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@@ -1,15 +1,16 @@
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<?php
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+
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+require_once "parseInterpro.inc";
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+
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/*******************************************************************************
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* Tripal Interpro lets users show/hide iprscan results associated with a tripal
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* feature
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******************************************************************************/
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function tripal_analysis_interpro_init(){
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// Add javascript and style sheet
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- drupal_add_css(drupal_get_path('theme', 'tripal').
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- '/css/tripal_analysis_interpro.css');
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+ drupal_add_css(drupal_get_path('theme', 'tripal').'/css/tripal_analysis_interpro.css');
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// Add javascript and style sheet
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- drupal_add_js(drupal_get_path('theme', 'tripal').
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- '/js/tripal_analysis_interpro.js');
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+ drupal_add_js(drupal_get_path('theme', 'tripal').'/js/tripal_analysis_interpro.js');
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}
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/*******************************************************************************
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* Provide information to drupal about the node types that we're creating
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@@ -60,99 +61,19 @@ function tripal_analysis_interpro_block($op = 'list', $delta = 0, $edit=array())
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*/
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function chado_analysis_interpro_form ($node){
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- $type = node_get_types('type', $node);
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- $form = array();
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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['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->analysisname,
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- '#weight' => 1
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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' => $node->program,
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- '#weight' => 2
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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->programversion,
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- '#weight' => 3
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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->algorithm,
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- '#weight' => 4
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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' => FALSE,
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- '#default_value' => $node->sourcename,
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- '#weight' => 5
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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' => $node->sourceversion,
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- '#weight' => 6
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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->sourceuri,
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- '#weight' => 7
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- );
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- // Get time saved in chado
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- $default_time = $node->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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- '#weight' => 8
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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('Description and/or Program Settings'),
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- '#required' => FALSE,
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- '#default_value' => $node->description,
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- '#weight' => 9
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- );
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+ // add in the default fields for the analysis
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+ $form = chado_analysis_form($node);
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+
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+ $analysis = $node->analysis;
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+
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+ $interprofile = $analysis->tripal_analysis_interpro->interprofile;
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+ $interproparameters = $analysis->tripal_analysis_interpro->interproparameters;
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+ $parsego = $analysis->tripal_analysis_interpro->parsego;
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+ $query_re = $analysis->tripal_analysis_interpro->query_re;
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+ $query_type = $analysis->tripal_analysis_interpro->query_type;
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+ $query_uniquename = $analysis->tripal_analysis_interpro->query_uniquename;
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+
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- //----InterProScan Settings (Shown only when Tripal Interpro is enabled) ----
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- if (preg_match("/.*\|.*/",$node->interprofile)) {
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- $prop_values = explode("|", $node->interprofile);
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- $node->interprofile = $prop_values[0];
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- $node->interproparameters = $prop_values[1];
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- }
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$moreSettings ['interpro'] = 'Interpro Settings';
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$form['interpro'] = array(
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'#title' => t('Interpro Settings'),
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@@ -163,19 +84,19 @@ function chado_analysis_interpro_form ($node){
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'#weight' => 11
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);
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$form['interpro']['interprofile'] = array(
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- '#title' => t('Interproscan Output File (in html format)'),
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+ '#title' => t('Interproscan Output File (in XML format)'),
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'#type' => 'textfield',
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- '#description' => t('The html output file generated by Interproscan in full path.'),
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- '#default_value' => $node->interprofile,
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+ '#description' => t('Please provide the full path to the XML output file generated by InterProScan.'),
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+ '#default_value' => $interprofile,
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);
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$form['interpro']['interprojob'] = array(
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'#type' => 'checkbox',
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- '#title' => t('Submit a job to parse the Interpro html output'),
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+ '#title' => t('Submit a job to parse the InterProScan XML file'),
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'#description' => t('Note: features associated with the interpro results must '.
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'exist in chado before parsing the file. Otherwise, interpro '.
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'results that cannot be linked to a feature will be '.
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- 'discarded. Also, Triapl Interpro module needs to be enabled.'),
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- '#default_value' => $node->interprojob,
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+ 'discarded.'),
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+ '#default_value' => $interprojob,
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'#attributes' => array(
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'onclick' => 'return isSubmittingJob(this)'
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)
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@@ -184,290 +105,167 @@ function chado_analysis_interpro_form ($node){
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'#type' => 'checkbox',
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'#title' => t('Load GO terms to the database'),
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'#description' => t('Check the box to load GO terms to chado database'),
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- '#default_value' => $node->parsego
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+ '#default_value' => $parsego
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);
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$form['interpro']['interproparameters'] = array(
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'#title' => t('Parameters'),
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'#type' => 'textfield',
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- '#description' => t('The parameters for running the interpro analysis.'),
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- '#default_value' => $node->interproparameters,
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+ '#description' => t('The parameters used when running the InterProScan analysis.'),
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+ '#default_value' => $interproparameters,
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+ );
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+
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+ $form['interpro']['query_re'] = array(
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+ '#title' => t('Query Name RE'),
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+ '#type' => 'textfield',
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+ '#description' => t('Enter the regular expression that will extract the '.
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+ 'feature name from the query line in the interpro results. This should be '.
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+ 'the same as the definition line in the query FASTA file. This option is '.
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+ 'is only required when the query does not identically match a feature '.
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+ 'in the database.'),
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+ '#default_value' => $query_re,
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+ );
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+
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+ $form['interpro']['query_type'] = array(
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+ '#title' => t('Query Type'),
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+ '#type' => 'textfield',
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+ '#description' => t('Please enter the Sequence Ontology term that describes '.
