diff --git a/model/src/main/java/lcsb/mapviewer/model/Project.java b/model/src/main/java/lcsb/mapviewer/model/Project.java index 9ae046103c4493dd572cfcc03c3f82e5a5134ad2..11c7642c20406ecae8fb379adc00b15f5072249c 100644 --- a/model/src/main/java/lcsb/mapviewer/model/Project.java +++ b/model/src/main/java/lcsb/mapviewer/model/Project.java @@ -19,7 +19,6 @@ import javax.persistence.JoinColumn; import javax.persistence.OneToMany; import javax.persistence.OneToOne; import javax.persistence.OrderBy; -import javax.persistence.Table; import org.apache.log4j.Appender; import org.apache.log4j.Logger; @@ -48,7 +47,6 @@ import lcsb.mapviewer.model.map.model.ModelData; * */ @Entity -@Table(name = "project_table") public class Project implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java b/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java index 34d4910b899a7ccaf7b2e5b0abf8ab12ccaa8faf..51a320daf6f7314aac9fb502ee4ee0ddf165fe8a 100644 --- a/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java +++ b/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java @@ -16,7 +16,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "cache_type") public class CacheType implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java b/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java index 9a02e7dec1bad802de064c0725514732b93274c7..4e6e86518e93d675398244126b9e8c028286c26a 100644 --- a/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java +++ b/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java @@ -24,7 +24,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "file_entry") @Inheritance(strategy = InheritanceType.SINGLE_TABLE) @DiscriminatorColumn(name = "file_type_db", discriminatorType = DiscriminatorType.STRING) public abstract class FileEntry implements Serializable { diff --git a/model/src/main/java/lcsb/mapviewer/model/map/Comment.java b/model/src/main/java/lcsb/mapviewer/model/map/Comment.java index 6b057ef82ab3d943a1fad966257c849f53196ae4..19e25b0b6b57a22aca93f3ac17be39e283b4002f 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/Comment.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/Comment.java @@ -10,7 +10,6 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.ManyToOne; -import javax.persistence.Table; import org.hibernate.annotations.Type; @@ -25,7 +24,6 @@ import lcsb.mapviewer.model.user.User; * */ @Entity -@Table(name = "feedback") public class Comment implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java index 920ae38639a838e3524879da75f38d76992ae987..0438dc2fe50eba4dc598cceb7fed93aee41f0e71 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java @@ -8,7 +8,6 @@ import javax.persistence.Enumerated; import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; -import javax.persistence.Table; import javax.xml.bind.annotation.XmlRootElement; import org.apache.log4j.Logger; @@ -23,7 +22,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException; * */ @Entity -@Table(name = "miriam_data_table") @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment") @XmlRootElement public class MiriamData implements Comparable<MiriamData>, Serializable { diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java index fee5414deba29d0225cfeecdca6cb8a62514e65f..72e0ee423dbd8d04fa610bc67442629fc36e7e79 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java @@ -12,7 +12,6 @@ import javax.persistence.Id; import javax.persistence.ManyToOne; import javax.persistence.OneToMany; import javax.persistence.OrderBy; -import javax.persistence.Table; import org.hibernate.annotations.Cascade; import org.hibernate.annotations.CascadeType; @@ -31,7 +30,6 @@ import lcsb.mapviewer.model.map.model.ModelData; * */ @Entity -@Table(name = "overview_image_table") public class OverviewImage implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java index 055badb567897543dff728614b0f6a1d296a0d70..150de91e50a556e20ff108156381ba7d0a79cc77 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java @@ -16,7 +16,6 @@ import javax.persistence.Id; import javax.persistence.Inheritance; import javax.persistence.InheritanceType; import javax.persistence.ManyToOne; -import javax.persistence.Table; /** * Abstract class representing link that connects {@link OverviewImage parent @@ -34,7 +33,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "overview_link_table") @Inheritance(strategy = InheritanceType.SINGLE_TABLE) @DiscriminatorColumn(name = "link_type", discriminatorType = DiscriminatorType.STRING) @DiscriminatorValue("GENERIC_VIEW") diff --git a/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java b/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java index 2da6290762fa5d0c4e5a4f6b08f8a5dfac9acc18..d50ff698b3cb706c3d034c6ea261a5b839b9097a 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java @@ -7,7 +7,6 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.ManyToOne; -import javax.persistence.Table; import org.apache.log4j.Logger; @@ -23,7 +22,6 @@ import lcsb.mapviewer.model.map.species.Element; * */ @Entity -@Table(name = "search_index_table") public class SearchIndex implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java index e2ba0bf1a17760808838f5fe0f64fba90f66d6b1..1a078a021b42bcea4417d4261d6c96b9eca5cad8 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java @@ -15,7 +15,6 @@ import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.ManyToOne; import javax.persistence.OrderColumn; -import javax.persistence.Table; import javax.xml.bind.annotation.XmlRootElement; import org.apache.log4j.Logger; @@ -29,7 +28,6 @@ import lcsb.mapviewer.model.map.model.ModelData; * */ @Entity -@Table(name = "sbml_function") @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment") @XmlRootElement public class SbmlFunction implements Serializable, SbmlArgument { diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java index 1ea1d20a6f15bd5def74cdc73432f845e9b45fec..90340d4fba701fe3f78da9ea0dcaba3f7c04a641 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java @@ -16,7 +16,6 @@ import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.JoinTable; import javax.persistence.ManyToMany; -import javax.persistence.Table; import javax.xml.bind.annotation.XmlRootElement; import org.apache.log4j.Logger; @@ -32,7 +31,6 @@ import lcsb.mapviewer.model.map.species.Element; * */ @Entity -@Table(name = "sbml_kinetics") @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment") @XmlRootElement public class SbmlKinetics implements Serializable { diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java index 038ef26ac8a73cc4212990488478fe46b028312d..4114af3054c34d5539d5d90b7fee35cd48383f1b 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java @@ -7,7 +7,6 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.ManyToOne; -import javax.persistence.Table; import javax.xml.bind.annotation.XmlRootElement; import org.apache.log4j.Logger; @@ -19,7 +18,6 @@ import org.apache.log4j.Logger; * */ @Entity -@Table(name = "sbml_parameter") @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment") @XmlRootElement public class SbmlParameter implements Serializable, SbmlArgument { diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java index ad9be0855a013087b6d53f371a40f0f71fdef2af..93c5ab53eb1575f6bc6bb93ae3248c89138bcf0b 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java @@ -11,7 +11,6 @@ import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.ManyToOne; import javax.persistence.OneToMany; -import javax.persistence.Table; import javax.xml.bind.annotation.XmlRootElement; import org.apache.log4j.Logger; @@ -27,7 +26,6 @@ import lcsb.mapviewer.model.map.model.ModelData; * */ @Entity -@Table(name = "sbml_unit") @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment") @XmlRootElement public class SbmlUnit implements Serializable { diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java index 6b3f6783d2ee7a40a026d0c3c0b06ad0ad720a06..64e876549ce72db3cde7ad9d7ce938aeda524928 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java @@ -10,7 +10,6 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.ManyToOne; -import javax.persistence.Table; import javax.xml.bind.annotation.XmlRootElement; import org.apache.log4j.Logger; @@ -27,7 +26,6 @@ import org.apache.log4j.Logger; * */ @Entity -@Table(name = "sbml_unit_factor") @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment") @XmlRootElement public class SbmlUnitTypeFactor implements Serializable { diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java index e3540fa4db3f5eda3e25c3129f67c1f529310a08..ea3a0fbeae5dbaf603f82875e407afe64570983e 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java @@ -14,7 +14,6 @@ import javax.persistence.Id; import javax.persistence.OneToMany; import javax.persistence.OneToOne; import javax.persistence.OrderBy; -import javax.persistence.Table; import org.hibernate.annotations.Cascade; import org.hibernate.annotations.CascadeType; @@ -30,7 +29,6 @@ import lcsb.mapviewer.model.map.MiriamData; * */ @Entity -@Table(name = "reference_genome") public class ReferenceGenome implements Serializable { /** * diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java index 158b26a66e7810494c7edaa9d2ef4cb8dff8113c..c69adf638d3ef2e44f830092e5c2622fa3bbdd1c 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java @@ -8,7 +8,6 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.ManyToOne; -import javax.persistence.Table; /** * This object defines information about mapping genes to gene. This data is @@ -21,7 +20,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "reference_genome_gene_mapping") public class ReferenceGenomeGeneMapping implements Serializable { /** * diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java index a3bf929397c0d4544645dd7f9171722b7434bcd5..d3ca569b69050d4deee73b9e76e1e0a055f552a4 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java @@ -15,7 +15,6 @@ import javax.persistence.JoinTable; import javax.persistence.ManyToOne; import javax.persistence.OneToMany; import javax.persistence.OrderColumn; -import javax.persistence.Table; import org.apache.log4j.Logger; import org.hibernate.annotations.Cascade; @@ -33,7 +32,6 @@ import lcsb.mapviewer.model.map.model.ModelData; * */ @Entity -@Table(name = "layer_table") public class Layer implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java index 64a8d09c13549e99f6bb8099827b8a6c1c4536e1..cfccd82386b6d5eb683fafd16d7a14eb707b1e52 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java @@ -20,7 +20,6 @@ import javax.persistence.ManyToMany; import javax.persistence.ManyToOne; import javax.persistence.OneToMany; import javax.persistence.OrderBy; -import javax.persistence.Table; import javax.persistence.Transient; import javax.xml.bind.annotation.XmlTransient; @@ -56,7 +55,6 @@ import lcsb.mapviewer.model.map.species.Element; * */ @Entity -@Table(name = "model_table") public class ModelData implements Serializable { /** @@ -117,7 +115,7 @@ public class ModelData implements Serializable { @Cascade({ CascadeType.ALL }) @ManyToMany(fetch = FetchType.EAGER) - @JoinTable(name = "model_parameters", joinColumns = { + @JoinTable(name = "model_parameters_table", joinColumns = { @JoinColumn(name = "model_id", referencedColumnName = "id", nullable = false, updatable = false) }, inverseJoinColumns = { @JoinColumn(name = "parameter_id", referencedColumnName = "id", nullable = true, updatable = true) }) private Set<SbmlParameter> parameters = new HashSet<>(); diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java index d3fbc2027ff027de8c95169fd4c399baca2115ce..406aa59362f98cd6b9a3fc97ec4e90b2daffec11 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java @@ -27,7 +27,6 @@ import org.apache.log4j.Logger; * */ @Entity -@Table(name = "submodel_connection_table") @Inheritance(strategy = InheritanceType.SINGLE_TABLE) @DiscriminatorColumn(name = "submodel_connections_type_db", discriminatorType = DiscriminatorType.STRING) @DiscriminatorValue("SUBMODEL_CONNECTION") diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java index 4b19c5a06cd182b830fdb28ef00566c8c36d2210..ffd6962b23b1924a0b1a745604304731ae29434c 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java @@ -38,10 +38,10 @@ import lcsb.mapviewer.model.graphics.PolylineData; * */ @Entity -@Table(name = "node_table") @Inheritance(strategy = InheritanceType.SINGLE_TABLE) @DiscriminatorColumn(name = "node_type_db", discriminatorType = DiscriminatorType.STRING) @DiscriminatorValue("GENERIC_NODE") +@Table(name = "reaction_node_table") public abstract class AbstractNode implements Serializable { /** * diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java index 3eccdb2b155c3c1889ee105f2a405e15a032fbe4..3820a84ddcbceff5390c13e4fbd63266aea202c1 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java @@ -30,7 +30,6 @@ import javax.persistence.OneToMany; import javax.persistence.OneToOne; import javax.persistence.OrderBy; import javax.persistence.OrderColumn; -import javax.persistence.Table; import javax.xml.bind.annotation.XmlTransient; import org.apache.log4j.Logger; @@ -73,7 +72,6 @@ import lcsb.mapviewer.model.map.species.Element; * */ @Entity -@Table(name = "reaction_table") @Inheritance(strategy = InheritanceType.SINGLE_TABLE) @DiscriminatorColumn(name = "reaction_type_db", discriminatorType = DiscriminatorType.STRING) @DiscriminatorValue("GENERIC_REACTION") diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java index 81623b6a082880eea3f8a624f7f5ec4921f50348..ab8c1b997cd4661068732b00f555684bf545fb74 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java @@ -30,7 +30,6 @@ import javax.persistence.ManyToMany; import javax.persistence.ManyToOne; import javax.persistence.OneToMany; import javax.persistence.OrderColumn; -import javax.persistence.Table; import javax.xml.bind.annotation.XmlTransient; import org.apache.log4j.Logger; @@ -57,7 +56,6 @@ import lcsb.mapviewer.model.map.model.ModelData; * */ @Entity -@Table(name = "element_table") @Inheritance(strategy = InheritanceType.SINGLE_TABLE) @DiscriminatorColumn(name = "element_type_db", discriminatorType = DiscriminatorType.STRING) @DiscriminatorValue("GENERIC") diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java index ed4820c79257070944cbede32a10258f669eedc3..6696a13000f88ddae64514fb45ea4847cd82332e 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java @@ -16,7 +16,6 @@ import javax.persistence.Inheritance; import javax.persistence.InheritanceType; import javax.persistence.JoinColumn; import javax.persistence.ManyToOne; -import javax.persistence.Table; import org.apache.log4j.Logger; import org.hibernate.annotations.Type; @@ -32,7 +31,6 @@ import lcsb.mapviewer.model.map.species.Species; */ @Entity -@Table(name = "modification_residue_table") @Inheritance(strategy = InheritanceType.SINGLE_TABLE) @DiscriminatorColumn(name = "modification_type", discriminatorType = DiscriminatorType.STRING) @DiscriminatorValue("GENERIC_MODIFICATION_RESIDUE") diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java index 4dc712a3b875c69d506eb994aadeaa13da45ecea..6eaa87c618234f5e06b53a7f874c070239fc34d7 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Structure.java @@ -11,7 +11,6 @@ import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.ManyToOne; -import javax.persistence.Table; import lcsb.mapviewer.common.exception.NotImplementedException; @@ -32,9 +31,6 @@ import