From a470db1bcf171f718549d4c8f8166f638cc76cf5 Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Sat, 27 May 2023 21:19:44 +0200
Subject: [PATCH] Fixed the label retrieval
---
.../dbrepo-realm.json | 70 +++++----
.../table/columns/concepts/ConceptDto.java | 3 +-
.../columns/concepts/ConceptSaveDto.java | 6 +
.../table/columns/concepts/UnitDto.java | 3 +-
.../table/columns/concepts/UnitSaveDto.java | 6 +
.../at/tuwien/api/semantics/EntityDto.java | 3 +-
.../api/semantics/TableColumnEntityDto.java | 2 +-
.../table/columns/TableColumnConcept.java | 3 +
.../table/columns/TableColumnUnit.java | 3 +
dbrepo-metadata-db/setup-schema.sql | 41 +++---
.../tuwien/endpoints/SemanticsEndpoint.java | 41 ++----
.../at/tuwien/endpoints/TableEndpoint.java | 2 +-
.../java/at/tuwien/mapper/OntologyMapper.java | 83 +++++++----
.../tuwien/service/impl/QueryServiceImpl.java | 21 ++-
.../service/impl/SemanticServiceImpl.java | 6 +-
.../tuwien/service/impl/TableServiceImpl.java | 2 +-
.../tuwien/endpoints/TableColumnEndpoint.java | 4 +-
.../endpoint/TableColumnEndpointUnitTest.java | 18 ++-
.../SemanticEntityNotFoundException.java | 21 +++
.../gateway/SemanticServiceGateway.java | 8 ++
.../impl/SemanticServiceGatewayImpl.java | 49 +++++++
.../java/at/tuwien/mapper/TableMapper.java | 9 +-
.../repository/jpa/OntologyRepository.java | 10 ++
.../at/tuwien/service/SemanticService.java | 32 +++++
.../java/at/tuwien/service/TableService.java | 8 +-
.../service/impl/SemanticServiceImpl.java | 107 ++++++++++++++
.../tuwien/service/impl/TableServiceImpl.java | 77 +++-------
dbrepo-ui/.env.example | 1 +
dbrepo-ui/Dockerfile | 1 +
dbrepo-ui/api/semantic.service.js | 34 +++++
.../components/dialogs/EditSemantics.vue | 96 -------------
dbrepo-ui/components/dialogs/Semantics.vue | 135 +++++++++++-------
.../components/dialogs/ViewSemanticEntity.vue | 72 ++++++++++
dbrepo-ui/config.js | 1 +
dbrepo-ui/layouts/default.vue | 5 +-
dbrepo-ui/nuxt.config.js | 5 +-
dbrepo-ui/pages/semantic/index.vue | 35 +++--
.../semantic/ontology/_ontology_id/index.vue | 17 +--
dbrepo-ui/pages/semantic/ontology/index.vue | 5 +
39 files changed, 673 insertions(+), 372 deletions(-)
create mode 100644 dbrepo-table-service/services/src/main/java/at/tuwien/exception/SemanticEntityNotFoundException.java
create mode 100644 dbrepo-table-service/services/src/main/java/at/tuwien/gateway/SemanticServiceGateway.java
create mode 100644 dbrepo-table-service/services/src/main/java/at/tuwien/gateway/impl/SemanticServiceGatewayImpl.java
create mode 100644 dbrepo-table-service/services/src/main/java/at/tuwien/repository/jpa/OntologyRepository.java
create mode 100644 dbrepo-table-service/services/src/main/java/at/tuwien/service/SemanticService.java
create mode 100644 dbrepo-table-service/services/src/main/java/at/tuwien/service/impl/SemanticServiceImpl.java
delete mode 100644 dbrepo-ui/components/dialogs/EditSemantics.vue
create mode 100644 dbrepo-ui/components/dialogs/ViewSemanticEntity.vue
diff --git a/dbrepo-authentication-service/dbrepo-realm.json b/dbrepo-authentication-service/dbrepo-realm.json
index d6f63ede24..359cfccf6c 100644
--- a/dbrepo-authentication-service/dbrepo-realm.json
+++ b/dbrepo-authentication-service/dbrepo-realm.json
@@ -66,6 +66,14 @@
"clientRole" : false,
"containerId" : "82c39861-d877-4667-a0f3-4daa2ee230e0",
"attributes" : { }
+ }, {
+ "id" : "143ba359-5fa2-451e-8296-43ecf20bb251",
+ "name" : "update-semantic-concept",
+ "description" : "${update-semantic-concept}",
+ "composite" : false,
+ "clientRole" : false,
+ "containerId" : "82c39861-d877-4667-a0f3-4daa2ee230e0",
+ "attributes" : { }
}, {
"id" : "5136d7a3-e3f0-4585-bacd-15cb8a56095c",
