<?php
// This conditional is added to prevent errors in the biomaterial TOC admin page.
if (property_exists($variables['node'], 'biomaterial')) {
$biomaterial = $variables['node']->biomaterial;
$biomaterial = chado_expand_var($biomaterial, 'field', 'biomaterial.description');
$ontology_terms = $variables['biomaterial_ontology_terms'];
?>
<div class="tripal_biomaterial-data-block-desc tripal-data-block-desc"></div>
<?php
$analysis_name = $variables['analysis_name'];
$analysis_nid = $variables['analysis_nid'];
$headers = array();
$rows = array();
// The biomaterial name.
$rows[] = array(array('data' => 'Biomaterial', 'header' => TRUE, 'width' => '20%'), '<i>' . $biomaterial->name . '</i>');
// The organism from which the biomaterial was collected
if ($biomaterial->taxon_id) {
$organism = '<i>' . $biomaterial->taxon_id->genus . ' ' . $biomaterial->taxon_id->species . '</i> (' . $biomaterial->taxon_id->common_name . ')';
if (property_exists($biomaterial->taxon_id, 'nid')) {
$organism = l('<i>' . $biomaterial->taxon_id->genus . ' ' . $biomaterial->taxon_id->species . '</i> (' . $biomaterial->taxon_id->common_name . ')', 'node/' . $biomaterial->taxon_id->nid, array('html' => TRUE));
}
$rows[] = array(array('data' => 'Organism', 'header' => TRUE, 'width' => '20%'), $organism);
}
// The analysis
if ($analysis_name) {
$analysis = $analysis_name;
if ($analysis_nid) {
$analysis = l($analysis_name, 'node/' . $analysis_nid, array('html' => TRUE));
<?php
// This line is added so that no errors show in the TOC admin page.
if (property_exists($variables['node'], 'arraydesign')) {
$arraydesign = $variables['node']->arraydesign;
$arraydesign = chado_expand_var($arraydesign, 'table', 'arraydesignprop', array('return_array' => 1));
$properties = $arraydesign->arraydesignprop;
// Check for properties.
if (count($properties) > 0) {
?>
<div class="tripal_arraydesign-data-block-desc tripal-data-block-desc">Additional information about this array design:</div><?php
$header = array('Property Name', 'Value');
$rows = array();
foreach ($properties as $property) {
$rows[] = array(ucfirst(preg_replace('/_/', ' ', $property->type_id->name)), $property->value);
}
$table = array('header' => $headers, 'rows' => $rows, 'attributes' => array('id' => 'tripal_arraydesign-table-properties', 'class' => 'tripal-data-table'), 'sticky' => FALSE, 'caption' => '', 'colgroups' => array(), 'empty' => '');
print theme_table($table);
}
}
<?php
// This conditional is added to prevent errors in the array design TOC admin page.
if (property_exists($variables['node'], 'protocol')) {
$protocol = $variables['node']->protocol;
$protocol = chado_expand_var($protocol, 'field', 'protocol.protocoldescription');
$protocol = chado_expand_var($protocol, 'field', 'protocol.hardwaredescription');
$protocol = chado_expand_var($protocol, 'field', 'protocol.softwaredescription');
//$protocol = chado_expand_var($protocol, 'field', 'arraydesign.description');
?>
<div class="tripal_protocol-data-block-desc tripal-data-block-desc"></div>
<?php
$headers = array();
$rows = array();
// The protocol name.
$rows[] = array(array('data' => 'Protocol', 'header' => TRUE, 'width' => '20%'), '<i>' . $protocol->name . '</i>');
// The protocol type
$rows[] = array(array('data' => 'Protocol Type', 'header' => TRUE, 'width' => '20%'), '<i>' . $protocol->type_id->name . '</i>');
// The protocol link.
if ($protocol->uri) {
$rows[] = array(array('data' => 'Protocol Link', 'header' => TRUE, 'width' => '20%'), '<i><a href="' . $protocol->uri . '"> Protocol </a></i>');
}
// The protocol link.
if ($protocol->pub_id) {
$rows[] = array(array('data' => 'Publication', 'header' => TRUE, 'width' => '20%'), '<i>' . l($protocol->pub_id->title, '/node/' . $protocol->pub_id->nid) . '</i>');
}
// allow site admins to see the protocol ID
if (user_access('view ids')) {
// Protocol ID
$dbname_accession = $feature_dbxref->dbxref_id->db_id->name . ":" . $feature_dbxref->dbxref_id->accession;
if ($feature_dbxref->dbxref_id->db_id->urlprefix) {
$references .= l($dbname_accession, $feature_dbxref->dbxref_id->db_id->urlprefix . $feature_dbxref->dbxref_id->accession, array('attributes' => array('target' => '_blank'))) . "<br>";
} else {
$references .= $dbname_accession . "<Br>";
}
}
// if closes
}
// foreach closes
}
// if cound closes
// Dbxref row
$references = !empty($references) ? $references : 'None';
$rows[] = array(array('data' => 'Dbxref', 'header' => TRUE), $references);
$feature = chado_expand_var($feature, 'table', 'analysisfeature', $options);
$analyses = $feature->subject_id->analysisfeature;
$src_values = array('feature_id' => $feature->subject_id->featureloc->feature_id->srcfeature_id->feature_id);
$srcfeature = chado_generate_var('analysisfeature', $src_values, $options);
//echo "<prE>"; print_r($analyses); echo "</prE>";
// Analyses - if and else statements cause the anaylses having different array formats.
