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@@ -19,7 +19,7 @@
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// form elements (e.g. buttons) and the form is being rebuilt but has not yet
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// been validated
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//
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- // The properties elements added by this function do use AJAX calls from buttons,
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+ // The reference elements added by this function do use AJAX calls from buttons,
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// therefore, it is important to check for form values in the $form_state['values']
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// for case #2 above, and in the $form_state['input'] for case #3.
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// See the chado analysis node form for an example.
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@@ -27,68 +27,21 @@
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// Next, add in all the form array definition particular to your node type
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- // To add in the properties form elements, you first need to prepare the arguments
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- // for the function call. One inportant argument is a list of properties that
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- // will be made avaialble for the user to select from. You should query the
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- // database to retrieve the applicable terms from the cvterm table and store them in an array
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- // of where the cvterm.cvterm_id field is the key and the cvterm.name is the value.
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- // these terms should all be from the same vocabulary.
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- $properties = array();
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- $properties[] = 'Select a Property';
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- $sql = "
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- SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
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- FROM {cvterm} CVT
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- INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
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- WHERE
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- CV.name = :ontology_name AND
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- NOT CVT.is_obsolete = 1
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- ORDER BY CVT.name ASC
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- ";
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-
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- $ontology_name = 'name_of_proptype_ontology'; //you need to set this variable with the cv.name of the ontology governing your prop tables type_id
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- $prop_types = chado_query($sql, array(':ontology_name' => $ontology_name));
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- while ($prop = $prop_types->fetchObject()) {
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- $properties[$prop->cvterm_id] = $prop->name;
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- }
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+ // To add in the chado properties form elements, you first need to prepare the arguments
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+ // for the function call.
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- // the properties form will add a select dropdown of terms containing the items in the $properties array
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- // constructed above, but it will also pre-populate rows of properties that already are associated
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- // with the object. If you would like to pre-populated properties regardless if they exist in the database
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- // or not, you can create an $include array which has the following format:
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- // array(
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- // array('cvterm' => $obj1, 'value' => $val1),
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- // array('cvterm' => $obj2, 'value' => $val2),
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- // ... etc
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- // );
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- // The 'cvterm' key should have as a value an object with these properties: 'name', 'cvterm_id', 'definition'.
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- $include = array();
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-
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- // sometimes a property exists in the database and is properly associated with the object, but we do
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- // not want it to appear in the list of properties that are pre-populated. It may be handled in some
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- // other way. For example, for contacts, the description field is stored as a property because
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- // the actual contact.description field is only 255 characters. The 'contact_description' property 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. This array holds the value of the cvterm.name column of the cvterms
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- // to exclude
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- $exclude = array();
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-
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- // the instructions argument provides additional instructions to the user beyond the default instructions.
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- $instructions = t('To add additional properties to the drop down. ' . l("Add terms to the $ontology_name vocabulary", "admin/tripal/chado/tripal_cv/cvterm/add") . ".");
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-
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- // Finally, and add the properties form elements to the form
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- tripal_core_properties_form(
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- $form, $form_state, // form and form_state of the current form
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- 'exampleprop', // properties table name
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- 'example_id', // key to link to the chado content created by this node
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- $ontology_name, // name of ontology governing your prop table type_id column
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- $properties, // an array of properties to use in the drop-down
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- $example_id, // the value of the above key
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- $exclude, // elements from the ontology you don't want to be available as property types
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- $include, // additional elements not in the ontology that you do what in the drop-down
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- $instructions, // form specific instructions
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- 'Properties' // name of the fieldset
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+ $details = array(
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+ 'property_table' => 'example_property', // the name of the table linking additional properties to this node
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+ 'base_foreign_key' => 'example_id', // key to link to the chado content created by this node
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+ 'base_key_value' => $example_id, // the value of the above key
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+ 'cv_name' => 'example_prop_cv', // the name of the cv governing the _prop.type_id
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+ 'fieldset_title' => 'Additional References', // the non-translated title for this fieldset
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+ 'additional_instructions' => '' // a non-stranslated string providing additional instructions
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);
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+ // Finally, and add the additional form elements to the form
