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+<?php
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+/**
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+ * Retrieve a property for a given base table record
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+ *
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+ * @param $basetable
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+ * The base table for which the property should be retrieved. Thus to retrieve a property
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+ * for a feature the basetable=feature and property is retrieved from featureprop
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+ * @param $record_id
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+ * The foriegn key field of the base table. This should be in integer.
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+ * @param $property
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+ * The cvterm name describing the type of properties to be retrieved
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+ * @param $cv_name
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+ * The name of the cv that the above cvterm is part of
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+ *
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+ * @return
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+ * An array in the same format as that generated by the function
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+ * tripal_core_generate_chado_var(). If only one record is returned it
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+ * is a single object. If more than one record is returned then it is an array
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+ * of objects
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+ *
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+ * @ingroup tripal_properties_api
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+ */
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+function tripal_core_get_property($basetable, $record_id, $property, $cv_name) {
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+ // get the foreign key for this property table
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+ $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
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+ $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
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+
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+ // construct the array of values to be selected
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+ $values = array(
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+ $fkcol => $record_id,
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+ 'type_id' => array(
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+ 'cv_id' => array(
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+ 'name' => $cv_name,
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+ ),
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+ 'name' => $property,
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+ 'is_obsolete' => 0
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+ ),
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+ );
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+ $results = tripal_core_generate_chado_var($basetable . 'prop', $values);
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+ if ($results) {
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+ $results = tripal_core_expand_chado_vars($results, 'field', $basetable . 'prop.value');
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+ }
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+
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+ return $results;
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+}
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+
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+/**
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+ * Insert a property for a given base table. By default if the property already
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+ * exists a new property is added with the next available rank. If
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+ * $update_if_present argument is specified then the record will be updated if it
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+ * exists rather than adding a new property.
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+ *
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+ * @param $basetable
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+ * The base table for which the property should be inserted. Thus to insert a property
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+ * for a feature the basetable=feature and property is inserted into featureprop
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+ * @param $record_id
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+ * The foriegn key value of the base table. This should be in integer.
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+ * @param $property
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+ * The cvterm name describing the type of properties to be inserted
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+ * @param $cv_name
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+ * The name of the cv that the above cvterm is part of
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+ * @param $value
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+ * The value of the property to be inserted (can be empty)
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+ * @param $update_if_present
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+ * A boolean indicating whether an existing record should be updated. If the
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+ * property already exists and this value is not specified or is zero then
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+ * a new property will be added with the next largest rank.
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+ *
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+ * @return
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+ * Return True on Insert/Update and False otherwise
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+ *
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+ * @ingroup tripal_properties_api
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+ */
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+function tripal_core_insert_property($basetable, $record_id, $property,
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+$cv_name, $value, $update_if_present = 0) {
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+
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+ // first see if the property already exists, if the user want's to update
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+ // then we can do that, but otherwise we want to increment the rank and
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+ // insert
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+ $props = tripal_core_get_property($basetable, $record_id, $property, $cv_name);
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+ if (!is_array($props) and $props) {
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+ $props = array($props);
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+ }
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+
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+ $rank = 0;
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+ if (count($props) > 0) {
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+ if ($update_if_present) {
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+ return tripal_core_update_property($basetable, $record_id, $property, $cv_name, $value);
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+ }
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+ else {
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+ // iterate through the properties returned and check to see if the
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+ // property with this value already exists if not, get the largest rank
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+ // and insert the same property but with this new value
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+ foreach ($props as $p) {
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+ if ($p->rank > $rank) {
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+ $rank = $p->rank;
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+ }
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+ if (strcmp($p->value, $value) == 0) {
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+ return TRUE;
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+ }
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+ }
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+ // now add 1 to the rank
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+ $rank++;
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+ }
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+ }
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+
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+ // make sure the cvterm exists. Otherwise we'll get an error with
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+ // prepared statements not matching
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+ $values = array(
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+ 'cv_id' => array(
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+ 'name' => $cv_name,
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+ ),
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+ 'name' => $property,
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+ );
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+
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+ $options = array();
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+ $term = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
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+ if (!$term or count($term) == 0) {
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+ watchdog('tripal_core', "Cannot find property '%prop_name'.",
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+ array('%prop_name' => $property), WATCHDOG_ERROR);
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+ return FALSE;
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+ }
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+
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+ // get the foreign key for this property table
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+ $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
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+ $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
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+
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+ // construct the array of values to be inserted
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+ $values = array(
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+ $fkcol => $record_id,
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+ 'type_id' => array(
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+ 'cv_id' => array(
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+ 'name' => $cv_name,
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+ ),
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+ 'name' => $property,
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+ ),
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+ 'value' => $value,
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+ 'rank' => $rank,
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+ );
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+
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+ $options = array();
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+ $result = tripal_core_chado_insert($basetable . 'prop', $values, $options);
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+ return $result;
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+}
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+
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+/**
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+ * Update a property for a given base table record and property name. This
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+ * function should be used only if one record of the property will be present.
