tpps.queries.api.inc File Reference

Go to the source code of this file.

Functions
	tpps_api_author_pid_query (array $authors)
	tpps_api_organism_pid_query (array $orgs)
	tpps_api_organization_pid_query (array $orgs)
	tpps_api_project_author_query (array $pids, $entities=FALSE)
	tpps_api_project_design_query (array $pids)
	tpps_api_project_genotype_query (array $pids, $entities=FALSE)
	tpps_api_project_organism_query (array $pids, $entities=FALSE)
	tpps_api_project_phenotype_query (array $pids, $entities=FALSE)
	tpps_api_project_publication_query (array $pids, $entities=FALSE)
	tpps_api_project_query (array $pids, $entities=FALSE)
	tpps_api_project_stats_query (array $states)
	tpps_api_project_stock_query (array $pids, $entities=FALSE)
	tpps_api_query_or (array $vals, array $fields, $override_op=NULL)
	tpps_api_record_entities ($label, array $record_ids)

Detailed Description

Defines queries for the TPPS API.

Most queries get information based on a list of project ids, but some can produce a list of project ids based on some conditions. Query functions with names like "tpps_api_*_pid_query" will produce a list of pids based on the provided conditions. For example, the function "tpps_api_author_pid_query" will return a list of pids with authors that match at least one of the provided names. Query functions with names like "tpps_api_project_*_query" will produce a list of ids or entities based on a list of pids. For example, the function "tpps_api_project_organism_query" will return a list of organism ids or, if the entities parameter is set to true, will return a list of organism entities associated with the provided pids.

Definition in file tpps.queries.api.inc.

Function Documentation

tpps_api_author_pid_query()

tpps_api_author_pid_query

(

array

$authors

)

Returns array of project ids associated with provided authors.

Parameters

array

$authors

An array of author names.

Returns

array An array of associated project ids.

Definition at line 28 of file tpps.queries.api.inc.

                                                   {
  $query = db_select('chado.pubauthor', 'pa');
  $query->join('chado.project_pub', 'pp', 'pp.pub_id = pa.pub_id');
  $query->fields('pp', array('project_id'));
  $or = tpps_api_query_or($orgs, array(
    'pa.givennames',
    'pa.surname',
  ));
  $query->condition($or);
  return $query->execute();
}

tpps_api_organism_pid_query()

tpps_api_organism_pid_query

(

array

$orgs

)

Returns array of project ids associated with provided species.

Parameters

array

$orgs

An array of species names.

Returns

array An array of associated project ids.

Definition at line 49 of file tpps.queries.api.inc.

                                                  {
  $query = db_select('chado.organism', 'o');
  $query->join('chado.project_organism', 'po', 'po.organism_id = o.organism_id');
  $query->fields('po', array('project_id'));
  $or = tpps_api_query_or($orgs, array(
    'o.genus',
    'o.species',
  ));
  $query->condition($or);
  return $query->execute();
}

tpps_api_organization_pid_query()

tpps_api_organization_pid_query

(

array

$orgs

)

Returns array of project ids associated with provided organizations.

Parameters

array

$orgs

An array of organization names.

Returns

array An array of associated project ids.

Definition at line 70 of file tpps.queries.api.inc.

                                                      {
  $query = db_select('chado.contact', 'c');
  $query->join('chado.contact_relationship', 'cr', 'c.contact_id = cr.object_id');
  $query->join('chado.project_contact', 'pc', 'pc.contact_id = cr.subject_id');
  $query->fields('pc', array('project_id'));
  $or = tpps_api_query_or($orgs, array(
    'c.name',
  ));
  $and = db_and()
    ->condition('c.type_id', tpps_load_cvterm('organization')->cvterm_id)
    ->condition($or);
  $query->condition($and);
  return $query->execute();
}

tpps_api_project_author_query()

tpps_api_project_author_query	(	array	$pids,
			$entities = FALSE
	)

Returns array of authors associated with provided project ids.

This function currently does not support returning Tripal Entities.

Parameters

array	$pids	An array of project ids.
bool	$entities	(Placeholder) Whether or not to return entities.

Returns

array An array of pubauthor table record ids.

Definition at line 146 of file tpps.queries.api.inc.

