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Merge pull request #1618 from tripal/tv4g4-1586-Newick-importer
Newick Importer
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tripal_chado/src/Plugin/TripalImporter/NewickImporter.php
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| <?php | ||
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| namespace Drupal\tripal_chado\Plugin\TripalImporter; | ||
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| use Drupal\tripal_chado\TripalImporter\ChadoImporterBase; | ||
| use Drupal\tripal\TripalVocabTerms\TripalTerm; | ||
| use Drupal\Core\Ajax\AjaxResponse; | ||
| use Drupal\Core\Ajax\InvokeCommand; | ||
| use Drupal\Core\Ajax\ReplaceCommand; | ||
| use Drupal\Core\Link; | ||
| use Drupal\Core\Url; | ||
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| /** | ||
| * Taxonomy Importer implementation of the TripalImporterBase. | ||
| * | ||
| * @TripalImporter( | ||
| * id = "chado_newick_tree_loader", | ||
| * label = @Translation("Newick Tree Loader"), | ||
| * description = @Translation("Import Newick Tree into Chado"), | ||
| * file_types = {"tree","txt","newick"}, | ||
| * upload_description = @Translation("Please provide the Newick formatted tree file (one tree per file only). The file must have a .txt or .tree extension"), | ||
| * upload_title = @Translation("Newick Tree File"), | ||
| * use_analysis = True, | ||
| * require_analysis = True, | ||
| * button_text = @Translation("Import Newick Tree file"), | ||
| * file_upload = True, | ||
| * file_load = False, | ||
| * file_remote = False, | ||
| * file_required = False, | ||
| * cardinality = 1, | ||
| * menu_path = "", | ||
| * callback = "", | ||
| * callback_module = "", | ||
| * callback_path = "", | ||
| * ) | ||
| */ | ||
| class NewickImporter extends ChadoImporterBase { | ||
| /** | ||
| * @see TripalImporter::form() | ||
| */ | ||
| public function form($form, &$form_state) { | ||
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| $chado = $this->getChadoConnection(); | ||
| // Always call the parent form to ensure Chado is handled properly. | ||
| $form = parent::form($form, $form_state); | ||
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| // Default values can come in the following ways: | ||
| // | ||
| // 1) as elements of the $node object. This occurs when editing an existing phylotree | ||
| // 2) in the $form_state['values'] array which occurs on a failed validation or | ||
| // ajax callbacks from non submit form elements | ||
| // 3) in the $form_state['input'] array which occurs on ajax callbacks from submit | ||
| // form elements and the form is being rebuilt | ||
| // | ||
| // set form field defaults | ||
| $phylotree = NULL; | ||
| $phylotree_id = NULL; | ||
| $tree_name = ''; | ||
| $leaf_type = ''; | ||
| $analysis_id = ''; | ||
| $dbxref = ''; | ||
| $comment = ''; | ||
| $tree_required = TRUE; | ||
| $tree_file = ''; | ||
| $name_re = ''; | ||
| $match = ''; | ||
| // $load_later = FALSE; // Default is to combine tree import with current job | ||
|
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| // get the sequence ontology CV ID | ||
| $cv_results = $chado->select('1:cv', 'cv') | ||
| ->fields('cv') | ||
| ->condition('name', 'sequence') | ||
| ->execute(); | ||
| $cv_id = $cv_results->fetchObject()->cv_id; | ||
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| $form_state_values = $form_state->getValues(); | ||
| $form_state_input = $form_state->getUserInput(); | ||
| // If we are re constructing the form from a failed validation or ajax callback | ||
| // then use the $form_state['values'] values. | ||
| if (isset($form_state_values['tree_name'])) { | ||
| $tree_name = $form_state_values['tree_name']; | ||
| $leaf_type = $form_state_values['leaf_type']; | ||
| $analysis_id = $form_state_values['analysis_id']; | ||
| $dbxref = $form_state_values['dbxref']; | ||
| $comment = $form_state_values['description']; | ||
| } | ||
| // If we are re building the form from after submission (from ajax call) then | ||
| // the values are in the $form_state['input'] array. | ||
| if (!empty($form_state_input)) { | ||
| $tree_name = $form_state_input['tree_name']; | ||
| $leaf_type = $form_state_input['leaf_type']; | ||
| $analysis_id = $form_state_input['analysis_id']; | ||