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+ tripal_api_chado_node_properties_form($form, $form_state, $details);
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+
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return $form;
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}
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@@ -103,37 +56,15 @@
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// Add to any other tables needed
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- // Add each property (exampleprop table). The tripal_core_properties_form_retrieve()
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- // function retrieves all of the properties and returns them in an array of the format:
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- //
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- // $properties[<property name>][<rank>] = <value
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- //
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- // This array can then be used for inserting or updating properties using the API call
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- // tripal_hook_insert_property()
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- //
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- // example_property = controlled vocab name for exampleprop.type_id
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- $properties = tripal_core_properties_form_retreive($node, 'example_property');
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- foreach ($properties as $property => $elements) {
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- foreach ($elements as $rank => $value) {
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-
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- $success = tripal_core_insert_property(
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- 'example', //base table name
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- $example_id, // key to link to the chado content created by this node
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- $property, // cvterm.name of the property to be added
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- $ontology_name, // name of the ontology the cvterm is from
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- $value // the value o the property
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- );
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-
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- if (!$success) {
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- watchdog(
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- 'tripal_example',
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- 'Example Update: Unable to insert property %cvterm %value.',
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- array('%cvterm' => $property, '%value' => $value),
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- WATCHDOG_ERROR
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- );
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- }
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- }
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- }
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+ // Add all properties
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+ // Existing _property links will be cleared and then re-added
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+ tripal_api_chado_node_properties_form_update_properties(
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+ $node, // the node object passed in via hook_insert()
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+ 'example_property', // the name of the _property linking table
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+ 'example', // the name of the base chado table for the node
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+ 'example_id', // key to link to the chado content created by this node
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+ $node->example_id // value of the above key
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+ );
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}
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// Add record to chado_example linking example_id to new node
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@@ -147,38 +78,16 @@
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// Update any other tables needed
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- // First delete any existing properties
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- tripal_core_chado_delete(
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- 'exampleprop', // the name of the prop table
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- array('example_id' => $example_id) // name of your key and the current value used to determine which to delete
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+ // Update all properties
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+ // Existing _property links will be cleared and then re-added
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+ tripal_api_chado_node_properties_form_update_properties(
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+ $node, // the node object passed in via hook_insert()
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+ 'example_property', // the name of the _property linking table
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+ 'example', // the name of the base chado table for the node
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+ 'example_id', // key to link to the chado content created by this node
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+ $node->example_id // value of the above key
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);
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- // Add each property (exampleprop table)
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- // example_property = controlled vocab name for exampleprop.type_id
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- $properties = tripal_core_properties_form_retreive($node, 'example_property');
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- foreach ($properties as $property => $elements) {
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- foreach ($elements as $rank => $value) {
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-
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- $success = tripal_core_insert_property(
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- 'example', //base table name
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- $example_id, // key to link to the chado content created by this node
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- $property, // cvterm.name of the property to be added
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- $ontology_name, // name of the ontology the cvterm is from
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- $value // the value o the property
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- );
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-
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- if (!$success) {
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- watchdog(
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- 'tripal_example',
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- 'Example Update: Unable to insert property %cvterm %value.',
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- array('%cvterm' => $property, '%value' => $value),
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- WATCHDOG_ERROR
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- );
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- }
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- }
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- }
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- }
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-
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// Don't need to update chado_example linking table since niether example_id or nid can be changed in update
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}
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@@ -514,3 +423,544 @@ function tripal_core_delete_property_by_id($basetable, $record_id) {
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return tripal_core_chado_delete($basetable . 'prop', $match);
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}
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+
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+/**
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+ * @section
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+ * Properties Form to be added to node forms
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+ */
