'; $output .= 'All Relationships should include the CURRENT Individual (' . $node->uniquename . ')
'; $output .= '
Current Relationships
'; $output .= list_relationships_for_node($node->uniquename, $node->subject_relationships, $node->object_relationships); $output .= '

'; $output .= drupal_get_form('tripal_feature_add_ONE_relationship_form', $node); $output .= '
'; $output .= drupal_get_form('tripal_feature_implement_add_chado_properties_navigate', 'relationships', $node->nid); return $output; } /** * Implements Hook_form() * Handles adding of Relationships to Features * * @ingroup tripal_feature */ function tripal_feature_add_ONE_relationship_form($form_state, $node) { $feature_id = $node->feature_id; $organism_id = $node->organism->organism_id; $_SESSION['organism'] = $organism_id; //needed for autocomplete enter feature to work $form['rel_nid'] = array( '#type' => 'hidden', '#value' => $node->nid ); $form['add_relationships'] = array( '#type' => 'fieldset', '#title' => t('Add Relationships') . '(optional)', ); $form['add_relationships']['description'] = array( '#type' => 'item', '#value' => t('Relationships are specified as follows: (Subject) (Type of Relationship) (Object). For example, X part_of Y, where X & Y are genomic features.') ); $form['add_relationships']['subject_id'] = array( '#type' => 'textfield', '#title' => t('Subject'), '#description' => 'The Uniquename, Name, Database Reference or Synonym of a Feature can be used here', ); $cv = tripal_cv_get_cv_by_name('relationship'); $type_options = tripal_cv_get_cvterm_options($cv->cv_id); $type_options[0] = 'Select a Type'; ksort($type_options); $form['add_relationships']['type_id'] = array( '#type' => 'select', '#title' => t('Type of Relationship'), '#options' => $type_options ); $form['add_relationships']['object_id'] = array( '#type' => 'textfield', '#title' => t('Object'), '#description' => 'The Uniquename, Name, Database Reference or Synonym of a Feature can be used here', ); $form['add_relationships']['r_description'] = array( '#type' => 'textarea', '#title' => t('Notes on the relationship') . '+', '#description' => t('Should not include Genotypes and Phenotypes'), ); $form['add_relationships']['submit'] = array( '#type' => 'submit', '#value' => t('Add a Relationship') ); $form['add_relationships']['r_feature_id'] = array( '#type' => 'value', '#value' => $feature_id, '#required' => TRUE ); $form['add_relationships']['r_feature_uniquename'] = array( '#type' => 'value', '#value' => $node->uniquename, '#required' => TRUE ); return $form; } /** * * * @ingroup tripal_feature */ function tripal_feature_add_ONE_relationship_form_validate($form, &$form_state) { //Require Validation if adding if ($form_state['clicked_button']['#value'] == t('Add a Relationship') ) { // check valid feature selected for subject $criteria = array('unknown' => array('value' => $form_state['values']['subject_id'], 'columns' => array('name', 'uniquename', 'accession', 'synonym') )); $subject_results = get_chado_stocks($criteria, 'ANY', $_SESSION['organism']); if (sizeof($subject_results) > 1) { $links= array(); for ($i=0; $inid); } $message = t("Too many features match '%object'! Please refine your input to match ONLY ONE feature.
To aid in this process, here are the features that match your initial input: %features", array('%object' => $form_state['values']['subject_id'], '%features' => join(', ', $links) ) ); form_set_error('subject_id', $message); } elseif (sizeof($subject_results) < 1) { form_set_error('subject_id', t("There are no features matching your input. Please check your input for typos and/or lookup the feature here", array('!url' => url('features')))); } elseif (sizeof($subject_results) == 1) { $form_state['values']['subject_id'] = $subject_results[0]->stock_id; } // check valid stock selected for object $criteria = array('unknown' => array('value' => $form_state['values']['object_id'], 'columns' => array('name', 'uniquename', 'accession', 'synonym') )); $object_results = get_chado_stocks($criteria, 'ANY', $_SESSION['organism']); if (sizeof($object_results) > 1) { $links= array(); for ($i=0; $inid); } $message = t("Too many features match '%object'! Please refine your input to match ONLY ONE stock.
