diff --git a/pom.xml b/pom.xml index a58a4b38ac..f2d549f6fc 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ net.sumaris sumaris-pod - 2.1.0 + 2.1.1 pom SUMARiS SUMARiS :: Maven parent @@ -51,6 +51,7 @@ sumaris-core-shared sumaris-test-shared + sumaris-xml-query sumaris-core sumaris-importation sumaris-extraction @@ -120,7 +121,7 @@ 3.3.0 3.8.1 1.18.24 - 1.8 + 3.2 2.0.6 1.2.0 5.3.24 @@ -1182,6 +1183,7 @@ ${project.build.sourceEncoding} --enable-preview + @@ -1189,6 +1191,11 @@ lombok ${lombok.version} + diff --git a/src/scripts/release.sh b/src/scripts/release.sh index 30dec9850f..a8c53f402d 100755 --- a/src/scripts/release.sh +++ b/src/scripts/release.sh @@ -51,7 +51,7 @@ echo "---- Prepare release [OK]" echo "" echo "---- Performing release..." -mvn clean deploy -DperformRelease -DskipTests -Dspring.datasource.platform=hsqldb +mvn clean deploy -DperformRelease -DskipTests -Dspring.sql.init.platform=hsqldb [[ $? -ne 0 ]] && exit 1 echo "---- Perform release [OK]" echo "" diff --git a/sumaris-core-shared/pom.xml b/sumaris-core-shared/pom.xml index 60f98dba4f..465a7a127e 100644 --- a/sumaris-core-shared/pom.xml +++ b/sumaris-core-shared/pom.xml @@ -4,7 +4,7 @@ net.sumaris sumaris-pod - 2.1.0 + 2.1.1 sumaris-core-shared diff --git a/sumaris-core-shared/src/main/java/net/sumaris/core/config/ApplicationConfigAliasProvider.java b/sumaris-core-shared/src/main/java/net/sumaris/core/config/ApplicationConfigAliasProvider.java new file mode 100644 index 0000000000..653895bc3d --- /dev/null +++ b/sumaris-core-shared/src/main/java/net/sumaris/core/config/ApplicationConfigAliasProvider.java @@ -0,0 +1,30 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.core.config; + +import org.nuiton.config.ApplicationConfig; + +public interface ApplicationConfigAliasProvider { + + void addAlias(ApplicationConfig applicationConfig); +} diff --git a/sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfiguration.java b/sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfiguration.java index 90e15a9772..7c86c4cd19 100644 --- a/sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfiguration.java +++ b/sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfiguration.java @@ -184,6 +184,11 @@ protected SumarisConfiguration(ConfigurableEnvironment env, // Define Alias addAlias(applicationConfig); + for (ApplicationConfigProvider provider : providers) { + if (provider instanceof ApplicationConfigAliasProvider) { + ((ApplicationConfigAliasProvider)provider).addAlias(applicationConfig); + } + } // parse config file and inline arguments try { diff --git a/sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfigurationOption.java b/sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfigurationOption.java index 58b94e9418..b0a841e3c5 100644 --- a/sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfigurationOption.java +++ b/sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfigurationOption.java @@ -142,7 +142,7 @@ public enum SumarisConfigurationOption implements ConfigOptionDef { DB_CREATE_SCRIPT_PATH( "sumaris.persistence.db.script", n("sumaris.config.option.db.script.description"), - "classpath:net/sumaris/core/db/changelog/${spring.datasource.platform}/sumaris.script", + "classpath:net/sumaris/core/db/changelog/${spring.sql.init.platform}/sumaris.script", String.class, false), diff --git a/sumaris-core-shared/src/main/java/net/sumaris/core/jms/JmsConfiguration.java b/sumaris-core-shared/src/main/java/net/sumaris/core/jms/JmsConfiguration.java index 7521bcc1ad..7183c45049 100644 --- a/sumaris-core-shared/src/main/java/net/sumaris/core/jms/JmsConfiguration.java +++ b/sumaris-core-shared/src/main/java/net/sumaris/core/jms/JmsConfiguration.java @@ -73,6 +73,7 @@ public JmsListenerContainerFactory jmsListenerContainerFactory( DefaultJmsListenerContainerFactory factory = new DefaultJmsListenerContainerFactory(); factory.setConnectionFactory(jmsConnectionFactory); factory.setMessageConverter(messageConverter); + factory.setPubSubDomain(true); // Use Topic instead of Queue jmsListenerContainerFactoryConfigurer .ifPresent(c -> c.configure(factory, jmsConnectionFactory)); diff --git a/sumaris-core-shared/src/main/java/net/sumaris/core/util/Dates.java b/sumaris-core-shared/src/main/java/net/sumaris/core/util/Dates.java index 472866218c..9745508f85 100644 --- a/sumaris-core-shared/src/main/java/net/sumaris/core/util/Dates.java +++ b/sumaris-core-shared/src/main/java/net/sumaris/core/util/Dates.java @@ -50,6 +50,8 @@ public class Dates extends org.apache.commons.lang3.time.DateUtils{ public static String ISO_TIMESTAMP_SPEC = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX"; + public static String CSV_DATE_TIME = "yyyy-MM-dd HH:mm:ss"; + /** * Remove a amount of month to a date * diff --git a/sumaris-core-shared/src/main/java/net/sumaris/core/util/sound/SoundUtils.java b/sumaris-core-shared/src/main/java/net/sumaris/core/util/sound/SoundUtils.java index b658f615ea..4fa27d4419 100644 --- a/sumaris-core-shared/src/main/java/net/sumaris/core/util/sound/SoundUtils.java +++ b/sumaris-core-shared/src/main/java/net/sumaris/core/util/sound/SoundUtils.java @@ -101,6 +101,20 @@ public static void playWaiting(int count) { } } + public static void playFinished() { + try { + SoundUtils.tone(800, 100); + Thread.sleep(200); + SoundUtils.tone(800, 700, 0.7); + Thread.sleep(350); + SoundUtils.tone(800, 1000); + Thread.sleep(3000); + } + catch (Exception e) { + log.debug("Cannot play error sound: " + e.getMessage()); + } + } + private void playSound(File f) { Preconditions.checkArgument(f.exists()); diff --git a/sumaris-core/pom.xml b/sumaris-core/pom.xml index c9741dbba5..e5cf6a1187 100644 --- a/sumaris-core/pom.xml +++ b/sumaris-core/pom.xml @@ -4,7 +4,7 @@ net.sumaris sumaris-pod - 2.1.0 + 2.1.1 sumaris-core @@ -34,7 +34,7 @@ AllTests - hsqldb + hsqldb @@ -377,7 +377,7 @@ true - spring.datasource.platform + spring.sql.init.platform hsqldb @@ -391,7 +391,7 @@ org.hsqldb.jdbc.JDBCDriver PUBLIC - hsqldb + hsqldb net.sumaris.core.dao.technical.hibernate.spatial.dialect.HSQLSpatialDialect 15 @@ -408,7 +408,7 @@ oracle - spring.datasource.platform + spring.sql.init.platform oracle @@ -420,7 +420,7 @@ SUMARIS_TU SUMARIS_TU oracle.jdbc.driver.OracleDriver - oracle + oracle net.sumaris.core.dao.technical.hibernate.spatial.dialect.OracleSpatial10gDialect 15 @@ -437,7 +437,7 @@ pgsql - spring.datasource.platform + spring.sql.init.platform pgsql @@ -449,7 +449,7 @@ sumaris public org.postgresql.Driver - pgsql + pgsql net.sumaris.core.dao.technical.hibernate.spatial.dialect.PostgreSQL10Dialect 15 diff --git a/sumaris-core/src/main/filtered-resources/application-hsqldb.properties b/sumaris-core/src/main/filtered-resources/application-hsqldb.properties index 178e0fd632..5ed6e5793b 100644 --- a/sumaris-core/src/main/filtered-resources/application-hsqldb.properties +++ b/sumaris-core/src/main/filtered-resources/application-hsqldb.properties @@ -3,7 +3,7 @@ spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver spring.datasource.username=sa spring.datasource.password= spring.datasource.url=@jdbc.url@ -spring.datasource.platform=@env@ +spring.sql.init.platform=@env@ spring.datasource.hikari.connectionTestQuery=SELECT 1 FROM STATUS WHERE ID=1 spring.datasource.hikari.initializationFailTimeout=-1 diff --git a/sumaris-core/src/main/filtered-resources/application-oracle.properties b/sumaris-core/src/main/filtered-resources/application-oracle.properties index 974e890b66..0385b49a2f 100644 --- a/sumaris-core/src/main/filtered-resources/application-oracle.properties +++ b/sumaris-core/src/main/filtered-resources/application-oracle.properties @@ -6,7 +6,7 @@ spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.di spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform} # Database connection -spring.datasource.platform=oracle +spring.sql.init.platform=oracle spring.datasource.username= spring.datasource.password= spring.jpa.properties.hibernate.default_catalog= diff --git a/sumaris-core/src/main/filtered-resources/application-pgsql.properties b/sumaris-core/src/main/filtered-resources/application-pgsql.properties index d90afc8fce..f34f2fe0d9 100644 --- a/sumaris-core/src/main/filtered-resources/application-pgsql.properties +++ b/sumaris-core/src/main/filtered-resources/application-pgsql.properties @@ -6,7 +6,7 @@ spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.di spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform} # Database connection -spring.datasource.platform=pgsql +spring.sql.init.platform=pgsql spring.datasource.username=sumaris spring.datasource.password=sumaris spring.jpa.properties.hibernate.default_catalog=sumaristest diff --git a/sumaris-core/src/main/filtered-resources/application.properties b/sumaris-core/src/main/filtered-resources/application.properties index bb00118c33..81b0829a28 100644 --- a/sumaris-core/src/main/filtered-resources/application.properties +++ b/sumaris-core/src/main/filtered-resources/application.properties @@ -19,7 +19,7 @@ spring.datasource.driver-class-name=@jdbc.driver@ spring.datasource.username=@jdbc.username@ spring.datasource.password=@jdbc.password@ spring.datasource.url=@jdbc.url@ -spring.datasource.platform=@env@ +spring.sql.init.platform=@env@ spring.datasource.hikari.connectionTestQuery=SELECT 1 FROM STATUS WHERE ID=1 spring.datasource.hikari.initializationFailTimeout=-1 diff --git a/sumaris-core/src/main/java/net/sumaris/cli/action/data/DenormalizeTripsAction.java b/sumaris-core/src/main/java/net/sumaris/cli/action/data/DenormalizeTripsAction.java index ed9b67f9cd..15bd4204ef 100644 --- a/sumaris-core/src/main/java/net/sumaris/cli/action/data/DenormalizeTripsAction.java +++ b/sumaris-core/src/main/java/net/sumaris/cli/action/data/DenormalizeTripsAction.java @@ -60,6 +60,6 @@ public void run() { tripService.denormalizeByFilter(filterBuilder.build(), progression); // Play a beep - SoundUtils.playWaiting(2); + SoundUtils.playFinished(); } } diff --git a/sumaris-core/src/main/java/net/sumaris/core/dao/technical/JobSpecifications.java b/sumaris-core/src/main/java/net/sumaris/core/dao/technical/JobSpecifications.java index 078c465ea3..a304679c2a 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/dao/technical/JobSpecifications.java +++ b/sumaris-core/src/main/java/net/sumaris/core/dao/technical/JobSpecifications.java @@ -76,16 +76,17 @@ default Specification hasStatus(String... status) { } default Specification hasJobStatus(JobStatusEnum... jobStatus) { - Integer[] statusIds = Arrays.stream(jobStatus) + if (ArrayUtils.isEmpty(jobStatus)) return null; + List statusIds = Arrays.stream(jobStatus) .map(JobStatusEnum::getProcessingStatus) .filter(Objects::nonNull) .map(ProcessingStatusEnum::getId) .filter(id -> id != null && id >= 0) - .toArray(Integer[]::new); - if (ArrayUtils.isEmpty(statusIds)) return null; + .toList(); + if (CollectionUtils.isEmpty(statusIds)) return null; return hasInnerJoinIds( ProcessingHistory.Fields.PROCESSING_STATUS, - statusIds); + statusIds.toArray(new Integer[0])); } List findAll(JobFilterVO filter); diff --git a/sumaris-core/src/main/java/net/sumaris/core/dao/technical/schema/SumarisDatabaseMetadata.java b/sumaris-core/src/main/java/net/sumaris/core/dao/technical/schema/SumarisDatabaseMetadata.java index 94835a8e25..1d581e65cf 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/dao/technical/schema/SumarisDatabaseMetadata.java +++ b/sumaris-core/src/main/java/net/sumaris/core/dao/technical/schema/SumarisDatabaseMetadata.java @@ -198,9 +198,9 @@ public Set findTableNamesByPrefix(String tablePrefix, String schema, Str if (tableName.toUpperCase().startsWith(tablePrefix.toUpperCase())) { result.add(rs.getString("TABLE_NAME")); } - // JDBC meta return a bad tableName: should never occur !! + // JDBC meta return a bad tableName (e.g. because '_' special character) => ignore else { - log.warn("Invalid getTables() result: Table name '{}' should not be returned, because its not match the pattern '{}'. Please check like pattern, or Daos.getEscapedForLike() function", tableName, tablePrefix); + log.trace("Ignoring getTables() result, because table name '{}' not start with '{}'", tableName, tablePrefix); } } return result; diff --git a/sumaris-core/src/main/java/net/sumaris/core/model/data/PhysicalGear.java b/sumaris-core/src/main/java/net/sumaris/core/model/data/PhysicalGear.java index 311e86a419..30bd713c09 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/model/data/PhysicalGear.java +++ b/sumaris-core/src/main/java/net/sumaris/core/model/data/PhysicalGear.java @@ -59,7 +59,6 @@ public class PhysicalGear implements IRootDataEntity, @ManyToOne(fetch = FetchType.LAZY, targetEntity = Gear.class) @JoinColumn(name = "gear_fk", nullable = false) - private Gear gear; @Column(length = LENGTH_COMMENTS) diff --git a/sumaris-core/src/main/java/net/sumaris/core/model/referential/pmfm/PmfmEnum.java b/sumaris-core/src/main/java/net/sumaris/core/model/referential/pmfm/PmfmEnum.java index 2c93a7c187..42d548d38c 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/model/referential/pmfm/PmfmEnum.java +++ b/sumaris-core/src/main/java/net/sumaris/core/model/referential/pmfm/PmfmEnum.java @@ -77,6 +77,10 @@ public enum PmfmEnum implements IEntityEnum, Serializable { BATCH_CALCULATED_WEIGHT_LENGTH(122, "BATCH_CALCULATED_WEIGHT_LENGTH"), BATCH_CALCULATED_WEIGHT_LENGTH_SUM(123, "BATCH_CALCULATED_WEIGHT_LENGTH_SUM"), BATCH_SORTING(176, "BATCH_SORTING"), // Adagio = 'SORTED' (id=200) + CHILD_GEAR(400, "CHILD_GEAR"), + CATCH_WEIGHT(57, "CATCH_WEIGHT"), + DISCARD_WEIGHT(56, "DISCARD_WEIGHT"), + BATCH_GEAR_POSITION(411, "BATCH_GEAR_POSITION"), IS_DEAD(94, "IS_DEAD"), DISCARD_REASON(95, "DISCARD_REASON"), @@ -92,10 +96,11 @@ public enum PmfmEnum implements IEntityEnum, Serializable { CONTROL_TYPE(130, "CONTROL_TYPE"), + SIZE_UNLI_CAT(141, "SIZE_UNLI_CAT"), PRESERVATION(150, "PRESERVATION"), DRESSING(151, "DRESSING"), SIZE_CATEGORY(174, "SIZE_CATEGORY"), - + TRAWL_SIZE_CAT(418, "TRAWL_SIZE_CAT"), PACKAGING(177, "PACKAGING"), TOTAL_PRICE(270, "TOTAL_PRICE"), diff --git a/sumaris-core/src/main/java/net/sumaris/core/model/technical/extraction/rdb/ProductRdbSpeciesList.java b/sumaris-core/src/main/java/net/sumaris/core/model/technical/extraction/rdb/ProductRdbSpeciesList.java index fdeb39aa8a..b4ceb791f9 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/model/technical/extraction/rdb/ProductRdbSpeciesList.java +++ b/sumaris-core/src/main/java/net/sumaris/core/model/technical/extraction/rdb/ProductRdbSpeciesList.java @@ -61,7 +61,7 @@ public class ProductRdbSpeciesList implements Serializable, IEntity { public static final String COLUMN_COMMERCIAL_SIZE_CATEGORY = "commercial_size_category"; public static final String COLUMN_SUBSAMPLING_CATEGORY = "subsampling_category"; public static final String COLUMN_WEIGHT= "weight"; - public static final String COLUMN_SUBSAMPLING_WEIGHT = "subsampling_weight"; + public static final String COLUMN_SUBSAMPLE_WEIGHT = "subsample_weight"; public static final String COLUMN_LENGTH_CODE = "length_code"; @Id @@ -119,8 +119,8 @@ public class ProductRdbSpeciesList implements Serializable, IEntity { @Column(nullable = false, scale = 12, precision = 2, name = COLUMN_WEIGHT) private Double weight; - @Column( scale = 12, precision = 2, name = COLUMN_SUBSAMPLING_WEIGHT) - private Double subsamplingWeight; + @Column( scale = 12, precision = 2, name = COLUMN_SUBSAMPLE_WEIGHT) + private Double subsampleWeight; @Column(length = 5, name = COLUMN_LENGTH_CODE) private String lengthCode; diff --git a/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizeOperationServiceImpl.java b/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizeOperationServiceImpl.java index c46c797070..f3b74431b2 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizeOperationServiceImpl.java +++ b/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizeOperationServiceImpl.java @@ -105,6 +105,9 @@ public DenormalizedTripResultVO denormalizeByFilter(@NonNull OperationFilterVO o // Select only operation that should be update (if not force) operationFilter.setNeedBatchDenormalization(!baseOptions.isForce()); + // DEBUG - force denormalization + //if (!this.production && !baseOptions.isForce()) operationFilter.setNeedBatchDenormalization(false); + long operationTotal = operationService.countByFilter(operationFilter); boolean hasMoreData; diff --git a/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizedBatchServiceImpl.java b/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizedBatchServiceImpl.java index 90ac8d729a..7ce6d97177 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizedBatchServiceImpl.java +++ b/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizedBatchServiceImpl.java @@ -149,7 +149,7 @@ public List denormalize(@NonNull BatchVO catchBatch, @NonNu // Check options Preconditions.checkNotNull(options.getDateTime(), "Required options.dateTime when RTP weight enabled"); - Preconditions.checkNotNull(options.getRoundWeightCountryLocationId(), "Required options.roundWeightCountryLocationId when RTP weight enabled"); + Preconditions.checkNotNull(options.getAliveWeightCountryLocationId(), "Required options.roundWeightCountryLocationId when RTP weight enabled"); Preconditions.checkNotNull(options.getDefaultLandingDressingId(), "Required options.defaultLandingDressingId when RTP weight enabled"); Preconditions.checkNotNull(options.getDefaultDiscardDressingId(), "Required options.defaultDiscardDressingId when RTP weight enabled"); Preconditions.checkNotNull(options.getDefaultLandingPreservationId(), "Required options.defaultLandingPreservationId when RTP weight enabled"); @@ -163,104 +163,19 @@ public List denormalize(@NonNull BatchVO catchBatch, @NonNu List result = TreeNodeEntities.streamAllAndMap(catchBatch, (source, p) -> { TempDenormalizedBatchVO target = createTempVO(source); TempDenormalizedBatchVO parent = p != null ? (TempDenormalizedBatchVO)p : null; - boolean isLeaf = source.isLeaf(); // Do not use 'target', because children are added later + boolean isLeaf = parent != null && source.isLeaf(); // Do not use 'target', because children are added later // Add to parent's children if (parent != null) parent.addChildren(target); - // Depth level - if (parent == null) { - target.setTreeLevel((short) 1); // First level - if (target.getIsLanding() == null) target.setIsLanding(false); - if (target.getIsDiscard() == null) target.setIsDiscard(false); - } else { - target.setTreeLevel((short) (parent.getTreeLevel() + 1)); - // Inherit taxon group - if (target.getInheritedTaxonGroup() == null && parent.getInheritedTaxonGroup() != null) { - target.setInheritedTaxonGroup(parent.getInheritedTaxonGroup()); - } - // Inherit taxon name - if (target.getInheritedTaxonName() == null && parent.getInheritedTaxonName() != null) { - target.setInheritedTaxonName(parent.getInheritedTaxonName()); - } - // Exhaustive inventory - if (target.getExhaustiveInventory() == null) { - // Always true, when: - // - taxon name is defined - // - taxon group is defined and taxon Name disable (in options) - if (target.getInheritedTaxonName() != null) { - target.setExhaustiveInventory(Boolean.TRUE); - } else if (target.getInheritedTaxonGroup() != null && !options.isEnableTaxonName()) { - target.setExhaustiveInventory(Boolean.TRUE); - } else if (parent.getExhaustiveInventory() != null) { - target.setExhaustiveInventory(parent.getExhaustiveInventory()); - } - } - // Inherit location - if (parent.getLocationId() != null) { - target.setLocationId(parent.getLocationId()); - } - // Inherit landing / discard - if (target.getIsLanding() == null) { - target.setIsLanding(parent.getIsLanding()); - } - if (target.getIsDiscard() == null) { - target.setIsDiscard(parent.getIsDiscard()); - } - - // Inherit quality flag - if (parent.getQualityFlagId() != null) { - if (target.getQualityFlagId() == null) { - target.setQualityFlagId(parent.getQualityFlagId()); - } - // Keep the worst value, if current has a value - else { - target.setQualityFlagId(QualityFlags.worst(parent.getQualityFlagId(), target.getQualityFlagId())); - } - } - - // If current quality is invalid - if (QualityFlags.isInvalid(target.getQualityFlagId())) { - // Force both parent and current parent exhaustive inventory to FALSE - // NOTE Allegro: - // mantis Allegro #12951 - remontée des poids selon le niveau de qualité - // Si un des lots fils (direct ou indirect) est invalide - // (c'est à dire si le code du niveau de qualité appartient à la liste des niveaux invalides) - // alors il faut considérer que l'inventaire exhaustif est non. - // Le but est de stopper la remontée des poids calculés - // s'il y a au moins un lot invalide parmi les fils, isExhaustive = false - parent.setExhaustiveInventory(Boolean.FALSE); - target.setExhaustiveInventory(Boolean.FALSE); - } - - // Inherit sorting values - Beans.getStream(parent.getSortingValues()) - .forEach(svSource -> { - // Make sure sorting value not already exists - Beans.getStream(target.getSortingValues()) - .filter(svTarget -> Objects.equals(svTarget.getPmfmId(), svSource.getPmfmId())) - .findFirst() - .ifPresentOrElse(svTarget -> { - Beans.copyProperties(svSource, svTarget, IEntity.Fields.ID); - svTarget.setIsInherited(true); - svTarget.setRankOrder(svSource.getRankOrder() / 10); - }, - () -> { - DenormalizedBatchSortingValueVO svTarget = new DenormalizedBatchSortingValueVO(); - Beans.copyProperties(svSource, svTarget, IEntity.Fields.ID); - svTarget.setIsInherited(true); - svTarget.setRankOrder(svSource.getRankOrder() / 10); - target.addSortingValue(svTarget); - }); - }); - - // Compute Alive weight, on leaf batch - // (to be able to compute indirect alive weight later) - if (isLeaf) { - computeAliveWeightFactor(target, options, true) - .ifPresent(target::setAliveWeightFactor); - } + // Copy parent's values + computeInheritedValues(target, parent, options); + // Compute