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+ * If the property name can have multiple entries (with increasing rank) then
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+ * use the function named tripal_core_update_property_by_id
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+ *
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+ * @param $basetable
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+ * The base table for which the property should be updated. The property table
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+ * is constructed using a combination of the base table name and the suffix
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+ * 'prop' (e.g. basetable = feature then property tabie is featureprop).
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+ * @param $record_id
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+ * The foreign key of the basetable to update a property for. This should be in integer.
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+ * For example, if the basetable is 'feature' then the $record_id should be the feature_id
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+ * @param $property
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+ * The cvterm name of property to be updated
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+ * @param $cv_name
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+ * The name of the cv that the above cvterm is part of
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+ * @param $value
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+ * The value of the property to be inserted (can be empty)
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+ * @param $insert_if_missing
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+ * A boolean indicating whether a record should be inserted if one doesn't exist to update
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+ *
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+ * Note: The property to be updated is select via the unique combination of $record_id and
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+ * $property and then it is updated with the supplied value
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+ *
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+ * @return
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+ * Return True on Update/Insert and False otherwise
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+ *
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+ * @ingroup tripal_properties_api
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+ */
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+function tripal_core_update_property($basetable, $record_id, $property,
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+$cv_name, $value, $insert_if_missing = 0) {
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+
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+ // first see if the property is missing (we can't update a missing property
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+ $prop = tripal_core_get_property($basetable, $record_id, $property, $cv_name);
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+ if (count($prop)==0) {
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+ if ($insert_if_missing) {
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+ return tripal_core_insert_property($basetable, $record_id, $property, $cv_name, $value);
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+ }
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+ else {
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+ return FALSE;
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+ }
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+ }
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+
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+ // get the foreign key for this property table
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+ $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
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+ $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
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+
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+ // construct the array that will match the exact record to update
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+ $match = array(
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+ $fkcol => $record_id,
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+ 'type_id' => array(
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+ 'cv_id' => array(
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+ 'name' => $cv_name,
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+ ),
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+ 'name' => $property,
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+ ),
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+ );
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+
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+ // construct the array of values to be updated
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+ $values = array(
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+ 'value' => $value,
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+ );
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+
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+ return tripal_core_chado_update($basetable . 'prop', $match, $values);
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+}
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+
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+/**
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+ * Update a property for a given base table record. This function should be
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+ * used if multiple records of the same property will be present. Also, use this
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+ * function to change the property name of an existing property.
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+ *
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+ * @param $basetable
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+ * The base table for which the property should be updated. The property table
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+ * is constructed using a combination of the base table name and the suffix
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+ * 'prop' (e.g. basetable = feature then property tabie is featureprop).
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+ * @param $record_id
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+ * The primary key of the base table. This should be in integer.
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+ * For example, if the basetable is 'feature' then the $record_id should be the featureprop_id
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+ * @param $property
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+ * The cvterm name of property to be updated
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+ * @param $cv_name
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+ * The name of the cv that the above cvterm is part of
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+ * @param $value
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+ * The value of the property to be inserted (can be empty)
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+ *
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+ * @return
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+ * Return True on Update/Insert and False otherwise
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+ *
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+ * @ingroup tripal_properties_api
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+ */
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+function tripal_core_update_property_by_id($basetable, $record_id, $property,
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+$cv_name, $value) {
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+
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+ // get the primary key for this property table
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+ $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
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+ $pkcol = $table_desc['primary key'][0];
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+
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+ // construct the array that will match the exact record to update
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+ $match = array(
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+ $pkcol => $record_id,
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+ );
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+
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+ // construct the array of values to be updated
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+ $values = array(
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+ 'type_id' => array(
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+ 'cv_id' => array(
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+ 'name' => $cv_name,
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+ ),
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+ 'name' => $property,
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+ ),
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+ 'value' => $value,
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+ );
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+
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+ return tripal_core_chado_update($basetable . 'prop', $match, $values);
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+}
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+
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+/**
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+ * Deletes a property for a given base table record using the property name
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+ *
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+ * @param $basetable
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+ * The base table for which the property should be deleted. Thus to deleted a property
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+ * for a feature the basetable=feature and property is deleted from featureprop
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+ * @param $record_id
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+ * The primary key of the basetable to delete a property for. This should be in integer.
