From a9160249a5b44c905f1761eadaaf2d90037a186b Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Mon, 27 Feb 2023 15:34:58 +0000
Subject: [PATCH 1/3] Update export_atlas_ebeye_xml.pl

---
 bin/export_atlas_ebeye_xml.pl | 53 ++++++++++++++++++++++++++++-------
 1 file changed, 43 insertions(+), 10 deletions(-)

diff --git a/bin/export_atlas_ebeye_xml.pl b/bin/export_atlas_ebeye_xml.pl
index 16024c8..3061655 100755
--- a/bin/export_atlas_ebeye_xml.pl
+++ b/bin/export_atlas_ebeye_xml.pl
@@ -906,19 +906,52 @@ sub get_privacy{
   my ( $expId ) =  @_;
 
   if ( ! exists $exptPrivacies->{ $expId } ){
-    my $url = "http://peach.ebi.ac.uk:8480/api/privacy.txt?acc=$expId";
+    my $url = "https://www.ebi.ac.uk/biostudies/api/v1/search?type=study&accession=$expId";
     my $ua = LWP::UserAgent->new;
-    my $response = $ua->get($url)->content;
-    my ($privacy) = $response =~ m/privacy:(\w+)\s/g;
-
-    if (! $privacy ){
-      $privacy='unknown';
-    }
-    elsif ($privacy ne 'public' && $privacy ne 'private'){
-      $logger->logdie( "Invalid privacy \"$privacy\" for \"$expId\"" );
+    my $response = $ua->get($url);
+    
+    my $privacy;
+    
+    if( $response->is_success ) {
+        my $data = decode_json($response->content);
+        my $total_hit = $data->{totalHits};
+ 	    if ($total_hit > 0){
+            my $is_public = $data->{hits}[0]->{isPublic};
+
+            if ($is_public) {
+                $privacy="public";
+            } else {
+                $privacy="private";
+            }
+        }
+        else{
+            $logger->error(
+                "Accession ",
+                $expId,
+                " not found: \"",
+                $response->decoded_content,
+                "\". Defaulting to unknown."
+                );
+
+                $privacy="unknown";
+
+ 	    }
     }
-    $exptPrivacies->{ $expId } = $privacy;
+    
+    else {
+     	$logger->error(
+              "Problem querying ArrayExpress for $expId privacy status: ",
+              $response->status_line,
+              ". Defaulting to unknown."
+          );
+
+ 	$privacy="unknown";
+   
+    
   }
+  
+  $exptPrivacies->{ $expId } = $privacy;
+  
   return $exptPrivacies->{ $expId };
 }
 

From b472a2c2b57088ffe7117131d1d2b5ed163aa209 Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Wed, 15 Mar 2023 13:38:48 +0000
Subject: [PATCH 2/3] Update export_atlas_ebeye_xml.pl

---
 bin/export_atlas_ebeye_xml.pl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/export_atlas_ebeye_xml.pl b/bin/export_atlas_ebeye_xml.pl
index 3061655..b1059bf 100755
--- a/bin/export_atlas_ebeye_xml.pl
+++ b/bin/export_atlas_ebeye_xml.pl
@@ -948,10 +948,10 @@ sub get_privacy{
  	$privacy="unknown";
    
     
-  }
-  
-  $exptPrivacies->{ $expId } = $privacy;
+    }
   
+    $exptPrivacies->{ $expId } = $privacy;
+  }
   return $exptPrivacies->{ $expId };
 }
 

From da9a589159c2a5eb9ad18024d4858ba5faa8929c Mon Sep 17 00:00:00 2001
From: Anil Thanki <thanki.anil@gmail.com>
Date: Tue, 30 May 2023 16:26:18 +0100
Subject: [PATCH 3/3] Update export_atlas_ebeye_xml.pl

---
 bin/export_atlas_ebeye_xml.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/export_atlas_ebeye_xml.pl b/bin/export_atlas_ebeye_xml.pl
index b1059bf..c0f59ed 100755
--- a/bin/export_atlas_ebeye_xml.pl
+++ b/bin/export_atlas_ebeye_xml.pl
@@ -913,7 +913,7 @@ sub get_privacy{
     my $privacy;
     
     if( $response->is_success ) {
-        my $data = decode_json($response->content);
+        my $data = parse_json(decode ('UTF-8', $response->content));
         my $total_hit = $data->{totalHits};
  	    if ($total_hit > 0){
             my $is_public = $data->{hits}[0]->{isPublic};