To aid in this process, here are the stocks that match your initial input: %features", array('%object' => $form_state['values']['object_id'], '%features' => join(', ', $links) ) ); form_set_error('object_id', $message); } elseif (sizeof($object_results) < 1) { form_set_error('object_id', t("There are no features matching your input. Please check your input for typos and/or lookup the feature here", array('!url' => url('features')))); } elseif (sizeof($object_results) == 1) { $form_state['values']['object_id'] = $object_results[0]->stock_id; } // check valid type selected if ($form_state['values']['type_id'] == 0) { form_set_error('type_id', 'Please select a type of relationship.'); } else { $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']['type_id'])); if ($tmp_obj->count != 1) { form_set_error('type_id', 'The type you selected is not valid. Please choose another one.'); } } // check either subject or object is the current stock if ( $subject_results[0]->nid != $form_state['values']['rel_nid'] ) { if ( $object_results[0]->nid != $form_state['values']['rel_nid'] ) { form_set_error('subject_id', 'Either Subject or Object must be the current stock (' . $form_state['values']['r_stock_uniquename'] . ').'); } } } //end of require validation if adding relationship } /** * * * @ingroup tripal_feature */ function tripal_feature_add_ONE_relationship_form_submit($form, &$form_state) { if ($form_state['values']['subject_id'] > 0) { $previous_db = db_set_active('chado'); db_query( "INSERT INTO {stock_relationship} (subject_id, type_id, object_id, value) VALUES (%d, %d, %d, '%s')", $form_state['values']['subject_id'], $form_state['values']['type_id'], $form_state['values']['object_id'], $form_state['values']['r_description'] ); db_set_active($previous_db); drupal_set_message(t('Successfully Added Relationship.')); } //end of insert relationship } /** * * * @ingroup tripal_feature */ function tripal_feature_edit_ALL_relationships_page($node) { $output = ''; $output .= drupal_get_form('tripal_feature_edit_ALL_relationships_form', $node); $output .= '
'; $output .= drupal_get_form('tripal_feature_add_ONE_relationship_form', $node); $output .= '
'; $output .= drupal_get_form('tripal_feature_implement_back_to_feature_button', $node->nid); return $output; } /** * Implements Hook_form() * Handles adding of Properties & Synonyms to Stocks * * @ingroup tripal_feature */ function tripal_feature_edit_ALL_relationships_form($form_state, $node) { $form = array(); $form['nid'] = array( '#type' => 'hidden', '#value' => $node->nid ); $form['r_feature_uniquename'] = array( '#type' => 'hidden', '#value' => $node->uniquename ); $i=0; $feature = $node->feature; $orelationships = tripal_feature_load_relationships($feature->feature_id, 'as_object'); $srelationships = tripal_feature_load_relationships($feature->feature_id, 'as_subject'); $relationships = array_merge($orelationships, $srelationships); if (sizeof($relationships) != 0) { foreach ($relationships as $r) { $i++; $form["num-$i"] = array( '#type' => 'fieldset', '#title' => t("Relationship %i", array('%i' => $i)), ); $form["num-$i"]["id-$i"] = array( '#type' => 'hidden', '#value' => $r->stock_relationship_id ); //Enter relationship specific fields if ( !empty($r->subject_id) ) { $default = $r->subject_uniquename; $description = l($r->subject_name, 'node/' . $r->subject_nid); } else { $default = $node->uniquename; $description = "Current Feature"; } $description .