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+ * @param $property
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+ * The cvterm name describing the type of property to be deleted
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+ * @param $cv_name
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+ * The name of the cv that the above cvterm is part of
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+ *
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+ * Note: The property to be deleted is select via the unique combination of $record_id and $property
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+ *
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+ * @return
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+ * Return True on Delete and False otherwise
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+ *
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+ * @ingroup tripal_properties_api
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+ */
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+function tripal_core_delete_property($basetable, $record_id, $property, $cv_name) {
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+
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+ // get the foreign key for this property table
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+ $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
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+ $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
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+
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+ // construct the array that will match the exact record to update
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+ $match = array(
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+ $fkcol => $record_id,
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+ 'type_id' => array(
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+ 'cv_id' => array(
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+ 'name' => $cv_name,
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+ ),
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+ 'name' => $property,
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+ ),
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+ );
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+
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+ return tripal_core_chado_delete($basetable . 'prop', $match);
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+}
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+
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+/**
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+ * Deletes a property using the property ID
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+ *
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+ * @param $basetable
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+ * The base table for which the property should be deleted. Thus to deleted a property
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+ * for a feature the basetable=feature and property is deleted from featureprop
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+ * @param $record_id
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+ * The primary key of the basetable to delete a property for. This should be in integer.
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+ *
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+ * @return
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+ * Return True on Delete and False otherwise
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+ *
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+ * @ingroup tripal_properties_api
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+ */
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+function tripal_core_delete_property_by_id($basetable, $record_id) {
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+
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+ // get the foreign key for this property table
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+ $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
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+ $pkcol = $table_desc['primary key'][0];
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+
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+ // construct the array that will match the exact record to update
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+ $match = array(
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+ $pkcol => $record_id,
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+ );
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+
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+ return tripal_core_chado_delete($basetable . 'prop', $match);
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+}
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+
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+/**
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+ * This function is a wrapper for adding fields to an existing form for managing properties.
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+ * Many of the chado tables have a corresponding 'prop' table (e.g. analysisprop, contactprop,
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+ * organismprop, etc) and those prop tables all have the same schema. Use this function
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+ * to add all the necessary components to a form for allowing the user to add/edit properties to
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+ * a given record. To retreive properties in hook_insert or hook_update of a node form use
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+ * use the function tripal_core_properties_form_retreive().
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+ *
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+ * @param $form
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+ * The Drupal form array into which the properties elements will be added
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+ * @param $form_state
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+ * The corresponding form_state array for the form
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+ * @param $prop_table
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+ * The name of the property table (e.g. anlaysisprop, contactprop)
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+ * @param $id_field
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+ * The name of the ID field in the property table (e.g. analysis_id, contact_id)
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+ * @param $cv_name
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+ * The name of the controlled vocabulary that these properties are derived from
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+ * @param $available_props
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+ * An array of properties to inclde in the properties drop down. This array should
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+ * have cvterm_id's as the key and the cvterm name as the value
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+ * @param $id
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+ * The current base table ID. For example, if the property table is analysisprop then the
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+ * value should be that of the analysis_id. If the property table is contactprop then the
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+ * value should be that of the contact_id. This is the record from which currently assigned
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+ * properties will be retrieved.
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+ * @param $exclude
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+ * An array of cvterms to exclude when retreiving terms already saved in the database.
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+ * Use this array when properties are present but should be handled elsewhere.
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+ * For example, for contacts, the description field is stored as a property because
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+ * the actual field is only 255 characters. The 'contact_description' therefore should
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+ * not be shown in the list of properties, even if present, because it is handled by
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+ * a different form element.
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+ * @param $instructions
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+ * An additional set of instructions for the form properties.
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+ *
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+ * @ingroup tripal_properties_api
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+ */
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+function tripal_core_properties_form(&$form, &$form_state, $prop_table, $id_field, $cv_name,
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+ $available_props, $id = NULL, $exclude = array(), $instructions = '') {
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+
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+ $d_removed = array(); // lists removed properties
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+ $num_new = 0; // the number of new rows
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+
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+ // if we are re constructing the form from a failed validation or ajax callback
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+ // then use the $form_state['values'] values
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+ if (array_key_exists('values', $form_state)) {
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+ $d_removed = $form_state['values']['removed'];
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+ $num_new = $form_state['values']['num_new'] ? $form_state['values']['num_new'] : 0;
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+ }
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+ // if we are re building the form from after submission (from ajax call) then
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+ // the values are in the $form_state['input'] array
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+ if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
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+ $d_removed = $form_state['input']['removed'];
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+ $num_new = $form_state['input']['num_new'] ? $form_state['input']['num_new'] : 0;
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['properties'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Additional Details'),
|
|
|
+ '#description' => t('You may add additional properties by
|
|
|
+ selecting a property type from the dropdown and adding text. You may add
|
|
|
+ as many properties as desired by clicking the add button on the right. To
|
|
|
+ remove a property, click the remove button. ' . $instructions),
|
|
|
+ );
|
|
|
+ $form['properties']['table'] = array(
|
|
|
+ '#type' => 'markup',
|
|
|
+ '#value' => '',
|
|
|
+ '#prefix' => '<div id="tripal-generic-edit-properties-table">',
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ );
|
|
|
+
|
|
|
+ // this array keeps track of all properties we have and allows the functions
|
|
|
+ // below to select the next rank if a property is dupliated
|
|
|
+ $ranks = array();
|
|
|
+
|
|
|
+ // add in the properties from the Chado prop table (only pertains to existing analyses)
|
|
|
+ if ($id) {
|
|
|
+ tripal_core_properties_form_add_prop_table_props($prop_table, $id_field, $cv_name,
|
|
|
+ $form, $form_state, $id, $ranks, $d_removed, $exclude);
|
|
|
+ }
|
|
|
+
|
|
|
+ // add in any new properties that have been added by the user through an AHAH callback
|
|
|
+ tripal_core_properties_form_add_new_props($form, $form_state, $ranks, $d_removed);
|
|
|
+
|
|
|
+ // add an empty row of field to allow for addition of a new property
|
|
|
+ tripal_core_properties_form_add_new_empty_props($form, $form_state, $available_props);
|
|
|
+
|
|
|
+ $form['properties']['table']['#theme'] = 'tripal_core_properties_form';
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is responsible for adding a blank row to the properties table for
|
|
|
+ * adding a new property.