"name" : "escalated-container-handling",
@@ -220,6 +228,14 @@
"clientRole" : false,
"containerId" : "82c39861-d877-4667-a0f3-4daa2ee230e0",
"attributes" : { }
+ }, {
+ "id" : "b60a5694-4099-4f7d-a7e9-4c433e0eb9c9",
+ "name" : "update-semantic-unit",
+ "description" : "${update-semantic-unit}",
+ "composite" : false,
+ "clientRole" : false,
+ "containerId" : "82c39861-d877-4667-a0f3-4daa2ee230e0",
+ "attributes" : { }
}, {
"id" : "e9854bbb-4580-4757-b1ae-305934173249",
"name" : "create-database-access",
@@ -258,7 +274,7 @@
"description" : "${default-data-steward-roles}",
"composite" : true,
"composites" : {
- "realm" : [ "escalated-identifier-handling", "escalated-semantics-handling", "default-user-handling" ]
+ "realm" : [ "escalated-identifier-handling", "default-semantics-handling", "escalated-semantics-handling", "default-user-handling" ]
},
"clientRole" : false,
"containerId" : "82c39861-d877-4667-a0f3-4daa2ee230e0",
@@ -293,7 +309,7 @@
"description" : "${escalated-semantics-handling}",
"composite" : true,
"composites" : {
- "realm" : [ "create-ontology", "update-ontology", "list-ontologies", "delete-ontology", "modify-foreign-table-column-semantics" ]
+ "realm" : [ "update-semantic-unit", "create-ontology", "update-ontology", "list-ontologies", "delete-ontology", "modify-foreign-table-column-semantics", "update-semantic-concept" ]
},
"clientRole" : false,
"containerId" : "82c39861-d877-4667-a0f3-4daa2ee230e0",
@@ -1054,7 +1070,7 @@
"otpPolicyLookAheadWindow" : 1,
"otpPolicyPeriod" : 30,
"otpPolicyCodeReusable" : false,
- "otpSupportedApplications" : [ "totpAppMicrosoftAuthenticatorName", "totpAppGoogleName", "totpAppFreeOTPName" ],
+ "otpSupportedApplications" : [ "totpAppGoogleName", "totpAppFreeOTPName", "totpAppMicrosoftAuthenticatorName" ],
"webAuthnPolicyRpEntityName" : "keycloak",
"webAuthnPolicySignatureAlgorithms" : [ "ES256" ],
"webAuthnPolicyRpId" : "",
@@ -2077,7 +2093,7 @@
"subType" : "authenticated",
"subComponents" : { },
"config" : {
- "allowed-protocol-mapper-types" : [ "saml-user-attribute-mapper", "oidc-address-mapper", "saml-user-property-mapper", "oidc-usermodel-property-mapper", "saml-role-list-mapper", "oidc-sha256-pairwise-sub-mapper", "oidc-usermodel-attribute-mapper", "oidc-full-name-mapper" ]
+ "allowed-protocol-mapper-types" : [ "oidc-sha256-pairwise-sub-mapper", "oidc-address-mapper", "oidc-usermodel-attribute-mapper", "oidc-full-name-mapper", "saml-user-attribute-mapper", "saml-role-list-mapper", "oidc-usermodel-property-mapper", "saml-user-property-mapper" ]
}
}, {
"id" : "3ab11d74-5e76-408a-b85a-26bf8950f979",
@@ -2086,7 +2102,7 @@
"subType" : "anonymous",
"subComponents" : { },
"config" : {
- "allowed-protocol-mapper-types" : [ "saml-role-list-mapper", "oidc-full-name-mapper", "oidc-usermodel-property-mapper", "oidc-sha256-pairwise-sub-mapper", "oidc-address-mapper", "oidc-usermodel-attribute-mapper", "saml-user-property-mapper", "saml-user-attribute-mapper" ]
+ "allowed-protocol-mapper-types" : [ "saml-user-property-mapper", "saml-role-list-mapper", "oidc-usermodel-property-mapper", "oidc-full-name-mapper", "saml-user-attribute-mapper", "oidc-address-mapper", "oidc-usermodel-attribute-mapper", "oidc-sha256-pairwise-sub-mapper" ]
}
} ],
"org.keycloak.keys.KeyProvider" : [ {
@@ -2138,7 +2154,7 @@
"internationalizationEnabled" : false,
"supportedLocales" : [ ],
"authenticationFlows" : [ {
- "id" : "7dddcfca-7bcd-477f-8329-50a43455fd87",
+ "id" : "b21432ee-a5a0-44f1-89a5-0a7649bb5e99",
"alias" : "Account verification options",
"description" : "Method with which to verity the existing account",
"providerId" : "basic-flow",
@@ -2160,7 +2176,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "8dffaa2e-8dbe-4276-8cd9-7a81eaece233",
