From 9dca1232c9d8a47e7b651a920ac5e879fca8698f Mon Sep 17 00:00:00 2001
From: Brendan Le Ny <bleny@codelutin.com>
Date: Thu, 3 Feb 2022 16:30:36 +0100
Subject: [PATCH 1/3] =?UTF-8?q?=C3=89chappement=20des=20composants=20des?=
=?UTF-8?q?=20cl=C3=A9s=20(ltree)=20en=20utilisant=20le=20nom=20du=20carac?=
=?UTF-8?q?t=C3=A8re=20unicode?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.../fr/inra/oresing/rest/OreSiService.java | 46 ++++++++++++++-----
1 file changed, 35 insertions(+), 11 deletions(-)
diff --git a/src/main/java/fr/inra/oresing/rest/OreSiService.java b/src/main/java/fr/inra/oresing/rest/OreSiService.java
index aa3c7c380..e2301459c 100644
--- a/src/main/java/fr/inra/oresing/rest/OreSiService.java
+++ b/src/main/java/fr/inra/oresing/rest/OreSiService.java
@@ -98,22 +98,46 @@ public class OreSiService {
private RelationalService relationalService;
public static String escapeKeyComponent(String key) {
- String toEscape = StringUtils.stripAccents(key.toLowerCase());
- String escaped = StringUtils.remove(
- RegExUtils.replaceAll(
- StringUtils.replace(toEscape, " ", "_"),
- "[^a-z0-9_]",
- ""
- ), "-"
- );
+ String lowerCased = key.toLowerCase();
+ String withAccentsStripped = StringUtils.stripAccents(lowerCased);
+ String toEscape = StringUtils.replace(withAccentsStripped, " ", "_");
+ String escaped = toEscape.chars()
+ .mapToObj(x -> (char) x)
+ .map(OreSiService::escapeSymbolFromKeyComponent)
+ .collect(Collectors.joining());
checkNaturalKeySyntax(escaped);
return escaped;
}
public static void checkNaturalKeySyntax(String keyComponent) {
- if (keyComponent.isEmpty())
- Preconditions.checkState(keyComponent.matches("[a-z0-9_]+"), "La clé naturelle ne peut être vide. vérifier le nom des colonnes.");
- Preconditions.checkState(keyComponent.matches("[a-z0-9_]+"), keyComponent + " n'est pas un élément valide pour une clé naturelle");
+ Preconditions.checkState(keyComponent.length() <= 256, "Un label dans un ltree ne peut pas être plus long que 256 caractères à cause de PG");
+ Preconditions.checkState(!keyComponent.isEmpty(), "La clé naturelle ne peut être vide. vérifier le nom des colonnes.");
+ Preconditions.checkState(keyComponent.matches("[a-zA-Z0-9_]+"), keyComponent + " n'est pas un élément valide pour une clé naturelle");
+ }
+
+ private static String escapeSymbolFromKeyComponent(Character aChar) {
+ String escapedChar;
+ if (characterCanBeUsedInLtreeLabel(aChar)) {
+ escapedChar = String.valueOf(aChar);
+ } else {
+ escapedChar = RegExUtils.replaceAll(
+ Character.getName(aChar),
+ "[^a-zA-Z0-9_]",
+ ""
+ );
+ }
+ return escapedChar;
+ }
+
+ /**
+ * D'après la documentation PostgreSQL sur ltree
+ *
+ * <blockquote>
+ * A label is a sequence of alphanumeric characters and underscores (for example, in C locale the characters A-Za-z0-9_ are allowed). Labels must be less than 256 characters long.
+ * </blockquote>
+ */
+ private static boolean characterCanBeUsedInLtreeLabel(Character aChar) {
+ return Character.isAlphabetic(aChar) || Character.isDigit(aChar) || '_' == aChar;
}
private void checkHierarchicalKeySyntax(String compositeKey) {
--
GitLab
From cf75f22ddaf741b168ac95bd2ea64f9826f32271 Mon Sep 17 00:00:00 2001
From: Brendan Le Ny <bleny@codelutin.com>
Date: Fri, 4 Feb 2022 20:05:23 +0100
Subject: [PATCH 2/3] Introduit une classe Ltree
---
.../fr/inra/oresing/persistence/Ltree.java | 94 +++++++++++++++++++
.../fr/inra/oresing/rest/OreSiService.java | 79 ++++------------
.../inra/oresing/persistence/LtreeTest.java | 15 +++
3 files changed, 125 insertions(+), 63 deletions(-)
create mode 100644 src/main/java/fr/inra/oresing/persistence/Ltree.java
create mode 100644 src/test/java/fr/inra/oresing/persistence/LtreeTest.java
diff --git a/src/main/java/fr/inra/oresing/persistence/Ltree.java b/src/main/java/fr/inra/oresing/persistence/Ltree.java
new file mode 100644
index 000000000..8caaf2ebb
--- /dev/null
+++ b/src/main/java/fr/inra/oresing/persistence/Ltree.java
@@ -0,0 +1,94 @@
+package fr.inra.oresing.persistence;
+
+import com.google.common.base.Preconditions;
+import com.google.common.base.Splitter;
+import lombok.Value;
+import org.apache.commons.lang3.CharUtils;
+import org.apache.commons.lang3.RegExUtils;
+import org.apache.commons.lang3.StringUtils;
+
+import java.util.stream.Collectors;
+
+@Value
+public class Ltree {
+
+ /**
+ * Déliminateur entre les différents niveaux d'un ltree postgresql.
