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@@ -0,0 +1,668 @@
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+<?php
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+/**
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+ * When editing or creating a new node of type 'chado_analysis' we need
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+ * a form. This function creates the form that will be used for this.
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+ *
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+ * @ingroup tripal_analysis
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+ */
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+function chado_analysis_form(&$node, $form_state) {
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+ tripal_core_ahah_init_form();
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+ $form = array();
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+
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+ $analysis = $node->analysis;
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+
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+ // add in the description column. It is a text field and may not be included
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+ // if the text is too big.
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+ $analysis = tripal_core_expand_chado_vars($analysis, 'field', 'analysis.description');
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+
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+ // get form defaults
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+ $analysis_id = $node->analysis_id;
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+ if (!$analysis_id) {
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+ $analysis_id = $analysis->analysis_id;
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+ }
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+ $analysisname = $node->analysisname;
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+ if (!$analysisname) {
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+ $analysisname = $analysis->name;
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+ }
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+ $program = $node->program;
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+ if (!$program) {
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+ $program = $analysis->program;
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+ }
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+ $programversion = $node->programversion;
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+ if (!$programversion) {
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+ $programversion = $analysis->programversion;
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+ }
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+ $algorithm = $node->algorithm;
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+ if (!$algorithm) {
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+ $algorithm = $analysis->algorithm;
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+ }
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+ $sourcename = $node->sourcename;
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+ if (!$sourcename) {
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+ $sourcename = $analysis->sourcename;
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+ }
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+ $sourceversion = $node->sourceversion;
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+ if (!$sourceversion) {
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+ $sourceversion = $analysis->sourceversion;
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+ }
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+ $sourceuri = $node->sourceuri;
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+ if (!$sourceuri) {
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+ $sourceuri = $analysis->sourceuri;
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+ }
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+ $timeexecuted = $node->timeexecuted;
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+ if (!$timeexecuted) {
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+ $timeexecuted = $analysis->timeexecuted;
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+ }
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+ $description = $node->description;
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+ if (!$description) {
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+ $description = $analysis->description;
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+ }
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+
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+ // on AHAH callbacks we want to keep a list of all the properties that have been removed
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+ // we'll store this info in a hidden field and retrieve it here
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+ $d_removed = $form_state['values']['removed'];
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+
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+ // get the number of new fields that have been aded via AHAH callbacks
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+ $num_new = $form_state['values']['num_new'] ? $form_state['values']['num_new'] : 0;
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+
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+ // initialze default properties array. This is where we store the property defaults
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+ $d_properties = array();
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+
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+
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+ $form['title']= array(
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+ '#type' => 'hidden',
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+ '#default_value' => $node->title,
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+ );
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+ $form['analysis_id']= array(
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+ '#type' => 'hidden',
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+ '#default_value' => $analysis_id,
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+ );
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+ $form['analysisname']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Analysis Name'),
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+ '#required' => TRUE,
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+ '#default_value' => $analysisname,
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+ '#description' => t("This should be a brief name that
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+ describes the analysis succintly. This name will helps the user find analyses."),
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+ );
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+ $form['program']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Program'),
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+ '#required' => TRUE,
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+ '#default_value' => $program,
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+ '#description' => t("Program name, e.g. blastx, blastp, sim4, genscan."),
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+ );
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+ $form['programversion']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Program Version'),
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+ '#required' => TRUE,
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+ '#default_value' => $programversion,
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+ '#description' => t("Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]. Enter 'n/a' if no version is available."),
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+ );
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+ $form['algorithm']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Algorithm'),
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+ '#required' => FALSE,
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+ '#default_value' => $algorithm,
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+ '#description' => t("Algorithm name, e.g. blast."),
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+ );
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+ $form['sourcename']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Source Name'),
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+ '#required' => TRUE,
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+ '#default_value' => $sourcename,
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+ '#description' => t('The name of the source data. This could be a file name, data set name or a
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+ small description for how the data was collected. For long descriptions use the description field below'),
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+
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+ );
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+ $form['sourceversion']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Source Version'),
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+ '#required' => FALSE,
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+ '#default_value' => $sourceversion,
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+ '#description' => t('If the source dataset has a version, include it here'),
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+ );
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+ $form['sourceuri']= array(
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+ '#type' => 'textfield',
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+ '#title' => t('Source URI'),
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+ '#required' => FALSE,
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+ '#default_value' => $sourceuri,
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+ '#description' => t("This is a permanent URL or URI for the source of the analysis.
