3232import org .slf4j .LoggerFactory ;
3333import org .springframework .stereotype .Service ;
3434
35- import com .fasterxml .jackson .annotation .JsonCreator ;
36- import com .fasterxml .jackson .annotation .JsonProperty ;
3735import com .fasterxml .jackson .core .JsonProcessingException ;
3836import com .fasterxml .jackson .databind .ObjectMapper ;
3937
4038import eu .openanalytics .phaedra .calculationservice .exception .CalculationException ;
4139import eu .openanalytics .phaedra .calculationservice .execution .CalculationContext ;
40+ import eu .openanalytics .phaedra .calculationservice .execution .input .CalculationInputHelper ;
4241import eu .openanalytics .phaedra .calculationservice .execution .progress .CalculationStage ;
4342import eu .openanalytics .phaedra .calculationservice .execution .progress .CalculationStateEventCode ;
4443import eu .openanalytics .phaedra .calculationservice .execution .script .ScriptExecutionRequest ;
6059 * but also stats for each welltype present in the plate.
6160 *
6261 * Feature Stats can be calculated as soon as the Feature itself has been calculated.
62+ *
63+ * TODO: wellType is still named "welltype" in protocol-service and resultdata-service. Fix naming across all services
6364 */
6465@ Service
6566public class FeatureStatExecutorService {
@@ -133,31 +134,36 @@ private FeatureStatDTO findStat(CalculationContext ctx, long featureId, long sta
133134
134135 private Map <String , Object > collectStatInputData (CalculationContext ctx , FeatureDTO feature , FeatureStatDTO featureStat ) {
135136 Map <String , Object > input = new HashMap <String , Object >();
136- input .put ("lowWelltype" , ctx .getProtocolData ().protocol .getLowWelltype ());
137- input .put ("highWelltype" , ctx .getProtocolData ().protocol .getHighWelltype ());
138- input .put ("welltypes" , ctx .getWells ().stream ().map (WellDTO ::getWellType ).toList ());
137+ CalculationInputHelper .addWellInfo (input , ctx , ctx .getWells ());
138+ // Note: assuming here that the feature values are already sorted by well nr
139139 input .put ("featureValues" , ctx .getFeatureResults ().get (feature .getId ()).getValues ());
140140 input .put ("isPlateStat" , featureStat .getPlateStat ());
141- input .put ("isWelltypeStat " , featureStat .getWelltypeStat ());
141+ input .put ("isWellTypeStat " , featureStat .getWelltypeStat ());
142142 return input ;
143143 }
144144
145- private List <ResultFeatureStatDTO > parseResults (CalculationContext ctx , FeatureDTO feature , FeatureStatDTO featureStat , ScriptExecutionOutputDTO output ) {
145+ private List <ResultFeatureStatDTO > parseResults (CalculationContext ctx , FeatureDTO feature , FeatureStatDTO featureStat , ScriptExecutionOutputDTO output ) {
146146 List <ResultFeatureStatDTO > results = new ArrayList <>();
147147
148148 float plateValue = Float .NaN ;
149- Map <String , Float > wellTypeValues = null ;
149+ Map <String , Float > wellTypeValues = new HashMap <>();
150+
150151 try {
151- OutputWrapper outputWrapper = objectMapper .readValue (output .getOutput (), OutputWrapper .class );
152- plateValue = outputWrapper .getPlateValue ().orElse (Float .NaN );
153- wellTypeValues = outputWrapper .getWelltypeOutputs ();
152+ Map <?,?> outputMap = objectMapper .readValue (output .getOutput (), Map .class );
153+ outputMap = (Map <?,?>) outputMap .get ("output" ); // Output string contains a nested 'output' key, e.g. output = "{\"output\":{\"plateValue\":384,\"wellTypeValues\":{\"HC\":32,\"LC\":32,\"SAMPLE\":320}}}\n"
154+ if (outputMap .get ("plateValue" ) instanceof Number ) plateValue = ((Number ) outputMap .get ("plateValue" )).floatValue ();
155+ if (outputMap .get ("wellTypeValues" ) instanceof Map ) {
156+ Map <?,?> wellTypeValuesMap = (Map <?,?>) outputMap .get ("wellTypeValues" );
157+ wellTypeValuesMap .entrySet ().stream ().filter (e -> e .getValue () instanceof Number ).forEach (e -> wellTypeValues .put ((String ) e .getKey (), ((Number ) e .getValue ()).floatValue ()));
158+ }
154159 } catch (JsonProcessingException e ) {
155160 throw new CalculationException ("Invalid response JSON" , e );
156161 }
157162
158163 if (featureStat .getPlateStat ()) {
159164 results .add (createResultStatDTO (feature , featureStat , output , plateValue , null ));
160165 }
166+
161167 if (featureStat .getWelltypeStat ()) {
162168 List <String > wellTypes = ctx .getWells ().stream ().map (WellDTO ::getWellType ).distinct ().toList ();
163169 for (String wellType : wellTypes ) {
@@ -181,29 +187,4 @@ private ResultFeatureStatDTO createResultStatDTO(FeatureDTO feature, FeatureStat
181187 .exitCode (output .getExitCode ())
182188 .build ();
183189 }
184-
185- private static class OutputWrapper {
186-
187- private final Float plateValue ;
188- private final Map <String , Float > welltypeValues ;
189-
190- @ JsonCreator
191- private OutputWrapper (
192- @ JsonProperty (value = "plateValue" , required = true ) Float plateValue ,
193- @ JsonProperty (value = "welltypeValues" , required = true ) Map <String , Float > welltypeValues ) {
194- this .plateValue = plateValue ;
195- this .welltypeValues = welltypeValues ;
196- }
197-
198- public Optional <Float > getPlateValue () {
199- return Optional .ofNullable (plateValue );
200- }
201-
202-
203- public Map <String , Float > getWelltypeOutputs () {
204- return welltypeValues ;
205- }
206-
207- }
208-
209190}
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