+ * <p>
+ * https://www.postgresql.org/docs/current/ltree.html
+ */
+ public static final String SEPARATOR = ".";
+
+ String sql;
+
+ private Ltree(String sql) {
+ this.sql = sql;
+ }
+
+ public static Ltree fromSql(String sql) {
+ checkSyntax(sql);
+ return new Ltree(sql);
+ }
+
+ public static String escapeLabel(String key) {
+ String lowerCased = key.toLowerCase();
+ String withAccentsStripped = StringUtils.stripAccents(lowerCased);
+ String toEscape = StringUtils.replace(withAccentsStripped, " ", "_");
+ String escaped = toEscape.chars()
+ .mapToObj(x -> (char) x)
+ .map(Ltree::escapeSymbolFromKeyComponent)
+ .collect(Collectors.joining());
+ checkLabelSyntax(escaped);
+ return escaped;
+ }
+
+ public static void checkLabelSyntax(String keyComponent) {
+ Preconditions.checkState(keyComponent.length() <= 256, "Un label dans un ltree ne peut pas être plus long que 256 caractères à cause de PG");
+ Preconditions.checkState(!keyComponent.isEmpty(), "La clé naturelle ne peut être vide. vérifier le nom des colonnes.");
+ Preconditions.checkState(keyComponent.matches("[a-zA-Z0-9_]+"), keyComponent + " n'est pas un élément valide pour une clé naturelle");
+ }
+
+ private static String escapeSymbolFromKeyComponent(Character aChar) {
+ String escapedChar;
+ if (characterCanBeUsedInLabel(aChar)) {
+ escapedChar = CharUtils.toString(aChar);
+ } else {
+ escapedChar = RegExUtils.replaceAll(
+ Character.getName(aChar),
+ "[^a-zA-Z0-9_]",
+ ""
+ );
+ }
+ return escapedChar;
+ }
+
+ /**
+ * D'après la documentation PostgreSQL sur ltree
+ *
+ * <blockquote>
+ * A label is a sequence of alphanumeric characters and underscores (for example, in C locale the characters A-Za-z0-9_ are allowed). Labels must be less than 256 characters long.
+ * </blockquote>
+ */
+ private static boolean characterCanBeUsedInLabel(Character aChar) {
+ return CharUtils.isAsciiAlphanumeric(aChar) || '_' == aChar;
+ }
+
+ public static void checkSyntax(String sql) {
+ Splitter.on(SEPARATOR).split(sql).forEach(Ltree::checkLabelSyntax);
+ }
+
+ public static Ltree join(String prefix, String suffix) {
+ checkSyntax(prefix);
+ checkSyntax(suffix);
+ return fromSql(prefix + SEPARATOR + suffix);
+ }
+
+ public static Ltree join(Ltree prefix, Ltree suffix) {
+ return join(prefix.getSql(), suffix.getSql());
+ }
+
+ public static Ltree parseLabel(String labelToEscape) {
+ String escaped = escapeLabel(labelToEscape);
+ return fromSql(escaped);
+ }
+}
diff --git a/src/main/java/fr/inra/oresing/rest/OreSiService.java b/src/main/java/fr/inra/oresing/rest/OreSiService.java
index e2301459c..8c7f0e439 100644
--- a/src/main/java/fr/inra/oresing/rest/OreSiService.java
+++ b/src/main/java/fr/inra/oresing/rest/OreSiService.java
@@ -3,7 +3,6 @@ package fr.inra.oresing.rest;
import com.google.common.base.Charsets;
import com.google.common.base.Preconditions;
import com.google.common.base.Predicate;
-import com.google.common.base.Splitter;
import com.google.common.collect.*;
import com.google.common.primitives.Ints;
import fr.inra.oresing.OreSiTechnicalException;
@@ -25,7 +24,6 @@ import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVPrinter;
import org.apache.commons.csv.CSVRecord;
-import org.apache.commons.lang3.RegExUtils;
import org.apache.commons.lang3.StringUtils;
import org.assertj.core.util.Streams;
import org.assertj.core.util.Strings;
@@ -66,12 +64,6 @@ public class OreSiService {
public static final DateTimeFormatter DATE_TIME_FORMATTER = DateTimeFormatter.ofPattern("yyyy-MM-dd hh:mm:ss").withZone(ZoneOffset.UTC);
public static final DateTimeFormatter DATE_FORMATTER_DDMMYYYY = DateTimeFormatter.ofPattern("dd/MM/yyyy");
- /**
- * Déliminateur entre les différents niveaux d'un ltree postgresql.
