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@@ -266,9 +266,7 @@ function tripal_chado_populate_chado_semweb_table() {
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/**
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* Adds defaults to the chado_semweb table.
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*/
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-function tripal_chado_semweb_form($form, &$form_state) {
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-
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- $chado_table = '';
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+function tripal_chado_semweb_form($form, &$form_state, $chado_table = NULL) {
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if (array_key_exists('values', $form_state)) {
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$chado_table = $form_state['values']['chado_table'];
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}
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@@ -290,54 +288,223 @@ function tripal_chado_semweb_form($form, &$form_state) {
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),
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);
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- // If the user has selected a content type, then we need to
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- // show some filters.
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+ // If the user has selected a chado table, then we need to
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+ // show the columns for setting terms.
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if ($chado_table) {
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- $form['filters'] = array(
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- '#type' => 'fieldset',
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- '#title' => 'Filters',
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+ $schema = chado_get_schema($chado_table);
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+ $pk = $schema['primary key'][0];
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+ $cv_default =
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+ db_select('tripal_cv_defaults', 'tc')
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+ ->fields('tc', array('field_name'))
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+ ->condition('table_name', $chado_table)
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+ ->execute()
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+ ->fetchField();
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+ $columns = $schema['fields'];
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+ $headers = array('Field Name', 'Term', 'Description', 'Action');
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+ $rows = array();
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+ foreach ($columns AS $column => $detail) {
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+ // Do not show column if it's the primary key or default cv
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+ if ($column != $pk && $column != $cv_default) {
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+ $cvterm_id =
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+ db_select('chado_semweb', 'cs')
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+ ->fields('cs', array('cvterm_id'))
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+ ->condition('chado_table', $chado_table)
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+ ->condition('chado_column', $column)
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+ ->execute()
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+ ->fetchField();
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+ $sw_term = '';
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+ $sw_desc = '';
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+ if($cvterm_id) {
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+ $term = tripal_get_cvterm(array(
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+ 'cvterm_id' => $cvterm_id
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+ ));
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+ $sw_term = $term->name;
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+ $sw_desc = $term->definition;
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+ }
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+ $rows[] = array(
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+ $column,
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+ $sw_term,
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+ $sw_desc,
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+ l('Edit', '/admin/tripal/storage/chado/semweb/edit/' . $chado_table . '/' . $column)
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+ );
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+ }
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+ }
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+ $output = theme('table', array(
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+ 'header' => $headers,
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+ 'rows' => $rows,
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+ ));
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+ $form['table'] = array(
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+ '#markup' => $output,
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+ '#title' => 'Table',
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'#description' => t('Please provide any filters for limiting
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- the records. Only those that match the filters specified
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- below will be published. To publish all records of this
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- type, leave all filters blank.'),
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- '#collapsed' => TRUE,
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- '#collapsible' => TRUE,
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+ the records. Only those that match the filters specified
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+ below will be published. To publish all records of this
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+ type, leave all filters blank.'),
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);
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+ }
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- $form['publish_btn'] = array(
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+ $form['#prefix'] = '<div id="tripal-chado-semweb-form">';
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+ $form['#suffix'] = '</div>';
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+ return $form;
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+}
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+
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+/**
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+ * Adds defaults to the chado_semweb table.
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+ */
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+function tripal_chado_semweb_edit_form($form, &$form_state, $table = NULL, $column = NULL) {
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+
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+ $term_name = array_key_exists('values', $form_state) ? $form_state['values']['term_name'] : '';
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+
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+ $form['chado_table'] = array(
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+ '#markup' => 'Term used for the <strong>' . t($column) . '</strong> column of the chado <strong>' . t($table) . '</strong> table:',
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+ );
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+ $form['table_name'] = array(
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+ '#type' => 'value',
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+ '#value' => $table
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+ );
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+ $form['column'] = array(
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+ '#type' => 'value',
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+ '#value' => $column
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+ );
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+ // If no term has been selected yet then provide the auto complete field.
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+ $form['term_name'] = array(
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+ '#title' => t('Term'),
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+ '#type' => 'textfield',
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+ '#description' => t("The content type must be the name of a term in
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+ a controlled vocabulary and the controlled vocabulary should
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+ already be loaded into Tripal. For example, to create a content
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+ type for storing 'genes', use the 'gene' term from the
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+ Sequence Ontology (SO)."),
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+ '#required' => TRUE,
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+ '#default_value' => $term_name,
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+ '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/",
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+ );
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+ $form['select_button'] = array(
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+ '#type' => 'button',
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+ '#value' => t('Lookup Term'),
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+ '#name' => 'select_cvterm',
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+ '#ajax' => array(
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+ 'callback' => "tripal_chado_semweb_form_ajax_callback",
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+ 'wrapper' => "tripal-chado-semweb-edit-form",
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+ 'effect' => 'fade',
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+ 'method' => 'replace'
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+ ),
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+ );
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+ if ($term_name) {
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+ $form['terms_list'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Matching Terms'),
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+ '#description' => t('Please select the term the best matches the
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+ content type you want to create. If the same term exists in
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+ multiple vocabularies you will see more than one option below.')