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+ 'the query sequences used for InterProScan. This is only necessary if two '.
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+ 'or more sequences have the same name.'),
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+ '#default_value' => $query_type,
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+ );
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+
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+ $form['interpro']['query_uniquename'] = array(
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+ '#title' => t('Use Unique Name'),
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+ '#type' => 'checkbox',
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+ '#description' => t('Select this checboxk if the query name in the results file '.
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+ 'matches the uniquename of the feature. By default, the blast results will '.
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+ 'mapped to the "name" of the feature.'),
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+ '#default_value' => $query_uniquename,
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);
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return $form;
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}
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-/*******************************************************************************
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+/**
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+ *
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+ *
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+ */
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+function chado_analysis_interpro_load($node){
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+
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+ // load the default set of analysis fields
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+ $additions = chado_analysis_load($node);
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+
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+ // create some variables for easier lookup
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+ $analysis = $additions->analysis;
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+ $analysis_id = $analysis->analysis_id;
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+
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+ $intepro_settings = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_settings');
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+ $interprofile = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_interprofile');
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+ $interproparameters= tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_interproparameters');
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+ $parsego = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_parsego');
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+ $query_re = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_query_re');
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+ $query_type = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_query_type');
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+ $query_uniquename = tripal_analysis_get_property($analysis->analysis_id,'analysis_interpro_query_uniquename');
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+
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+ $analysis->tripal_analysis_interpro->interprofile = $interprofile->value;
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+ $analysis->tripal_analysis_interpro->interproparameters= $interproparameters->value;
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+ $analysis->tripal_analysis_interpro->parsego = $parsego->value;
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+ $analysis->tripal_analysis_interpro->query_re = $query_re->value;
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+ $analysis->tripal_analysis_interpro->query_type = $query_type->value;
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+ $analysis->tripal_analysis_interpro->query_uniquename = $query_uniquename->value;
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+
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+ // if there is an old style 'interpro_settings' array, then break these out for
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+ // use in the new format
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+ if(count($interpro_settings)>0){
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+ $prop_values = explode ("|", $interpro_settings->value);
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+ $analysis->tripal_analysis_interpro->interprofile = $prop_values[0];
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+ $analysis->tripal_analysis_interpro->interproparameters = $prop_values[1];
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+ }
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+ return $additions;
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+}
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+/**
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*
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*/
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function chado_analysis_interpro_insert($node){
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- global $user;
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- // Create a timestamp so we can insert it into the chado database
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- $time = $node->timeexecuted;
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- $month = $time['month'];
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- $day = $time['day'];
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- $year = $time['year'];
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- $timestamp = $month.'/'.$day.'/'.$year;
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-
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- // If this analysis already exists then don't recreate it in chado
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- $analysis_id = $node->analysis_id;
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- if ($analysis_id) {
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- $sql = "SELECT analysis_id ".
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- "FROM {Analysis} ".
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- "WHERE analysis_id = %d ";
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- $previous_db = tripal_db_set_active('chado');
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- $analysis = db_fetch_object(db_query($sql, $node->analysis_id));
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- tripal_db_set_active($previous_db);
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- }
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+ // insert the analysistripal_core_generate_chado_var
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+ chado_analysis_insert($node);
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+
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+ // set the type for this analysis
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_type','tripal_analysis_interpro');
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+
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+ // now add in the remaining settings as a single property but separated by bars
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_interprofile',$node->interprofile);
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_interproparameters',$node->interproparameters);
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_parsego',$node->parsego);
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_query_re',$node->query_re);
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_query_type',$node->query_type);
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+ tripal_analysis_insert_property($node->analysis_id,'analysis_interpro_query_uniquename',$node->query_uniquename);
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+
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+ // submit the parsing jobs
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+ chado_analysis_interpro_submit_job($node);
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- // If the analysis doesn't exist then let's create it in chado.
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- if(!$analysis){
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- // First add the item to the chado analysis table
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- $sql = "INSERT INTO {analysis} ".
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- " (name, description, program, programversion, algorithm, ".
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- " sourcename, sourceversion, sourceuri, timeexecuted) ".
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- "VALUES ('%s','%s','%s','%s','%s','%s','%s','%s','%s')";
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- $previous_db = tripal_db_set_active('chado'); // use chado database
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- db_query($sql,$node->analysisname, $node->description,
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- $node->program,$node->programversion,$node->algorithm,
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- $node->sourcename, $node->sourceversion, $node->sourceuri,
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- $timestamp);
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-
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- // find the newly entered analysis_id
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- $sql = "SELECT analysis_id ".
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- "FROM {Analysis} ".
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- "WHERE program='%s'".
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- "AND programversion='%s'".
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- "AND sourcename='%s'";
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- $analysis_id = db_result(db_query($sql, $node->program,
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- $node->programversion, $node->sourcename));
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-
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- // Get cvterm_id for 'analysis_interpro_settings'
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- $sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
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- "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
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- "WHERE CVT.name = 'analysis_interpro_settings' ".
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- "AND CV.name = 'tripal'";
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- $type_id = db_result(db_query($sql));
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-
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- // Insert into chado {analysisprop} table
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- $sql = "INSERT INTO {analysisprop} (analysis_id, type_id, value) ".
