Added compound quality flags as array/set and integrated it into Comp…

…oundController

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/compounds/CompoundController.java

@@ -44,7 +44,6 @@
 import de.unijena.bioinf.projectspace.ProjectSpaceManager;
 import de.unijena.bioinf.projectspace.fingerid.FBCandidateNumber;
 import io.swagger.v3.oas.annotations.tags.Tag;
-import org.checkerframework.checker.units.qual.C;
 import org.jetbrains.annotations.NotNull;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -59,6 +58,7 @@
 import java.io.StringReader;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.EnumSet;
 import java.util.List;
 import java.util.Optional;
 import java.util.function.Function;
@@ -87,12 +87,12 @@ public CompoundController(ComputeContext context) {
      * @return CompoundIds with additional annotations and MS/MS data (if specified).
      */
     @GetMapping(value = "/compounds", produces = MediaType.APPLICATION_JSON_VALUE)
-    public List<CompoundId> getCompounds(@PathVariable String projectId, @RequestParam(required = false, defaultValue = "false") boolean topAnnotation, @RequestParam(required = false, defaultValue = "false") boolean msData) {
+    public List<CompoundId> getCompounds(@PathVariable String projectId, @RequestParam(required = false, defaultValue = "false") boolean topAnnotation, @RequestParam(required = false, defaultValue = "false") boolean msData, @RequestParam(required = false,defaultValue = "false") boolean msQuality) {
         LoggerFactory.getLogger(CompoundController.class).info("Started collecting compounds...");
         final ProjectSpaceManager<?> space = projectSpace(projectId);
 
         final ArrayList<CompoundId> compoundIds = new ArrayList<>();
-        space.projectSpace().forEach(ccid -> compoundIds.add(asCompoundId(ccid, space, topAnnotation, msData)));
+        space.projectSpace().forEach(ccid -> compoundIds.add(asCompoundId(ccid, space, topAnnotation, msData,msQuality)));
 
         LoggerFactory.getLogger(CompoundController.class).info("Finished parsing compounds...");
         return compoundIds;
@@ -175,10 +175,11 @@ public List<CompoundId> importCompoundsFromString(@PathVariable String projectId
     @GetMapping(value = "/compounds/{cid}", produces = MediaType.APPLICATION_JSON_VALUE)
     public CompoundId getCompound(@PathVariable String projectId, @PathVariable String cid,
                                   @RequestParam(required = false, defaultValue = "false") boolean topAnnotation,
-                                  @RequestParam(required = false, defaultValue = "false") boolean msData) {
+                                  @RequestParam(required = false, defaultValue = "false") boolean msData,
+                                  @RequestParam(required = false, defaultValue = "false") boolean msQuality) {
         final ProjectSpaceManager<?> space = projectSpace(projectId);
         final CompoundContainerId ccid = parseCID(space, cid);
-        return asCompoundId(ccid, space, topAnnotation, msData);
+        return asCompoundId(ccid, space, topAnnotation, msData,msQuality);
     }
 
     /**
@@ -240,14 +241,27 @@ private MsData asCompoundMsData(Instance instance) {
                         "Compound with ID '" + instance + "' has no input Data!"));
     }
 
-    private CompoundId asCompoundId(CompoundContainerId cid, ProjectSpaceManager<?> ps, boolean includeSummary, boolean includeMsData) {
+    private EnumSet<CompoundQuality.CompoundQualityFlag> asCompoundQualityData(Instance instance){
+        return instance.loadCompoundContainer(Ms2Experiment.class)
+                .getAnnotation(Ms2Experiment.class)
+                .flatMap(exp -> exp.getAnnotation(CompoundQuality.class))
+                .map(CompoundQuality::getFlags)
+                .orElseThrow(()-> new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR,
+                        "Compound with ID '" + instance+ "' has no Quality information!"));
+    }
+
+
+
+    private CompoundId asCompoundId(CompoundContainerId cid, ProjectSpaceManager<?> ps, boolean includeSummary, boolean includeMsData, boolean includeMsQuality) {
         final CompoundId compoundId = CompoundId.of(cid);
         if (includeSummary || includeMsData) {
             Instance instance = ps.getInstanceFromCompound(cid);
             if (includeSummary)
                 compoundId.setTopAnnotation(asCompoundSummary(instance));
             if (includeMsData)
                 compoundId.setMsData(asCompoundMsData(instance));
+            if (includeMsQuality)
+                compoundId.setQualityFlags(asCompoundQualityData(instance));
         }
         return compoundId;
     }

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/compounds/model/CompoundAnnotation.java

@@ -47,10 +47,10 @@
 
 /**
  * Summary of the results of a Compound. Can be added to a CompoundId.
- * It is not null within a CompoundId if it was not requested und non null otherwise
- * The different summary fields within this summary are null if the corresponding
- * compound does not contain the represented results. The content of  non NULL
- * summary field id the result was computed but is empty.
+ * It is null within a CompoundId if it was not requested und non-null otherwise.
+ * The different summary fields within this summary object are null if the corresponding
+ * compound does not contain the represented results. If fields are non-null
+ * the corresponding result has been computed but might still be empty.
  * */
 @Getter
 @Setter

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/compounds/model/CompoundId.java

@@ -20,10 +20,13 @@
 package de.unijena.bioinf.ms.middleware.compounds.model;
 
 import de.unijena.bioinf.ChemistryBase.chem.PrecursorIonType;
+import de.unijena.bioinf.ChemistryBase.ms.CompoundQuality;
 import de.unijena.bioinf.projectspace.CompoundContainerId;
 import lombok.Getter;
 import lombok.Setter;
 
+import java.util.EnumSet;
+
 /**
  * The CompoundId contains the ID of a compound together with some read-only information that might be displayed in
  * some summary view.
@@ -50,6 +53,17 @@ public class CompoundId {
     protected CompoundAnnotation topAnnotation;
     protected MsData msData;
 
+    // Data and Result quality
+    /**
+     * Contains all pre-computation quality information that belong to
+     * this compound, such as information about the quality of the peak shape, MS2 spectrum etc.,
+     * see ({@link CompoundQuality.CompoundQualityFlag})
+     * <p>
+     * Each Compound has a Set of Quality assessment flags.
+     */
+    protected EnumSet<CompoundQuality.CompoundQualityFlag> qualityFlags;
+    //todo we will add an additional MSQuality Object with many different quality checks produced by LCMS Compound// Summary.
+
     //todo handle computing flag
     protected boolean computing = false;