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@@ -0,0 +1,145 @@
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+<?php
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+
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+class operation__analysis extends ChadoField {
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+
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+ // The default lable for this field.
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+ public static $default_label = 'Analysis';
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+
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+ // The default description for this field.
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+ public static $description = 'Application of analytical methods to existing data of a specific type.';
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+
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+ // Provide a list of instance specific settings. These can be access within
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+ // the instanceSettingsForm. When the instanceSettingsForm is submitted
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+ // then Drupal with automatically change these settings for the instnace.
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+ // It is recommended to put settings at the instance level whenever possible.
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+ // If you override this variable in a child class be sure to replicate the
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+ // term_name, term_vocab, term_accession and term_fixed keys as these are
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+ // required for all TripalFields.
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+ public static $default_instance_settings = [
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+ // The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).
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+ 'term_vocabulary' => 'operation',
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+ // The name of the term.
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+ 'term_name' => 'Analysis',
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+ // The unique ID (i.e. accession) of the term.
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+ 'term_accession' => '2945',
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+ // Set to TRUE if the site admin is allowed to change the term
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+ // type. This will create form elements when editing the field instance
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+ // to allow the site admin to change the term settings above.
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+ 'term_fixed' => FALSE,
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+ ];
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+
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+ // The default widget for this field.
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+ public static $default_widget = 'operation__analysis_widget';
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+
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+ // The default formatter for this field.
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+ public static $default_formatter = 'operation__analysis_formatter';
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+
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+
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+ /**
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+ * @see TripalField::load()
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+ */
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+ public function load($entity) {
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+ $record = $entity->chado_record;
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+ $settings = $this->instance['settings'];
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+
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+ $field_name = $this->field['field_name'];
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+ $field_type = $this->field['type'];
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+ $field_table = $this->instance['settings']['chado_table'];
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+ $field_column = $this->instance['settings']['chado_column'];
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+
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+ // Get the terms for each of the keys for the 'values' property.
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+ $name_term = chado_get_semweb_term('analysis', 'name');
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+
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+ // Set some defaults for the empty record.
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+ $entity->{$field_name}['und'][0] = [
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+ 'value' => [],
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+ ];
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+
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+ if (!$record or !$record->analysis_id) {
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+ return;
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+ }
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+ $linker_field = 'chado-' . $field_table . '__' . $field_column;
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+ $entity->{$field_name}['und'][0]['value'] = [
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+ $name_term => $record->{$field_column}->name,
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+ ];
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+ $entity->{$field_name}['und'][0][$linker_field] = $record->{$field_column}->analysis_id;
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+
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+ // Is there a published entity for this analysis?
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+ if (property_exists($record->{$field_column}, 'entity_id')) {
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+ $entity->{$field_name}['und'][0]['value']['entity'] = 'TripalEntity:' . $record->{$field_column}->entity_id;
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+ }
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+ }
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+
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+
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+ /**
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+ * @see TripalField::elementInfo()
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+ */
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+ public function elementInfo() {
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+ $field_term = $this->getFieldTermID();
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+
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+ $name_term = chado_get_semweb_term('analysis', 'name');
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+
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+ return [
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+ $field_term => [
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+ 'operations' => ['eq', 'contains', 'starts'],
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+ 'sortable' => TRUE,
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+ 'searchable' => TRUE,
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+ 'readonly' => FALSE,
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+ 'type' => 'xs:complexType',
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+ 'elements' => [
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+ $name_term => [
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+ 'searchable' => TRUE,
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+ 'name' => 'name',
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+ 'operations' => ['eq', 'ne', 'contains', 'starts'],
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+ 'sortable' => FALSE,
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+ 'type' => 'xs:string',
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+ 'readonly' => TRUE,
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+ 'required' => FALSE,
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+ ],
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+ 'entity' => [
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+ 'searchable' => FALSE,
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+ ],
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+ ],
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+ ],
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+ ];
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+ }
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+
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+ /**
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+ * @see ChadoField::query()
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+ */
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+ public function query($query, $condition) {
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+ $alias = $this->field['field_name'];
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+ $operator = $condition['operator'];
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+
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+ $field_term_id = $this->getFieldTermID();
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+ $name_term = $field_term_id . ',' . chado_get_semweb_term('analysis', 'name');
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+
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+ // Join to the organism table for this field.
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+ $this->queryJoinOnce($query, 'analysis', $alias, "base.analysis_id = $alias.analysis_id");
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+
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+ // If the column is the field name then we're during a search on the full
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+ // scientific name.
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+ if ($condition['column'] == $field_term_id or
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+ $condition['column'] == $name_term) {
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+ $query->condition("$alias.name", $condition['value'], $operator);
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+ }
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+ }
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+
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+ /**
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+ * @see ChadoField::queryOrder()
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+ */
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+ public function queryOrder($query, $order) {
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+ $alias = $this->field['field_name'];
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+
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+ $field_term_id = $this->getFieldTermID();
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+ $name_term = $field_term_id . ',' . chado_get_semweb_term('analysis', 'name');
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+
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+ // Join to the organism table for this field.
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+ $this->queryJoinOnce($query, 'analysis', $alias, "base.analysis_id = $alias.analysis_id");
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+
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+ // Now perform the sort.
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+ if ($order['column'] == $name_term) {
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+ $query->orderBy("$alias.name", $order['direction']);
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+ }
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+ }
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+}
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Stephen Ficklin