lcsb.mapviewer.common.exception.NotImplementedException; * */ @Entity -@Table(name = "structure_table") -// @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", -// strategy = "increment") public class Structure implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java index f595b130089139fb54b125b6df4d602afc512d6a..b735554f7a3b61e67d9b7a37e280263a2115b1ac 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/UniprotRecord.java @@ -14,7 +14,6 @@ import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.ManyToOne; import javax.persistence.OneToMany; -import javax.persistence.Table; import org.hibernate.annotations.Cascade; import org.hibernate.annotations.CascadeType; @@ -31,9 +30,6 @@ import lcsb.mapviewer.model.map.species.Species; */ @Entity -@Table(name = "uniprot_table") -// @org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", -// strategy = "increment") public class UniprotRecord implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchHistory.java b/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchHistory.java index 6fe5be58b183679bb4f0f5d55a111a303a48ae01..4769fddc83c1e47164da8a7c9eeb7f21e40372ff 100644 --- a/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchHistory.java +++ b/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchHistory.java @@ -10,7 +10,6 @@ import javax.persistence.Enumerated; import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; -import javax.persistence.Table; /** * This object describe single search event entry. It's used for gathering some @@ -20,7 +19,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "history_table") public class SearchHistory implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java index 11d48d1df1b7c7ea3520560e1cc107eafee8be17..9a7500d06159759171d529f6f75a03bfce497513 100644 --- a/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java +++ b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java @@ -13,7 +13,6 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.JoinColumn; -import javax.persistence.Table; import lcsb.mapviewer.common.comparator.IntegerComparator; @@ -24,7 +23,6 @@ import lcsb.mapviewer.common.comparator.IntegerComparator; * */ @Entity -@Table(name = "plugin_table") public class Plugin implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java b/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java index 87ce8fdf032de28279ba1f1b194961279d47fa48..27c0e6b03b067e9bd219ae0f1f5b47816cccddb0 100644 --- a/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java +++ b/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java @@ -9,7 +9,6 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.ManyToOne; -import javax.persistence.Table; import lcsb.mapviewer.model.user.User; @@ -20,7 +19,6 @@ import lcsb.mapviewer.model.user.User; * */ @Entity -@Table(name = "plugin_data_entry") public class PluginDataEntry implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java index 859747533a20f19f4b3fa5610cc17de3c2b4168a..2c5c863b00e7dedb2f72cd819c13289b49e97b6d 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java @@ -8,7 +8,6 @@ import javax.persistence.Enumerated; import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; -import javax.persistence.Table; /** * This class represents one configurable parameter of the system. @@ -17,7 +16,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "configuration_table") public class ConfigurationOption implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ObjectPrivilege.java b/model/src/main/java/lcsb/mapviewer/model/user/ObjectPrivilege.java index 085b035727befa7a8f1480f1abe0c49f33071602..7501a98380ac2a2fe012db814e43146401e537e8 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/ObjectPrivilege.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/ObjectPrivilege.java @@ -9,7 +9,7 @@ import lcsb.mapviewer.common.ObjectUtils; import lcsb.mapviewer.common.comparator.IntegerComparator; /** - * This class extends {@link BasicPrivilege} class which define typical user + * This class extends {@link Privilege} class which define typical user * privilege. The extension introduces specific object in the model to which * privilege is given. * @@ -18,7 +18,7 @@ import lcsb.mapviewer.common.comparator.IntegerComparator; */ @Entity @DiscriminatorValue("OBJECT_PRIVILEGE") -public class ObjectPrivilege extends BasicPrivilege implements Serializable { +public class ObjectPrivilege extends Privilege implements Serializable { /** * @@ -57,7 +57,7 @@ public class ObjectPrivilege extends BasicPrivilege implements Serializable { } @Override - public boolean equalsPrivilege(BasicPrivilege privilege) { + public boolean equalsPrivilege(Privilege privilege) { if (privilege == null) { return false; } diff --git a/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java b/model/src/main/java/lcsb/mapviewer/model/user/Privilege.java similarity index 88% rename from model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java rename to model/src/main/java/lcsb/mapviewer/model/user/Privilege.java index 8d7e39c7759e0defec1db56c67556fbaa71c3e84..1aca90abddbda8d02b6a58830bad4ef78173ca88 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/Privilege.java @@ -16,7 +16,6 @@ import javax.persistence.Id; import javax.persistence.Inheritance; import javax.persistence.InheritanceType; import javax.persistence.ManyToOne; -import javax.persistence.Table; import lcsb.mapviewer.common.comparator.IntegerComparator; @@ -28,21 +27,20 @@ import lcsb.mapviewer.common.comparator.IntegerComparator; * */ @Entity -@Table(name = "privilege_table") @Inheritance(strategy = InheritanceType.SINGLE_TABLE) @DiscriminatorColumn(name = "privilege_class_type_db", discriminatorType = DiscriminatorType.STRING) @DiscriminatorValue("BASIC_PRIVILEGE") -public class BasicPrivilege implements Serializable { +public class Privilege implements Serializable { /** * */ private static final long serialVersionUID = 1L; - public static final Comparator<? super BasicPrivilege> ID_COMPARATOR = new Comparator<BasicPrivilege>() { + public static final Comparator<? super Privilege> ID_COMPARATOR = new Comparator<Privilege>() { @Override - public int compare(BasicPrivilege o1, BasicPrivilege o2) { + public int compare(Privilege o1, Privilege o2) { return new IntegerComparator().compare(o1.getId(), o2.getId()); } }; @@ -83,7 +81,7 @@ public class BasicPrivilege implements Serializable { * @param user * user for which this privilege is set */ - public BasicPrivilege(int level, PrivilegeType type, User user) { + public Privilege(int level, PrivilegeType type, User user) { this.level = level; this.type = type; this.user = user; @@ -92,7 +90,7 @@ public class BasicPrivilege implements Serializable { /** * Default constructor. */ - public BasicPrivilege() { + public Privilege() { } /** @@ -104,7 +102,7 @@ public class BasicPrivilege implements Serializable { * @return <code>true</code> if privilege is of the same type as an argument, * <code>false</code> otherwise */ - public boolean equalsPrivilege(BasicPrivilege privilege) { + public boolean equalsPrivilege(Privilege privilege) { if (privilege == null) { return false; } diff --git a/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java b/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java index b53d20049dab0cafc4c111aeaee33164b233fb98..aba1b94652f7e4ff4dea856a5dfb72c4a734b2de 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java @@ -19,7 +19,7 @@ public enum PrivilegeType { /** * User can add project. */ - ADD_MAP(BasicPrivilege.class, null, "Add project"), + ADD_MAP(Privilege.class, null, "Add project"), /** * User can edit comments in the project. @@ -29,17 +29,17 @@ public enum PrivilegeType { /** * User