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+
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+/**
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+ * Provides a form for adding to BASEprop table
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+ *
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+ * @param $form
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+ * The Drupal form array into which the property form 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 $details
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+ * An array defining details needed by this form. Required Keys are:
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+ * - property_table: the name of the property linking table (ie: featureprop)
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+ * - base_foreign_key: the name of the foreign key linking this table to the non-property table (ie: feature_id)
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+ * - base_key_value: the value of the base_foreign_key for the current form (ie: 999 if the feature_id=999)
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+ * Require ONE of the following:
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+ * The controlled vocabulary governing the property types
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+ * -cv_id: the unique key from the cv table
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+ * -cv_name: the cv.name field uniquely identifying the controlled vocab
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+ * Optional keys include:
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+ * - fieldset_title: the non-translated title for this fieldset
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+ * - additional_instructions: a non-translated string providing additional instructions
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+ */
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+function chado_node_properties_form(&$form, &$form_state, $details) {
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+
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+ // Set Defaults for optional fields
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+ $details['fieldset_title'] = 'Properties';
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+ $details['additional_instructions'] = '';
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+
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+ // Get Property Types for the Select List
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+ if (isset($details['cv_name'])) {
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+ $property_options = array();
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+ $property_options[] = 'Select a Property';
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+ $sql = "
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+ SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
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+ FROM {cvterm} CVT
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+ INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
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+ WHERE
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+ CV.name = :cv_name AND
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+ NOT CVT.is_obsolete = 1
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+ ORDER BY CVT.name ASC
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+ ";
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+ $prop_types = chado_query($sql, array(':cv_name' => $details['cv_name']));
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+ while ($prop = $prop_types->fetchObject()) {
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+ $property_options[$prop->cvterm_id] = $prop->name;
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+ }
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+ } elseif (isset($details['cv_id'])) {
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+ $property_options = array();
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+ $property_options[] = 'Select a Property';
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+ $sql = "
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+ SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
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+ FROM {cvterm} CVT
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+ INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
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+ WHERE
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+ CV.cv_id = :cv_id AND
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+ NOT CVT.is_obsolete = 1
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+ ORDER BY CVT.name ASC
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+ ";
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+ $prop_types = chado_query($sql, array(':cv_id' => $details['cv_id']));
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+ while ($prop = $prop_types->fetchObject()) {
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+ $property_options[$prop->cvterm_id] = $prop->name;
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+ }
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+ }
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+
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+ // the fieldset of the property elements
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+ $form['properties'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t($details['fieldset_title']),
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+ '#description' => t('You may add additional properties by selecting a property type
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+ from the dropdown and adding text. You may add as many properties as desired by
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+ clicking the add button on the right. To remove a property, click the remove button.
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+ To add additional properties to the drop down. ' . $details['additional_instructions']),
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+ '#prefix' => "<div id='properties-fieldset'>",
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+ '#suffix' => '</div>'
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+ );
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+
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+ // this form element is a tree, so that we don't puke all of the values into then node variable
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+ // it is set as a tree, and keeps them in the $form_state['values']['property_table'] heading.
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+ $form['properties']['property_table'] = array(
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+ '#type' => 'markup',
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+ '#tree' => TRUE,
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+ '#prefix' => '<div id="tripal-generic-edit-properties-table">',
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+ '#suffix' => '</div>',
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+ '#theme' => 'chado_node_properties_form_table'
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+ );
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+
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+ // Add defaults into form_state to be used elsewhere
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+ $form['properties']['property_table']['details'] = array(
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+ '#type' => 'hidden',
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+ '#value' => serialize($details)
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+ );
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+
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+ /* Properties can come to us in two ways:
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+ *
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+ * 1) In the form state in the $form_state['chado_properties']. Data is in this field
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+ * when an AJAX call updates the form state or a validation error.
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+ *
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+ * 2) Directly from the database if the record already has properties associated. This
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+ * data is only used the first time the form is loaded. On AJAX calls or validation
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+ * errors the fields on the form are populated from the $form_state['chado_properties']
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+ * entry.