- * <p>
- * https://www.postgresql.org/docs/current/ltree.html
- */
- private static final String LTREE_SEPARATOR = ".";
private static final String KEYCOLUMN_SEPARATOR = "__";
@Autowired
private OreSiRepository repo;
@@ -97,51 +89,12 @@ public class OreSiService {
@Autowired
private RelationalService relationalService;
- public static String escapeKeyComponent(String key) {
- String lowerCased = key.toLowerCase();
- String withAccentsStripped = StringUtils.stripAccents(lowerCased);
- String toEscape = StringUtils.replace(withAccentsStripped, " ", "_");
- String escaped = toEscape.chars()
- .mapToObj(x -> (char) x)
- .map(OreSiService::escapeSymbolFromKeyComponent)
- .collect(Collectors.joining());
- checkNaturalKeySyntax(escaped);
- return escaped;
- }
-
- public static void checkNaturalKeySyntax(String keyComponent) {
- Preconditions.checkState(keyComponent.length() <= 256, "Un label dans un ltree ne peut pas être plus long que 256 caractères à cause de PG");
- Preconditions.checkState(!keyComponent.isEmpty(), "La clé naturelle ne peut être vide. vérifier le nom des colonnes.");
- Preconditions.checkState(keyComponent.matches("[a-zA-Z0-9_]+"), keyComponent + " n'est pas un élément valide pour une clé naturelle");
- }
-
- private static String escapeSymbolFromKeyComponent(Character aChar) {
- String escapedChar;
- if (characterCanBeUsedInLtreeLabel(aChar)) {
- escapedChar = String.valueOf(aChar);
- } else {
- escapedChar = RegExUtils.replaceAll(
- Character.getName(aChar),
- "[^a-zA-Z0-9_]",
- ""
- );
- }
- return escapedChar;
- }
-
/**
- * D'après la documentation PostgreSQL sur ltree
- *
- * <blockquote>
- * A label is a sequence of alphanumeric characters and underscores (for example, in C locale the characters A-Za-z0-9_ are allowed). Labels must be less than 256 characters long.
- * </blockquote>
+ * @deprecated utiliser directement {@link Ltree#escapeLabel(String)}
*/
- private static boolean characterCanBeUsedInLtreeLabel(Character aChar) {
- return Character.isAlphabetic(aChar) || Character.isDigit(aChar) || '_' == aChar;
- }
-
- private void checkHierarchicalKeySyntax(String compositeKey) {
- Splitter.on(LTREE_SEPARATOR).split(compositeKey).forEach(OreSiService::checkNaturalKeySyntax);
+ @Deprecated
+ public static String escapeKeyComponent(String key) {
+ return Ltree.escapeLabel(key);
}
protected UUID storeFile(Application app, MultipartFile file) throws IOException {
@@ -380,10 +333,10 @@ public class OreSiService {
parentHierarchicalKeyColumn = referenceComponentDescription.getParentKeyColumn();
parentHierarchicalParentReference = compositeReferenceDescription.getComponents().get(compositeReferenceDescription.getComponents().indexOf(referenceComponentDescription) - 1).getReference();
getHierarchicalKeyFn = (naturalKey, referenceValues) -> {
- String parentHierarchicalKey = escapeKeyComponent(referenceValues.get(parentHierarchicalKeyColumn));
- return parentHierarchicalKey + LTREE_SEPARATOR + naturalKey;
+ String parentHierarchicalKey = Ltree.escapeLabel(referenceValues.get(parentHierarchicalKeyColumn));
+ return parentHierarchicalKey + Ltree.SEPARATOR + naturalKey;
};
- getHierarchicalReferenceFn = (reference) -> parentHierarchicalParentReference + LTREE_SEPARATOR + reference;
+ getHierarchicalReferenceFn = (reference) -> parentHierarchicalParentReference + Ltree.SEPARATOR + reference;
}
} else {
getHierarchicalKeyFn = (naturalKey, referenceValues) -> naturalKey;
@@ -439,7 +392,7 @@ public class OreSiService {
UUID referenceId = referenceValidationCheckResult.getReferenceId();
refValues.put((String) referenceValidationCheckResult.getTarget().getTarget(), (String) referenceValidationCheckResult.getValue());
refsLinkedTo
- .computeIfAbsent(escapeKeyComponent(reference), k -> new LinkedHashSet<>())
+ .computeIfAbsent(Ltree.escapeLabel(reference), k -> new LinkedHashSet<>())
.add(referenceId);
}
} else {
@@ -450,15 +403,15 @@ public class OreSiService {
String naturalKey;
String technicalId = e.getId().toString();
if (ref.getKeyColumns().isEmpty()) {
- naturalKey = escapeKeyComponent(technicalId);
+ naturalKey = Ltree.escapeLabel(technicalId);
} else {
naturalKey = ref.getKeyColumns().stream()
.map(kc -> refValues.get(kc))
.filter(key -> !Strings.isNullOrEmpty(key))
- .map(key -> escapeKeyComponent(key))
+ .map(key -> Ltree.escapeLabel(key))
