analysis; $analysis = tripal_core_expand_chado_vars($analysis, 'field', 'analysis.description'); $analysis_id = $analysis->analysis_id; // get form defaults $analysisname = $analysis->name; $program = $analysis->program; $programversion = $analysis->programversion; $algorithm = $analysis->algorithm; $sourcename = $analysis->sourcename; $sourceversion = $analysis->sourceversion; $sourceuri = $analysis->sourceuri; $timeexecuted = $analysis->timeexecuted; $description = $analysis->description; // set the organism_id in the form $form['analysis_id'] = array( '#type' => 'value', '#value' => $analysis->analysis_id, ); } // if we are re constructing the form from a failed validation or ajax callback // then use the $form_state['values'] values if (array_key_exists('values', $form_state)) { $analysisname = $form_state['values']['analysisname']; $program = $form_state['values']['program']; $programversion = $form_state['values']['programversion']; $algorithm = $form_state['values']['algorithm']; $sourcename = $form_state['values']['sourcename']; $sourceversion = $form_state['values']['sourceversion']; $sourceuri = $form_state['values']['sourceuri']; $timeexecuted = $form_state['values']['timeexecuted']; $description = $form_state['values']['description']; $d_removed = $form_state['values']['removed']; $num_new = $form_state['values']['num_new'] ? $form_state['values']['num_new'] : 0; } // if we are re building the form from after submission (from ajax call) then // the values are in the $form_state['input'] array if (array_key_exists('input', $form_state) and !empty($form_state['input'])) { $analysisname = $form_state['input']['analysisname']; $program = $form_state['input']['program']; $programversion = $form_state['input']['programversion']; $algorithm = $form_state['input']['algorithm']; $sourcename = $form_state['input']['sourcename']; $sourceversion = $form_state['input']['sourceversion']; $sourceuri = $form_state['input']['sourceuri']; $timeexecuted = $form_state['input']['timeexecuted']; $description = $form_state['input']['description']; $d_removed = $form_state['input']['removed']; $num_new = $form_state['input']['num_new'] ? $form_state['input']['num_new'] : 0; } $form['title']= array( '#type' => 'value', '#default_value' => $node->title, ); $form['instructions'] = array( '#markup' => t('Note: When adding any type of data it is good to associate it with an analysis so that site visitors can identify the source of the data including necessary materials and methods. The fields below imply that all analyses are derived from some software package. But, data can also be derived via retreival from an external source or an analysis pipeline with multipel software components. In these cases, provide values for the fields below that best makes sense '), ); $form['analysisname']= array( '#type' => 'textfield', '#title' => t('Analysis Name'), '#required' => TRUE, '#default_value' => $analysisname, '#description' => t("This should be a brief name that describes the analysis succintly. This name will helps the user find analyses."), ); $form['program']= array( '#type' => 'textfield', '#title' => t('Program, Pipeline Name or Method Name'), '#required' => TRUE, '#default_value' => $program, '#description' => t("Program name, e.g. blastx, blastp, sim4, genscan. If the analysis was not derived from a software package, provide a very brief description of the pipeline or method."), ); $form['programversion']= array( '#type' => 'textfield', '#title' => t('Program, Pipeline or Method version'), '#required' => TRUE, '#default_value' => $programversion, '#description' => t("Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]. Enter 'n/a' if no version is available or applicable."), ); $form['algorithm']= array( '#type' => 'textfield', '#title' => t('Algorithm'), '#required' => FALSE, '#default_value' => $algorithm, '#description' => t("Algorithm name, e.g. blast."), ); $form['sourcename']= array( '#type' => 'textfield', '#title' => t('Source Name'), '#required' => TRUE, '#default_value' => $sourcename, '#description' => t('The name of the source data. This could be a file name, data set name or a small description for how the data was collected. For long descriptions use the description field below'), ); $form['sourceversion']= array( '#type' => 'textfield', '#title' => t('Source Version'), '#required' => FALSE, '#default_value' => $sourceversion, '#description' => t('If the source dataset has a version, include it here'), ); $form['sourceuri']= array( '#type' => 'textfield', '#title' => t('Source URI'), '#required' => FALSE, '#default_value' => $sourceuri, '#description' => t("This is a permanent URL or URI for the source of the analysis. Someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model)."), ); // Get time saved in chado $default_time = $timeexecuted; $year = preg_replace("/^(\d+)-\d+-\d+ .*/", "$1", $default_time); $month = preg_replace("/^\d+-0?(\d+)-\d+ .*/", "$1", $default_time); $day = preg_replace("/^\d+-\d+-0?(\d+) .*/", "$1", $default_time); // If the time is not set, use current time if (!