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Merge branch '59-paras-vs-params' into 'master'
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Renaming typos and bad name Choices

Closes #53, #54, #58, #57, and #59

See merge request bright-giant/sirius/sirius-frontend!18
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Markus Fleischauer committed Oct 30, 2023
2 parents fa73ed0 + d9ab081 commit 4a37c65
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Showing 10 changed files with 23 additions and 37 deletions.
4 changes: 2 additions & 2 deletions ...e/src/main/java/de/unijena/bioinf/ms/middleware/controller/AlignedFeaturesController.java
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Expand Up @@ -101,7 +101,7 @@ public void deleteAlignedFeature(@PathVariable String projectId, @PathVariable S

/**
* List of StructureCandidates for the given 'alignedFeatureId' with minimal information.
* StructureCandidates can be enriched with molecular fingerprint, structure database links and pubmed ids.
* StructureCandidates can be enriched with molecular fingerprint, structure database links.
*
* @param projectId project-space to read from.
* @param alignedFeatureId feature (aligned over runs) the structure candidates belong to.
Expand Down Expand Up @@ -166,7 +166,7 @@ public FormulaCandidate getFormulaCandidate(

/**
* List of StructureCandidates the given 'formulaId' with minimal information.
* StructureCandidates can be enriched with molecular fingerprint, structure database links and pubmed ids,
* StructureCandidates can be enriched with molecular fingerprint, structure database links.
*
* @param projectId project-space to read from.
* @param alignedFeatureId feature (aligned over runs) the formula result belongs to.
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2 changes: 1 addition & 1 deletion ..._service/src/main/java/de/unijena/bioinf/ms/middleware/controller/CompoundController.java
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Expand Up @@ -93,7 +93,7 @@ public Compound getCompound(@PathVariable String projectId, @PathVariable String
* @param compoundId identifier of the compound to delete.
*/
@DeleteMapping(value = "/{compoundId}")
public void deleteAlignedFeature(@PathVariable String projectId, @PathVariable String compoundId) {
public void deleteCompound(@PathVariable String projectId, @PathVariable String compoundId) {
projectsProvider.getProjectOrThrow(projectId).deleteCompoundById(compoundId);
}
}
4 changes: 2 additions & 2 deletions ...ice/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/FormulaCandidate.java
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Expand Up @@ -66,8 +66,8 @@ public enum OptFields {statistics, fragmentationTree, simulatedIsotopePattern, p
*/
protected Double zodiacScore;

protected Integer numOfexplainedPeaks;
protected Integer numOfexplainablePeaks;
protected Integer numOfExplainedPeaks;
protected Integer numOfExplainablePeaks;

protected Double totalExplainedIntensity;
protected Deviation medianMassDeviation;
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2 changes: 1 addition & 1 deletion ...service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/FragmentNode.java
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Expand Up @@ -33,7 +33,7 @@ public class FragmentNode {
String molecularFormula;
String ionType;
double massDeviationDa;
double massErrorPpm;
double massDeviationPpm;
double score;

double intensity;
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2 changes: 1 addition & 1 deletion ...ce/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/FragmentationTree.java
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Expand Up @@ -61,7 +61,7 @@ public static FragmentationTree fromFtree(FTree sourceTree) {
if (anoPeak.get(f).isMeasured()) {
Deviation dev = sourceTree.getMassError(f);
fn.setMassDeviationDa(dev.getAbsolute());
fn.setMassErrorPpm(dev.getPpm());
fn.setMassDeviationPpm(dev.getPpm());
}
}

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6 changes: 0 additions & 6 deletions ...e/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/StructureCandidate.java
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Expand Up @@ -37,7 +37,6 @@ public class StructureCandidate {
protected String structureName;
protected String smiles;

protected Integer numOfPubMedIds;
protected Double xlogP;
protected String inchiKey;

Expand All @@ -52,11 +51,6 @@ public class StructureCandidate {
* OPTIONAL: needs to be added by parameter
*/
List<DBLink> refSpectraLinks;
/**
* PubMed IDs belonging to this structure candidate
* OPTIONAL: needs to be added by parameter
*/
int[] pubmedIds;