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+ */
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+ if (isset($form_state['chado_properties'])) {
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+ $existing_properties = $form_state['chado_properties'];
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+ }
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+ else {
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+ if (isset($details['cv_name'])) {
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+ $existing_properties = chado_query(
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+ "SELECT CVT.cvterm_id, CVT.name as type_name, CVT.definition, PP.value, PP.rank
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+ FROM {" . $details['property_table'] . "} PP
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+ INNER JOIN {cvterm} CVT ON CVT.cvterm_id = PP.type_id
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+ INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
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+ WHERE
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+ PP." . $details['base_foreign_key'] . " = :base_key_value AND
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+ CV.name = '" .$details['cv_name']. "'
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+ ORDER BY CVT.name, PP.rank",
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+ array(':base_key_value' => $details['base_key_value'])
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+ );
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+ } elseif (isset($details['cv_id'])) {
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+ $existing_properties = chado_query(
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+ "SELECT PP.".$details['property_table']."_id property_id, CVT.cvterm_id as type_id, CVT.name as type_name, CVT.definition, PP.value, PP.rank
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+ FROM {" . $details['property_table'] . "} PP
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+ INNER JOIN {cvterm} CVT ON CVT.cvterm_id = PP.type_id
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+ INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
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+ WHERE
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+ PP." . $details['base_foreign_key'] . " = :base_key_value AND
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+ CV.cv_id = '" .$details['cv_id']. "'
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+ ORDER BY CVT.name, PP.rank",
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+ array(':base_key_value' => $details['base_key_value'])
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+ );
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+ }
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+ }
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+
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+ /* The format of the $existing_properties array is either:
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+ *
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+ * From the chado_properties array:
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+ * $form_state['chado_properties'] = array(
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+ * '[type_id]-[rank]' => array(
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+ * 'type_id' => [the cvterm.cvterm_id value]
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+ * 'type_name' => [the cvterm.name value]
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+ * 'property_id' => [the property.property_id value, or NULL if it doesn't yet exist],
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+ * 'value' => [the BASEprop.value value],
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+ * 'rank' => [the BASEprop.rank value],
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+ * ),
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+ * );
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+ *
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+ * OR
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+ * Populated from the database:
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+ * $existing_property = array(
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+ * 0 => array(
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+ * 'property_id' => [the property.property_id value, or NULL if it doesn't yet exist],
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+ * 'type_id' => [the cvterm.cvterm_id value]
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+ * 'type_name' => [the cvterm.name value]
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+ * 'value' => [the BASEprop.value value],
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+ * 'rank' => [the BASEprop.rank value],
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+ * ),
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+ * );
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+ *
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+ * NOTE: The main difference is the key
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+ *
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+ * Loop on the array elements of the $existing_properties array and add
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+ * an element to the form for each one.
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+ */
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+ foreach ($existing_properties as $property) {
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+
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+ $form['properties']['property_table'][$property->type_id]['#type'] = 'markup';
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+ $form['properties']['property_table'][$property->type_id]['#value'] = '';
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+
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+ $form['properties']['property_table'][$property->type_id][$property->rank]['#type'] = 'markup';
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+ $form['properties']['property_table'][$property->type_id][$property->rank]['#value'] = '';
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|
+
|
|
|
+ $form['properties']['property_table'][$property->type_id][$property->rank]['prop_type_id'] = array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $property->type_id
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['property_table'][$property->type_id][$property->rank]['prop_value'] = array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $property->value
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['property_table'][$property->type_id][$property->rank]['property_id'] = array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $property->property_id
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['property_table'][$property->type_id][$property->rank]['type'] = array(
|
|
|
+ '#type' => 'markup',
|
|
|
+ '#markup' => $property->type_name
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['property_table'][$property->type_id][$property->rank]['value'] = array(
|
|
|
+ '#type' => 'markup',
|
|
|
+ '#markup' => $property->value
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['property_table'][$property->type_id][$property->rank]['rank'] = array(
|
|
|
+ '#type' => 'markup',
|
|
|
+ '#markup' => $property->rank
|
|
|
+ );
|
|
|
+ // remove button
|
|
|
+ $form['properties']['property_table'][$property->type_id][$property->rank]['property_action'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => t('Remove'),
|
|
|
+ '#name' => "property_remove-".$property->type_id.'-'.$property->rank,
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "chado_node_properties_form_ajax_update",
|
|
|
+ 'wrapper' => 'tripal-generic-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 node form submit. In the validate function we validate only the
|
|
|
+ // property fields and in the submit we remove the indicated property
|
|
|
+ // from the chado_properties array. In order to keep validate errors
|
|
|
+ // from the node form validate and Drupal required errors for non-property fields
|
|
|
+ // preventing the user from removing properties we set the #limit_validation_errors below
|
|
|
+ '#validate' => array('chado_node_properties_form_remove_button_validate'),
|
|
|
+ '#submit' => array('chado_node_properties_form_remove_button_submit'),
|
|
|
+ // Limit the validation of the form upon clicking this button to the property_table tree
|
|
|
+ // No other fields will be validated (ie: no fields from the main form or any other api
|
|
|
+ // added form).
