Merge pull request #712 from USGCRP/MoreAuditFixes

Fixed more sources of audit user/note errors.

README.docker.md

@@ -12,16 +12,18 @@ used for production instances.
   1. Install [docker compose](https://docs.docker.com/compose/install/)
   1. run `docker build -t gcis .` 
      - Go get some tea.
+  1. run `mkdir -p files/assets-back`
   1. Setup postgres *alone* first
+     1. If you have an existing postgres container, run `docker rm gcis_postgres_1`
      1. Download the latest [public content release](https://github.com/USGCRP/gcis/releases)
      1. Untar the files
         1. the `schema` file should be moved to `./db/docker/2_schema.sql`
         1. the `content_1` file should be moved to `./db/docker/3_content_1.sql`
         1. the `content_2` file should be moved to `./db/docker/4_content_2.sql`
            - if you want an empty GCIS instance, only copy the schema & content 1.
-     1. run `docker-compose up postgres` 
+     1. run `docker-compose up postgres &` 
         - Refresh your tea.
-     1. after the previous command finishes loading, exit the command
+     1. after the previous command finishes loading, run `docker-compose stop`
   1. Start the full docker set
      1. run `docker-compose up`
      1. GCIS should be available at `127.0.0.1` with all content available

docker-compose.yml

@@ -1,4 +1,4 @@
-version: '2'
+version: '3'
 services:
   nginx:
     image: nginx:latest
@@ -18,6 +18,8 @@ services:
       - PGHOST=postgres
       - PGUSER=gcisops
       - MOJO_MODE=development
+    volumes:
+      - ./files:/var/local/www
 
   postgres:
     image: postgres:9.6

lib/Tuba/Activity.pm

@@ -132,8 +132,8 @@ sub update_rel {
     for my $id ($c->param('delete_publication')) {
         next unless $id;
         Tuba::DB::Object::Methodology::Manager->delete_objects(
-            { activity_identifier => $activity->identifier,
-              publication_id => $id });
+            where => [{activity_identifier => $activity->identifier, publication_id => $id}],
+            audit_user => $c->audit_user, audit_note => $c->audit_note);
         $c->flash(message => 'Saved changes');
     }
 

lib/Tuba/Array.pm

@@ -64,7 +64,9 @@ sub update_rel {
     }
 
     for my $id ($c->param('delete_table')) {
-        ArrayTableMaps->delete_objects({ table_identifier => $id, array_identifier => $object->identifier });
+        ArrayTableMaps->delete_objects(
+            where => [{table_identifier => $id, array_identifier => $object->identifier}],
+            audit_user => $c->audit_user, audit_note => $c->audit_note);
         $c->flash(message => 'Saved changes');
     }
 

lib/Tuba/Controller.pm

@@ -974,11 +974,13 @@ PUT files.
 
 sub put_files {
     my $c = shift;
+
     my $file = Mojo::Upload->new(asset => Mojo::Asset::File->new->add_chunk($c->req->body));
     $file->filename($c->stash("filename") ||  'asset');
     my $obj = $c->_this_object or return $c->reply->not_found;
     my $pub = $obj->get_publication(autocreate => 1);
-    my $tfile = $pub->upload_file(c => $c, upload => $file) or do {
+
+    my $tfile = $pub->upload_file(c => $c, upload => $file, audit_user => $c->user, audit_note => $c->audit_note) or do {
         return $c->render(status => 500, text => $pub->error);
     };
     $tfile->generate_thumbnail(); 
@@ -1219,8 +1221,8 @@ sub update_rel {
         for my $id ($c->param("delete_$dwhat")) {
             next unless $id;
             $mwhat->delete_objects(
-                { "${dwhat}_identifier" => $id,
-                  publication_id => $pub->id });
+                where => [{"${dwhat}_identifier" => $id, publication_id => $pub->id}],
+                audit_user => $c->user, audit_note => $c->audit_note);
             $c->flash(message => 'Saved changes');
         }
     }
@@ -1404,7 +1406,7 @@ sub remove {
           or return $c->redirect_with_error('update_form',"couldn't find $json->{replacement}");
         @replacement = (replacement => $rpl);
     }
-    $object->delete(audit_user => $c->user, @replacement)
+    $object->delete(audit_user => $c->user, audit_note => $c->audit_note, @replacement)
       or return $c->redirect_with_error('update_form', $object->error);
     return $c->render(text => 'ok');
 }

