Merge branch 'master' into issue-2758-disable-edits-for-existing-alleles

pombase · Aug 30, 2023 · c8b4e3c · c8b4e3c
2 parents d88f23b + 42fd96c
commit c8b4e3c
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Showing 4 changed files with 24 additions and 19 deletions.
diff --git a/canto.yaml b/canto.yaml
@@ -25,7 +25,7 @@ header_image: logos/curation_tool.png
 
 canto_url: https://curation.pombase.org/
 
-app_version: v1760
+app_version: v1762
 
 schema_version: 35
 
@@ -1488,87 +1488,87 @@ allele_type_list:
     export_type: amino_acid_insertion
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: e.g. A858AMKGYP (insertion of MKGYP after A858, note A before and after number)
   - name: "amino acid substitution(s)"
     export_type: amino_acid_mutation
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: eg. K132A or F256A,F310A
   - name: amino acid insertion and substitution
     export_type: amino_acid_insertion_and_mutation
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: e.g. A858AMKGYP,F124D
   - name: amino acid insertion and deletion
     export_type: amino_acid_insertion_and_deletion
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: e.g. A858AMKGYP,100-200,P500*
   - name: partial deletion and amino acid change
     export_type: amino_acid_deletion_and_mutation
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: e.g. 100-200,F124D,P500*
   - name: partial deletion, amino acid
     export_type: partial_amino_acid_deletion
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: "Specify deleted residues - eg. 100-200 OR 10-20,40-50. Use P500* for nonsense mutation"
   - name: nucleotide insertion
     export_type: nucleotide_insertion
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: e.g. C132CAATTT (insertion of AATTT after C132, note C before and after number))
   - name: "nucleotide substitution(s)"
     export_type: nucleotide_mutation
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: eg. A25G, OR A(-25)G (for residues upstream of ATG -protein coding- or transcription start -RNA genes-)
   - name: partial deletion, nucleotide
     export_type: partial_nucleotide_deletion
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: "Specify deleted residues - eg. 100-200 OR (-20)-(-30) (for residues upstream of ATG -protein coding- or transcription start -RNA genes-)"
   - name: partial deletion and nucleotide change
     export_type: nucleotide_deletion_and_mutation
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: e.g. 100-200,A124T,C128G (for residues upstream of ATG -protein coding- or transcription start -RNA genes- use negative numbers in parenthesis)
   - name: nucleotide insertion and substitution
     export_type: nucleotide_insertion_and_mutation
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: e.g. T858TAAGA,T(-124)A (for residues upstream of ATG -protein coding- or transcription start -RNA genes- use negative numbers in parenthesis)
@@ -1593,7 +1593,7 @@ allele_type_list:
     export_type: other
     show_description: true
     description_required: true
-    allele_name_required: false
+    allele_name_required: true
     allow_expression_change: true
     expression_required: true
     placeholder: Please provide a description

diff --git a/lib/Canto/Chado/GenotypeInteractionLookup.pm b/lib/Canto/Chado/GenotypeInteractionLookup.pm
@@ -133,8 +133,13 @@ sub lookup
   $ua->default_header('Accept', 'text/plain');
   my $res = $ua->get($url);
 
+  if ($res->status_line() =~ /^404\s.*/) {
+    return (0, []);
+  }
+
   if (!$res->is_success && $res->status_line() !~ /^404\s.*/) {
     warn $res->status_line();
+    return (0, []);
   }
 
   my $content = $res->decoded_content();

diff --git a/t/50_config.t b/t/50_config.t
@@ -240,14 +240,14 @@ my $config_for_json = $config_with_suffix->for_json('allele_types');
 
 my $description_required =
   $config_for_json->{'nucleotide substitution(s)'}->{description_required};
-my $allele_name_required =
-  $config_for_json->{'nucleotide substitution(s)'}->{allele_name_required};
+my $show_description =
+  $config_for_json->{'deletion'}->{show_description};
 
 ok ($description_required);
-ok (!$allele_name_required);
+ok (!$show_description);
 
 ok ($description_required == JSON::true);
-ok ($allele_name_required == JSON::false);
+ok ($show_description == JSON::false);
 
 # species taxon ID lookup
 is ($config_single->get_species_taxon_of_strain_taxon(1238467), 168172);

diff --git a/t/80_web_service.t b/t/80_web_service.t
@@ -230,11 +230,11 @@ test_psgi $app, sub {
       die "$@\n", $res->content();
     }
 
-    like($res->content(), qr/"allele_name_required"\s*:\s*false/);
+    like($res->content(), qr/"description_required"\s*:\s*false/);
     like($res->content(), qr/"allele_name_required"\s*:\s*true/);
 
     ok ($obj->{'partial deletion, nucleotide'}->{allow_expression_change});
-    ok (!$obj->{'partial deletion, nucleotide'}->{allele_name_required});
+    ok (!$obj->{'unknown'}->{description_required});
   }
 
   {