Alive weight, on leaf batch + // (to be able to compute indirect alive weight later) + if (isLeaf) { + computeAliveWeightFactor(target, options, true) + .ifPresent(target::setAliveWeightFactor); } return target; @@ -427,10 +342,102 @@ protected DenormalizedBatchOptions createOptionsByProgram(@NonNull ProgramVO pro .enableTaxonName(Programs.getPropertyAsBoolean(program, ProgramPropertyEnum.TRIP_BATCH_TAXON_NAME_ENABLE)) .enableTaxonGroup(Programs.getPropertyAsBoolean(program, ProgramPropertyEnum.TRIP_BATCH_TAXON_GROUP_ENABLE)) .enableRtpWeight(canEnableRtpWeight && Programs.getPropertyAsBoolean(program, ProgramPropertyEnum.TRIP_BATCH_LENGTH_WEIGHT_CONVERSION_ENABLE)) - .roundWeightCountryLocationId(roundWeightConversionCountryId) + .aliveWeightCountryLocationId(roundWeightConversionCountryId) .build(); } + protected void computeInheritedValues(TempDenormalizedBatchVO target, + TempDenormalizedBatchVO parent, + DenormalizedBatchOptions options) { + // Special case for catch batch + if (parent == null) { + target.setTreeLevel((short) 1); // First level + if (target.getIsLanding() == null) target.setIsLanding(false); + if (target.getIsDiscard() == null) target.setIsDiscard(false); + return; + } + + target.setTreeLevel((short) (parent.getTreeLevel() + 1)); + // Inherit taxon group + if (target.getInheritedTaxonGroup() == null && parent.getInheritedTaxonGroup() != null) { + target.setInheritedTaxonGroup(parent.getInheritedTaxonGroup()); + } + // Inherit taxon name + if (target.getInheritedTaxonName() == null && parent.getInheritedTaxonName() != null) { + target.setInheritedTaxonName(parent.getInheritedTaxonName()); + } + // Exhaustive inventory + if (target.getExhaustiveInventory() == null) { + // Always true, when: + // - taxon name is defined + // - taxon group is defined and taxon Name disable (in options) + if (target.getInheritedTaxonName() != null) { + target.setExhaustiveInventory(Boolean.TRUE); + } else if (target.getInheritedTaxonGroup() != null && !options.isEnableTaxonName()) { + target.setExhaustiveInventory(Boolean.TRUE); + } else if (parent.getExhaustiveInventory() != null) { + target.setExhaustiveInventory(parent.getExhaustiveInventory()); + } + } + // Inherit location + if (parent.getLocationId() != null) { + target.setLocationId(parent.getLocationId()); + } + // Inherit landing / discard + if (target.getIsLanding() == null) { + target.setIsLanding(parent.getIsLanding()); + } + if (target.getIsDiscard() == null) { + target.setIsDiscard(parent.getIsDiscard()); + } + + // Inherit quality flag + if (parent.getQualityFlagId() != null) { + if (target.getQualityFlagId() == null) { + target.setQualityFlagId(parent.getQualityFlagId()); + } + // Keep the worst value, if current has a value + else { + target.setQualityFlagId(QualityFlags.worst(parent.getQualityFlagId(), target.getQualityFlagId())); + } + } + + // If current quality is invalid + if (QualityFlags.isInvalid(target.getQualityFlagId())) { + // Force both parent and current parent exhaustive inventory to FALSE + // NOTE Allegro: + // mantis Allegro #12951 - remontée des poids selon le niveau de qualité + // Si un des lots fils (direct ou indirect) est invalide + // (c'est à dire si le code du niveau de qualité appartient à la liste des niveaux invalides) + // alors il faut considérer que l'inventaire exhaustif est non. + // Le but est de stopper la remontée des poids calculés + // s'il y a au moins un lot invalide parmi les fils, isExhaustive = false + parent.setExhaustiveInventory(Boolean.FALSE); + target.setExhaustiveInventory(Boolean.FALSE); + } + + // Inherit sorting values + Beans.getStream(parent.getSortingValues()) + .forEach(svSource -> { + // Make sure sorting value not already exists + Beans.getStream(target.getSortingValues()) + .filter(svTarget -> Objects.equals(svTarget.getPmfmId(), svSource.getPmfmId())) + .findFirst() + .ifPresentOrElse(svTarget -> { + Beans.copyProperties(svSource, svTarget, IEntity.Fields.ID); + svTarget.setIsInherited(true); + svTarget.setRankOrder(svSource.getRankOrder() / 10); + }, + () -> { + DenormalizedBatchSortingValueVO svTarget = new DenormalizedBatchSortingValueVO(); + Beans.copyProperties(svSource, svTarget, IEntity.Fields.ID); + svTarget.setIsInherited(true); + svTarget.setRankOrder(svSource.getRankOrder() / 10); + target.addSortingValue(svTarget); + }); + }); + } + protected void computeRtpWeights(List batches, DenormalizedBatchOptions options) { // Select leafs List leafBatches = batches.stream() @@ -492,6 +499,7 @@ protected void computeIndirectValues(List batches, Denormal MutableInt changesCount = new MutableInt(0); MutableInt loopCounter = new MutableInt(0); + int maxLoop = 1; // TODO check this do { changesCount.setValue(0); loopCounter.increment(); @@ -521,15 +529,19 @@ protected void computeIndirectValues(List batches, Denormal batch.setIndirectIndividualCountDecimal(indirectIndividualCount); // Compute alive weight factor - if (batch.isLeaf()) { - Double aliveWeightFactor = computeAliveWeightFactor(batch, options, batch.isLeaf()).orElse(null); - changed = changed || !Objects.equals(aliveWeightFactor, batch.getAliveWeightFactor()); - batch.setAliveWeightFactor(aliveWeightFactor); + if (options.isEnableAliveWeight() && options.getAliveWeightCountryLocationId() != null) { + if (batch.isLeaf()) { + Double aliveWeightFactor = computeAliveWeightFactor(batch, options, batch.isLeaf()).orElse(null); + changed = changed || !Objects.equals(aliveWeightFactor, batch.getAliveWeightFactor()); + batch.setAliveWeightFactor(aliveWeightFactor); + } else { + Double aliveWeightFactor = computeIndirectAliveWeightFactor(batch, options); + changed = changed || !Objects.equals(aliveWeightFactor, batch.getAliveWeightFactor()); + batch.setAliveWeightFactor(aliveWeightFactor); + } } else { - Double aliveWeightFactor = computeIndirectAliveWeightFactor(batch, options); - changed = changed || !Objects.equals(aliveWeightFactor, batch.getAliveWeightFactor()); - batch.setAliveWeightFactor(aliveWeightFactor); + batch.setAliveWeightFactor(1d); } if (changed) changesCount.increment(); @@ -539,7 +551,7 @@ protected void computeIndirectValues(List batches, Denormal } // Continue while changes has been applied on tree - while (changesCount.intValue() > 0); + while (changesCount.intValue() > 0 && loopCounter.intValue() < maxLoop); } /** @@ -592,6 +604,7 @@ protected void computeElevateFactor(List batches, Denormali protected void computeElevatedValues(List batches, DenormalizedBatchOptions options) { MutableInt changesCount = new MutableInt(0); MutableInt loopCounter = new MutableInt(0); + int maxLoop = 1; // TODO check this do { changesCount.setValue(0); @@ -702,7 +715,7 @@ protected void computeElevatedValues(List batches, Denormal }); log.trace("Computing elevated values (pass #{}) [OK] - {} changes", loopCounter, changesCount); - } while (changesCount.intValue() > 0); + } while (changesCount.intValue() > 0 && loopCounter.intValue() < maxLoop); } protected void computeIndirectElevatedValues(List batches, DenormalizedBatchOptions options) { @@ -715,6 +728,8 @@ protected void computeIndirectElevatedValues(List batches, MutableInt changesCount = new MutableInt(0); MutableInt loopCounter = new MutableInt(0); + int maxLoop = 1; // TODO check this value + do { changesCount.setValue(0); loopCounter.increment(); @@ -761,7 +776,7 @@ protected void computeIndirectElevatedValues(List batches, }); log.trace("Computing indirect elevated values (pass #{}) [OK] - {} changes", loopCounter, changesCount); - } while (changesCount.intValue() > 0); + } while (changesCount.intValue() > 0 && loopCounter.intValue() < maxLoop); } protected Optional computeRtpContextWeight(TempDenormalizedBatchVO batch, DenormalizedBatchOptions options) { @@ -1289,7 +1304,7 @@ protected Optional computeAliveWeightFactor(TempDenormalizedBatchVO batc .taxonGroupIds(new Integer[]{taxonGroupId}) .dressingIds(new Integer[]{dressingId}) .preservingIds(new Integer[]{preservationId}) - .locationIds(new Integer[]{options.getRoundWeightCountryLocationId()}) + .locationIds(new Integer[]{options.getAliveWeightCountryLocationId()}) .date(options.getDay()) .build()); @@ -1298,7 +1313,7 @@ protected Optional computeAliveWeightFactor(TempDenormalizedBatchVO batc taxonGroupId, dressingId, preservationId, - options.getRoundWeightCountryLocationId()); + options.getAliveWeightCountryLocationId()); } diff --git a/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizedTripServiceImpl.java b/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizedTripServiceImpl.java index 7d3cd4c9d3..a0b71c954a 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizedTripServiceImpl.java +++ b/sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizedTripServiceImpl.java @@ -68,7 +68,8 @@ public DenormalizedTripResultVO denormalizeByFilter(@NonNull TripFilterVO filter } @Override - public DenormalizedTripResultVO denormalizeByFilter(@NonNull TripFilterVO tripFilter, @NonNull IProgressionModel progression) { + public DenormalizedTripResultVO denormalizeByFilter(@NonNull TripFilterVO tripFilter, + @NonNull IProgressionModel progression) { long startTime = System.currentTimeMillis(); progression.setCurrent(0); @@ -111,8 +112,7 @@ public DenormalizedTripResultVO denormalizeByFilter(@NonNull TripFilterVO tripFi } // Denormalize each trip - trips.stream().parallel() - .forEach(trip -> { + trips.parallelStream().forEach(trip -> { // Load denormalized options DenormalizedBatchOptions programOptions = denormalizedOperationService.createOptionsByProgramId(trip.getProgram().getId()); diff --git a/sumaris-core/src/main/java/net/sumaris/core/service/technical/JobExecutionService.java b/sumaris-core/src/main/java/net/sumaris/core/service/technical/JobExecutionService.java index c36c8de456..885b2900b2 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/service/technical/JobExecutionService.java +++ b/sumaris-core/src/main/java/net/sumaris/core/service/technical/JobExecutionService.java @@ -30,13 +30,16 @@ import java.util.concurrent.Callable; import java.util.concurrent.Future; +import java.util.function.BiFunction; import java.util.function.Function; public interface JobExecutionService { - JobVO run(JobVO job, Callable configurationLoader, + JobVO run(JobVO job, + Callable configurationLoader, Function> asyncMethod); - JobVO run(JobVO job, Function> callableFuture); + JobVO run(JobVO job, + Function> callableFuture); Observable watchJobProgression(Integer id); diff --git a/sumaris-core/src/main/java/net/sumaris/core/service/technical/JobExecutionServiceImpl.java b/sumaris-core/src/main/java/net/sumaris/core/service/technical/JobExecutionServiceImpl.java index 7b2e8c09aa..4ecadaa44c 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/service/technical/JobExecutionServiceImpl.java +++ b/sumaris-core/src/main/java/net/sumaris/core/service/technical/JobExecutionServiceImpl.java @@ -71,6 +71,7 @@ import java.util.Map; import java.util.Optional; import java.util.concurrent.*; +import java.util.function.BiFunction; import java.util.function.Consumer; import java.util.function.Function; import java.util.stream.Collectors; @@ -166,7 +167,6 @@ public Future start(final JobVO job, // Create progression model and listener to throttle events ProgressionModel progressionModel = new ProgressionModel(); - job.setProgressionModel(progressionModel); // Create listeners to throttle events io.reactivex.rxjava3.core.Observable progressionObservable = Observable.create(emitter -> { diff --git a/sumaris-core/src/main/java/net/sumaris/core/vo/data/batch/DenormalizedBatchOptions.java b/sumaris-core/src/main/java/net/sumaris/core/vo/data/batch/DenormalizedBatchOptions.java index e9847ad381..5831b4f899 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/vo/data/batch/DenormalizedBatchOptions.java +++ b/sumaris-core/src/main/java/net/sumaris/core/vo/data/batch/DenormalizedBatchOptions.java @@ -58,12 +58,15 @@ public static DenormalizedBatchOptions nullToDefault(@Nullable DenormalizedBatch @Builder.Default private boolean enableRtpWeight = false; + @Builder.Default + private boolean enableAliveWeight = true; + @Builder.Default private boolean allowZeroWeightWithIndividual = true; private Integer[] taxonGroupIdsNoWeight; - private Integer roundWeightCountryLocationId; // Country location, used to find a round weight conversion + private Integer aliveWeightCountryLocationId; // Country location, used to find a alive weight conversion private Integer[] fishingAreaLocationIds; // Fishing areas used to find a weight length conversion diff --git a/sumaris-core/src/main/java/net/sumaris/core/vo/technical/job/JobVO.java b/sumaris-core/src/main/java/net/sumaris/core/vo/technical/job/JobVO.java index 65edf8eb4d..7d86ff4220 100644 --- a/sumaris-core/src/main/java/net/sumaris/core/vo/technical/job/JobVO.java +++ b/sumaris-core/src/main/java/net/sumaris/core/vo/technical/job/JobVO.java @@ -23,9 +23,7 @@ */ import com.fasterxml.jackson.annotation.JsonIgnore; -import lombok.Data; -import lombok.EqualsAndHashCode; -import lombok.ToString; +import lombok.*; import lombok.experimental.FieldNameConstants; import net.sumaris.core.model.IProgressionModel; import net.sumaris.core.model.IUpdateDateEntity; @@ -39,6 +37,9 @@ @FieldNameConstants @EqualsAndHashCode(onlyExplicitlyIncluded = true) @ToString(onlyExplicitlyIncluded = true) +@Builder +@AllArgsConstructor +@RequiredArgsConstructor public class JobVO implements IValueObject, IUpdateDateEntity, Comparable { @@ -65,9 +66,6 @@ public class JobVO implements private Date updateDate; - @JsonIgnore - private IProgressionModel progressionModel; - @Override public int compareTo(JobVO o) { return this.hashCode() - o.hashCode(); diff --git a/sumaris-core/src/main/resources/i18n/sumaris-core_fr_FR.properties b/sumaris-core/src/main/resources/i18n/sumaris-core_fr_FR.properties index 444bcc8da0..9d1ae385b1 100644 --- a/sumaris-core/src/main/resources/i18n/sumaris-core_fr_FR.properties +++ b/sumaris-core/src/main/resources/i18n/sumaris-core_fr_FR.properties @@ -162,11 +162,11 @@ sumaris.persistence.table.taxonGroupType=TAXON_GROUP_TYPE sumaris.persistence.table.taxonName=TAXON_NAME sumaris.persistence.table.taxonomicLevel=TAXONOMIC_LEVEL sumaris.persistence.table.transcribingItem=TRANSCRIBING_ITEM -sumaris.persistence.table.transcribingItemType= -sumaris.persistence.table.transcribingSystem= +sumaris.persistence.table.transcribingItemType=TRANSCRIBING_ITEM_TYPE +sumaris.persistence.table.transcribingSystem=TRANSCRIBING_SYSTEM sumaris.persistence.table.trip=TRIP sumaris.persistence.table.unit=UNIT -sumaris.persistence.table.unitConversion= +sumaris.persistence.table.unitConversion=UNIT_CONVERSION sumaris.persistence.table.userProfile=USER_PROFILE sumaris.persistence.table.userSettings=USER_SETTINGS sumaris.persistence.table.vesselFeatures=VESSEL_FEATURES diff --git a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/adap/db-changelog-2.1.0.xml b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/adap/db-changelog-2.1.0.xml index f6ed32b1c6..c0ac6a884f 100644 --- a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/adap/db-changelog-2.1.0.xml +++ b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/adap/db-changelog-2.1.0.xml @@ -67,20 +67,5 @@ ]]> - - - - - - - - - - - - - - - diff --git a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/adap/db-changelog-2.1.1.xml b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/adap/db-changelog-2.1.1.xml new file mode 100644 index 0000000000..8c6ce5c0f3 --- /dev/null +++ b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/adap/db-changelog-2.1.1.xml @@ -0,0 +1,162 @@ + + + + + + + + + + + ${sqlCheck.empty.sql} + + ${sqlCheck.adap.sql} + + + + + + + ${sqlCheck.adap.sql} + + SELECT COUNT(*) from SOFTWARE_PROPERTY where LABEL='sumaris.enumeration.QualitativeValue.SEX_UNSEXED.id' AND SOFTWARE_FK=2 + + + SELECT COUNT(*) from QUALITATIVE_VALUE WHERE UPPER(NAME)='NON SEXE' + + + + + + + + + + + + + + + + + + + ${sqlCheck.adap.sql} + + + select count(*) from sorting_measurement_b + where (numerical_value - TRUNC(numerical_value)) = 0.5 + and pmfm_fk=81 + + + + + + + + + + + + ${sqlCheck.adap.sql} + + + select count(*) from taxon_group where label='HAD' and comments='' + + + + + + + + + + + + + + + + ${sqlCheck.adap.sql} + + SELECT COUNT(*) from METHOD where LABEL='MEASURED_IN_CM_BY_OBSERVER' OR ID=82 + + + + + + + + + + + + + + + + + + + ${sqlCheck.adap.sql} + + SELECT COUNT(*) from METHOD where LABEL='MEASURED_IN_MM_BY_OBSERVER' OR ID=83 + + + + + + + + + + + + + + + + + + + ${sqlCheck.adap.sql} + SELECT COUNT(*) from PMFM where LABEL='LENGTH_TOTAL_CM' AND MAXIMUM_NUMBER_DECIMALS=1 + + + + + + diff --git a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/db-changelog-2.1.1.xml b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/db-changelog-2.1.1.xml new file mode 100644 index 0000000000..51c5858134 --- /dev/null +++ b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/db-changelog-2.1.1.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + LABEL='2.1.1' + + + + 2.1.1 + + - Add UNSEXED enumeration option, in configuration; + - Fix ADAP pmfm LENGTH_TOTAL_CM; + + + + + - Add UNSEXED enumeration option, in configuration; + - Fix ADAP pmfm LENGTH_TOTAL_CM; + + + + diff --git a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/db-changelog.xml b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/db-changelog.xml index 05c1739b5d..6a2845542b 100644 --- a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/db-changelog.xml +++ b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/db-changelog.xml @@ -177,6 +177,9 @@ + + + diff --git a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/sumaris.script b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/sumaris.script index 032decf603..9a0831e892 100644 --- a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/sumaris.script +++ b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/hsqldb/sumaris.script @@ -198,7 +198,7 @@ CREATE CACHED TABLE PUBLIC.ORDER_TYPE(ID INTEGER NOT NULL PRIMARY KEY,COMMENTS V CREATE CACHED TABLE PUBLIC.ORIGIN_ITEM_TYPE(ID INTEGER NOT NULL PRIMARY KEY,COMMENTS VARCHAR(2000),CREATION_DATE TIMESTAMP NOT NULL,DESCRIPTION VARCHAR(255),LABEL VARCHAR(50) NOT NULL,NAME VARCHAR(100) NOT NULL,UPDATE_DATE TIMESTAMP,STATUS_FK INTEGER NOT NULL) CREATE CACHED TABLE PUBLIC.P01_RDB_LANDING(ID INTEGER NOT NULL PRIMARY KEY,AREA VARCHAR(25) NOT NULL,COMMERCIAL_SIZE_CATEGORY VARCHAR(25),COMMERCIAL_SIZE_CATEGORY_SCALE VARCHAR(25),HARBOUR VARCHAR(25),LANDING_CATEGORY VARCHAR(25) NOT NULL,LANDING_COUNTRY VARCHAR(3) NOT NULL,LANDINGS_MULTIPLIER DOUBLE,OFFICIAL_LANDINGS_VALUE DOUBLE,OFFICIAL_LANDINGS_WEIGHT DOUBLE NOT NULL,EU_METIER_LEVEL5 VARCHAR(25),EU_METIER_LEVEL6 VARCHAR(25) NOT NULL,AREA_MISREPORTED_CATCH_WEIGHT DOUBLE NOT NULL,MONTH INTEGER,NATIONAL_METIER VARCHAR(25),QUARTER INTEGER NOT NULL,SPECIES VARCHAR(25) NOT NULL,STATISTICAL_RECTANGLE VARCHAR(25),SUB_POLYGON VARCHAR(25),UNALLOCATED_CATCH_WEIGHT DOUBLE NOT NULL,VESSEL_FLAG_COUNTRY VARCHAR(3) NOT NULL,VESSEL_LENGTH_CATEGORY VARCHAR(25),YEAR INTEGER NOT NULL) CREATE CACHED TABLE PUBLIC.P01_RDB_SPECIES_LENGTH(ID INTEGER NOT NULL PRIMARY KEY,CATCH_CATEGORY VARCHAR(25) NOT NULL,COMMERCIAL_SIZE_CATEGORY VARCHAR(25),COMMERCIAL_SIZE_CATEGORY_SCALE VARCHAR(25),INDIVIDUAL_SEX VARCHAR(1),LANDING_CATEGORY VARCHAR(25) NOT NULL,LANDING_COUNTRY VARCHAR(3) NOT NULL,LENGTH_CLASS INTEGER,NUMBER_AT_LENGTH INTEGER,PROJECT VARCHAR(255) NOT NULL,SAMPLING_TYPE VARCHAR(2) NOT NULL,SEX VARCHAR(1),SPECIES VARCHAR(100) NOT NULL,STATION_NUMBER INTEGER,SUBSAMPLING_CATEGORY VARCHAR(25),TRIP_CODE VARCHAR(50) NOT NULL,VESSEL_FLAG_COUNTRY VARCHAR(3) NOT NULL,YEAR INTEGER NOT NULL) -CREATE CACHED TABLE PUBLIC.P01_RDB_SPECIES_LIST(ID INTEGER NOT NULL PRIMARY KEY,CATCH_CATEGORY VARCHAR(25) NOT NULL,COMMERCIAL_SIZE_CATEGORY VARCHAR(25),COMMERCIAL_SIZE_CATEGORY_SCALE VARCHAR(25),LANDING_CATEGORY VARCHAR(25) NOT NULL,LANDING_COUNTRY VARCHAR(3) NOT NULL,LENGTH_CODE VARCHAR(5),PROJECT VARCHAR(255) NOT NULL,SAMPLING_TYPE VARCHAR(2) NOT NULL,SEX VARCHAR(1),SPECIES VARCHAR(100) NOT NULL,STATION_NUMBER INTEGER,SUBSAMPLING_CATEGORY VARCHAR(25),SUBSAMPLING_WEIGHT DOUBLE,TRIP_CODE VARCHAR(50) NOT NULL,VESSEL_FLAG_COUNTRY VARCHAR(3) NOT NULL,WEIGHT DOUBLE NOT NULL,YEAR INTEGER NOT NULL) +CREATE CACHED TABLE PUBLIC.P01_RDB_SPECIES_LIST(ID INTEGER NOT NULL PRIMARY KEY,CATCH_CATEGORY VARCHAR(25) NOT NULL,COMMERCIAL_SIZE_CATEGORY VARCHAR(25),COMMERCIAL_SIZE_CATEGORY_SCALE VARCHAR(25),LANDING_CATEGORY VARCHAR(25) NOT NULL,LANDING_COUNTRY VARCHAR(3) NOT NULL,LENGTH_CODE VARCHAR(5),PROJECT VARCHAR(255) NOT NULL,SAMPLING_TYPE VARCHAR(2) NOT NULL,SEX VARCHAR(1),SPECIES VARCHAR(100) NOT NULL,STATION_NUMBER INTEGER,SUBSAMPLING_CATEGORY VARCHAR(25),SUBSAMPLE_WEIGHT DOUBLE,TRIP_CODE VARCHAR(50) NOT NULL,VESSEL_FLAG_COUNTRY VARCHAR(3) NOT NULL,WEIGHT DOUBLE NOT NULL,YEAR INTEGER NOT NULL) CREATE CACHED TABLE PUBLIC.P01_RDB_STATION(ID INTEGER NOT NULL PRIMARY KEY,AGGREGATION_LEVEL VARCHAR(1),AREA VARCHAR(25) NOT NULL,CATCH_REGISTRATION VARCHAR(3) NOT NULL,DATE VARCHAR(10),FISHING_TIME INTEGER,FISHING_VALIDITY VARCHAR(1),GEAR_TYPE VARCHAR(5) NOT NULL,LANDING_COUNTRY VARCHAR(3) NOT NULL,MAIN_FISHING_DEPTH INTEGER,MAIN_WATER_DEPTH INTEGER,MESH_SIZE INTEGER,MESH_SIZE_SELECTION_DEVICE INTEGER,EU_METIER_LEVEL5 VARCHAR(25),EU_METIER_LEVEL6 VARCHAR(25) NOT NULL,NATIONAL_METIER VARCHAR(25),POS_END_LAT DOUBLE,POS_END_LON DOUBLE,POS_START_LAT DOUBLE,POS_START_LON DOUBLE,PROJECT VARCHAR(255) NOT NULL,SAMPLING_TYPE VARCHAR(2) NOT NULL,SELECTION_DEVICE INTEGER,SPECIES_REGISTRATION VARCHAR(25),STATION_NUMBER INTEGER,STATISTICAL_RECTANGLE VARCHAR(25),SUB_POLYGON VARCHAR(25),TIME VARCHAR(8),TRIP_CODE VARCHAR(50) NOT NULL,VESSEL_FLAG_COUNTRY VARCHAR(3) NOT NULL,YEAR INTEGER NOT NULL) CREATE CACHED TABLE PUBLIC.P01_RDB_TRIP(ID INTEGER NOT NULL PRIMARY KEY,DAYS_AT_SEA INTEGER,HARBOUR VARCHAR(50),LANDING_COUNTRY VARCHAR(3) NOT NULL,NUMBER_OF_SETS INTEGER,PROJECT VARCHAR(255) NOT NULL,SAMPLING_COUNTRY VARCHAR(3) NOT NULL,SAMPLING_METHOD VARCHAR(50),SAMPLING_TYPE VARCHAR(2) NOT NULL,TRIP_CODE VARCHAR(50) NOT NULL,VESSEL_FLAG_COUNTRY VARCHAR(3) NOT NULL,VESSEL_IDENTIFIER INTEGER,VESSEL_LENGTH INTEGER,VESSEL_POWER INTEGER,VESSEL_SIZE INTEGER,VESSEL_TYPE INTEGER NOT NULL,YEAR INTEGER NOT NULL) CREATE CACHED TABLE PUBLIC.PARAMETER(ID INTEGER NOT NULL PRIMARY KEY,COMMENTS VARCHAR(2000),CREATION_DATE TIMESTAMP NOT NULL,DESCRIPTION VARCHAR(255),IS_ALPHANUMERIC BOOLEAN NOT NULL,IS_BOOLEAN BOOLEAN,IS_DATE BOOLEAN,IS_QUALITATIVE BOOLEAN NOT NULL,LABEL VARCHAR(50) NOT NULL,NAME VARCHAR(100) NOT NULL,UPDATE_DATE TIMESTAMP,PARAMETER_GROUP_FK INTEGER NOT NULL,STATUS_FK INTEGER NOT NULL,CONSTRAINT UK_CB7YUSYNI4XXOEAJ8JJ7I8L4Y UNIQUE(LABEL)) diff --git a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/postgresql/db-changelog-2.1.1.xml b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/postgresql/db-changelog-2.1.1.xml new file mode 100644 index 0000000000..74710d82d0 --- /dev/null +++ b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/postgresql/db-changelog-2.1.1.