create Extension SPI, merge ValueFormatterLoader into LPhyCoreLoader #…

…400 #431

lphy-base/src/main/java/lphy/base/spi/LPhyBaseImpl.java

@@ -35,7 +35,7 @@
 import lphy.base.function.tree.PruneTree;
 import lphy.core.model.BasicFunction;
 import lphy.core.model.GenerativeDistribution;
-import lphy.core.spi.LPhyExtension;
+import lphy.core.spi.LPhyCoreImpl;
 
 import java.util.Arrays;
 import java.util.List;
@@ -46,67 +46,73 @@
  * It requires a public no-args constructor.
  * @author Walter Xie
  */
-public class LPhyBaseImpl implements LPhyExtension {
+public class LPhyBaseImpl extends LPhyCoreImpl { //implements LPhyExtension {
 
     static {
         SequenceTypeLoader sequenceTypeLoader = new SequenceTypeLoader();
         sequenceTypeLoader.loadAllExtensions();
     }
 
-    List<Class<? extends GenerativeDistribution>> genDists = Arrays.asList(
-            // probability distribution
-            Bernoulli.class, BernoulliMulti.class, Beta.class, Categorical.class, Cauchy.class, Dirichlet.class,
-            DiscretizedGamma.class, Exp.class, Gamma.class, Geometric.class, InverseGamma.class, LogNormal.class,
-            NegativeBinomial.class, Normal.class, NormalGamma.class, Poisson.class,
-            Uniform.class, UniformDiscrete.class, Weibull.class, WeightedDirichlet.class,
-            // tree distribution
-            Yule.class, BirthDeathTree.class, FullBirthDeathTree.class, BirthDeathTreeDT.class,
-            BirthDeathSamplingTree.class, BirthDeathSamplingTreeDT.class, BirthDeathSerialSamplingTree.class,
-            RhoSampleTree.class, FossilBirthDeathTree.class,
-            SimBDReverse.class, SimFBDAge.class, SimFossilsPoisson.class,
-            SerialCoalescent.class, StructuredCoalescent.class, MultispeciesCoalescent.class,
-            // skyline
-            SkylineCoalescent.class, ExpMarkovChain.class, RandomComposition.class,
-            // alignment
-            Sequence.class, ErrorModel.class, MissingSites.class,
-            // others
-            RandomBooleanArray.class, Sample.class,
-            // phylogenetic distribution
-            PhyloBrownian.class, PhyloMultivariateBrownian.class, PhyloOU.class,
-            PhyloCTMC.class, PhyloCTMCSiteModel.class, bSiteRates.class);
+    @Override
+    public List<Class<? extends GenerativeDistribution>> declareDistributions() {
+        return Arrays.asList(
+                // probability distribution
+                Bernoulli.class, BernoulliMulti.class, Beta.class, Categorical.class, Cauchy.class, Dirichlet.class,
+                DiscretizedGamma.class, Exp.class, Gamma.class, Geometric.class, InverseGamma.class, LogNormal.class,
+                NegativeBinomial.class, Normal.class, NormalGamma.class, Poisson.class,
+                Uniform.class, UniformDiscrete.class, Weibull.class, WeightedDirichlet.class,
+                // tree distribution
+                Yule.class, BirthDeathTree.class, FullBirthDeathTree.class, BirthDeathTreeDT.class,
+                BirthDeathSamplingTree.class, BirthDeathSamplingTreeDT.class, BirthDeathSerialSamplingTree.class,
+                RhoSampleTree.class, FossilBirthDeathTree.class,
+                SimBDReverse.class, SimFBDAge.class, SimFossilsPoisson.class,
+                SerialCoalescent.class, StructuredCoalescent.class, MultispeciesCoalescent.class,
+                // skyline
+                SkylineCoalescent.class, ExpMarkovChain.class, RandomComposition.class,
+                // alignment
+                Sequence.class, ErrorModel.class, MissingSites.class,
+                // others
+                RandomBooleanArray.class, Sample.class,
+                // phylogenetic distribution
+                PhyloBrownian.class, PhyloMultivariateBrownian.class, PhyloOU.class,
+                PhyloCTMC.class, PhyloCTMCSiteModel.class, bSiteRates.class);
+    }
 
-    List<Class<? extends BasicFunction>> functions = Arrays.asList(ARange.class, ArgI.class,
-            // Substitution models
-            JukesCantor.class, K80.class, F81.class, HKY.class, GTR.class, WAG.class,
-            GeneralTimeReversible.class, LewisMK.class,
-            NucleotideModel.class,
-            BModelSetFunction.class,
-            bSiteModelFunction.class,
+    @Override
+    public List<Class<? extends BasicFunction>> declareFunctions() {
+        return Arrays.asList(ARange.class, ArgI.class,
+                // Substitution models
+                JukesCantor.class, K80.class, F81.class, HKY.class, GTR.class, WAG.class,
+                GeneralTimeReversible.class, LewisMK.class,
+                NucleotideModel.class,
+                BModelSetFunction.class,
+                bSiteModelFunction.class,
 
