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Merge pull request #88 from UofS-Pulse-Binfo/rawphenotypes-germplasm-…
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…field

Creates rawphenotypes germplasm field
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@laceysanderson
laceysanderson authored Jun 24, 2022
2 parents 8ec5a1a + 755be53 commit 75addd0
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255 changes: 255 additions & 0 deletions includes/TripalFields/ncit__raw_data/ncit__raw_data.inc
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<?php
/**
* @class
* Purpose: Provide quick browse functionality for entity pages
*
* Data: No data.
* Assumptions:
*/
class ncit__raw_data extends TripalField {
// --------------------------------------------------------------------------
// EDITABLE STATIC CONSTANTS
//
// The following constants SHOULD be set for each descendant class. They are
// used by the static functions to provide information to Drupal about
// the field and it's default widget and formatter.
// --------------------------------------------------------------------------
// The default label for this field.
public static $default_label = 'Germplasm Raw Phenotypes';
// The default description for this field.
public static $default_description = 'Show available raw phenotypes of a germplasm';
// The default widget for this field.
public static $default_widget = 'ncit__raw_data_widget';
// The default formatter for this field.
public static $default_formatter = 'ncit__raw_data_formatter';
// The module that manages this field.
public static $module = 'rawphenotypes';

// A list of global settings. These can be accessed within the
// globalSettingsForm. When the globalSettingsForm is submitted then
// Drupal will automatically change these settings for all fields.
// Once instances exist for a field type then these settings cannot be
// changed.
public static $default_settings = array(
'storage' => 'tripal_no_storage',
// It is expected that all fields set a 'value' in the load() function.
// In many cases, the value may be an associative array of key/value pairs.
// In order for Tripal to provide context for all data, the keys should
// be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
// function that are supported by the query() function should be
// listed here.
'browseable_keys' => array(),
);

// Provide a list of instance specific settings. These can be access within
// the instanceSettingsForm. When the instanceSettingsForm is submitted
// then Drupal with automatically change these settings for the instance.
// It is recommended to put settings at the instance level whenever possible.
// If you override this variable in a child class be sure to replicate the
// term_name, term_vocab, term_accession and term_fixed keys as these are
// required for all TripalFields.
public static $default_instance_settings = array(
// The short name for the vocabulary (e.g. schema, SO, GO, PATO, etc.).
'term_vocabulary' => 'NCIT',
// The name of the term.
'term_name' => 'Raw Data',
// The unique ID (i.e. accession) of the term.
'term_accession' => 'C142663',
// Set to TRUE if the site admin is not allowed to change the term
// type, otherwise the admin can change the term mapped to a field.
'term_fixed' => FALSE,
// Indicates if this field should be automatically attached to display
// or web services or if this field should be loaded separately. This
// is convenient for speed. Fields that are slow should for loading
// should have auto_attach set to FALSE so tha their values can be
// attached asynchronously.
'auto_attach' => FALSE,
// The table where the options for this specific field are stored.
// This can be one of trpfancy_browse_options or trpfancy_browse_options_per_entity
// based on admin configuration. Default: trpfancy_browse_options.
'option_storage' => '',
// A list of browser types this field intends to provide.
'browser_types' => '',
);

// A boolean specifying that users should not be allowed to create
// fields and instances of this field type through the UI. Such
// fields can only be created programmatically with field_create_field()
// and field_create_instance().
public static $no_ui = FALSE;
// A boolean specifying that the field will not contain any data. This
// should exclude the field from web services or downloads. An example
// could be a quick browse field that appears on the page that redirects
// the user but otherwise provides no data.
public static $no_data = TRUE;

/**
* Loads the field values from the underlying data store.
*
* @param $entity
*
* @return
* An array of the following format:
* $entity->{$field_name}['und'][0]['value'] = $value;
* where:
* - $entity is the entity object to which this field is attached.
* - $field_name is the name of this field
* - 'und' is the language code (in this case 'und' == undefined)
* - 0 is the cardinality. Increment by 1 when more than one item is
* available.
* - 'value' is the key indicating the value of this field. It should
* always be set. The value of the 'value' key will be the contents
* used for web services and for downloadable content. The value
* should be of the follow format types: 1) A single value (text,
* numeric, etc.) 2) An array of key value pair. 3) If multiple entries
* then cardinality should incremented and format types 1 and 2 should
* be used for each item.
* The array may contain as many other keys at the same level as 'value'
* but those keys are for internal field use and are not considered the
* value of the field.
*/
public function load($entity) {
global $user;

// User permissions.
$rawpheno_permission = array('access rawpheno', 'download rawpheno');
$count_permission = 0;
foreach($rawpheno_permission as $permission) {
if (user_access($permission, $user)) {
$count_permission++;
}
}