$analysis_name = '';
if (count($analyses) == 2) {
foreach ($analyses as $analysis) {
$a_name = $analysis->analysis_id->name;
if (property_exists($analysis->analysis_id, 'nid')) {
//$options['target'] = '_blank';
$analysis_name .= l($a_name, "node/" . $analysis->analysis_id->nid) . "<bR>";
}
}
} else {
<?php
// This line is added so that no errors show in the TOC admin page.
if (property_exists($variables['node'], 'biomaterial')) {
$biomaterial = $variables['node']->biomaterial;
$biomaterial = chado_expand_var($biomaterial, 'table', 'biomaterialprop', array('return_array' => 1));
$properties = $biomaterial->biomaterialprop;
// Check for properties.
if (count($properties) > 0) {
?>
<div class="tripal_biomaterial-data-block-desc tripal-data-block-desc">Additional information about this biomaterial:</div><?php
$headers = array('Property Name', 'Value');
$rows = array();
foreach ($properties as $property) {
$rows[] = array(ucfirst(preg_replace('/_/', ' ', $property->type_id->name)), $property->value);
}
$table = array('header' => $headers, 'rows' => $rows, 'attributes' => array('id' => 'tripal_biomaterial-table-properties', 'class' => 'tripal-data-table'), 'sticky' => FALSE, 'caption' => '', 'colgroups' => array(), 'empty' => '');
print theme_table($table);
}
}
<?php
$node = $variables['node'];
$protocol = $variables['node']->protocol;
$protocol = chado_expand_var($protocol, 'field', 'protocol.protocoldescription');
?>
<div class="tripal_protocol-teaser tripal-teaser">
<div class="tripal-protocol-teaser-title tripal-teaser-title"><?php
print l($node->title, "node/{$node->nid}", array('html' => TRUE));
?>
</div>
<div class="tripal_protocol-teaser-text tripal-teaser-text"><?php
print substr($protocol->protocoldescription, 0, 650);
if (strlen($protocol->protocoldescription > 650)) {
print "... " . l("[more]", "node/{$node->nid}");
}
?>
</div>
</div>
<?php
$node = $variables['node'];
$analysis = $variables['node']->analysis;
$analysis = chado_expand_var($analysis, 'table', 'analysisprop', array('return_array' => 1));
$properties = $analysis->analysisprop;
$expression = $node->analysis->tripal_analysis_expression;
if ($variables['assay_protocol'] != '' or $variables['acquisition_protocol'] != '' or $variables['quantification_protocol'] != 0) {
?>
<div class="tripal__analysis-data-block-desc tripal-data-block-desc">Protocols used in the process of the experiment.</div><?php
$header = array('Protocol', 'Type', 'Date Run');
$rows = array();
if ($variables['assay_protocol'] != '') {
$rows[] = array($variables['assay_protocol'][0]->name, 'Assay', preg_replace("/^(\\d+-\\d+-\\d+) .*/", "\$1", $variables['assaydate']));
}
if ($variables['acquisition_protocol'] != '') {
$rows[] = array($variables['acquisition_protocol'][0]->name, 'Acquistion', preg_replace("/^(\\d+-\\d+-\\d+) .*/", "\$1", $variables['acquisitiondate']));
}
if ($variables['quantification_protocol'] != '') {
$rows[] = array($variables['quantification_protocol'][0]->name, 'Quantification', preg_replace("/^(\\d+-\\d+-\\d+) .*/", "\$1", $variables['quantificationdate']));
}
if (!empty($rows)) {
$table = array('header' => $header, 'rows' => $rows, 'attributes' => array('id' => 'tripal_protocol-table-properties', 'class' => 'tripal_data_table'), 'sticky' => FALSE, 'caption' => '', 'colgroups' => array(), 'empty' => '');
print theme_table($table);
}
}
?>
<?php
/*
* phylotree analyis template
*/
$node = $variables['node'];
$phylotree = $node->phylotree;
$header = array('Name', 'Description', 'Metadata');
$analysis = $phylotree->analysis_id;
$rows = array();
if ($analysis) {
$analysis = chado_expand_var($analysis, 'field', 'analysis.description');
$rows[] = array($analysis->name, $analysis->description, sprintf('%s %s %s %s %s %s %s', $analysis->program, $analysis->programversion, $analysis->algorithm, $analysis->sourcename, $analysis->sourceversion, $analysis->sourceuri, $analysis->timeexecuted));
} else {
// degrade gracefully if no analysis is present
$rows[] = array('n/a', '', '');
}
$table = array('header' => $header, 'rows' => $rows, 'attributes' => array('id' => 'tripal_phylotree-table-analysis', 'class' => 'tripal-data-table'), 'sticky' => FALSE, 'caption' => '', 'colgroups' => array(), 'empty' => '');
print theme_table($table);
<?php
// This conditional is added to prevent errors in the array design TOC admin page.