.collect(Collectors.joining(KEYCOLUMN_SEPARATOR));
}
- OreSiService.checkNaturalKeySyntax(naturalKey);
+ Ltree.checkLabelSyntax(naturalKey);
String recursiveNaturalKey = naturalKey;
if (isRecursive) {
selfLineChecker
@@ -468,7 +421,7 @@ public class OreSiService {
.ifPresent(key -> e.setId(key));
String parentKey = parentreferenceMap.getOrDefault(recursiveNaturalKey, null);
while (!Strings.isNullOrEmpty(parentKey)) {
- recursiveNaturalKey = parentKey + LTREE_SEPARATOR + recursiveNaturalKey;
+ recursiveNaturalKey = parentKey + Ltree.SEPARATOR + recursiveNaturalKey;
parentKey = parentreferenceMap.getOrDefault(parentKey, null);
}
}
@@ -483,7 +436,7 @@ public class OreSiService {
getHierarchicalReferenceFn.apply(selfHierarchicalReference);
refValues.putAll(InternationalizationDisplay.getDisplays(displayPattern, displayColumns, refValues));
buildedHierarchicalKeys.put(naturalKey, hierarchicalKey);
- checkHierarchicalKeySyntax(hierarchicalKey);
+ Ltree.checkSyntax(hierarchicalKey);
e.setBinaryFile(fileId);
e.setReferenceType(refType);
e.setHierarchicalKey(hierarchicalKey);
@@ -533,11 +486,11 @@ public class OreSiService {
if (!Strings.isNullOrEmpty(s)) {
String naturalKey;
try {
- s = OreSiService.escapeKeyComponent(s);
+ s = Ltree.escapeLabel(s);
naturalKey = ref.getKeyColumns()
.stream()
.map(kc -> columns.indexOf(kc))
- .map(k -> OreSiService.escapeKeyComponent(csvrecord.get(k)))
+ .map(k -> Ltree.escapeLabel(csvrecord.get(k)))
.collect(Collectors.joining("__"));
} catch (IllegalArgumentException e) {
return;
@@ -827,7 +780,7 @@ public class OreSiService {
Map<String, String> requiredAuthorizations = new LinkedHashMap<>();
dataTypeDescription.getAuthorization().getAuthorizationScopes().forEach((authorizationScope, variableComponentKey) -> {
String requiredAuthorization = values.get(variableComponentKey);
- checkHierarchicalKeySyntax(requiredAuthorization);
+ Ltree.checkSyntax(requiredAuthorization);
requiredAuthorizations.put(authorizationScope, requiredAuthorization);
});
checkTimescopRangeInDatasetRange(timeScope, errors, binaryFileDataset, rowWithData.getLineNumber());
diff --git a/src/test/java/fr/inra/oresing/persistence/LtreeTest.java b/src/test/java/fr/inra/oresing/persistence/LtreeTest.java
new file mode 100644
index 000000000..0e1479f09
--- /dev/null
+++ b/src/test/java/fr/inra/oresing/persistence/LtreeTest.java
@@ -0,0 +1,15 @@
+package fr.inra.oresing.persistence;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class LtreeTest {
+
+ @Test
+ public void parseLabel() {
+ String sql = Ltree.parseLabel("composition <5%/µg").getSql();
+ Assert.assertEquals("composition_LESSTHANSIGN5PERCENTSIGNSOLIDUSMICROSIGNg", sql);
+ }
+}
\ No newline at end of file
--
GitLab
From a7d7538546bebaeb679119f5a2e4877b2ffbc1b3 Mon Sep 17 00:00:00 2001
From: Brendan Le Ny <bleny@codelutin.com>
Date: Mon, 7 Feb 2022 15:01:52 +0100
Subject: [PATCH 3/3] =?UTF-8?q?Utilise=20Ltree=20dans=20les=20entit=C3=A9s?=
=?UTF-8?q?=20et=20dans=20la=20couche=20service=20pour=20le=20calcul=20des?=
=?UTF-8?q?=20cl=C3=A9s?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.../fr/inra/oresing/model/ReferenceValue.java | 7 +-
.../oresing/persistence/JsonRowMapper.java | 12 ++++
.../JsonTableRepositoryTemplate.java | 1 +
.../fr/inra/oresing/persistence/Ltree.java | 6 ++
.../persistence/ReferenceValueRepository.java | 4 +-
.../oresing/rest/AuthorizationService.java | 2 +-
.../fr/inra/oresing/rest/OreSiResources.java | 6 +-
.../fr/inra/oresing/rest/OreSiService.java | 65 ++++++++++---------
.../migration/application/V1__init_schema.sql | 4 +-
.../data/monsore/monsore-with-repository.yaml | 6 +-
src/test/resources/data/monsore/monsore.yaml | 6 +-
11 files changed, 71 insertions(+), 48 deletions(-)
diff --git a/src/main/java/fr/inra/oresing/model/ReferenceValue.java b/src/main/java/fr/inra/oresing/model/ReferenceValue.java
index 88ea349bd..9a0b18b54 100644
--- a/src/main/java/fr/inra/oresing/model/ReferenceValue.java
+++ b/src/main/java/fr/inra/oresing/model/ReferenceValue.java
@@ -1,5 +1,6 @@
package fr.inra.oresing.model;
+import fr.inra.oresing.persistence.Ltree;
import lombok.Getter;
import lombok.Setter;
import lombok.ToString;
@@ -14,9 +15,9 @@ import java.util.UUID;
public class ReferenceValue extends OreSiEntity {
private UUID application;
private String referenceType;
- private String hierarchicalKey;