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+ Someone could recreate the analysis directly by going to this URI and
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+ fetching the source data (e.g. the blast database, or the training model)."),
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+ );
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+ // Get time saved in chado
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+ $default_time = $timeexecuted;
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+ $year = preg_replace("/^(\d+)-\d+-\d+ .*/", "$1", $default_time);
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+ $month = preg_replace("/^\d+-0?(\d+)-\d+ .*/", "$1", $default_time);
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+ $day = preg_replace("/^\d+-\d+-0?(\d+) .*/", "$1", $default_time);
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+ // If the time is not set, use current time
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+ if (!$default_time) {
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+ $default_time = time();
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+ $year = format_date($default_time, 'custom', 'Y');
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+ $month = format_date($default_time, 'custom', 'n');
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+ $day = format_date($default_time, 'custom', 'j');
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+ }
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+ $form['timeexecuted']= array(
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+ '#type' => 'date',
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+ '#title' => t('Time Executed'),
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+ '#required' => TRUE,
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+ '#default_value' => array(
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+ 'year' => $year,
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+ 'month' => $month,
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+ 'day' => $day,
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+ ),
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+ );
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+ $form['description']= array(
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+ '#type' => 'textarea',
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+ '#rows' => 15,
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+ '#title' => t('Materials & Methods (Description and/or Program Settings)'),
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+ '#required' => FALSE,
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+ '#default_value' => $description,
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+ '#description' => t('Please provide all necessary information to allow
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+ someone to recreate the analysis, including materials and methods
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+ for collection of the source data and performing the analysis'),
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+ );
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+
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+ // get the analysis properties
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+ $properties_select = array();
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+ $properties_select[] = 'Select a Property';
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+ $properties_list = array();
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+ $sql = "
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+ SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
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+ FROM {cvterm} CVT
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+ INNER JOIN {cv} ON CVT.cv_id = CV.cv_id
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+ WHERE
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+ CV.name = 'analysis_property' AND
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+ NOT CVT.is_obsolete = 1
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+ ORDER BY CVT.name ASC
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+ ";
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+ $prop_types = chado_query($sql);
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+ while ($prop = db_fetch_object($prop_types)) {
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+ $properties_select[$prop->cvterm_id] = $prop->name;
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+ $properties_list[$prop->cvterm_id] = $prop;
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+ }
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+ // add in the properties from the analysisprop table
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+ $num_properties += chado_analysis_node_form_add_analysisprop_table_props($form, $form_state, $analysis_id, $d_properties, $d_removed);
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+
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+ // add in any new properties that have been added by the user through an AHAH callback
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+ $num_new = chado_analysis_node_form_add_new_props($form, $form_state, $d_properties, $d_removed);
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+
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+ // add an empty row of field to allow for addition of a new property
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+ chado_analysis_node_form_add_new_empty_props($form, $properties_select);
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+
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+ return $form;
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+}
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+
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+/**
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+ * Validates the user input before creating an analysis node