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- "VALUES (%d, %d, '%s')";
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- $interprosettings = $node->interprofile."|".$node->interproparameters;
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- db_query($sql, $analysis_id, $type_id, $interprosettings);
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-
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- tripal_db_set_active($previous_db); // switch back to drupal database
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- // Add a job if the user wants to parse the html output
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- if($node->interprojob) {
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- $job_args[0] = $analysis_id;
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- $job_args[1] = $node->interprofile;
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- if ($node->parsego) {
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- $job_args[2] = 1;
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- } else {
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- $job_args[2] = 0;
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- }
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- if (is_readable($node->interprofile)) {
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- $fname = preg_replace("/.*\/(.*)/", "$1", $node->interprofile);
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- tripal_add_job("Parse interpro: $fname",'tripal_analysis_interpro',
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- 'tripal_analysis_interpro_parseHTMLFile', $job_args, $user->uid);
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- } else {
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- drupal_set_message("Can not open interpro output file. Job not scheduled.");
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- }
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- }
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- }
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-
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- // Make sure the entry for this analysis doesn't already exist in the
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- // chado_analysis table if it doesn't exist then we want to add it.
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- $node_check_sql = "SELECT * FROM {chado_analysis} ".
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- "WHERE analysis_id = %d";
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- $node_check = db_fetch_object(db_query($node_check_sql, $analysis_id));
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- if(!$node_check){
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- // next add the item to the drupal table
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- $sql = "INSERT INTO {chado_analysis} (nid, vid, analysis_id) ".
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- "VALUES (%d, %d, %d)";
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- db_query($sql,$node->nid,$node->vid,$analysis_id);
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- // Create a title for the analysis node using the unique keys so when the
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- // node is saved, it will have a title
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- $record = new stdClass();
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- // If the analysis has a name, use it as the node title. If not, construct
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- // the title using program, programversion, and sourcename
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- if ($node->analysisname) {
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- $record->title = $node->analysisname;
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- } else {
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- //Construct node title as "program (version)
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- $record->title = "$node->program ($node->programversion)";
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- }
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- $record->nid = $node->nid;
|
|
|
- drupal_write_record('node',$record,'nid');
|
|
|
- drupal_write_record('node_revisions',$record,'nid');
|
|
|
- }
|
|
|
}
|
|
|
-/*******************************************************************************
|
|
|
- * Delete interpro anlysis
|
|
|
+/**
|
|
|
+ *
|
|
|
*/
|
|
|
-function chado_analysis_interpro_delete($node){
|
|
|
- // Before removing, get analysis_id so we can remove it from chado database
|
|
|
- // later
|
|
|
- $sql_drupal = "SELECT analysis_id ".
|
|
|
- "FROM {chado_analysis} ".
|
|
|
- "WHERE nid = %d ".
|
|
|
- "AND vid = %d";
|
|
|
- $analysis_id = db_result(db_query($sql_drupal, $node->nid, $node->vid));
|
|
|
-
|
|
|
- // Remove data from the {chado_analysis}, {node}, and {node_revisions} tables
|
|
|
- $sql_del = "DELETE FROM {chado_analysis} ".
|
|
|
- "WHERE nid = %d ".
|
|
|
- "AND vid = %d";
|
|
|
- db_query($sql_del, $node->nid, $node->vid);
|
|
|
- $sql_del = "DELETE FROM {node} ".
|
|
|
- "WHERE nid = %d ".
|
|
|
- "AND vid = %d";
|
|
|
- db_query($sql_del, $node->nid, $node->vid);
|
|
|
- $sql_del = "DELETE FROM {node_revisions} ".
|
|
|
- "WHERE nid = %d ".
|
|
|
- "AND vid = %d";
|
|
|
- db_query($sql_del, $node->nid, $node->vid);
|
|
|
-
|
|
|
- //Remove from analysisfeatureprop, analysisfeature, analysis, and analysisprop tables
|
|
|
- $previous_db = tripal_db_set_active('chado');
|
|
|
- $sql = "SELECT analysisfeature_id FROM {analysisfeature} WHERE analysis_id=%d";
|
|
|
- $results = db_query($sql, $analysis_id);
|
|
|
- while ($af = db_fetch_object($results)) {
|
|
|
- db_query("DELETE FROM {analysisfeatureprop} WHERE analysisfeature_id = %d", $af->analysisfeature_id);
|
|
|
+function chado_analysis_interpro_update($node){
|
|
|
+ // insert the analysistripal_core_generate_chado_var
|
|
|
+ chado_analysis_update($node);
|
|
|
+
|
|
|
+ // set the type for this analysis
|
|
|
+ tripal_analysis_update_property($node->analysis_id,'analysis_type','tripal_analysis_interpro',1);
|
|
|
+
|
|
|
+ // now add in the remaining settings as a single property but separated by bars
|
|
|
+ tripal_analysis_update_property($node->analysis_id,'analysis_interpro_interprofile',$node->interprofile,1);
|
|
|
+ tripal_analysis_update_property($node->analysis_id,'analysis_interpro_interproparameters',$node->interproparameters,1);
|
|
|
+ tripal_analysis_update_property($node->analysis_id,'analysis_interpro_parsego',$node->parsego,1);
|
|
|
+ tripal_analysis_update_property($node->analysis_id,'analysis_interpro_query_re',$node->query_re,1);
|
|
|
+ tripal_analysis_update_property($node->analysis_id,'analysis_interpro_query_type',$node->query_type,1);
|
|
|
+ tripal_analysis_update_property($node->analysis_id,'analysis_interpro_query_uniquename',$node->query_uniquename,1);
|
|
|
+
|
|
|
+ // if this analysis uses the old style settings cvterm then remove that term
|
|
|
+ $old = tripal_analysis_get_property($node->analysis_id,'analysis_interpro_settings');
|
|
|
+ if(count($old) > 0){
|
|
|
+ tripal_analysis_delete_property($node->analysis_id,'analysis_interpro_settings');
|
|
|
}
|
|
|
- db_query("DELETE FROM {analysisfeature} WHERE analysis_id = %d", $analysis_id);
|
|
|
- db_query("DELETE FROM {analysisprop} WHERE analysis_id = %d", $analysis_id);
|
|
|
- db_query("DELETE FROM {analysis} WHERE analysis_id = %d", $analysis_id);
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
+
|
|
|
+ // submit the parsing jobs
|
|
|
+ chado_analysis_interpro_submit_job($node);
|
|
|
}
|
|
|
-
|
|
|
/*******************************************************************************
|
|
|
- * Update interpro analysis
|
|
|
+ * Delete interpro anlysis
|
|
|
*/
|
|
|
-function chado_analysis_interpro_update($node){
|
|
|
- global $user;
|
|
|
- if($node->revision){
|
|
|
- // TODO -- decide what to do about revisions
|
|
|
- } else {
|
|
|
- // Create a timestamp so we can insert it into the chado database
|
|
|
- $time = $node->timeexecuted;
|
|
|
- $month = $time['month'];
|
|
|
- $day = $time['day'];
|
|
|
- $year = $time['year'];
|
|
|
- $timestamp = $month.'/'.$day.'/'.$year;
|
|
|
-
|
|
|
- // get the analysis_id for this node:
|
|
|
- $sql = "SELECT analysis_id ".
