Write curator ORCID to GPAD file

Refs pombase/pombase-chado#787
pombase · Dec 12, 2023 · eac7914 · eac7914
1 parent 8c43862
commit eac7914
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Showing 3 changed files with 18 additions and 2 deletions.
diff --git a/src/pombase/bio/go_format_writer.rs b/src/pombase/bio/go_format_writer.rs
@@ -480,12 +480,19 @@ pub fn write_gene_product_annotation(gpad_writer: &mut dyn io::Write,
                         } else {
                           &db_object_id
                         };
-                    let line = format!("{}\t{}\t{}\t{}\t{}\t{}\t{}\t\t{}\t{}\t{}\t\n",
+                    let annotation_props =
+                        if let Some(ref curator_orcid) = annotation_detail.curator {
+                            flex_fmt!("contributor-id=orcid:{}", curator_orcid)
+                        } else {
+                            flex_str!("")
+                        };
+
+                    let line = format!("{}\t{}\t{}\t{}\t{}\t{}\t{}\t\t{}\t{}\t{}\t{}\n",
                                        db_object_id,
                                        not, relation, ontology_class_id,
                                        reference_uniquename, evidence_type,
                                        with_or_from, date, assigned_by,
-                                       annotation_extensions);
+                                       annotation_extensions, annotation_props);
                     gpad_writer.write_all(line.as_bytes())?;
                 } else {
                     println!("WARNING while writing GAF file: \

diff --git a/src/pombase/data_types.rs b/src/pombase/data_types.rs
@@ -727,6 +727,8 @@ impl PartialOrd for WithFromValue {
     }
 }
 
+pub type CuratorOrcid = FlexStr;
+
 #[derive(Serialize, Deserialize, Clone, Debug)]
 pub struct OntAnnotationDetail {
     pub id: i32,
@@ -767,6 +769,8 @@ pub struct OntAnnotationDetail {
     pub assigned_by: Option<FlexStr>,
     #[serde(skip_serializing_if="Option::is_none")]
     pub throughput: Option<Throughput>,
+    #[serde(skip_serializing_if="Option::is_none")]
+    pub curator: Option<CuratorOrcid>,
 }
 
 impl PartialEq for OntAnnotationDetail {

diff --git a/src/pombase/web/data_build.rs b/src/pombase/web/data_build.rs
@@ -3853,6 +3853,7 @@ phenotypes, so just the first part of this extension will be used:
             let mut eco_evidence: Option<FlexStr> = None;
             let mut genotype_background: Option<FlexStr> = None;
             let mut throughput: Option<Throughput> = None;
+            let mut curator_orcid: Option<CuratorOrcid> = None;
 
             // need to get evidence first as it's used later
             // See: https://github.com/pombase/website/issues/455
@@ -3942,6 +3943,9 @@ phenotypes, so just the first part of this extension will be used:
                             froms.insert(self.make_with_or_from_value(&value));
                         }
                     },
+                    "curator_orcid" => {
+                        curator_orcid = prop.value.clone();
+                    },
                     "annotation_throughput_type" => {
                         if let Some(throughput_type) = prop.value.clone() {
                             throughput = Some(match throughput_type.as_ref() {
@@ -4081,6 +4085,7 @@ phenotypes, so just the first part of this extension will be used:
                 date,
                 assigned_by,
                 throughput,
+                curator: curator_orcid,
             };
 
             if &feature.feat_type.name == "genotype_interaction" {