if (property_exists($variables['node'], 'arraydesign')) {
$arraydesign = $variables['node']->arraydesign;
$arraydesign = chado_expand_var($arraydesign, 'field', 'arraydesign.description');
?>
<div class="tripal_arraydesign-data-block-desc tripal-data-block-desc"></div>
<?php
$headers = array();
$rows = array();
// The array design name
$rows[] = array(array('data' => 'Array Design', 'header' => TRUE, 'width' => '20%'), '<i>' . $arraydesign->name . '</i>');
// The name of the manufacturer. The manufacturer is an entry in the contact table.
$rows[] = array(array('data' => 'Manufacturer', 'header' => TRUE, 'width' => '20%'), '<i>' . $arraydesign->manufacturer_id->name . '</i>');
// The version of the array design.
if ($arraydesign->version) {
$rows[] = array(array('data' => 'Version', 'header' => TRUE, 'width' => '20%'), '<i>' . $arraydesign->version . '</i>');
}
//The array dimensions, number of array columns and number of array rows are all displayed in a single field.
if ($arraydesign->array_dimensions or $arraydesign->num_array_columns or $arraydesign->num_array_rows) {
$afield = '';
if ($arraydesign->array_dimensions) {
$afield = $afield . $arraydesign->array_dimensions;
}
if ($arraydesign->array_dimensions and $arraydesign->num_array_columns and $arraydesign->num_array_rows) {
$afield = $afield . ' - ';
}
if ($arraydesign->num_array_columns) {
<?php
$biomaterial = $variables['node']->biomaterial;
$references = array();
if ($biomaterial->dbxref_id) {
$biomaterial->dbxref_id->is_primary = 1;
$references[] = $biomaterial->dbxref_id;
}
$options = array('return_array' => 1);
$biomaterial = chado_expand_var($biomaterial, 'table', 'biomaterial_dbxref', $options);
$biomaterial_dbxrefs = $biomaterial->biomaterial_dbxref;
if (count($biomaterial_dbxrefs) > 0) {
foreach ($biomaterial_dbxrefs as $biomaterial_dbxref) {
$references[] = $biomaterial_dbxref->dbxref_id;
}
}
if (count($references) > 0) {
?>
<div class="tripal_biomaterial-data-block-desc tripal-data-block-desc">External references for this biomaterial:</div><?php
$headers = array('Database', 'Accession');
$rows = array();
foreach ($references as $dbxref) {
$dbname = $dbxref->db_id->name;
if ($dbxref->db_id->url) {
$dbname = l($dbname, $dbxref->db_id->url, array('attributes' => array('target' => '_blank')));
}
$accession = $dbxref->accession;
if ($dbxref->db_id->urlprefix) {
$accession = l($accession, $dbxref->db_id->urlprefix . $dbxref->accession, array('attributes' => array('target' => "_blank")));
}
if (property_exists($dbxref, 'is_primary')) {
}
// second add in the object relationships.
foreach ($object_rels as $rel_type => $rels) {
foreach ($rels as $subject_type => $subjects) {
// the $headers array is an array of fields to use as the colum headers.
// additional documentation can be found here
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$headers = array('Name', 'Genome', 'Transcript', 'CDS', 'Protein');
// the $rows array contains an array of rows where each row is an array
// of values for each column of the table in that row. Additional documentation
// can be found here:
// https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
$rows = array();
foreach ($subjects as $subject) {
// Below tripal function is used to get seqlen from featureloc relationship
$obj_feature = chado_expand_var($subject, 'table', 'featureloc');
//echo "<pre>"; print_r($subject);echo "</pre>";
// Genomic sequence - nothing but co-ordinates sequence
$genomic_link = "<a href='#' onclick=\"popup_message_display_popup(" . $subject->record->object_id->feature_id . ", '" . $subject->record->object_id->type_id->name . "', 680, 300, '0', '" . $subject->record->object_id->featureloc->feature_id->strand . "');\">Genomic Fasta</a>";
// cDNA sequence
$type_id_cdna = CDNA_TYPE_ID;
//'585';
$cdna_args = array(':feature_id' => $subject->record->subject_id->feature_id);
$cdna_sql = "select * from chado.feature where uniquename=(select uniquename from chado.feature where feature_id=:feature_id) and type_id=" . $type_id_cdna;
$cdna_sequence = chado_query($cdna_sql, $cdna_args)->fetchObject();
$cDNA_link = "-";
if (!empty($cdna_sequence->residues)) {
$cDNA_link = "<a href='#' onclick=\"popup_message_display_popup(" . $subject->record->subject_id->feature_id . ", '" . $subject->record->subject_id->type_id->name . "', 680, 300, '0', '" . $subject->record->subject_id->featureloc->feature_id->strand . "');\">cDNA Fasta</a>";
}
// CDS sequence
$type_id_cds = CDS_TYPE_ID;