|
|
|
- "FROM {chado_analysis} ".
|
|
|
- "WHERE vid = %d";
|
|
|
- $analysis_id = db_fetch_object(db_query($sql, $node->vid))->analysis_id;
|
|
|
-
|
|
|
- $sql = "UPDATE {analysis} ".
|
|
|
- "SET name = '%s', ".
|
|
|
- " description = '%s', ".
|
|
|
- " program = '%s', ".
|
|
|
- " programversion = '%s', ".
|
|
|
- " algorithm = '%s', ".
|
|
|
- " sourcename = '%s', ".
|
|
|
- " sourceversion = '%s', ".
|
|
|
- " sourceuri = '%s', ".
|
|
|
- " timeexecuted = '%s' ".
|
|
|
- "WHERE analysis_id = %d ";
|
|
|
-
|
|
|
- $previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
- db_query($sql, $node->analysisname, $node->description, $node->program,
|
|
|
- $node->programversion,$node->algorithm,$node->sourcename,
|
|
|
- $node->sourceversion, $node->sourceuri, $timestamp, $analysis_id);
|
|
|
-
|
|
|
- // Get cvterm_id for 'analysis_interpro_settings'
|
|
|
- $sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
|
|
|
- "INNER JOIN cv CV ON CV.cv_id = CVT.cv_id ".
|
|
|
- "WHERE CVT.name = 'analysis_interpro_settings' ".
|
|
|
- "AND CV.name = 'tripal'";
|
|
|
- $type_id = db_result(db_query($sql));
|
|
|
-
|
|
|
- $sql = "UPDATE {analysisprop} ".
|
|
|
- "SET value = '%s' ".
|
|
|
- "WHERE analysis_id = %d AND type_id = %d";
|
|
|
- $interprosettings = $node->interprofile."|".$node->interproparameters;
|
|
|
- db_query($sql, $interprosettings, $analysis_id, $type_id);
|
|
|
- tripal_db_set_active($previous_db); // switch back to drupal database
|
|
|
- // Add a job if the user wants to parse the html output
|
|
|
- if($node->interprojob) {
|
|
|
- $job_args[0] = $analysis_id;
|
|
|
- $job_args[1] = $node->interprofile;
|
|
|
- if ($node->parsego) {
|
|
|
- $job_args[2] = 1;
|
|
|
- } else {
|
|
|
- $job_args[2] = 0;
|
|
|
- }
|
|
|
- if (is_readable($node->interprofile)) {
|
|
|
- $fname = preg_replace("/.*\/(.*)/", "$1", $node->interprofile);
|
|
|
- tripal_add_job("Parse interpro: $fname",'tripal_analysis_interpro',
|
|
|
- 'tripal_analysis_interpro_parseHTMLFile', $job_args, $user->uid);
|
|
|
- } else {
|
|
|
- drupal_set_message("Can not open interpro output file. Job not scheduled.");
|
|
|
- }
|
|
|
- }
|
|
|
+function chado_analysis_interpro_delete($node){
|
|
|
+ chado_analysis_delete($node);
|
|
|
+}
|
|
|
|
|
|
- // Create a title for the analysis node using the unique keys so when the
|
|
|
- // node is saved, it will have a title
|
|
|
- $record = new stdClass();
|
|
|
- // If the analysis has a name, use it as the node title. If not, construct
|
|
|
- // the title using program, programversion, and sourcename
|
|
|
- if ($node->analysisname) {
|
|
|
- $record->title = $node->analysisname;
|
|
|
+/**
|
|
|
+*
|
|
|
+*/
|
|
|
+function chado_analysis_interpro_submit_job($node){
|
|
|
+ global $user;
|
|
|
+
|
|
|
+ // Add a job if the user wants to parse the html output
|
|
|
+ if($node->interprojob) {
|
|
|
+ $job_args[0] = $node->analysis_id;
|
|
|
+ $job_args[1] = $node->interprofile;
|
|
|
+ if ($node->parsego) {
|
|
|
+ $job_args[2] = 1;
|
|
|
+ } else {
|
|
|
+ $job_args[2] = 0;
|
|
|
+ }
|
|
|
+ $job_args[3] = $node->query_re;
|
|
|
+ $job_args[4] = $node->query_type;
|
|
|
+ $job_args[5] = $node->query_uniquename;
|
|
|
+
|
|
|
+ if (is_readable($node->interprofile)) {
|
|
|
+ $fname = preg_replace("/.*\/(.*)/", "$1", $node->interprofile);
|
|
|
+ tripal_add_job("Parse interpro: $fname",'tripal_analysis_interpro',
|
|
|
+ 'tripal_analysis_interpro_parseXMLFile', $job_args, $user->uid);
|
|
|
} else {
|
|
|
- //Construct node title as "program (version)
|
|
|
- $record->title = "$node->program ($node->programversion)";
|
|
|
+ drupal_set_message("Can not open interpro output file. Job not scheduled.");
|
|
|
}
|
|
|
- $record->nid = $node->nid;
|
|
|
- drupal_write_record('node',$record,'nid');
|
|
|
- drupal_write_record('node_revisions',$record,'nid');
|
|
|
}
|
|
|
}
|
|
|
-/*******************************************************************************
|
|
|
- * When a node is requested by the user this function is called to allow us
|
|
|
- * to add auxiliary data to the node object.