can manage projects. */ - PROJECT_MANAGEMENT(BasicPrivilege.class, null, "Map management"), + PROJECT_MANAGEMENT(Privilege.class, null, "Map management"), /** * User can manage users. */ - USER_MANAGEMENT(BasicPrivilege.class, null, "User management"), + USER_MANAGEMENT(Privilege.class, null, "User management"), /** * User can have custom layouts (access level defines how many). */ - CUSTOM_LAYOUTS(BasicPrivilege.class, null, "Custom overlays", true), + CUSTOM_LAYOUTS(Privilege.class, null, "Custom overlays", true), /** * User can view non-public layout. @@ -49,7 +49,7 @@ public enum PrivilegeType { /** * User can manage configuration. */ - CONFIGURATION_MANAGE(BasicPrivilege.class, null, "Manage configuration"), + CONFIGURATION_MANAGE(Privilege.class, null, "Manage configuration"), /** * User can manage layouts of all users in the project. @@ -59,17 +59,17 @@ public enum PrivilegeType { /** * User can manage reference genomes. */ - MANAGE_GENOMES(BasicPrivilege.class, null, "Manage genomes"), + MANAGE_GENOMES(Privilege.class, null, "Manage genomes"), /** * User can manage preferences */ - MANAGE_PLUGINS(BasicPrivilege.class, null, "Manage plugins"); + MANAGE_PLUGINS(Privilege.class, null, "Manage plugins"); /** * Type of privilege (basic or privilege to the object). */ - private Class<? extends BasicPrivilege> privilegeClassType; + private Class<? extends Privilege> privilegeClassType; /** * Type of the object to which privilege refers. @@ -96,7 +96,7 @@ public enum PrivilegeType { * @param commonName * {@link #commonName} */ - PrivilegeType(Class<? extends BasicPrivilege> privilegeClazz, Class<?> objectClazz, String commonName) { + PrivilegeType(Class<? extends Privilege> privilegeClazz, Class<?> objectClazz, String commonName) { this.privilegeClassType = privilegeClazz; this.privilegeObjectType = objectClazz; this.commonName = commonName; @@ -114,7 +114,7 @@ public enum PrivilegeType { * @param numeric * {@link #numeric} */ - PrivilegeType(Class<? extends BasicPrivilege> privilegeClazz, Class<?> objectClazz, String commonName, + PrivilegeType(Class<? extends Privilege> privilegeClazz, Class<?> objectClazz, String commonName, boolean numeric) { this.privilegeClassType = privilegeClazz; this.privilegeObjectType = objectClazz; @@ -126,7 +126,7 @@ public enum PrivilegeType { * * @return {@link #privilegeClassType} */ - public Class<? extends BasicPrivilege> getPrivilegeClassType() { + public Class<? extends Privilege> getPrivilegeClassType() { return privilegeClassType; } diff --git a/model/src/main/java/lcsb/mapviewer/model/user/User.java b/model/src/main/java/lcsb/mapviewer/model/user/User.java index aab0ff98254c4421045804d68766b4531f1cc4f0..4909435c87cea418119de48fd1c9bfb73213c8fe 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/User.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java @@ -19,7 +19,6 @@ import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.OneToMany; import javax.persistence.OneToOne; -import javax.persistence.Table; import org.hibernate.annotations.Cascade; @@ -32,7 +31,6 @@ import lcsb.mapviewer.common.comparator.StringComparator; * */ @Entity -@Table(name = "user_table") public class User implements Serializable { /** @@ -139,7 +137,7 @@ public class User implements Serializable { * Set of user privileges. */ @OneToMany(fetch = FetchType.EAGER, mappedBy = "user", orphanRemoval = true, cascade = CascadeType.ALL) - private Set<BasicPrivilege> privileges = new HashSet<>(); + private Set<Privilege> privileges = new HashSet<>(); /** * Default annotations schema used by this user. @@ -160,7 +158,7 @@ public class User implements Serializable { * @param privilege * privilege to add */ - public void addPrivilege(BasicPrivilege privilege) { + public void addPrivilege(Privilege privilege) { privileges.add(privilege); } @@ -270,7 +268,7 @@ public class User implements Serializable { * @return the privileges * @see #privileges */ - public Set<BasicPrivilege> getPrivileges() { + public Set<Privilege> getPrivileges() { return privileges; } @@ -279,7 +277,7 @@ public class User implements Serializable { * the privileges to set * @see #privileges */ - public void setPrivileges(Set<BasicPrivilege> privileges) { + public void setPrivileges(Set<Privilege> privileges) { this.privileges = privileges; } diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java index eb4f5b5faef4ee653755d4a7e36d95ba21c12471..3da219851c429049ad3f537c79255c77c9898250 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java @@ -14,7 +14,6 @@ import javax.persistence.Id; import javax.persistence.OneToMany; import javax.persistence.OneToOne; import javax.persistence.OrderBy; -import javax.persistence.Table; import javax.persistence.Transient; import org.apache.log4j.Logger; @@ -33,7 +32,6 @@ import lcsb.mapviewer.model.map.MiriamType; * */ @Entity -@Table(name = "user_annotation_schema_table") public class UserAnnotationSchema implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParam.java b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParam.java index ec367568a293c421b846f607cb5611e22d4c885d..787ba75e919dfcc69df14b13f4bb4111c9153276 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParam.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParam.java @@ -8,7 +8,6 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.ManyToOne; -import javax.persistence.Table; /** * This class defines set of annotators parameters that are used by a user. @@ -17,7 +16,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "annotators_params_table") public class UserAnnotatorsParam implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java b/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java index fae45c19b9441bf6b633b355cd7c692d59891237..958d3df52e6680d7138d0b88ea03093d3a2e7691 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java @@ -15,7 +15,6 @@ import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.ManyToOne; import javax.persistence.OrderColumn; -import javax.persistence.Table; /** * This class defines set of default class annotators for a single class type @@ -25,7 +24,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "class_annotator_table") public class UserClassAnnotators implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java b/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java index 8224dcfaf58d1148713172e56faf0691e08ee335..787e584d14cf99dd4e59d8ae2e0c8b7e3573560a 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java @@ -17,7 +17,6 @@ import javax.persistence.JoinColumn; import javax.persistence.JoinTable; import javax.persistence.ManyToOne; import javax.persistence.OrderColumn; -import javax.persistence.Table; import javax.persistence.Transient; import org.apache.log4j.Logger; @@ -32,7 +31,6 @@ import lcsb.mapviewer.model.map.MiriamType; * */ @Entity -@Table(name = "class_required_annotation_table") public class UserClassRequiredAnnotations implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java b/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java index e9672ccf45829b429c009ece011247ab4d3f4c02..97907dd6aac5c7ddf353bb8a6528a683ff7c1fdf 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java @@ -17,7 +17,6 @@ import javax.persistence.JoinColumn; import javax.persistence.JoinTable; import javax.persistence.ManyToOne; import javax.persistence.OrderColumn; -import javax.persistence.Table; import lcsb.mapviewer.model.map.MiriamType; @@ -28,7 +27,6 @@ import lcsb.mapviewer.model.map.MiriamType; * */ @Entity -@Table(name = "class_valid_annotation_table") public class UserClassValidAnnotations implements Serializable { /** diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserGuiPreference.java