+ "id" : "fe07cb6c-0ffe-4353-9184-6a7bd51940ea",
"alias" : "Authentication Options",
"description" : "Authentication options.",
"providerId" : "basic-flow",
@@ -2189,7 +2205,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "7e3d1f77-19a9-421c-b58c-d38f4d03fe63",
+ "id" : "ebefc325-3ee1-45ea-8837-0503a13784b1",
"alias" : "Browser - Conditional OTP",
"description" : "Flow to determine if the OTP is required for the authentication",
"providerId" : "basic-flow",
@@ -2211,7 +2227,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "e60fa1bd-3905-4c5d-a754-396dbf02d3db",
+ "id" : "006c167c-32bf-41fe-80a2-0e01f9f158d5",
"alias" : "Direct Grant - Conditional OTP",
"description" : "Flow to determine if the OTP is required for the authentication",
"providerId" : "basic-flow",
@@ -2233,7 +2249,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "6570bc4c-7804-4a5c-87da-4ae57e9e26dd",
+ "id" : "b00fef58-fcdb-4e63-8efc-7f45b2d916fa",
"alias" : "First broker login - Conditional OTP",
"description" : "Flow to determine if the OTP is required for the authentication",
"providerId" : "basic-flow",
@@ -2255,7 +2271,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "6c011108-9cf4-4973-8bb4-afbf15dd44a2",
+ "id" : "ac9e7d88-fef2-4292-9e92-469a3b44b252",
"alias" : "Handle Existing Account",
"description" : "Handle what to do if there is existing account with same email/username like authenticated identity provider",
"providerId" : "basic-flow",
@@ -2277,7 +2293,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "9acc6184-a192-44b1-aed8-9cf500456c68",
+ "id" : "b346f859-4f7c-4383-ad6e-22ee648568f7",
"alias" : "Reset - Conditional OTP",
"description" : "Flow to determine if the OTP should be reset or not. Set to REQUIRED to force.",
"providerId" : "basic-flow",
@@ -2299,7 +2315,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "78dac59d-dca1-401e-973b-083694df75df",
+ "id" : "44618916-6ad5-4d89-98b5-02ca56c4e94e",
"alias" : "User creation or linking",
"description" : "Flow for the existing/non-existing user alternatives",
"providerId" : "basic-flow",
@@ -2322,7 +2338,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "fe5875af-12d3-4027-b6dc-62aa2e4f4ec9",
+ "id" : "cd705e48-31b2-4b44-93a1-ac64366d99e7",
"alias" : "Verify Existing Account by Re-authentication",
"description" : "Reauthentication of existing account",
"providerId" : "basic-flow",
@@ -2344,7 +2360,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "9a61c442-6393-4d10-bbb4-bb19a03f4560",
+ "id" : "1f8c5799-9c25-490d-bc81-8a75fcf88ce3",
"alias" : "browser",
"description" : "browser based authentication",
"providerId" : "basic-flow",
@@ -2380,7 +2396,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "76db50d0-143c-499a-8256-e4229c5f81d6",
+ "id" : "6ac53bd6-6665-42f6-8c9b-4bc0d6e39b83",
"alias" : "clients",
"description" : "Base authentication for clients",
"providerId" : "client-flow",
@@ -2416,7 +2432,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "4529a603-cc30-46e4-b821-f8fe88352048",
+ "id" : "76b187f5-0c6c-4cb8-ac56-b54712ca290d",
"alias" : "direct grant",
"description" : "OpenID Connect Resource Owner Grant",
"providerId" : "basic-flow",
@@ -2445,7 +2461,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "dc9cda33-523a-4b76-ba21-7055c0f1aaea",
+ "id" : "42e03bec-71a8-4517-8fc0-1601397f8e17",
"alias" : "docker auth",
"description" : "Used by Docker clients to authenticate against the IDP",
"providerId" : "basic-flow",
@@ -2460,7 +2476,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "27eb9e18-c28b-43c1-8148-9b46b3ed103e",
+ "id" : "9ec63a08-04e2-4736-a87a-46057598466e",