|
|
|
- */
|
|
|
-function chado_analysis_interpro_load($node){
|
|
|
- // get the analysis_id for this node:
|
|
|
- $sql = "SELECT analysis_id FROM {chado_analysis} WHERE vid = %d";
|
|
|
- $ana_node = db_fetch_object(db_query($sql, $node->vid));
|
|
|
- $additions = new stdClass();
|
|
|
- if ($ana_node) {
|
|
|
- // get analysis information
|
|
|
- $sql = "SELECT Analysis_id, name AS analysisname, description, program, ".
|
|
|
- " programversion, algorithm, sourcename, sourceversion, ".
|
|
|
- " sourceuri, timeexecuted ".
|
|
|
- "FROM {Analysis} ".
|
|
|
- "WHERE Analysis_id = $ana_node->analysis_id";
|
|
|
- $previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
- $additions = db_fetch_object(db_query($sql));
|
|
|
-
|
|
|
- // get cvterm_id for 'analysis_interpro_settings'
|
|
|
- $sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
|
|
|
- "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
|
|
|
- "WHERE CVT.name = 'analysis_interpro_settings' ".
|
|
|
- "AND CV.name = 'tripal'";
|
|
|
- $type_id = db_result(db_query($sql));
|
|
|
- // get analysisprop information
|
|
|
- $sql = "SELECT value FROM {analysisprop} ".
|
|
|
- "WHERE analysis_id = %d ".
|
|
|
- "AND type_id = %d";
|
|
|
- $analysisprop = db_result(db_query($sql, $ana_node->analysis_id, $type_id));
|
|
|
- $prop_values = explode ("|", $analysisprop, 1);
|
|
|
- $additions->interprofile = $prop_values[0];
|
|
|
- $additions->interproparameters = $prop_values[1];
|
|
|
-
|
|
|
- tripal_db_set_active($previous_db); // now use drupal database
|
|
|
- }
|
|
|
- // If the analysis has a name, use it as the node title. If not, construct
|
|
|
- // the title using program programversion, and sourcename
|
|
|
- if ($additions->analysisname) {
|
|
|
- $additions->title = $additions->analysisname;
|
|
|
- } else {
|
|
|
- // Construct node title as "program version (source)
|
|
|
- $additions->title = "$additions->program ($additions->programversion)";
|
|
|
- }
|
|
|
- return $additions;
|
|
|
-}
|
|
|
+
|
|
|
|
|
|
/*******************************************************************************
|
|
|
* This function customizes the view of the chado_analysis node. It allows
|
|
|
@@ -498,244 +296,6 @@ function chado_analysis_interpro_view ($node, $teaser = FALSE, $page = FALSE) {
|
|
|
return $node;
|
|
|
}
|
|
|
|
|
|
-/*******************************************************************************
|
|
|
- * Parse Interpro HTML Output file into analysisfeatureprop table
|
|
|
- */
|
|
|
-function tripal_analysis_interpro_parseHTMLFile ($analysis_id, $interprofile, $parsego, $job_id) {
|
|
|
-
|
|
|
- // Prepare log
|
|
|
- $filename = preg_replace("/.*\/(.*)/", "$1", $interprofile);
|
|
|
- $logfile = file_directory_path() . "/tripal/tripal_analysis_interpro/load_$filename.log";
|
|
|
- $log = fopen($logfile, 'a'); // append parsing results to log file
|
|
|
-
|
|
|
- // Parsing started
|
|
|
- print "Parsing File:".$interprofile." ...\n";
|
|
|
- fwrite($log, date("D M j G:i:s Y").". Loading $interprofile\n");
|
|
|
-
|
|
|
- // Get cvterm_id for 'analysis_interpro_output_iteration_hits' which is required
|
|
|
- // for inserting into the analysisfeatureprop table
|
|
|
- $previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
- $sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
|
|
|
- "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
|
|
|
- "WHERE CVT.name = 'analysis_interpro_output_hit' ".
