fixed "all" database label bug in cli. fixes #92

sirius-ms · Jan 10, 2023 · 887c96d · 887c96d
1 parent e3e0c73
commit 887c96d
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Showing 4 changed files with 7 additions and 13 deletions.
diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/completion/DataSourceCandidates.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/completion/DataSourceCandidates.java
@@ -32,7 +32,7 @@ public class DataSourceCandidates implements Iterable<String> {
             DataSource.values()).filter(it -> it != DataSource.TRAIN).map(DataSource::name)
             .collect(Collectors.toList()));
 
-    public static final String VALID_DATA_STRING = "Example: possible DBs: 'ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE'";
+    public static final String VALID_DATA_STRING = "Example: possible DBs: 'ALL,ALL_BUT_INSILICO,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE'";
     public static final String PATAM_LABEL = "<dbName>[,<dbName>...]";
 
     @NotNull

diff --git a/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/compute/DBSelectionList.java b/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/compute/DBSelectionList.java
@@ -21,6 +21,7 @@
 
 import de.unijena.bioinf.chemdb.DataSource;
 import de.unijena.bioinf.chemdb.DataSources;
+import de.unijena.bioinf.chemdb.SearchableDatabases;
 import de.unijena.bioinf.chemdb.custom.CustomDataSources;
 import de.unijena.bioinf.ms.gui.utils.GuiUtils;
 import de.unijena.bioinf.ms.gui.utils.jCheckboxList.JCheckBoxList;
@@ -30,15 +31,11 @@
 import java.util.Comparator;
 import java.util.List;
 import java.util.Objects;
-import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 public class DBSelectionList extends JCheckBoxList<CustomDataSources.Source> {
-    public final static Set<String> BLACK_LIST = Set.of(DataSource.ADDITIONAL.realName, DataSource.TRAIN.realName, DataSource.LIPID.realName(), DataSource.ALL.realName, DataSource.ALL_BUT_INSILICO.realName,
-            DataSource.PUBCHEMANNOTATIONBIO.realName, DataSource.PUBCHEMANNOTATIONDRUG.realName, DataSource.PUBCHEMANNOTATIONFOOD.realName, DataSource.PUBCHEMANNOTATIONSAFETYANDTOXIC.realName,
-            DataSource.SUPERNATURAL.realName
-    );
+
 
     public DBSelectionList() {
         this(true);
@@ -49,7 +46,7 @@ public DBSelectionList( boolean includeCustom) {
 
     public DBSelectionList(@Nullable String descriptionKey, boolean includeCustom) {
         this(descriptionKey, CustomDataSources.sourcesStream().
-                filter(db -> !BLACK_LIST.contains(db.name())).
+                filter(db -> !SearchableDatabases.NON_SLECTABLE_LIST.contains(db.name())).
                 filter(db -> includeCustom || !db.isCustomSource()).sorted(Comparator.comparing(CustomDataSources.Source::name)).
                 collect(Collectors.toList()));
     }

diff --git a/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/compute/FingerblastConfigPanel.java b/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/compute/FingerblastConfigPanel.java
@@ -20,6 +20,7 @@
 package de.unijena.bioinf.ms.gui.compute;
 
 import de.unijena.bioinf.chemdb.DataSource;
+import de.unijena.bioinf.chemdb.SearchableDatabases;
 import de.unijena.bioinf.chemdb.custom.CustomDataSources;
 import de.unijena.bioinf.ms.frontend.subtools.fingerblast.FingerblastOptions;
 import de.unijena.bioinf.ms.gui.utils.GuiUtils;
@@ -30,7 +31,6 @@
 import org.jetbrains.annotations.Nullable;
 
 import javax.swing.*;
-import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;
@@ -89,9 +89,7 @@ public List<String> getStructureSearchDBStrings() {
     List<CustomDataSources.Source> allButInsilico = null;
     private List<CustomDataSources.Source> allButInsilico(){
        if (allButInsilico == null){
-           allButInsilico = CustomDataSources.getSourcesFromNames(
-                   Arrays.stream(DataSource.valuesNoALLNoMINES()).map(DataSource::realName)
-                           .filter(s -> !DBSelectionList.BLACK_LIST.contains(s)).collect(Collectors.toList()));
+           allButInsilico = SearchableDatabases.getNonInSilicoSelectableSources();
        }
        return allButInsilico;
 

diff --git a/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/fingerid/custom_db/DatabaseDialog.java b/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/fingerid/custom_db/DatabaseDialog.java
@@ -25,7 +25,6 @@
 import de.unijena.bioinf.chemdb.custom.CustomDatabase;
 import de.unijena.bioinf.ms.frontend.subtools.InputFilesOptions;
 import de.unijena.bioinf.ms.frontend.subtools.custom_db.CustomDBOptions;
-import de.unijena.bioinf.ms.gui.compute.DBSelectionList;
 import de.unijena.bioinf.ms.gui.compute.jjobs.Jobs;
 import de.unijena.bioinf.ms.gui.configs.Buttons;
 import de.unijena.bioinf.ms.gui.configs.Icons;
@@ -217,7 +216,7 @@ public void updateContent(CustomDatabase<?> c) {
                 content.setText("<html>Custom database. Containing "
                         + c.getStatistics().getCompounds() + " compounds with " + c.getStatistics().getFormulas()
                         + " different molecular formulas." +
-                        ((c.getSettings().isInheritance() ? "<br>This database will also include all compounds from '" + DataSources.getDataSourcesFromBitFlags(c.getFilterFlag()).stream().filter(n -> !DBSelectionList.BLACK_LIST.contains(n)).collect(Collectors.joining("', '")) + "'." : "")
+                        ((c.getSettings().isInheritance() ? "<br>This database will also include all compounds from '" + DataSources.getDataSourcesFromBitFlags(c.getFilterFlag()).stream().filter(n -> !SearchableDatabases.NON_SLECTABLE_LIST.contains(n)).collect(Collectors.joining("', '")) + "'." : "")
                                 + (c.needsUpgrade() ? "<br><b>This database schema is outdated. You have to upgrade the database before you can use it.</b>" : "") + "</html>"));
             } else {
                 content.setText("Empty custom database.");