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Test and fix all db indices problems
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128 changes: 128 additions & 0 deletions
128
includes/TripalFields/local__feature_search/local__feature_search.inc
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,128 @@ | ||
| <?php | ||
| /** | ||
| * @class | ||
| * Purpose: | ||
| * | ||
| * Data: | ||
| * Assumptions: | ||
| */ | ||
| class local__feature_search extends ChadoField { | ||
|
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| // -------------------------------------------------------------------------- | ||
| // 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. | ||
| // -------------------------------------------------------------------------- | ||
|
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| // The default label for this field. | ||
| public static $default_label = 'Feature Search'; | ||
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| // The default description for this field. | ||
| public static $default_description = 'Search features related to an organism (search by property)'; | ||
|
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| // The default widget for this field. | ||
| public static $default_widget = 'local__feature_search_widget'; | ||
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| // The default formatter for this field. | ||
| public static $default_formatter = 'local__feature_search_formatter'; | ||
|
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| // The module that manages this field. | ||
| public static $module = 'tripal_elasticsearch'; | ||
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| // 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' => 'field_chado_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. | ||
| 'searchable_keys' => array(), | ||
| ); | ||
|
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| // 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 DATABASE name, as it appears in chado.db. This also builds the link-out url. In most cases this will simply be the CV name. In some cases (EDAM) this will be the SUBONTOLOGY. | ||
| 'term_vocabulary' => 'local', | ||
| // The name of the term. | ||
| 'term_name' => 'feature_search', | ||
| // The unique ID (i.e. accession) of the term. | ||
| 'term_accession' => 'feature_search', | ||
| // 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 in Chado that the instance maps to. | ||
| 'chado_table' => 'organism', | ||
| // The column of the table in Chado where the value of the field comes from. | ||
| 'chado_column' => 'organism_id', | ||
| // The base table. | ||
| 'base_table' => 'organism', | ||
| ); | ||
|
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| // 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; | ||
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| // 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 search field that appears on the page that redirects | ||
| // the user but otherwise provides no data. | ||
| public static $no_data = FALSE; | ||
|
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||
| /** | ||
| * 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) { | ||
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| // ChadoFields automatically load the chado column specified in the | ||
| // default settings above. If that is all you need then you don't even | ||
| // need to implement this function. However, if you need to add any | ||
| // additional data to be used in the display, you should add it here. | ||
| parent::load($entity); | ||
| } | ||
| } |
131 changes: 131 additions & 0 deletions
131
includes/TripalFields/local__feature_search/local__feature_search_formatter.inc
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,131 @@ | ||
| <?php | ||
|
|
||
| /** | ||
| * @class | ||
| * Purpose: | ||
| * | ||
| * Display: | ||
| * Configuration: | ||
| */ | ||
| class local__feature_search_formatter extends ChadoFieldFormatter { | ||
|
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| // The default label for this field. | ||
| public static $default_label = 'Feature Search'; | ||
|
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| // The list of field types for which this formatter is appropriate. | ||
| public static $field_types = ['local__feature_search']; | ||
|
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| // The list of default settings for this formatter. | ||
| public static $default_settings = [ | ||
| 'setting1' => 'default_value', | ||
| ]; | ||
|
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| /** | ||
| * Provides the field's setting form. | ||
| * | ||
| * This function corresponds to the hook_field_formatter_settings_form() | ||
| * function of the Drupal Field API. | ||
| * | ||
| * The settings form appears on the 'Manage Display' page of the content | ||
| * type administration page. This function provides the form that will | ||
| * appear on that page. | ||
| * | ||
| * To add a validate function, please create a static function in the | ||
| * implementing class, and indicate that this function should be used | ||
| * in the form array that is returned by this function. | ||
| * | ||
| * This form will not be displayed if the formatter_settings_summary() | ||
| * function does not return anything. | ||
| * | ||
| * param $field | ||
| * The field structure being configured. | ||
| * param $instance | ||
| * The instance structure being configured. | ||
| * param $view_mode | ||
| * The view mode being configured. | ||
| * param $form | ||
| * The (entire) configuration form array, which will usually have no use | ||
| * here. Typically for reference only. | ||
| * param $form_state | ||
| * The form state of the (entire) configuration form. | ||
| * | ||
| * @return | ||
| * A Drupal Form array containing the settings form for this field. | ||
| */ | ||
| public function settingsForm($view_mode, $form, &$form_state) { | ||
|
|
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| } | ||
|
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| /** | ||
| * 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) { | ||
| // Get the settings | ||
| $settings = $display['settings']; | ||
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| $organism = $entity->chado_record; | ||
| $form = drupal_get_form('tripal_elasticsearch_gene_search_form', TRUE, "$organism->genus $organism->species", [ | ||
| 'ds_pane' => 'Feature Search', | ||
| ]); | ||
|
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| $content = '<p>You can search this organism’s features in the database by entering search terms in the box. You can search by feature name or annotation, for example, (Heat Shock, IPR020575, GO:0016049, etc.)</p>'; | ||
| $content .= drupal_render($form); | ||
| $element[] = [ | ||
| '#type' => 'markup', | ||
| '#markup' => $content, | ||
| ]; | ||
| } | ||
|
|
||
| /** | ||
| * Provides a summary of the formatter settings. | ||
| * | ||
| * This function corresponds to the hook_field_formatter_settings_summary() | ||
| * function of the Drupal Field API. | ||
| * | ||
| * On the 'Manage Display' page of the content type administration page, | ||
| * fields are allowed to provide a settings form. This settings form can | ||
| * be used to allow the site admin to define how the field should be | ||
| * formatted. The settings are then available for the formatter() | ||
| * function of this class. This function provides a text-based description | ||
| * of the settings for the site developer to see. It appears on the manage | ||
| * display page inline with the field. A field must always return a | ||
| * value in this function if the settings form gear button is to appear. | ||
| * | ||
| * See the hook_field_formatter_settings_summary() function for more | ||
| * information. | ||
| * | ||
| * @param $field | ||
| * @param $instance | ||
| * @param $view_mode | ||
| * | ||
| * @return string | ||
| * A string that provides a very brief summary of the field settings | ||
| * to the user. | ||
| * | ||
| */ | ||
| public function settingsSummary($view_mode) { | ||
| return ''; | ||
| } | ||
|
|
||
| } |
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