|
|
|
- "AND CV.name = 'tripal'";
|
|
|
- $type_id = db_result(db_query($sql));
|
|
|
- print "cvterm_id for analysis_interpro_output_iteration_hits is $type_id\n";
|
|
|
-
|
|
|
- // Load the HTML file and convert it into XML for loading
|
|
|
- $dom = new domDocument;
|
|
|
- $dom->loadHTMLFile($interprofile);
|
|
|
- $xml = $dom->saveXML();
|
|
|
- $interproput = simplexml_load_string($xml);
|
|
|
-
|
|
|
- // Get html tables for parsing
|
|
|
- $tables = $interproput->children()->children();
|
|
|
-
|
|
|
- // Count the number of tables to be processed
|
|
|
- $no_iterations = 0;
|
|
|
- foreach($tables as $tmp) {
|
|
|
- if ($tmp->getName() == 'table') {
|
|
|
- $no_iterations ++;
|
|
|
- }
|
|
|
- }
|
|
|
- print "$no_iterations html tables to be processed.\n";
|
|
|
- $interval = intval($no_iterations * 0.01);
|
|
|
- $idx_iterations = 0;
|
|
|
-
|
|
|
- // Processed the tables
|
|
|
- foreach ($tables as $table) {
|
|
|
- //if (preg_match('/No hits reported/', $table->asXML()) ) {
|
|
|
- //print "skipping this table b/c no hits are reported\n";
|
|
|
- //}
|
|
|
- // make sure we are looking at a table and its not an empty table
|
|
|
- if ($table->getName() == 'table' && !preg_match('/No hits reported/', $table->asXML()) ) {
|
|
|
- $idx_iterations ++;
|
|
|
- if ($idx_iterations % $interval == 0) {
|
|
|
- $percentage = (int) ($idx_iterations / $no_iterations * 100);
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
- tripal_job_set_progress($job_id, $percentage);
|
|
|
- $previous_db = tripal_db_set_active('chado');
|
|
|
- print $percentage."% ";
|
|
|
- }
|
|
|
-
|
|
|
- // Set job status
|
|
|
- // Get the first row and match its name with the feature name
|
|
|
- $firsttd = $table->children()->children()->children();
|
|
|
- $feature_id = 0;
|
|
|
- foreach($firsttd as $b) {
|
|
|
- foreach($b->children() as $a) {
|
|
|
- if ($a->getName() == 'a') {
|
|
|
- // Remove _ORF from the sequence name
|
|
|
- $seqname = preg_replace('/^(.+?)_\d_.+/', "$1", $a);
|
|
|
- print "seqname is $seqname\n";
|
|
|
-
|
|
|
- // Find out how many features match this uniquename
|
|
|
- $sql = "SELECT count(feature_id) FROM {feature} ".
|
|
|
- "WHERE uniquename = '%s' ";
|
|
|
- $no_features = db_result(db_query($sql, $seqname));
|
|
|
-
|
|
|
- // If there is only one match, get the feature_id
|
|
|
- if ($no_features == 1) {
|
|
|
- $sql = "SELECT feature_id FROM {feature} ".
|
|
|
- "WHERE uniquename = '%s' ";
|
|
|
- $feature_id = db_result(db_query($sql, $seqname));
|
|
|
- print "\tfeature id is $feature_id\n";
|
|
|
-
|
|
|
- // If the uniquename matches more than one features then skip and print 'Ambiguous'
|
|
|
- } else if ($no_features > 1) {
|
|
|
- fwrite($log, "Ambiguous: ".$seqname." matches more than one feature and is not processed.\n");
|
|
|
- continue;
|
|
|
-
|
|
|
- // If the uniquename did not match, skip and print 'Failed'
|
|
|
- } else {
|
|
|
- fwrite($log, "Failed: ".$seqname."\n");
|
|
|
- }
|
|
|
-
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Successfully matched. print 'Succeeded'. Add analysis_id and
|
|
|
- // feature_id to analysisfeature. Add the table as XML to analysisfeatureprop
|
|
|
- if ($feature_id) {
|
|
|
-
|
|
|
- //------------------------------------
|
|
|
- // Clease unwanted rows from the table
|
|
|
- //------------------------------------
|
|
|
-
|
|
|
- $parent_row = "/<tr><td valign=\"top\"><b>Parent<\/b><\/td>\s*<td valign=\"top\">\s*no.*?parent<\/td>\s*<\/tr>/";
|
|
|
- $children_row = "/<tr><td valign=\"top\"><b>Children<\/b><\/td>\s*<td valign=\"top\">\s*no.*?children<\/td>\s*<\/tr>/";
|
|
|
- $found_row = "/<tr><td valign=\"top\"><b>Found.*?in<\/b><\/td>\s*<td valign=\"top\">\s*no.*?entries<\/td>\s*<\/tr>/";
|
|
|
- $contains_row = "/<tr><td valign=\"top\"><b>Contains<\/b><\/td>\s*<td valign=\"top\">\s*no.*?entries<\/td>\s*<\/tr>/";
|
|
|
- $go_row = "/<tr><td valign=\"top\"><b>GO.*?terms<\/b><\/td>\s*<td valign=\"top\">\s*none<\/td>\s*<\/tr>/";
|
|
|
-
|
|
|
- $table_txt = $table->asXML();
|
|
|
- $table_txt = preg_replace($parent_row, "", $table_txt);
|
|
|
- $table_txt = preg_replace($children_row, "", $table_txt);
|
|
|
- $table_txt = preg_replace($found_row, "", $table_txt);
|
|
|
- $table_txt = preg_replace($contains_row, "", $table_txt);
|
|
|
- $table_txt = preg_replace($go_row, "", $table_txt);
|
|
|
-
|
|
|
- //------------------------------------
|
|
|
- // Clease unwanted ORF link from table
|
|
|
- //------------------------------------
|
|
|
- $orf_link = "/<b><a href=\"\/iprscan\/wget.*?\">(.*?)<\/a><\/b>/";
|
|
|
- $table_txt = preg_replace($orf_link, "$1", $table_txt);
|
|
|
-
|
|
|
- //print "----------------------------\n";
|
|
|
- //print "old: ".$table->asXML()."\n\n\n";
|
|
|
- //print "----------------------------\n";
|
|
|
- //print "Fixed: $table_txt\n";
|
|
|
- //print "----------------------------\n";
|
|
|
-
|
|
|
- //------------------------------------
|
|
|
- // If this feature has already been associated with this analysis, do not reinsert
|
|
|
- // Otherwise, Insert into analysisfeature table
|
|
|
- //------------------------------------
|
|
|
- $sql = "Select analysisfeature_id as id from {analysisfeature} where feature_id = %d and analysis_id = %d";
|
|
|
- $analysisfeature = db_fetch_object(db_query($sql, $feature_id, $analysis_id));
|
|
|
- if($analysisfeature){ $analysisfeature_id = $analysisfeature->id; }
|
|
|
- if(!$analysisfeature_id){
|
|
|
- print "inserting analysisfeature\n";
|
|
|
- $sql = "INSERT INTO {analysisfeature} (feature_id, analysis_id) ".