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+ *
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+ * @ingroup tripal_analysis
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+ */
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+function chado_analysis_validate($node, &$form) {
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+ // use the analysis parent to validate the node
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+ tripal_analysis_validate($node, $form);
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+}
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+
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+/**
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+ * This validation is being used for three activities:
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+ * CASE A: Update a node that exists in both drupal and chado
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+ * CASE B: Synchronizing a node from chado to drupal
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+ * CASE C: Inserting a new node that exists in niether drupal nor chado
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+ *
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+ * @ingroup tripal_analysis
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+ */
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+function tripal_analysis_validate($node, &$form) {
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+
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+
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+ // Only nodes being updated will have an nid already
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+ if (!is_null($node->nid)) {
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+ // CASE A: We are validating a form for updating an existing node
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+
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+ // get the existing node
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+ $values = array('analysis_id' => $node->analysis_id);
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+ $result = tripal_core_chado_select('analysis', array('*'), $values);
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+ $analysis = $result[0];
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+
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+ // if the name has changed make sure it doesn't conflict with an existing name
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+ if($analysis->name != $node->analysisname) {
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+ $values = array('name' => $node->analysisname);
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+ $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
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+ if($result and count($result) > 0) {
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+ form_set_error('analysisname', 'Cannot update the analysis with this analysis name. An analysis with this name already exists.');
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+ return;
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+ }
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+ }
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+
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+ // if the unique constraint has changed check to make sure it doesn't conflict with an
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+ // existing record
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+ if($analysis->program != $node->program or $analysis->programversion != $node->programversion or
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+ $analysis->sourcename != $node->sourcename) {
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+ $values = array(
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+ 'program' => $node->program,
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+ 'programversion' => $node->programversion,
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+ 'sourcename' => $node->sourcename,
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+ );
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+ $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
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+ if ($result and count($result) > 0) {
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+ if ($analysis->program != $node->program) {
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+ $field = 'program';
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+ }
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+ if ($analysis->programversion != $node->programversion) {
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+ $field = 'programversion';
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+ }
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+ if ($analysis->sourcename != $node->sourcename) {
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+ $field = 'sourcename';
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+ }
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+ form_set_error($field, 'Cannot update the analysis with this program,
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+ program version and source name. An analysis with these values already exists.');
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+ return;
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+ }
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+ }
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+ }
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+ else{
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+ // To differentiate if we are syncing or creating a new analysis altogther, see if an
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+ // analysis_id already exists
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+ if ($node->analysis_id and $node->analysis_id != 0) {