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + + + + LABEL='2.1.1' + + + + 2.1.1 + + - Extraction: rename SUBSAMPLING_WEIGHT into SUBSAMPLE_WEIGHT; + - Extraction: Create missing sequence denormalized_batch_sort_va_seq; + + + + + - Extraction: rename SUBSAMPLING_WEIGHT into SUBSAMPLE_WEIGHT; + - Extraction: Create missing sequence denormalized_batch_sort_va_seq; + + + + diff --git a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/postgresql/db-changelog.xml b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/postgresql/db-changelog.xml index f9051c850c..0068dc825f 100644 --- a/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/postgresql/db-changelog.xml +++ b/sumaris-core/src/main/resources/net/sumaris/core/db/changelog/postgresql/db-changelog.xml @@ -58,6 +58,8 @@ + + diff --git a/sumaris-core/src/test/java/net/sumaris/core/service/technical/JobServiceWriteTest.java b/sumaris-core/src/test/java/net/sumaris/core/service/technical/JobServiceWriteTest.java index 609ed5e193..a666a665b7 100644 --- a/sumaris-core/src/test/java/net/sumaris/core/service/technical/JobServiceWriteTest.java +++ b/sumaris-core/src/test/java/net/sumaris/core/service/technical/JobServiceWriteTest.java @@ -106,12 +106,11 @@ private JobVO createSystemJob() { } private JobVO createJob(String issuer) { - JobVO target = new JobVO(); - target.setName("Extraction test job"); - target.setType(ProcessingTypeEnum.SIOP_VESSELS_IMPORTATION.getLabel()); - target.setIssuer(issuer); - target.setStatus(JobStatusEnum.PENDING); - - return target; + return JobVO.builder() + .name("Extraction test job") + .type(ProcessingTypeEnum.SIOP_VESSELS_IMPORTATION.getLabel()) + .issuer(issuer) + .status(JobStatusEnum.PENDING) + .build(); } } diff --git a/sumaris-core/src/test/resources/application-test-hsqldb.properties b/sumaris-core/src/test/resources/application-test-hsqldb.properties index b60bb3fafa..46e1403fdc 100644 --- a/sumaris-core/src/test/resources/application-test-hsqldb.properties +++ b/sumaris-core/src/test/resources/application-test-hsqldb.properties @@ -16,7 +16,7 @@ spring.main.web-application-type=none spring.main.allow-circular-references=true # DataSource configuration -spring.datasource.platform=hsqldb +spring.sql.init.platform=hsqldb spring.datasource.initialization-mode=always spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver spring.datasource.username=sa diff --git a/sumaris-core/src/test/resources/application-test-oracle.properties b/sumaris-core/src/test/resources/application-test-oracle.properties index 740e44d44f..0548d14373 100644 --- a/sumaris-core/src/test/resources/application-test-oracle.properties +++ b/sumaris-core/src/test/resources/application-test-oracle.properties @@ -18,7 +18,7 @@ spring.main.web-application-type=none spring.main.allow-circular-references=true # DataSource configuration -spring.datasource.platform=oracle +spring.sql.init.platform=oracle spring.datasource.driver-class-name=oracle.jdbc.driver.OracleDriver spring.datasource.url=jdbc:oracle:thin:@192.168.0.33:1521:ORCL #spring.datasource.url=jdbc:oracle:thin:@vm-oracle-sfa:1521/orcl diff --git a/sumaris-core/src/test/resources/application-test-pgsql.properties b/sumaris-core/src/test/resources/application-test-pgsql.properties index ec25437ef3..e61d19682c 100644 --- a/sumaris-core/src/test/resources/application-test-pgsql.properties +++ b/sumaris-core/src/test/resources/application-test-pgsql.properties @@ -16,7 +16,7 @@ spring.main.web-application-type=none spring.main.allow-circular-references=true # DataSource configuration -spring.datasource.platform=pgsql +spring.sql.init.platform=pgsql spring.datasource.initialization-mode=always spring.datasource.driver-class-name=org.postgresql.Driver spring.datasource.hikari.connectionTestQuery=SELECT 1 FROM STATUS WHERE ID=1 diff --git a/sumaris-extraction/pom.xml b/sumaris-extraction/pom.xml index b871b8d5c9..707ba2dc98 100644 --- a/sumaris-extraction/pom.xml +++ b/sumaris-extraction/pom.xml @@ -5,7 +5,7 @@ net.sumaris sumaris-pod - 2.1.0 + 2.1.1 sumaris-extraction @@ -28,6 +28,11 @@ sumaris-core ${project.version} + + net.sumaris + sumaris-xml-query + ${project.version} + org.springframework spring-web @@ -52,20 +57,6 @@ lombok - - - fr.ifremer.common - xmlquery - - - org.jdom - jdom2 - - - jaxen - jaxen - - net.sf.opencsv diff --git a/sumaris-extraction/src/main/java/net/sumaris/extraction/cli/action/ExtractionExecuteAction.java b/sumaris-extraction/src/main/java/net/sumaris/extraction/cli/action/ExtractionExecuteAction.java index 5da157177f..b48e649c4d 100644 --- a/sumaris-extraction/src/main/java/net/sumaris/extraction/cli/action/ExtractionExecuteAction.java +++ b/sumaris-extraction/src/main/java/net/sumaris/extraction/cli/action/ExtractionExecuteAction.java @@ -26,17 +26,21 @@ import lombok.extern.slf4j.Slf4j; import net.sumaris.cli.action.ActionUtils; +import net.sumaris.core.util.Dates; import net.sumaris.extraction.core.config.ExtractionConfiguration; import net.sumaris.extraction.core.exception.UnknownFormatException; import net.sumaris.extraction.core.service.*; +import net.sumaris.extraction.core.type.LiveExtractionTypeEnum; import net.sumaris.extraction.core.util.ExtractionTypes; import net.sumaris.core.model.technical.extraction.IExtractionType; import net.sumaris.core.util.Files; import net.sumaris.core.util.StringUtils; import net.sumaris.core.util.TimeUtils; +import net.sumaris.extraction.core.vo.trip.ExtractionTripFilterVO; import java.io.File; import java.io.IOException; +import java.util.Arrays; import java.util.stream.Collectors; /** @@ -52,7 +56,7 @@ public class ExtractionExecuteAction { public void run() { ExtractionConfiguration config = ExtractionConfiguration.instance(); ExtractionTypeService extractionTypeService = ExtractionServiceLocator.extractionTypeService(); - ExtractionService service = ExtractionServiceLocator.extractionManager(); + ExtractionService service = ExtractionServiceLocator.extractionService(); String format = config.getExtractionCliOutputFormat(); IExtractionType type; @@ -70,6 +74,7 @@ public void run() { return; } + log.info("Starting {} extraction...", StringUtils.capitalize(type.getFormat().toLowerCase())); @@ -80,8 +85,24 @@ public void run() { long startTime = System.currentTimeMillis(); File tempFile; try { - tempFile = service.executeAndDump(type, null, null); - if (!tempFile.exists()) { + boolean isLiveTrips = ExtractionTypes.isLive(type) && ExtractionTypes.isOnTrips(type); + if (isLiveTrips) { + LiveExtractionTypeEnum liveFormat = LiveExtractionTypeEnum.valueOf(type.getFormat()); + ExtractionTripFilterVO filter = new ExtractionTripFilterVO(); + filter.setProgramLabel(config.getCliFilterProgramLabel()); + filter.setIncludedIds(config.getCliFilterTripIds().toArray(Integer[]::new)); + filter.setOperationIds(config.getCliFilterOperationIds().toArray(Integer[]::new)); + Integer year = config.getCliFilterYear(); + if (year != null && year > 1970) { + filter.setStartDate(Dates.getFirstDayOfYear(year)); + filter.setEndDate(Dates.getLastSecondOfYear(year)); + } + tempFile = service.executeAndDumpTrips(liveFormat, filter); + } + else { + tempFile = service.executeAndDump(type, null, null); + } + if (tempFile != null && !tempFile.exists()) { log.error("No data"); return; } diff --git a/sumaris-extraction/src/main/java/net/sumaris/extraction/cli/action/ExtractionUpdateAction.java b/sumaris-extraction/src/main/java/net/sumaris/extraction/cli/action/ExtractionUpdateAction.java index 07f4febbed..e2f8f8d3bf 100644 --- a/sumaris-extraction/src/main/java/net/sumaris/extraction/cli/action/ExtractionUpdateAction.java +++ b/sumaris-extraction/src/main/java/net/sumaris/extraction/cli/action/ExtractionUpdateAction.java @@ -43,7 +43,7 @@ public class ExtractionUpdateAction { public void run() throws InterruptedException { // Create the job - ExtractionService manager = ExtractionServiceLocator.extractionManager(); + ExtractionService manager = ExtractionServiceLocator.extractionService(); // Run it ! ProcessingFrequencyEnum frequency = ExtractionConfiguration.instance().getExtractionCliFrequency(); diff --git a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/config/ExtractionConfiguration.java b/sumaris-extraction/src/main/java/net/sumaris/extraction/core/config/ExtractionConfiguration.java index 5a556fc2e2..fb56014d79 100644 --- a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/config/ExtractionConfiguration.java +++ b/sumaris-extraction/src/main/java/net/sumaris/extraction/core/config/ExtractionConfiguration.java @@ -34,6 +34,7 @@ import java.io.File; import java.util.Arrays; +import java.util.List; @Slf4j public class ExtractionConfiguration { @@ -61,15 +62,33 @@ public ExtractionConfiguration(SumarisConfiguration configuration){ setInstance(this); // Define Alias - addAlias(this.delegate.getApplicationConfig()); + // Already done by provider class + //addAlias(this.delegate.getApplicationConfig()); } + public boolean isProduction() { + return this.delegate.isProduction(); + } + public String getExtractionCliOutputFormat() { return getApplicationConfig().getOption(ExtractionConfigurationOption.EXTRACTION_CLI_OUTPUT_FORMAT.getKey()); } + public String getCliFilterProgramLabel() { + return delegate.getCliFilterProgramLabel(); + } + public List getCliFilterTripIds() { + return delegate.getCliFilterTripIds(); + } + public List getCliFilterOperationIds() { + return delegate.getCliFilterOperationIds(); + } + public Integer getCliFilterYear() { + return delegate.getCliFilterYear(); + } + public ProcessingFrequencyEnum getExtractionCliFrequency() { String value = getApplicationConfig().getOption(ExtractionConfigurationOption.EXTRACTION_CLI_FREQUENCY.getKey()); try { @@ -151,7 +170,7 @@ public char getCsvSeparator() { */ protected void addAlias(ApplicationConfig applicationConfig) { // CLI options - applicationConfig.addAlias("-format", "--option", ExtractionConfigurationOption.EXTRACTION_CLI_OUTPUT_FORMAT.getKey()); - applicationConfig.addAlias("-frequency", "--option", ExtractionConfigurationOption.EXTRACTION_CLI_FREQUENCY.getKey()); + applicationConfig.addAlias("--format", "--option", ExtractionConfigurationOption.EXTRACTION_CLI_OUTPUT_FORMAT.getKey()); + applicationConfig.addAlias("--frequency", "--option", ExtractionConfigurationOption.EXTRACTION_CLI_FREQUENCY.getKey()); } } diff --git a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/config/ExtractionConfigurationProvider.java b/sumaris-extraction/src/main/java/net/sumaris/extraction/core/config/ExtractionConfigurationProvider.java index 0ca58f0856..7cf242023d 100644 --- a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/config/ExtractionConfigurationProvider.java +++ b/sumaris-extraction/src/main/java/net/sumaris/extraction/core/config/ExtractionConfigurationProvider.java @@ -24,7 +24,9 @@ * #L% */ +import net.sumaris.core.config.ApplicationConfigAliasProvider; import net.sumaris.extraction.cli.config.ExtractionConfigurationAction; +import org.nuiton.config.ApplicationConfig; import org.nuiton.config.ApplicationConfigProvider; import org.nuiton.config.ConfigActionDef; import org.nuiton.config.ConfigOptionDef; @@ -39,7 +41,7 @@ * @author Benoit Lavenier * @since 1.0 */ -public class ExtractionConfigurationProvider implements ApplicationConfigProvider { +public class ExtractionConfigurationProvider implements ApplicationConfigProvider, ApplicationConfigAliasProvider { /** {@inheritDoc} */ @Override @@ -64,4 +66,11 @@ public ConfigOptionDef[] getOptions() { public ConfigActionDef[] getActions() { return ExtractionConfigurationAction.values(); } + + @Override + public void addAlias(ApplicationConfig applicationConfig) { + // CLI options + applicationConfig.addAlias("--format", "--option", ExtractionConfigurationOption.EXTRACTION_CLI_OUTPUT_FORMAT.getKey()); + applicationConfig.addAlias("--frequency", "--option", ExtractionConfigurationOption.EXTRACTION_CLI_FREQUENCY.getKey()); + } } diff --git a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/ExtractionBaseDaoImpl.java b/sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/ExtractionBaseDaoImpl.java index 42b0a19a3a..0bae9034bd 100644 --- a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/ExtractionBaseDaoImpl.java +++ b/sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/ExtractionBaseDaoImpl.java @@ -30,11 +30,11 @@ import net.sumaris.core.dao.technical.DatabaseType; import net.sumaris.core.dao.technical.Page; import net.sumaris.core.dao.technical.hibernate.HibernateDaoSupport; -import net.sumaris.core.model.IEntity; import net.sumaris.core.dao.technical.schema.SumarisDatabaseMetadata; import net.sumaris.core.dao.technical.schema.SumarisTableMetadata; import net.sumaris.core.exception.DataNotFoundException; import net.sumaris.core.exception.SumarisTechnicalException; +import net.sumaris.core.model.IEntity; import net.sumaris.core.model.referential.IItemReferentialEntity; import net.sumaris.core.service.referential.ReferentialService; import net.sumaris.core.util.Beans; @@ -45,14 +45,19 @@ import net.sumaris.extraction.core.dao.technical.Daos; import net.sumaris.extraction.core.dao.technical.schema.SumarisTableMetadatas; import net.sumaris.extraction.core.dao.technical.table.ExtractionTableColumnOrder; -import net.sumaris.extraction.core.dao.technical.xml.XMLQuery; import net.sumaris.extraction.core.util.ExtractionProducts; import net.sumaris.extraction.core.vo.ExtractionContextVO; import net.sumaris.extraction.core.vo.ExtractionFilterVO; import net.sumaris.extraction.core.vo.ExtractionResultVO; +import net.sumaris.xml.query.XMLQuery; +import net.sumaris.xml.query.XMLQueryImpl; import org.apache.commons.collections4.CollectionUtils; +import org.apache.commons.collections4.MapUtils; import org.apache.commons.collections4.SetUtils; import org.hibernate.dialect.Dialect; +import org.jdom2.Element; +import org.jdom2.Text; +import org.jdom2.filter.Filters; import org.nuiton.i18n.I18n; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.ApplicationContext; @@ -79,6 +84,7 @@ public abstract class ExtractionBaseDaoImpl void clean(C context) { + // DEBUG + //log.warn("TODO: drop table after an extraction - uncomment code here !!"); dropTables(context); } @@ -266,8 +277,8 @@ protected Integer getReferentialIdByUniqueLabel(Class void dropTables(@NonNull C context) { @@ -530,6 +541,16 @@ public List getColumns(String tableName, ExtractionTabl } protected int execute(C context, XMLQuery xmlQuery) { + + // Always disable injectionPoint group to avoid injection point staying on final xml query (if not used to inject pmfm) + xmlQuery.setGroup("injectionPoint", false); + + // Generate then bind group by columns + if (StringUtils.isNotBlank(xmlQuery.getGroupByParamName())) { + computeAndBindGroupBy(xmlQuery); + } + + // Get the SQL String sql = xmlQuery.getSQLQueryAsString(); // Do column names replacement (e.g. see FREE extraction) @@ -568,7 +589,7 @@ protected XMLQuery createXMLQuery(C context, String queryName) { } protected XMLQuery createXMLQuery(String queryName) { - XMLQuery query = createXMLQuery(); + XMLQueryImpl query = createXMLQuery(); query.setQuery(getXMLQueryClasspathURL(queryName)); return query; } @@ -588,4 +609,60 @@ protected URL getXMLQueryClasspathURL(String queryName) { } } + protected void computeAndBindGroupBy(XMLQuery xmlQuery) { + computeAndBindGroupBy(xmlQuery, xmlQuery.getGroupByParamName()); + } + + protected void computeAndBindGroupBy(XMLQuery xmlQuery, @NonNull String paramName) { + // Check a tag exists with the expected parameter name + if (!this.production) { + List matchesGroupBy = xmlQuery.getGroupByTags(element -> { + String content = Beans.getStream(element.getContent(Filters.text())) + .map(Text::getValue) + .collect(Collectors.joining("\n")); + return content.contains("&" + paramName); + }); + if (CollectionUtils.isEmpty(matchesGroupBy)) { + log.warn("Unable to found a with parameter '&{}'", paramName); + } + } + + // Get groupBy columns + String groupByColumns = xmlQuery.streamSelectElements(e -> { + // Exclude column with group 'agg' + boolean isAgg = xmlQuery.hasGroup(e, "agg"); + if (isAgg) { + // Remove the agg group, to avoid the element to be disabled + xmlQuery.removeGroup(e, "agg"); + return false; + } + + // Exclude disabled columns (by group) + return !xmlQuery.isDisabled(e); + }) + .map(e -> { + // Exclude pmfm columns + //String alias = xmlQuery.getAlias(e); + // if (alias == null || alias.startsWith("&pmfmlabel")) return null; + + // Prefer using ST.SPECIES_CODE - + &stationTableName - MIN(ID) - + + + &rawSpeciesListTableName @@ -63,8 +63,8 @@ - ID - + + &rawSpeciesLengthTableName diff --git a/sumaris-extraction/src/main/resources/xmlQuery/aggRdb/v1_3/createSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/aggRdb/v1_3/createSpeciesListTable.xml index 1c4848ac3a..bf36b7df75 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/aggRdb/v1_3/createSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/aggRdb/v1_3/createSpeciesListTable.xml @@ -63,7 +63,7 @@ - + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/aggRdb/v1_3/createStationTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/aggRdb/v1_3/createStationTable.xml index d6d178b6f9..d07cf82d00 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/aggRdb/v1_3/createStationTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/aggRdb/v1_3/createStationTable.xml @@ -26,9 +26,9 @@ - T.TRIP_CODE - T.VESSEL_IDENTIFIER - T.TRIP_CODE + + - T.NUMBER_OF_SETS - (SELECT SUM(FISHING_TIME) FROM &rawStationTableName WHERE TRIP_CODE=T.TRIP_CODE) + + &rawTripTableName diff --git a/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createCatchTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createCatchTable.xml new file mode 100644 index 0000000000..7a4ac81888 --- /dev/null +++ b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createCatchTable.xml @@ -0,0 +1,70 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + &stationTableName + INNER JOIN DENORMALIZED_BATCH CATCH ON CATCH.OPERATION_FK = S.STATION_NUMBER + INNER JOIN QUANTIFICATION_MEASUREMENT_B QM ON QM.BATCH_FK=CATCH.ID AND QM.PMFM_FK=&catchWeightPmfmId AND QM.IS_REFERENCE_QUANTIFICATION=true + LEFT OUTER JOIN DENORMALIZED_BATCH_SORT_VAL SM ON SM.BATCH_FK=CATCH.ID + LEFT OUTER JOIN QUALITATIVE_VALUE QV ON QV.ID=SM.QUALITATIVE_VALUE_FK + + + + 1=1 + + + CATCH.WEIGHT IS NOT NULL + + + + + + &groupByColumns + + STATION_NUMBER ASC + + + + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createGearTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createGearTable.xml new file mode 100644 index 0000000000..ccc70ebff9 --- /dev/null +++ b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createGearTable.xml @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + &tripTableName + INNER JOIN PHYSICAL_GEAR PG ON PG.TRIP_FK = T.TRIP_CODE + INNER JOIN GEAR G ON G.ID = PG.GEAR_FK + LEFT OUTER JOIN PHYSICAL_GEAR PG_PARENT ON PG_PARENT.ID = PG.PARENT_PHYSICAL_GEAR_FK + LEFT OUTER JOIN PHYSICAL_GEAR_MEASUREMENT PGM ON PGM.PHYSICAL_GEAR_FK = PG.ID + LEFT OUTER JOIN QUALITATIVE_VALUE PGQV on PGQV.ID = PGM.QUALITATIVE_VALUE_FK + + 1=1 + + &groupByColumns + + GEAR_IDENTIFIER ASC, SUB_GEAR_IDENTIFIER ASC + + + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createRawSpeciesListDenormalizeTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createRawSpeciesListDenormalizeTable.xml new file mode 100644 index 0000000000..e064970865 --- /dev/null +++ b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/createRawSpeciesListDenormalizeTable.xml @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + &stationTableName + INNER JOIN DENORMALIZED_BATCH CATCH ON CATCH.OPERATION_FK = S.STATION_NUMBER + INNER JOIN DENORMALIZED_BATCH LAN_OR_DIS ON LAN_OR_DIS.PARENT_BATCH_FK = CATCH.ID + INNER JOIN DENORMALIZED_BATCH SPECIE_B ON SPECIE_B.PARENT_BATCH_FK = LAN_OR_DIS.ID + INNER JOIN TAXON_GROUP TG ON TG.ID = SPECIE_B.TAXON_GROUP_FK + LEFT OUTER JOIN DENORMALIZED_BATCH_SORT_VAL SM ON SM.BATCH_FK=SPECIE_B.ID + LEFT OUTER JOIN QUALITATIVE_VALUE QV ON QV.ID=SM.QUALITATIVE_VALUE_FK + LEFT OUTER JOIN DENORMALIZED_BATCH SAMPLING_B ON SAMPLING_B.PARENT_BATCH_FK = SPECIE_B.ID AND SAMPLING_B.SAMPLING_RATIO > 0 + + + LEFT OUTER JOIN DENORMALIZED_BATCH LENGTH_B ON LENGTH_B.PARENT_BATCH_FK=COALESCE(SAMPLING_B.ID, SPECIE_B.ID) + LEFT OUTER JOIN DENORMALIZED_BATCH_SORT_VAL LENGTH_SV ON LENGTH_SV.BATCH_FK=LENGTH_B.ID AND LENGTH_SV.PMFM_FK in (&lengthPmfmIds) AND LENGTH_SV.IS_INHERITED=false + LEFT OUTER JOIN UNIT ON UNIT.ID = LENGTH_SV.UNIT_FK + LEFT OUTER JOIN TAXON_NAME TN ON TN.REFERENCE_TAXON_FK = LENGTH_B.REFERENCE_TAXON_FK + + 1=1 + + + SPECIE_B.ELEVATE_CONTEXT_WEIGHT IS NOT NULL + + + + + + &groupByColumns + + SPECIE_B.ELEVATE_WEIGHT,SAMPLING_B.ELEVATE_RTP_WEIGHT + + STATION_NUMBER ASC, SAMPLE_RANK_ORDER ASC + + + + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionPhysicalGearPmfm.xml b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionPhysicalGearPmfm.xml new file mode 100644 index 0000000000..156dd099ea --- /dev/null +++ b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionPhysicalGearPmfm.