Merge branch 'master' into testing

.github/workflows/test-with-docker.yml

@@ -17,6 +17,6 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: pull base image
-      run: docker pull pombase/canto-base:v14
+      run: docker pull pombase/canto-base:v17
     - name: run make test inside a Docker container
       run: ./etc/docker-run-tests.sh

canto.yaml

@@ -25,7 +25,7 @@ header_image: logos/curation_tool.png
 
 canto_url: https://curation.pombase.org/
 
-app_version: v1789
+app_version: v1797
 
 schema_version: 35
 
@@ -1462,6 +1462,10 @@ implementation_classes:
   organism_adaptor: Canto::Track::OrganismLookup
   strain_adaptor: Canto::Track::StrainLookup
 
+# Possible values for "feature_pub_source" in Chado when pre-populating
+# sessions.  Ignored if the feature_pub_lookup adaptor isn't configured.
+feature_pub_sources: []
+
 wildtype_name_template: '@@gene_display_name@@+'
 deletion_name_template: '@@gene_display_name@@delta'
 transformant_name_template: '@@gene_display_name@@ transformant'

etc/docker-run-tests.sh

@@ -1,4 +1,4 @@
 #!/bin/sh -
 
 docker run --rm --net="host" --mount type=bind,source=$(pwd)/,target=/canto -w=/canto \
-    pombase/canto-base:v15 /bin/bash -c "cd /canto && perl Makefile.PL && make test"
+    pombase/canto-base:v17 /bin/bash -c "cd /canto && perl Makefile.PL && make test"

lib/Canto/Controller/Curs.pm

@@ -216,8 +216,8 @@ sub top : Chained('/') PathPart('curs') CaptureArgs(1)
   $st->{submitter_email} = $submitter_email;
   $st->{submitter_name} = $submitter_name;
 
-  $st->{message_to_curators} =
-    $self->get_metadata($schema, MESSAGE_FOR_CURATORS_KEY);
+  my $message_to_curators = $self->get_metadata($schema, MESSAGE_FOR_CURATORS_KEY);
+  $st->{message_to_curators} = $message_to_curators;
 
   my $external_notes = $self->get_metadata($schema, Canto::Curs->EXTERNAL_NOTES_KEY);
 
@@ -258,6 +258,12 @@ sub top : Chained('/') PathPart('curs') CaptureArgs(1)
     $st->{current_user_is_admin} = 0;
   }
 
+  if ($st->{current_user_is_admin} &&
+      ($state eq NEEDS_APPROVAL || $state eq APPROVAL_IN_PROGRESS || $state eq APPROVED) &&
+      defined $message_to_curators && $message_to_curators !~ /^\s*$/) {
+    push @{$st->{notice}}, qq|This session has a message to curators|;
+  }
+
   if ($config->{canto_offline} && !$st->{read_only_curs} &&
         (!defined $current_user || !$current_user->is_admin()) &&
         $path !~ m:/(ws/\w+/list):) {
@@ -341,6 +347,19 @@ sub top : Chained('/') PathPart('curs') CaptureArgs(1)
     $use_dispatch = 0;
   }
 
+  if ($state eq CURATION_IN_PROGRESS) {
+    my $existing_genes =
+      $self->get_metadata($schema, Canto::Curs::MetadataStorer::SESSION_HAS_EXISTING_GENES);
+
+    if (defined $existing_genes) {
+      $self->unset_metadata($schema, Canto::Curs::MetadataStorer::SESSION_HAS_EXISTING_GENES);
+      my $pub_uniquename = $st->{pub}->uniquename();
+      push @{$st->{message}}, qq|Warning: this session has been populated with $pub_uniquename genes known from other sources.  Use the "Add more genes from $pub_uniquename" link to add missing genes|;
+      $c->detach('edit_genes');
+      $use_dispatch = 0;
+    }
+  }
+
   if ($use_dispatch) {
     my $dispatch_dest = $state_dispatch{$state};
     if (defined $dispatch_dest) {

lib/Canto/Curs/MetadataStorer.pm

@@ -51,6 +51,12 @@ has state => (is => 'ro', init_arg => undef,
               isa => 'Canto::Curs::State',
               lazy_build => 1);
 
