simplified Modularization

app/ix/core/controllers/CoreSubstanceFactory.java

@@ -0,0 +1,127 @@
+package ix.core.controllers;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+
+import ix.core.util.CachedSupplier;
+import ix.ginas.models.v1.Substance;
+import ix.ginas.models.v1.SubstanceReference;
+import ix.utils.UUIDUtil;
+import ix.utils.Util;
+
+import play.Logger;
+import play.db.ebean.Model;
+
+public class CoreSubstanceFactory extends EntityFactory {
+	private static final String CODE_TYPE_PRIMARY = "PRIMARY";
+	static public CachedSupplier<Model.Finder<UUID, Substance>> finder = Util.finderFor(UUID.class, Substance.class);
+
+	/**
+	 * Get a Substance by it's UUID
+	 * @param uuid
+	 * @return
+	 */
+	public static Substance getSubstance(String uuid) {
+		if (uuid == null ||!UUIDUtil.isUUID(uuid)) {
+			return null;
+	}
+		return getSubstance(UUID.fromString(uuid));
+	}
+	public static Substance getSubstance(UUID uuid) {
+		return getEntity(uuid, finder.get());
+	}
+
+	public static Substance getFullSubstance(SubstanceReference subRef) {
+		try {
+			if (subRef == null)
+				return null;
+			return getSubstanceByApprovalIDOrUUID(subRef.approvalID, subRef.refuuid);
+		}catch(Exception e){
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	public static List<Substance> getSubstanceWithAlternativeDefinition(Substance altSub) {
+		List<Substance> sublist = new ArrayList<Substance>();
+		sublist = finder.get().where()
+				.and(com.avaje.ebean.Expr.eq("relationships.relatedSubstance.refuuid",
+						altSub.getOrGenerateUUID().toString()),
+				com.avaje.ebean.Expr.eq("relationships.type", Substance.ALTERNATE_SUBSTANCE_REL)).findList();
+
+		List<Substance> realList = new ArrayList<Substance>();
+		for (Substance sub : sublist) {
+			for (SubstanceReference sref : sub.getAlternativeDefinitionReferences()) {
+				if (sref.refuuid.equals(altSub.getUuid().toString())) {
+					realList.add(sub);
+					break;
+				}
+			}
+		}
+		return realList;
+	}
+
+	/**
+	 * Returns the substance corresponding to the supplied uuid or approvalID.
+	 * 
+	 * If either is null, it will not be used in resolving. This method returns
+	 * first based on the UUID, and falls back to the approvalID if nothing is
+	 * found.
+	 * 
+	 * @param approvalID
+	 * @param uuid
+	 * @return
+	 */
+	private static Substance getSubstanceByApprovalIDOrUUID(String approvalID, String uuid) {
+		try {
+			if (approvalID == null && uuid == null)
+				return null;
+			Substance s = null;
+
+			if(uuid != null){
+				try{
+					s=getSubstance(uuid);
+				}catch(Exception e){
+					e.printStackTrace();
+				}
+			}
+
+			if (s == null && approvalID != null) {
+				s = getSubstanceByApprovalID(approvalID);
+			}
+			return s;
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+		return null;
+		// return finder.where().eq("approvalID", approvalID).findUnique();
+	}
+	public static Substance getSubstanceByApprovalID(String approvalID) {
+		List<Substance> list = finder.get().where().ieq("approvalID", approvalID).findList();
+		if (list != null && list.size() > 0) {
+			return list.get(0);
+		}
+		return null;
+	}
+
+	public static List<Substance> getSubstances(int top, int skip, String filter) {
+		List<Substance> substances = filter(new FetchOptions(top, skip, filter), finder.get());
+		return substances;
+	}
+
+	// TODO: Doesn't support top/skip
+	public static List<Substance> getSubstancesWithExactName(int top, int skip, String name) {
+		return finder.get().where().eq("names.name", name).findList();
+	}
+
+	// TODO: Doesn't support top/skip
+	public static List<Substance> getSubstancesWithExactCode(int top, int skip, String code, String codeSystem) {
+		return finder.get().where(Util.andAll(
+				 com.avaje.ebean.Expr.eq("codes.code", code),
+				 com.avaje.ebean.Expr.eq("codes.codeSystem", codeSystem),
+				 com.avaje.ebean.Expr.eq("codes.type", CODE_TYPE_PRIMARY)
+				))
+				.findList();
+	}
+}