b/model/src/main/java/lcsb/mapviewer/model/user/UserGuiPreference.java index 0282d1fedbd9d30e61b0f97a41108a10d97ec593..4b1dffd79d32be883d6bc6d3f0b893f2465e5804 100644 --- a/model/src/main/java/lcsb/mapviewer/model/user/UserGuiPreference.java +++ b/model/src/main/java/lcsb/mapviewer/model/user/UserGuiPreference.java @@ -10,7 +10,6 @@ import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.ManyToOne; -import javax.persistence.Table; /** * This class defines GUI preference for the {@link User}. @@ -19,7 +18,6 @@ import javax.persistence.Table; * */ @Entity -@Table(name = "user_gui_preferences") public class UserGuiPreference implements Serializable { /** diff --git a/model/src/test/java/lcsb/mapviewer/model/user/BasicPrivilegeTest.java b/model/src/test/java/lcsb/mapviewer/model/user/BasicPrivilegeTest.java index 8a226413bb0b55b715c2b7c8eb50dc9c6b09efa9..22522353bda2c6e5f044be106f790c5bbe3cc9de 100644 --- a/model/src/test/java/lcsb/mapviewer/model/user/BasicPrivilegeTest.java +++ b/model/src/test/java/lcsb/mapviewer/model/user/BasicPrivilegeTest.java @@ -21,7 +21,7 @@ public class BasicPrivilegeTest { @Test public void testSerialization() { try { - SerializationUtils.serialize(new BasicPrivilege()); + SerializationUtils.serialize(new Privilege()); } catch (Exception e) { e.printStackTrace(); throw e; @@ -31,7 +31,7 @@ public class BasicPrivilegeTest { @Test public void testGetters() { try { - BasicPrivilege privilege = new BasicPrivilege(); + Privilege privilege = new Privilege(); int id = 25; int level = 26; PrivilegeType type = PrivilegeType.ADD_MAP; @@ -55,7 +55,7 @@ public class BasicPrivilegeTest { @Test public void testEqualsPrivilege() { try { - BasicPrivilege privilege = new BasicPrivilege(); + Privilege privilege = new Privilege(); assertFalse(privilege.equalsPrivilege(null)); } catch (Exception e) { e.printStackTrace(); diff --git a/model/src/test/java/lcsb/mapviewer/model/user/ObjectPrivilegeTest.java b/model/src/test/java/lcsb/mapviewer/model/user/ObjectPrivilegeTest.java index 3820cdc171954f6e797691888d50960f195b8812..ff1bcfde7b8eef0e0d56985f0b5da07f95408a5a 100644 --- a/model/src/test/java/lcsb/mapviewer/model/user/ObjectPrivilegeTest.java +++ b/model/src/test/java/lcsb/mapviewer/model/user/ObjectPrivilegeTest.java @@ -70,7 +70,7 @@ public class ObjectPrivilegeTest { ObjectPrivilege privilege = new ObjectPrivilege(); privilege.setType(PrivilegeType.ADD_MAP); assertFalse(privilege.equalsPrivilege(null)); - assertFalse(privilege.equalsPrivilege(new BasicPrivilege())); + assertFalse(privilege.equalsPrivilege(new Privilege())); privilege.setIdObject(2); ObjectPrivilege privilege2 = new ObjectPrivilege(); diff --git a/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java b/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java index 863536f39f290974ff8bed3205e482be63b1cf4d..532a723eab443d4eb4d5cf34e393a07eee6de6fa 100644 --- a/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java +++ b/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java @@ -46,7 +46,7 @@ public class UserTest { public void testAddPrivilege() { try { User user = new User(); - user.addPrivilege(new BasicPrivilege()); + user.addPrivilege(new Privilege()); assertEquals(1, user.getPrivileges().size()); } catch (Exception e) { e.printStackTrace(); @@ -64,7 +64,7 @@ public class UserTest { String name = "ccr"; String email= "a.a@pl.pl"; String surname = "cccv"; - Set<BasicPrivilege> privileges = new HashSet<>(); + Set<Privilege> privileges = new HashSet<>(); boolean removed = true; UserAnnotationSchema annotationSchema = new UserAnnotationSchema(); Color minColor = Color.BLACK; diff --git a/persist/src/main/java/lcsb/mapviewer/persist/CustomImplicitNamingStrategy.java b/persist/src/main/java/lcsb/mapviewer/persist/CustomImplicitNamingStrategy.java new file mode 100644 index 0000000000000000000000000000000000000000..31bcb2caaae9025de0a08452735b17cc96b155d8 --- /dev/null +++ b/persist/src/main/java/lcsb/mapviewer/persist/CustomImplicitNamingStrategy.java @@ -0,0 +1,30 @@ +package lcsb.mapviewer.persist; + +import org.apache.log4j.Logger; +import org.hibernate.boot.model.naming.Identifier; +import org.hibernate.boot.model.naming.ImplicitEntityNameSource; +import org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy; + +/** + * This naming strategy adds "Table" suffix to table names when there is no + * table name defined. + * + * @author Piotr Gawron + * + */ +public class CustomImplicitNamingStrategy extends SpringImplicitNamingStrategy { + /** + * + */ + private static final long serialVersionUID = 1L; + + Logger logger = Logger.getLogger(CustomImplicitNamingStrategy.class); + + private static final String TABLE_NAME_SUFFIX = "Table"; + + @Override + public Identifier determinePrimaryTableName(ImplicitEntityNameSource source) { + Identifier newIdentifier = super.determinePrimaryTableName(source); + return new Identifier(newIdentifier.getText() + TABLE_NAME_SUFFIX, newIdentifier.isQuoted()); + } +} diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml index dd83728553450d85c0ff5295110ddabf4ba1c8bb..ed36014a24a8b5071a33a4d596cca5f0754d6b9f 100644 --- a/persist/src/main/resources/applicationContext-persist.xml +++ b/persist/src/main/resources/applicationContext-persist.xml @@ -81,9 +81,9 @@ <value>lcsb.mapviewer.model.graphics.PolylineData</value> - <value>lcsb.mapviewer.model.user.BasicPrivilege</value> <value>lcsb.mapviewer.model.user.ConfigurationOption</value> <value>lcsb.mapviewer.model.user.ObjectPrivilege</value> + <value>lcsb.mapviewer.model.user.Privilege</value> <value>lcsb.mapviewer.model.user.User</value> <value>lcsb.mapviewer.model.user.UserAnnotatorsParam</value> <value>lcsb.mapviewer.model.user.UserAnnotationSchema</value> @@ -206,7 +206,7 @@ <bean class="org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy" /> </property> <property name="ImplicitNamingStrategy"> - <bean class="org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy" /> + <bean class="lcsb.mapviewer.persist.CustomImplicitNamingStrategy" /> </property> </bean> diff --git a/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181029.3__arrow_type_data_is_serialized_in_a_string.sql b/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181029.3__arrow_type_data_is_serialized_in_a_string.sql index 6f0991ee3fd3b8724c2ade273ec80b462d196012..6c21f47873ecd909ba153baa069048146e9cad4d 100644 --- a/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181029.3__arrow_type_data_is_serialized_in_a_string.sql +++ b/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181029.3__arrow_type_data_is_serialized_in_a_string.sql @@ -6,3 +6,5 @@ update polyline_data set end_atd = (select concat(angle,';',len,';',arrow_type,' alter table polyline_data drop column begin_atd_id; alter table polyline_data drop column end_atd_id; + +drop table arrow_type_data; \ No newline at end of file diff --git a/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181030.3__normalization_of_table_names.sql b/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181030.3__normalization_of_table_names.sql new file mode 100644 index 0000000000000000000000000000000000000000..7ef03d4c79d92ae0a0fe7021796498e906c5c695 --- /dev/null +++ b/persist/src/main/resources/db/migration/12.2.0~alpha.0/V12.2.0.20181030.3__normalization_of_table_names.sql @@ -0,0 +1,77 @@ +-- rename table names to match implicit class name mapping +alter table model_table rename to model_data_table; +alter table model_parameters rename to model_parameters_table; +alter table sbml_parameter rename to sbml_parameter_table; +alter table sbml_unit rename to sbml_unit_table; +alter table sbml_kinetics rename to sbml_kinetics_table; +alter