"alias" : "first broker login",
"description" : "Actions taken after first broker login with identity provider account, which is not yet linked to any Keycloak account",
"providerId" : "basic-flow",
@@ -2483,7 +2499,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "9f83ad1f-cb1a-422b-802e-b4d7f2800fc5",
+ "id" : "715aef9a-fbc1-4a8a-969b-0df5e81ea536",
"alias" : "forms",
"description" : "Username, password, otp and other auth forms.",
"providerId" : "basic-flow",
@@ -2505,7 +2521,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "fadcf245-9bab-4b43-ae93-5a2fe685970f",
+ "id" : "ad7f41c0-abb5-492d-9de1-f11a9c0e3090",
"alias" : "http challenge",
"description" : "An authentication flow based on challenge-response HTTP Authentication Schemes",
"providerId" : "basic-flow",
@@ -2527,7 +2543,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "3509bd76-4ae6-4f70-816c-415668d7000d",
+ "id" : "96d9faa7-7c92-4b34-9433-6b8198cab651",
"alias" : "registration",
"description" : "registration flow",
"providerId" : "basic-flow",
@@ -2543,7 +2559,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "e18b1d97-8ce5-43f1-bb4e-9540c303f6da",
+ "id" : "6cfc2735-d8a8-41da-ab4f-5c8f2c6d3ff1",
"alias" : "registration form",
"description" : "registration form",
"providerId" : "form-flow",
@@ -2579,7 +2595,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "bf867f8e-95a7-4dc3-8569-07b53874b41c",
+ "id" : "2bc9fcb2-2b4a-480d-a4f8-d41885ef4bf9",
"alias" : "reset credentials",
"description" : "Reset credentials for a user if they forgot their password or something",
"providerId" : "basic-flow",
@@ -2615,7 +2631,7 @@
"userSetupAllowed" : false
} ]
}, {
- "id" : "74b260ac-7de8-41f0-a0ab-3b26bc6b4d75",
+ "id" : "4e4b9e79-7aff-4de8-869f-04dbd1a5bd1e",
"alias" : "saml ecp",
"description" : "SAML ECP Profile Authentication Flow",
"providerId" : "basic-flow",
@@ -2631,13 +2647,13 @@
} ]
} ],
"authenticatorConfig" : [ {
- "id" : "e22bf5a6-9a63-425c-91f2-684a10f7f436",
+ "id" : "b65b03a6-9a9e-49f0-9887-7942996c8345",
"alias" : "create unique user config",
"config" : {
"require.password.update.after.registration" : "false"
}
}, {
- "id" : "a06a0326-c8e5-4c05-bb63-545b9f4932f2",
+ "id" : "33d1c568-b4cd-43e1-870a-f14778834744",
"alias" : "review profile config",
"config" : {
"update.profile.on.first.login" : "missing"
diff --git a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptDto.java b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptDto.java
index e031cf5944..590cd825e7 100644
--- a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptDto.java
+++ b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptDto.java
@@ -25,9 +25,10 @@ public class ConceptDto {
@NotBlank
private String uri;
- @NotBlank
private String name;
+ private String description;
+
@NotNull
@JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
private Instant created;
diff --git a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptSaveDto.java b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptSaveDto.java
index e38927af8f..159e07823c 100644
--- a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptSaveDto.java
+++ b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptSaveDto.java
@@ -16,4 +16,10 @@ public class ConceptSaveDto {
@NotBlank
private String uri;
+ @NotBlank
+ private String name;
+
+ @NotBlank
+ private String description;
+
}
diff --git a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/UnitDto.java b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/UnitDto.java
index 65b6c2a0bd..9e0fd69360 100644
--- a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/UnitDto.java
+++ b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/UnitDto.java