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+ // CASE B: Synchronizing a node from chado to drupal
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+ // we don't need to do anything.
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+ }
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+ else {
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+ // CASE C: We are validating a form for inserting a new node
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+ // The unique constraint for the chado analysis table is: program, programversion, sourcename
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+ $values = array(
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+ 'program' => $node->program,
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+ 'programversion' => $node->programversion,
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+ 'sourcename' => $node->sourcename,
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+ );
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+ $analysis = tripal_core_chado_select('analysis', array('analysis_id'), $values);
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+ if ($analysis and count($analysis) > 0) {
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+ form_set_error('program', 'Cannot add the analysis with this program,
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+ program version and source name. An analysis with these values already exists.');
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+ return;
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+ }
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+
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+ // make sure we have a unique analysis name. This is not a requirement
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+ // for the analysis table but we use the analysis name for the Drupal node
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+ // title, so it should be unique
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+ $values = array('name' => $node->analysisname);
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+ $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
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+ if($result and count($result) > 0) {
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+ form_set_error('analysisname', 'Cannot add the analysis with this analysis name. An analysis with this name already exists.');
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+ return;
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+ }
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+ }
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+ }
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+}
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+
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+/*
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+ *
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+ */
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+function chado_analysis_node_form_add_new_empty_props(&$form, $properties_select) {
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+
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+ // add one more blank set of property fields
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+ $form['properties']['new']["new_id"] = array(
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+ '#type' => 'select',
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+ '#options' => $properties_select,
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+ '#ahah' => array(
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+ 'path' => "tripal_analysis/properties/description",
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+ 'wrapper' => 'tripal-analysis-new_value-desc',
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+ 'event' => 'change',
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+ 'method' => 'replace',
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+ ),
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+ );
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+ $form['properties']['new']["new_value"] = array(
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+ '#type' => 'textarea',
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+ '#default_value' => '',
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+ '#cols' => 5,
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+ '#rows' => $rows,
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+ '#description' => '<div id="tripal-analysis-new_value-desc"></div>'
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+ );
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+ $form['properties']['new']["add"] = array(
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+ '#type' => 'image_button',
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+ '#value' => t('Add'),
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+ '#src' => drupal_get_path('theme', 'tripal') . '/images/add.png',
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+ '#ahah' => array(
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+ 'path' => "tripal_analysis/properties/add",
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+ 'wrapper' => 'tripal-analysis-edit-properties-table',
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+ 'event' => 'click',
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+ 'method' => 'replace',
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+ ),
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+ '#attributes' => array('onClick' => 'return false;'),
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+ );
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+}
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+/*
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+ *
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+ */
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+function chado_analysis_node_form_add_new_props(&$form, $form_state, &$d_properties, &$d_removed) {
