hotfix for ig variants

Author: pnrobinson

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ga4ghphetools"
-version = "0.5.16"
+version = "0.5.17"
 edition = "2021"
 keywords = ["GA4GH", "Phenopacket Schema", "Human Phenotype Ontology"]
 description = "Generate GA4GH phenopackets from tabular data"

src/etl/etl_tools.rs

@@ -611,7 +611,6 @@ impl EtlTools {
     } else {
         return Err("No disease data available".to_string());
     };
-    println!("process_allele_column {} - {} - {}", symbol, hgnc, transcript);
     let mut vmanager = VariantManager::new(&symbol, &hgnc, &transcript);
     let pb = |p:u32,q:u32|{ println!("{}/{} variants validated", p, q)};
     vmanager.validate_all_variants(&all_alleles, pb)?;

src/variant/intergenic_hgvs_validator.rs

@@ -49,7 +49,7 @@ fn get_variant_validator_url(
     let encoded_hgvs = urlencoding::encode(&hgvs);
 
 
-    let full_url = format!("{}/{}/{}/mane?content-type=application%2Fjson", 
+    let full_url = format!("{}/{}/{}/select?content-type=application%2Fjson", 
         BASE_URL, 
         genome_assembly, 
         encoded_hgvs
@@ -88,7 +88,7 @@ impl IntergenicHgvsValidator {
         let hgvs = &vv_dto.variant_string;
         let url = get_variant_validator_url(&self.genome_assembly, hgvs);
         let response: Value = get(&url)
-            .map_err(|e| format!("Could not map {hgvs}: {e}"))?
+            .map_err(|e| format!("Could not map intergenic {hgvs}: {e}"))?
             .json()
             .map_err(|e| format!("Could not parse JSON for {hgvs}: {e}"))?;
         let mut ig = self.from_json(response)?;
@@ -102,7 +102,7 @@ impl IntergenicHgvsValidator {
     pub fn from_json(&mut self, response: Value) -> Result<IntergenicHgvsVariant, String> {
         self.extract_variant_validator_warnings(&response)?;
         if let Some(flag) = response.get("flag") {
-            if flag != "intergenic" {
+            if flag != "gene_variant" {
                 return Err(format!("Expecting to get an intergenic variant but got {}", flag));
             }
         }
@@ -291,7 +291,7 @@ response
         vvdto: VariantDto
     ){
         let intergenic = "NC_000019.10:g.12887294G>A";
-        let expected = "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NC_000019.10%3Ag.12887294G%3EA/mane?content-type=application%2Fjson";
+        let expected = "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NC_000019.10%3Ag.12887294G%3EA/select?content-type=application%2Fjson";
         let my_url = get_variant_validator_url("hg38",  intergenic);
         assert_eq!(expected, my_url);
     }

src/variant/variant_manager.rs

@@ -95,7 +95,7 @@ impl VariantManager {
                 } else if allele.starts_with("NC_") {
                     if self.validate_intergenic(allele).is_ok() {
                         n_validated += 1;
-                    }
+                    } 
                 } else if self.validate_sv(&allele).is_ok() {
                      n_validated += 1;
                 }
@@ -394,6 +394,7 @@ mod tests {
     }   
 
     #[test]
+     #[ignore = "API call"]
     fn test_malformed_sv() {
         // Note this test does not make it to the API and thus does not touch the network
         let label = "deletion:c.[6236 + 1_6237–1]_[6432 + 1_6433–1]del";
@@ -410,6 +411,7 @@ mod tests {
 
 
     #[test]
+    #[ignore = "API call"]
     fn test_intergenic() {
         let symbol = "KLF1";
         let transcript = "NM_006563.5";
@@ -422,5 +424,19 @@ mod tests {
         println!("{:?}", ig);
     }
 
+     #[test]
+      #[ignore = "API call"]
+     fn test_intergenic_TMEM216() {
+        let symbol = "TMEM216";
+        let transcript = "NM_001173990.3";
+        let hgnc = "HGNC:25018";
+        let allele = "NC_000011.10:g.61392563G>T";
+        let mut manager = VariantManager::new(symbol, hgnc, transcript);
+        let result = manager.get_validated_intergenic_hgvs(allele);
+        assert!(result.is_ok());
+       let ig = result.unwrap();
+        println!("{:?}", ig);
+    }
+
 
 }