                                                                       {
  $query = db_select('chado.project_pub', 'pp');
  $query->join('chado.pubauthor', 'pa', 'pa.pub_id = pp.pub_id');
  $query->fields('pa', array('pubauthor_id'));
  $or = tpps_api_query_or($pids, array(
    'pp.project_id',
  ), '=');
  $query->condition($or);
  $query = $query->execute();
  return $query->fetchCol();
}

tpps_api_project_design_query()

tpps_api_project_design_query

(

array

$pids

)

Returns array of design information associated with provided project ids.

This function does not support returning Tripal Entities.

Parameters

array

$pids

An array of project ids.

Returns

array An array of study design information.

Definition at line 198 of file tpps.queries.api.inc.

                                                    {
  $query = db_select('chado.projectprop', 'pp');
  $query->join('chado.cvterm', 'c', 'c.cvterm_id = pp.type_id');
  $query->fields('c', array('name'))
    ->fields('pp', array('value'));
  $or = tpps_api_query_or($pids, array(
    'pp.project_id',
  ), '=');
  $query->condition($or);
  $query = $query->execute();

  $results = array();
  while (($result = $query->fetchObject())) {
    $results[$result->name][] = $result->value;
  }

  return $results;
}

tpps_api_project_genotype_query()

tpps_api_project_genotype_query	(	array	$pids,
			$entities = FALSE
	)

Returns array of genotypes associated with provided project ids.

Parameters

array	$pids	An array of project ids.
bool	$entities	Whether or not to return entities.

Returns

array An array of genotype ids or entities.

Definition at line 284 of file tpps.queries.api.inc.

                                                                         {
  $query = db_select('chado.project_stock', 'ps');
  $query->join('chado.stock_genotype', 'sg', 'sg.stock_id = ps.stock_id');
  $or = tpps_api_query_or($pids, array(
    'ps.project_id',
  ), '=');
  $query->fields('sg', array('genotype_id'))
    ->condition($or);
  $query = $query->execute();

  $results = $query->fetchCol();

  if (!$entities) {
    return $results;
  }
  return tpps_api_record_entities('Genotype', $results);
}

tpps_api_project_organism_query()

tpps_api_project_organism_query	(	array	$pids,
			$entities = FALSE
	)

Returns array of species associated with provided project ids.

Parameters

array	$pids	An array of project ids.
bool	$entities	Whether or not to return entities.

Returns

array An array of organism ids or entities.

Definition at line 169 of file tpps.queries.api.inc.

                                                                         {
  $query = db_select('chado.project_organism', 'po')
    ->fields('po', array('organism_id'));
  $or = tpps_api_query_or($pids, array(
    'po.project_id',
  ), '=');
  $query->condition($or);
  $query = $query->execute();

  $results = $query->fetchCol();

  if (!$entities) {
    return $results;
  }

  return tpps_api_record_entities('Organism', $results);
}

tpps_api_project_phenotype_query()

tpps_api_project_phenotype_query	(	array	$pids,
			$entities = FALSE
	)

Returns array of phenotype ids associated with provided project ids.

This function currently does not support returning Tripal Entities.

Parameters

array	$pids	An array of project ids.
bool	$entities	(Placeholder) Whether or not to return entities.

Returns

array An array of study design information.

Definition at line 259 of file tpps.queries.api.inc.

                                                                          {
  $query = db_select('chado.project_stock', 'ps');
  $query->join('chado.stock_phenotype', 'sp', 'sp.stock_id = ps.stock_id');
  $or = tpps_api_query_or($pids, array(
    'ps.project_id',
  ), '=');
  $query->fields('sp', array('phenotype_id'))
    ->condition($or);
  $query = $query->execute();

  $results = $query->fetchCol();
  return $results;
}

tpps_api_project_publication_query()

tpps_api_project_publication_query	(	array	$pids,
			$entities = FALSE
	)

Returns array of publications associated with provided project ids.

Parameters

array	$pids	An array of project ids.
bool	$entities	Whether or not to return entities.

Returns

array An array of publication ids or entities.

Definition at line 115 of file tpps.queries.api.inc.