table sbml_function rename to sbml_function_table; +alter table sbml_unit_factor rename to sbml_unit_type_factor_table; +alter table layout rename to layout_table; +alter table uniprot_table rename to uniprot_record_table; +alter table layer_rect rename to layer_rect_table; +alter table layer_text rename to layer_text_table; +alter table layer_oval rename to layer_oval_table; +alter table polyline_data rename to polyline_data_table; +alter table cache_query rename to cache_query_table; +alter table class_annotator_table rename to user_class_annotators_table; +alter table class_valid_annotation_table rename to user_class_valid_annotations_table; +alter table annotators_params_table rename to user_annotators_param_table; +alter table class_required_annotation_table rename to user_class_required_annotations_table; +alter table user_gui_preferences rename to user_gui_preference_table; +alter table history_table rename to search_history_table; +alter table file_entry rename to file_entry_table; +alter table configuration_table rename to configuration_option_table; +alter table plugin_data_entry rename to plugin_data_entry_table; +alter table node_table rename to reaction_node_table; +alter table cache_type rename to cache_type_table; +alter table feedback rename to comment_table; +alter table reference_genome rename to reference_genome_table; +alter table reference_genome_gene_mapping rename to reference_genome_gene_mapping_table; + +--rename sequences to match table names +alter sequence annotators_params_table_iddb_seq rename to user_annotators_param_sequence; +alter sequence big_file_entry_iddb_seq rename to file_entry_sequence; +alter sequence cachequery_iddb_seq rename to cache_query_sequence; +alter sequence cache_type_iddb_seq rename to cache_type_sequence; +alter sequence class_annotator_iddb_seq rename to user_class_annotators_sequence; +alter sequence class_required_annotation_iddb_seq rename to user_class_required_annotations_sequence; +alter sequence class_valid_annotation_iddb_seq rename to user_class_valid_annotations_sequence; +alter sequence modification_residue_table_iddb_seq rename to modification_residue_sequence; +alter sequence overview_image_iddb_seq rename to overview_image_sequence; +alter sequence overview_link_iddb_seq rename to overview_link_sequence; +alter sequence feedback_iddb_seq rename to comment_sequence; +alter sequence configuration_table_iddb_seq rename to configuration_option_sequence; +alter sequence element_table_iddb_seq rename to element_sequence; +alter sequence layeroval_iddb_seq rename to layer_oval_sequence; +alter sequence layerrect_iddb_seq rename to layer_rect_sequence; +alter sequence layer_table_iddb_seq rename to layer_sequence; +alter sequence layertext_iddb_seq rename to layer_text_sequence; +alter sequence layout_iddb_seq rename to layout_sequence; +alter sequence miriam_data_table_iddb_seq rename to miriam_data_sequence; +alter sequence model_table_iddb_seq rename to model_data_sequence; +alter sequence plugin_table_iddb_seq rename to plugin_sequence; +alter sequence polylinedata_iddb_seq rename to polyline_data_sequence; +alter sequence privilege_table_iddb_seq rename to privilege_sequence; +alter sequence node_table_iddb_seq rename to reaction_node_sequence; +alter sequence reaction_table_iddb_seq rename to reaction_sequence; +alter sequence reference_genome_gene_mapping_iddb_seq rename to reference_genome_gene_mapping_sequence; +alter sequence reference_genome_iddb_seq rename to reference_genome_sequence; +alter sequence sbml_function_iddb_seq rename to sbml_function_sequence; +alter sequence sbml_parameter_iddb_seq rename to sbml_parameter_sequence; +alter sequence sbml_unit_iddb_seq rename to sbml_unit_sequence; +alter sequence sbml_unit_factor_iddb_seq rename to sbml_unit_type_factor_sequence; +alter sequence history_table_iddb_seq rename to search_history_sequence; +alter sequence search_index_table_iddb_seq rename to search_index_sequence; +alter sequence structure_table_iddb_seq rename to structure_sequence; +alter sequence submodel_connection_table_iddb_seq rename to submodel_connection_sequence; +alter sequence uniprot_table_iddb_seq rename to uniprot_record_sequence; +alter sequence user_annotation_schema_iddb_seq rename to user_annotation_schema_sequence; +alter sequence user_gui_preferences_iddb_seq rename to user_gui_preference_sequence; +alter sequence user_table_iddb_seq rename to user_sequence; +alter sequence project_table_id_seq rename to project_sequence; +alter sequence plugin_data_entry_iddb_seq rename to plugin_data_entry_sequence; + + +--drop unused sequences +drop sequence antisense_rna_region_table_iddb_seq; +drop sequence rna_region_table_iddb_seq; diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java index e1c95d96fab921e59326545e0907eb7ae81d7f33..e35c3001917c347644e50d998bd9c764d46ab07d 100644 --- a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java +++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java @@ -19,7 +19,7 @@ import org.springframework.security.crypto.password.PasswordEncoder; import lcsb.mapviewer.model.map.MiriamType; import lcsb.mapviewer.model.map.reaction.Reaction; import lcsb.mapviewer.model.map.species.Species; -import lcsb.mapviewer.model.user.BasicPrivilege; +import lcsb.mapviewer.model.user.Privilege; import lcsb.mapviewer.model.user.PrivilegeType; import lcsb.mapviewer.model.user.User; import lcsb.mapviewer.model.user.UserAnnotationSchema; @@ -65,7 +65,7 @@ public class UserDaoTest extends PersistTestFunctions { user = new User(); user.setLogin(testLogin); - user.addPrivilege(new BasicPrivilege(0, PrivilegeType.ADD_MAP, user)); + user.addPrivilege(new Privilege(0, PrivilegeType.ADD_MAP, user)); userDao.add(user); long counter2 = userDao.getCount(); diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java index 3ee62cd1c649594650180a0c3b38d91637b90cbb..b5b4336657f9237cc06c5fcfd168bf5bd51cca54 100644 --- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java +++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java @@ -20,9 +20,9 @@ import lcsb.mapviewer.common.Configuration; import lcsb.mapviewer.common.exception.InvalidArgumentException; import lcsb.mapviewer.model.Project; import lcsb.mapviewer.model.map.MiriamType; -import lcsb.mapviewer.model.user.BasicPrivilege; import lcsb.mapviewer.model.user.ConfigurationOption; import lcsb.mapviewer.model.user.ObjectPrivilege; +import lcsb.mapviewer.model.user.Privilege; import lcsb.mapviewer.model.user.PrivilegeType; import lcsb.mapviewer.model.user.User; import lcsb.mapviewer.model.user.UserAnnotationSchema; @@ -335,10 +335,10 @@ public class UserRestImpl extends BaseRestImpl { private List<Map<String, Object>> preparePrivileges(User user) { List<Map<String, Object>> result = new ArrayList<>(); Set<PrivilegeType> definedDefaultProjectPrivilegeTypes = new HashSet<>(); - List<BasicPrivilege> privileges = new ArrayList<>(); + List<Privilege> privileges = new ArrayList<>(); privileges.addAll(user.getPrivileges()); - privileges.sort(BasicPrivilege.ID_COMPARATOR); - for (BasicPrivilege privilege : privileges) { + privileges.sort(Privilege.ID_COMPARATOR); + for (Privilege privilege : privileges) { if (privilege instanceof ObjectPrivilege) { if (Project.class.equals(privilege.getType().getPrivilegeObjectType()) && ((ObjectPrivilege) privilege).getIdObject() == null) { @@ -346,7 +346,7 @@ public class UserRestImpl extends BaseRestImpl { } result.add(prepareObjectPrivilege((ObjectPrivilege) privilege)); } else { - result.add(prepareBasicPrivilege(privilege)); + result.add(preparePrivilege(privilege)); } } for (PrivilegeType privilegeType : PrivilegeType.values()) { @@ -387,9 +387,9 @@ public class UserRestImpl extends BaseRestImpl { return result; } - private Map<String, Object> prepareBasicPrivilege(BasicPrivilege privilege) { + private Map<String, Object> preparePrivilege(Privilege privilege) { Map<String, Object> result = new TreeMap<>(); - if (privilege.getClass().equals(BasicPrivilege.class)) { + if (privilege.getClass().equals(Privilege.class)) { result.put("type", privilege.getType()); result.put("value", privilege.getLevel()); return result; @@ -445,7 +445,7 @@ public class UserRestImpl extends BaseRestImpl { PrivilegeType type = PrivilegeType.valueOf(key); - if (type.getPrivilegeClassType().equals(BasicPrivilege.class)) { + if (type.getPrivilegeClassType().equals(Privilege.class)) { getUserService().setUserPrivilege(modifiedUser, type, value, token); } else if (type.getPrivilegeClassType().equals(ObjectPrivilege.class)) { if (value instanceof Map) { @@ -615,7 +615,7 @@ public class UserRestImpl extends BaseRestImpl { } } getUserService().addUser(user); - getUserService().createDefaultBasicPrivilegesForUser(user); + getUserService().createDefaultPrivilegesForUser(user); for (Project project : getProjectService().getAllProjects()) { getUserService().createDefaultProjectPrivilegesForUser(project, user); } diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/plugins/PluginRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/plugins/PluginRestImplTest.java index 209e40162bd605713f64fccabc857a29f7a71fd8..e378aa92c9c26591872c275ade5782c5336a873f 100644 --- a/rest-api/src/test/java/lcsb/mapviewer/api/plugins/PluginRestImplTest.java +++ b/rest-api/src/test/java/lcsb/mapviewer/api/plugins/PluginRestImplTest.java @@ -4,7 +4,7 @@ import org.junit.Test; import org.springframework.beans.factory.annotation.Autowired; import lcsb.mapviewer.api.RestTestFunctions; -import lcsb.mapviewer.model.user.BasicPrivilege; +import lcsb.mapviewer.model.user.Privilege; import lcsb.mapviewer.model.user.PrivilegeType; import lcsb.mapviewer.model.user.User; @@ -22,7 +22,7 @@ public class PluginRestImplTest extends RestTestFunctions { public void testCreatePlugin() throws Exception { try { User admin = userService.getUserByToken(adminToken); - userService.setUserPrivilege(admin, new BasicPrivilege(1, PrivilegeType.MANAGE_PLUGINS, admin)); + userService.setUserPrivilege(admin, new Privilege(1, PrivilegeType.MANAGE_PLUGINS, admin)); pluginRestImpl.createPlugin(adminToken, "x", "x", "x", "x", "true"); } catch (Exception e) { e.printStackTrace(); @@ -34,7 +34,7 @@ public class PluginRestImplTest extends RestTestFunctions { public void testRemovePlugin() throws Exception { try { User admin = userService.getUserByToken(adminToken); - userService.setUserPrivilege(admin, new BasicPrivilege(1, PrivilegeType.MANAGE_PLUGINS, admin)); + userService.setUserPrivilege(admin, new Privilege(1, PrivilegeType.MANAGE_PLUGINS, admin)); pluginRestImpl.createPlugin(adminToken, "x", "x", "x", "x", "true"); pluginRestImpl.removePlugin(adminToken, "x"); } catch (Exception e) { diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java index 726992b97babeabba8c479a985ec3a213000b6ef..94e6941ca0410fc960ae95a773116183261cf293 100644 --- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java +++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java @@ -463,7 +463,7 @@ public class ProjectService implements IProjectService { for (User user : userDao.getAll()) { if (!processedUser.contains(user)) { processedUser.add(user); - userService.createDefaultBasicPrivilegesForUser(user); + userService.createDefaultPrivilegesForUser(user); userService.createDefaultProjectPrivilegesForUser(project, user); } } diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java index c2d7624ceb56de2d851d3a816942fee228379c75..1736ec0cd3327e2347e199ec54daaa0bceac166f 100644 --- a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java +++ b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java @@ -28,7 +28,7 @@ import lcsb.mapviewer.common.comparator.IntegerComparator; import lcsb.mapviewer.common.exception.InvalidArgumentException; import lcsb.mapviewer.common.geometry.ColorParser; import lcsb.mapviewer.model.Project; -import lcsb.mapviewer.model.user.BasicPrivilege; +import lcsb.mapviewer.model.user.Privilege; import lcsb.mapviewer.model.user.ConfigurationElementType; import lcsb.mapviewer.model.user.ConfigurationOption; import lcsb.mapviewer.model.user.ObjectPrivilege; @@ -108,15 +108,15 @@ public class UserService implements IUserService { } @Override - public void setUserPrivilege(User user, BasicPrivilege privilege) { + public void setUserPrivilege(User user, Privilege privilege) { updateUserPrivilegesWithoutDbModification(user, privilege); updateUser(user); userDao.flush(); } - private void updateUserPrivilegesWithoutDbModification(User user, BasicPrivilege privilege) { - BasicPrivilege oldPrivilege = null; - for (BasicPrivilege privilegeIter : user.getPrivileges()) { + private void updateUserPrivilegesWithoutDbModification(User user, Privilege privilege) { + Privilege oldPrivilege = null; + for (Privilege privilegeIter : user.getPrivileges()) { if (privilegeIter.equalsPrivilege(privilege)) { oldPrivilege = privilegeIter; } @@ -163,8 +163,8 @@ public class UserService implements IUserService { // users and drop privileges one by one) List<User> users = userDao.getAll(); for (User user : users) { - List<BasicPrivilege> toRemove = new ArrayList<>(); - for (BasicPrivilege privilege : user.getPrivileges()) { + List<Privilege> toRemove = new ArrayList<>(); + for (Privilege privilege : user.getPrivileges()) { if (privilege.getType().equals(type) && privilege instanceof ObjectPrivilege && integerComparator.compare(((ObjectPrivilege) privilege).getIdObject(), id) == 0) { toRemove.add(privilege); @@ -179,10 +179,10 @@ public class UserService implements IUserService { @Override public int getUserPrivilegeLevel(User user, PrivilegeType type) { - if (type.getPrivilegeClassType() != BasicPrivilege.class) { + if (type.getPrivilegeClassType() != Privilege.class) { throw new InvalidArgumentException("This privilege requires additional information"); } - for (BasicPrivilege privilege : user.getPrivileges()) { + for (Privilege privilege : user.getPrivileges()) { if (privilege.getType().equals(type)) { return privilege.getLevel(); } @@ -221,7 +221,7 @@ public class UserService implements IUserService { user = userDao.getById(user.getId()); } IntegerComparator integerComparator = new IntegerComparator(); - for (BasicPrivilege privilege : user.getPrivileges()) { + for (Privilege privilege : user.getPrivileges()) { if (privilege.getClass() == ObjectPrivilege.class) { ObjectPrivilege oPrivilege = (ObjectPrivilege) privilege; if (oPrivilege.getType().equals(type) && integerComparator.compare(oPrivilege.getIdObject(), id) == 0) { @@ -234,10 +234,10 @@ public class UserService implements IUserService { @Override public void setUserPrivilege(User user, PrivilegeType type, Integer value) { - BasicPrivilege privilege = new BasicPrivilege(value, type, user); + Privilege privilege = new Privilege(value, type, user); - BasicPrivilege oldPrivilege = null; - for (BasicPrivilege privilegeIter : user.getPrivileges()) { + Privilege oldPrivilege = null; + for (Privilege privilegeIter : user.getPrivileges()) { if (privilegeIter.getType().equals(type)) { oldPrivilege = privilegeIter; } @@ -527,7 +527,7 @@ public class UserService implements IUserService { user.setEmail(ldapUserData.getEmail()); user.setConnectedToLdap(true); addUser(user); - createDefaultBasicPrivilegesForUser(user); + createDefaultPrivilegesForUser(user); for (Project project : projectDao.getAll()) { createDefaultProjectPrivilegesForUser(project, user); } @@ -569,9 +569,9 @@ public class UserService implements IUserService { } @Override - public void createDefaultBasicPrivilegesForUser(User user) { + public void createDefaultPrivilegesForUser(User user) { for (PrivilegeType type : PrivilegeType.values()) { - if (BasicPrivilege.class.equals(type.getPrivilegeClassType())) { + if (Privilege.class.equals(type.getPrivilegeClassType())) { int level = 0; ConfigurationOption option = configurationService.getValue(type); if (option != null) { @@ -580,7 +580,7 @@ public class UserService implements IUserService { } else if (StringUtils.isNumeric(option.getValue())) { level = Integer.valueOf(option.getValue()); } - BasicPrivilege privilege = new BasicPrivilege(level, type, user); + Privilege privilege = new Privilege(level, type, user); updateUserPrivilegesWithoutDbModification(user, privilege); } } diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java index 49f5ad04bc5f652887c0fb010b07c6933a4c8f5b..a97215e9d34c15283813caa7a4310598762c7fcd 100644 --- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java +++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java @@ -6,7 +6,7 @@ import java.util.Map; import lcsb.mapviewer.commands.ColorExtractor; import lcsb.mapviewer.model.Project; -import lcsb.mapviewer.model.user.BasicPrivilege; +import lcsb.mapviewer.model.user.Privilege; import lcsb.mapviewer.model.user.PrivilegeType; import lcsb.mapviewer.model.user.User; import lcsb.mapviewer.services.SecurityException; @@ -95,7 +95,7 @@ public interface IUserService { * @param privilege * user privilege */ - void setUserPrivilege(User user, BasicPrivilege privilege); + void setUserPrivilege(User user, Privilege privilege); /** * Adds user to the system. @@ -184,7 +184,7 @@ public interface IUserService { void setLdapService(ILdapService ldapService); void createDefaultProjectPrivilegesForUser(Project project, User user); - void createDefaultBasicPrivilegesForUser(User user); + void createDefaultPrivilegesForUser(User user); Map<String, Boolean> ldapAccountExistsForLogin(Collection<User> logins); } diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java index 036b1f99f9922f83913c9fe4b1743f134447c046..ad76543a9dc3a1a471d13399bf3f19babccd763a 100644 --- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java +++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java @@ -27,7 +27,7 @@ import lcsb.mapviewer.model.map.layout.LayoutStatus; import lcsb.mapviewer.model.map.model.Model; import lcsb.mapviewer.model.map.model.ModelSubmodelConnection; import lcsb.mapviewer.model.map.model.SubmodelType; -import lcsb.mapviewer.model.user.BasicPrivilege; +import lcsb.mapviewer.model.user.Privilege; import lcsb.mapviewer.model.user.ObjectPrivilege; import lcsb.mapviewer.model.user.PrivilegeType; import lcsb.mapviewer.model.user.User; @@ -116,7 +116,7 @@ public class LayoutServiceTest extends ServiceTestFunctions { try { int initialSize = model.getLayouts().size(); assertFalse(layoutService.userCanAddLayout(model, user)); - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); assertFalse(layoutService.userCanAddLayout(model, user)); @@ -133,11 +133,11 @@ public class LayoutServiceTest extends ServiceTestFunctions { assertFalse(layoutService.userCanAddLayout(model, user)); - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); assertFalse(layoutService.userCanAddLayout(model, user)); - userService.setUserPrivilege(user, new BasicPrivilege(2, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(2, PrivilegeType.CUSTOM_LAYOUTS, user)); assertTrue(layoutService.userCanAddLayout(model, user)); @@ -156,7 +156,7 @@ public class LayoutServiceTest extends ServiceTestFunctions { @Test public void testGetAvailable() throws Exception { try { - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); assertEquals(1, layoutService.getAvailableCustomLayoutsNumber(user)); CreateLayoutParams params = new CreateLayoutParams().name("Test").// @@ -192,7 +192,7 @@ public class LayoutServiceTest extends ServiceTestFunctions { assertNotNull(layouts); assertEquals(0, layouts.size()); - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); CreateLayoutParams params = new CreateLayoutParams().name("Test").// directory("testDir").// @@ -226,7 +226,7 @@ public class LayoutServiceTest extends ServiceTestFunctions { assertNotNull(layouts); assertEquals(0, layouts.size()); - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); CreateLayoutParams params = new CreateLayoutParams().name("Test").// directory("testDir").// @@ -262,7 +262,7 @@ public class LayoutServiceTest extends ServiceTestFunctions { assertNotNull(layouts); assertEquals(0, layouts.size()); - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); CreateLayoutParams params = new CreateLayoutParams().name("Test").// directory("testDir").// model(model).// @@ -323,7 +323,7 @@ public class LayoutServiceTest extends ServiceTestFunctions { projectService.addProject(localProject); - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); userService.setUserPrivilege(user, new ObjectPrivilege(localProject, 1, PrivilegeType.VIEW_PROJECT, user)); CreateLayoutParams params = new CreateLayoutParams().name("Test").// @@ -363,7 +363,7 @@ public class LayoutServiceTest extends ServiceTestFunctions { assertNotNull(layouts); assertEquals(0, layouts.size()); - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); CreateLayoutParams params = new CreateLayoutParams().name("Test").// directory("testDir").// model(model).// @@ -396,7 +396,7 @@ public class LayoutServiceTest extends ServiceTestFunctions { assertNotNull(layouts); assertEquals(0, layouts.size()); - userService.setUserPrivilege(user, new BasicPrivilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); + userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user)); ByteArrayInputStream bais = new ByteArrayInputStream( "name reactionIdentifier Color\ns1 #CC0000\ns2 #CCCC00\n re1 #CCCC00\n" .getBytes(StandardCharsets.UTF_8)); diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java index 9e11fe58f00ba897c0fd50c84e79743eb4ec863f..a88b5900d35b3afd17e55770c2eaaf6144c72b8f 100644 --- a/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java +++ b/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java @@ -22,7 +22,7 @@ import com.unboundid.ldap.sdk.LDAPConnection; import com.unboundid.ldap.sdk.LDAPException; import lcsb.mapviewer.model.Project; -import lcsb.mapviewer.model.user.BasicPrivilege; +import lcsb.mapviewer.model.user.Privilege; import lcsb.mapviewer.model.user.ConfigurationElementType; import lcsb.mapviewer.model.user.ObjectPrivilege; import lcsb.mapviewer.model.user.PrivilegeType; @@ -145,7 +145,7 @@ public class UserServiceTest extends ServiceTestFunctions { @Test public void testUserHasPrivilegeUserPrivilegeType2() { try { - BasicPrivilege privilege = new BasicPrivilege(); + Privilege privilege = new Privilege(); privilege.setLevel(1); privilege.setType(PrivilegeType.ADD_MAP); userService.setUserPrivilege(user, privilege); @@ -230,12 +230,12 @@ public class UserServiceTest extends ServiceTestFunctions { } @Test - public void testCreateDefaultBasicPrivilegesForUser() throws Exception { + public void testCreateDefaultPrivilegesForUser() throws Exception { String originalValue = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_CUSTOM_LAYOUTS); try { configurationService.setConfigurationValue(ConfigurationElementType.DEFAULT_CUSTOM_LAYOUTS, "127"); createUser(); - userService.createDefaultBasicPrivilegesForUser(user); + userService.createDefaultPrivilegesForUser(user); assertEquals(127, userService.getUserPrivilegeLevel(user, PrivilegeType.CUSTOM_LAYOUTS)); } catch (Exception e) {