lib/Tuba/DB/Mixin/Object/Publication.pm

@@ -219,9 +219,9 @@ sub upload_file {
     };
     $tfile->size($file->size);
     $pub->add_files($tfile);
-    $pub->save(audit_user => $c->user);
+    $pub->save(audit_user => $c->user, audit_note => $c->audit_note);
     $tfile->meta->error_mode('return');
-    $tfile->save(audit_user => $c->user) or do {
+    $tfile->save(audit_user => $c->user, audit_note => $c->audit_note) or do {
         $pub->error($tfile->error);
         return;
     };

lib/Tuba/DB/Object/Manager.pm

@@ -69,5 +69,53 @@ sub dbgrep {
 }
 
 
+sub delete_objects
+{
+  # Get the arguments.
+  #
+  my $object = shift;
+  my %args = @_;
+
+  # Get the database and database handle objects.
+  #
+  my $db  = $object->object_class->init_db;
+  my $dbh = $db->retain_dbh;
+
+  # Add the database and database handle to the args.
+  #
+  $args{db}  = $db;
+  $args{dbh} = $dbh;
+
+  # Remove the audit user and audit note arguments. Throw an error if there is
+  # no audit user argument.
+  #
+  my $audit_user = delete $args{audit_user} or die "missing audit_user for $object";
+  my $audit_note = delete $args{audit_note};
+
+  # Do the database transaction.
+  #
+  my $count= 0;
+
+  $db->do_transaction( sub {
+      # Add the audit user and audit note.
+      #
+      $dbh->do("set local audit.username = ?",{},$audit_user);
+      $dbh->do("set local audit.note = ?",{},$audit_note) if $audit_note;
+
+      # Call the super-class delete_objects method with the arguments.
+      #
+      $count = $object->SUPER::delete_objects(%args);
+    }
+  ) or do {
+    # Record an error if the transaction didn't succeed.
+    #
+    $object->error($db->error) unless $object->error;
+  };
+
+  # Return the object count result from the parent delete_objects method.
+  #
+  return $count;
+}
+
 
 1;

lib/Tuba/Figure.pm

@@ -207,13 +207,23 @@ sub update_rel {
     }
 
     my $report_identifier = $c->stash('report_identifier');
-    my @delete_images = $c->param('delete_image');
+
+    my @delete_images;
+
+    @delete_images = $c->param('delete_image') if $c->param('delete_image');
+
     if (my $nother = $json->{delete_image_identifier}) {
         push @delete_images, $nother;
     }
-    for my $id (@delete_images) {
-        ImageFigureMaps->delete_objects({ image_identifier => $id, figure_identifier => $object->identifier, report_identifier => $report_identifier });
-        $c->flash(message => 'Saved changes');
+
+    if (0 < scalar @delete_images) {
+        for my $id (@delete_images) {
+            ImageFigureMaps->delete_objects(
+                where => [{figure_identifier => $object->identifier,
+                          report_identifier => $report_identifier}],
+                audit_user => $c->audit_user, audit_note => $c->audit_note);
+            $c->flash(message => 'Saved changes');
+        }
     }
 
     return $c->SUPER::update_rel(@_);

lib/Tuba/Image.pm

@@ -63,7 +63,9 @@ sub update_rel {
     }
 
     for my $id ($c->param('delete_figure')) {
-        ImageFigureMaps->delete_objects({ figure_identifier => $id, image_identifier => $object->identifier });
+        ImageFigureMaps->delete_objects(
+            where => [{figure_identifier => $id, image_identifier => $object->identifier}],
+            audit_user => $c->audit_user, audit_note => $c->audit_note);
         $c->flash(message => 'Saved changes');
     }
 

