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@@ -33,33 +33,132 @@ function tripal_cv_obo_form($form, &$form_state) {
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$results = db_query($sql);
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$obos = array();
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- $obos[] = '';
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+ $obos[] = 'Select a Vocabulary';
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foreach ($results as $obo) {
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-// $obos[$obo->obo_id] = "$obo->name | $obo->path";
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$obos[$obo->obo_id] = $obo->name;
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}
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- $form['obo_existing'] = array(
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+ $obo_id = '';
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+ if (array_key_exists('values', $form_state)) {
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+ $obo_id = array_key_exists('obo_id', $form_state['values']) ? $form_state['values']['obo_id'] : '';
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+ }
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+
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+ $form['instructions'] = array(
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'#type' => 'fieldset',
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- '#title' => t('Use a Saved Ontology OBO Reference')
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+ '#title' => 'instructions',
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+ '#collapsible' => TRUE,
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+ '#collapsed' => FALSE,
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+ );
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+ $form['instructions']['info'] = array(
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+ '#type' => 'item',
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+ '#markup' => t('This page allows you to load vocabularies and ontologies
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+ that are in OBO format. Once loaded, the terms from these
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+ vocabularies can be used to categorize data in the database.
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+ You may use the form below to either reload a vocabulary that is already
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+ loaded (as when new updates to that vocabulary are available) or load a new
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+ vocabulary.'),
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);
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- $form['obo_new'] = array(
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+ $form['obo_existing'] = array(
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'#type' => 'fieldset',
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- '#title' => t('Use a New Ontology OBO Reference')
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+ '#title' => t('Use a Saved Ontology OBO Reference'),
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+ '#prefix' => '<span id="obo-existing-fieldset">',
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+ '#suffix' => '</span>'
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);
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$form['obo_existing']['existing_instructions']= array(
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- '#value' => t('The Ontology OBO files listed in the drop down below have been automatically added upon
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- installation of the Tripal CV module or were added from a previous upload. Select
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- an OBO, then click the submit button to load the vocabulary into the database. If the
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- vocabularies already exist then the ontology will be updated.'),
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+ '#type' => 'item',
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+ '#markup' => t('The vocabularies listed in the select box below have bene pre-populated
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+ upon installation of Tripal or have been previously loaded. Select one to edit
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+ its settings or submit for loading. You may reload any vocabulary that has
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+ already been loaded to retrieve any new updates.'),
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);
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$form['obo_existing']['obo_id'] = array(
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'#title' => t('Ontology OBO File Reference'),
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'#type' => 'select',
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'#options' => $obos,
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+ '#ajax' => array(
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+ 'callback' => 'tripal_cv_obo_form_ajax_callback',
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+ 'wrapper' => 'obo-existing-fieldset',
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+ ),
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+ );
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+
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+ // If the user has selected an OBO ID then get the form elements for
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+ // updating.
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+ if ($obo_id) {
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+ $uobo_name = '';
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+ $uobo_url = '';
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+ $uobo_file = '';
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+
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+ $vocab = db_select('tripal_cv_obo', 't')
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+ ->fields('t', array('name', 'path'))
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+ ->condition('obo_id', $obo_id)
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+ ->execute()
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+ ->fetchObject();
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+ $uobo_name = $vocab->name;
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+ if (preg_match('/^http/', $vocab->path)) {
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+ $uobo_url = $vocab->path;
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+ }
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+ else {
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+ $uobo_file = trim($vocab->path);
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+ $matches = array();
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+ if (preg_match('/\{(.*?)\}/', $uobo_file, $matches)) {
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+ $modpath = drupal_get_path('module', $matches[1]);
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+ $uobo_file = '/' . preg_replace('/\{.*?\}/', $modpath, $uobo_file);
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+ }
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+ }
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+ // We don't want the previous value to remain. We want the new default to
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+ // show up, so remove the input values
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+ unset($form_state['input']['uobo_name']);
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+ unset($form_state['input']['uobo_url']);
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+ unset($form_state['input']['uobo_file']);
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+
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+ $form['obo_existing']['uobo_name']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Vocabulary Name'),
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+ '#description' => t('Please provide a name for this vocabulary. After upload, this name will appear in the drop down
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+ list above for use again later.'),
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+ '#default_value' => $uobo_name,
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+ );
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+
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+ $form['obo_existing']['uobo_url']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Remote URL'),
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+ '#description' => t('Please enter a URL for the online OBO file. The file will be downloaded and parsed.