// If user has no permission to begin with, skip all and report
// raw phenotypes not available.
$field_name = $this->instance['field_name'];
$entity->{$field_name}['und'][0]['value'] = array();

if (user_is_logged_in() && $count_permission == 2) {
// # TRAITS/EXPERIMENT/LOCATION:
$traits = array();
// This query is identical to the rawphenotypes download page.
// Get all experiments (by plant id) where germplasm was used.
$all_experiment_locations = chado_query("
SELECT p2.project_id, p2.name, value AS location
FROM pheno_plantprop
INNER JOIN pheno_plant_project AS p1 USING (plant_id)
INNER JOIN {project} AS p2 ON p1.project_id = p2.project_id
WHERE
type_id = (SELECT cvterm_id FROM {cvterm} cvt LEFT JOIN {cv} cv ON cv.cv_id = cvt.cv_id
WHERE cvt.name = 'Location' AND cv.name = 'phenotype_plant_property_types') AND
plant_id IN (SELECT plant_id FROM pheno_plant WHERE stock_id = :germplasm GROUP BY plant_id)
GROUP BY p2.project_id, p2.name, value
", array(':germplasm' => $entity->chado_record->stock_id));
$experiment_locations = $all_experiment_locations->fetchAll();

// Only when germplasm returned rawphenotypic data.
if (count($experiment_locations) > 0) {
// User appointed experiments.
// See includes/rawpheno.function.measurements.inc file for function definition
// Given the user id this function returns an array of chado projects keyed by project_id
// that the user has permission to see.
$user_experiment = rawpheno_function_user_project($user->uid);
$user_experiment = array_keys($user_experiment);

// All traits in experiment and location.
$sql_cvterm = "
SELECT c_j.cvterm_json->>'id', c_j.cvterm_json->>'name' FROM (
SELECT JSON_BUILD_OBJECT('id', cvterm_id, 'name', name) AS cvterm_json FROM {cvterm} WHERE cvterm_id = ANY ((
SELECT STRING_TO_ARRAY(list_id.all_traits, ',') FROM (
SELECT string_agg(DISTINCT all_traits, ',') AS all_traits
FROM {rawpheno_rawdata_mview}
WHERE
location IN(:location)
AND plant_id IN (SELECT plant_id FROM pheno_plant_project WHERE project_id = :project_id)
) AS list_id
)::int[])
) AS c_j
WHERE c_j.cvterm_json->>'name' NOT IN ('Rep', 'Entry', 'Location', 'Name', 'Plot', 'Planting Date (date)', '# of Seeds Planted (count)')
ORDER BY c_j.cvterm_json->>'name' ASC
";

$trait_experiment_location = array();
$cache_exp = array();
$cache_loc = array();

foreach($experiment_locations as $item) {
$cache_exp[] = $item->project_id;
$cache_loc[] = $item->location;

$trait_set = chado_query($sql_cvterm, array(':location' => $item->location, ':project_id' => $item->project_id))
->fetchAllKeyed(0, 1);

if ($trait_set) {
foreach($trait_set as $trait_id => $trait_name) {
$allow = (in_array($item->project_id, $user_experiment)) ? 1 : 0;

// Save basic information about the trait (name + id key) and all experiment + location it was measured.
$entity->{$field_name}['und'][0]['value']['hydra:member'][ $trait_name . '_' . $trait_id ][] = array(
'phenotype_customfield_terms:id' => $item->project_id, // Project id number.
'phenotype_customfield_terms:name' => $item->name, // Project name.
'phenotype_customfield_terms:location' => $item->location, // Location in a project trait was measured.
'phenotype_customfield_terms:user_experiment' => $allow // Does user have permission?
);
}
}
}

// Save a complete summary count as a quick raw phenotypic data summary related to the germplasm.
$entity->{$field_name}['und'][0]['value']['phenotype_customfield_terms:summary'] = array(
'phenotype_customfield_terms:experiment' => count(array_unique($cache_exp)), // Summary count of experiments.
'phenotype_customfield_terms:location' => count(array_unique($cache_loc)), // Summary count of locations.
'phenotype_customfield_terms:trait' => count($entity->{$field_name}['und'][0]['value']['hydra:member']), // Summary count of traits.
);
}
}
}

/**
* Provides a form for the 'Field Settings' of an instance of this field.
*
* This function corresponds to the hook_field_instance_settings_form()
* function of the Drupal Field API.
*
* Validation of the instance settings form is not supported by Drupal, but
* the TripalField class does provide a mechanism for supporting validation.
* To allow for validation of your setting form you must call the parent
* in your child class:
*
* @code
* $element = parent::instanceSettingsForm();
* @endcode
*
* Please note, the form generated with this function does not easily
* support AJAX calls in the same way that other Drupal forms do. If you
* need to use AJAX you must manually alter the $form in your ajax call.
* The typical way to handle updating the form via an AJAX call is to make
* the changes in the form function itself but that doesn't work here.
*/
public function instanceSettingsForm() {

// Retrieve the current settings.
// If this field was just created these will contain the default values.
$settings = $this->instance['settings'];

// Allow the parent Tripal Field to set up the form element for us.
$element = parent::instanceSettingsForm();

return $element;
}

/**
* @see ChadoField::elementInfo()
*
*/
public function elementInfo() {
$field_term = $this->getFieldTermID();
return array(
$field_term => array(
'operations' => array('eq', 'ne', 'contains', 'starts'),
'sortable' => TRUE,
'searchable' => TRUE,
),
);
}
}
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