@@ -23,9 +23,10 @@ public class UnitDto {
@NotBlank
private String uri;
- @NotBlank
private String name;
+ private String description;
+
@NotNull
@JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
private Instant created;
diff --git a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/UnitSaveDto.java b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/UnitSaveDto.java
index 41cfd8caaf..326efc48b5 100644
--- a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/UnitSaveDto.java
+++ b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/UnitSaveDto.java
@@ -16,4 +16,10 @@ public class UnitSaveDto {
@NotBlank
private String uri;
+ @NotBlank
+ private String name;
+
+ @NotBlank
+ private String description;
+
}
diff --git a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/semantics/EntityDto.java b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/semantics/EntityDto.java
index 728b9979da..5c1d6cc13a 100644
--- a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/semantics/EntityDto.java
+++ b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/semantics/EntityDto.java
@@ -22,8 +22,7 @@ public class EntityDto {
@Schema(example = "Apache Jena")
private String label;
- @NotBlank
@Schema(example = "open source semantic web framework for Java")
- private String comment;
+ private String description;
}
diff --git a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/semantics/TableColumnEntityDto.java b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/semantics/TableColumnEntityDto.java
index 6e314aba1c..b71a0ae0be 100644
--- a/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/semantics/TableColumnEntityDto.java
+++ b/dbrepo-metadata-db/api/src/main/java/at/tuwien/api/semantics/TableColumnEntityDto.java
@@ -35,6 +35,6 @@ public class TableColumnEntityDto {
private String label;
@Schema(example = "open source semantic web framework for Java")
- private String comment;
+ private String description;
}
diff --git a/dbrepo-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnConcept.java b/dbrepo-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnConcept.java
index fa2ae5a066..8304898a1d 100644
--- a/dbrepo-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnConcept.java
+++ b/dbrepo-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnConcept.java
@@ -33,6 +33,9 @@ public class TableColumnConcept {
@Column(name = "name")
private String name;
+ @Column(name = "description")
+ private String description;
+
@Column(nullable = false, updatable = false, columnDefinition = "TIMESTAMP")
@CreatedDate
private Instant created;
diff --git a/dbrepo-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnUnit.java b/dbrepo-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnUnit.java
index aecbcd9dd3..922f48217f 100644
--- a/dbrepo-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnUnit.java
+++ b/dbrepo-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumnUnit.java
@@ -33,6 +33,9 @@ public class TableColumnUnit {
@Column(name = "name")
private String name;
+ @Column(name = "description")
+ private String description;
+
@Column(nullable = false, updatable = false, columnDefinition = "TIMESTAMP")
@CreatedDate
private Instant created;
diff --git a/dbrepo-metadata-db/setup-schema.sql b/dbrepo-metadata-db/setup-schema.sql
index 9642c98f61..92afa5c8ca 100644
--- a/dbrepo-metadata-db/setup-schema.sql
+++ b/dbrepo-metadata-db/setup-schema.sql
@@ -275,19 +275,21 @@ CREATE TABLE IF NOT EXISTS `fda`.`mdb_constraints_checks`
CREATE TABLE IF NOT EXISTS `fda`.`mdb_concepts`
(
- uri text not null,
- name VARCHAR(255) null,
- created timestamp NOT NULL DEFAULT NOW(),