-            // Data types
-            BinaryDatatypeFunction.class, NucleotidesFunction.class, StandardDatatypeFunction.class,
-            AminoAcidsFunction.class,
-            // Taxa
-            CreateTaxa.class, ExtantTaxa.class, NCharFunction.class, NTaxaFunction.class, TaxaFunction.class,
-            // Alignment
-            SelectSitesByMissingFraction.class, RemoveTaxa.class,
-            VariableSites.class, InvariableSites.class, CopySites.class,
-            // Tree
-            LocalBranchRates.class, ExtantTree.class, PruneTree.class, //NodeCount.class, TreeLength.class,
-            // Matrix
-            BinaryRateMatrix.class, MigrationMatrix.class, MigrationCount.class,
-            // IO
-            Newick.class, ReadNexus.class, ReadFasta.class, ReadDelim.class, ExtractTrait.class, SpeciesTaxa.class,
-            // Math
-            SumBoolean.class, SumRows.class, SumCols.class, Sum2dArray.class, Sum.class,// Product.class,
-            // Set Op
-            Intersect.class,
-            // cast
-            ToDouble.class,
-            // Utils
-            Length.class, Unique.class, Sort.class, IfElse.class, //ConcatStr.class,
-            Get.class, Select.class, Split.class, ParseInt.class, Rep.class, RepArray.class,  //Copy.class,
-            ConcatArray.class, Concat2Str.class);
+                // Data types
+                BinaryDatatypeFunction.class, NucleotidesFunction.class, StandardDatatypeFunction.class,
+                AminoAcidsFunction.class,
+                // Taxa
+                CreateTaxa.class, ExtantTaxa.class, NCharFunction.class, NTaxaFunction.class, TaxaFunction.class,
+                // Alignment
+                SelectSitesByMissingFraction.class, RemoveTaxa.class,
+                VariableSites.class, InvariableSites.class, CopySites.class,
+                // Tree
+                LocalBranchRates.class, ExtantTree.class, PruneTree.class, //NodeCount.class, TreeLength.class,
+                // Matrix
+                BinaryRateMatrix.class, MigrationMatrix.class, MigrationCount.class,
+                // IO
+                Newick.class, ReadNexus.class, ReadFasta.class, ReadDelim.class, ExtractTrait.class, SpeciesTaxa.class,
+                // Math
+                SumBoolean.class, SumRows.class, SumCols.class, Sum2dArray.class, Sum.class,// Product.class,
+                // Set Op
+                Intersect.class,
+                // cast
+                ToDouble.class,
+                // Utils
+                Length.class, Unique.class, Sort.class, IfElse.class, //ConcatStr.class,
+                Get.class, Select.class, Split.class, ParseInt.class, Rep.class, RepArray.class,  //Copy.class,
+                ConcatArray.class, Concat2Str.class);
+    }
 
     /**
      * Required by ServiceLoader.
@@ -115,15 +121,26 @@ public LPhyBaseImpl() {
         //TODO do something here, e.g. print package or classes info ?
     }
 
-    @Override
-    public List<Class<? extends GenerativeDistribution>> getDistributions() {
-        return genDists;
-    }
 
-    @Override
-    public List<Class<? extends BasicFunction>> getFunctions() {
-        return functions;
-    }
+//    @Override
+//    public void register() {
+//
+//    }
+//
+//    @Override
+//    public Map<String, Set<Class<?>>> getDistributions() {
+//        return null;
+//    }
+//
+//    @Override
+//    public Map<String, Set<Class<?>>> getFunctions() {
+//        return null;
+//    }
+//
+//    @Override
+//    public TreeSet<Class<?>> getTypes() {
+//        return null;
+//    }
 
     public String getExtensionName() {
         return "LPhy standard library";

lphy-base/src/main/java/lphy/base/spi/LPhyBaseValueFormatterImpl.java → lphy-base/src/main/java/lphy/base/spi/LPhyValueFormatterBaseImpl.java

@@ -3,7 +3,7 @@
 import lphy.base.logger.NexusAlignmentFormatter;
 import lphy.base.logger.NexusTreeFormatter;
 import lphy.core.logger.ValueFormatter;
-import lphy.core.spi.LPhyValueFormatter;
+import lphy.core.spi.LPhyValueFormatterCoreImpl;
 
 import java.util.Set;
 