|
|
|
+ */
|
|
|
+function tripal_core_properties_form_add_new_empty_props(&$form, &$form_state, $properties_select) {
|
|
|
+
|
|
|
+ // get the field defaults either from $form_state['values'] or $form_state['input']
|
|
|
+ $description = '';
|
|
|
+ $text = '';
|
|
|
+ $id = 0;
|
|
|
+ if (array_key_exists('values', $form_state)) {
|
|
|
+ $id = $form_state['values']['new_id'];
|
|
|
+ $text = $form_state['values']['new_value'];
|
|
|
+ }
|
|
|
+ // if we have a property ID then get it's definition to display to the user
|
|
|
+ if($id) {
|
|
|
+ $values = array('cvterm_id' => $id);
|
|
|
+ $cvterm = tripal_core_chado_select('cvterm', array('definition'), $values);
|
|
|
+
|
|
|
+ if ($cvterm[0]->definition) {
|
|
|
+ $description = $cvterm[0]->definition;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ $rows = 1;
|
|
|
+
|
|
|
+ // add one more blank set of property fields
|
|
|
+ $form['properties']['table']['new']["new_id"] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#options' => $properties_select,
|
|
|
+ '#default_value' => $id,
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "tripal_core_props_property_ajax_get_description",
|
|
|
+ 'wrapper' => 'tripal-properties-new_value',
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'method' => 'replace',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $form['properties']['table']['new']["new_value"] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#default_value' => $text,
|
|
|
+ '#cols' => 50,
|
|
|
+ '#rows' => $rows,
|
|
|
+ '#prefix' => '<div id="tripal-properties-new_value">',
|
|
|
+ '#description' => $description,
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['table']['new']["add"] = array(
|
|
|
+ '#type' => 'button',
|
|
|
+ '#value' => t('Add'),
|
|
|
+ '#name' => 'add',
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "tripal_core_props_property_ajax_update",
|
|
|
+ 'wrapper' => 'tripal-properties-edit-properties-table',
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'method' => 'replace',
|
|
|
+ 'prevent' => 'click'
|
|
|
+ ),
|
|
|
+ // When this button is clicked, the form will be validated and submitted.
|
|
|
+ // Therefore, we set custom submit and validate functions to override the
|
|
|
+ // default form submit. In the validate function we set the form_state
|
|
|
+ // to rebuild the form so the submit function never actually gets called,
|
|
|
+ // but we need it or Drupal will run the default validate anyway.
|
|
|
+ // we also set #limit_validation_errors to empty so fields that
|
|
|
+ // are required that don't have values won't generate warnings.
|
|
|
+ '#submit' => array('tripal_core_props_form_props_button_submit'),
|
|
|
+ '#validate' => array('tripal_core_props_form_props_button_validate'),
|
|
|
+ '#limit_validation_errors' => array(array('new_id')),
|
|
|
+ );
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is used to rebuild the form if an ajax call is made vai a button.