lib/Tuba/Methodology.pm

@@ -79,8 +79,8 @@ sub update_rel {
     for my $id ($c->param('delete_publication')) {
         next unless $id;
         Methodology->delete_objects(
-            { activity_identifier => $activity->identifier,
-              publication_id => $id });
+            where => [{activity_identifier => $activity->identifier, publication_id => $id}],
+            audit_user => $c->audit_user, audit_note => $c->audit_note);
         $c->flash(message => 'Saved changes');
     }
 

lib/Tuba/Organization.pm

@@ -47,14 +47,16 @@ sub update_rel {
     if (my $pub_id = $json->{delete_publication} || $c->param('delete_publication')) {
         my $con_id = $json->{contributor_id} || $c->param('contributor_id');
         die "person does not match contributor" unless Contributor->new(id => $con_id)->load->organization_identifier eq $org->identifier;
-        PublicationContributorMaps->delete_objects({
-                contributor_id => $con_id,
-                publication_id => $pub_id,
-            }) or return $c->update_error("Failed to remove publication");
+        PublicationContributorMaps->delete_objects(
+            where => [{ contributor_id => $con_id, publication_id => $pub_id }],
+            audit_user => $c->audit_user, audit_note => $c->audit_note)
+        or return $c->update_error("Failed to remove publication");
     } elsif (my $id = $json->{delete_contributor} || $c->param('delete_contributor')) {
         die "person does not match contributor" unless Contributor->new(id => $id)->load->organization_identifier eq $org->identifier;
-        Contributors->delete_objects({ id => $id })
-            or return $c->update_error("Failed to remove contributor");
+        Contributors->delete_objects(
+            where => [{ id => $id }],
+            audit_user => $c->audit_user, audit_note => $c->audit_note)
+        or return $c->update_error("Failed to remove contributor");
         $c->flash(info => "Saved changes.");
     }
 

lib/Tuba/Person.pm

@@ -143,14 +143,16 @@ sub update_rel {
     if (my $pub_id = $json->{delete_publication} || $c->param('delete_publication')) {
         my $con_id = $json->{contributor_id} || $c->param('contributor_id');
         die "person does not match contributor" unless Contributor->new(id => $con_id)->load->person_id == $person->id;
-        PublicationContributorMaps->delete_objects({
-                contributor_id => $con_id,
-                publication_id => $pub_id,
-            }) or return $c->update_error("Failed to remove publication");
+        PublicationContributorMaps->delete_objects(
+            where => [{contributor_id => $con_id, publication_id => $pub_id}],
+            audit_user => $c->audit_user, audit_note => $c->audit_note)
+        or return $c->update_error("Failed to remove publication");
     } elsif (my $id = $json->{delete_contributor} || $c->param('delete_contributor')) {
         die "person does not match contributor" unless Contributor->new(id => $id)->load->person_id == $person->id;
-        Contributors->delete_objects({ id => $id })
-            or return $c->update_error("Failed to remove contributor");
+        Contributors->delete_objects(
+            where => [{ id => $id }],
+            audit_user => $c->audit_user, audit_note => $c->audit_note)
+        or return $c->update_error("Failed to remove contributor");
         $c->flash(info => "Saved changes.");
     }
 

lib/Tuba/Table.pm

@@ -138,7 +138,11 @@ sub update_rel {
 
     my $report_identifier = $c->stash('report_identifier');
     for my $id (grep { defined && length } $c->param('delete_array')) {
-        ArrayTableMaps->delete_objects({ array_identifier => $id, table_identifier => $object->identifier, report_identifier => $report_identifier });
+        ArrayTableMaps->delete_objects(
+            where => [{array_identifier => $id,
+                       table_identifier => $object->identifier,
+                       report_identifier => $report_identifier}],
+            audit_user => $c->audit_user, audit_note => $c->audit_note);
         my $array = Array->new(identifier => $id);
         $array->load;
         if (!@{ $array->tables }) {