@@ -13,23 +13,19 @@
  * It requires a public no-args constructor.
  * @author Walter Xie
  */
-public class LPhyBaseValueFormatterImpl implements LPhyValueFormatter {
+public class LPhyValueFormatterBaseImpl extends LPhyValueFormatterCoreImpl {//implements LPhyValueFormatter {
 
-    /**
-     * Required by ServiceLoader.
-     */
-    public LPhyBaseValueFormatterImpl() {
-    }
 
     @Override
-    public Set<Class<? extends ValueFormatter>> getValueFormatters() {
+    public Set<Class<? extends ValueFormatter>> declareValueFormatters() {
         return Set.of(NexusAlignmentFormatter.class, NexusTreeFormatter.class);
     }
-//    public Map<Class<?>, Set<Class<? extends ValueFormatter>>> getValueFormatterMap() {
-//        return Map.of( SimpleAlignment.class, Set.of(NexusAlignmentFormatter.class),
-//                TimeTree.class, Set.of(NexusTreeFormatter.class) );
-//    }
 
+    /**
+     * Required by ServiceLoader.
+     */
+    public LPhyValueFormatterBaseImpl() {
+    }
 
     public String getExtensionName() {
         return "LPhy base loggers";

lphy-base/src/main/java/lphy/base/spi/SequenceTypeBaseImpl.java

@@ -23,7 +23,7 @@ public SequenceTypeBaseImpl() {
     }
 
     @Override
-    public Map<String, ? extends SequenceType> getSequenceTypes() {
+    public Map<String, ? extends SequenceType> declareSequenceTypes() {
         Map<String, SequenceType> dataTypeMap = new ConcurrentHashMap<>();
         dataTypeMap.put("rna", SequenceType.NUCLEOTIDE);
         dataTypeMap.put("dna", SequenceType.NUCLEOTIDE);
@@ -37,6 +37,11 @@ public SequenceTypeBaseImpl() {
         return dataTypeMap;
     }
 
+    @Override
+    public void register() {
+
+    }
+
     public String getExtensionName() {
         return "LPhy base";
     }

lphy-base/src/main/java/lphy/base/spi/SequenceTypeExtension.java

@@ -20,6 +20,6 @@ public interface SequenceTypeExtension extends Extension {
      *         The string key is a keyword to represent this SequenceType.
      *         The keyword can be used to identify and initialise the corresponding sequence type.
      */
-    Map<String, ? extends SequenceType> getSequenceTypes();
+    Map<String, ? extends SequenceType> declareSequenceTypes();
 
 }

lphy-base/src/main/java/lphy/base/spi/SequenceTypeLoader.java

@@ -52,7 +52,7 @@ private void registerExtensions(String extClsName) {
                 System.out.println("Registering extension from " + sequenceTypeExtension.getClass().getName());
 
                 // sequence types
-                Map<String, ? extends SequenceType> newDataTypes = sequenceTypeExtension.getSequenceTypes();
+                Map<String, ? extends SequenceType> newDataTypes = sequenceTypeExtension.declareSequenceTypes();
                 if (newDataTypes != null)
                     // TODO validate same sequence type?
                     newDataTypes.forEach(dataTypeMap::putIfAbsent);

lphy-base/src/main/java/module-info.java

@@ -1,5 +1,5 @@
 import lphy.base.spi.LPhyBaseImpl;
-import lphy.base.spi.LPhyBaseValueFormatterImpl;
+import lphy.base.spi.LPhyValueFormatterBaseImpl;
 import lphy.base.spi.SequenceTypeBaseImpl;
 
 /**
@@ -52,12 +52,9 @@
     exports lphy.base.logger;
 
     // LPhy extensions
-    uses lphy.core.spi.LPhyExtension;
+    uses lphy.core.spi.Extension;
     // declare what service interface the provider intends to use
-    provides lphy.core.spi.LPhyExtension with LPhyBaseImpl;
-
-    uses lphy.core.spi.LPhyValueFormatter;
-    provides lphy.core.spi.LPhyValueFormatter with LPhyBaseValueFormatterImpl;
+    provides lphy.core.spi.Extension with LPhyBaseImpl, LPhyValueFormatterBaseImpl;
 
     uses lphy.base.spi.SequenceTypeExtension;
     // declare what service interface the provider intends to use

lphy-studio/src/main/java/lphystudio/app/docgenerator/GenerateDocs.java

@@ -66,7 +66,7 @@ public static void main(String[] args) throws IOException {
             // class name with package that implements {@link LPhyExtension}
             String clsName = args[2];
             // require init ParserLoader
-            LoaderManager.getLphyCoreLoader().loadExtension(clsName);
+            LoaderManager.getLphyCoreLoader().loadExtensions(); //TODO broken
         }
         System.out.println("Creating doc for " + extName + " ...\n");
 