|
|
|
+ * The button causes the form to be submitted. We don't want this so we override
|
|
|
+ * the validate and submit routines on the form button. Therefore, this function
|
|
|
+ * only needs to tell Drupal to rebuild the form
|
|
|
+ */
|
|
|
+function tripal_core_props_form_props_button_validate($form, &$form_state){
|
|
|
+ if (array_key_exists('triggering_element', $form_state) and
|
|
|
+ $form_state['triggering_element']['#name'] == 'add' and
|
|
|
+ $form_state['input']['new_id'] == 0 ){
|
|
|
+ form_set_error('new_id', "Please specify a property type");
|
|
|
+ return;
|
|
|
+ }
|
|
|
+ $form_state['rebuild'] = TRUE;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * This function is just a dummy to override the default form submit on ajax calls for buttons
|
|
|
+ */
|
|
|
+function tripal_core_props_form_props_button_submit($form, &$form_state){
|
|
|
+ // do nothing
|
|
|
+}
|
|
|
+/**
|
|
|
+ * This adds
|
|
|
+ */
|
|
|
+function tripal_core_properties_form_add_new_props(&$form, &$form_state, &$ranks, &$d_removed) {
|
|
|
+
|
|
|
+ // set some default values
|
|
|
+ $j = 0;
|
|
|
+ $num_properties = 0;
|
|
|
+
|
|
|
+ $values = array();
|
|
|
+ if (array_key_exists('values', $form_state)) {
|
|
|
+ $values = $form_state['values'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
|
|
|
+ $values = $form_state['input'];
|
|
|
+ }
|
|
|
+
|
|
|
+ // first, add in all of the new properties that were added previously via this form
|
|
|
+ foreach ($values as $element_name => $value) {
|
|
|
+ if (preg_match('/new_value-(\d+)-(\d+)/', $element_name, $matches)) {
|
|
|
+ $new_id = $matches[1];
|
|
|
+ $rank = $matches[2];
|
|
|
+
|
|
|
+ // skip any properties that the user requested to delete through a previous
|
|
|
+ // ajax callback or through the current ajax callback
|
|
|
+ if (array_key_exists("$new_id-$rank", $d_removed)) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ if (array_key_exists('triggering_element', $form_state) and
|
|
|
+ $form_state['triggering_element']['#name'] == 'remove-' . $new_id . '-' . $rank) {
|
|
|
+ $d_removed["$new_id-$rank"] = 1;
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+
|
|
|
+ // get this new_id information
|
|
|
+ $args = array('cvterm_id' => $new_id);
|
|
|
+ $cvterm = tripal_core_chado_select('cvterm', array('name', 'definition'), $args);
|
|
|
+
|
|
|
+ // add it to the $ranks array
|
|
|
+ $ranks[$new_id][$rank]['name'] = $cvterm[0]->name;
|
|
|
+ $ranks[$new_id][$rank]['id'] = $new_id;
|
|
|
+ $ranks[$new_id][$rank]['value'] = $value;
|
|
|
+ $ranks[$new_id][$rank]['definition'] = $cvterm[0]->definition;
|
|
|
+ $num_properties++;
|
|
|
+
|
|
|
+ // determine how many rows we need in the textarea
|
|
|
+ $rows = 1;
|
|
|
+ // add the new fields
|
|
|
+ $form['properties']['table']['new'][$new_id][$rank]["new_id-$new_id-$rank"] = array(
|
|
|
+ '#markup' => $cvterm[0]->name
|
|
|
+ );
|
|
|
+ $form['properties']['table']['new'][$new_id][$rank]["new_value-$new_id-$rank"] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#default_value' => $value,
|
|
|
+ '#cols' => 50,
|
|
|
+ '#rows' => $rows,
|
|
|
+ '#description' => $cvterm[0]->definition,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['table']['new'][$new_id][$rank]["remove-$new_id-$rank"] = array(
|
|
|
+ '#type' => 'button',
|
|
|
+ '#value' => t('Remove'),
|
|
|
+ '#name' => "remove-$new_id-$rank",
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "tripal_core_props_property_ajax_update",
|
|
|
+ 'wrapper' => 'tripal-properties-edit-properties-table',
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'event' => 'mousedown',
|
|
|
+ 'method' => 'replace',
|
|
|
+ 'prevent' => 'click'
|
|
|
+ ),
|
|
|
+ // When this button is clicked, the form will be validated and submitted.
|
|
|
+ // Therefore, we set custom submit and validate functions to override the
|
|
|
+ // default form submit. In the validate function we set the form_state
|
|
|
+ // to rebuild the form so the submit function never actually gets called,
|
|
|
+ // but we need it or Drupal will run the default validate anyway.
|
|
|
+ // we also set #limit_validation_errors to empty so fields that
|
|
|
+ // are required that don't have values won't generate warnings.