- private String hierarchicalReference;
- private String naturalKey;
+ private Ltree hierarchicalKey;
+ private Ltree hierarchicalReference;
+ private Ltree naturalKey;
private Map<String, String> refValues;
private Map<String, Set<UUID>> refsLinkedTo;
private UUID binaryFile;
diff --git a/src/main/java/fr/inra/oresing/persistence/JsonRowMapper.java b/src/main/java/fr/inra/oresing/persistence/JsonRowMapper.java
index 75c99bd50..10a0fc062 100644
--- a/src/main/java/fr/inra/oresing/persistence/JsonRowMapper.java
+++ b/src/main/java/fr/inra/oresing/persistence/JsonRowMapper.java
@@ -55,6 +55,18 @@ public class JsonRowMapper<T> implements RowMapper<T> {
return LocalDateTimeRange.parseSql(p.getText());
}
})
+ .addSerializer(Ltree.class, new JsonSerializer<>() {
+ @Override
+ public void serialize(Ltree value, JsonGenerator gen, SerializerProvider serializers) throws IOException {
+ gen.writeString(value.getSql());
+ }
+ })
+ .addDeserializer(Ltree.class, new JsonDeserializer<>() {
+ @Override
+ public Ltree deserialize(JsonParser p, DeserializationContext ctxt) throws IOException {
+ return Ltree.fromSql(p.getText());
+ }
+ })
;
jsonMapper.registerModule(module);
}
diff --git a/src/main/java/fr/inra/oresing/persistence/JsonTableRepositoryTemplate.java b/src/main/java/fr/inra/oresing/persistence/JsonTableRepositoryTemplate.java
index fcd7c5902..e74a926d3 100644
--- a/src/main/java/fr/inra/oresing/persistence/JsonTableRepositoryTemplate.java
+++ b/src/main/java/fr/inra/oresing/persistence/JsonTableRepositoryTemplate.java
@@ -55,6 +55,7 @@ abstract class JsonTableRepositoryTemplate<T extends OreSiEntity> implements Ini
}
});
String json = getJsonRowMapper().toJson(entities);
+ System.out.println("machin " + json);
List<UUID> result = namedParameterJdbcTemplate.queryForList(
query, new MapSqlParameterSource("json", json), UUID.class);
});
diff --git a/src/main/java/fr/inra/oresing/persistence/Ltree.java b/src/main/java/fr/inra/oresing/persistence/Ltree.java
index 8caaf2ebb..a13148ef3 100644
--- a/src/main/java/fr/inra/oresing/persistence/Ltree.java
+++ b/src/main/java/fr/inra/oresing/persistence/Ltree.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.CharUtils;
import org.apache.commons.lang3.RegExUtils;
import org.apache.commons.lang3.StringUtils;
+import java.util.UUID;
import java.util.stream.Collectors;
@Value
@@ -91,4 +92,9 @@ public class Ltree {
String escaped = escapeLabel(labelToEscape);
return fromSql(escaped);
}
+
+ public static Ltree toLabel(UUID uuid) {
+ String escaped = escapeLabel(StringUtils.remove(uuid.toString(), "-"));
+ return fromSql(escaped);
+ }
}
diff --git a/src/main/java/fr/inra/oresing/persistence/ReferenceValueRepository.java b/src/main/java/fr/inra/oresing/persistence/ReferenceValueRepository.java
index f97c428e2..7b24cf31c 100644
--- a/src/main/java/fr/inra/oresing/persistence/ReferenceValueRepository.java
+++ b/src/main/java/fr/inra/oresing/persistence/ReferenceValueRepository.java
@@ -115,11 +115,11 @@ public class ReferenceValueRepository extends JsonTableInApplicationSchemaReposi
public ImmutableMap<String, ApplicationResult.Reference.ReferenceUUIDAndDisplay> getReferenceIdAndDisplayPerKeys(String referenceType, String locale) {
return findAllByReferenceType(referenceType).stream()
- .collect(ImmutableMap.toImmutableMap(ReferenceValue::getHierarchicalKey,result->new ApplicationResult.Reference.ReferenceUUIDAndDisplay(result.getRefValues().get("__display_"+locale), result.getId(), result.getRefValues())));
+ .collect(ImmutableMap.toImmutableMap(referenceValue -> referenceValue.getHierarchicalKey().getSql(),result->new ApplicationResult.Reference.ReferenceUUIDAndDisplay(result.getRefValues().get("__display_"+locale), result.getId(), result.getRefValues())));
}
public ImmutableMap<String, UUID> getReferenceIdPerKeys(String referenceType) {
return findAllByReferenceType(referenceType).stream()
- .collect(ImmutableMap.toImmutableMap(ReferenceValue::getHierarchicalKey, ReferenceValue::getId));
+ .collect(ImmutableMap.toImmutableMap(referenceValue -> referenceValue.getHierarchicalKey().getSql(), ReferenceValue::getId));
}
}
\ No newline at end of file
diff --git a/src/main/java/fr/inra/oresing/rest/AuthorizationService.java b/src/main/java/fr/inra/oresing/rest/AuthorizationService.java
index a667a59a9..7223f5651 100644
--- a/src/main/java/fr/inra/oresing/rest/AuthorizationService.java