lphy-studio/src/main/java/lphystudio/app/manager/ExtManager.java

@@ -1,7 +1,6 @@
 package lphystudio.app.manager;
 
 import lphy.core.spi.LPhyCoreLoader;
-import lphy.core.spi.LPhyExtension;
 import org.xml.sax.SAXException;
 
 import javax.xml.parsers.ParserConfigurationException;
@@ -24,15 +23,15 @@ public class ExtManager {
     // pin lphy on the top of the list
     public final static String LPHY_ID = "lphy";
 
-    final List<LPhyExtension> extensions;
+    final List<lphy.core.spi.Extension> extensions;
     Set<String> jarDirSet = new HashSet<>();
 
     public ExtManager()  {
         //TODO other loaders ?
         LPhyCoreLoader lphyCoreLoader = new LPhyCoreLoader();
-        lphyCoreLoader.loadAllExtensions();
+        lphyCoreLoader.loadExtensions();
 
-        extensions = lphyCoreLoader.getExtensions();
+        extensions = lphyCoreLoader.getExtensionMap().values().stream().toList();
         System.out.println(extensions);
     }
 
@@ -44,7 +43,7 @@ public List<Extension> getLoadedLPhyExts() {
         List<Extension> extList = new ArrayList<>();
 
         // find all loaded lphy exts
-        for (LPhyExtension ext : extensions) {
+        for (lphy.core.spi.Extension ext : extensions) {
             Class<?> cls = ext.getClass();
 //            String pkgNm = "/" + cls.getPackageName().replace(".", "/");
             // include jar name

lphy-studio/src/main/java/lphystudio/spi/LPhyStudioImpl.java

@@ -2,7 +2,7 @@
 
 import lphy.core.model.BasicFunction;
 import lphy.core.model.GenerativeDistribution;
-import lphy.core.spi.LPhyExtension;
+import lphy.core.spi.LPhyCoreImpl;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -11,7 +11,7 @@
  * Empty class to show studio ext in the Extension Manager.
  * @author Walter Xie
  */
-public class LPhyStudioImpl implements LPhyExtension {
+public class LPhyStudioImpl extends LPhyCoreImpl { //} implements LPhyExtension {
 
     /**
      * Required by ServiceLoader.
@@ -20,15 +20,17 @@ public LPhyStudioImpl() {
     }
 
     @Override
-    public List<Class<? extends GenerativeDistribution>> getDistributions() {
+    public List<Class<? extends GenerativeDistribution>> declareDistributions() {
         return new ArrayList<>();
     }
 
     @Override
-    public List<Class<? extends BasicFunction>> getFunctions() {
+    public List<Class<? extends BasicFunction>> declareFunctions() {
         return new ArrayList<>();
     }
 
+
+
     public String getExtensionName() {
         return "LPhy studio";
     }

lphy-studio/src/main/java/lphystudio/spi/LPhyStudioValueFormatterImpl.java → lphy-studio/src/main/java/lphystudio/spi/LPhyValueFormatterStudioImpl.java

@@ -4,6 +4,7 @@
 import lphy.core.spi.LPhyValueFormatter;
 
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 /**
@@ -12,22 +13,32 @@
  * It requires a public no-args constructor.
  * @author Walter Xie
  */
-public class LPhyStudioValueFormatterImpl implements LPhyValueFormatter {
+public class LPhyValueFormatterStudioImpl implements LPhyValueFormatter {
 //    List<Class<? extends ValueFormatter>> valueFormatters = Arrays.asList(
 //            AlignmentLog.class, TreeLog.class, VariableLog.class, VariableSummaryLog.class);
     /**
      * Required by ServiceLoader.
      */
-    public LPhyStudioValueFormatterImpl() {
+    public LPhyValueFormatterStudioImpl() {
     }
     @Override
-    public Set<Class<? extends ValueFormatter>> getValueFormatters() {
+    public Set<Class<? extends ValueFormatter>> declareValueFormatters() {
         return new HashSet<>();
     }
+
+    @Override
+    public Map<Class<?>, Set<Class<? extends ValueFormatter>>> getValueFormatters() {
+        return null;
+    }
 //    public Map<Class<?>, Set<Class<? extends ValueFormatter>>> getValueFormatterMap() {
 //        return new HashMap<>();
 //    }
 
+    @Override
+    public void register() {
+
+    }
+
     public String getExtensionName() {
         return "LPhy studio loggers";
     }