'organism',
    'phylotree', 'project', 'pub', 'stock', 'stockcollection', 'study'
  ];
}

/**
 * Creates the set of supported linker tables.
 */
function tripal_file_add_linker_tables() {

  $linked_tables = tripal_file_get_linked_tables();
  foreach ($linked_tables as $linked_table) {
    $linked_schema = chado_get_schema($linked_table);
    $pkey = $linked_schema['primary key'][0];
    $linker_table = $linked_table . '_file';
    $schema = [
      'table' => $linker_table,
      'fields' => [
        $linker_table . '_id' => [
          'size' => 'big',
          'type' => 'serial',
          'not null' => TRUE
        ],
        'file_id' => [
          'size' => 'big',
          'type' => 'int',
          'not null' => TRUE
        ],
        $pkey => [
          'size' => 'big',
          'type' => 'int',
          'not null' => TRUE
        ],
        'rank' => [
          'type' => 'int',
          'not null' => TRUE,
          'default' => 0
        ],
      ],
      'primary key' => [$linker_table . '_id'],
      'unique keys' => [
        $linker_table . '_c1' => ['file_id', $pkey],
      ],
      'indexes' => [
        $linker_table . '_idx1' => ['file_id'],
        $linker_table . '_idx2' => [$pkey],
      ],
      'foreign keys' => [
        'file' => [
          'table' => 'file',
          'columns' => [
            'file_id' => 'file_id',
          ],
        ],
        $linked_table => [
          'table' => $linked_table,
          'columns' => [
            $pkey => $pkey,
          ],
        ],
      ],
    ];
    chado_create_custom_table($linker_table, $schema, TRUE, NULL, FALSE);
  }
}

/**
 *
 */
function tripal_file_add_default_licenses() {

  // Public Domain license
  $license = new ChadoRecord('license');
  $license->setValues([
    'name' => 'Public Domain',
  ]);
  if (!$license->find()) {
    $license->setValues([
      'name' => 'Public Domain',
      'summary' => 'The data have no known copyrights or restrictions and ' .
        'can be freely used by anyone.'
    ]);
    $license->insert();
  }

  // CC 1.0 license
  $license = new ChadoRecord('license');
  $uri = 'https://creativecommons.org/publicdomain/zero/1.0/legalcode';
  $license->setValues([
    'uri' => $uri,
  ]);
  if (!$license->find()) {
    $license->setValues([
      'name' => 'CC0 1.0 Universal (CC0 1.0) Public Domain Dedication',
      'summary' => 'The person who associated a work with this deed has ' .
        'dedicated the work to the public domain by waiving all of his or ' .
        'her rights to the work worldwide under copyright law, including all ' .
        'related and neighboring rights, to the extent allowed by law. ' .
        'You can copy, modify, distribute and perform the work, even for ' .
        'commercial purposes, all without asking permission.',
      'uri' => $uri,
    ]);
    $license->insert();
  }

  // CC 4.0 license
  $license = new ChadoRecord('license');
  $uri = 'https://creativecommons.org/licenses/by/4.0/legalcode';
  $license->setValues([
    'uri' => $uri,
  ]);
  if (!$license->find()) {
    $license->setValues([
      'name' => 'Creative Commons Attribution 4.0 International Public License',
      'summary' => 'You are free to copy and redistribute the material ' .
        'in any medium or format, remix, transform, and build upon the '.
        'material for any purpose, even commercially. The licensor cannot '.
        'revoke these freedoms as long as you follow the license terms. ' .
        'You must give appropriate credit, provide a link to the license, '.
        'and indicate if changes were made. You may do so in any reasonable ' .
        'manner, but not in any way that suggests the licensor endorses you ' .
        'or your use. You may not apply legal terms or technological measures ' .
        'that legally restrict others from doing anything the license permits.',
      'uri' => $uri,
    ]);
    $license->insert();
  }

  global $user;
  $bundle = tripal_load_bundle_entity(['accession' => 'schema:license']);
  $args = [
    [
      'bundle_name' => $bundle->name,
      'filters' => [],
    ],
  ];
  return tripal_add_job("Publish " . $bundle->label . " records.",
      'tripal_chado', 'chado_publish_records', $args,
      $user->uid, 10, $includes);
}