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8 changes: 0 additions & 8 deletions ...ain/java/de/unijena/bioinf/ms/middleware/model/annotations/StructureCandidateFormula.java
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Expand Up @@ -27,7 +27,6 @@
import de.unijena.bioinf.ChemistryBase.chem.PrecursorIonType;
import de.unijena.bioinf.ChemistryBase.fp.Fingerprint;
import de.unijena.bioinf.chemdb.CompoundCandidate;
import de.unijena.bioinf.chemdb.PubmedLinks;
import de.unijena.bioinf.fingerid.ConfidenceScore;
import de.unijena.bioinf.projectspace.FormulaResultId;
import de.unijena.bioinf.projectspace.FormulaScoring;
Expand Down Expand Up @@ -103,13 +102,6 @@ public static StructureCandidateFormula of(Scored<CompoundCandidate> can, @Nulla
sSum.setXlogP(can.getCandidate().getXlogp());

//meta data
PubmedLinks pubMedIds = can.getCandidate().getPubmedIDs();
if (pubMedIds != null) {
sSum.setNumOfPubMedIds(pubMedIds.getNumberOfPubmedIDs());
if (optFields.contains(OptFields.pubmedIds))
sSum.setPubmedIds(pubMedIds.getCopyOfPubmedIDs());
}

if (optFields.contains(OptFields.dbLinks))
sSum.setDbLinks(can.getCandidate().getLinks());

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2 changes: 1 addition & 1 deletion ...main/java/de/unijena/bioinf/ms/middleware/model/annotations/StructureCandidateScored.java
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Expand Up @@ -30,7 +30,7 @@
@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonIgnoreProperties({ "molecularFormula", "adduct"})
public class StructureCandidateScored extends StructureCandidate {
public enum OptFields {fingerprint, dbLinks, refSpectraLinks, pubmedIds}
public enum OptFields {fingerprint, dbLinks, refSpectraLinks}

protected Double csiScore;
protected Double tanimotoSimilarity;
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22 changes: 11 additions & 11 deletions ...st_service/src/main/java/de/unijena/bioinf/ms/middleware/model/compute/JobSubmission.java
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Expand Up @@ -109,27 +109,27 @@ public class JobSubmission {
* Parameter Object for molecular formula identification tool (CLI-Tool: formula, sirius).
* If NULL the tool will not be executed.
*/
Sirius formulaIdParas;
Sirius formulaIdParams;
/**
* Parameter Object for network based molecular formula re-ranking (CLI-Tool: zodiac).
* If NULL the tool will not be executed.
*/
Zodiac zodiacParas;
Zodiac zodiacParams;
/**
* Parameter Object for Fingerprint prediction with CSI:FingerID (CLI-Tool: fingerint).
* If NULL the tool will not be executed.
*/
FingerprintPrediction fingerprintPredictionParas;
FingerprintPrediction fingerprintPredictionParams;
/**
* Parameter Object for structure database search with CSI:FingerID (CLI-Tool: structure).
* If NULL the tool will not be executed.
*/
StructureDbSearch structureDbSearchParas;
StructureDbSearch structureDbSearchParams;
/**
* Parameter Object for CANOPUS compound class prediction tool (CLI-Tool: canopus).
* If NULL the tool will not be executed.
*/
Canopus canopusParas;
Canopus canopusParams;

//todo passatutto api.