app/ix/core/exporters/AbstractSpreadsheetFormat.java

@@ -0,0 +1,30 @@
+package ix.core.exporters;
+
+import java.io.OutputStream;
+import java.util.Objects;
+import java.util.function.Function;
+
+public abstract class AbstractSpreadsheetFormat extends OutputFormat {
+
+    public AbstractSpreadsheetFormat(String extension, String displayname) {
+        super(extension, displayname);
+    }
+
+    abstract Spreadsheet createSpeadsheet(OutputStream out);
+
+    public AbstractSpreadsheetFormat withInfo(Function<StringBuilder, String> extension, Function<StringBuilder, String> displayName){
+        Objects.requireNonNull(extension);
+        Objects.requireNonNull(displayName);
+
+        return newSubclass(this, extension.apply(new StringBuilder(this.getExtension())), displayName.apply(new StringBuilder(this.getDisplayName())));
+    }
+
+    private AbstractSpreadsheetFormat newSubclass(AbstractSpreadsheetFormat parentClass, String ext, String display){
+        return new AbstractSpreadsheetFormat(ext, display) {
+            @Override
+            Spreadsheet createSpeadsheet(OutputStream out) {
+                return parentClass.createSpeadsheet(out);
+            }
+        };
+    }
+}

modules/ginas/app/ix/ginas/exporters/BasicColumnValueRecipe.java → app/ix/core/exporters/BasicColumnValueRecipe.java

@@ -1,4 +1,4 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
 import java.util.Objects;
 

modules/ginas/app/ix/ginas/exporters/Column.java → app/ix/core/exporters/Column.java

@@ -1,4 +1,4 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
 /**
  * Created by katzelda on 8/19/16.

modules/ginas/app/ix/ginas/exporters/ColumnValueRecipe.java → app/ix/core/exporters/ColumnValueRecipe.java

@@ -1,4 +1,4 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
 /**
  * Created by katzelda on 8/19/16.

modules/ginas/app/ix/ginas/exporters/Exporter.java → app/ix/core/exporters/Exporter.java

@@ -1,4 +1,4 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
 import java.io.Closeable;
 import java.io.IOException;

modules/ginas/app/ix/ginas/exporters/GroupColumnValueRecipe.java → app/ix/core/exporters/GroupColumnValueRecipe.java

@@ -1,4 +1,4 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
 import java.util.*;
 

modules/ginas/app/ix/ginas/exporters/SingleColumnValueRecipe.java → app/ix/core/exporters/SingleColumnValueRecipe.java

@@ -1,4 +1,4 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
 import java.util.function.BiFunction;
 

modules/ginas/app/ix/ginas/exporters/Spreadsheet.java → app/ix/core/exporters/Spreadsheet.java

@@ -1,4 +1,4 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
 import java.io.Closeable;
 

modules/ginas/app/ix/ginas/exporters/SpreadsheetCell.java → app/ix/core/exporters/SpreadsheetCell.java

@@ -1,4 +1,4 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
 import java.util.Date;
 

modules/ginas/app/ix/ginas/exporters/SubstanceExporterFactory.java → app/ix/core/exporters/SubstanceExporterFactory.java

@@ -1,6 +1,5 @@
-package ix.ginas.exporters;
+package ix.core.exporters;
 
-import ix.core.exporters.OutputFormat;
 import ix.ginas.models.v1.Substance;
 
 import java.io.IOException;

modules/ginas/app/ix/ginas/initializers/LoadValidatorInitializer.java → app/ix/core/initializers/LoadValidatorInitializer.java

@@ -1,13 +1,12 @@
-package ix.ginas.initializers;
+package ix.core.initializers;
 
 import com.fasterxml.jackson.annotation.JsonValue;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.type.TypeFactory;
-import ix.core.initializers.Initializer;
 import ix.core.util.IOUtil;
+import ix.core.validator.ValidatorFactory;
+import ix.core.validator.ValidatorPlugin;
 import ix.ginas.models.v1.Substance;
-import ix.ginas.utils.validation.ValidatorFactory;
-import ix.ginas.utils.validation.ValidatorPlugin;
 import play.Application;
 
 import java.util.Collections;

modules/ginas/app/ix/ginas/initializers/ScheduledTaskInitializer.java → app/ix/core/initializers/ScheduledTaskInitializer.java