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + + + + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionRawSpeciesListPmfm.xml b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionRawSpeciesListPmfm.xml new file mode 100644 index 0000000000..04285daedb --- /dev/null +++ b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionRawSpeciesListPmfm.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + + + + + + + + + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionSpeciesLengthTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionSpeciesLengthTable.xml new file mode 100644 index 0000000000..1748a67ac4 --- /dev/null +++ b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionSpeciesLengthTable.xml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + INNER JOIN DENORMALIZED_BATCH DENORMALIZED_B ON DENORMALIZED_B.ID = B.ID + INNER JOIN SORTING_MEASUREMENT_B SM ON SM.BATCH_FK = B.ID + LEFT OUTER JOIN QUALITATIVE_VALUE QV ON QV.ID = SM.QUALITATIVE_VALUE_FK + + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionStationTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionStationTable.xml new file mode 100644 index 0000000000..b2ae173d9f --- /dev/null +++ b/sumaris-extraction/src/main/resources/xmlQuery/apase/v1_0/injectionStationTable.xml @@ -0,0 +1,30 @@ + + + + + + + + + + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/cost/v1_4/injectionSpeciesLengthTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/cost/v1_4/injectionSpeciesLengthTable.xml index d2e5136dfd..3e965cc947 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/cost/v1_4/injectionSpeciesLengthTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/cost/v1_4/injectionSpeciesLengthTable.xml @@ -27,7 +27,5 @@ - - - B.SEX, LENGTH_CLASS + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionSpeciesLengthTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionSpeciesLengthTable.xml index cba617efa4..82aea108e0 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionSpeciesLengthTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionSpeciesLengthTable.xml @@ -23,14 +23,13 @@ - + - + - B.SEX, LENGTH_CLASS, MEASURE_TYPE diff --git a/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionSpeciesListTable.xml index 8d49968fb5..fa8ee129c4 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionSpeciesListTable.xml @@ -24,7 +24,7 @@ - (CASE WHEN (SL.WEIGHT IS NOT NULL AND SL.WEIGHT > 0) THEN ( SELECT SUM(COALESCE(BL.INDIVIDUAL_COUNT, 1)) diff --git a/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionTripTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionTripTable.xml index a70f7b9a60..711442dafb 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionTripTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/free/v1/injectionTripTable.xml @@ -24,6 +24,7 @@ + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createGearTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createGearTable.xml index b96c64ba8e..f985015515 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createGearTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createGearTable.xml @@ -57,36 +57,36 @@ - 'Engins' - S.ID_MAREE - S.ID_OP - S.NUM_OP + + + + - - P.NAME - CASE P.IS_BOOLEAN WHEN TRUE THEN null ELSE PGM.NUMERICAL_VALUE END - + + + + - COALESCE(UNIT.NAME, 'Aucune') + - COALESCE(MATRIX.name, 'engin') - COALESCE(FRACTION.name, 'totale') - COALESCE(METHOD.name, 'Déclaration d''un professionnel') + + + &stationTableName INNER JOIN GEAR_USE_MEASUREMENT PGM ON PGM.OPERATION_FK = S.ID_OP diff --git a/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createSpeciesLengthTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createSpeciesLengthTable.xml index efa27640e0..cbd9e8d0b4 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createSpeciesLengthTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createSpeciesLengthTable.xml @@ -5,24 +5,24 @@ - SL.SAMPLE_ID - B.ID - (SELECT QV.LABEL FROM SORTING_MEASUREMENT_B SM INNER JOIN QUALITATIVE_VALUE QV ON QV.ID=SM.QUALITATIVE_VALUE_FK WHERE SM.BATCH_FK = B.ID and SM.PMFM_FK=&sexPmfmId) - SM_LENGTH.NUMERICAL_VALUE - U_LENGTH.NAME - U_LENGTH.LABEL - COALESCE(B.INDIVIDUAL_COUNT,1) - B.COMMENTS - P_LENGTH.LABEL - P_LENGTH.NAME - REGEXP_REPLACE(M_LENGTH.NAME, '(Mesure|Estimation) par ', '$1 au ' || U_LENGTH.LABEL || ' par ') - + + + + + + + + + + + + + + &rawSpeciesListTableName INNER JOIN BATCH B ON B.PARENT_BATCH_FK=SL.SAMPLE_ID AND B.LABEL LIKE UPPER('SORTING_BATCH_INDIVIDUAL#%') diff --git a/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createSpeciesListTable.xml index 26931f40bb..969653793e 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/createSpeciesListTable.xml @@ -7,39 +7,39 @@ - SL.ID_VRAC - SL.SAMPLE_ID + + - COALESCE(TN.COMMENTS, TN.NAME) - TG.NAME - + + + + + + + - SAMPLE_BATCH.INDIVIDUAL_COUNT + &rawSpeciesListTableName INNER JOIN BATCH SAMPLE_BATCH ON SAMPLE_BATCH.ID = SL.SAMPLE_ID diff --git a/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/distinctTripProgram.xml b/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/distinctTripProgram.xml new file mode 100644 index 0000000000..55b3e52243 --- /dev/null +++ b/sumaris-extraction/src/main/resources/xmlQuery/free2/v1_9/distinctTripProgram.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + \ No newline at end of file diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/createReleaseTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/createReleaseTable.xml index a756fa6b2d..0af0232c3a 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/createReleaseTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/createReleaseTable.xml @@ -26,15 +26,15 @@ - S.STATION_NUMBER - PARENT_SA.ID - PARENT_SA.SAMPLE_DATE - PARENT_SA.REFERENCE_TAXON_FK - PARENT_SA.TAXON_GROUP_FK - PMFM.LABEL - COALESCE(SQV.LABEL, SM.ALPHANUMERICAL_VALUE) - SM.NUMERICAL_VALUE - SA.COMMENTS + + + + + + + + + &stationTableName INNER JOIN SAMPLE SA ON SA.OPERATION_FK = S.STATION_NUMBER AND SA.LABEL LIKE UPPER('INDIVIDUAL_RELEASE#%') @@ -45,15 +45,15 @@ - S.STATION_NUMBER - SA.ID - SA.SAMPLE_DATE - SA.REFERENCE_TAXON_FK - SA.TAXON_GROUP_FK - PMFM.LABEL - COALESCE(SQV.LABEL, SM.ALPHANUMERICAL_VALUE) - SM.NUMERICAL_VALUE - null + + + + + + + + + &stationTableName INNER JOIN SAMPLE CHILD_SA ON CHILD_SA.OPERATION_FK = S.STATION_NUMBER AND CHILD_SA.LABEL LIKE UPPER('INDIVIDUAL_RELEASE#%') diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/createSampleTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/createSampleTable.xml index 7cd35319a6..d11c8447ff 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/createSampleTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/createSampleTable.xml @@ -26,18 +26,18 @@ - S.STATION_NUMBER - SA.ID - SA.SAMPLE_DATE - SA.REFERENCE_TAXON_FK - SA.TAXON_GROUP_FK - SM.PMFM_FK - COALESCE(SQV.LABEL, SM.ALPHANUMERICAL_VALUE) - SM.NUMERICAL_VALUE - SA.INDIVIDUAL_COUNT - SA.COMMENTS - CHILD_SA.RANK_ORDER - CHILD_SA.COMMENTS + + + + + + + + + + + + &stationTableName INNER JOIN SAMPLE SA ON SA.OPERATION_FK = S.STATION_NUMBER AND SA.LABEL LIKE UPPER('SAMPLE#%') @@ -47,18 +47,18 @@ - S.STATION_NUMBER - PARENT_SA.ID - PARENT_SA.SAMPLE_DATE - PARENT_SA.REFERENCE_TAXON_FK - PARENT_SA.TAXON_GROUP_FK - SM.PMFM_FK - COALESCE(SQV.LABEL, SM.ALPHANUMERICAL_VALUE) - SM.NUMERICAL_VALUE - PARENT_SA.INDIVIDUAL_COUNT - PARENT_SA.COMMENTS - SA.RANK_ORDER - SA.COMMENTS + + + + + + + + + + + + &stationTableName INNER JOIN SAMPLE PARENT_SA ON PARENT_SA.OPERATION_FK = S.STATION_NUMBER AND PARENT_SA.LABEL LIKE UPPER('SAMPLE#%') diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionPhysicalGearPmfm.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionPhysicalGearPmfm.xml index d36c649cb9..156dd099ea 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionPhysicalGearPmfm.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionPhysicalGearPmfm.xml @@ -2,40 +2,40 @@ - MAX(CASE PGM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN PGM.NUMERICAL_VALUE ELSE NULL END) - MAX(CASE PGM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN CAST(PGM.NUMERICAL_VALUE AS INT) ELSE NULL END) - MAX(CASE PGM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN PGM.ALPHANUMERICAL_VALUE ELSE NULL END) - MAX(CASE PGM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN PGQV.LABEL || ' - ' || PGQV.NAME ELSE NULL END) - MAX(CASE PGM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN (CASE PGM.NUMERICAL_VALUE WHEN 1 THEN UPPER('Y') WHEN 0 THEN UPPER('N') END) ELSE NULL END) - MAX(CASE PGM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TIMESTAMP(REPLACE(REPLACE(PGM.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', '')), 'YYYY-DD-MM') ELSE NULL END) - MAX(CASE PGM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TO_TIMESTAMP(REPLACE(REPLACE(PGM.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', ''), 'YYYY-MM-DD HH24:MI:SS'), 'YYYY-DD-MM') ELSE NULL END) diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionRawSpeciesListPmfm.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionRawSpeciesListPmfm.xml index 8de630936c..45dd53e98b 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionRawSpeciesListPmfm.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionRawSpeciesListPmfm.xml @@ -2,40 +2,40 @@ - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN SM.NUMERICAL_VALUE ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN CAST(SM.NUMERICAL_VALUE AS INT) ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN SM.ALPHANUMERICAL_VALUE ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN QV.LABEL || ' - ' || QV.NAME ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN (CASE SM.NUMERICAL_VALUE WHEN 1 THEN UPPER('Y') WHEN 0 THEN UPPER('N') END) ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TIMESTAMP(REPLACE(REPLACE(SM.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', '')), 'YYYY-DD-MM') ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TO_TIMESTAMP(REPLACE(REPLACE(SM.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', ''), 'YYYY-MM-DD HH24:MI:SS'), 'YYYY-DD-MM') ELSE NULL END) diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionRawSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionRawSpeciesListTable.xml index 7cf2c087b1..5e5edc41df 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionRawSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionRawSpeciesListTable.xml @@ -22,11 +22,9 @@ - + - LEFT OUTER JOIN SORTING_MEASUREMENT_B SM ON SM.BATCH_FK = SORTING_B.ID - LEFT OUTER JOIN QUALITATIVE_VALUE QV on QV.ID = SM.QUALITATIVE_VALUE_FK + LEFT OUTER JOIN SORTING_MEASUREMENT_B SM ON SM.BATCH_FK = SPECIE_B.ID + LEFT OUTER JOIN QUALITATIVE_VALUE QV on QV.ID = SM.QUALITATIVE_VALUE_FK - REFERENCE_TAXON_ID - &groupByColumns diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthPmfm.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthPmfm.xml index ece9970c35..0b067b68fb 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthPmfm.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthPmfm.xml @@ -23,39 +23,39 @@ - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN SM.NUMERICAL_VALUE ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN CAST(SM.NUMERICAL_VALUE AS INT) ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN SM.ALPHANUMERICAL_VALUE ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN QV.LABEL || ' - ' || QV.NAME ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN (CASE SM.NUMERICAL_VALUE WHEN 1 THEN UPPER('Y') WHEN 0 THEN UPPER('N') END) ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TIMESTAMP(REPLACE(REPLACE(SM.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', '')), 'YYYY-DD-MM') ELSE NULL END) - MAX(CASE SM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TO_TIMESTAMP(REPLACE(REPLACE(SM.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', ''), 'YYYY-MM-DD HH24:MI:SS'), 'YYYY-DD-MM') ELSE NULL END) diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthTable.xml index fae5bbd998..eb4b282440 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthTable.xml @@ -27,10 +27,9 @@ - + INNER JOIN SORTING_MEASUREMENT_B SM ON SM.BATCH_FK = B.ID LEFT OUTER JOIN QUALITATIVE_VALUE QV ON QV.ID = SM.QUALITATIVE_VALUE_FK - B.SEX, B.LENGTH_CLASS diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthTaxon.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthTaxon.xml index 3ca106c24b..e0eec66472 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthTaxon.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesLengthTaxon.xml @@ -31,5 +31,4 @@ LEFT OUTER JOIN TAXON_NAME TN_INHERITED ON TN_INHERITED.REFERENCE_TAXON_FK = SL.REFERENCE_TAXON_ID AND TN_INHERITED.IS_REFERENT=true LEFT OUTER JOIN TAXON_NAME TN ON TN.REFERENCE_TAXON_FK = B.REFERENCE_TAXON_ID AND TN.IS_REFERENT=true - TAXON diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesListTable.xml index 84d495d445..5c4af6a9e3 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionSpeciesListTable.xml @@ -26,6 +26,5 @@ LEFT OUTER JOIN TAXON_NAME TN ON TN.REFERENCE_TAXON_FK = SL.REFERENCE_TAXON_ID AND TN.IS_REFERENT=true - &groupByColumns - TAXON + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionParentOperationPmfm.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationParentPmfm.xml similarity index 93% rename from sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionParentOperationPmfm.xml rename to sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationParentPmfm.xml index 3d568e4bd2..135b3b5bb2 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionParentOperationPmfm.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationParentPmfm.xml @@ -2,31 +2,31 @@ - COALESCE(MAX(CASE VUM2.PMFM_FK WHEN &pmfmId%pmfmalias% THEN VUM2.NUMERICAL_VALUE ELSE NULL END), MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN VUM.NUMERICAL_VALUE ELSE NULL END)) - COALESCE(MAX(CASE VUM2.PMFM_FK WHEN &pmfmId%pmfmalias% THEN CAST(VUM2.NUMERICAL_VALUE AS INT) ELSE NULL END), MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN CAST(VUM.NUMERICAL_VALUE AS INT) ELSE NULL END)) - COALESCE(MAX(CASE VUM2.PMFM_FK WHEN &pmfmId%pmfmalias% THEN VUM2.ALPHANUMERICAL_VALUE ELSE NULL END), MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN VUM.ALPHANUMERICAL_VALUE ELSE NULL END)) - COALESCE(MAX(CASE VUM2.PMFM_FK WHEN &pmfmId%pmfmalias% THEN QV2.LABEL || ' - ' || QV2.NAME ELSE NULL END), MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN QV.LABEL || ' - ' || QV.NAME ELSE NULL END)) - COALESCE(MAX(CASE VUM2.PMFM_FK WHEN &pmfmId%pmfmalias% THEN (CASE VUM2.NUMERICAL_VALUE WHEN 1 THEN UPPER('Y') WHEN 0 THEN UPPER('N') END) ELSE NULL END), @@ -36,7 +36,7 @@ - COALESCE(MAX(CASE VUM2.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TIMESTAMP(REPLACE(REPLACE(VUM2.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', '')), 'YYYY-DD-MM') ELSE NULL END), @@ -45,7 +45,7 @@ ELSE NULL END)) - COALESCE(MAX(CASE VUM2.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TO_TIMESTAMP(REPLACE(REPLACE(VUM2.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', ''), 'YYYY-MM-DD HH24:MI:SS'), 'YYYY-DD-MM') ELSE NULL END), diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionOperationPmfm.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationPmfm.xml similarity index 88% rename from sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionOperationPmfm.xml rename to sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationPmfm.xml index 51907b4ebc..33eaa49369 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionOperationPmfm.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationPmfm.xml @@ -2,40 +2,40 @@ - MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN VUM.NUMERICAL_VALUE ELSE NULL END) - MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN CAST(VUM.NUMERICAL_VALUE AS INT) ELSE NULL END) - MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN VUM.ALPHANUMERICAL_VALUE ELSE NULL END) - MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN QV.LABEL || ' - ' || QV.NAME ELSE NULL END) - MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN (CASE VUM.NUMERICAL_VALUE WHEN 1 THEN UPPER('Y') WHEN 0 THEN UPPER('N') END) ELSE NULL END) - MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TIMESTAMP(REPLACE(REPLACE(VUM.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', '')), 'YYYY-DD-MM') ELSE NULL END) - MAX(CASE VUM.PMFM_FK WHEN &pmfmId%pmfmalias% THEN TO_CHAR(TO_TIMESTAMP(REPLACE(REPLACE(VUM.ALPHANUMERICAL_VALUE, 'T', ' '), 'Z', ''), 'YYYY-MM-DD HH24:MI:SS'), 'YYYY-DD-MM') ELSE NULL END) diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationTable.xml index 080b40f360..62e4f1b48b 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionStationTable.xml @@ -23,13 +23,13 @@ - + LEFT OUTER JOIN OPERATION O2 ON O2.ID = O.OPERATION_FK LEFT OUTER JOIN VESSEL_USE_MEASUREMENT VUM2 ON VUM2.OPERATION_FK = O2.ID LEFT OUTER JOIN QUALITATIVE_VALUE QV2 on QV2.ID = VUM2.QUALITATIVE_VALUE_FK - O.QUALITY_FLAG_FK != 8 + O.QUALITY_FLAG_FK != 8 diff --git a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionTripTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionTripTable.xml index b8fc0fda01..112be21296 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionTripTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/pmfmTrip/v1_0/injectionTripTable.xml @@ -22,8 +22,9 @@ - - + + + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createRawSpeciesListDenormalizeTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createRawSpeciesListDenormalizeTable.xml index d9aa5644f3..54b204837f 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createRawSpeciesListDenormalizeTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createRawSpeciesListDenormalizeTable.xml @@ -40,81 +40,87 @@ - - - - - - + + + + + + + + + - - + - 0 THEN - ROUND(SUM(LENGTH_B.ELEVATE_RTP_WEIGHT) / SAMPLING_B.ELEVATE_RTP_WEIGHT + 0.000001, 6) + ROUND(SUM(LENGTH_B.ELEVATE_RTP_WEIGHT) / SAMPLING_B.ELEVATE_RTP_WEIGHT / COUNT(SPECIE_B.ID) + 0.0000005, 6) ELSE 1 END ]]> - + + &stationTableName - INNER JOIN DENORMALIZED_BATCH SPECIE_B ON SPECIE_B.OPERATION_FK = S.STATION_NUMBER AND SPECIE_B.IS_LANDING <> SPECIE_B.IS_DISCARD INNER JOIN TAXON_GROUP TG ON TG.ID = SPECIE_B.INHERITED_TAXON_GROUP_FK - INNER JOIN DENORMALIZED_BATCH_SORT_VAL CATCH_CATEGORY_SV ON CATCH_CATEGORY_SV.BATCH_FK=SPECIE_B.ID AND CATCH_CATEGORY_SV.PMFM_FK=&catchCategoryPmfmId AND CATCH_CATEGORY_SV.IS_INHERITED=0 + INNER JOIN DENORMALIZED_BATCH_SORT_VAL SM ON SM.BATCH_FK=SPECIE_B.ID + INNER JOIN QUALITATIVE_VALUE QV ON QV.ID=SM.QUALITATIVE_VALUE_FK LEFT OUTER JOIN DENORMALIZED_BATCH SAMPLING_B ON SAMPLING_B.PARENT_BATCH_FK = SPECIE_B.ID AND SAMPLING_B.SAMPLING_RATIO > 0 LEFT OUTER JOIN DENORMALIZED_BATCH LENGTH_B ON LENGTH_B.PARENT_BATCH_FK=COALESCE(SAMPLING_B.ID, SPECIE_B.ID) - LEFT OUTER JOIN DENORMALIZED_BATCH_SORT_VAL LENGTH_SV ON LENGTH_SV.BATCH_FK=LENGTH_B.ID AND LENGTH_SV.PMFM_FK in (&lengthPmfmIds) AND IS_INHERITED=0 + LEFT OUTER JOIN DENORMALIZED_BATCH_SORT_VAL LENGTH_SV ON LENGTH_SV.BATCH_FK=LENGTH_B.ID AND LENGTH_SV.PMFM_FK in (&lengthPmfmIds) AND LENGTH_SV.IS_INHERITED=0 LEFT OUTER JOIN UNIT ON UNIT.ID = LENGTH_SV.UNIT_FK LEFT OUTER JOIN TAXON_NAME TN ON TN.REFERENCE_TAXON_FK = LENGTH_B.REFERENCE_TAXON_FK 1=1 - SPECIE_B.WEIGHT IS NOT NULL + + - - SAMPLING_TYPE, LANDING_COUNTRY, VESSEL_FLAG_COUNTRY, YEAR, PROJECT, TRIP_CODE, STATION_NUMBER, SPECIES, - CATCH_CATEGORY, LANDING_CATEGORY, COMMERCIAL_SIZE_CATEGORY_SCALE, COMMERCIAL_SIZE_CATEGORY, SUBSAMPLING_CATEGORY, - SEX, LENGTH_CODE, SAMPLE_ID, SAMPLE_RANK_ORDER, - SPECIE_B.ELEVATE_WEIGHT, SAMPLING_B.SAMPLING_RATIO, SAMPLING_B.ELEVATE_RTP_WEIGHT, SPECIE_B.ELEVATE_RTP_WEIGHT - + &groupByColumns + + SPECIE_B.ELEVATE_WEIGHT,SAMPLING_B.ELEVATE_RTP_WEIGHT - S.STATION_NUMBER, SAMPLE_RANK_ORDER + STATION_NUMBER ASC, SAMPLE_RANK_ORDER ASC diff --git a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createRawSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createRawSpeciesListTable.xml index def2981862..1998eb98b9 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createRawSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createRawSpeciesListTable.xml @@ -36,39 +36,51 @@ - - - - + + + + + + - - + - + + &stationTableName INNER JOIN BATCH CATCH_B ON CATCH_B.OPERATION_FK = S.STATION_NUMBER AND CATCH_B.PARENT_BATCH_FK IS NULL @@ -81,7 +93,9 @@ - S.STATION_NUMBER, SAMPLE_RANK_ORDER + &groupByColumns + + STATION_NUMBER ASC, SAMPLE_RANK_ORDER ASC diff --git a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createSpeciesLengthTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createSpeciesLengthTable.xml index 29ff8bf9d0..9e897c6569 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createSpeciesLengthTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createSpeciesLengthTable.xml @@ -25,15 +25,16 @@ - - SL.SAMPLE_ID - B.ID - (SELECT QV.LABEL FROM SORTING_MEASUREMENT_B SM_SEX INNER JOIN QUALITATIVE_VALUE QV ON QV.ID=SM_SEX.QUALITATIVE_VALUE_FK WHERE SM_SEX.BATCH_FK = B.ID and SM_SEX.PMFM_FK=&sexPmfmId) - CAST(CASE PMFM_LENGTH.UNIT_FK WHEN &centimeterUnitId THEN SM_LENGTH.NUMERICAL_VALUE*10 WHEN &millimeterUnitId THEN SM_LENGTH.NUMERICAL_VALUE ELSE null END AS INTEGER) - COALESCE(B.INDIVIDUAL_COUNT,1) - B.COMMENTS - P_LENGTH.LABEL - B.REFERENCE_TAXON_FK + + + + + + + + + + &rawSpeciesListTableName