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+
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+ // first, add in all of the new properties that were added through a previous AHAH callback
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+ $j = 0;
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+ $num_properties++;
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+
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+ // we need to find the
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+ if ($form_state['values']) {
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+ foreach ($form_state['values'] as $element_name => $value) {
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+ if (preg_match('/new_value-(\d+)-(\d+)/', $element_name, $matches)) {
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+ $new_id = $matches[1];
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+ $rank = $matches[2];
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+
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+ // skip any properties that the user requested to delete through a previous
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+ // AHAH callback or through the current AHAH callback
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+ if($d_removed["$new_id-$rank"]) {
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+ continue;
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+ }
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+ if($form_state['post']['remove-' . $new_id . '-' . $rank]) {
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+ $d_removed["$new_id-$rank"] = 1;
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+ continue;
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+ }
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+
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+ // get this new_id information
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+ $cvterm = tripal_core_chado_select('cvterm', array('name', 'definition'), array('cvterm_id' => $new_id));
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+
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+ // add it to the $d_properties array
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+ $d_properties[$new_id][$rank]['name'] = $cvterm->name;
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+ $d_properties[$new_id][$rank]['id'] = $new_id;
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+ $d_properties[$new_id][$rank]['value'] = $value;
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+ $d_properties[$new_id][$rank]['definition'] = $cvterm->definition;
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+ $num_properties++;
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+
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+ // determine how many rows we need in the textarea
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+ $rows = 1;
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+
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+
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+ // add the new fields
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+ $form['properties']['new'][$new_id][$rank]["new_id-$new_id-$rank"] = array(
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+ '#type' => 'item',
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+ '#value' => $cvterm[0]->name
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+ );
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+ $form['properties']['new'][$new_id][$rank]["new_value-$new_id-$rank"] = array(
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+ '#type' => 'textarea',
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+ '#default_value' => $value,
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+ '#cols' => 50,
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+ '#rows' => $rows,
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+ '#description' => $cvterm->definition,
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+ );
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+
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|
+ $form['properties']['new'][$new_id][$rank]["remove-$new_id-$rank"] = array(
|
|
|
+ '#type' => 'image_button',
|
|
|
+ '#value' => t('Remove'),
|
|
|
+ '#src' => drupal_get_path('theme', 'tripal') . '/images/minus.png',
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => "tripal_analysis/properties/minus/$new_id/$rank",
|
|
|
+ 'wrapper' => 'tripal-analysis-edit-properties-table',
|
|
|
+ 'event' => 'click',
|
|
|
+ 'method' => 'replace',
|
|
|
+ ),
|
|
|
+ '#attributes' => array('onClick' => 'return false;'),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+
|
|
|
+ // second add in any new properties added during this callback
|
|
|
+ if($form_state['post']['add']) {
|
|
|
+ $new_id = $form_state['values']['new_id'];
|
|
|
+ $new_value = $form_state['values']['new_value'];
|
|
|
+
|
|
|
+ // get the rank by counting the number of entries
|
|
|
+ $rank = count($d_properties[$new_id]);
|
|
|
+
|
|
|
+ // get this new_id information
|
|
|
+ $cvterm = tripal_core_chado_select('cvterm', array('name', 'definition'), array('cvterm_id' => $new_id));
|
|
|
+
|
|
|
+ // add it to the $d_properties array
|
|
|
+ $d_properties[$new_id][$rank]['name'] = $cvterm->name;
|
|
|
+ $d_properties[$new_id][$rank]['id'] = $new_id;
|
|
|
+ $d_properties[$new_id][$rank]['value'] = $value;
|
|
|
+ $d_properties[$new_id][$rank]['definition'] = $cvterm->definition;
|
|
|
+ $num_properties++;
|
|
|
+
|
|
|
+ // determine how many rows we need in the textarea
|
|
|
+ $rows = 1;
|
|
|
+
|
|
|
+ // add the new fields
|
|
|
+ $form['properties']['new'][$new_id][$rank]["new_id-$new_id-$rank"] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => $cvterm[0]->name
|
|
|
+ );
|
|
|
+ $form['properties']['new'][$new_id][$rank]["new_value-$new_id-$rank"] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#default_value' => $new_value,
