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Merge pull request #99 from UofS-Pulse-Binfo/phenotype-ontology
Phenotype ontology
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,220 @@ | ||
| <?php | ||
| /** | ||
| * @class | ||
| * Purpose: Provide quick browse functionality for entity pages | ||
| * | ||
| * Data: No data. | ||
| * Assumptions: | ||
| */ | ||
| class ncit__synonym extends ChadoField { | ||
| // -------------------------------------------------------------------------- | ||
| // 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 = 'Crop Ontology'; | ||
| // The default description for this field. | ||
| public static $default_description = 'Crop Ontology'; | ||
| // The default widget for this field. | ||
| public static $default_widget = 'ncit__synonym_widget'; | ||
| // The default formatter for this field. | ||
| public static $default_formatter = 'ncit__synonym_formatter'; | ||
| // The module that manages this field. | ||
| public static $module = 'analyzedphenotypes'; | ||
|
|
||
| // 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' => 'Synonym', | ||
| // The unique ID (i.e. accession) of the term. | ||
| 'term_accession' => 'c52469', | ||
| // 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' => '', | ||
|
|
||
| 'chado_table' => 'cvterm_relationship', | ||
| 'chado_column' => 'cvterm_relationship_id', | ||
| 'base_table' => 'cvterm_relationship' | ||
|
|
||
| ); | ||
|
|
||
| // 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) { | ||
| $record = $entity->chado_record_id; | ||
|
|
||
| if ($record) { | ||
| // We need the term configuration for term Related used when creating relationship. | ||
| $sysvar = ap_get_variablenames( | ||
| array('variablename' => 'related'), | ||
| array('set' => 'terms') | ||
| ); | ||
| $sysvar_related = variable_get($sysvar); | ||
|
|
||
| if ($sysvar_related) { | ||
| // Inspect to see if this trait has crop ontology set in chado.cvterm_relationship | ||
| // using what is known - type_id of ontology Related (in configuration) and the object_id | ||
| // which is the current trait. | ||
|
|
||
| $identifiers = array( | ||
| 'column' => array('cvterm_relationship_id', 'subject_id'), | ||
| 'value' => array('type_id' => $sysvar_related, 'object_id' => $record) | ||
| ); | ||
| $rel = chado_select_record('cvterm_relationship', $identifiers['column'], $identifiers['value']); | ||
|
|
||
| $field_name = $this->field['field_name']; | ||
| $field_table = 'chado-cvterm_relationship__'; | ||
|
|
||
| if ($rel) { | ||
| // Has crop ontology. | ||
|
|
||
| // For chado mechnanism. | ||
| $entity->{$field_name}['und'][0] = array( | ||
| // Row id #. | ||
| $field_table . 'cvterm_relationship_id' => $rel[0]->cvterm_relationship_id, | ||
| // Relationship details. | ||
| $field_table . 'type_id' => $sysvar_related, | ||
| $field_table . 'object_id' => $entity->chado_record_id, | ||
| $field_table . 'subject_id' => $rel[0]->subject_id | ||
| ); | ||
|
|
||
| // For end user. | ||
| // Sending the term, accession and cv name. Last two items are used to constuct | ||
| // direct link to vocabulary lookup to a more details about a term. | ||
| $termprop = chado_generate_var('cvterm', array( | ||
| 'cvterm_id' => $rel[0]->subject_id | ||
| )); | ||
|
|
||
| // Term. | ||
| $relationship_term = tripal_get_chado_semweb_term('cvterm_relationship', 'subject_id'); | ||
| $entity->{$field_name}['und'][0]['value'][ $relationship_term ] = $termprop->name; | ||
|
|
||
| // Accession. | ||
| $accession = tripal_get_chado_semweb_term('dbxref', 'accession'); | ||
| $entity->{$field_name}['und'][0]['value'][ $accession ] = $termprop->dbxref_id->accession; | ||
|
|
||
| // CV. | ||
| $cv_term = tripal_get_chado_semweb_term('cv', 'name'); | ||
| $entity->{$field_name}['und'][0]['value'][ $cv_term ] = $termprop->cv_id->name; | ||
| } | ||
| else { | ||
| // Crop ontology not set. | ||
| // Nothing here, just forward what we know so far, Related term and the trait id. | ||
| $entity->{$field_name}['und'][0] = array( | ||
| 'value' => array(), | ||
| $field_table . 'object_id' => $entity->chado_record_id, | ||
| $field_table . 'type_id' => $sysvar_related, | ||
| ); | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * 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; | ||
| } | ||
| } |
77 changes: 77 additions & 0 deletions
77
includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| <?php | ||
| /** | ||
| * @class | ||
| * Purpose: Provide a quick search on entity pages which submits/redirects to a full search. | ||
| * | ||
| * Display: A simple textfield search form. | ||
| * Configuration: | ||
| * - path to the full search. | ||
| * - the URL token (query parameter) the value applies to. | ||
| * - help text. | ||
| * - textfield placeholder. | ||
| * - search button text. | ||
| * - autocomplete path. | ||
| */ | ||
| class ncit__synonym_formatter extends TripalFieldFormatter { | ||
| // The default label for this field. | ||
| public static $default_label = 'Crop Ontology'; | ||
|
|
||
| // The list of field types for which this formatter is appropriate. | ||
| public static $field_types = array('ncit__synonym'); | ||
|
|
||
| /** | ||
| * Provides the display for a field | ||
| * | ||
| * This function corresponds to the hook_field_formatter_view() | ||
| * function of the Drupal Field API. | ||
| * | ||
| * This function provides the display for a field when it is viewed on | ||
| * the web page. The content returned by the formatter should only include | ||
| * what is present in the $items[$delta]['values] array. This way, the | ||
| * contents that are displayed on the page, via webservices and downloaded | ||
| * into a CSV file will always be identical. The view need not show all | ||
| * of the data in the 'values' array. | ||
| * | ||
| * @param $element | ||
| * @param $entity_type | ||
| * @param $entity | ||
| * @param $langcode | ||
| * @param $items | ||
| * @param $display | ||
| * | ||
| * @return | ||
| * An element array compatible with that returned by the | ||
| * hook_field_formatter_view() function. | ||
| */ | ||
| public function view(&$element, $entity_type, $entity, $langcode, $items, $display) { | ||
| // No show when no crop ontology for a trait. | ||
| $element = null; | ||
|
|
||
| // Render crop ontology for this trait. | ||
| if ($items[0]['value']) { | ||
| // Style information. | ||
| drupal_add_css(drupal_get_path('module', 'analyzedphenotypes') . '/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css'); | ||
|
|
||
| // Refer to this ID for CSS styling. | ||
| $id = 'ap-field-crop_ontology_synonym'; | ||
|
|
||
| list($term, $accession, $cv) = array_values($items[0]['value']); | ||
|
|
||
| // If we can't find the term then do not provide the link as it will just cause a term not found | ||
| // in the term lookup module. | ||
| // @see tripal_vocabulary_lookup_term_page() | ||
| // Tripal.term_lookup.inc. | ||
| $lookterm = tripal_get_term_details($cv, $accession); | ||
|
|
||
| $cvterm_lookup = (!$lookterm) ? '' | ||
| : l('Vocabulary Details', 'cv/lookup/' . $cv . '/' . $accession, array('attributes' => array('target' => '_blank'))); | ||
|
|
||
| $element[0] = array( | ||
| '#type' => 'markup', | ||
| '#markup' => '<div id="' . $id . '">' . $term . '</div> ' . $cvterm_lookup, | ||
| ); | ||
| } | ||
|
|
||
| return $element; | ||
| } | ||
| } |
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