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+<?php
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+
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+class NewickImporter extends TripalImporter {
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+
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+ /**
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+ * The name of this loader. This name will be presented to the site
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+ * user.
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+ */
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+ public static $name = 'Newick Tree Loader';
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+
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+ /**
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+ * The machine name for this loader. This name will be used to construct
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+ * the URL for the loader.
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+ */
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+ public static $machine_name = 'chado_newick_loader';
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+
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+ /**
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+ * A brief description for this loader. This description will be
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+ * presented to the site user.
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+ */
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+ public static $description = 'Load Newick formatted phylogenetic trees.';
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+
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+ /**
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+ * An array containing the extensions of allowed file types.
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+ */
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+ public static $file_types = ['tree', 'txt'];
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+
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+ /**
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+ * Provides information to the user about the file upload. Typically this
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+ * may include a description of the file types allowed.
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+ */
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+ public static $upload_description = 'Please provide the Newick formatted tree file. The file must have a .txt or .tree extension.';
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+
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+ /**
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+ * The title that should appear above the file upload section.
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+ */
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+ public static $upload_title = 'Newick Upload';
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+
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+ /**
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+ * Text that should appear on the button at the bottom of the importer
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+ * form.
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+ */
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+ public static $button_text = 'Import Newick file';
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+
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+
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+ /**
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+ * Indicates the methods that the file uploader will support.
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+ */
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+ public static $methods = [
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+ // Allow the user to upload a file to the server.
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+ 'file_upload' => TRUE,
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+ // Allow the user to provide the path on the Tripal server for the file.
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+ 'file_local' => TRUE,
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+ // Allow the user to provide a remote URL for the file.
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+ 'file_remote' => TRUE,
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+ ];
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+
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+ /**
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+ * @see TripalImporter::form()
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+ */
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+ public function form($form, &$form_state) {
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+ // Default values can come in the following ways:
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+ //
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+ // 1) as elements of the $node object. This occurs when editing an existing phylotree
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+ // 2) in the $form_state['values'] array which occurs on a failed validation or
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+ // ajax callbacks from non submit form elements
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+ // 3) in the $form_state['input'[ array which occurs on ajax callbacks from submit
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+ // form elements and the form is being rebuilt
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+ //
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+ // set form field defaults
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+ $phylotree = NULL;
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+ $phylotree_id = NULL;
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+ $tree_name = '';
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+ $leaf_type = '';
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+ $analysis_id = '';
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+ $dbxref = '';
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+ $comment = '';
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+ $tree_required = TRUE;
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+ $tree_file = '';
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+ $name_re = '';
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+ $match = '';
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+
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+ // If we are re constructing the form from a failed validation or ajax callback
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+ // then use the $form_state['values'] values.
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+ if (array_key_exists('values', $form_state) and isset($form_state['values']['tree_name'])) {
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+ $tree_name = $form_state['values']['tree_name'];
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+ $leaf_type = $form_state['values']['leaf_type'];
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+ $analysis_id = $form_state['values']['analysis_id'];
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+ $dbxref = $form_state['values']['dbxref'];
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+ $comment = $form_state['values']['description'];
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+ }
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+ // If we are re building the form from after submission (from ajax call) then
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+ // the values are in the $form_state['input'] array.
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+ if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
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+ $tree_name = $form_state['input']['tree_name'];
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+ $leaf_type = $form_state['input']['leaf_type'];
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+ $analysis_id = $form_state['input']['analysis_id'];
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+ $comment = $form_state['input']['description'];
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+ $dbxref = $form_state['input']['dbxref'];
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+ }
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+
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+ $form['tree_name'] = [
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+ '#type' => 'textfield',
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+ '#title' => t('Tree Name'),
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+ '#required' => TRUE,
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+ '#default_value' => $tree_name,
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+ '#description' => t('Enter the name used to refer to this phylogenetic tree.'),
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+ '#maxlength' => 255,
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+ ];
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+
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+ $type_cv = tripal_get_default_cv('phylotree', 'type_id');
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+ $so_cv = tripal_get_cv(['name' => 'sequence']);
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+ $cv_id = $so_cv->cv_id;
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+ if (!$so_cv) {
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+ drupal_set_message('The Sequence Ontolgoy does not appear to be imported.
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+ Please import the Sequence Ontology before adding a tree.', 'error');
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+ }
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+
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+ $form['leaf_type'] = [
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+ '#title' => t('Tree Type'),
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+ '#type' => 'textfield',
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+ '#description' => t("Choose the tree type. The type is
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+ a valid Sequence Ontology (SO) term. For example, trees derived
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+ from protein sequences should use the SO term 'polypeptide'.