|
|
|
+ '#limit_validation_errors' => array(
|
|
|
+ array('property_table') // Validate all fields within $form_state['values']['property_table']
|
|
|
+ )
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+ // Form elements for adding a new property
|
|
|
+ //---------------------------------------------
|
|
|
+ $form['properties']['property_table']['new'] = array(
|
|
|
+ '#type' => 'markup',
|
|
|
+ '#prefix' => '<span class="addtl-properties-add-new-property">',
|
|
|
+ '#suffix' => '</span>'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['property_table']['new']['type'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#options' => $property_options, // Set at top of form
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['property_table']['new']['value'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ );
|
|
|
+
|
|
|
+ // add button
|
|
|
+ $form['properties']['property_table']['new']['property_action'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => t('Add'),
|
|
|
+ '#name' => "property-add",
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "chado_node_properties_form_ajax_update",
|
|
|
+ 'wrapper' => 'tripal-generic-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 node form submit. In the validate function we validate only the
|
|
|
+ // additional property fields and in the submit we add them to the chado_properties
|
|
|
+ // array. In order to keep validate errors from the node form validate and Drupal
|
|
|
+ // required errors for non-property fields preventing the user from adding properties we
|
|
|
+ // set the #limit_validation_errors below
|
|
|
+ '#validate' => array('chado_node_properties_form_add_button_validate'),
|
|
|
+ '#submit' => array('chado_node_properties_form_add_button_submit'),
|
|
|
+ // Limit the validation of the form upon clicking this button to the property_table tree
|
|
|
+ // No other fields will be validated (ie: no fields from the main form or any other api
|
|
|
+ // added form).
|
|
|
+ '#limit_validation_errors' => array(
|
|
|
+ array('property_table') // Validate all fields within $form_state['values']['property_table']
|
|
|
+ )
|
|
|
+ );
|
|
|
+
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Validate the user input for creating a new property
|
|
|
+ * Called by the add button in chado_node_properties_form
|
|
|
+ */
|
|
|
+function chado_node_properties_form_add_button_validate($form, &$form_state) {
|
|
|
+
|
|
|
+ // Ensure the type_id is supplied & Valid
|
|
|
+ $cvterm = tripal_core_chado_select(
|
|
|
+ 'cvterm',
|
|
|
+ array('cvterm_id', 'name'),
|
|
|
+ array('cvterm_id' => $form_state['values']['property_table']['new']['type'])
|
|
|
+ );
|
|
|
+ if (!isset($cvterm[0])) {
|
|
|
+ form_set_error('property_table][new][cvterm', 'Please select a property type before attempting to add a new property.');
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $form_state['values']['property_table']['new']['type_name'] = $cvterm[0]->name;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Ensure value is supplied
|
|
|
+ if (empty($form_state['values']['property_table']['new']['value'])) {
|
|
|
+ form_set_error('property_table][new][value','You must enter the property value before attempting to add a new property.');
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Called by the add button in chado_node_properties_form
|
|
|
+ *
|
|
|
+ * Create an array of properties in the form state. This array will then be
|
|
|
+ * used to rebuild the form in subsequent builds
|
|
|
+ */
|
|
|
+function chado_node_properties_form_add_button_submit(&$form, &$form_state) {
|
|
|
+
|
|
|
+ $details = unserialize($form_state['values']['property_table']['details']);
|
|
|
+
|
|
|
+ // if the chado_additional_properties array is not set then this is the first time modifying the
|
|
|
+ // property table. this means we need to include all the properties from the db
|
|
|
+ if (!isset($form_state['chado_properties'])) {
|
|
|
+ chado_node_properties_form_create_property_formstate_array($form, $form_state);
|
|
|
+ }
|
|
|
+
|
|
|
+ // get details for the new property
|
|
|
+ $property = array(
