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Generate correct links to polypeptide feature pages for phylotr... #1

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Generate correct links to polypeptide feature pages for phylotr... #1

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7d7582b
fix: Generate correct links to polypeptide feature pages for phylo tr…
Jun 2, 2022
569c9e4
fix: Assign name instead of uniquename for linkout
Jun 28, 2022
3b57d78
test: Don't display gcv link
Oct 11, 2022
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39 changes: 18 additions & 21 deletions includes/tripal_linkout.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ function gene_linkout_json($gene) {
$result = chado_query($sql, $args);
$fields = $result->fetchAssoc();


// Get mRNA from gene
$sql = "SELECT f2.uniquename AS mrna_uniquename, f2.feature_id AS mrna_id
FROM chado.feature f, chado.feature_relationship fr, chado.feature f2
Expand Down Expand Up @@ -52,7 +51,7 @@ function gene_linkout_json($gene) {
$fields['pep_uniquename'] = $new_fields['pep_uniquename'];
$fields['pep_name'] = $new_fields['pep_name'];

full_gene_linkout_json($fields['genus'], $fields['species'], $fields['pep_name'], $fields['pep_uniquename'], $fields['mrna_uniquename'], $gene, FALSE, $fields['organism_id']);
full_gene_linkout_json($fields['genus'], $fields['species'], $fields['species_split'], $fields['pep_name'], $fields['pep_uniquename'], $fields['mrna_uniquename'], $gene, FALSE, $fields['organism_id']);
}

function family_representative_linkout_json($genus, $species, $family_representative) {
Expand Down Expand Up @@ -89,7 +88,7 @@ function family_representative_linkout_json($genus, $species, $family_representa
full_gene_linkout_json($genus, $species, $fields['pep_name'], $fields['pep_uniquename'], $family_representative, $fields['gene_uniquename'], TRUE, $fields['organism_id']);
}

function full_gene_linkout_json($genus, $species, $pep_name, $pep_uniquename, $transcript_name, $gene_name, $show_gcv=TRUE, $organism_id=NULL) {
function full_gene_linkout_json($genus, $species, $species_split, $pep_name, $pep_uniquename, $transcript_name, $gene_name, $show_gcv=FALSE, $organism_id=NULL) {
$link = [];
global $base_url;

Expand All @@ -105,10 +104,13 @@ function full_gene_linkout_json($genus, $species, $pep_name, $pep_uniquename, $t
if(getenv("MAIN_TRIPAL_URL")){
$gogepp_url = getenv("MAIN_TRIPAL_URL");
} else {
$gogepp_url = 'https://'.$current_gogepp.'.genouest.org';
$gogepp_url = 'https://'.$current_gogepp.'.genouest.org'; // change for production?
}

$species = str_replace(' ', '-', $species);
// Split species var to get only the first part of the string (containing only the "species" name)
$species_exploded = explode("-", $species);
$species_split = $species_exploded[0];

$sp_links = array();
$sp_links['bombyx_mori'] = array('http://sgp.dna.affrc.go.jp/KAIKObase/keyword_search.php?keyword=%pep_uniquename%&field=all&chr_id=all&scaf_id=&data_set%5B%5D=gene&graph_view=on');
Expand Down Expand Up @@ -145,38 +147,33 @@ function full_gene_linkout_json($genus, $species, $pep_name, $pep_uniquename, $t
'%genus%' => $genus,
'%lower_genus%' => strtolower($genus),
'%species%' => $species,
'%species_split%' => $species_split,
'%pep_name%' => $pep_name,
'%pep_uniquename%' => $pep_uniquename,
'%pep_uniquename_noPA%' => $pep_uniquename_noPA,
'%gene_name%' => $gene_name,
'%transcript_name%' => $transcript_name,
);

if (array_key_exists($org_str, $sp_links)) {
foreach ($sp_links[$org_str] as $key => $linkstr) {
$link[] = array(
'href' => str_replace(array_keys($replacements), $replacements, $linkstr),
'text' => 'View page for: ' . $pep_uniquename,
);
}
}
else if (! in_array($org_str, $no_links)) {
if (isset($pep_uniquename)) {
$default_url = $gogepp_url . '/sp/%lower_genus%_%species%/feature/%genus%/%species%/polypeptide/%pep_uniquename%';
$link[] = array(
'href' => str_replace(array_keys($replacements), $replacements, $default_url),
'text' => 'View page for: ' . $pep_uniquename,
);
}
if (isset($pep_uniquename)) {
$default_url = $gogepp_url . '/sp/%lower_genus%_%species_split%/feature/%genus%/%species%/polypeptide/%pep_name%';
$link[] = array(
'href' => str_replace(array_keys($replacements), $replacements, $default_url),
'text' => 'View page for: ' . $pep_uniquename,
);
}

// Don't display gcv link
$show_gcv = False;


if (!empty($gene_name) && $show_gcv) {
$org = '';
if (!empty($organism_id)) {
$org = "/$organism_id";
}
if (substr($base_url, -6) === 'tripal')
$default_url = $base_url . '/../gcv/#/search/'.$current_gogepp.$org.'/%gene_name%';
$default_url = $base_url . '/../gcv#/search/'.$current_gogepp.$org.'/%gene_name%';
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Is this removal necessary or a mistake ?

else
$default_url = $base_url . '/gcv/#/search/'.$current_gogepp.$org.'/%gene_name%';

Expand Down