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@@ -303,6 +303,49 @@ function chado_analysis_update($node){
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*/
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function chado_analysis_form ($node){
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+ $analysis = $node->analysis;
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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 = $analysis->description;
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+ }
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$form = array();
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$form['title']= array(
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'#type' => 'hidden',
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@@ -310,13 +353,13 @@ function chado_analysis_form ($node){
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);
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$form['analysis_id']= array(
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'#type' => 'hidden',
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- '#default_value' => $node->analysis->analysis_id,
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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' => FALSE,
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- '#default_value' => $node->analysis->name,
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+ '#default_value' => $analysisname,
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'#description' => t("This should be a handy short identifier that
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describes the analysis succintly as possible which helps the user find analyses."),
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);
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@@ -324,28 +367,28 @@ function chado_analysis_form ($node){
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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' => $node->analysis->program,
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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' => $node->analysis->programversion,
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+ '#default_value' => $programversion,
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'#description' => t("Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]"),
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);
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$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' => $node->analysis->algorithm,
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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' => $node->analysis->sourcename,
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+ '#default_value' => $sourcename,
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'#description' => t('The name of the source data. This could be a file name, data set name or a
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small description for how the data was collected. For long descriptions use the description field below'),
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@@ -354,20 +397,20 @@ function chado_analysis_form ($node){
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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' => $node->analysis->sourceversion,
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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' => $node->analysis->sourceuri,
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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 = $node->analysis->timeexecuted;
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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", $default_time);
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@@ -393,7 +436,7 @@ function chado_analysis_form ($node){
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'#rows' => 15,
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'#title' => t('Description and/or Program Settings'),
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'#required' => FALSE,
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- '#default_value' => $node->analysis->description,
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+ '#default_value' => $description,
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'#description' => t('Please provide all necessary information to allow
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someone to recreate the analysis, including materials and methods
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for collection of the source data and performing the analysis'),
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@@ -409,38 +452,15 @@ function chado_analysis_form ($node){
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* @ingroup tripal_analysis
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*/
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function chado_analysis_load($node){
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- $additions = new stdClass();
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- // get the analysis_id for this node:
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- $sql = "SELECT analysis_id FROM {chado_analysis} WHERE nid = %d";
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- $ana_node = db_fetch_object(db_query($sql, $node->nid));
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- if ($ana_node) {
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- // get analysis information
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- $sql = "SELECT Analysis_id, name, description, program, ".
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- " programversion, algorithm, sourcename, sourceversion, ".
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- " sourceuri, timeexecuted ".
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- "FROM {Analysis} ".
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- "WHERE Analysis_id = $ana_node->analysis_id";
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- $previous_db = tripal_db_set_active('chado'); // use chado database
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- $additions->analysis = db_fetch_object(db_query($sql));
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+ // get the feature details from chado
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+ $analysis_id = chado_get_id_for_node('analysis',$node);
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- // get number of features assc with this analysis
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-// $sql = "SELECT count(feature_id) as featurecount ".
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-// "FROM {Analysisfeature} ".
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-// "WHERE Analysis_id = %d";
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-// $additions->featurecount = db_result(db_query($sql, $ana_node->analysis_id));
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+ $values = array('analysis_id' => $analysis_id);
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+ $analysis = tripal_core_generate_chado_var('analysis',$values);
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- tripal_db_set_active($previous_db); // now use drupal database
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- }
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- // If the analysis has a name, use it as the node title. If not, construct
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- // the title using program programversion, and sourcename
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- if ($additions->analysis->name) {
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- $additions->title = $additions->analysis->name;
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- } else {
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- // Construct node title as "program version (source)
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- $additions->title = "$additions->analysis->program ($additions->analysis->programversion)";
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- }
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- return $additions;
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+ $additions->analysis = $analysis;
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+ return $additions;
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}
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/*******************************************************************************
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spficklin