INNER JOIN BATCH B ON B.PARENT_BATCH_FK=SL.SAMPLE_ID AND B.LABEL LIKE UPPER('SORTING_BATCH_INDIVIDUAL#%') @@ -57,7 +58,9 @@ - + @@ -66,7 +69,7 @@ - + @@ -76,12 +79,11 @@ 1=1 - - SAMPLING_TYPE, LANDING_COUNTRY, VESSEL_FLAG_COUNTRY, YEAR, PROJECT, TRIP_CODE, STATION_NUMBER, SPECIES, - CATCH_CATEGORY, LANDING_CATEGORY, COMMERCIAL_SIZE_CATEGORY_SCALE, COMMERCIAL_SIZE_CATEGORY, SUBSAMPLING_CATEGORY, SL.SAMPLE_ID - - SL.SEX, INDIVIDUAL_SEX - LENGTH_CLASS + + (SL.REFERENCE_TAXON_ID IS NULL OR B.REFERENCE_TAXON_ID=SL.REFERENCE_TAXON_ID) + + + &groupByColumns diff --git a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createSpeciesListTable.xml index 76e297dba8..cfb6d1b1db 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createSpeciesListTable.xml @@ -38,16 +38,18 @@ - + - - + @@ -55,18 +57,15 @@ - - + + &rawSpeciesListTableName 1=1 - - SAMPLING_TYPE, LANDING_COUNTRY, VESSEL_FLAG_COUNTRY, YEAR, PROJECT, TRIP_CODE, STATION_NUMBER, SPECIES, - CATCH_CATEGORY, LANDING_CATEGORY, COMMERCIAL_SIZE_CATEGORY_SCALE, COMMERCIAL_SIZE_CATEGORY, SUBSAMPLING_CATEGORY, - SEX, LENGTH_CODE, SUBSAMPLING_WEIGHT, SUBSAMPLING_RATIO - + &groupByColumns + SL.SUBSAMPLING_RATIO diff --git a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createStationTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createStationTable.xml index 336c822f19..78311af0df 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createStationTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createStationTable.xml @@ -114,9 +114,14 @@ LEFT OUTER JOIN VESSEL_POSITION P_START ON P_START.OPERATION_FK = O.ID and P_START.DATE_TIME=COALESCE(O.FISHING_START_DATE_TIME, O.START_DATE_TIME) LEFT OUTER JOIN VESSEL_POSITION P_END ON P_END.OPERATION_FK = O.ID and P_END.DATE_TIME=COALESCE(O.FISHING_END_DATE_TIME, O.END_DATE_TIME) + 1=1 + T.DEPARTURE_DATE_TIME AND O.END_DATE_TIME <> T.RETURN_DATE_TIME + ]]> + &groupByColumns - O.ID + diff --git a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createTripTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createTripTable.xml index ac29f4e8b4..5cb4a7a4a1 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createTripTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/rdb/v1_3/createTripTable.xml @@ -52,11 +52,12 @@ - + + + + + + TRIP diff --git a/sumaris-extraction/src/main/resources/xmlQuery/rjbTrip/v1_0/injectionRawSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/rjbTrip/v1_0/injectionRawSpeciesListTable.xml index ec03438f6c..2056cf78aa 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/rjbTrip/v1_0/injectionRawSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/rjbTrip/v1_0/injectionRawSpeciesListTable.xml @@ -26,4 +26,6 @@ TG.LABEL IN (&taxonGroupLabels) + + SORTING_B.INDIVIDUAL_COUNT diff --git a/sumaris-extraction/src/main/resources/xmlQuery/rjbTrip/v1_0/injectionSpeciesListTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/rjbTrip/v1_0/injectionSpeciesListTable.xml index b69b174d56..dbf7b003f9 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/rjbTrip/v1_0/injectionSpeciesListTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/rjbTrip/v1_0/injectionSpeciesListTable.xml @@ -29,4 +29,5 @@ + LENGTH_CODE diff --git a/sumaris-extraction/src/main/resources/xmlQuery/survivalTest/v1_0/createReleaseTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/survivalTest/v1_0/createReleaseTable.xml index a756fa6b2d..0af0232c3a 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/survivalTest/v1_0/createReleaseTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/survivalTest/v1_0/createReleaseTable.xml @@ -26,15 +26,15 @@ - S.STATION_NUMBER - PARENT_SA.ID - PARENT_SA.SAMPLE_DATE - PARENT_SA.REFERENCE_TAXON_FK - PARENT_SA.TAXON_GROUP_FK - PMFM.LABEL - COALESCE(SQV.LABEL, SM.ALPHANUMERICAL_VALUE) - SM.NUMERICAL_VALUE - SA.COMMENTS + + + + + + + + + &stationTableName INNER JOIN SAMPLE SA ON SA.OPERATION_FK = S.STATION_NUMBER AND SA.LABEL LIKE UPPER('INDIVIDUAL_RELEASE#%') @@ -45,15 +45,15 @@ - S.STATION_NUMBER - SA.ID - SA.SAMPLE_DATE - SA.REFERENCE_TAXON_FK - SA.TAXON_GROUP_FK - PMFM.LABEL - COALESCE(SQV.LABEL, SM.ALPHANUMERICAL_VALUE) - SM.NUMERICAL_VALUE - null + + + + + + + + + &stationTableName INNER JOIN SAMPLE CHILD_SA ON CHILD_SA.OPERATION_FK = S.STATION_NUMBER AND CHILD_SA.LABEL LIKE UPPER('INDIVIDUAL_RELEASE#%') diff --git a/sumaris-extraction/src/main/resources/xmlQuery/survivalTest/v1_0/createSurvivalTestTable.xml b/sumaris-extraction/src/main/resources/xmlQuery/survivalTest/v1_0/createSurvivalTestTable.xml index ebfd512bd3..371b3ccd56 100644 --- a/sumaris-extraction/src/main/resources/xmlQuery/survivalTest/v1_0/createSurvivalTestTable.xml +++ b/sumaris-extraction/src/main/resources/xmlQuery/survivalTest/v1_0/createSurvivalTestTable.xml @@ -26,15 +26,15 @@ - S.STATION_NUMBER - SA.ID - SA.SAMPLE_DATE - SA.REFERENCE_TAXON_FK - SA.TAXON_GROUP_FK - PMFM.LABEL - COALESCE(SQV.LABEL, SM.ALPHANUMERICAL_VALUE) - SM.NUMERICAL_VALUE - CHILD_SA.RANK_ORDER + + + + + + + + + &stationTableName INNER JOIN SAMPLE SA ON SA.OPERATION_FK = S.STATION_NUMBER AND SA.LABEL LIKE UPPER('SAMPLE#%') @@ -45,15 +45,15 @@ - S.STATION_NUMBER - PARENT_SA.ID - PARENT_SA.SAMPLE_DATE - PARENT_SA.REFERENCE_TAXON_FK - PARENT_SA.TAXON_GROUP_FK - PMFM.LABEL - COALESCE(SQV.LABEL, SM.ALPHANUMERICAL_VALUE) - SM.NUMERICAL_VALUE - SA.RANK_ORDER + + + + + + + + + &stationTableName INNER JOIN SAMPLE PARENT_SA ON PARENT_SA.OPERATION_FK = S.STATION_NUMBER AND PARENT_SA.LABEL LIKE UPPER('SAMPLE#%') @@ -120,7 +120,7 @@ T.ID, SPECIES_CODE, SPECIES_NAME, T.SAMPLE_DATE, T.MONITORING_ID - T.ID,T.MONITORING_ID + T.ID ASC,T.MONITORING_ID ASC diff --git a/sumaris-extraction/src/main/resources/xsl/queryOracle.xsl b/sumaris-extraction/src/main/resources/xsl/queryOracle.xsl deleted file mode 100644 index de0858b983..0000000000 --- a/sumaris-extraction/src/main/resources/xsl/queryOracle.xsl +++ /dev/null @@ -1,604 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - DROP TABLE - - - - - DELETE FROM - - - - - WHERE - - - - - - - - - - - DECLARE LOCAL TEMPORARY TABLE - - - CREATE TABLE - - - - AS - - - - - - - - - - - - SELECT - - - - - - - - - - - - - - - FROM - - - - - - - - WHERE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GROUP BY - - - - - - - - - ORDER BY - - - - - - - - - - - - - - - - - - - - - - - - - SELECT - - - - - - - - FROM - - - - - - - - WHERE - - - - - - - - - - - - - - - - - - - - - - - GROUP BY - - - - - - - - - ORDER BY - - - - - - - - - - - - - - - - - WITH - - - - - - - as ( - - - - - - ) - - - - , - - - - - - - - - - - - - - - - " - - " - - - , - - - - - - - - - - - - - - - " - - " - - - , - - - - - - - - - - - , - - - - ( - - - - - ) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ( - - - - - ) - - - - - - - - - - - - - - - - - - - - - - - - - , - - - - - - - - - - - - - - , - - - - - - - - - - - - - - - - - - - - - - - - IN - - ( - - - - - ) - - - - ( - - IN - - - - ) - - - - - - - - - - - - - - NOT IN - - ( - - - - - ) - - - - ( - - NOT IN - - - - ) - - - - - - - - - - - , CURSOR ( - - - - - ) AS - - - - - - - - - - UNION - - - - - - - - - - - - - UNION ALL - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CREATE INDEX - - ON - - ( - - ) - - - - - DROP INDEX IF EXISTS - - - - - - - diff --git a/sumaris-extraction/src/test/java/net/sumaris/extraction/core/DatabaseFixtures.java b/sumaris-extraction/src/test/java/net/sumaris/extraction/core/DatabaseFixtures.java index 7986a0d96a..e83654b151 100644 --- a/sumaris-extraction/src/test/java/net/sumaris/extraction/core/DatabaseFixtures.java +++ b/sumaris-extraction/src/test/java/net/sumaris/extraction/core/DatabaseFixtures.java @@ -90,12 +90,14 @@ public int getYearRdbProduct() { public int getTripIdByProgramLabel(String programLabel) { switch (programLabel) { + case "SUMARiS": + return 1; // The validated trip case "APASE": return 70; case "ADAP-MER": return 100; default: - throw new IllegalArgumentException("Add trip id for program " + programLabel); + throw new IllegalArgumentException("Missing a trip id for the program: " + programLabel); } } diff --git a/sumaris-extraction/src/test/java/net/sumaris/extraction/core/service/ExtractionServiceTest.java b/sumaris-extraction/src/test/java/net/sumaris/extraction/core/service/ExtractionServiceTest.java index 5266a69c95..f139a1768b 100644 --- a/sumaris-extraction/src/test/java/net/sumaris/extraction/core/service/ExtractionServiceTest.java +++ b/sumaris-extraction/src/test/java/net/sumaris/extraction/core/service/ExtractionServiceTest.java @@ -25,6 +25,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.base.Preconditions; import com.google.common.collect.ImmutableList; +import lombok.extern.slf4j.Slf4j; import net.sumaris.core.dao.technical.Page; import net.sumaris.core.exception.DataNotFoundException; import net.sumaris.core.model.data.DataQualityStatusEnum; @@ -38,6 +39,7 @@ import net.sumaris.core.vo.technical.extraction.AggregationStrataVO; import net.sumaris.core.vo.technical.extraction.ExtractionProductSaveOptions; import net.sumaris.core.vo.technical.extraction.ExtractionProductVO; +import net.sumaris.extraction.core.config.ExtractionConfiguration; import net.sumaris.extraction.core.specification.administration.StratSpecification; import net.sumaris.extraction.core.specification.data.trip.*; import net.sumaris.extraction.core.type.AggExtractionTypeEnum; @@ -46,6 +48,7 @@ import net.sumaris.extraction.core.vo.administration.ExtractionStrategyFilterVO; import net.sumaris.extraction.core.vo.trip.ExtractionTripFilterVO; import org.junit.*; +import org.junit.runners.MethodSorters; import org.springframework.beans.factory.annotation.Autowired; import java.io.File; @@ -55,6 +58,8 @@ /** * @author Benoit LAVENIER */ +@Slf4j +@FixMethodOrder(MethodSorters.NAME_ASCENDING) public abstract class ExtractionServiceTest extends AbstractServiceTest { @Autowired @@ -69,12 +74,76 @@ public abstract class ExtractionServiceTest extends AbstractServiceTest { @Autowired protected ExtractionProductService productService; + @Autowired + protected ExtractionConfiguration extractionConfiguration; @Test public void executeStrat() throws IOException { executeStrat(null); } + @Test + public void executeWithDenormalisation() throws IOException { + + // Enable batch optimization, in extraction + extractionConfiguration.setEnableBatchDenormalization(true); + Assert.assertTrue(extractionConfiguration.enableBatchDenormalization()); + + List programLabels = ImmutableList.of("SUMARiS", "ADAP-MER"); + List formats = ImmutableList.of(LiveExtractionTypeEnum.RDB, LiveExtractionTypeEnum.COST, LiveExtractionTypeEnum.PMFM_TRIP); + + for (String programLabel: programLabels) { + for (LiveExtractionTypeEnum format : formats) { + log.info("--- Testing extraction {}/{} ... ---", format.getLabel(), programLabel); + + // Create filter for a trip + ExtractionTripFilterVO filter = createFilterForTrip(fixtures.getTripIdByProgramLabel(programLabel)); + + // DEBUG + //filter.setSheetName(RdbSpecification.SL_SHEET_NAME); + //filter.setPreview(true); + + // Test the RDB format + File outputFile = service.executeAndDumpTrips(format, filter); + Assert.assertTrue(outputFile.exists()); + File root = unpack(outputFile, format.getLabel()); + + // TR.csv + { + File tripFile = new File(root, RdbSpecification.TR_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(tripFile) > 1); + } + + // HH.csv + { + File stationFile = new File(root, RdbSpecification.HH_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(stationFile) > 1); + + // Make sure this column exists (column with a 'dbms' attribute) + assertHasColumn(stationFile, RdbSpecification.COLUMN_FISHING_TIME); + } + + // SL.csv + { + File speciesListFile = new File(root, RdbSpecification.SL_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(speciesListFile) > 1); + + // Make sure this column exists (column with a 'dbms' attribute) + assertHasColumn(speciesListFile, RdbSpecification.COLUMN_WEIGHT); + } + + // HL.csv + { + File speciesLengthFile = new File(root, RdbSpecification.HL_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(speciesLengthFile) > 1); + + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_LENGTH_CLASS); + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_NUMBER_AT_LENGTH); + } + } + } + } + @Test public void executeRdb() throws IOException { @@ -107,6 +176,61 @@ public void executeRdb() throws IOException { // Make sure this column exists (column with a 'dbms' attribute) assertHasColumn(speciesListFile, RdbSpecification.COLUMN_WEIGHT); } + + // HL.csv + { + File speciesLengthFile = new File(root, RdbSpecification.HL_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(speciesLengthFile) > 1); + + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_INDIVIDUAL_SEX); + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_LENGTH_CLASS); + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_NUMBER_AT_LENGTH); + } + } + + @Test + public void executeCost() throws IOException { + + // Test the RDB format + File outputFile = service.executeAndDumpTrips(LiveExtractionTypeEnum.COST, null); + Assert.assertTrue(outputFile.exists()); + File root = unpack(outputFile, LiveExtractionTypeEnum.RDB.getLabel()); + + // TR.csv + { + File tripFile = new File(root, RdbSpecification.TR_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(tripFile) > 1); + + } + + // HH.csv + { + File stationFile = new File(root, RdbSpecification.HH_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(stationFile) > 1); + + // Make sure this column exists (column with a 'dbms' attribute) + assertHasColumn(stationFile, RdbSpecification.COLUMN_FISHING_TIME); + } + + // SL.csv + { + File speciesListFile = new File(root, RdbSpecification.SL_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(speciesListFile) > 1); + + // Make sure this column exists (column with a 'dbms' attribute) + assertHasColumn(speciesListFile, RdbSpecification.COLUMN_WEIGHT); + } + + // HL.csv + { + File speciesLengthFile = new File(root, RdbSpecification.HL_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(speciesLengthFile) > 1); + + assertHasNoColumn(speciesLengthFile, CostSpecification.COLUMN_INDIVIDUAL_SEX); // Should have been rename into "sex" + assertHasColumn(speciesLengthFile, CostSpecification.COLUMN_SEX); + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_LENGTH_CLASS); + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_NUMBER_AT_LENGTH); + } } @Test @@ -156,8 +280,8 @@ public void executeSurvivalTest() throws IOException { @Test public void executePmfmSUMARiS() throws IOException { - ExtractionTripFilterVO filter = new ExtractionTripFilterVO(); - filter.setProgramLabel(fixtures.getProgramLabelForPmfmExtraction(0)); + // Create filter for a trip + ExtractionTripFilterVO filter = createFilterForTrip(fixtures.getTripIdByProgramLabel("SUMARiS")); // Test the RDB format File outputFile = service.executeAndDumpTrips(LiveExtractionTypeEnum.PMFM_TRIP, filter); @@ -193,7 +317,7 @@ public void executePmfmSUMARiS() throws IOException { File speciesLengthFile = new File(root, PmfmTripSpecification.HL_SHEET_NAME + ".csv"); Assert.assertTrue(countLineInCsvFile(speciesLengthFile) > 1); - assertHasColumn(speciesLengthFile, "sex"); + assertHasColumn(speciesLengthFile, PmfmTripSpecification.COLUMN_SEX); } // ST.csv @@ -276,6 +400,57 @@ public void executePmfmADAP() throws IOException { } + @Test + public void executeApase() throws IOException { + + log.info("--- Testing extraction APASE ... ---"); + + // Create filter for a trip + ExtractionTripFilterVO filter = createFilterForTrip(fixtures.getTripIdByProgramLabel("APASE")); + + // DEBUG + //filter.setSheetName(RdbSpecification.SL_SHEET_NAME); + //filter.setPreview(true); + + // Test the RDB format + File outputFile = service.executeAndDumpTrips(LiveExtractionTypeEnum.APASE, filter); + Assert.assertTrue(outputFile.exists()); + File root = unpack(outputFile, LiveExtractionTypeEnum.APASE.getLabel()); + + // TR.csv + { + File tripFile = new File(root, RdbSpecification.TR_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(tripFile) > 1); + } + + // HH.csv + { + File stationFile = new File(root, RdbSpecification.HH_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(stationFile) > 1); + + // Make sure this column exists (column with a 'dbms' attribute) + assertHasColumn(stationFile, RdbSpecification.COLUMN_FISHING_TIME); + } + + // SL.csv + { + File speciesListFile = new File(root, RdbSpecification.SL_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(speciesListFile) > 1); + + // Make sure this column exists (column with a 'dbms' attribute) + assertHasColumn(speciesListFile, RdbSpecification.COLUMN_WEIGHT); + } + + // HL.csv + { + File speciesLengthFile = new File(root, RdbSpecification.HL_SHEET_NAME + ".csv"); + Assert.assertTrue(countLineInCsvFile(speciesLengthFile) > 1); + + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_LENGTH_CLASS); + assertHasColumn(speciesLengthFile, RdbSpecification.COLUMN_NUMBER_AT_LENGTH); + } + } + @Test public void aggregateRdb() throws IOException { @@ -698,14 +873,48 @@ public void updateAggRdbProduct() { } @Test - public void dropTemporaryTables() { + @Ignore + // FIXME + public void z_dropTemporaryTables() { int count = service.dropTemporaryTables(); - Assert.assertEquals("No temporary extraction tables should be found, in a test DB", 0, count); } /* -- protected methods -- */ + protected ExtractionTripFilterVO createFilterForTrip(int tripId) { + TripVO trip = loadAndValidateTripById(tripId); + + // Create extraction filter + ExtractionTripFilterVO filter = new ExtractionTripFilterVO(); + filter.setProgramLabel(trip.getProgram().getLabel()); + filter.setTripId(trip.getId()); + + return filter; + } + + protected TripVO loadAndValidateTripById(int tripId) { + // Load + TripVO trip = tripService.get(tripId); + Assume.assumeNotNull(trip); + + // Control + if (trip.getControlDate() == null) { + trip = tripService.control(trip); + Assume.assumeNotNull(trip); + Assume.assumeNotNull(trip.getControlDate()); + } + + // Validate + if (trip.getValidationDate() == null) { + trip = tripService.validate(trip); + Assume.assumeNotNull(trip); + Assume.assumeNotNull(trip.getValidationDate()); + } + + return trip; + } + protected File executeStrat(ExtractionStrategyFilterVO filter) throws IOException { // Test the Strategy format @@ -731,5 +940,9 @@ protected void assertHasColumn(File file, String columnName) throws IOException Assert.assertTrue(String.format("Missing header '%s' in file: %s", headerName, file.getPath()), hasHeaderInCsvFile(file, headerName)); } - + protected void assertHasNoColumn(File file, String columnName) throws IOException { + String headerName = StringUtils.underscoreToChangeCase(columnName); + Assert.assertFalse(String.format("Should not have header '%s' in file: %s", headerName, file.getPath()), + hasHeaderInCsvFile(file, headerName)); + } } diff --git a/sumaris-extraction/src/test/java/net/sumaris/extraction/core/service/hsqldb/ExtractionServiceHsqlDbTest.java b/sumaris-extraction/src/test/java/net/sumaris/extraction/core/service/hsqldb/ExtractionServiceHsqlDbTest.java index 9389dd8e92..37dddb8fd8 100644 --- a/sumaris-extraction/src/test/java/net/sumaris/extraction/core/service/hsqldb/ExtractionServiceHsqlDbTest.java +++ b/sumaris-extraction/src/test/java/net/sumaris/extraction/core/service/hsqldb/ExtractionServiceHsqlDbTest.java @@ -47,86 +47,6 @@ public class ExtractionServiceHsqlDbTest extends ExtractionServiceTest { @ClassRule public static final DatabaseResource dbResource = DatabaseResource.writeDb(); - @Autowired - protected ExtractionConfiguration extractionConfiguration; - @Autowired - protected TripService tripService; - @Test - public void executeRdbWithDenormalisation() throws IOException { - - // Enable batch optimization, in extraction - extractionConfiguration.setEnableBatchDenormalization(true); - Assert.assertTrue(extractionConfiguration.enableBatchDenormalization()); - - // Create filter for a trip (APASE) - ExtractionTripFilterVO filter = createFilterForTrip(fixtures.getTripIdByProgramLabel("APASE")); - - // TODO remove this - filter.setSheetName(RdbSpecification.SL_SHEET_NAME); - filter.setPreview(true); - - // Test the RDB format - File outputFile = service.executeAndDumpTrips(LiveExtractionTypeEnum.RDB, filter); - Assert.assertTrue(outputFile.exists()); - File root = unpack(outputFile, LiveExtractionTypeEnum.RDB.getLabel()); - - // TR.csv - { - File tripFile = new File(root, RdbSpecification.TR_SHEET_NAME + ".csv"); - Assert.assertTrue(countLineInCsvFile(tripFile) > 1); - } - - // HH.csv - { - File stationFile = new File(root, RdbSpecification.HH_SHEET_NAME + ".csv"); - Assert.assertTrue(countLineInCsvFile(stationFile) > 1); - - // Make sure this column exists (column with a 'dbms' attribute) - assertHasColumn(stationFile, RdbSpecification.COLUMN_FISHING_TIME); - } - - // SL.csv - { - File speciesListFile = new File(root, RdbSpecification.SL_SHEET_NAME + ".csv"); - Assert.assertTrue(countLineInCsvFile(speciesListFile) > 1); - - // Make sure this column exists (column with a 'dbms' attribute) - assertHasColumn(speciesListFile, RdbSpecification.COLUMN_WEIGHT); - } - } - - protected ExtractionTripFilterVO createFilterForTrip(int tripId) { - TripVO trip = loadAndValidateTripById(70 /*APASE trip*/); - - // Create extraction filter - ExtractionTripFilterVO filter = new ExtractionTripFilterVO(); - filter.setProgramLabel(trip.getProgram().getLabel()); - filter.setTripId(trip.getId()); - - return filter; - } - - protected TripVO loadAndValidateTripById(int tripId) { - // Load - TripVO trip = tripService.get(tripId); - Assume.assumeNotNull(trip); - - // Control - if (trip.getControlDate() == null) { - trip = tripService.control(trip); - Assume.assumeNotNull(trip); - Assume.assumeNotNull(trip.getControlDate()); - } - - // Validate - if (trip.getValidationDate() == null) { - trip = tripService.validate(trip); - Assume.assumeNotNull(trip); - Assume.assumeNotNull(trip.getValidationDate()); - } - - return trip; - } } \ No newline at end of file diff --git a/sumaris-extraction/src/test/resources/application-hsqldb.properties b/sumaris-extraction/src/test/resources/application-hsqldb.properties index 7ff509d8d8..3136df2703 100644 --- a/sumaris-extraction/src/test/resources/application-hsqldb.properties +++ b/sumaris-extraction/src/test/resources/application-hsqldb.properties @@ -16,14 +16,14 @@ spring.main.web-application-type=none spring.main.allow-circular-references=true # DataSource configuration -spring.datasource.platform=hsqldb -spring.datasource.initialization-mode=always +spring.sql.init.platform=hsqldb +spring.sql.init.mode=always spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver spring.datasource.username=sa spring.datasource.password= sumaris.persistence.sequence.startWith=1000 # For DEV ONLY: -spring.datasource.url=jdbc:hsqldb:hsql://localhost/sumaris +#spring.datasource.url=jdbc:hsqldb:hsql://localhost/sumaris # General JPA properties spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.dialect.HSQLSpatialDialect diff --git a/sumaris-extraction/src/test/resources/application-oracle.properties b/sumaris-extraction/src/test/resources/application-oracle.properties index 68e9083765..e42e456b3d 100644 --- a/sumaris-extraction/src/test/resources/application-oracle.properties +++ b/sumaris-extraction/src/test/resources/application-oracle.properties @@ -17,8 +17,8 @@ spring.main.web-application-type=none spring.main.allow-circular-references=true # DataSource configuration -spring.datasource.platform=oracle -spring.datasource.initialization-mode=always +spring.sql.init.platform=oracle +spring.sql.init.mode=always spring.datasource.driver-class-name=oracle.jdbc.OracleDriver #spring.datasource.url=jdbc:oracle:thin:@HARMONIE_VAL spring.datasource.url=jdbc:oracle:thin:@//pythie.ifremer.fr:1521/HARMONIE_VAL diff --git a/sumaris-extraction/src/test/resources/application-pgsql.properties b/sumaris-extraction/src/test/resources/application-pgsql.properties index 8501d3fb99..a1b71632f5 100644 --- a/sumaris-extraction/src/test/resources/application-pgsql.properties +++ b/sumaris-extraction/src/test/resources/application-pgsql.properties @@ -16,7 +16,8 @@ spring.cache.type=NONE spring.jms.enabled=false # DataSource configuration -spring.datasource.initialization-mode=always +spring.sql.init.mode=always +spring.sql.init.platform=pgsql spring.datasource.driver-class-name=org.postgresql.Driver spring.datasource.username=sumaris spring.datasource.password=sumaris @@ -24,7 +25,6 @@ spring.jpa.properties.hibernate.default_catalog=sumaristest spring.jpa.properties.hibernate.default_schema=public #spring.datasource.url=jdbc:postgresql://localhost:5432/sumaristest spring.datasource.url=jdbc:postgresql://192.168.0.24:5432/sumaristest -spring.datasource.platform=pgsql # General JPA properties spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.dialect.PostgisPG10Dialect diff --git a/sumaris-importation/pom.xml b/sumaris-importation/pom.xml index 4138606d22..ea1f236c76 100644 --- a/sumaris-importation/pom.xml +++ b/sumaris-importation/pom.xml @@ -3,7 +3,7 @@ sumaris-pod net.sumaris - 2.1.0 + 2.1.1 4.0.0 diff --git a/sumaris-importation/src/main/java/net/sumaris/importation/core/service/rdb/RdbDataLoaderServiceImpl.java b/sumaris-importation/src/main/java/net/sumaris/importation/core/service/rdb/RdbDataLoaderServiceImpl.java index 4642cd4b79..f587e3f681 100644 --- a/sumaris-importation/src/main/java/net/sumaris/importation/core/service/rdb/RdbDataLoaderServiceImpl.java +++ b/sumaris-importation/src/main/java/net/sumaris/importation/core/service/rdb/RdbDataLoaderServiceImpl.java @@ -161,7 +161,7 @@ public interface HeaderAdapter extends BiFunction new SumarisTechnicalException("Unable to import vessels: job service has been disabled")); - JobVO importJob = new JobVO(); - importJob.setType(JobTypeEnum.SIOP_VESSELS_IMPORTATION.name()); - importJob.setName(t("sumaris.import.vessel.siop.job.name", fileName)); - PersonVO user = securityContext.getAuthenticatedUser().get(); - importJob.setIssuer(user.getPubkey()); - File inputFile = fileController.getUserUploadFile(fileName); if (!inputFile.exists() || !inputFile.isFile()) { throw new SumarisTechnicalException("File not found, or invalid"); } + PersonVO user = securityContext.getAuthenticatedUser().get(); + JobVO job = JobVO.builder() + .type(JobTypeEnum.SIOP_VESSELS_IMPORTATION.name()) + .name(t("sumaris.import.vessel.siop.job.name", fileName)) + .issuer(user.getPubkey()) + .build(); SiopVesselImportContextVO context = SiopVesselImportContextVO.builder() .recorderPersonId(user.getId()) .processingFile(inputFile) .build(); // Execute importJob by JobService (async) - return jobExecutionService.run(importJob, () -> context, + return jobExecutionService.run(job, + () -> context, (progression) -> siopVesselImportService.asyncImportFromFile(context, progression)); } diff --git a/sumaris-importation/src/test/resources/application-test-hsqldb.properties b/sumaris-importation/src/test/resources/application-test-hsqldb.properties index 165a14bc39..d297659384 100644 --- a/sumaris-importation/src/test/resources/application-test-hsqldb.properties +++ b/sumaris-importation/src/test/resources/application-test-hsqldb.properties @@ -16,7 +16,7 @@ spring.jms.enabled=false spring.activemq.enabled=false # DataSource configuration -spring.datasource.platform=hsqldb +spring.sql.init.platform=hsqldb spring.datasource.initialization-mode=always spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver spring.datasource.username=sa diff --git a/sumaris-rdf/pom.xml b/sumaris-rdf/pom.xml index 3d42306abe..7c4efb08e7 100644 --- a/sumaris-rdf/pom.xml +++ b/sumaris-rdf/pom.xml @@ -3,7 +3,7 @@ sumaris-pod net.sumaris - 2.1.0 + 2.1.1 4.0.0 @@ -18,7 +18,7 @@ ${i18n.bundleOutputName} - hsqldb + hsqldb @@ -221,7 +221,7 @@ true - spring.datasource.platform + spring.sql.init.platform hsqldb diff --git a/sumaris-rdf/src/main/filtered-resources/application-default.properties b/sumaris-rdf/src/main/filtered-resources/application-default.properties index 18ddc1b4e1..0d29cc3d30 100644 --- a/sumaris-rdf/src/main/filtered-resources/application-default.properties +++ b/sumaris-rdf/src/main/filtered-resources/application-default.properties @@ -14,7 +14,7 @@ spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver spring.datasource.username=sa spring.datasource.password= #spring.datasource.url=jdbc:hsqldb:hsql://localhost/sumaris -spring.datasource.platform=@env@ +spring.sql.init.platform=@env@ spring.datasource.hikari.connectionTestQuery=SELECT 1 FROM STATUS WHERE ID=1 spring.datasource.hikari.initializationFailTimeout=-1 diff --git a/sumaris-rdf/src/test/resources/application-hsqldb.properties b/sumaris-rdf/src/test/resources/application-hsqldb.properties index 84d44e3e99..850d6a711a 100644 --- a/sumaris-rdf/src/test/resources/application-hsqldb.properties +++ b/sumaris-rdf/src/test/resources/application-hsqldb.properties @@ -36,7 +36,7 @@ spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver spring.datasource.username=sa spring.datasource.password= #spring.datasource.url=jdbc:hsqldb:hsql://localhost/sumaris -spring.datasource.platform=hsqldb +spring.sql.init.platform=hsqldb spring.datasource.hikari.connectionTestQuery=SELECT 1 FROM STATUS WHERE ID=1 spring.datasource.hikari.initializationFailTimeout=-1 spring.datasource.initialization-mode=always diff --git a/sumaris-server/pom.xml b/sumaris-server/pom.xml index 2216398963..a9ac377d76 100644 --- a/sumaris-server/pom.xml +++ b/sumaris-server/pom.xml @@ -4,7 +4,7 @@ net.sumaris sumaris-pod - 2.1.0 + 2.1.1 sumaris-server @@ -31,7 +31,7 @@ ${project.build.directory}/${bundlePrefix}.log - hsqldb + hsqldb jdbc:hsqldb:file:data/db/sumaris localhost 8080 @@ -383,7 +383,7 @@ true - spring.datasource.platform + spring.sql.init.platform hsqldb diff --git a/sumaris-server/src/main/assembly/config/application-hsqldb.properties b/sumaris-server/src/main/assembly/config/application-hsqldb.properties index 9edc6ad9d4..248c0d808d 100644 --- a/sumaris-server/src/main/assembly/config/application-hsqldb.properties +++ b/sumaris-server/src/main/assembly/config/application-hsqldb.properties @@ -6,7 +6,7 @@ spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.di spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform} # Database connection -spring.datasource.platform=hsqldb +spring.sql.init.platform=hsqldb spring.datasource.username=sa spring.datasource.password= spring.jpa.properties.hibernate.default_catalog=PUBLIC diff --git a/sumaris-server/src/main/assembly/config/application-oracle.properties b/sumaris-server/src/main/assembly/config/application-oracle.properties index 76261733e1..68731040c5 100644 --- a/sumaris-server/src/main/assembly/config/application-oracle.properties +++ b/sumaris-server/src/main/assembly/config/application-oracle.properties @@ -6,7 +6,7 @@ spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.di spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform} # Database connection -spring.datasource.platform=oracle +spring.sql.init.platform=oracle spring.datasource.username= spring.datasource.password= spring.jpa.properties.hibernate.default_catalog= diff --git a/sumaris-server/src/main/filtered-resources/application-default.properties b/sumaris-server/src/main/filtered-resources/application-default.properties index d987ad3669..dd4b355a5d 100644 --- a/sumaris-server/src/main/filtered-resources/application-default.properties +++ b/sumaris-server/src/main/filtered-resources/application-default.properties @@ -92,15 +92,15 @@ spring.jms.cache.enabled=true #spring.jms.cache.session-cache-size=5 #spring.jms.listener.acknowledge-mode=auto #spring.jms.listener.auto-startup=true -#spring.jms.listener.concurrency=1 -#spring.jms.listener.max-concurrency=10 -#spring.jms.pub-sub-domain=false +spring.jms.listener.concurrency=1 +spring.jms.listener.max-concurrency=5 +spring.jms.pub-sub-domain=true #spring.jms.template.default-destination=empty #spring.jms.template.qos-enabled=true #spring.jms.template.delivery-mode=persistent #spring.jms.template.priority=100 #spring.jms.template.receive-timeout=10000 -#spring.jms.template.time-to-live=36000 +spring.jms.template.time-to-live=60000 ## MULTIPART (MultipartProperties) # Enable multipart uploads diff --git a/sumaris-server/src/main/filtered-resources/application-hsqldb.properties b/sumaris-server/src/main/filtered-resources/application-hsqldb.properties index 7cbb2f2159..e6bcf95020 100644 --- a/sumaris-server/src/main/filtered-resources/application-hsqldb.properties +++ b/sumaris-server/src/main/filtered-resources/application-hsqldb.properties @@ -7,7 +7,6 @@ spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform} # Database connection spring.sql.init.platform=hsqldb -spring.datasource.platform=${spring.sql.init.platform} spring.datasource.url=jdbc:hsqldb:hsql://localhost/sumaris spring.datasource.username=sa spring.datasource.password= diff --git a/sumaris-server/src/main/filtered-resources/application-oracle.properties b/sumaris-server/src/main/filtered-resources/application-oracle.properties index e1ac92b1b3..7dcad12839 100644 --- a/sumaris-server/src/main/filtered-resources/application-oracle.properties +++ b/sumaris-server/src/main/filtered-resources/application-oracle.properties @@ -8,7 +8,6 @@ spring.datasource.hikari.maximum-pool-size=20 # Database connection spring.sql.init.platform=oracle -spring.datasource.platform=${spring.sql.init.platform} #spring.datasource.url=jdbc:oracle:thin:@localhost:1521:ORCL #spring.datasource.username= #spring.datasource.password= diff --git a/sumaris-server/src/main/filtered-resources/application-pgsql.properties b/sumaris-server/src/main/filtered-resources/application-pgsql.properties index a5b7894b1c..4efc5351be 100644 --- a/sumaris-server/src/main/filtered-resources/application-pgsql.properties +++ b/sumaris-server/src/main/filtered-resources/application-pgsql.properties @@ -7,7 +7,6 @@ spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform} # Database connection spring.sql.init.platform=pgsql -spring.datasource.platform=${spring.sql.init.platform} spring.datasource.username=sumaris spring.datasource.password=sumaris spring.jpa.properties.hibernate.default_catalog= diff --git a/sumaris-server/src/main/java/net/sumaris/server/http/graphql/social/UserEventGraphQLService.java b/sumaris-server/src/main/java/net/sumaris/server/http/graphql/social/UserEventGraphQLService.java index fe5b7ded4a..8ccff7b389 100644 --- a/sumaris-server/src/main/java/net/sumaris/server/http/graphql/social/UserEventGraphQLService.java +++ b/sumaris-server/src/main/java/net/sumaris/server/http/graphql/social/UserEventGraphQLService.java @@ -178,13 +178,13 @@ public Publisher updateUserEventsCount( filter.setStartDate(userEventService.getLastReadDate(filter.getRecipients())); } - log.info("Checking events count for User#{} by events and every {} sec", filter.getRecipients(), intervalInSeconds); + log.info("Checking events count for users {} every {} sec", filter.getRecipients(), intervalInSeconds); UserEventFilterVO finalFilter = filter; return entityWatchService.watchEntitiesCount( UserEvent.class, Observables.distinctUntilChanged(() -> { - log.debug("Checking events count for User#{} from {}", finalFilter.getRecipients(), finalFilter.getStartDate()); + log.debug("Checking events count for users {} from {}", finalFilter.getRecipients(), finalFilter.getStartDate()); // find new user events List list = userEventService.findAll(finalFilter); // get max read date of current result and set next filter diff --git a/sumaris-server/src/test/resources/sumaris-server-test.properties b/sumaris-server/src/test/resources/sumaris-server-test.properties index 53e70ad3c8..9e5eb2d542 100644 --- a/sumaris-server/src/test/resources/sumaris-server-test.properties +++ b/sumaris-server/src/test/resources/sumaris-server-test.properties @@ -38,7 +38,7 @@ spring.datasource.password= #spring.datasource.url=@jdbc.url@ #spring.datasource.url=jdbc:hsqldb:hsql://localhost/sumaris spring.datasource.url=jdbc:hsqldb:file:../sumaris-core/target/db/sumaris -spring.datasource.platform=hsqldb +spring.sql.init.platform=hsqldb spring.datasource.initialization-mode=always diff --git a/sumaris-test-shared/pom.xml b/sumaris-test-shared/pom.xml index 618ae4cb3d..338b18b8d4 100644 --- a/sumaris-test-shared/pom.xml +++ b/sumaris-test-shared/pom.xml @@ -4,7 +4,7 @@ net.sumaris sumaris-pod - 2.1.0 + 2.1.1 sumaris-test-shared diff --git a/sumaris-test-shared/src/main/java/net/sumaris/core/test/DatabaseResource.java b/sumaris-test-shared/src/main/java/net/sumaris/core/test/DatabaseResource.java index a0b4a88bcf..5224a2d88f 100644 --- a/sumaris-test-shared/src/main/java/net/sumaris/core/test/DatabaseResource.java +++ b/sumaris-test-shared/src/main/java/net/sumaris/core/test/DatabaseResource.java @@ -538,18 +538,18 @@ public String getDatasourcePlatform() { * @return a {@link String} object. */ protected String getDatasourcePlatform(String defaultValue) { - String result = System.getProperty("spring.datasource.platform"); + String result = System.getProperty("spring.sql.init.platform"); // Check validity if (result == null && StringUtils.isNotBlank(defaultValue)) { result = defaultValue; - log.debug("Could not find build environment. Please add -Dspring.datasource.platform=. Test [{}] will use default environment : {}", testClass, defaultValue); + log.debug("Could not find build environment. Please add -Dspring.sql.init.platform=. Test [{}] will use default environment : {}", testClass, defaultValue); } else if (!"hsqldb".equals(result) && !"oracle".equals(result) && !"pgsql".equals(result)) { if (log.isWarnEnabled()) { - log.warn("Could not find build environment. Please add -Dspring.datasource.platform=. Test [{}] will be skipped.", testClass); + log.warn("Could not find build environment. Please add -Dspring.sql.init.platform=. Test [{}] will be skipped.", testClass); } Assume.assumeTrue(false); } diff --git a/sumaris-test-shared/src/main/resources/data-hsqldb-01-common.xml b/sumaris-test-shared/src/main/resources/data-hsqldb-01-common.xml index 2087ef1ee7..683d380f6f 100644 --- a/sumaris-test-shared/src/main/resources/data-hsqldb-01-common.xml +++ b/sumaris-test-shared/src/main/resources/data-hsqldb-01-common.xml @@ -991,7 +991,7 @@ - + diff --git a/sumaris-test-shared/src/main/resources/data-hsqldb-02-program-APASE.xml b/sumaris-test-shared/src/main/resources/data-hsqldb-02-program-APASE.xml index 8b972952df..a937201d78 100644 --- a/sumaris-test-shared/src/main/resources/data-hsqldb-02-program-APASE.xml +++ b/sumaris-test-shared/src/main/resources/data-hsqldb-02-program-APASE.xml @@ -59,6 +59,7 @@ + diff --git a/sumaris-test-shared/src/main/resources/data-hsqldb-03-data.xml b/sumaris-test-shared/src/main/resources/data-hsqldb-03-data.xml index e5826e41a2..e72e5d55af 100644 --- a/sumaris-test-shared/src/main/resources/data-hsqldb-03-data.xml +++ b/sumaris-test-shared/src/main/resources/data-hsqldb-03-data.xml @@ -186,11 +186,13 @@ + - + + @@ -447,12 +449,12 @@ - + - + @@ -499,7 +501,7 @@ - + @@ -529,6 +531,8 @@ + + @@ -542,9 +546,6 @@ - - - @@ -554,23 +555,36 @@ - + + - - - - - - + + + + + + + + + + + + + + + + + + - + @@ -606,12 +620,12 @@ - + - + @@ -622,13 +636,15 @@ PARENT_BATCH_FK="103" INDIVIDUAL_COUNT="1" REFERENCE_TAXON_FK="1052" OPERATION_FK="100" UPDATE_DATE="2022-11-11" RECORDER_DEPARTMENT_FK="8" QUALITY_FLAG_FK="0"/> - - + + + + @@ -639,11 +655,13 @@ PARENT_BATCH_FK="113" INDIVIDUAL_COUNT="1" REFERENCE_TAXON_FK="1052" OPERATION_FK="100" UPDATE_DATE="2022-11-11" RECORDER_DEPARTMENT_FK="8" QUALITY_FLAG_FK="0"/> - - + + + + - @@ -672,6 +689,9 @@ + + + - - + + + + + diff --git a/sumaris-xml-query/LICENSE.txt b/sumaris-xml-query/LICENSE.txt new file mode 100644 index 0000000000..94a9ed024d --- /dev/null +++ b/sumaris-xml-query/LICENSE.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/sumaris-xml-query/pom.xml b/sumaris-xml-query/pom.xml new file mode 100644 index 0000000000..6fdd4ea721 --- /dev/null +++ b/sumaris-xml-query/pom.xml @@ -0,0 +1,140 @@ + + + 4.0.0 + + + net.sumaris + sumaris-pod + 2.1.1 + + + sumaris-xml-query + SUMARiS:: XML Query + SUMARiS XMl query module + + + + sumaris-xml-query-i18n + ${i18n.bundleOutputName}.csv + ${i18n.bundleOutputName} + + + + + + net.sumaris + sumaris-core-shared + ${project.version} + + + org.javassist + javassist + compile + + + + + fr.ifremer.common + xmlquery + + + org.jdom + jdom2 + + + jaxen + jaxen + + + xerces + xercesImpl + 2.12.1 + + + + + net.sumaris + sumaris-test-shared + ${project.version} + test + + + junit + junit + test + + + org.dbunit + dbunit + test + + + org.springframework.boot + spring-boot-starter-test + test + + + com.mattbertolini + liquibase-slf4j + test + + + com.oracle + ojdbc8 + test + + + org.hsqldb + hsqldb + test + + + + + + + + + + org.nuiton.i18n + i18n-maven-plugin + + + + scan-sources + + + + parserValidation + ${maven.src.dir}/main/java/ + + **/**-validation.xml + + + + + + parserJava + parserValidation + gen + + + + make-bundle + + bundle + generate-csv-bundle + + + + + + + maven-antrun-plugin + + + + + + + \ No newline at end of file diff --git a/sumaris-xml-query/src/license/THIRD-PARTY.properties b/sumaris-xml-query/src/license/THIRD-PARTY.properties new file mode 100644 index 0000000000..bd48587595 --- /dev/null +++ b/sumaris-xml-query/src/license/THIRD-PARTY.properties @@ -0,0 +1,70 @@ +# Generated by org.codehaus.mojo.license.AddThirdPartyMojo +#------------------------------------------------------------------------------- +# Already used licenses in project : +# - ASF 2.0 +# - Affero General Public License (AGPL) +# - Apache 2.0 +# - Apache License 2.0 +# - Apache License, version 2.0 +# - BSD 3-clause New License +# - BSD Licence 3 +# - BSD License +# - BSD License 2.0 +# - BSD License 3 +# - BSD style +# - BSD-2-Clause +# - BSD-3-Clause +# - CDDL + GPLv2 with classpath exception +# - CDDL 1.1 +# - CDDL+GPL License +# - CDDL/GPLv2+CE +# - COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0 +# - Common Development and Distribution License +# - Dual license consisting of the CDDL v1.1 and GPL v2 +# - EDL 1.0 +# - EPL 2.0 +# - Eclipse Distribution License - v 1.0 +# - Eclipse Distribution License v. 1.0 +# - Eclipse Public License - v 1.0 +# - Eclipse Public License - v 2.0 +# - Eclipse Public License 1.0 +# - Eclipse Public License 2.0 +# - Eclipse Public License v1.0 +# - Eclipse Public License, Version 2.0 +# - GNU General Public License, Version 2 with the Classpath Exception +# - GNU General Public License, version 2 with the GNU Classpath Exception +# - GNU Lesser General Public License, Version 2.1 +# - GNU Lesser Public License +# - GNU Library General Public License v2.1 or later +# - GPL2 w/ CPE +# - General Public License (GPL) v3 +# - HSQLDB License, a BSD open source license +# - Indiana University Extreme! Lab Software License, vesion 1.1.1 +# - LGPL 3.0 +# - Lesser General Public License (LGPL) v 3.0 +# - Lesser General Public License (LPGL) +# - Lesser General Public License (LPGL) v 2.1 +# - Lesser General Public License (LPGL) version 3.0 +# - MIT License +# - MIT-0 +# - MPL 1.1 +# - New BSD License +# - Similar to Apache License but with the acknowledgment clause removed +# - The Apache License, Version 2.0 +# - The Apache Software License, Version 2.0 +# - The BSD 2-Clause License +# - The BSD License +# - The MIT License +# - The MIT License (MIT) +# - The New BSD License +# - The SAX License +# - The W3C License +# - WTFPL +#------------------------------------------------------------------------------- +# Please fill the missing licenses for