= " (" . $r->subject_type . ")"; $form["num-$i"]["subject_id-$i"] = array( '#type' => 'textfield', //'#title' => t('Subject'), '#required' => TRUE, '#size' => 30, '#default_value' => $default, '#description' => t('%description', array('%description' => $description)), ); $cv = tripal_cv_get_cv_by_name('relationship'); $type_options = tripal_cv_get_cvterm_options($cv->cv_id); ksort($type_options); $form["num-$i"]["type_id-$i"] = array( '#type' => 'select', //'#title' => t('Type of Relationship'), '#options' => $type_options, '#required' => TRUE, '#default_value' => $r->relationship_type_id ); if (!empty($r->object_id) ) { $default = $r->object_uniquename; $description = l($r->object_name, 'node/' . $r->object_nid); } else { $default = $node->uniquename; $description = 'Current Feature'; } $description .= " (" . $r->object_type . ")"; $form["num-$i"]["object_id-$i"] = array( '#type' => 'textfield', //'#title' => t('Object'), '#required' => TRUE, '#size' => 30, '#default_value' => $default, '#description' => $description ); $form["num-$i"]["delete-$i"] = array( '#type' => 'submit', '#value' => t("Delete"), '#name' => "delete-$i", ); } //end of foreach relationship $form['num_relationships'] = array( '#type' => 'hidden', '#value' => $i ); $form["submit-edits"] = array( '#type' => 'submit', '#value' => t('Update All Relationships') ); } else { $form["info"] = array( '#type' => 'markup', '#value' => t('No relationships currently exist for this feature.') ); } return $form; } /** * * * @ingroup tripal_feature */ function tripal_feature_edit_ALL_relationships_form_validate($form, &$form_state) { // Only Require if Updating Relationships if ($form_state['clicked_button']['#value'] == t('Update All Relationships') ) { for ($i=1; $i<=$form_state['values']['num_relationships']; $i++) { // check valid stock selected for subject $criteria = array('unknown' => array('value' => $form_state['values']["subject_id-$i"], 'columns' => array('name', 'uniquename', 'accession', 'synonym') )); $subject_results = get_chado_stocks($criteria, 'ANY', $_SESSION['organism']); if (sizeof($subject_results) > 1) { $links= array(); for ($j=0; $jnid); } $message = t("Too many features match '%subject'! Please refine your input to match ONLY ONE feature.
To aid in this process, here are the features that match your initial input: %features", array('%subject' => $form_state['values']["subject_id-$i"], '%features' => join(', ', $links) ) ); form_set_error("subject_id-$i", $message); } elseif (sizeof($subject_results) < 1) { form_set_error("subject_id-$i", t("There are no features matching your input. Please check your input for typos and/or lookup the here", array('!url' => url('features')))); } elseif (sizeof($subject_results) == 1) { $form_state['values']["subject_id-$i"] = $subject_results[0]->stock_id; } // check valid stock selected for object $criteria = array('unknown' => array('value' => $form_state['values']["object_id-$i"], 'columns' => array('name', 'uniquename', 'accession', 'synonym') )); $object_results = get_chado_stocks($criteria, 'ANY' , $_SESSION['organism']); if (sizeof($object_results) > 1) { $links= array(); for ($j=0; $jnid); } $message = "Too many stocks match '" . $form_state['values']["object_id-$i"] . "'! " . "Please refine your input to match ONLY ONE stock.