@@ -1,4 +1,4 @@
-package ix.ginas.initializers;
+package ix.core.initializers;
 
 import java.io.BufferedOutputStream;
 import java.io.File;

modules/ginas/app/ix/ginas/utils/AbstractNoDependencyIDGenerator.java → app/ix/core/utils/AbstractNoDependencyIDGenerator.java

@@ -1,4 +1,4 @@
-package ix.ginas.utils;
+package ix.core.utils;
 
 /**
  * An ID Generator that can generate a new ID without relying on any

modules/ginas/app/ix/ginas/utils/IdGeneratorForType.java → app/ix/core/utils/IdGeneratorForType.java

@@ -1,4 +1,4 @@
-package ix.ginas.utils;
+package ix.core.utils;
 
 /**
  * An ID Generator which may use properties of a given type

modules/ginas/app/ix/ginas/utils/NamedIdGenerator.java → app/ix/core/utils/NamedIdGenerator.java

@@ -1,4 +1,4 @@
-package ix.ginas.utils;
+package ix.core.utils;
 
 public interface NamedIdGenerator<T, K> extends IdGeneratorForType<T,K> {
     /**

modules/ginas/app/ix/ginas/utils/RandomAlphaNumericIDGenerator.java → app/ix/core/utils/RandomAlphaNumericIDGenerator.java

@@ -1,4 +1,4 @@
-package ix.ginas.utils;
+package ix.core.utils;
 
 import java.util.HashSet;
 import java.util.Objects;

modules/ginas/app/ix/ginas/utils/SequentialNumericIDGenerator.java → app/ix/core/utils/SequentialNumericIDGenerator.java

@@ -1,6 +1,4 @@
-package ix.ginas.utils;
-
-
+package ix.core.utils;
 
 public abstract class SequentialNumericIDGenerator<T> extends AbstractNoDependencyIDGenerator<T, String> implements NamedIdGenerator<T, String> {
 

modules/ginas/app/ix/ginas/utils/validation/ValidatorFactory.java → app/ix/core/validator/ValidatorFactory.java

@@ -1,8 +1,7 @@
-package ix.ginas.utils.validation;
+package ix.core.validator;
 
-import ix.core.validator.Validator;
 import ix.core.util.CachedSupplier;
-import ix.ginas.initializers.LoadValidatorInitializer;
+import ix.core.initializers.LoadValidatorInitializer;
 
 import java.util.LinkedHashMap;
 import java.util.List;

modules/ginas/app/ix/ginas/utils/validation/ValidatorPlugin.java → app/ix/core/validator/ValidatorPlugin.java

@@ -1,7 +1,6 @@
-package ix.ginas.utils.validation;
+package ix.core.validator;
 
-import ix.core.validator.Validator;
-import ix.ginas.initializers.LoadValidatorInitializer;
+import ix.core.initializers.LoadValidatorInitializer;
 
 /**
  * Created by katzelda on 5/7/18.

modules/ginas/app/ix/ginas/controllers/GinasApp.java

@@ -25,7 +25,10 @@
 import gov.nih.ncats.molwitch.Chemical;
 import gov.nih.ncats.molwitch.io.ChemFormat;
 import ix.core.controllers.v1.GsrsApiUtil;
+import ix.core.exporters.Exporter;
 import ix.core.exporters.OutputFormat;
+import ix.core.exporters.SubstanceExporterFactory;
+import ix.core.exporters.SubstanceExporterFactory.Parameters;
 import ix.core.validator.GinasProcessingMessage;
 import ix.core.UserFetcher;
 import ix.core.adapters.EntityPersistAdapter;

modules/ginas/app/ix/ginas/controllers/plugins/GinasSubstanceExporterFactoryPlugin.java

@@ -19,7 +19,7 @@
 
 import ix.core.util.IOUtil;
 import ix.core.exporters.OutputFormat;
-import ix.ginas.exporters.SubstanceExporterFactory;
+import ix.core.exporters.SubstanceExporterFactory;
 import org.apache.poi.util.DefaultTempFileCreationStrategy;
 import org.apache.poi.util.TempFile;
 import org.apache.poi.util.TempFileCreationStrategy;