Commit d357d2b2 authored by piotr.gawron's avatar piotr.gawron
Browse files

cell designer structures moved to celldesigner module, in progress

parent c406fa56
......@@ -32,13 +32,13 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
/**
* This class is responsible for connection to Vencata annotation service. The
......
......@@ -20,13 +20,13 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Chemical;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import uk.ac.ebi.chebi.webapps.chebiWS.client.ChebiWebServiceClient;
import uk.ac.ebi.chebi.webapps.chebiWS.model.ChebiWebServiceFault_Exception;
......
......@@ -7,6 +7,8 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Chemical;
import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
......@@ -14,8 +16,6 @@ import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.model.map.species.Species;
/**
* Interface that allows to annotate {@link AnnotatedObject elements} in the
......
......@@ -20,6 +20,10 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
......@@ -28,10 +32,6 @@ import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
......
......@@ -23,6 +23,7 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
......@@ -32,7 +33,6 @@ import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
......
......@@ -21,17 +21,17 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
import lcsb.mapviewer.converter.model.celldesigner.structure.Phenotype;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
import lcsb.mapviewer.model.map.species.ComplexSpecies;
import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
......
......@@ -15,6 +15,10 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
......@@ -24,10 +28,6 @@ import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
......
......@@ -17,16 +17,16 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Chemical;
import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
......
......@@ -17,15 +17,15 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
......
......@@ -13,10 +13,10 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class ImproperAnnotationsTest {
......
......@@ -7,8 +7,8 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class MissingAnnotationTest {
......
......@@ -11,9 +11,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class MissingRequiredAnnotationsTest {
......
......@@ -29,6 +29,8 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
......@@ -42,8 +44,6 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.persist.dao.map.ModelDao;
public class ModelAnnotatorTest extends AnnotationTestFunctions {
......
......@@ -25,13 +25,13 @@ import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.data.Chebi;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Chemical;
import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
import uk.ac.ebi.chebi.webapps.chebiWS.client.ChebiWebServiceClient;
import uk.ac.ebi.chebi.webapps.chebiWS.model.ChebiWebServiceFault_Exception;
import uk.ac.ebi.chebi.webapps.chebiWS.model.DataItem;
......
......@@ -11,12 +11,12 @@ import org.junit.Test;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.IonAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
public class ElementAnnotatorTest extends AnnotationTestFunctions {
......
......@@ -24,12 +24,12 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
......
......@@ -28,11 +28,11 @@ import lcsb.mapviewer.annotation.data.EntrezData;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class EntrezAnnotatorTest extends AnnotationTestFunctions {
......
......@@ -25,10 +25,10 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.data.Go;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
public class GoAnnotatorTest extends AnnotationTestFunctions {
......
......@@ -16,11 +16,11 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class HgncAnnotatorTest extends AnnotationTestFunctions {
......
......@@ -21,10 +21,10 @@ import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
public class ReconAnnotatorTest extends AnnotationTestFunctions {
Logger logger = Logger.getLogger(ReconAnnotatorTest.class);
......
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