" . "To aid in this process, here are the stocks that match your initial input: " . join(', ', $links); form_set_error("object_id-$i", $message); } elseif (sizeof($object_results) < 1) { form_set_error("object_id-$i", t("There are no features matching your input. Please check your input for typos and/or lookup the here", array('!url' => url('features')))); } elseif (sizeof($object_results) == 1) { $form_state['values']["object_id-$i"] = $object_results[0]->stock_id; } // check valid type selected if ($form_state['values']["type_id-$i"] == 0) { form_set_error('type_id', 'Please select a type of relationship.'); } else { $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d" , $form_state['values']["type_id-$i"])); if ($tmp_obj->count != 1) { form_set_error("type_id-$i", 'The type you selected is not valid. Please choose another one.'); } } // check either subject or object is the current stock if ( $subject_results[0]->nid != $form_state['values']['nid'] ) { if ( $object_results[0]->nid != $form_state['values']['nid'] ) { form_set_error("subject_id-$i", 'Either Subject or Object must be the current stock (' . $form_state['values']['r_stock_uniquename'] . ').'); } } } // end of for each relationship } //end of if updating relationships } /** * * * @ingroup tripal_feature */ function tripal_feature_edit_ALL_relationships_form_submit($form, &$form_state) { if ($form_state['clicked_button']['#value'] == t('Update Relationships') ) { //Update all for ($i=1; $i<=$form_state['values']['num_relationships']; $i++) { //process stock textfields tripal_feature_update_relationship( $form_state['values']["id-$i"], $form_state['values']["subject_id-$i"], $form_state['values']["type_id-$i"], $form_state['values']["object_id-$i"] ); } drupal_set_message(t("Updated all Relationships")); drupal_goto('node/' . $form_state['values']['nid']); } elseif ( preg_match('/Delete #(\d+)/', $form_state['clicked_button']['#value'], $matches) ) { $i = $matches[1]; tripal_feature_delete_relationship($form_state['values']["id-$i"]); drupal_set_message(t("Deleted Relationship")); } elseif ($form_state['clicked_button']['#value'] == t('Back to Stock') ) { drupal_goto('node/' . $form_state['values']['nid']); } else { drupal_set_message(t("Unrecognized Button Pressed"), 'error'); } } /** * * * @ingroup tripal_feature */ function tripal_feature_update_relationship($stock_relationship_id, $subject_id, $cvterm_id, $object_id) { $previous_db = db_set_active('chado'); db_query( "UPDATE {stock_relationship} SET subject_id=%d, type_id=%d, object_id=%d WHERE stock_relationship_id=%d", $subject_id, $cvterm_id, $object_id, $stock_relationship_id ); db_set_active($previous_db); } /** * * * @ingroup tripal_feature */ function tripal_feature_delete_relationship($stock_relationship_id) { $previous_db = db_set_active('chado'); db_query( "DELETE FROM {stock_relationship} WHERE stock_relationship_id=%d", $stock_relationship_id ); db_set_active($previous_db); } /** * * * @ingroup tripal_feature */ function theme_tripal_feature_edit_ALL_relationships_form($form) { $output = ''; $output .= '
'; $output .= 'Edit Already Existing Relationships(optional)'; $output .= '

Each relationship for this stock is listed below, one per line. The textboxes indicating ' .'the subject and object of the relationship can contain the uniquename, name, database ' .'reference or synonym of a stock of the same organism.

'; $output .= ''; $output .= ''; for ($i=1; $i <= $form['num_relationships']['#value']; $i++) { $output .= '' . '' . '' . '' . ''; } $output .= '
#SubjectTypeObject
' . drupal_render($form["num-$i"]) . '' . drupal_render($form["subject_id-$i"]) . '' . drupal_render($form["type_id-$i"]) . '' . drupal_render($form["object_id-$i"]) . '' . drupal_render($form["submit-$i"]) . '

'; $output .= drupal_render($form); $output .= '
'; return $output; } /** * * * @ingroup tripal_feature */ function tripal_feature_list_relationships_for_node($feature_name, $subject_relationships, $object_relationships) { if (!empty($subject_relationships) OR !empty($object_relationships) ) { $output = ''; $output .= ''; if (!empty($subject_relationships) ) { foreach ($subject_relationships as $s) { $output .= ''; } } if (!empty($object_relationships) ) { foreach ($object_relationships as $o) { $output .= ''; } // end of foreach property } $output .= '
SubjectRelationship TypeObject
' . $s->subject_name . '' . $s->relationship_type . '' . $feature_name . '
' . $feature_name . '' . $o->relationship_type . '' . $o->object_name . '
'; } else { $output = 'No Relationships For the Current Feature'; } return $output; }