+++ b/src/main/java/fr/inra/oresing/rest/AuthorizationService.java
@@ -300,6 +300,6 @@ public class AuthorizationService {
ImmutableSortedSet<GetGrantableResult.AuthorizationScope.Option> options = tree.getChildren(referenceValue).stream()
.map(child -> toOption(tree, child))
.collect(ImmutableSortedSet.toImmutableSortedSet(Comparator.comparing(GetGrantableResult.AuthorizationScope.Option::getId)));
- return new GetGrantableResult.AuthorizationScope.Option(referenceValue.getHierarchicalKey(), referenceValue.getHierarchicalKey(), options);
+ return new GetGrantableResult.AuthorizationScope.Option(referenceValue.getHierarchicalKey().getSql(), referenceValue.getHierarchicalKey().getSql(), options);
}
}
\ No newline at end of file
diff --git a/src/main/java/fr/inra/oresing/rest/OreSiResources.java b/src/main/java/fr/inra/oresing/rest/OreSiResources.java
index d59af7505..e8cb0de81 100644
--- a/src/main/java/fr/inra/oresing/rest/OreSiResources.java
+++ b/src/main/java/fr/inra/oresing/rest/OreSiResources.java
@@ -197,9 +197,9 @@ public class OreSiResources {
ImmutableSet<GetReferenceResult.ReferenceValue> referenceValues = list.stream()
.map(referenceValue ->
new GetReferenceResult.ReferenceValue(
- referenceValue.getHierarchicalKey(),
- referenceValue.getHierarchicalReference(),
- referenceValue.getNaturalKey(),
+ referenceValue.getHierarchicalKey().getSql(),
+ referenceValue.getHierarchicalReference().getSql(),
+ referenceValue.getNaturalKey().getSql(),
referenceValue.getRefValues()
)
)
diff --git a/src/main/java/fr/inra/oresing/rest/OreSiService.java b/src/main/java/fr/inra/oresing/rest/OreSiService.java
index 8c7f0e439..60d074e34 100644
--- a/src/main/java/fr/inra/oresing/rest/OreSiService.java
+++ b/src/main/java/fr/inra/oresing/rest/OreSiService.java
@@ -316,10 +316,10 @@ public class OreSiService {
String parentHierarchicalKeyColumn, parentHierarchicalParentReference;
Optional<Configuration.CompositeReferenceComponentDescription> recursiveComponentDescription = getRecursiveComponent(conf.getCompositeReferences(), refType);
boolean isRecursive = recursiveComponentDescription.isPresent();
- BiFunction<String, Map<String, String>, String> getHierarchicalKeyFn;
- Function<String, String> getHierarchicalReferenceFn;
- Map<String, String> buildedHierarchicalKeys = new HashMap<>();
- Map<String, String> parentreferenceMap = new HashMap<>();
+ BiFunction<Ltree, Map<String, String>, Ltree> getHierarchicalKeyFn;
+ Function<Ltree, Ltree> getHierarchicalReferenceFn;
+ Map<Ltree, Ltree> buildedHierarchicalKeys = new HashMap<>();
+ Map<Ltree, Ltree> parentreferenceMap = new HashMap<>();
if (toUpdateCompositeReference.isPresent()) {
Configuration.CompositeReferenceDescription compositeReferenceDescription = toUpdateCompositeReference.get();
boolean root = Iterables.get(compositeReferenceDescription.getComponents(), 0).getReference().equals(refType);
@@ -333,10 +333,10 @@ public class OreSiService {
parentHierarchicalKeyColumn = referenceComponentDescription.getParentKeyColumn();
parentHierarchicalParentReference = compositeReferenceDescription.getComponents().get(compositeReferenceDescription.getComponents().indexOf(referenceComponentDescription) - 1).getReference();
getHierarchicalKeyFn = (naturalKey, referenceValues) -> {
- String parentHierarchicalKey = Ltree.escapeLabel(referenceValues.get(parentHierarchicalKeyColumn));
- return parentHierarchicalKey + Ltree.SEPARATOR + naturalKey;
+ Ltree parentHierarchicalKey = Ltree.parseLabel(referenceValues.get(parentHierarchicalKeyColumn));
+ return Ltree.join(parentHierarchicalKey, naturalKey);
};
- getHierarchicalReferenceFn = (reference) -> parentHierarchicalParentReference + Ltree.SEPARATOR + reference;
+ getHierarchicalReferenceFn = (reference) -> Ltree.join(Ltree.parseLabel(parentHierarchicalParentReference), reference);
}
} else {
getHierarchicalKeyFn = (naturalKey, referenceValues) -> naturalKey;
@@ -368,7 +368,7 @@ public class OreSiService {
if (isRecursive) {
recordStream = addMissingReferences(recordStream, selfLineChecker, recursiveComponentDescription, columns, ref, parentreferenceMap);
}
- List<String> hierarchicalKeys = new LinkedList<>();
+ List<Ltree> hierarchicalKeys = new LinkedList<>();
Optional<InternationalizationReferenceMap> internationalizationReferenceMap = Optional.ofNullable(conf)