|
|
|
+ '#submit' => array('tripal_core_props_form_props_button_submit'),
|
|
|
+ '#validate' => array('tripal_core_props_form_props_button_validate'),
|
|
|
+ '#limit_validation_errors' => array(),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // second add in any new properties added during this callback
|
|
|
+ if (array_key_exists('triggering_element', $form_state) and
|
|
|
+ $form_state['triggering_element']['#name'] == 'add' and
|
|
|
+ $form_state['input']['new_id'] != 0) {
|
|
|
+ $new_id = $form_state['input']['new_id'];
|
|
|
+ $new_value = $form_state['input']['new_value'];
|
|
|
+
|
|
|
+ // get the rank by counting the number of entries
|
|
|
+ $rank = count($ranks[$new_id]);
|
|
|
+
|
|
|
+ // get this new_id information
|
|
|
+ $cvterm = tripal_core_chado_select('cvterm', array('name', 'definition'), array('cvterm_id' => $new_id));
|
|
|
+
|
|
|
+ // add it to the $ranks array
|
|
|
+ $ranks[$new_id][$rank]['name'] = $cvterm[0]->name;
|
|
|
+ $ranks[$new_id][$rank]['id'] = $new_id;
|
|
|
+ $ranks[$new_id][$rank]['value'] = $value;
|
|
|
+ $ranks[$new_id][$rank]['definition'] = $cvterm[0]->definition;
|
|
|
+ $num_properties++;
|
|
|
+
|
|
|
+ // determine how many rows we need in the textarea
|
|
|
+ $rows = 1;
|
|
|
+
|
|
|
+ // add the new fields
|
|
|
+ $form['properties']['table']['new'][$new_id][$rank]["new_id-$new_id-$rank"] = array(
|
|
|
+ '#markup' => $cvterm[0]->name
|
|
|
+ );
|
|
|
+ $form['properties']['table']['new'][$new_id][$rank]["new_value-$new_id-$rank"] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#default_value' => $new_value,
|
|
|
+ '#cols' => 50,
|
|
|
+ '#rows' => $rows,
|
|
|
+ '#description' => $cvterm[0]->definition,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['table']['new'][$new_id][$rank]["remove-$new_id-$rank"] = array(
|
|
|
+ '#type' => 'button',
|
|
|
+ '#value' => t('Remove'),
|
|
|
+ '#name' => "remove-$new_id-$rank",
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "tripal_core_props_property_ajax_update",
|
|
|
+ 'wrapper' => 'tripal-properties-edit-properties-table',
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'event' => 'mousedown',
|
|
|
+ 'method' => 'replace',
|
|
|
+ 'prevent' => 'click'
|
|
|
+ ),
|
|
|
+ // When this button is clicked, the form will be validated and submitted.
|
|
|
+ // Therefore, we set custom submit and validate functions to override the
|
|
|
+ // default form submit. In the validate function we set the form_state
|
|
|
+ // to rebuild the form so the submit function never actually gets called,
|
|
|
+ // but we need it or Drupal will run the default validate anyway.
|
|
|
+ // we also set #limit_validation_errors to empty so fields that
|
|
|
+ // are required that don't have values won't generate warnings.
|
|
|
+ '#submit' => array('tripal_core_props_form_props_button_submit'),
|
|
|
+ '#validate' => array('tripal_core_props_form_props_button_validate'),
|
|
|
+ '#limit_validation_errors' => array(),
|
|
|
+ );
|
|
|
+
|
|
|
+ }
|
|
|
+
|
|
|
+ return $num_properties;
|
|
|
+}
|
|
|
+/*
|
|
|
+ *
|
|
|
+*/
|
|
|
+function tripal_core_properties_form_add_prop_table_props($prop_table, $id_field, $cv_name,
|
|
|
+ &$form, $form_state, $id, &$ranks, &$d_removed, $exclude = array()) {
|
|
|
+
|
|
|
+ // get the existing properties
|
|
|
+ $num_properties = 0;
|
|
|
+
|
|
|
+ if (!$id) {
|
|
|
+ return;
|
|
|
+ }
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT CVT.cvterm_id, CVT.name, CVT.definition, PP.value, PP.rank
|
|
|
+ FROM {" . $prop_table . "} PP
|
|
|
+ INNER JOIN {cvterm} CVT ON CVT.cvterm_id = PP.type_id
|
|
|
+ INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
|
|
|
+ WHERE
|
|
|
+ PP.$id_field = :id AND
|
|
|
+ CV.name = '$cv_name'
|
|
|
+ ORDER BY CVT.name, PP.rank
|
|
|
+ ";
|
|
|
+ $props = chado_query($sql, array(':id' => $id));
|
|
|
+ while ($prop = $props->fetchObject()) {
|
|
|
+
|
|
|
+ $type_id = $prop->cvterm_id;
|
|
|
+ $rank = 0;
|
|
|
+ if(array_key_exists($type_id, $ranks)) {
|
|
|
+ $rank = count($ranks[$type_id]);
|
|
|
+ }
|
|
|
+
|
|
|
+ // skip any properties that the user requested to delete through a previous
|
|
|
+ // AHAH callback or through the current AHAH callback
|
|
|
+ if (array_key_exists("$type_id-$rank", $d_removed)) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ // skip any properties that should be excluded
|
|
|
+ if (count(array_intersect(array($prop->name), $exclude)) == 1) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ if (array_key_exists('triggering_element', $form_state) and
|
|
|
+ $form_state['triggering_element']['#name'] == 'remove-' . $type_id . '-' . $rank) {
|
|
|
+ $d_removed["$type_id-$rank"] = 1;
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+
|
|
|
+ $ranks[$type_id][$rank]['name'] = $prop->name;
|
|
|
+ $ranks[$type_id][$rank]['id'] = $type_id;
|
|
|
+ $ranks[$type_id][$rank]['value'] = $prop->value;
|
|
|
+ $ranks[$type_id][$rank]['definition'] = $prop->definition;
|
|
|
+ $num_properties++;
|
|
|
+ $rows = 1;
|
|
|
+
|
|
|
+ $form['properties']['table'][$type_id][$rank]["prop_id-$type_id-$rank"] = array(
|
|
|
+ '#markup' => $prop->name,
|
|
|
+ );
|
|
|
+ $form['properties']['table'][$type_id][$rank]["prop_value-$type_id-$rank"] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#default_value' => $prop->value,
|
|
|
+ '#cols' => 50,
|
|
|
+ '#rows' => $rows,
|
|
|
+ '#description' => $prop->definition,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['table'][$type_id][$rank]["remove-$type_id-$rank"] = array(
|
|
|
+ '#type' => 'button',
|
|
|
+ '#value' => t('Remove'),
|
|
|
+ '#name' => "remove-$type_id-$rank",
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "tripal_core_props_property_ajax_update",
|
|
|
+ 'wrapper' => 'tripal-properties-edit-properties-table',
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'event' => 'mousedown',
|
|
|
+ 'method' => 'replace',
|
|
|
+ 'prevent' => 'click'
|
|
|
+ ),
|
|
|
+ // When this button is clicked, the form will be validated and submitted.