| $comment = $form_state_input['description']; | ||
| $dbxref = $form_state_input['dbxref']; | ||
| } | ||
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| $form['tree_name'] = [ | ||
| '#type' => 'textfield', | ||
| '#title' => t('Tree Name'), | ||
| '#required' => TRUE, | ||
| '#default_value' => $tree_name, | ||
| '#description' => t('Enter the name used to refer to this phylogenetic tree.'), | ||
| '#maxlength' => 255, | ||
| ]; | ||
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| $so_cv = chado_get_cv(['name' => 'sequence']); | ||
| $cv_id = $so_cv->cv_id; | ||
| if (!$so_cv) { | ||
| \Drupal::messenger()->addError(t("The Sequence Ontolgoy does not appear to be imported. | ||
| Please import the Sequence Ontology before adding a tree.")); | ||
| } | ||
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| $form['leaf_type'] = [ | ||
| '#title' => t('Tree Type'), | ||
| '#type' => 'textfield', | ||
| '#description' => t("Choose the tree type. The type is | ||
| a valid Sequence Ontology (SO) term. For example, trees derived | ||
| from protein sequences should use the SO term 'polypeptide'. | ||
| Alternatively, a phylotree can be used for representing a taxonomic | ||
| tree. In this case, the word 'taxonomy' should be used."), | ||
| '#required' => TRUE, | ||
| '#default_value' => $leaf_type, | ||
| '#autocomplete_route_name' => 'tripal_chado.cvterm_autocomplete', | ||
| '#autocomplete_route_parameters' => ['count' => 5, 'cv_id' => $cv_id] | ||
| ]; | ||
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| $form['dbxref'] = [ | ||
| '#title' => t('Database Cross-Reference'), | ||
| '#type' => 'textfield', | ||
| '#description' => t("Enter a database cross-reference of the form | ||
| [DB name]:[accession]. The database name must already exist in the | ||
| database. If the accession does not exist it is automatically added."), | ||
| '#required' => FALSE, | ||
| '#default_value' => $dbxref, | ||
| ]; | ||
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| $form['description'] = [ | ||
| '#type' => 'textarea', | ||
| '#title' => t('Description'), | ||
| '#required' => TRUE, | ||
| '#default_value' => $comment, | ||
| '#description' => t('Enter a description for this tree.'), | ||
| ]; | ||
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| $form['name_re'] = [ | ||
| '#title' => t('Feature Name Regular Expression'), | ||
| '#type' => 'textfield', | ||
| '#description' => t('The tree nodes will be automatically associated with | ||
| features, or in the case of taxonomic trees, with organisms. However, | ||
| if the nodes in the tree file are not exactly as the names of features | ||
| or organisms but have enough information to uniquely identify them, | ||
| then you may provide a regular expression that the importer will use to | ||
| extract the appropriate names from the node names. For example, remove | ||
| a prefix ABC_ with ^ABC_(.*)$'), | ||
| '#default_value' => $name_re, | ||
| ]; | ||
| $form['match'] = [ | ||
| '#title' => t('Use Unique Feature Name'), | ||
| '#type' => 'checkbox', | ||
| '#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.'), | ||
| '#default_value' => $match, | ||
| ]; | ||
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| return $form; | ||
| } | ||
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| /** | ||
| * @see TripalImporter::formValidate() | ||
| */ | ||
| public function formValidate($form, &$form_state) { | ||
| $chado = $this->getChadoConnection(); | ||
| // $values = $form_state['values']; | ||
| $values = $form_state->getValues(); | ||
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| // TRIPAL 4 - The type option is from an autocomplete which seems to include (SO:*) part | ||
| // Temporarily, remove this part | ||
| $leaf_type = $values["leaf_type"]; | ||
| $leaf_type = explode(' ', $leaf_type)[0]; // splits the string by space and takes the first part | ||
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| $options = [ | ||
| 'name' => trim($values["tree_name"]), | ||
| 'description' => trim($values["description"]), | ||
| 'analysis_id' => $values["analysis_id"], | ||
| 'leaf_type' => $leaf_type, | ||
| 'format' => 'newick', | ||
| 'dbxref' => trim($values["dbxref"]), | ||
| 'match' => $values["match"], | ||
| 'name_re' => $values["name_re"], | ||