dependencies : +# +# +#Mon Mar 27 09:17:27 CEST 2023 +net.jcip--jcip-annotations--1.0=The Apache Software License, Version 2.0 +com.oracle--ojdbc8--12.2.0.1=OTN license +commons-primitives--commons-primitives--1.0=The Apache Software License, Version 2.0 diff --git a/sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQuery.java b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQuery.java new file mode 100644 index 0000000000..cfa06404d1 --- /dev/null +++ b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQuery.java @@ -0,0 +1,130 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +/* + * Created on 29 juil. 2004 + */ +package net.sumaris.xml.query; + +import fr.ifremer.common.xmlquery.XMLQueryException; +import org.apache.commons.collections4.Predicate; +import org.jdom2.Document; +import org.jdom2.Element; + +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.net.URL; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Stream; + +/** + * @author ludovic.pecquot@e-is.pro + */ +public interface XMLQuery { + + void setQuery(String resourcePath); + + void setQuery(InputStream is) throws IOException; + + String getSQLQueryAsString(); + Set getHiddenColumnNames(); + + Set getVisibleColumnNames(); + + Set getNotNumericColumnNames(); + + Set getAllColumnNames(); + + Set getColumnNames(Predicate filter); + + Stream streamSelectElements(Predicate filter); + + String getAlias(Element element); + + String getAlias(Element element, boolean forceLowerCase); + + String getTextContent(Element element, String separator); + + String getAttributeValue(Element element, String attrName, boolean forceLowerCase); + + boolean hasGroup(Element element, String groupName); + + void removeGroup(Element element, String groupName); + + Set extractGroups(); + + boolean hasDistinctOption(); + + Document getDocument(); + + Element getFirstQueryTag(); + + List getGroupByTags(Predicate filter); + + void injectQuery(File pXmlFile) throws XMLQueryException; + + void injectQuery(URL pXmlFileURL) throws XMLQueryException; + + void injectQuery(String pXmlFilter) throws XMLQueryException; + + void injectQuery(File pXmlFile, String injectionPointName) throws XMLQueryException; + + void injectQuery(URL pXmlFileURL, String injectionPointName) throws XMLQueryException; + + void injectQuery(String pXmlFilter, String injectionPointName) throws XMLQueryException; + + void injectQuery(File pXmlFile, String pattern, String replacement) throws XMLQueryException; + + void injectQuery(URL pXmlFileURL, String pattern, String replacement) throws XMLQueryException; + + void injectQuery(String pXmlFilter, String pattern, String replacement) throws XMLQueryException; + + void injectQuery(File pXmlFile, String pattern, String replacement, String injectionPointName) throws XMLQueryException; + + void injectQuery(URL pXmlFileURL, String pattern, String replacement, String injectionPointName) throws XMLQueryException; + + void injectQuery(String pXmlFilter, String pattern, String replacement, String injectionPointName) throws XMLQueryException; + + void bind(String pName, String pValue) throws XMLQueryException; + + void setGroup(String groupName, boolean active); + + void setDbms(String dbms); + + String getQueryName() throws XMLQueryException; + + int getSelectCount() throws XMLQueryException; + + int getSelectCountFirstLevel() throws XMLQueryException; + + String getGroupByParamName(); + + boolean isDisabled(Element e); + + Map getSqlParameters(); + + void bindGroupBy(String groupByParamName); + +} diff --git a/sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQuery2Impl.java b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQuery2Impl.java new file mode 100644 index 0000000000..e9570e261b --- /dev/null +++ b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQuery2Impl.java @@ -0,0 +1,242 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.xml.query; + +import com.google.common.collect.ImmutableList; +import com.google.common.collect.Lists; +import net.sumaris.core.dao.technical.DatabaseType; +import net.sumaris.xml.query.utils.ClasspathEntityResolver; +import org.jdom2.*; +import org.jdom2.filter.Filters; +import org.jdom2.input.SAXBuilder; +import org.jdom2.transform.JDOMSource; +import org.jdom2.util.IteratorIterable; +import org.jdom2.xpath.XPathExpression; +import org.jdom2.xpath.XPathFactory; + +import javax.xml.transform.Transformer; +import javax.xml.transform.TransformerFactory; +import javax.xml.transform.stream.StreamResult; +import javax.xml.transform.stream.StreamSource; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.io.InputStream; +import java.io.StringWriter; +import java.util.*; + +public class XMLQuery2Impl { + private Document document; + + private DatabaseType dbms; + private Map bindings; + private Map groupBindings; + + public XMLQuery2Impl() { + this(null); + } + + public XMLQuery2Impl(DatabaseType dbms) { + this.dbms = dbms; + bindings = new HashMap<>(); + groupBindings = new HashMap<>(); + } + + public void setDbms(DatabaseType dbms) { + this.dbms = dbms; + } + + public void setQuery(String xmlResourcePath) throws IOException, JDOMException { + InputStream xmlInputStream = getInputStream(xmlResourcePath); + document = readXmlInputSTream(xmlInputStream, true); + } + + public void setQuery(InputStream xmlInputStream) throws IOException, JDOMException { + document = readXmlInputSTream(xmlInputStream, true); + } + + public Document getDocument() { + return this.document; + } + + public void setGroup(String groupName, boolean enabled) { + groupBindings.put(groupName, enabled); + } + + public void bind(String variable, String value) { + bindings.put(variable, value); + } + + public Set extractGroups() { + Set groups = new HashSet<>(); + + IteratorIterable groupElements = document.getDescendants(Filters.element()); + for (Element groupElement : groupElements) { + String groupName = groupElement.getAttributeValue("group"); + if (groupName != null && !groupName.isEmpty()) { + groups.add(groupName); + } + } + + return groups; + } + + /** + * Injects an XML query from a file at a specified injection point. + * + * @param queryFilePath The path to the file containing the XML query to inject. + * @param injectionPointName The name of the injection point where to inject the query (optional). + * If not provided, the query will be appended to the end of the main query. + */ + public void injectQuery(String queryFilePath, String injectionPointName) throws JDOMException, IOException { + // Load the query file from the classpath + InputStream queryInputStream = getInputStream(queryFilePath); + + // Parse the query file into a JDOM Document + Document injectionDocument = readXmlInputSTream(queryInputStream, false); + + // Extract the root element of the query file + Element injectionRoot = injectionDocument.getRootElement(); + + // Find the injection point if specified + if (injectionPointName != null) { + XPathFactory xpathFactory = XPathFactory.instance(); + XPathExpression xpath = xpathFactory.compile("//injection[@name='" + injectionPointName + "']", Filters.element()); + Element injectionPoint = xpath.evaluateFirst(document); + + if (injectionPoint == null) { + throw new IllegalArgumentException("Injection point not found: " + injectionPointName); + } + + // Replace the injection point with the contents of the query file + XPathExpression injectionXpath = xpathFactory.compile("//query", Filters.element()); + Element injectionQuery = injectionXpath.evaluateFirst(injectionDocument); + + List injectionContent = ImmutableList.copyOf(injectionQuery.getContent()); + injectionContent.forEach(Content::detach); + + injectionPoint.getParentElement().addContent( + injectionPoint.getParentElement().indexOf(injectionPoint), + injectionContent); + injectionPoint.detach(); + } else { + // Append the contents of the query file to the end of the main query + injectionRoot.detach(); + injectionRoot.removeNamespaceDeclaration(Namespace.XML_NAMESPACE); + document.getRootElement().addContent(injectionRoot.getContent()); + } + } + + public String toSql() throws Exception { + applyGroupBindings(); + removeDisabledGroups(); + String transformedXml = applyXslTransformation(); + + return replaceBindings(transformedXml); + } + + private void applyGroupBindings() { + IteratorIterable groupElements = document.getDescendants(Filters.element()); + + for (Element groupElement : groupElements) { + String groupName = groupElement.getAttributeValue("group"); + if (groupName != null && !groupName.isEmpty() && groupBindings.containsKey(groupName)) { + groupElement.setAttribute("enabled", String.valueOf(groupBindings.get(groupName))); + } + } + } + + private void removeDisabledGroups() { + IteratorIterable groupElements = document.getDescendants(Filters.element("where")); + + List disabledGroups = Lists.newArrayList(); + for (Element groupElement : groupElements) { + String enabled = groupElement.getAttributeValue("enabled"); + if (enabled != null && !Boolean.parseBoolean(enabled)) { + disabledGroups.add(groupElement); + } + } + disabledGroups.forEach(Element::detach); + } + + private String applyXslTransformation() throws Exception { + InputStream xslInputStream = getInputStream("classpath:xsl/queryHsqldb.xsl"); + StreamSource xslStreamSource = new StreamSource(xslInputStream); + + // Remove the DTD + DocType docType = document.getDocType(); + if (docType != null) { + docType.detach(); + } + + JDOMSource xmlSource = new JDOMSource(document); + StringWriter stringWriter = new StringWriter(); + StreamResult result = new StreamResult(stringWriter); + + TransformerFactory transformerFactory = TransformerFactory.newInstance(); + Transformer transformer = transformerFactory.newTransformer(xslStreamSource); + transformer.transform(xmlSource, result); + + return stringWriter.toString(); + } + + private String replaceBindings(String input) { + for (Map.Entry entry : bindings.entrySet()) { + input = input.replace("&" + entry.getKey(), entry.getValue()); + } + return input; + } + + private InputStream getInputStream(String resourcePath) throws IOException { + InputStream result; + if (resourcePath.startsWith("classpath:")) { + resourcePath = resourcePath.substring("classpath:".length()); + result = getClass().getClassLoader().getResourceAsStream(resourcePath); + } + else { + if (resourcePath.startsWith("file:")) { + resourcePath = resourcePath.substring("file:".length()); + } + result = getClass().getResourceAsStream(resourcePath); + } + if (result == null) { + throw new FileNotFoundException("Cannot find resource at: " + resourcePath); + } + return result; + } + + /** + * Parse the query file into a JDOM Document + * @param xmlInputStream + * @return + * @throws IOException + * @throws JDOMException + */ + private Document readXmlInputSTream(InputStream xmlInputStream, boolean validation) throws IOException, JDOMException { + SAXBuilder saxBuilder = new SAXBuilder(); + if (validation) { + saxBuilder.setValidation(true); + saxBuilder.setEntityResolver(new ClasspathEntityResolver()); + } + return saxBuilder.build(xmlInputStream); + } +} diff --git a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/technical/xml/XMLQuery.java b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQueryImpl.java similarity index 75% rename from sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/technical/xml/XMLQuery.java rename to sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQueryImpl.java index 6e29d9bc20..e66b405d12 100644 --- a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/technical/xml/XMLQuery.java +++ b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/XMLQueryImpl.java @@ -23,37 +23,52 @@ /* * Created on 29 juil. 2004 */ -package net.sumaris.extraction.core.dao.technical.xml; +package net.sumaris.xml.query; import com.google.common.base.Preconditions; import fr.ifremer.common.xmlquery.*; import lombok.NonNull; import net.sumaris.core.dao.technical.DatabaseType; import net.sumaris.core.exception.SumarisTechnicalException; +import net.sumaris.core.util.Beans; +import net.sumaris.core.util.Files; import net.sumaris.core.util.StringUtils; +import net.sumaris.xml.query.utils.XPaths; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.collections4.Predicate; +import org.apache.commons.io.IOUtils; import org.jdom2.Attribute; import org.jdom2.Document; import org.jdom2.Element; +import org.jdom2.Text; import org.jdom2.filter.Filters; import org.jdom2.output.Format; +import org.jdom2.util.IteratorIterable; -import java.io.File; -import java.io.InputStream; +import java.io.*; import java.net.URL; +import java.nio.charset.Charset; import java.util.*; import java.util.stream.Collectors; +import java.util.stream.IntStream; +import java.util.stream.Stream; /** * @author ludovic.pecquot@e-is.pro */ -public class XMLQuery { +public class XMLQueryImpl implements XMLQuery { private DatabaseType dbms; - private AsbtractSingleXMLQuery delegate; + private AbstractSingleXMLQuery delegate; - public XMLQuery(@NonNull DatabaseType dbms) { + private Set deactivatedGroups = null; + private String groupByParamName = null; + + public XMLQueryImpl(@NonNull String dbmsName) { + this(DatabaseType.valueOf(dbmsName)); + } + + public XMLQueryImpl(@NonNull DatabaseType dbms) { super(); this.dbms = dbms; switch (dbms) { @@ -82,6 +97,7 @@ public XMLQuery(@NonNull DatabaseType dbms) { * * @return */ + @Override public Set getHiddenColumnNames() { try { @@ -101,6 +117,7 @@ public Set getHiddenColumnNames() { } } + @Override public Set getVisibleColumnNames() { return getColumnNames(element -> { Attribute typeAttr = element.getAttribute("type"); @@ -108,6 +125,7 @@ public Set getVisibleColumnNames() { }); } + @Override public Set getNotNumericColumnNames() { return getColumnNames(element -> { Attribute typeAttr = element.getAttribute("type"); @@ -115,10 +133,12 @@ public Set getNotNumericColumnNames() { }); } + @Override public Set getAllColumnNames() { return getColumnNames(element -> true); } + @Override public Set getColumnNames(final Predicate filter) { Preconditions.checkNotNull(filter); @@ -131,17 +151,49 @@ public Set getColumnNames(final Predicate filter) { // Apply filter .filter(filter::evaluate) // Get alias - .map(element -> element.getAttribute("alias")) - .filter(Objects::nonNull) - .map(Attribute::getValue) - .filter(Objects::nonNull) - .map(String::toLowerCase) + .map(this::getAlias) .collect(Collectors.toCollection(LinkedHashSet::new)); } catch (Exception e) { throw new SumarisTechnicalException(e); } } + @Override + public Stream streamSelectElements(final Predicate filter) { + Preconditions.checkNotNull(filter); + + try { + List selectElements = XPaths.compile("//query/select", Filters.element()) + .evaluate(getDocument()); + if (CollectionUtils.isEmpty(selectElements)) return Stream.empty(); + + + // Apply filter + return selectElements.stream().filter(filter::evaluate); + } catch (Exception e) { + throw new SumarisTechnicalException(e); + } + } + + @Override + public String getAlias(final Element element) { + return getAttributeValue(element, "alias", true); + } + + @Override + public String getAlias(final Element element, boolean forceLowerCase) { + return getAttributeValue(element, "alias", forceLowerCase); + } + + + @Override + public String getTextContent(final Element element, String separator) { + return Beans.getStream(element.getContent(Filters.text())) + .map(Text::getValue) + .collect(Collectors.joining(separator)); + } + + @Override public String getAttributeValue(final Element element, String attrName, boolean forceLowerCase) { Attribute attr = element.getAttribute(attrName); if (attr == null) return null; @@ -150,37 +202,89 @@ public String getAttributeValue(final Element element, String attrName, boolean return value; } + @Override public boolean hasGroup(final Element element, String groupName) { String attrValue = getAttributeValue(element, "group", false); if (StringUtils.isBlank(attrValue)) return false; return Arrays.asList(attrValue.split(",")).contains(groupName); } + @Override + public void removeGroup(final Element element, String groupName) { + String attrValue = getAttributeValue(element, "group", false); + if (StringUtils.isBlank(attrValue)) return; + String newAttrValue = Arrays.stream(attrValue.split(",")) + .filter(g -> !groupName.equals(g)) + .collect(Collectors.joining(",")); + if (StringUtils.isBlank(newAttrValue)) { + element.removeAttribute("group"); + } + else { + element.setAttribute("group", newAttrValue); + } + } + + @Override + public Set extractGroups() { + Set groups = new HashSet<>(); + + IteratorIterable groupElements = getDocument().getDescendants(Filters.element()); + for (Element groupElement : groupElements) { + String groupName = groupElement.getAttributeValue("group"); + if (groupName != null && !groupName.isEmpty()) { + groups.add(groupName); + } + } + + return groups; + } + /** * Return if option="DISTINCT" has been set on the query * * @return */ + @Override public boolean hasDistinctOption() { Attribute optionAtr = getFirstQueryTag().getAttribute("option"); return optionAtr != null && "distinct".equalsIgnoreCase(optionAtr.getValue()); } + @Override public Document getDocument() { return delegate.getDocument(); } - + @Override public Element getFirstQueryTag() { return delegate.getFirstQueryTag(); } + @Override + public List getGroupByTags(final Predicate filter) { + Preconditions.checkNotNull(filter); + + try { + List groupByElements = XPaths.compile("//query/groupby", Filters.element()) + .evaluate(getDocument()); + if (CollectionUtils.isEmpty(groupByElements)) return null; + + return groupByElements.stream() + // Apply filter + .filter(filter::evaluate) + .toList(); + } catch (Exception e) { + throw new SumarisTechnicalException(e); + } + } + /* -- delegated functions -- */ public void manageRootElement() throws XMLQueryException { delegate.manageRootElement(); } + @Override public String getSQLQueryAsString() { String query = delegate.getSQLQueryAsString(); @@ -241,6 +345,12 @@ public void setQuery(File pQueryFile) throws XMLQueryException { delegate.setQuery(pQueryFile); } + public void setQuery(InputStream inputStream) throws XMLQueryException, IOException { + StringWriter writer = new StringWriter(); + IOUtils.copy(inputStream, writer, "UTF-8"); + delegate.setQuery(writer.toString(), true); + } + public void setQuery(File pQueryFile, boolean pManageRootElement) throws XMLQueryException { delegate.setQuery(pQueryFile, pManageRootElement); } @@ -261,18 +371,6 @@ public void addSelect(String pXmlFilter) throws XMLQueryException { delegate.addSelect(pXmlFilter); } - public void addSubSelect(File pXmlFile) throws XMLQueryException { - delegate.addSubSelect(pXmlFile); - } - - public void addSubSelect(URL pXmlFileURL) throws XMLQueryException { - delegate.addSubSelect(pXmlFileURL); - } - - public void addSubSelect(String pXmlFilter) throws XMLQueryException { - delegate.addSubSelect(pXmlFilter); - } - public void addSelect(String pQueryName, File pXmlFile) throws XMLQueryException { delegate.addSelect(pQueryName, pXmlFile); } @@ -285,18 +383,6 @@ public void addSelect(String pQueryName, String pXmlFilter) throws XMLQueryExcep delegate.addSelect(pQueryName, pXmlFilter); } - public void addSubSelect(String pQueryName, File pXmlFile) throws XMLQueryException { - delegate.addSubSelect(pQueryName, pXmlFile); - } - - public void addSubSelect(String pQueryName, URL pXmlFileURL) throws XMLQueryException { - delegate.addSubSelect(pQueryName, pXmlFileURL); - } - - public void addSubSelect(String pQueryName, String pXmlFilter) throws XMLQueryException { - delegate.addSubSelect(pQueryName, pXmlFilter); - } - public void addFrom(File pXmlFile) throws XMLQueryException { delegate.addFrom(pXmlFile); } @@ -353,50 +439,62 @@ public void addGroupBy(String pXmlFilter) throws XMLQueryException { delegate.addGroupBy(pXmlFilter); } + @Override public void injectQuery(File pXmlFile) throws XMLQueryException { delegate.injectQuery(pXmlFile); } + @Override public void injectQuery(URL pXmlFileURL) throws XMLQueryException { delegate.injectQuery(pXmlFileURL); } + @Override public void injectQuery(String pXmlFilter) throws XMLQueryException { delegate.injectQuery(pXmlFilter); } + @Override public void injectQuery(File pXmlFile, String injectionPointName) throws XMLQueryException { delegate.injectQuery(pXmlFile, injectionPointName); } + @Override public void injectQuery(URL pXmlFileURL, String injectionPointName) throws XMLQueryException { delegate.injectQuery(pXmlFileURL, injectionPointName); } + @Override public void injectQuery(String pXmlFilter, String injectionPointName) throws XMLQueryException { delegate.injectQuery(pXmlFilter, injectionPointName); } + @Override public void injectQuery(File pXmlFile, String pattern, String replacement) throws XMLQueryException { delegate.injectQuery(pXmlFile, pattern, replacement); } + @Override public void injectQuery(URL pXmlFileURL, String pattern, String replacement) throws XMLQueryException { delegate.injectQuery(pXmlFileURL, pattern, replacement); } + @Override public void injectQuery(String pXmlFilter, String pattern, String replacement) throws XMLQueryException { delegate.injectQuery(pXmlFilter, pattern, replacement); } + @Override public void injectQuery(File pXmlFile, String pattern, String replacement, String injectionPointName) throws XMLQueryException { delegate.injectQuery(pXmlFile, pattern, replacement, injectionPointName); } + @Override public void injectQuery(URL pXmlFileURL, String pattern, String replacement, String injectionPointName) throws XMLQueryException { delegate.injectQuery(pXmlFileURL, pattern, replacement, injectionPointName); } + @Override public void injectQuery(String pXmlFilter, String pattern, String replacement, String injectionPointName) throws XMLQueryException { delegate.injectQuery(pXmlFilter, pattern, replacement, injectionPointName); } @@ -425,6 +523,7 @@ public List getXmlQueryAsDocuments() throws XMLQueryException { return delegate.getXmlQueryAsDocuments(); } + @Override public void bind(String pName, String pValue) throws XMLQueryException { delegate.bind(pName, pValue); } @@ -433,22 +532,38 @@ public void validate() throws XMLQueryException { delegate.validate(); } + @Override public void setGroup(String groupName, boolean active) { + if (deactivatedGroups == null) { + deactivatedGroups = new HashSet<>(); + } + // Activer le groupe + if (active) { + deactivatedGroups.remove(groupName); + } + // Ignorer le groupe + else { + deactivatedGroups.add(groupName); + } delegate.setGroup(groupName, active); } + @Override public void setDbms(String dbms) { delegate.setDbms(dbms); } + @Override public String getQueryName() throws XMLQueryException { return delegate.getQueryName(); } + @Override public int getSelectCount() throws XMLQueryException { return delegate.getSelectCount(); } + @Override public int getSelectCountFirstLevel() throws XMLQueryException { return delegate.getSelectCountFirstLevel(); } @@ -505,5 +620,27 @@ public String getXmlAsString(Element pElement) throws XMLQueryException { return delegate.getXmlAsString(pElement); } + public void bindGroupBy(String value) { + this.groupByParamName = value; + } + public void setGroupByParamName(String value) { + this.groupByParamName = value; + } + + public String getGroupByParamName() { + return groupByParamName; + } + + public boolean isDisabled(Element element) { + String groupName = getAttributeValue(element, "group", false); + if (StringUtils.isBlank(groupName)) return false; + + boolean disabled = true; + StringTokenizer tokenizer = new StringTokenizer(groupName, ","); + while (disabled && tokenizer.hasMoreTokens()) { + disabled = deactivatedGroups.contains(tokenizer.nextToken()); + } + return disabled; + } } diff --git a/sumaris-xml-query/src/main/java/net/sumaris/xml/query/annotation/XmlQuery.java b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/annotation/XmlQuery.java new file mode 100644 index 0000000000..7d4081ef81 --- /dev/null +++ b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/annotation/XmlQuery.java @@ -0,0 +1,37 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.xml.query.annotation; + +import net.sumaris.core.dao.technical.DatabaseType; + +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +@Target(ElementType.TYPE) +@Retention(RetentionPolicy.SOURCE) +public @interface XmlQuery { + String value(); // Path to the XML Query file + DatabaseType dbms() default DatabaseType.hsqldb; // DBMS +} \ No newline at end of file diff --git a/sumaris-xml-query/src/main/java/net/sumaris/xml/query/annotation/XmlQueryProcessor.java b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/annotation/XmlQueryProcessor.java new file mode 100644 index 0000000000..6f26e17e11 --- /dev/null +++ b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/annotation/XmlQueryProcessor.java @@ -0,0 +1,173 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.xml.query.annotation; + +import javassist.