.map(configuration -> conf.getInternationalization())
.map(inter -> inter.getReferences())
@@ -400,43 +400,46 @@ public class OreSiService {
}
});
ReferenceValue e = new ReferenceValue();
- String naturalKey;
- String technicalId = e.getId().toString();
+ Ltree naturalKey;
if (ref.getKeyColumns().isEmpty()) {
- naturalKey = Ltree.escapeLabel(technicalId);
+ UUID technicalId = e.getId();
+ naturalKey = Ltree.toLabel(technicalId);
} else {
- naturalKey = ref.getKeyColumns().stream()
+ naturalKey = Ltree.parseLabel(ref.getKeyColumns().stream()
.map(kc -> refValues.get(kc))
.filter(key -> !Strings.isNullOrEmpty(key))
.map(key -> Ltree.escapeLabel(key))
- .collect(Collectors.joining(KEYCOLUMN_SEPARATOR));
+ .collect(Collectors.joining(KEYCOLUMN_SEPARATOR)));
}
- Ltree.checkLabelSyntax(naturalKey);
- String recursiveNaturalKey = naturalKey;
+ Ltree recursiveNaturalKey = naturalKey;
+ final Ltree refTypeAsLabel = Ltree.parseLabel(refType);
if (isRecursive) {
selfLineChecker
.map(referenceLineChecker -> referenceLineChecker.getReferenceValues())
- .map(values -> values.get(naturalKey))
+ .map(values -> values.get(naturalKey.getSql()))
.filter(key -> key != null)
.ifPresent(key -> e.setId(key));
- String parentKey = parentreferenceMap.getOrDefault(recursiveNaturalKey, null);
- while (!Strings.isNullOrEmpty(parentKey)) {
- recursiveNaturalKey = parentKey + Ltree.SEPARATOR + recursiveNaturalKey;
+ Ltree parentKey = parentreferenceMap.getOrDefault(recursiveNaturalKey, null);
+ while (parentKey != null) {
+ recursiveNaturalKey = Ltree.join(parentKey, recursiveNaturalKey);
parentKey = parentreferenceMap.getOrDefault(parentKey, null);
+ //selfHierarchicalReference = Ltree.join(selfHierarchicalReference, refTypeAsLabel);
}
+// int x = StringUtils.countMatches(selfHierarchicalReference.getSql(), ".");
+// int y = StringUtils.countMatches(recursiveNaturalKey.getSql(), ".");
+// Preconditions.checkState(x == y);
}
- String hierarchicalKey = getHierarchicalKeyFn.apply(isRecursive ? recursiveNaturalKey : naturalKey, refValues);
- String selfHierarchicalReference = refType;
+ Ltree hierarchicalKey = getHierarchicalKeyFn.apply(isRecursive ? recursiveNaturalKey : naturalKey, refValues);
+ Ltree selfHierarchicalReference = refTypeAsLabel;
if (isRecursive) {
- for (int i = 1; i < recursiveNaturalKey.split("\\.").length; i++) {
- selfHierarchicalReference += ".".concat(refType);
+ for (int i = 1; i < recursiveNaturalKey.getSql().split("\\.").length; i++) {
+ selfHierarchicalReference = Ltree.fromSql(selfHierarchicalReference.getSql() + ".".concat(refType));
}
}
- String hierarchicalReference =
+ Ltree hierarchicalReference =
getHierarchicalReferenceFn.apply(selfHierarchicalReference);
refValues.putAll(InternationalizationDisplay.getDisplays(displayPattern, displayColumns, refValues));
buildedHierarchicalKeys.put(naturalKey, hierarchicalKey);
- Ltree.checkSyntax(hierarchicalKey);
e.setBinaryFile(fileId);
e.setReferenceType(refType);
e.setHierarchicalKey(hierarchicalKey);
@@ -447,7 +450,7 @@ public class OreSiService {
e.setRefValues(refValues);
return e;
})
- .sorted((a, b) -> a.getHierarchicalKey().compareTo(b.getHierarchicalKey()))
+ .sorted(Comparator.comparing(a -> a.getHierarchicalKey().getSql()))
.map(e -> {
if (hierarchicalKeys.contains(e.getHierarchicalKey())) {
/*envoyer un message de warning : le refType avec la clef e.getNaturalKey existe en plusieurs exemplaires
@@ -468,7 +471,7 @@ public class OreSiService {
return fileId;
}
- private Stream<CSVRecord> addMissingReferences(Stream<CSVRecord> recordStream, Optional<ReferenceLineChecker> selfLineChecker, Optional<Configuration.CompositeReferenceComponentDescription> recursiveComponentDescription, ImmutableList<String> columns, Configuration.ReferenceDescription ref, Map<String, String> referenceMap) {
+ private Stream<CSVRecord> addMissingReferences(Stream<CSVRecord> recordStream, Optional<ReferenceLineChecker> selfLineChecker, Optional<Configuration.CompositeReferenceComponentDescription> recursiveComponentDescription, ImmutableList<String> columns, Configuration.ReferenceDescription ref, Map<Ltree, Ltree> referenceMap) {
Integer parentRecursiveIndex = recursiveComponentDescription
.map(rcd -> rcd.getParentRecursiveKey())
.map(rck -> columns.indexOf(rck))
@@ -495,7 +498,7 @@ public class OreSiService {
} catch (IllegalArgumentException e) {