|
|
|
+ 'type_id' => $form_state['values']['property_table']['new']['type'],
|
|
|
+ 'type_name' => $form_state['values']['property_table']['new']['type_name'],
|
|
|
+ 'property_id' => NULL,
|
|
|
+ 'value' => $form_state['values']['property_table']['new']['value'],
|
|
|
+ 'rank' => '0',
|
|
|
+ );
|
|
|
+
|
|
|
+ // get max rank
|
|
|
+ $rank = tripal_core_get_max_chado_rank(
|
|
|
+ $details['property_table'],
|
|
|
+ array(
|
|
|
+ $details['base_foreign_key'] => $details['base_key_value'],
|
|
|
+ 'type_id' => $property['type_id']
|
|
|
+ )
|
|
|
+ );
|
|
|
+ $property['rank'] = strval($rank + 1);
|
|
|
+
|
|
|
+ $key = $property['type_id'] . '-' . $property['rank'];
|
|
|
+ $form_state['chado_properties'][$key] = (object) $property;
|
|
|
+
|
|
|
+ $form_state['rebuild'] = TRUE;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * There is no user input for the remove buttons so there is no need to validate
|
|
|
+ * However, both a submit & validate need to be specified so this is just a placeholder
|
|
|
+ *
|
|
|
+ * Called by the many remove buttons in chado_node_properties_form
|
|
|
+ */
|
|
|
+function chado_node_properties_form_remove_button_validate($form, $form_state) {
|
|
|
+ // No Validation needed for remove
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Remove the correct property from the form
|
|
|
+ * Called by the many remove buttons in chado_node_properties_form
|
|
|
+ */
|
|
|
+function chado_node_properties_form_remove_button_submit(&$form, &$form_state) {
|
|
|
+
|
|
|
+ // if the chado_properties array is not set then this is the first time modifying the
|
|
|
+ // property table. this means we need to include all the properties from the db
|
|
|
+ if (!isset($form_state['chado_properties'])) {
|
|
|
+ chado_node_properties_form_create_property_formstate_array($form, $form_state);
|
|
|
+ }
|
|
|
+
|
|
|
+ // remove the specified property from the form property table
|
|
|
+ if(preg_match('/property_remove-([^-]+-[^-]+)/',$form_state['triggering_element']['#name'],$match)) {
|
|
|
+ $key = $match[1];
|
|
|
+ if (array_key_exists($key, $form_state['chado_properties'])) {
|
|
|
+ unset($form_state['chado_properties'][$key]);
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ $form_state['rebuild'] = TRUE;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Ajax function which returns the section of the form to be re-rendered
|
|
|
+ */
|
|
|
+function chado_node_properties_form_ajax_update($form, $form_state) {
|
|
|
+ return $form['properties']['property_table'];
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Creates an array in form_state containing the existing properties. This array is
|
|
|
+ * then modified by the add/remove buttons and used as a source for rebuilding the form.
|
|
|
+ * This function get's called at each button (add and remove) button submits the first
|
|
|
+ * time one of the button's is clicked to instantiates the $form_state['chado_properties'] array
|
|
|
+ *
|
|
|
+ * $form_state['chado_properties'] = array(
|
|
|
+ * '[type_id]-[rank]' => array(
|
|
|
+ * 'type_id' => [the cvterm.cvterm_id value]
|
|
|
+ * 'type_name' => [the cvterm.name value]
|
|
|
+ * 'property_id' => [the property.property_id value, or NULL if it doesn't yet exist],
|
|
|
+ * 'value' => [the BASEprop.value value],
|
|
|
+ * 'rank' => [the BASEprop.rank value],
|
|
|
+ * ),
|
|
|
+ * );
|
|
|
+ */
|
|
|
+function chado_node_properties_form_create_property_formstate_array($form, &$form_state) {
|
|
|
+
|
|
|
+ $form_state['chado_properties'] = array();
|
|
|
+
|
|
|
+ foreach (element_children($form['properties']['property_table']) as $type_id) {
|
|
|
+ if ($type_id != 'new') {
|
|
|
+ foreach (element_children($form['properties']['property_table'][$type_id]) as $rank) {
|
|
|
+ $element = $form['properties']['property_table'][$type_id][$rank];
|
|
|
+ $property = array(
|
|
|
+ 'type_id' => $element['type_id']['#value'],
|
|
|
+ 'type_name' => $element['type']['#markup'],
|
|
|
+ 'property_id' => $element['property_id']['#value'],
|
|
|
+ 'value' => $element['value']['#markup'],
|
|
|
+ 'rank' => $element['rank']['#markup']