Expand All @@ -147,11 +147,11 @@ public static JobSubmission createDefaultInstance(boolean includeConfigMap) {
j.setEnforcedAdducts(settings.getEnforced().stream().map(PrecursorIonType::toString).collect(Collectors.toList()));
j.setDetectableAdducts(settings.getDetectable().stream().map(PrecursorIonType::toString).collect(Collectors.toList()));
j.setRecompute(false);
j.setFormulaIdParas(new Sirius());
j.setZodiacParas(new Zodiac());
j.setFingerprintPredictionParas(new FingerprintPrediction());
j.setStructureDbSearchParas(new StructureDbSearch());
j.setCanopusParas(new Canopus());
j.setFormulaIdParams(new Sirius());
j.setZodiacParams(new Zodiac());
j.setFingerprintPredictionParams(new FingerprintPrediction());
j.setStructureDbSearchParams(new StructureDbSearch());
j.setCanopusParams(new Canopus());
if (includeConfigMap) {
final Map<String, String> configMap = new HashMap<>();
PropertyManager.DEFAULTS.getConfigKeys().forEachRemaining(k ->
Expand All @@ -164,7 +164,7 @@ public static JobSubmission createDefaultInstance(boolean includeConfigMap) {

@JsonIgnore
public List<Tool<?>> getEnabledTools() {
return Stream.of(formulaIdParas, zodiacParas, fingerprintPredictionParas, structureDbSearchParas, canopusParas)
return Stream.of(formulaIdParams, zodiacParams, fingerprintPredictionParams, structureDbSearchParams, canopusParams)
.filter(Objects::nonNull).filter(Tool::isEnabled).collect(Collectors.toList());
}
}
8 changes: 4 additions & 4 deletions ...rc/main/java/de/unijena/bioinf/ms/middleware/service/projects/SiriusProjectSpaceImpl.java
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Expand Up @@ -483,8 +483,8 @@ public static FormulaCandidate asFormulaCandidate(@NotNull FormulaResult formula
formulaResult.getAnnotation(FTree.class).
ifPresent(fTree -> {
final FTreeMetricsHelper metrHelp = new FTreeMetricsHelper(fTree);
frs.setNumOfexplainedPeaks(metrHelp.getNumOfExplainedPeaks());
frs.setNumOfexplainablePeaks(metrHelp.getNumberOfExplainablePeaks());
frs.setNumOfExplainedPeaks(metrHelp.getNumOfExplainedPeaks());
frs.setNumOfExplainablePeaks(metrHelp.getNumberOfExplainablePeaks());
frs.setTotalExplainedIntensity(metrHelp.getExplainedIntensityRatio());
frs.setMedianMassDeviation(metrHelp.getMedianMassDeviation());
});
Expand Down Expand Up @@ -533,7 +533,7 @@ public static FeatureAnnotations extractTopAnnotationsDeNovo(Instance inst) {
// topHit.getAnnotation(FBCandidates.class).map(FBCandidates::getResults)
// .filter(l -> !l.isEmpty()).map(r -> r.get(0)).map(s ->
// StructureCandidateFormula.of(s, topHit.getAnnotationOrThrow(FormulaScoring.class),
// EnumSet.of(StructureCandidateScored.OptFields.dbLinks, StructureCandidateScored.OptFields.pubmedIds, StructureCandidateScored.OptFields.refSpectraLinks), topHit.getId()))
// EnumSet.of(StructureCandidateScored.OptFields.dbLinks, StructureCandidateScored.OptFields.refSpectraLinks), topHit.getId()))
// .ifPresent(cSum::setStructureAnnotation);

topHit.getAnnotation(CanopusResult.class).map(CompoundClasses::of).
Expand All @@ -557,7 +557,7 @@ public static FeatureAnnotations extractTopAnnotations(Instance inst) {
topHit.getAnnotation(FBCandidates.class).map(FBCandidates::getResults)
.filter(l -> !l.isEmpty()).map(r -> r.get(0)).map(s ->
StructureCandidateFormula.of(s, topHit.getAnnotationOrThrow(FormulaScoring.class),
EnumSet.of(StructureCandidateScored.OptFields.dbLinks, StructureCandidateScored.OptFields.pubmedIds, StructureCandidateScored.OptFields.refSpectraLinks), topHit.getId()))
EnumSet.of(StructureCandidateScored.OptFields.dbLinks, StructureCandidateScored.OptFields.refSpectraLinks), topHit.getId()))
.ifPresent(cSum::setStructureAnnotation);

topHit.getAnnotation(CanopusResult.class).map(CompoundClasses::of).
Expand Down

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