$default_time) { $default_time = REQUEST_TIME; $year = format_date($default_time, 'custom', 'Y'); $month = format_date($default_time, 'custom', 'n'); $day = format_date($default_time, 'custom', 'j'); } $form['timeexecuted']= array( '#type' => 'date', '#title' => t('Time Executed'), '#required' => TRUE, '#default_value' => array( 'year' => $year, 'month' => $month, 'day' => $day, ), ); $form['description']= array( '#type' => 'textarea', '#rows' => 15, '#title' => t('Materials & Methods (Description and/or Program Settings)'), '#required' => FALSE, '#default_value' => $description, '#description' => t('Please provide all necessary information to allow someone to recreate the analysis, including materials and methods for collection of the source data and performing the analysis'), ); // get the analysis properties $properties = array(); $properties[] = 'Select a Property'; $sql = " SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition FROM {cvterm} CVT INNER JOIN {cv} ON CVT.cv_id = CV.cv_id WHERE CV.name = 'analysis_property' AND NOT CVT.is_obsolete = 1 ORDER BY CVT.name ASC "; $prop_types = chado_query($sql); while ($prop = $prop_types->fetchObject()) { $properties[$prop->cvterm_id] = $prop->name; } $exclude = array(); $include = array(); $instructions = t('To add additional properties to the drop down. ' . l("Add terms to the analysis_property vocabulary", "admin/tripal/chado/tripal_cv/cvterm/add") . "."); tripal_core_properties_form($form, $form_state, 'analysisprop', 'analysis_id', 'analysis_property', $properties, $analysis_id, $exclude, $include, $instructions, 'Properties'); return $form; } /** * Validates the user input before creating an analysis node * * @ingroup tripal_analysis */ function chado_analysis_validate($node, $form, &$form_state) { // use the analysis parent to validate the node tripal_analysis_validate($node, $form, $form_state); } /** * This validation is being used for three activities: * CASE A: Update a node that exists in both drupal and chado * CASE B: Synchronizing a node from chado to drupal * CASE C: Inserting a new node that exists in niether drupal nor chado * * @ingroup tripal_analysis */ function tripal_analysis_validate($node, $form, &$form_state) { // remove surrounding white-space on submitted values $node->analysisname = trim($node->analysisname); $node->description = trim($node->description); $node->program = trim($node->program); $node->programversion = trim($node->programversion); $node->algorithm = trim($node->algorithm); $node->sourcename = trim($node->sourcename); $node->sourceversion = trim($node->sourceversion); $node->sourceuri = trim($node->sourceuri); // if this is a delete then don't validate if($node->op == 'Delete') { return; } // we are syncing if we do not have a node ID but we do have a analysis_id. We don't // need to validate during syncing so just skip it. if (is_null($node->nid) and property_exists($node, 'analysis_id') and $node->analysis_id != 0) { return; } // Validating for an update if (!is_null($node->nid)) { // get the existing node $values = array('analysis_id' => $node->analysis_id); $result = tripal_core_chado_select('analysis', array('*'), $values); $analysis = $result[0]; // if the name has changed make sure it doesn't conflict with an existing name if ($analysis->name != $node->analysisname) { $values = array('name' => $node->analysisname); $result = tripal_core_chado_select('analysis', array('analysis_id'), $values); if ($result and count($result) > 0) { form_set_error('analysisname', 'Cannot update the analysis with this analysis name. An analysis with this name already exists.'); return; } } // if the unique constraint has changed check to make sure it doesn't conflict with an // existing record if ($analysis->program != $node->program or $analysis->programversion != $node->programversion or $analysis->sourcename != $node->sourcename) { $values = array( 'program' => $node->program, 'programversion' => $node->programversion, 'sourcename' => $node->sourcename, ); $result = tripal_core_chado_select('analysis', array('analysis_id'), $values); if ($result and count($result) > 0) { if ($analysis->program != $node->program) { $field = 'program'; } if ($analysis->programversion != $node->programversion) { $field = 'programversion'; } if ($analysis->sourcename != $node->sourcename) { $field = 'sourcename'; } form_set_error($field, 'Cannot update the analysis with this program, program version and source name. An analysis with these values already exists.'); return; } } } // Validating for an insert else { $values = array( 'program' => $node->program, 'programversion' => $node->programversion, 'sourcename' => $node->sourcename, ); $analysis = tripal_core_chado_select('analysis', array('analysis_id'), $values); if ($analysis and count($analysis) > 0) { form_set_error('program', 'Cannot add the analysis with this program, program version and source name. An analysis with these values already exists.'); return; } // make sure we have a unique analysis name. This is not a requirement // for the analysis table but we use the analysis name for the Drupal node // title, so it should be unique $values = array('name' => $node->analysisname); $result = tripal_core_chado_select('analysis', array('analysis_id'), $values); if ($result and count($result) > 0) { form_set_error('analysisname', 'Cannot add the analysis with this analysis name. An analysis with this name already exists.'); return; } } }