/**
 * Adds the terms for the linked table columns.
 */
function tripal_file_add_linker_tables_terms() {
  // Terms for linker tables
  $linked_tables = tripal_file_get_linked_tables();

  foreach ($linked_tables as $linked_table) {
    $linked_schema = chado_get_schema($linked_table);
    $pkey = $linked_schema['primary key'][0];
    $linker_table = $linked_table . '_file';

    // Add the term for rank.
    $term = chado_get_cvterm(['id' => 'OBCS:0000117']);
    chado_associate_semweb_term($linker_table, 'rank', $term);
  }
}

/**
 * Repopulates db2cv materialized view.
 */
function tripal_file_repopulate_db2cv_mview($jobname='Repopulating db2cv_mview') {
  global $user;
  $sql = "SELECT mview_id FROM [tripal_mviews] WHERE modulename=:modulename AND name=:name";
  $args = [':modulename' => 'tripal_chado', ':name' => 'db2cv_mview'];
  $mview_id = chado_query($sql, $args)->fetchField();
  tripal_add_job(
    $jobname,
    'tripal_chado',
    'chado_populate_mview',
    [$mview_id],
    $user->uid
  );
}

/**
 * Add default licenses
 */
function tripal_file_update_7100() {
  try {
    tripal_file_add_default_licenses();
    tripal_file_repopulate_db2cv_mview('Repopulating db2cv_mview to fix legacy SOFP');
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Could not perform update: '. $error);
  }
}

/**
 * Add support for displayed filename.
 */
function tripal_file_update_7101() {

  $transaction = db_transaction();
  try {

    // Add 'filename' column to fileloc table, this holds the filename presented to
    // the user. Do nothing if it already exists, as will occur on a new install.
    if (!chado_column_exists('fileloc', 'filename')) {
      $sql = "ALTER TABLE ONLY {fileloc} ADD COLUMN filename TEXT";
      chado_query($sql, []);
      $sql = "COMMENT ON COLUMN {fileloc}.filename IS :comment";
      $column_comment = 'The short name of the uri as displayed to the user.';
      chado_query($sql, [':comment' => $column_comment]);

      // The CVterm for the new column is added as of this update, data:1050 = 'File name'.
      tripal_file_add_terms();
    }

  }
  catch (\PDOException $e) {
    $transaction->rollback();
    $error = $e->getMessage();
    throw new DrupalUpdateException('Could not perform update: '. $error);
  }

}

/**
 * Add missing schema for filename column
 */
function tripal_file_update_7102() {

  $filename_schema = [
    'type' => 'text',
    'not null' => FALSE,
    'description' => t('The short name of the uri as displayed to the user.'),
  ];

  $transaction = db_transaction();
  try {

    // Retrieve the table_id of the fileloc custom table, this will be
    // needed to update the schema.
    $sql = "SELECT table_id FROM [tripal_custom_tables] WHERE table_name='fileloc'";
    $fileloc_table_id = chado_query($sql, [])->fetchObject()->table_id;

    // Update the schema to add the new column for the fileloc custom table
    // by getting the current schema, adding in filename schema, and updating
    // the schema stored in public.tripal_custom_tables.
    $schema = chado_get_schema('fileloc');
    $schema['fields']['filename'] = $filename_schema;
    $fields = ['schema' => serialize($schema)];
    db_update('tripal_custom_tables')
      ->fields($fields)
      ->condition('table_id', $fileloc_table_id, '=')
      ->execute();

  }
  catch (\PDOException $e) {
    $transaction->rollback();
    $error = $e->getMessage();
    throw new DrupalUpdateException('Could not perform update: '. $error);
  }

}

/**
 * Add the file_relationship table.
 */
function tripal_file_update_7103() {

  $transaction = db_transaction();
  try {
    tripal_file_add_file_relationship_table();
  }
  catch (\PDOException $e) {
    $transaction->rollback();
    $error = $e->getMessage();
    throw new DrupalUpdateException('Could not perform update: '. $error);
  }
}