| // 'load_later' => $values["load_later"], | ||
| ]; | ||
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| $errors = []; | ||
| $warnings = []; | ||
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| // Validate DBXREF | ||
| if ($options['dbxref'] and ($options['dbxref'] != "null:local:null")) { | ||
| // The db in a dbxref must already exist, the accession can be new. | ||
| $dbxref_parts = explode(':', $options['dbxref'], 2); | ||
| $db = $dbxref_parts[0]; | ||
| if ((count($dbxref_parts) < 2) or (strlen($db) < 1) or (strlen($dbxref_parts[1]) < 1)) { | ||
| $form_state->setErrorByName('dbxref', "The dbxref must consist of a DB and an accession separated by a colon, specify a valid dbxref value."); | ||
| return; | ||
| } | ||
| // Lookup | ||
| $results = $chado->select('1:db', 'db') | ||
| ->fields('db') | ||
| ->condition('name', $db) | ||
| ->execute() | ||
| ->fetchAll(); | ||
| $count = count($results); | ||
| if ($count < 1) { | ||
| $form_state->setErrorByName('dbxref', "The DB \"$db\" in the dbxref value does not exist, specify a valid dbxref value."); | ||
| return; | ||
| } | ||
| } | ||
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| // Verify that a file has been supplied. | ||
| if ((!array_key_exists('tree_file', $options) or $options['tree_file'] == null) && $values['file_upload_existing'] <= 0) { | ||
| $form_state->setErrorByName('file_upload_existing', t('No tree file was submitted, please upload a file or choose one if it exists')); | ||
| return; | ||
| } | ||
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| // Perform API validation. | ||
| chado_validate_phylotree('insert', $options, $errors, $warnings, $chado->getSchemaName()); | ||
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| // Now set form errors if any errors were detected. | ||
| if (count($errors) > 0) { | ||
| foreach ($errors as $field => $message) { | ||
| if ($field == 'name') { | ||
| $field = 'tree_name'; | ||
| } | ||
| $form_state->setErrorByName($field, $message); | ||
| } | ||
| $form_state->setError($form, "Please fix these errors to continue creating a job"); | ||
| } | ||
| // Add any warnings if any were detected | ||
| if (count($warnings) > 0) { | ||
| foreach ($warnings as $field => $message) { | ||
| \Drupal::messenger()->addWarning(t("$message")); | ||
| } | ||
| } | ||
| } | ||
|
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| /** | ||
| * @see TripalImporter::run() | ||
| */ | ||
| public function run() { | ||
| $chado = $this->getChadoConnection(); | ||
| $arguments = $this->arguments['run_args']; | ||
|
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| // TRIPAL 4 - The type option is from an autocomplete which seems to include (SO:*) part | ||
| // Temporarily, remove this part | ||
| $leaf_type = $arguments["leaf_type"]; | ||
| $leaf_type = explode(' ', $leaf_type)[0]; // splits the string by space and takes the first part | ||
|
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| $options = [ | ||
| 'name' => $arguments["tree_name"], | ||
| 'description' => $arguments["description"], | ||
| 'analysis_id' => $arguments["analysis_id"], | ||
| 'leaf_type' => $leaf_type, | ||
| 'tree_file' => $this->arguments['files'][0]['file_path'], | ||
| 'format' => 'newick', | ||
| 'dbxref' => $arguments["dbxref"], | ||
| 'match' => $arguments["match"], | ||
| 'name_re' => $arguments["name_re"], | ||
| // 'load_later' => $arguments["load_later"], | ||
| ]; | ||
| // pass through the job, needed for log output to show up on the "jobs page" | ||
| if (property_exists($this, 'job')) { | ||
| $options['job'] = $this->job; | ||
| } | ||
| $errors = []; | ||
| $warnings = []; | ||
| chado_insert_phylotree($options, $errors, $warnings, $chado->getSchemaName()); | ||
| } | ||
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| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public function postRun() { | ||
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| } | ||
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| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public function formSubmit($form, &$form_state) { | ||
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| } | ||
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| } |
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