|
|
|
+ '#cols' => 50,
|
|
|
+ '#rows' => $rows,
|
|
|
+ '#description' => $cvterm->definition,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties']['new'][$new_id][$rank]["remove-$new_id-$rank"] = array(
|
|
|
+ '#type' => 'image_button',
|
|
|
+ '#value' => t('Remove'),
|
|
|
+ '#src' => drupal_get_path('theme', 'tripal') . '/images/minus.png',
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => "tripal_analysis/properties/minus/$new_id/$rank",
|
|
|
+ 'wrapper' => 'tripal-analysis-edit-properties-table',
|
|
|
+ 'event' => 'click',
|
|
|
+ 'method' => 'replace',
|
|
|
+ ),
|
|
|
+ '#attributes' => array('onClick' => 'return false;'),
|
|
|
+ );
|
|
|
+
|
|
|
+ }
|
|
|
+
|
|
|
+ return $num_properties;
|
|
|
+}
|
|
|
+/*
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_analysis_node_form_add_analysisprop_table_props(&$form, $form_state, $analysis_id, &$d_properties, &$d_removed) {
|
|
|
+
|
|
|
+ // get the properties for this analysis
|
|
|
+ $num_properties = 0;
|
|
|
+
|
|
|
+ if(!$analysis_id) {
|
|
|
+ return $num_properties;
|
|
|
+ }
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT CVT.cvterm_id, CVT.name, CVT.definition, PP.value, PP.rank
|
|
|
+ FROM {analysisprop} PP
|
|
|
+ INNER JOIN {cvterm} CVT on CVT.cvterm_id = PP.type_id
|
|
|
+ WHERE PP.analysis_id = %d
|
|
|
+ ORDER BY CVT.name, PP.rank
|
|
|
+ ";
|
|
|
+ $analysis_props = chado_query($sql, $analysis_id);
|
|
|
+ while ($prop = db_fetch_object($analysis_props)) {
|
|
|
+
|
|
|
+ $type_id = $prop->cvterm_id;
|
|
|
+ $rank = count($d_properties[$type_id]);
|
|
|
+
|
|
|
+ // skip any properties that the user requested to delete through a previous
|
|
|
+ // AHAH callback or through the current AHAH callback
|
|
|
+ if($d_removed["$type_id-$rank"]) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ if($form_state['post']['remove-' . $type_id . '-' . $rank]) {
|
|
|
+ $d_removed["$type_id-$rank"] = 1;
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+
|
|
|
+ $d_properties[$type_id][$rank]['name'] = $prop->name;
|
|
|
+ $d_properties[$type_id][$rank]['id'] = $type_id;
|
|
|
+ $d_properties[$type_id][$rank]['value'] = $prop->value;
|
|
|
+ $d_properties[$type_id][$rank]['definition'] = $prop->definition;
|
|
|
+ $num_properties++;
|
|
|
+
|
|
|
+ $form['properties'][$type_id][$rank]["prop_id-$type_id-$rank"] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => $prop->name,
|
|
|
+ );
|
|
|
+ $form['properties'][$type_id][$rank]["prop_value-$type_id-$rank"] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#default_value' => $prop->value,
|
|
|
+ '#cols' => 50,
|
|
|
+ '#rows' => $rows,
|
|
|
+ '#description' => $prop->definition,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['properties'][$type_id][$rank]["remove-$type_id-$rank"] = array(
|
|
|
+ '#type' => 'image_button',
|
|
|
+ '#value' => t('Remove'),
|
|
|
+ '#src' => drupal_get_path('theme', 'tripal') . '/images/minus.png',
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => "tripal_analysis/properties/minus/$type_id/$rank",
|
|
|
+ 'wrapper' => 'tripal-analysis-edit-properties-table',
|
|
|
+ 'event' => 'click',
|
|
|
+ 'method' => 'replace',
|
|
|
+ ),
|
|
|
+ '#attributes' => array('onClick' => 'return false;'),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ return $num_properties;
|
|
|
+}
|
|
|
+/*
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_analysis_theme_node_form_properties($form) {
|
|
|
+ $rows = array();
|
|
|
+
|
|
|
+ if ($form['properties']) {
|
|
|
+
|
|
|
+ // first add in the properties derived from the analysisprop table
|
|
|
+ // the array tree for these properties looks like this:
|
|
|
+ // $form['properties'][$type_id][$rank]["prop_id-$type_id-$rank"]
|
|
|
+ foreach ($form['properties'] as $type_id => $elements) {
|
|
|
+ // there are other fields in the properties array so we only
|
|
|
+ // want the numeric ones those are our type_id
|
|
|
+ if (is_numeric($type_id)) {
|
|
|
+ foreach ($elements as $rank => $element) {
|
|
|
+ if (is_numeric($rank)) {
|
|
|
+ $rows[] = array(
|
|
|
+ drupal_render($element["prop_id-$type_id-$rank"]),
|
|
|
+ drupal_render($element["prop_value-$type_id-$rank"]),
|
|
|
+ drupal_render($element["remove-$type_id-$rank"]),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // second, add in any new properties added by the user through AHAH callbacks
|
|
|
+ // the array tree for these properties looks like this:
|
|
|
+ // $form['properties']['new'][$type_id][$rank]["new_id-$new_id-$rank"]
|
|
|
+ foreach ($form['properties']['new'] as $type_id => $elements) {
|
|
|
+ if (is_numeric($type_id)) {
|
|
|
+ foreach ($elements as $rank => $element) {
|
|
|
+ if (is_numeric($rank)) {
|
|
|
+ $rows[] = array(
|
|
|
+ drupal_render($element["new_id-$type_id-$rank"]),
|
|
|
+ drupal_render($element["new_value-$type_id-$rank"]),
|
|
|
+ drupal_render($element["remove-$type_id-$rank"]),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // finally add in a set of blank field for adding a new property
|
|
|
+ $rows[] = array(
|
|
|
+ drupal_render($form['properties']['new']['new_id']),
|
|
|
+ drupal_render($form['properties']['new']['new_value']),
|
|
|
+ drupal_render($form['properties']['new']['add']),
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+ $headers = array('Property Type','Value', '');
|
|
|
+ return theme('table', $headers, $rows, array('id'=> "tripal-analysis-edit-properties-table"));
|
|
|
+}
|
|
|
+
|
|
|
+/*
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_analysis_property_add() {
|
|
|
+ $status = TRUE;
|
|
|
+
|
|
|
+ // prepare and render the form
|
|
|
+ $form = tripal_core_ahah_prepare_form();
|
|
|
+
|
|
|
+ // we only want to return the properties as that's all we'll replace with this AHAh callback
|
|
|
+ $data = tripal_analysis_theme_node_form_properties($form);
|
|
|
+
|
|
|
+ // bind javascript events to the new objects that will be returned
|
|
|
+ // so that AHAH enabled elements will work.