|
|
|
- "VALUES (%d, %d)";
|
|
|
- db_query ($sql, $feature_id, $analysis_id);
|
|
|
- $sql = "Select analysisfeature_id from {analysisfeature} where feature_id = %d and analysis_id = %d";
|
|
|
- $analysisfeature = db_fetch_object(db_query($sql, $feature_id, $analysis_id));
|
|
|
- $analysisfeature_id = $analysisfeature->id;
|
|
|
- }
|
|
|
-
|
|
|
- print "analysisfeature_id is $analysisfeature_id (analysis_id = $analysis_id; feature_id = $feature_id)\n";
|
|
|
-
|
|
|
-
|
|
|
- // Get the higest rank for this feature_id in analysisfeatureprop table.
|
|
|
- // If the value of the inserting content is not duplicate, add it to
|
|
|
- // analysisfeaturepro with 'higest_rank + 1'
|
|
|
- $sql = "SELECT MAX(rank) FROM {analysisfeatureprop} AFP ".
|
|
|
- "INNER JOIN analysisfeature AF ON AF.analysisfeature_id = AFP.analysisfeature_id ".
|
|
|
- "WHERE feature_id=%d ".
|
|
|
- "AND analysis_id=%d ".
|
|
|
- "AND type_id=%d ";
|
|
|
-
|
|
|
- $afp = db_fetch_object(db_query($sql, $feature_id, $analysis_id, $type_id));
|
|
|
- $hi_rank = 0;
|
|
|
- if ($afp) {
|
|
|
- $hi_rank = $afp->max + 1;
|
|
|
- }
|
|
|
-
|
|
|
- //------------------------------------------------------------
|
|
|
- // Insert interpro html tags into analysisfeatureprop table
|
|
|
- //------------------------------------------------------------
|
|
|
- // Before inserting, make sure it's not a duplicate
|
|
|
- $sql = "SELECT value FROM {analysisfeatureprop} WHERE analysisfeature_id = %d AND type_id = %d";
|
|
|
- $result = db_query($sql, $analysisfeature_id, $type_id);
|
|
|
- $duplicate = 0;
|
|
|
- while ($afp_value = db_fetch_object($result)) {
|
|
|
- if ($table_txt == $afp_value->value) {
|
|
|
- $duplicate = 1;
|
|
|
- }
|
|
|
- }
|
|
|
- if (!$duplicate) {
|
|
|
- $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank)".
|
|
|
- "VALUES (%d, %d, '%s', %d)";
|
|
|
- db_query($sql, $analysisfeature_id, $type_id, $table_txt, $hi_rank);
|
|
|
- fwrite($log, " (Insert)\n"); // write to log
|
|
|
- print "\twriting table\n";
|
|
|
- } else {
|
|
|
- fwrite($log, " (Skipped)\n");
|
|
|
- print "\tskipping table - dup\n";
|
|
|
- }
|
|
|
-
|
|
|
- // Parse GO terms. Make sure GO database schema is installed in chado
|
|
|
- $go_db_id = db_result(db_query("SELECT db_id FROM {db} WHERE name='GO'"));
|
|
|
- if (!$go_db_id) {
|
|
|
- print 'GO schema not installed in chado. GO terms are not processed.';
|
|
|
- }
|
|
|
- if ($go_db_id && $parsego) {
|
|
|
- $trs = $table->children();
|
|
|
- foreach ($trs as $tr) {
|
|
|
- $tds = $tr->children();
|
|
|
- foreach($tds as $td) {
|
|
|
- $gotags = $td->children();
|
|
|
- foreach ($gotags as $gotag) {
|
|
|
- // Look for 'GO:accession#'
|
|
|
- if (preg_match("/^.*?GO:(\d+).*$/", $gotag, $matches)) {
|
|
|
-
|
|
|
- // Find cvterm_id for the matched GO term
|
|
|
- $sql = "SELECT cvterm_id FROM {cvterm} CVT
|
|
|
- INNER JOIN dbxref DBX ON CVT.dbxref_id = DBX.dbxref_id
|
|
|
- WHERE DBX.accession = '%s' AND DBX.db_id = %d";
|
|
|
- $goterm_id = db_result(db_query($sql, $matches[1], $go_db_id));
|
|
|
-
|
|
|
- //-------------------------------------------
|
|
|
- // Insert GO terms into feature_cvterm table
|
|
|
- //-------------------------------------------
|
|
|
- // Default pub_id = 1 (NULL) was used
|
|
|
- $sql = "INSERT INTO {feature_cvterm} (feature_id, cvterm_id, pub_id)
|
|
|
- VALUES (%d, %d, 1)";
|
|
|
- db_query($sql, $feature_id, $goterm_id);
|
|
|
-
|
|
|
- //------------------------------------------------
|
|
|
- // Insert GO terms into analysisfeatureprop table
|
|
|
- //------------------------------------------------
|
|
|
- $sql = "INSERT INTO {analysisfeatureprop} (analysisfeature_id, type_id, value, rank) ".
