Merge pull request #64 from ebi-uniprot/dev

esm score endpoint

src/main/java/uk/ac/ebi/protvar/controller/PredictionController.java

@@ -115,4 +115,21 @@ public ResponseEntity<List<ConservScore>> getConservScoresByAccAndPos(
         List<ConservScore> scores = protVarDataRepo.getConservScores(accession, position);
         return new ResponseEntity<>(scores, HttpStatus.OK);
     }
+
+    /**
+     * Get ESM score.
+     *
+     * @param accession UniProt accession
+     * @param position  Amino acid position
+     * @return <code>ESMScore</code> information on accession
+     */
+    @Operation(summary = "Retrieve ESM1v scores for accession and position")
+    @GetMapping(value = "/esm/{accession}/{position}", produces = MediaType.APPLICATION_JSON_VALUE)
+    public ResponseEntity<List<ESMScore>> getEsmScores(
+            @Parameter(example = "Q9NUW8") @PathVariable String accession,
+            @Parameter(example = "493") @PathVariable Integer position) {
+
+        List<ConservScore> scores = protVarDataRepo.getConservScores(accession, position);
+        return new ResponseEntity<>(scores, HttpStatus.OK);
+    }
 }

src/main/java/uk/ac/ebi/protvar/model/data/ESMScore.java

@@ -0,0 +1,16 @@
+package uk.ac.ebi.protvar.model.data;
+
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.Setter;
+
+
+@AllArgsConstructor
+@Getter
+@Setter
+public class ESMScore {
+	private String accession;
+	private Integer position;
+	private String mtAA;
+	private Double score;
+}

src/main/java/uk/ac/ebi/protvar/repo/ProtVarDataRepo.java

@@ -54,4 +54,8 @@ public interface ProtVarDataRepo {
 
 	// Conservation score
 	List<ConservScore> getConservScores(String acc, Integer pos);
+
+	// ESM score
+	List<ESMScore> getEsmScores(String acc, Integer pos);
+
 }

src/main/java/uk/ac/ebi/protvar/repo/ProtVarDataRepoImpl.java

@@ -115,10 +115,14 @@ INNER JOIN (VALUES :accPosSet) AS t(acc,pos)
 	private static final String SELECT_INTERACTION_MODEL = "SELECT pdb_model FROM af2complexes_interaction WHERE a=:a AND b=:b";
 	private static final String SELECT_INTERACTION_MODEL_NEW = "SELECT pdb_model FROM interaction_v2 WHERE a=:a AND b=:b";
 
-	private static final String SELECT_CONSERV_SCORES = """
+	private static final String SELECT_FROM_CONSERV_SCORE = """
    			SELECT * FROM CONSERV_SCORE 
    			WHERE acc=:acc AND pos=:pos
    			""";
+	private static final String SELECT_FROM_ESM = """
+   			SELECT * FROM esm 
+   			WHERE accession=:acc AND position=:pos
+   			""";
 
 	private NamedParameterJdbcTemplate jdbcTemplate;
 
@@ -400,11 +404,26 @@ private List<Integer> getResidueList(ResultSet rs, String fieldName) throws SQLE
 	public List<ConservScore> getConservScores(String acc, Integer pos) {
 		SqlParameterSource parameters = new MapSqlParameterSource("acc", acc)
 				.addValue("pos", pos);
-		return jdbcTemplate.query(SELECT_CONSERV_SCORES, parameters, (rs, rowNum) -> createConservScore(rs));
+		return jdbcTemplate.query(SELECT_FROM_CONSERV_SCORE,
+				parameters,
+				(rs, rowNum) ->
+						new ConservScore(rs.getString("acc"),
+								rs.getString("aa"),
+								rs.getInt("pos"),
+								rs.getDouble("score"))
+		);
 	}
 
-	private ConservScore createConservScore(ResultSet rs) throws SQLException {
-		return new ConservScore(rs.getString("acc"), rs.getString("aa"),
-				rs.getInt("pos"), rs.getDouble("score"));
+	public List<ESMScore> getEsmScores(String acc, Integer pos) {
+		SqlParameterSource parameters = new MapSqlParameterSource("acc", acc)
+				.addValue("pos", pos);
+		return jdbcTemplate.query(SELECT_FROM_ESM,
+				parameters,
+				(rs, rowNum) ->
+						new ESMScore(rs.getString("accession"),
+								rs.getInt("position"),
+								rs.getString("mt_aa"),
+								rs.getDouble("score"))
+		);
 	}
 }