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+ );
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+ $match = array(
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+ 'name' => $term_name,
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+ );
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+ $terms = chado_generate_var('cvterm', $match, array('return_array' => TRUE));
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+ $terms = chado_expand_var($terms, 'field', 'cvterm.definition');
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+ $num_terms = 0;
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+ foreach ($terms as $term) {
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+ // Save the user a click by setting the default value as 1 if there's
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+ // only one matching term.
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+ $default = FALSE;
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+ $attrs = array();
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+ if ($num_terms == 0 and count($terms) == 1) {
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+ $default = TRUE;
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+ $attrs = array('checked' => 'checked');
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+ }
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+ $form['terms_list']['term-' . $term->cvterm_id] = array(
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+ '#type' => 'checkbox',
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+ '#title' => $term->name,
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+ '#default_value' => $default,
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+ '#attributes' => $attrs,
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+ '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name .
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+ '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '. ' .
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+ '<br><b>Definition:</b> ' . $term->definition,
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+ );
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+ $num_terms++;
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+ }
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+ if ($num_terms == 0) {
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+ $form['terms_list']['none'] = array(
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+ '#type' => 'item',
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+ '#markup' => '<i>' . t('There is no term that matches the entered text.') . '</i>'
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+ );
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+ }
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+ // Add in the button for the cases of no terms or too many.
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+ $form['submit_button'] = array(
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'#type' => 'submit',
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- '#name' => 'publish_btn',
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- '#value' => 'Publish',
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+ '#value' => t('Use this term'),
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+ '#name' => 'use_cvterm'
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);
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}
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-
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- $form['#prefix'] = '<div id="tripal-chado-publish-form">';
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+ $form['#prefix'] = '<div id = "tripal-chado-semweb-edit-form">';
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$form['#suffix'] = '</div>';
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+
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return $form;
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}
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-function tripal_chado_semweb_form_validate($form, &$form_state) {
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-
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+function tripal_chado_semweb_edit_form_validate($form, &$form_state) {
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+ if (array_key_exists('clicked_button', $form_state) && $form_state['clicked_button']['#name'] =='use_cvterm') {
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+ $cvterm_id = NULL;
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+ // Make sure we have a cvterm selected
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+ $num_selected = 0;
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+ foreach ($form_state['values'] as $key => $value) {
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+ $matches = array();
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+ if (preg_match("/^term-(\d+)$/", $key, $matches) and
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+ $form_state['values']['term-' . $matches[1]]) {
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+ $cvterm_id = $matches[1];
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+ $num_selected++;
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+ }
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+ }
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+ if ($num_selected == 0) {
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+ form_set_error('', 'Please select at least one term.');
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+ }
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+ else if ($num_selected > 1) {
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+ form_set_error('term-' . $cvterm_id, 'Please select only one term from the list below.');
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+ }
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+ else {
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+ $form_state['values']['#selected_cvterm_id'] = $cvterm_id;
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+ }
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+ }
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}
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-function tripal_chado_semweb_form_submit($form, &$form_state) {
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- if ($form_state['clicked_button']['#name'] == 'publish_btn') {
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- global $user;
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-
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- $chado_table = $form_state['values']['chado_table'];
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- $bundle_name = 'bio_data_' . $chado_table;
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- $bundle = tripal_load_bundle_entity(array('name' => $bundle_name));
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- $args = array(
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- array('bundle_name' => $bundle_name),
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- );
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- $includes = array(
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- module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.publish'),
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- );
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- return tripal_add_job("Publish " . $bundle->label . " records.",
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- 'tripal_chado', 'tripal_chado_publish_records', $args,
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- $user->uid, 10, $includes);
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- }
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+function tripal_chado_semweb_edit_form_submit($form, &$form_state) {
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+ if (array_key_exists('clicked_button', $form_state) && $form_state['clicked_button']['#name'] =='use_cvterm') {
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+ $table_name = $form_state['values']['table_name'];
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+ $column = $form_state['values']['column'];
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+ $cvterm_id = $form_state['values']['#selected_cvterm_id'];
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+ // Check if there is already a record
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+ $record_id =
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+ db_select('chado_semweb', 'cs')
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+ ->fields('cs', array('chado_semweb_id'))
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+ ->condition('chado_table', $table_name)
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+ ->condition('chado_column', $column)
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+ ->execute()
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+ ->fetchField();
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+
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+ // If the record exists, update it
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+ if ($record_id) {
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+ db_update('chado_semweb')
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+ ->fields(array(
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+ 'cvterm_id' => $cvterm_id
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+ ))
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+ ->condition('chado_semweb_id', $record_id)
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+ ->execute();
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+ }
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+ // Otherwise, insert a new record
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+ else {
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+ db_insert('chado_semweb')
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+ ->fields(array(
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+ 'chado_table' => $table_name,
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+ 'chado_column' => $column,
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+ 'cvterm_id' => $cvterm_id
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+ ))
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+ ->execute();
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+ }
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+ drupal_set_message('The term settings have been saved.');
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+ drupal_goto('/admin/tripal/storage/chado/semweb/' . $table_name);
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+ }
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}
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/**
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*
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Chun-Huai Cheng