|
|
|
+ );
|
|
|
+ $key = $property['type_id'] . '-' . $property['rank'];
|
|
|
+ $form_state['chado_properties'][$key] = (object) $property;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Function to theme the add/remove properties form into a table
|
|
|
+ */
|
|
|
+function theme_chado_node_properties_form_table($variables) {
|
|
|
+ $element = $variables['element'];
|
|
|
+
|
|
|
+ $header = array(
|
|
|
+ 'type' => t('Type'),
|
|
|
+ 'value' => t('Value'),
|
|
|
+ 'rank' => t('Rank'),
|
|
|
+ 'property_action' => t('Actions'),
|
|
|
+ );
|
|
|
+
|
|
|
+ $rows = array();
|
|
|
+ foreach (element_children($element) as $type_id) {
|
|
|
+ if ($type_id == 'new') {
|
|
|
+ $row = array();
|
|
|
+
|
|
|
+ $row['data'] = array();
|
|
|
+ foreach ($header as $fieldname => $title) {
|
|
|
+ $row['data'][] = drupal_render($element[$type_id][$fieldname]);
|
|
|
+ }
|
|
|
+ $rows[] = $row;
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ foreach (element_children($element[$type_id]) as $version) {
|
|
|
+ $row = array();
|
|
|
+
|
|
|
+ $row['data'] = array();
|
|
|
+ foreach ($header as $fieldname => $title) {
|
|
|
+ $row['data'][] = drupal_render($element[$type_id][$version][$fieldname]);
|
|
|
+ }
|
|
|
+ $rows[] = $row;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ return theme('table', array(
|
|
|
+ 'header' => $header,
|
|
|
+ 'rows' => $rows
|
|
|
+ ));
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is used in a hook_insert, hook_update for a node form
|
|
|
+ * when the chado node properties form has been added to the form. It retrieves all of the properties
|
|
|
+ * and returns them in an array of the format:
|
|
|
+ *
|
|
|
+ * $dbxefs[<type_id>][<rank>] = <value>
|
|
|
+ *
|
|
|
+ * This array can then be used for inserting or updating properties
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A property array
|
|
|
+ *
|
|
|
+ * @ingroup tripal_properties_api
|
|
|
+ */
|
|
|
+function chado_node_properties_form_retreive($node) {
|
|
|
+ $properties = array();
|
|
|
+ foreach ($node->property_table as $type_id => $elements) {
|
|
|
+ if ($type_id != 'new' AND $type_id != 'details') {
|
|
|
+ foreach ($elements as $rank => $element) {
|
|
|
+ $properties[$type_id][$rank] = $element['prop_value'];
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ return $properties;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * This function is used in hook_insert or hook_update and handles inserting of any new
|
|
|
+ * properties
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * The node passed into hook_insert & hook_update
|
|
|
+ * @param $details
|
|
|
+ * - property_table: the name of the _property linking table (ie: feature_property)
|
|
|
+ * - base_table: the name of the base table (ie: feature)
|
|
|
+ * - foreignkey_name: the name of the foreign key used to link to the node content (ie: feature_id)
|
|
|
+ * - foreignkey_value: the value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
|
|
|
+ */
|
|
|
+function chado_node_properties_form_update_properties($node, $details) {
|
|
|
+
|
|
|
+ // First remove existing property links
|
|
|
+ tripal_core_chado_delete($details['property_table'], array($details['foreignkey_name'] => $details['foreignkey_value']));
|
|
|
+
|
|
|
+ // Add back in property links and insert properties as needed
|
|
|
+ $properties = chado_node_properties_form_retreive($node);
|
|
|
+ foreach ($properties as $type_id => $ranks) {
|
|
|
+ foreach ($ranks as $rank => $value) {
|
|
|
+
|
|
|
+ $success = tripal_core_chado_insert(
|
|
|
+ $details['property_table'],
|
|
|
+ array(
|
|
|
+ $details['foreignkey_name'] => $details['foreignkey_value'],
|
|
|
+ 'type_id' => $type_id,
|
|
|
+ 'value' => $value,
|
|
|
+ 'rank' => $rank
|
|
|
+ )
|
|
|
+ );
|
|
|
+
|
|
|
+ if (!$success) {
|
|
|
+ watchdog(
|
|
|
+ 'tripal_' . $details['base_table'],
|
|
|
+ $details['base_table'] . ' Insert: Unable to insert property type_id %cvterm with value %value.',
|
|
|
+ array('%cvterm' => $type_id, '%value' => $value),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+ }
|
|
|
+ }
|
|
|
+}
|
Lacey Sanderson