|
|
|
- "VALUES (%d, %d, '%s', 0)";
|
|
|
- db_query($sql, $analysisfeature_id, $goterm_id, $matches[1]);
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- tripal_db_set_active ($previous_db); // Use drupal database
|
|
|
- print "Done.\nSuccessful and failed entries have been saved in the log file:\n $logfile\n";
|
|
|
-
|
|
|
- fwrite($log, "\n");
|
|
|
- fclose($log);
|
|
|
- return;
|
|
|
-}
|
|
|
|
|
|
/*******************************************************************************
|
|
|
* tripal_analysis_interpro_nodeapi()
|
|
|
@@ -798,7 +358,7 @@ function tripal_analysis_interpro_theme () {
|
|
|
|
|
|
function tripal_analysis_interpro_preprocess_tripal_feature_interpro_results(&$variables){
|
|
|
$feature = $variables['node']->feature;
|
|
|
- $variables['tripal_analysis_interpro']['results'] = tripal_get_interpro_results($feature->feature_id);
|
|
|
+ $variables['tripal_analysis_interpro']['results'] = tripal_get_interpro_XML_results($feature->feature_id);
|
|
|
}
|
|
|
|
|
|
/*******************************************************************************
|
|
|
@@ -809,12 +369,67 @@ function theme_parse_EBI_Interpro_XML_index_version ($node) {
|
|
|
$content = tripal_get_interpro_results_index_version($feature->feature_id);
|
|
|
return $content;
|
|
|
}
|
|
|
+/**
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_get_interpro_XML_results($feature_id){
|
|
|
+
|
|
|
+ // Get the blast results stored as XML from the analysisfeatureprop table
|
|
|
+ // the type for the property is named 'analysis_blast_output_iteration_hits'
|
|
|
+ // and is found in the 'tripal' controlled vocabulary. This CV term was
|
|
|
+ // added by this module.
|
|
|
+ $select = array(
|
|
|
+ 'analysisfeature_id' => array(
|
|
|
+ 'feature_id' => $feature_id,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'name' => 'analysis_interpro_xmloutput_hit',
|
|
|
+ 'cv_id' => array(
|
|
|
+ 'name' => 'tripal'
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $afeatureprops = tripal_core_chado_select('analysisfeatureprop',array('*'),$select);
|
|
|
+
|
|
|
+ // iterate through all of the interpro XML properties for this feature
|
|
|
+ $results = array ();
|
|
|
+ foreach ($afeatureprops as $index => $afeatureprop) {
|
|
|
+
|
|
|
+ // get the analysis feature record
|
|
|
+ $analysisfeature_arr = tripal_core_chado_select('analysisfeature',array('analysis_id'),
|
|
|
+ array('analysisfeature_id' => $afeatureprop->analysisfeature_id));
|
|
|
+ $analysisfeature = $analysisfeature_arr[0];
|
|
|
+
|
|
|
+ // get the analysis record and the analysis_id
|
|
|
+ $analysis = tripal_core_generate_chado_var('analysis',
|
|
|
+ array('analysis_id' => $analysisfeature->analysis_id));
|
|
|
+ $analysis_id = $analysis->analysis_id;
|
|
|
|
|
|
+
|
|
|
+ // parse the XML and add it to the array of blast results to be returned
|
|
|
+ $interpro_xml = $afeatureprop->value;
|
|
|
+ $orf = tripal_analysis_interpro_get_result_object($interpro_xml,$feature_id);
|
|
|
+ $results[$analysis->analysis_id]['protein_ORFs'][] = $orf;
|
|
|
+ $results[$analysis->analysis_id]['analysis'] = $analysis;
|
|
|
+
|
|
|
+ // iterate through all of the protein ORFs and combine the terms into one large list
|
|
|
+ if(!is_array($results[$analysis->analysis_id]['allterms'])){
|
|
|
+ $results[$analysis->analysis_id]['allterms'] = array();
|
|
|
+ }
|
|
|
+ if(!is_array($results[$analysis->analysis_id]['goterms'])){
|
|
|
+ $results[$analysis->analysis_id]['goterms'] = array();
|
|
|
+ }
|
|
|
+ $results[$analysis->analysis_id]['allterms'] = array_merge($results[$analysis->analysis_id]['allterms'],$orf['iprterms']);
|
|
|
+ $results[$analysis->analysis_id]['goterms'] = array_merge($results[$analysis->analysis_id]['goterms'],$orf['goterms']);
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+ return $results;
|
|
|
+}
|
|
|
/*******************************************************************************
|
|
|
* tripal_get_interpro_results()
|
|
|
* Get interpro result from featureprop table for the feature
|
|
|
*/
|
|
|
-function tripal_get_interpro_results($feature_id){
|
|
|
+function tripal_get_interpro_HTML_results($feature_id){
|
|
|
// Get cvterm_id for 'analysis_interpro_output_hit' which is required
|
|
|
// for inserting into the analysisfeatureprop table
|
|
|
$previous_db = tripal_db_set_active('chado');
|
spficklin