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+ (e.g. http://www.obofoundry.org/ro/ro.obo'),
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+ '#default_value' => $uobo_url,
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+ );
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+
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+ $form['obo_existing']['uobo_file']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Local File'),
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+ '#description' => t('Please enter the file system path for an OBO
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+ definition file. If entering a path relative to
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+ the Drupal installation you may use a relative path that excludes the
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+ Drupal installation directory (e.g. sites/default/files/xyz.obo). Note
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+ that Drupal relative paths have no preceeding slash.
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+ Otherwise, please provide the full path on the filesystem. The path
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+ must be accessible to the web server on which this Drupal instance is running.'),
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+ '#default_value' => $uobo_file,
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+ );
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+ $form['obo_existing']['update_obo_details']= array(
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+ '#type' => 'submit',
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+ '#value' => 'Update Ontology Details',
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+ '#name' => 'update_obo_details'
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+ );
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+ $form['obo_existing']['update_load_obo']= array(
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+ '#type' => 'submit',
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+ '#value' => 'Load Vocabulary',
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+ '#name' => 'update_load_obo'
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+ );
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+ }
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+
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+ $form['obo_new'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Add a New Ontology OBO Reference'),
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+ '#collapsible' => TRUE,
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+ '#collapsed' => TRUE,
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);
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$form['obo_new']['path_instructions']= array(
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@@ -83,17 +182,21 @@ function tripal_cv_obo_form($form, &$form_state) {
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);
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$form['obo_new']['obo_file']= array(
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- '#type' => 'textfield',
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- '#title' => t('Local File'),
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- '#description' => t('Please enter the full system path for an OBO definition file, or a path within the Drupal
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- installation (e.g. /sites/default/files/xyz.obo). The path must be accessible to the
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- server on which this Drupal instance is running.'),
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+ '#type' => 'textfield',
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+ '#title' => t('Local File'),
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+ '#description' => t('Please enter the file system path for an OBO
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+ definition file. If entering a path relative to
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+ the Drupal installation you may use a relative path that excludes the
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+ Drupal installation directory (e.g. sites/default/files/xyz.obo). Note
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+ that Drupal relative paths have no preceeding slash.
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+ Otherwise, please provide the full path on the filesystem. The path
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+ must be accessible to the web server on which this Drupal instance is running.'),
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);
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- $form['submit'] = array(
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- '#type' => 'submit',
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- '#value' => t('Submit'),
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- '#executes_submit_callback' => TRUE,
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+ $form['obo_new']['add_new_obo'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Add this vocabulary'),
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+ '#name' => 'add_new_obo',
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);
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$form['#redirect'] = 'admin/tripal/tripal_cv/obo_loader';
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@@ -101,6 +204,72 @@ function tripal_cv_obo_form($form, &$form_state) {
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return $form;
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}
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+/**
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+ *
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+ * @param $form
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+ * @param $form_state
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+ */
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+function tripal_cv_obo_form_validate($form, &$form_state) {
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+ $obo_id = $form_state['values']['obo_id'];
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+ $obo_name = trim($form_state['values']['obo_name']);
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+ $obo_url = trim($form_state['values']['obo_url']);
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+ $obo_file = trim($form_state['values']['obo_file']);
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+ $uobo_name = array_key_exists('uobo_name', $form_state['values']) ? trim($form_state['values']['uobo_name']) : '';
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+ $uobo_url = array_key_exists('uobo_url', $form_state['values']) ? trim($form_state['values']['uobo_url']) : '';
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+ $uobo_file = array_key_exists('uobo_file', $form_state['values']) ? trim($form_state['values']['uobo_file']) : '';
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+
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+ // Make sure if the name is changed it doesn't conflict with another OBO.