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+ Alternatively, a phylotree can be used for representing a taxonomic
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+ tree. In this case, the word 'taxonomy' should be used."),
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+ '#required' => TRUE,
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+ '#default_value' => $leaf_type,
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+ '#autocomplete_path' => "admin/tripal/legacy/tripal_cv/cvterm/auto_name/$cv_id",
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+ ];
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+
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+ $form['dbxref'] = [
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+ '#title' => t('Database Cross-Reference'),
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+ '#type' => 'textfield',
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+ '#description' => t("Enter a database cross-reference of the form
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+ [DB name]:[accession]. The database name must already exist in the
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+ database. If the accession does not exist it is automatically added."),
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+ '#required' => FALSE,
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+ '#default_value' => $dbxref,
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+ ];
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+
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+ $form['description'] = [
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+ '#type' => 'textarea',
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+ '#title' => t('Description'),
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+ '#required' => TRUE,
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+ '#default_value' => $comment,
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+ '#description' => t('Enter a description for this tree.'),
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+ ];
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+
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+ $form['name_re'] = [
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+ '#title' => t('Feature Name Regular Expression'),
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+ '#type' => 'textfield',
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+ '#description' => t('If this is a phylogenetic (non taxonomic) tree, then
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+ the tree nodes will be automatically associated with features. However,
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+ if the nodes in the tree file are not exactly as the names of features
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+ but have enough information to uniquely identify the feature then you
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+ may provide a regular expression that the importer will use to extract
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+ the feature names from the node names.'),
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+ '#default_value' => $name_re,
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+ ];
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+ $form['match'] = [
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+ '#title' => t('Use Unique Feature Name'),
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+ '#type' => 'checkbox',
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+ '#description' => t('If this is a phylogenetic (non taxonomic tree) and the nodes ' . 'should match the unique name of the feature rather than the name of the feature ' . 'then select this box. If unselected the loader will try to match the feature ' . 'using the feature name.'),
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+ '#default_value' => $match,
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+ ];
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+
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+ return $form;
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+ }
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+
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+ /**
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+ * @see TripalImporter::formValidate()
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+ */
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+ public function formValidate($form, &$form_state) {
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+
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+ $values = $form_state['values'];
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+
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+ $options = [
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+ 'name' => trim($values["tree_name"]),
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+ 'description' => trim($values["description"]),
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+ 'analysis_id' => $values["analysis_id"],
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+ 'leaf_type' => $values["leaf_type"],
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+ 'tree_file' => $this->arguments['files'][0]['file_path'],
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+ 'format' => 'newick',
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+ 'dbxref' => trim($values["dbxref"]),
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+ 'match' => $values["match"],
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+ 'name_re' => $values["name_re"],
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+ ];
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+
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+ $errors = [];
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+ $warnings = [];
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+
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+ tripal_validate_phylotree('insert', $options, $errors, $warnings);
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+
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+ // Now set form errors if any errors were detected.
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+ if (count($errors) > 0) {
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+ foreach ($errors as $field => $message) {
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+ if ($field == 'name') {
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+ $field = 'tree_name';
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+ }
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+ form_set_error($field, $message);
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+ }
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+ }
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+ // Add any warnings if any were detected
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+ if (count($warnings) > 0) {
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+ foreach ($warnings as $field => $message) {
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+ drupal_set_message($message, 'warning');
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+ }
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+ }
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+ }
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+
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+ /**
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+ * @see TripalImporter::run()
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+ */
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+ public function run() {
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+
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+ $arguments = $this->arguments['run_args'];
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+
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+ $options = array(
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+ 'name' => $this->arguments["tree_name"],
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+ 'description' => $this->arguments["description"],
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+ 'analysis_id' => $this->arguments["analysis_id"],
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+ 'leaf_type' => $this->arguments["leaf_type"],
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+ 'tree_file' => $this->arguments['files'][0]['file_path'],
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+ 'format' => 'newick',
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+ 'dbxref' => $this->arguments["dbxref"],
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+ 'match' => $this->arguments["match"],
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+ 'name_re' => $this->arguments["name_re"],
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+ );
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+ $errors = array();
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+ $warnings = array();
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+ tripal_insert_phylotree($options, $errors, $warnings);
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+ }
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+}
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Stephen Ficklin