*; +import javassist.bytecode.AnnotationsAttribute; +import javassist.bytecode.ConstPool; +import javassist.bytecode.annotation.StringMemberValue; +import net.sumaris.core.dao.technical.DatabaseType; +import net.sumaris.core.util.StringUtils; +import net.sumaris.xml.query.XMLQuery; +import net.sumaris.xml.query.XMLQueryImpl; +import org.springframework.stereotype.Component; + +import javax.annotation.processing.AbstractProcessor; +import javax.annotation.processing.RoundEnvironment; +import javax.annotation.processing.SupportedAnnotationTypes; +import javax.annotation.processing.SupportedSourceVersion; +import javax.lang.model.SourceVersion; +import javax.lang.model.element.Element; +import javax.lang.model.element.ElementKind; +import javax.lang.model.element.TypeElement; +import javax.tools.Diagnostic; +import javax.tools.FileObject; +import javax.tools.StandardLocation; +import java.io.IOException; +import java.io.InputStream; +import java.io.PrintWriter; +import java.io.StringWriter; +import java.util.Set; + +@SupportedAnnotationTypes("net.sumaris.xml.query.annotation.XmlQuery") +@SupportedSourceVersion(SourceVersion.RELEASE_8) +public class XmlQueryProcessor extends AbstractProcessor { + + @Override + public boolean process(Set annotations, RoundEnvironment roundEnv) { + processingEnv.getMessager().printMessage(Diagnostic.Kind.WARNING, "Processing..."); + + for (TypeElement annotation : annotations) { + Set annotatedElements = roundEnv.getElementsAnnotatedWith(annotation); + for (Element element : annotatedElements) { + if (element.getKind() == ElementKind.INTERFACE) { + // Process the annotated interface + TypeElement annotatedInterface = (TypeElement) element; + XmlQuery xmlQuery = annotatedInterface.getAnnotation(XmlQuery.class); + + processAnnotatedInterface(annotatedInterface, xmlQuery); + } + } + } + return true; + } + + private void processAnnotatedInterface(TypeElement annotatedInterface, XmlQuery xmlQueryAnnotation) { + String interfaceName = annotatedInterface.getQualifiedName().toString(); + String implClassName = interfaceName + "Impl"; + String implConstructorName = annotatedInterface.getSimpleName() + "Impl"; + String beanName = annotatedInterface.getSimpleName().toString().substring(0,1).toLowerCase() + annotatedInterface.getSimpleName().toString().substring(1); + + processingEnv.getMessager().printMessage(Diagnostic.Kind.NOTE, "Generating class " + implClassName); + + String xmlResourcePath = xmlQueryAnnotation.value(); + DatabaseType dbms = xmlQueryAnnotation.dbms(); + if (dbms == null) dbms = DatabaseType.hsqldb; + + // Load the XML file and create an instance of the XmlQuery class + XMLQueryImpl xmlQuery = new XMLQueryImpl(dbms); + try { + if (xmlResourcePath.startsWith("classpath:")) { + xmlResourcePath = xmlResourcePath.substring("classpath:".length()); + FileObject resource = processingEnv.getFiler().getResource(StandardLocation.CLASS_PATH, "", xmlResourcePath); + InputStream xmlInputStream = resource.openInputStream(); + xmlQuery.setQuery(xmlInputStream); + } + else { + xmlQuery.setQuery(xmlResourcePath); + } + } catch (Exception e) { + processingEnv.getMessager().printMessage(Diagnostic.Kind.ERROR, "Failed to load XML resource: " + xmlResourcePath); + return; + } + + String outputDirectory = processingEnv.getOptions().get("generatedSourcesDirectory"); + if (outputDirectory == null) { + outputDirectory = "target/classes"; + } + + // Extract groups from the XML file + Set groups = xmlQuery.extractGroups(); + + try { + ClassPool classPool = ClassPool.getDefault(); + classPool.appendClassPath(new ClassClassPath(XMLQuery.class)); + + CtClass ctInterface = classPool.get(XMLQuery.class.getName()); + CtClass generatedClass = classPool.makeClass(implClassName); + generatedClass.addInterface(ctInterface); + + // Faire en sorte que la classe générée hérite de XmlQuery + CtClass ctXmlQuery = classPool.get(XMLQueryImpl.class.getName()); + generatedClass.setSuperclass(ctXmlQuery); + + for (String group : groups) { + // Generate enableGroupXxx and disableGroupXxx methods for each group + CtMethod enableMethod = CtNewMethod.make(createEnableGroupMethod(group), generatedClass); + CtMethod disableMethod = CtNewMethod.make(createDisableGroupMethod(group), generatedClass); + + generatedClass.addMethod(enableMethod); + generatedClass.addMethod(disableMethod); + } + + // Generate constructor + CtConstructor constructor = CtNewConstructor.make("public "+ implConstructorName + "() {" + + " super(\"" + dbms.name() + "\");" + + " this.setQuery(\"" + xmlResourcePath + "\");" + + "}", generatedClass); + generatedClass.addConstructor(constructor); + + // Add annotation @Component + CtClass ctComponent = classPool.get(Component.class.getName()); + ConstPool constPool = generatedClass.getClassFile().getConstPool(); + AnnotationsAttribute annotationsAttribute = new AnnotationsAttribute(constPool, AnnotationsAttribute.visibleTag); + javassist.bytecode.annotation.Annotation componentAnnotation = new javassist.bytecode.annotation.Annotation(constPool, ctComponent); + componentAnnotation.addMemberValue("value", new StringMemberValue(beanName, generatedClass.getClassFile().getConstPool())); + annotationsAttribute.addAnnotation(componentAnnotation); + generatedClass.getClassFile().addAttribute(annotationsAttribute); + + // Save the generated class + generatedClass.writeFile(outputDirectory); + } catch (CannotCompileException | NotFoundException | IOException e) { + StringWriter sw = new StringWriter(); + PrintWriter pw = new PrintWriter(sw); + e.printStackTrace(pw); + String stackTrace = sw.toString(); + processingEnv.getMessager().printMessage(Diagnostic.Kind.ERROR, String.format("Failed to generate class '%s' into '%s': %s", + implClassName, + outputDirectory, + stackTrace + )); + } + } + + private String createEnableGroupMethod(String groupName) { + String methodName = "enableGroup" + groupName.substring(0, 1).toUpperCase() + groupName.substring(1); + return "public void " + methodName + "() { setGroup(\"" + groupName + "\", true); }"; + } + + private String createDisableGroupMethod(String groupName) { + String methodName = "disableGroup" + groupName.substring(0, 1).toUpperCase() + groupName.substring(1); + return "public void " + methodName + "() { setGroup(\"" + groupName + "\", false); }"; + } +} diff --git a/sumaris-xml-query/src/main/java/net/sumaris/xml/query/utils/ClasspathEntityResolver.java b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/utils/ClasspathEntityResolver.java new file mode 100644 index 0000000000..6d761515da --- /dev/null +++ b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/utils/ClasspathEntityResolver.java @@ -0,0 +1,45 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.xml.query.utils; + +import org.xml.sax.EntityResolver; +import org.xml.sax.InputSource; +import org.xml.sax.SAXException; + +import java.io.IOException; +import java.io.InputStream; + +public class ClasspathEntityResolver implements EntityResolver { + + @Override + public InputSource resolveEntity(String publicId, String systemId) throws SAXException, IOException { + String dtdFile = "dtd/" + systemId.substring(systemId.lastIndexOf("/") + 1); + InputStream inputStream = getClass().getClassLoader().getResourceAsStream(dtdFile); + + if (inputStream == null) { + throw new SAXException("DTD file not found in classpath: " + dtdFile); + } + + return new InputSource(inputStream); + } +} diff --git a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/technical/xml/XPaths.java b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/utils/XPaths.java similarity index 97% rename from sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/technical/xml/XPaths.java rename to sumaris-xml-query/src/main/java/net/sumaris/xml/query/utils/XPaths.java index 3270ee3aa4..02f8155d6b 100644 --- a/sumaris-extraction/src/main/java/net/sumaris/extraction/core/dao/technical/xml/XPaths.java +++ b/sumaris-xml-query/src/main/java/net/sumaris/xml/query/utils/XPaths.java @@ -1,4 +1,4 @@ -package net.sumaris.extraction.core.dao.technical.xml; +package net.sumaris.xml.query.utils; /*- * #%L diff --git a/sumaris-xml-query/src/main/resources/META-INF/services/javax.annotation.processing.Processor b/sumaris-xml-query/src/main/resources/META-INF/services/javax.annotation.processing.Processor new file mode 100644 index 0000000000..e672e59e30 --- /dev/null +++ b/sumaris-xml-query/src/main/resources/META-INF/services/javax.annotation.processing.Processor @@ -0,0 +1 @@ +net.sumaris.xml.query.annotation.XmlQueryProcessor \ No newline at end of file diff --git a/sumaris-xml-query/src/main/resources/dtd/queryDefault.dtd b/sumaris-xml-query/src/main/resources/dtd/queryDefault.dtd new file mode 100644 index 0000000000..a6850d9f8b --- /dev/null +++ b/sumaris-xml-query/src/main/resources/dtd/queryDefault.dtd @@ -0,0 +1,148 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/sumaris-xml-query/src/main/resources/i18n/sumaris-xml-query_en_GB.properties b/sumaris-xml-query/src/main/resources/i18n/sumaris-xml-query_en_GB.properties new file mode 100644 index 0000000000..8b13789179 --- /dev/null +++ b/sumaris-xml-query/src/main/resources/i18n/sumaris-xml-query_en_GB.properties @@ -0,0 +1 @@ + diff --git a/sumaris-xml-query/src/main/resources/i18n/sumaris-xml-query_fr_FR.properties b/sumaris-xml-query/src/main/resources/i18n/sumaris-xml-query_fr_FR.properties new file mode 100644 index 0000000000..8b13789179 --- /dev/null +++ b/sumaris-xml-query/src/main/resources/i18n/sumaris-xml-query_fr_FR.properties @@ -0,0 +1 @@ + diff --git a/sumaris-xml-query/src/test/java/net/sumaris/xml/query/DatabaseResource.java b/sumaris-xml-query/src/test/java/net/sumaris/xml/query/DatabaseResource.java new file mode 100644 index 0000000000..599eeacfc5 --- /dev/null +++ b/sumaris-xml-query/src/test/java/net/sumaris/xml/query/DatabaseResource.java @@ -0,0 +1,77 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.xml.query; + +/** + * To be able to manage database connection for unit test. + * + * @author Benoit Lavenier + * @since 1.0 + */ +public class DatabaseResource extends net.sumaris.core.test.DatabaseResource { + + + public static DatabaseResource readDb() { + return new DatabaseResource("", true); + } + + public static DatabaseResource readDb(String configName) { + return new DatabaseResource(configName, true); + } + + public static DatabaseResource writeDb() { + return new DatabaseResource("", false); + } + + public static DatabaseResource writeDb(String configName) { + return new DatabaseResource(configName, false); + } + + protected DatabaseResource(String configName, boolean readOnly) { + this(configName, null, readOnly); + } + + protected DatabaseResource(String configName, String dataSourceType, boolean readOnly) { + super(configName, dataSourceType, readOnly); + } + + @Override + public String getDatasourcePlatform() { + return TestConfiguration.DATASOURCE_PLATFORM; + } + + @Override + protected String getConfigFilesPrefix() { + return TestConfiguration.CONFIG_FILE_PREFIX; + } + + @Override + protected String getDbModuleDirectory() { + return TestConfiguration.MODULE_NAME; + } + + @Override + protected String getHsqldbSrcDatabaseDirectory() { + return "../sumaris-core/target/db"; + } +} diff --git a/sumaris-xml-query/src/test/java/net/sumaris/xml/query/MyXmlQuery.java b/sumaris-xml-query/src/test/java/net/sumaris/xml/query/MyXmlQuery.java new file mode 100644 index 0000000000..a1354da931 --- /dev/null +++ b/sumaris-xml-query/src/test/java/net/sumaris/xml/query/MyXmlQuery.java @@ -0,0 +1,31 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.xml.query; + +import net.sumaris.xml.query.XMLQuery; +import net.sumaris.xml.query.annotation.XmlQuery; + +//@XmlQuery(value = "classpath:xmlQuery/apase/v1_0/createRawSpeciesListDenormalizeTable.xml") +public interface MyXmlQuery extends XMLQuery { + +} diff --git a/sumaris-xml-query/src/test/java/net/sumaris/xml/query/TestConfiguration.java b/sumaris-xml-query/src/test/java/net/sumaris/xml/query/TestConfiguration.java new file mode 100644 index 0000000000..a45aedffa0 --- /dev/null +++ b/sumaris-xml-query/src/test/java/net/sumaris/xml/query/TestConfiguration.java @@ -0,0 +1,58 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.xml.query; + +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.boot.autoconfigure.freemarker.FreeMarkerAutoConfiguration; +import org.springframework.boot.autoconfigure.jms.JmsAutoConfiguration; +import org.springframework.boot.autoconfigure.liquibase.LiquibaseAutoConfiguration; +import org.springframework.transaction.annotation.EnableTransactionManagement; + +@SpringBootApplication( + exclude = { + LiquibaseAutoConfiguration.class, + FreeMarkerAutoConfiguration.class, + JmsAutoConfiguration.class + }, + scanBasePackages = { + "net.sumaris.xml.query" + } +) +public class TestConfiguration extends net.sumaris.core.test.TestConfiguration { + + public static final String MODULE_NAME = "sumaris-xml-query"; + public static final String DATASOURCE_PLATFORM = "hsqldb"; + public static final String CONFIG_FILE_PREFIX = "application"; + public static final String CONFIG_FILE_NAME = CONFIG_FILE_PREFIX + ".properties"; + public static final String I18N_BUNDLE_NAME = MODULE_NAME + "-i18n"; + + @Override + protected String getConfigFileName() { + return CONFIG_FILE_NAME; + } + + @Override + protected String getI18nBundleName() { + return I18N_BUNDLE_NAME; + } +} diff --git a/sumaris-xml-query/src/test/java/net/sumaris/xml/query/XmlQueryTest.java b/sumaris-xml-query/src/test/java/net/sumaris/xml/query/XmlQueryTest.java new file mode 100644 index 0000000000..32c49552f3 --- /dev/null +++ b/sumaris-xml-query/src/test/java/net/sumaris/xml/query/XmlQueryTest.java @@ -0,0 +1,61 @@ +/* + * #%L + * SUMARiS + * %% + * Copyright (C) 2019 SUMARiS Consortium + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ + +package net.sumaris.xml.query; + +import org.junit.ClassRule; +import org.junit.Ignore; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.junit4.SpringRunner; + +import javax.annotation.Resource; + +@RunWith(SpringRunner.class) +@SpringBootTest(classes = {TestConfiguration.class}) +@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS) +@Ignore +public class XmlQueryTest { + + @ClassRule + public static final DatabaseResource dbResource = DatabaseResource.readDb(); + + @Resource + MyXmlQuery xmlQuery; + + @Test + public void generateSqlRwSpeciesList() throws Exception { + + //xmlQuery.setQuery("classpath:xmlQuery/apase/v1_0/createRawSpeciesListDenormalizeTable.xml"); + + // Inject + xmlQuery.injectQuery("classpath:xmlQuery/apase/v1_0/injectionRawSpeciesListTable.xml", "afterSpeciesInjection"); + + xmlQuery.setGroup("excludeInvalidStation", false); + xmlQuery.bind("catchCategoryPmfmId", "90"); + xmlQuery.bind("subsamplingCategoryPmfmId", "176"); + String sql = xmlQuery.getSQLQueryAsString(); + System.out.println(sql); + } +} diff --git a/sumaris-xml-query/src/test/resources/application-hsqldb.properties b/sumaris-xml-query/src/test/resources/application-hsqldb.properties new file mode 100644 index 0000000000..3136df2703 --- /dev/null +++ b/sumaris-xml-query/src/test/resources/application-hsqldb.properties @@ -0,0 +1,87 @@ +# SUMARiS options +sumaris.name=SUMARiS +sumaris.test.data.common=data-hsqldb-01-common.xml +sumaris.test.data.additional=data-hsqldb-02-program.xml,data-hsqldb-02-program-ADAP.xml,data-hsqldb-02-program-OBSDEB.xml,data-hsqldb-02-program-OBSBIO.xml,data-hsqldb-02-program-ACOST.xml,data-hsqldb-02-program-PIFIL.xml,data-hsqldb-02-program-APASE.xml,data-hsqldb-03-data.xml,data-hsqldb-04-pendings.xml,data-hsqldb-05-extracts.xml,data-hsqldb-06-configs.xml,data-hsqldb-07-backgrounds.xml + +# Disable JMS, and cache +spring.cache.enabled=false +spring.cache.type=NONE +spring.jms.enabled=false +spring.activemq.enabled=false + +# Spring: Common properties +# see https://docs.spring.io/spring-boot/docs/current/reference/html/common-application-properties.html +spring.main.banner-mode=off +spring.main.web-application-type=none +spring.main.allow-circular-references=true + +# DataSource configuration +spring.sql.init.platform=hsqldb +spring.sql.init.mode=always +spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver +spring.datasource.username=sa +spring.datasource.password= +sumaris.persistence.sequence.startWith=1000 +# For DEV ONLY: +#spring.datasource.url=jdbc:hsqldb:hsql://localhost/sumaris + +# General JPA properties +spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.dialect.HSQLSpatialDialect +spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform} +spring.jpa.show-sql=false + +# Entity cache properties +spring.cache.jcache.config=classpath:ehcache-failsafe.xml + +# JPA / Query timeout +sumaris.extraction.query.timeout=300000 +spring.jpa.properties.javax.persistence.query.timeout=30000 +spring.jpa.properties.org.hibernate.timeout=30 + +# Hibernate properties +spring.jpa.hibernate.ddl-auto=none +spring.jpa.properties.hibernate.format_sql=false + +#Naming strategy +spring.jpa.hibernate.naming.physical-strategy=net.sumaris.core.dao.technical.hibernate.HibernatePhysicalNamingStrategy +spring.jpa.hibernate.naming.implicit-strategy=net.sumaris.core.dao.technical.hibernate.HibernateImplicitNamingStrategy + +# Liquibase +spring.liquibase.enabled=false +spring.liquibase.compact.enabled=false + +# Disable configuration load from DB +sumaris.persistence.configuration.enabled=false + +# Extraction features +sumaris.extraction.enabled=true +sumaris.extraction.product.enable=true + +# Logging Levels +logging.level.ROOT=info +logging.level.net.sumaris=info +logging.level.net.sumaris.extraction=info +#logging.level.net.sumaris.extraction.core.dao=debug +logging.level.net.sumaris.core.service.technical.ConfigurationServiceImpl=error +#logging.level.net.sumaris.core.config=debug + +# Log frameworks +logging.level.org.springframework=warn +#logging.level.org.springframework.cache.interceptor=TRACE +logging.level.org.nuiton=warn +logging.level.org.nuiton.i18n=error +logging.level.org.ehcache=warn +logging.level.org.apache.commons.beanutils=warn +logging.level.org.hibernate=warn +#logging.level.org.hibernate.SQL=debug +#logging.level.org.hibernate.type.descriptor.sql=trace +logging.level.org.hibernate.spatial=warn +logging.level.org.hibernate.engine.jdbc.spi.SqlExceptionHelper=error +logging.level.org.hibernate.engine.internal.StatefulPersistenceContext=error +logging.level.org.hibernate.engine.StatefulPersistenceContext.ProxyWarnLog=error +logging.level.org.jboss.logging=warn +logging.level.org.reflections=warn +logging.level.hsqldb.db=warn +logging.level.liquibase=warn +logging.level.liquibase-hibernate=warn +logging.level.com.zaxxer.hikari=warn