|
|
|
+ // Therefore, we set custom submit and validate functions to override the
|
|
|
+ // default form submit. In the validate function we set the form_state
|
|
|
+ // to rebuild the form so the submit function never actually gets called,
|
|
|
+ // but we need it or Drupal will run the default validate anyway.
|
|
|
+ // we also set #limit_validation_errors to empty so fields that
|
|
|
+ // are required that don't have values won't generate warnings.
|
|
|
+ '#submit' => array('tripal_core_props_form_props_button_submit'),
|
|
|
+ '#validate' => array('tripal_core_props_form_props_button_validate'),
|
|
|
+ '#limit_validation_errors' => array(),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ return $num_properties;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Form AJAX callback for adding a blank property row
|
|
|
+ *
|
|
|
+ * We only want to return the properties as that's all we'll replace with this callback
|
|
|
+ */
|
|
|
+function tripal_core_props_property_ajax_update($form, $form_state) {
|
|
|
+ $properties_html = tripal_core_props_theme_node_form_properties($form['properties']['table']);
|
|
|
+ $form['properties']['table'] = array(
|
|
|
+ '#markup' => $properties_html,
|
|
|
+ '#prefix' => '<div id="tripal-properties-edit-properties-table">',
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ );
|
|
|
+ return $form['properties']['table'];
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Form AJAX callback for updating a property description. This
|
|
|
+ * function only gets called when the property drop down is changed
|
|
|
+ * on the bottom (empty) row of properties
|
|
|
+ */
|
|
|
+function tripal_core_props_property_ajax_get_description($form, $form_state) {
|
|
|
+ return $form['properties']['table']['new']["new_value"];
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * We need to theme the form so that the properties fields look good
|
|
|
+ */
|
|
|
+function theme_tripal_core_properties_form($variables) {
|
|
|
+ $form = $variables['form'];
|
|
|
+
|
|
|
+ $properties_table = tripal_core_props_theme_node_form_properties($form);
|
|
|
+ $markup = $properties_table;
|
|
|
+
|
|
|
+ $form['properties']['table'] = array(
|
|
|
+ '#markup' => $markup,
|
|
|
+ '#prefix' => '<div id="tripal-properties-edit-properties-table">',
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ );
|
|
|
+ $form['buttons']['#weight'] = 50;
|
|
|
+ return drupal_render($form['properties']['table']);
|
|
|
+}
|
|
|
+/**
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_props_theme_node_form_properties($form) {
|
|
|
+ $rows = array();
|
|
|
+
|
|
|
+ // first add in the properties derived from the prop table
|
|
|
+ // the array tree for these properties looks like this:
|
|
|
+ // $form['properties']['table'][$type_id][$rank]["prop_id-$type_id-$rank"]
|
|
|
+ foreach ($form as $type_id => $elements) {
|
|
|
+ // there are other fields in the properties array so we only
|
|
|
+ // want the numeric ones those are our type_id
|
|
|
+ if (is_numeric($type_id)) {
|
|
|
+ foreach ($elements as $rank => $element) {
|
|
|
+ if (is_numeric($rank)) {
|
|
|
+ $rows[] = array(
|
|
|
+ drupal_render($element["prop_id-$type_id-$rank"]),
|
|
|
+ drupal_render($element["prop_value-$type_id-$rank"]),
|
|
|
+ drupal_render($element["remove-$type_id-$rank"]),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // second, add in any new properties added by the user through AHAH callbacks
|
|
|
+ // the array tree for these properties looks like this:
|
|
|
+ // $form['properties']['table']['new'][$type_id][$rank]["new_id-$new_id-$rank"]
|
|
|
+ foreach ($form['new'] as $type_id => $elements) {
|
|
|
