4.9.9 - backport of CandidateFormulas parameter

sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/sirius/SiriusOptions.java

@@ -1,22 +1,3 @@
-/*
- *  This file is part of the SIRIUS Software for analyzing MS and MS/MS data
- *
- *  Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer, Marvin Meusel and Sebastian Böcker,
- *  Chair of Bioinformatics, Friedrich-Schiller University.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Affero General Public License
- *  as published by the Free Software Foundation; either
- *  version 3 of the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Affero General Public License for more details.
- *
- *  You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
- */
-
 /*
  *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
@@ -37,7 +18,6 @@
 package de.unijena.bioinf.ms.frontend.subtools.sirius;
 
 import de.unijena.bioinf.ChemistryBase.ms.DetectedAdducts;
-import de.unijena.bioinf.ChemistryBase.ms.ft.model.Whiteset;
 import de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory;
 import de.unijena.bioinf.ms.frontend.DefaultParameter;
 import de.unijena.bioinf.ms.frontend.completion.DataSourceCandidates;
@@ -137,10 +117,9 @@ public void setDatabase(DefaultParameter dbList) throws Exception {
     }
 
     @Option(names = {"-f", "--formulas"}, description = "Specify a list of candidate formulas the method should use. Omit this option if you want to consider all possible molecular formulas")
-    public void setFormulaWhiteList(List<String> formulaWhiteList) {
-        formulaWhiteSet = Whiteset.of(formulaWhiteList);
+    public void setCandidateFormulas(DefaultParameter formulas) throws Exception {
+        defaultConfigOptions.changeOption("CandidateFormulas", formulas);
     }
-    public Whiteset formulaWhiteSet =  null;
 
 
     @Option(names = {"--no-isotope-filter"}, description = "Disable molecular formula filter. When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score.")
@@ -167,7 +146,7 @@ public void setIonsEnforced(DefaultParameter adductList) throws Exception {
     }
 
 
-    //heuristic threshods
+    //heuristic thresholds
     @Option(names = {"--heuristic"}, descriptionKey ="UseHeuristic.mzToUseHeuristic" , description = "Enable heuristic preprocessing for compounds >= the specified m/z.")
     public void setMzToUseHeuristic(DefaultParameter value) throws Exception {
         defaultConfigOptions.changeOption("UseHeuristic.mzToUseHeuristic", value);
@@ -230,10 +209,7 @@ public void setTrustGuessIonFromMS1(boolean trust) {
 
     @Override
     public InstanceJob.Factory<SiriusSubToolJob> call() throws Exception {
-        return new InstanceJob.Factory<>(
-                sub -> new SiriusSubToolJob(this, sub),
-                getInvalidator()
-        );
+        return new InstanceJob.Factory<>(SiriusSubToolJob::new, getInvalidator());
     }
 
     @Override

sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/sirius/SiriusSubToolJob.java

@@ -21,6 +21,7 @@
 
 import de.unijena.bioinf.ChemistryBase.ms.DetectedAdducts;
 import de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment;
+import de.unijena.bioinf.ChemistryBase.ms.ft.model.CandidateFormulas;
 import de.unijena.bioinf.ChemistryBase.ms.ft.model.Whiteset;
 import de.unijena.bioinf.ChemistryBase.ms.properties.FinalConfig;
 import de.unijena.bioinf.chemdb.annotations.FormulaSearchDB;
@@ -41,16 +42,10 @@
 import java.util.Optional;
 
 public class SiriusSubToolJob extends InstanceJob {
-    //todo this is only a temporary solution. parameters should be annotated to the exp
-    // we do not want to have the sub-tool management to be dependent on a cli parsing library
-    protected final SiriusOptions cliOptions;
-
-    public SiriusSubToolJob(SiriusOptions cliOptions, JobSubmitter jobSubmitter) {
+    public SiriusSubToolJob(JobSubmitter jobSubmitter) {
         super(jobSubmitter, false);
-        this.cliOptions = cliOptions;
     }
 
-
     @Override
     public boolean isAlreadyComputed(@NotNull Instance inst) {
         return !inst.loadCompoundContainer().getResults().isEmpty();
@@ -62,27 +57,29 @@ protected void computeAndAnnotateResult(final @NotNull Instance inst) throws Exc
         // set whiteSet or merge with whiteSet from db search if available
         Whiteset wSet = null;
 
-        checkForInterruption();
+        {
+            checkForInterruption();
 
-        // create WhiteSet from DB if necessary
-        //todo do we really want to restrict to organic even if the db is user selected
-        final Optional<FormulaSearchDB> searchDB = exp.getAnnotation(FormulaSearchDB.class);
-        if (searchDB.isPresent() && searchDB.get().containsDBs())
-            wSet = submitSubJob(new FormulaWhiteListJob(ApplicationCore.WEB_API.getChemDB(), searchDB.get().searchDBs, exp, true, false))
-                    .awaitResult();
+            // create WhiteSet from DB if necessary
+            //todo do we really want to restrict to organic even if the db is user selected
+            final Optional<FormulaSearchDB> searchDB = exp.getAnnotation(FormulaSearchDB.class);
+            if (searchDB.isPresent() && searchDB.get().containsDBs())
+                wSet = submitSubJob(new FormulaWhiteListJob(ApplicationCore.WEB_API.getChemDB(), searchDB.get().searchDBs, exp, true, false))
+                        .awaitResult();
 
-        checkForInterruption();
+            checkForInterruption();
 
 
-        // todo this should be moved to annotations at some point.
-        // so that the cli parser dependency can be removed
-        if (cliOptions.formulaWhiteSet != null) {
-            if (wSet != null)
-                wSet = wSet.add(cliOptions.formulaWhiteSet);
-            else
-                wSet = cliOptions.formulaWhiteSet;
+            // so that the cli parser dependency can be removed
+            if (exp.getAnnotation(CandidateFormulas.class).map(CandidateFormulas::formulas).map(Whiteset::notEmpty).orElse(false)) {
+                final Whiteset userFormulas = exp.getAnnotation(CandidateFormulas.class).map(CandidateFormulas::formulas).orElseThrow();
+                if (wSet != null)
+                    wSet = wSet.add(userFormulas);
+                else
+                    wSet = userFormulas;
+            }
+            exp.setAnnotation(Whiteset.class, wSet);
         }
-        exp.setAnnotation(Whiteset.class, wSet);
 
         checkForInterruption();
 

sirius_cli/src/main/resources/sirius_frontend.build.properties

@@ -1,5 +1,5 @@
 #here you can provide properties that may be needed during build- AND during runtime and should not be editable by the user at runtime
-de.unijena.bioinf.siriusFrontend.version=4.9.8
+de.unijena.bioinf.siriusFrontend.version=4.9.9
 
 de.unijena.bioinf.sirius.version=4.6.1
 de.unijena.bioinf.fingerid.version=1.6.0