                                                                            {
  $query = db_select('chado.project_pub', 'pp')
    ->fields('pp', array('pub_id'));
  $or = tpps_api_query_or($pids, array(
    'pp.project_id',
  ), '=');
  $query->condition($or);
  $query = $query->execute();

  $results = $query->fetchCol();

  if (!$entities) {
    return $results;
  }

  return tpps_api_record_entities('Publication', $results);
}

tpps_api_project_query()

tpps_api_project_query	(	array	$pids,
			$entities = FALSE
	)

Returns array of projects associated with provided project ids.

Parameters

array	$pids	An array of project ids.
bool	$entities	Whether or not to return entities.

Returns

array An array of project ids or entities.

Definition at line 96 of file tpps.queries.api.inc.

                                                                {
  if (!$entities) {
    return $pids;
  }

  return tpps_api_record_entities('Project', $pids);
}

tpps_api_project_stats_query()

tpps_api_project_stats_query

(

array

$states

)

Returns array of submission statistics based on provided submission states.

This function does not support returning Tripal Entities.

Parameters

array

$states

An array of TPPS submission states.

Returns

array An array of TPPS submission statistics.

Definition at line 313 of file tpps.queries.api.inc.

                                                     {
  $results = array();
  foreach ($states as $state) {
    $results[] = $state['stats'];
  }
  return $results;
}

tpps_api_project_stock_query()

tpps_api_project_stock_query	(	array	$pids,
			$entities = FALSE
	)

Returns array of stocks associated with provided project ids.

Parameters

array	$pids	An array of project ids.
bool	$entities	Whether or not to return entities.

Returns

array An array of stock ids or entities.

Definition at line 228 of file tpps.queries.api.inc.

                                                                      {
  $query = db_select('chado.project_stock', 'p')
    ->fields('p', array('stock_id'));
  $or = tpps_api_query_or($pids, array(
    'p.project_id',
  ), '=');
  $query->condition($or);
  $query = $query->execute();

  $results = $query->fetchCol();

  if (!$entities) {
    return $results;
  }

  return tpps_api_record_entities('Stock', $results);
}

tpps_api_query_or()

tpps_api_query_or	(	array	$vals,
		array	$fields,
			$override_op = NULL
	)

Constructs a db_or() condition object for use with other TPPS API functions.

The default comparison operator is '~*', but this can be overriden by either specifying a different argument in square brackets following the value being compared, or by specifying a condition-wide operator in the override_op function parameter.

Parameters

array	$vals	The values being compared in this condition.
array	$fields	The columns that the values should be compared against.
string	$override_op	The condition-wide overriding operator.

Returns

object The constructed db_or() condition object.

Definition at line 339 of file tpps.queries.api.inc.

                                                                            {
  $or = db_or();
  foreach ($vals as $val) {
    $op = '~*';
    if (preg_match('/^(.*)\[(.+)\]$/', $val, $matches)) {
      $val = $matches[1];
      $op = $matches[2];
    }
    $op = !empty($override_op) ? $override_op : $op;
    foreach ($fields as $field) {
      $or->condition($field, $val, $op);
    }
  }
  return $or;
}

tpps_api_record_entities()

tpps_api_record_entities	(		$label,
		array	$record_ids
	)

Loads and returns entities that refer to the provided record ids.

This function takes a Tripal Entity label and an array of record ids and attempts to load the associated Tripal Entities. It will also attach fields that are not automatically attached by the Tripal Entity loader.

Parameters

string	$label	The label of the Tripal Entity type.
array	$record_ids	The array of database record ids referred to by the Tripal Entities.

Returns

array An array of associated Tripal Entities.

Definition at line 370 of file tpps.queries.api.inc.

                                                             {
  $bundle = tripal_load_bundle_entity(array('label' => $label));
  $details = @tripal_get_bundle_details($bundle->name);

  $entity_ids = array();
  foreach ($record_ids as $id) {
    $entity_ids[] = chado_get_record_entity_by_bundle($bundle, $id);
  }

  $field_ids = array();
  if (!empty($details['fields'])) {
    foreach ($details['fields'] as $field) {
      $field_ids[] = field_info_field($field['name'])['id'];
    }
  }

  return tripal_load_entity('TripalEntity', $entity_ids, FALSE, $field_ids);
}