|
|
|
+ $settings = tripal_core_ahah_bind_events();
|
|
|
+
|
|
|
+ // return the updated JSON
|
|
|
+ drupal_json(
|
|
|
+ array(
|
|
|
+ 'status' => $status,
|
|
|
+ 'data' => $data,
|
|
|
+ 'settings' => $settings,
|
|
|
+ )
|
|
|
+ );
|
|
|
+}
|
|
|
+/*
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_analysis_property_delete() {
|
|
|
+ $status = TRUE;
|
|
|
+
|
|
|
+ // prepare and render the form
|
|
|
+ $form = tripal_core_ahah_prepare_form();
|
|
|
+
|
|
|
+ // we only want to return the properties as that's all we'll replace with this AHAh callback
|
|
|
+ $data = tripal_analysis_theme_node_form_properties($form);
|
|
|
+
|
|
|
+ // bind javascript events to the new objects that will be returned
|
|
|
+ // so that AHAH enabled elements will work.
|
|
|
+ $settings = tripal_core_ahah_bind_events();
|
|
|
+
|
|
|
+ // return the updated JSON
|
|
|
+ drupal_json(
|
|
|
+ array(
|
|
|
+ 'status' => $status,
|
|
|
+ 'data' => $data,
|
|
|
+ 'settings' => $settings,
|
|
|
+ )
|
|
|
+ );
|
|
|
+}
|
|
|
+/*
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_analysis_property_get_description() {
|
|
|
+ $new_id = $_POST['new_id'];
|
|
|
+
|
|
|
+ $values = array('cvterm_id' => $new_id);
|
|
|
+ $cvterm = tripal_core_chado_select('cvterm', array('definition'), $values);
|
|
|
+
|
|
|
+ $description = ' ';
|
|
|
+ if ($cvterm[0]->definition) {
|
|
|
+ $description = $cvterm[0]->definition;
|
|
|
+ }
|
|
|
+ drupal_json(
|
|
|
+ array(
|
|
|
+ 'status' => TRUE,
|
|
|
+ 'data' => '<div id="tripal-analysis-new_value-desc">' . $description . '</div>',
|
|
|
+ )
|
|
|
+ );
|
|
|
+}
|
|
|
+/*
|
|
|
+ *
|
|
|
+ */
|
|
|
+function theme_chado_analysis_node_form($form) {
|
|
|
+
|
|
|
+ $properties_table = tripal_analysis_theme_node_form_properties($form);
|
|
|
+
|
|
|
+ $markup = drupal_render($form['analysis_id']);
|
|
|
+ $markup .= drupal_render($form['title']);
|
|
|
+ $markup .= drupal_render($form['type_id']);
|
|
|
+ $markup .= drupal_render($form['description']);
|
|
|
+ $markup .= "<b>Include Additional Details</b><br>You may add additional properties to this analysis by scrolling to the bottom of this table, selecting a property type from the dropdown and adding text. You may add as many properties as desired by clicking the plus button on the right. To remove a property, click the minus button";
|
|
|
+ $markup .= $properties_table;
|
|
|
+
|
|
|
+ $form['properties'] = array(
|
|
|
+ '#type' => 'markup',
|
|
|
+ '#value' => $markup,
|
|
|
+ );
|
|
|
+ $form['buttons']['#weight'] = 50;
|
|
|
+ return drupal_render($form);
|
|
|
+}
|
spficklin