+use constant {
+  # the session was pre-populated with genes from Chado associated with
+  # the publication
+  SESSION_HAS_EXISTING_GENES => "session_has_existing_genes",
+};
+
 sub _build_state
 {
   my $self = shift;

lib/Canto/Role/MetadataAccess.pm

@@ -58,7 +58,7 @@ sub
   my $self = shift;
 
   if (@_ < 3) {
-    croak "not enough arguments to get_metadata()";
+    croak "not enough arguments to set_metadata()";
   }
 
   my $schema = shift;

lib/Canto/Track.pm

@@ -96,6 +96,69 @@ sub create_curs
   return ($curs, $curs_db);
 }
 
+=head2
+
+ Usage   : lookup_and_store_chado_genes($config, $curs_schema, $pub);
+ Function: If Chado is configured, lookup any genes that are known from
+           PMID keywords or other source (see feature_pub_sources in
+           config.yaml)
+ Args    :
+ Returns :
+
+=cut
+
+sub lookup_and_store_chado_genes
+{
+  my ($config, $state, $curs_schema, $pub_uniquename) = @_;
+
+  my $feature_pub_lookup = Canto::Track::get_adaptor($config, 'feature_pub');
+
+  if (!defined $feature_pub_lookup) {
+    return;
+  }
+
+  my $taxonid;
+
+  my $instance_organism = $config->{instance_organism};
+
+  if (defined $instance_organism) {
+    $taxonid = $instance_organism->{taxonid};
+  } else {
+    return;
+  }
+
+  my @results = $feature_pub_lookup->lookup(publication_uniquename => $pub_uniquename,
+                                            feature_type => 'gene');
+
+  if (@results == 0) {
+    return;
+  }
+
+  my @feature_pub_sources = @{$config->{feature_pub_sources}};
+
+  my %genes_to_add = ();
+
+  map {
+    my $row = $_;
+
+    if (grep { $row->{feature_pub_source} eq $_ } @feature_pub_sources) {
+      $genes_to_add{$row->{gene_uniquename}} = 1;
+    }
+  } @results;
+
+  my $organism =
+    Canto::CursDB::Organism::get_organism($curs_schema, $taxonid);
+
+  for my $gene_uniquename (keys %genes_to_add) {
+    $curs_schema->create_with_type('Gene', {
+      primary_identifier => $gene_uniquename,
+      organism => $organism,
+    });
+  }
+
+  $state->set_metadata($curs_schema, Canto::Curs::MetadataStorer::SESSION_HAS_EXISTING_GENES, scalar(keys %genes_to_add));
+}
+
 =head2 create_curs_db
 
  Usage   : Canto::Track::create_curs_db($config, $curs_object, );
@@ -179,6 +242,8 @@ sub create_curs_db
   my $state = Canto::Curs::State->new(config => $config);
   $state->store_statuses($curs_schema);
 
+  lookup_and_store_chado_genes($config, $state, $curs_schema, $pub->uniquename());
+
   if (wantarray) {
     return ($curs_schema, $db_file_name);
   } else {

lib/Canto/Track/OntologyLookup.pm

@@ -190,7 +190,7 @@ sub _make_term_hash
       if (!$seen{$child_cvterm->cvterm_id()}) {
         push @child_hashes,
           {$self->_make_term_hash($child_cvterm,
-                                  $child_cvterm->cv()->name(), 0, 0, 0, undef)};
+                                  $child_cvterm->cv()->name(), 1, 0, 0, undef)};
         $seen{$child_cvterm->cvterm_id()} = 1;
       }
     }

root/curs/modules/ontology.mhtml

@@ -59,6 +59,7 @@ Annotation extensions
                          term-id="{{currentTerm()}}"
                          is-valid="extensionBuilderIsValid"
                          annotation-type-name="<% $annotation_type_name %>"
+                         gene-systematic-id="<% $gene_systematic_id %>"
                          feature-type="finalFeatureType"></extension-builder>
     </div>
   </div>
@@ -95,8 +96,10 @@ Annotation extensions
 
 <%init>
 my $feature_display_name;
+my $gene_systematic_id = '';
 if ($feature_type eq 'gene') {
   $feature_display_name = $feature->display_name();
+  $gene_systematic_id = $feature->primary_identifier();
 } else {
   $feature_display_name = $feature->display_name($c->config());
 }

root/static/js/canto-modules.js

@@ -4289,7 +4289,6 @@ var alleleEditDialogCtrl =
       const alleleType = $scope.alleleData.type.trim();
 
       if (!qcUrl || !$scope.current_type_config ||
-          !$scope.userIsAdmin ||
           !$scope.current_type_config.check_description_with_api) {
         $scope.descriptionState = 'ok';
         return $q.when(null);

root/static/ng_templates/term_children.html

@@ -11,7 +11,8 @@
   <div class="curs-box-body">
     <ul>
       <li ng-repeat="child in termDetails.children">
-        <a href="#" ng-click="gotoChild(child.id)">{{child.name}}
+        <a href="#" ng-click="gotoChild(child.id)"
+           title="{{child.definition}}">{{child.name}}
           <img ng-src="{{CantoGlobals.application_root}}/static/images/right_arrow.png"></img>
         </a>
       </li>