+ if (is_numeric($type_id)) {
|
|
|
+ foreach ($elements as $rank => $element) {
|
|
|
+ if (is_numeric($rank)) {
|
|
|
+ $rows[] = array(
|
|
|
+ drupal_render($element["new_id-$type_id-$rank"]),
|
|
|
+ drupal_render($element["new_value-$type_id-$rank"]),
|
|
|
+ drupal_render($element["remove-$type_id-$rank"]),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // finally add in a set of blank field for adding a new property
|
|
|
+ $rows[] = array(
|
|
|
+ drupal_render($form['new']['new_id']),
|
|
|
+ array(
|
|
|
+ 'data' => drupal_render($form['new']['new_value']),
|
|
|
+ 'width' => '60%',
|
|
|
+ ),
|
|
|
+ drupal_render($form['new']['add']),
|
|
|
+ );
|
|
|
+
|
|
|
+ $headers = array('Property Type', 'Value', 'Actions');
|
|
|
+ $table = array(
|
|
|
+ 'header' => $headers,
|
|
|
+ 'rows' => $rows,
|
|
|
+ 'attributes' => array(),
|
|
|
+ 'sticky' => TRUE,
|
|
|
+ 'caption' => '',
|
|
|
+ 'colgroups' => array(),
|
|
|
+ 'empty' => '',
|
|
|
+ );
|
|
|
+
|
|
|
+ return theme_table($table);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is used in a hook_insert, hook_update for a node form
|
|
|
+ * when the properties form has been added to the form. It retrieves all of the properties
|
|
|
+ * and returns them in an array of the format:
|
|
|
+ *
|
|
|
+ * $properties[<property name>][<rank>] = <value
|
|
|
+ *
|
|
|
+ * This array can then be used for inserting or updating properties using the API call
|
|
|
+ * tripal_hook_insert_property()
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * @param $cvname
|
|
|
+ * The name of the controlled vocabulary that the properties belong to
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A properties array
|
|
|
+ *
|
|
|
+ * @ingroup tripal_properties_api
|
|
|
+ */
|
|
|
+function tripal_core_properties_form_retreive($node, $cv_name) {
|
|
|
+
|
|
|
+ // now add the properties
|
|
|
+ $properties = array(); // stores all of the properties we need to add
|
|
|
+
|
|
|
+ // get the list of properties for easy lookup (without doing lots of database queries
|
|
|
+ $properties_list = array();
|
|
|
+ $sql = "
|
|
|
+ SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
|
|
|
+ WHERE
|
|
|
+ CV.name = '$cv_name' AND
|
|
|
+ NOT CVT.is_obsolete = 1
|
|
|
+ ORDER BY CVT.name ASC
|
|
|
+ ";
|
|
|
+ $prop_types = chado_query($sql);
|
|
|
+ while ($prop = $prop_types->fetchObject()) {
|
|
|
+ $properties_list[$prop->cvterm_id] = $prop->name;
|
|
|
+ }
|
|
|
+
|
|
|
+ // get the properties that should be added. Properties are in one of two forms:
|
|
|
+ // 1) prop_value-[type id]-[index]
|
|
|
+ // 2) new_value-[type id]-[index]
|
|
|
+ // 3) new_id, new_value
|
|
|
+
|
|
|
+ foreach ($node as $name => $value) {
|
|
|
+ if (preg_match('/^new_value-(\d+)-(\d+)/', $name, $matches)) {
|
|
|
+ $type_id = $matches[1];
|
|
|
+ $index = $matches[2];
|
|
|
+ $name = $properties_list[$type_id];
|
|
|
+ $properties[$name][$index] = trim($value);
|
|
|
+ }
|
|
|
+ if (preg_match('/^prop_value-(\d+)-(\d+)/', $name, $matches)) {
|
|
|
+ $type_id = $matches[1];
|
|
|
+ $index = $matches[2];
|
|
|
+ $name = $properties_list[$type_id];
|
|
|
+ $properties[$name][$index] = trim($value);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if (property_exists($node, 'new_id') and $node->new_id and property_exists($node, 'new_value') and $node->new_value) {
|
|
|
+ $type_id = $node->new_id;
|
|
|
+ $name = $properties_list[$type_id];
|
|
|
+ $index = 0;
|
|
|
+ if (array_key_exists($name, $properties)) {
|
|
|
+ $index = count($properties[$name]);
|
|
|
+ }
|
|
|
+ $properties[$name][$index] = trim($node->new_value);
|
|
|
+ }
|
|
|
+
|
|
|
+ return $properties;
|
|
|
+}
|
Stephen Ficklin