return;
}
- referenceMap.put(naturalKey, s);
+ referenceMap.put(Ltree.parseLabel(naturalKey), Ltree.parseLabel(s));
if (!referenceUUIDs.containsKey(s)) {
referenceUUIDs.put(s, UUID.randomUUID());
}
@@ -524,8 +527,8 @@ public class OreSiService {
.getConfiguration()
.getCompositeReferencesUsing(lowestLevelReference)
.orElseThrow();
- BiMap<String, ReferenceValue> indexedByHierarchicalKeyReferenceValues = HashBiMap.create();
- Map<ReferenceValue, String> parentHierarchicalKeys = new LinkedHashMap<>();
+ BiMap<Ltree, ReferenceValue> indexedByHierarchicalKeyReferenceValues = HashBiMap.create();
+ Map<ReferenceValue, Ltree> parentHierarchicalKeys = new LinkedHashMap<>();
ImmutableList<String> referenceTypes = compositeReferenceDescription.getComponents().stream()
.map(Configuration.CompositeReferenceComponentDescription::getReference)
.collect(ImmutableList.toImmutableList());
@@ -539,7 +542,7 @@ public class OreSiService {
referenceValueRepository.findAllByReferenceType(reference).forEach(referenceValue -> {
indexedByHierarchicalKeyReferenceValues.put(referenceValue.getHierarchicalKey(), referenceValue);
if (parentKeyColumn != null) {
- String parentHierarchicalKey = referenceValue.getRefValues().get(parentKeyColumn);
+ Ltree parentHierarchicalKey = Ltree.fromSql(referenceValue.getRefValues().get(parentKeyColumn));
parentHierarchicalKeys.put(referenceValue, parentHierarchicalKey);
}
});
diff --git a/src/main/resources/migration/application/V1__init_schema.sql b/src/main/resources/migration/application/V1__init_schema.sql
index 9a0db35f8..c493aa71c 100644
--- a/src/main/resources/migration/application/V1__init_schema.sql
+++ b/src/main/resources/migration/application/V1__init_schema.sql
@@ -19,8 +19,8 @@ create table ReferenceValue
application EntityRef REFERENCES Application (id),
referenceType TEXT CHECK (name_check(application, 'referenceType', referenceType)),
hierarchicalKey ltree NOT NULL,
- hierarchicalReference TEXT NOT NULL,
- naturalKey TEXT NOT NULL,
+ hierarchicalReference ltree NOT NULL,
+ naturalKey ltree NOT NULL,
refsLinkedTo jsonb check (refs_check_for_reference('${applicationSchema}', application, refsLinkedTo)),
refValues jsonb,
binaryFile EntityRef REFERENCES BinaryFile (id),
diff --git a/src/test/resources/data/monsore/monsore-with-repository.yaml b/src/test/resources/data/monsore/monsore-with-repository.yaml
index d6d755471..351da6cca 100644
--- a/src/test/resources/data/monsore/monsore-with-repository.yaml
+++ b/src/test/resources/data/monsore/monsore-with-repository.yaml
@@ -352,8 +352,8 @@ dataTypes:
replace: true
defaultValue: >
return references.get("sites")
- .find{it.getNaturalKey().equals(datumByVariableAndComponent.get("site").get("bassin"))}
- .getHierarchicalKey();
+ .find{it.getNaturalKey().getSql().equals(datumByVariableAndComponent.get("site").get("bassin"))}
+ .getHierarchicalKey().getSql();
checker:
name: Reference
params:
@@ -365,7 +365,7 @@ dataTypes:
defaultValue: >
return references.get("sites")
.find{it.getRefValues().get("zet_chemin_parent").equals(datumByVariableAndComponent.get("site").get("bassin")) && it.getRefValues().get("zet_nom_key").equals(datumByVariableAndComponent.get("site").get("plateforme"))}
- .getHierarchicalKey();
+ .getHierarchicalKey().getSql();
checker:
name: Reference
params:
diff --git a/src/test/resources/data/monsore/monsore.yaml b/src/test/resources/data/monsore/monsore.yaml
index f11cc867b..fec3bc303 100644
--- a/src/test/resources/data/monsore/monsore.yaml
+++ b/src/test/resources/data/monsore/monsore.yaml
@@ -350,8 +350,8 @@ dataTypes:
replace: true
defaultValue: >
return references.get("sites")
- .find{it.getNaturalKey().equals(datumByVariableAndComponent.get("site").get("bassin"))}
- .getHierarchicalKey();
+ .find{it.getNaturalKey().getSql().equals(datumByVariableAndComponent.get("site").get("bassin"))}
+ .getHierarchicalKey().getSql();
checker:
name: Reference
params:
@@ -363,7 +363,7 @@ dataTypes:
defaultValue: >
return references.get("sites")
.find{it.getRefValues().get("zet_chemin_parent").equals(datumByVariableAndComponent.get("site").get("bassin")) && it.getRefValues().get("zet_nom_key").equals(datumByVariableAndComponent.get("site").get("plateforme"))}
- .getHierarchicalKey();
+ .getHierarchicalKey().getSql();
checker:
name: Reference
params:
--
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