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+ if ($form_state['clicked_button']['#name'] == 'update_obo_details' or
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+ $form_state['clicked_button']['#name'] == 'update_load_obo') {
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+ // Get the current record
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+ $vocab = db_select('tripal_cv_obo', 't')
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+ ->fields('t', array('obo_id', 'name', 'path'))
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+ ->condition('name', $uobo_name)
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+ ->execute()
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+ ->fetchObject();
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+ if ($vocab and $vocab->obo_id != $obo_id) {
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+ form_set_error('uobo_name', 'The vocabulary name must be different from existing vocabularies');
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+ }
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+ // Make sure the file exists. First check if it is a relative path
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+ $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $uobo_file;
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+ if (!file_exists($dfile)) {
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+ if (!file_exists($uobo_file)) {
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+ form_set_error('uobo_file', 'The specified path does not exist or cannot be read.');
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+ }
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+ }
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+ if (!$uobo_url and !$uobo_file) {
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+ form_set_error('uobo_url', 'Please provide a URL or a path for the vocabulary.');
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+ }
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+ if ($uobo_url and $uobo_file) {
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+ form_set_error('uobo_url', 'Please provide only a URL or a path for the vocabulary, but not both.');
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+ }
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+ }
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+ if ($form_state['clicked_button']['#name'] == 'add_new_obo') {
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+ // Get the current record
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+ $vocab = db_select('tripal_cv_obo', 't')
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+ ->fields('t', array('obo_id', 'name', 'path'))
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+ ->condition('name', $obo_name)
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+ ->execute()
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+ ->fetchObject();
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+ if ($vocab) {
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+ form_set_error('obo_name', 'The vocabulary name must be different from existing vocabularies');
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+ }
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+ // Make sure the file exists. First check if it is a relative path
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+ $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $obo_file;
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+ if (!file_exists($dfile)) {
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+ if (!file_exists($obo_file)) {
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+ form_set_error('obo_file', 'The specified path does not exist or cannot be read.');
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+ }
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+ }
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+ if (!$obo_url and !$obo_file) {
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+ form_set_error('obo_url', 'Please provide a URL or a path for the vocabulary.');
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+ }
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+ if ($obo_url and $obo_file) {
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+ form_set_error('obo_url', 'Please provide only a URL or a path for the vocabulary, but not both.');
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+ }
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+ }
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+}
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+
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/**
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* The submit function for the load ontology form. It registers a
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* tripal job to import the user specified ontology file
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@@ -114,17 +283,52 @@ function tripal_cv_obo_form($form, &$form_state) {
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* @ingroup tripal_obo_loader
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*/
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function tripal_cv_obo_form_submit($form, &$form_state) {
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+
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$obo_id = $form_state['values']['obo_id'];
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$obo_name = trim($form_state['values']['obo_name']);
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$obo_url = trim($form_state['values']['obo_url']);
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$obo_file = trim($form_state['values']['obo_file']);
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+ $uobo_name = array_key_exists('uobo_name', $form_state['values']) ? trim($form_state['values']['uobo_name']) : '';
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+ $uobo_url = array_key_exists('uobo_url', $form_state['values']) ? trim($form_state['values']['uobo_url']) : '';
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+ $uobo_file = array_key_exists('uobo_file', $form_state['values']) ? trim($form_state['values']['uobo_file']) : '';
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+
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+ // If the user requested to alter the details then do that.
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+ if ($form_state['clicked_button']['#name'] == 'update_obo_details' or
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+ $form_state['clicked_button']['#name'] == 'update_load_obo') {
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+ $success = db_update('tripal_cv_obo')
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+ ->fields(array(
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+ 'name' => $uobo_name,
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+ 'path' => $uobo_url ? $uobo_url : $uobo_file,
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+ ))
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+ ->condition('obo_id', $obo_id)
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+ ->execute();
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+ if ($success) {
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+ drupal_set_message(t("The vocabulary %vocab has been updated.", array('%vocab' => $uobo_name)));
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+ }
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+ else {
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+ drupal_set_message(t("The vocabulary %vocab could not be updated.", array('%vocab' => $uobo_name)), 'error');
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+ }
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- tripal_submit_obo_job(array(
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- 'obo_id' => $obo_id,
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- 'name' => $obo_name,
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- 'url' => $obo_url,
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- 'file' => $obo_file
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- ));
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+ }
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+ // If the user requested to update and load then we've already handled the
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+ // update now we just need to load.
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+ if ($form_state['clicked_button']['#name'] == 'update_load_obo') {
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+ tripal_submit_obo_job(array('obo_id' => $obo_id));
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+ }
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+ if ($form_state['clicked_button']['#name'] == 'add_new_obo') {
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+ $success = db_insert('tripal_cv_obo')
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+ ->fields(array(
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+ 'name' => $obo_name,
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+ 'path' => $obo_url ? $obo_url : $obo_file,
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+ ))
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+ ->execute();
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+ if ($success) {
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+ drupal_set_message(t("The vocabulary %vocab has been added.", array('%vocab' => $obo_name)));
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+ }
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+ else {
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+ drupal_set_message(t("The vocabulary %vocab could not be added.", array('%vocab' => $obo_name)), 'error');
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+ }
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+ }
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}
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/**
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@@ -1231,3 +1435,8 @@ function tripal_cv_obo_add_dbxref($db_id, $accession, $version='', $description=
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}
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return $result[0];
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}
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+
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+
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+function tripal_cv_obo_form_ajax_callback($form, $form_state) {
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+ return $form['obo_existing'];
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+}
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Stephen Ficklin