- created_by character varying(255),
+ uri text not null,
+ name VARCHAR(255) null,
+ description TEXT null,
+ created timestamp NOT NULL DEFAULT NOW(),
+ created_by character varying(255),
PRIMARY KEY (uri(200))
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `fda`.`mdb_units`
(
- uri text not null,
- name VARCHAR(255) null,
- created timestamp NOT NULL DEFAULT NOW(),
- created_by character varying(255),
+ uri text not null,
+ name VARCHAR(255) null,
+ description TEXT null,
+ created timestamp NOT NULL DEFAULT NOW(),
+ created_by character varying(255),
PRIMARY KEY (uri(200))
) WITH SYSTEM VERSIONING;
@@ -499,13 +501,18 @@ VALUES (1, '%Y-%c-%d %H:%i:%S.%f', 'yyyy-MM-dd HH:mm:ss.SSSSSS', '2022-01-30 13:
(1, '%Y-%c-%d %H:%i:%S', 'yyyy-MM-dd HH:mm:ss', '2022-01-30 13:44:25', true),
(1, '%Y-%c-%d', 'yyyy-MM-dd', '2022-01-30', false);
-INSERT INTO `fda`.`mdb_ontologies` (uri, prefix, sparql_endpoint)
-VALUES ('http://www.ontology-of-units-of-measure.org/resource/om-2/', 'om2', null),
- ('http://www.wikidata.org/', 'wd', 'https://query.wikidata.org/sparql'),
- ('http://purl.org/ontology/mo/', 'mo', null),
- ('http://purl.org/dc/elements/1.1/', 'dc', null),
- ('http://www.w3.org/2001/XMLSchema#', 'xsd', null),
- ('http://purl.org/NET/c4dm/timeline.owl#', 'tl', null),
- ('http://xmlns.com/foaf/0.1/', 'foaf', null),
- ('http://dbpedia.org', 'db', 'http://dbpedia.org/sparql');
+INSERT INTO `fda`.`mdb_ontologies` (prefix, uri, sparql_endpoint)
+VALUES ('om2', 'http://www.ontology-of-units-of-measure.org/resource/om-2/', null),
+ ('wd', 'http://www.wikidata.org/', 'https://query.wikidata.org/sparql'),
+ ('mo', 'http://purl.org/ontology/mo/', null),
+ ('dc', 'http://purl.org/dc/elements/1.1/', null),
+ ('xsd', 'http://www.w3.org/2001/XMLSchema#', null),
+ ('tl', 'http://purl.org/NET/c4dm/timeline.owl#', null),
+ ('foaf', 'http://xmlns.com/foaf/0.1/', null),
+ ('schema', 'http://schema.org/', null),
+ ('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', null),
+ ('rdfs', 'http://www.w3.org/2000/01/rdf-schema#', null),
+ ('owl', 'http://www.w3.org/2002/07/owl#', null),
+ ('prov', 'http://www.w3.org/ns/prov#', null),
+ ('db', 'http://dbpedia.org', 'http://dbpedia.org/sparql');
COMMIT;
diff --git a/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/SemanticsEndpoint.java b/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/SemanticsEndpoint.java
index 6567d5ee38..5bcf6abdf0 100644
--- a/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/SemanticsEndpoint.java
+++ b/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/SemanticsEndpoint.java
@@ -1,9 +1,6 @@
package at.tuwien.endpoints;
-import at.tuwien.api.database.table.columns.concepts.ConceptDto;
-import at.tuwien.api.database.table.columns.concepts.ConceptSaveDto;
-import at.tuwien.api.database.table.columns.concepts.UnitDto;
-import at.tuwien.api.database.table.columns.concepts.UnitSaveDto;
+import at.tuwien.api.database.table.columns.concepts.*;
import at.tuwien.mapper.OntologyMapper;
import at.tuwien.mapper.SemanticMapper;
import at.tuwien.service.SemanticService;
@@ -67,39 +64,19 @@ public class SemanticsEndpoint {
@PostMapping("/concept")
@Transactional
@PreAuthorize("hasAuthority('create-semantic-concept')")
- @Timed(value = "semantics.concept.save", description = "Time needed to create or update a semantic concept")
+ @Timed(value = "semantics.concept.save", description = "Time needed to save a semantic concept")
@Operation(summary = "Create or update a semantic concept", security = @SecurityRequirement(name = "bearerAuth"))
@ApiResponses(value = {
@ApiResponse(responseCode = "202",
- description = "Created or updated a semantic concept",
+ description = "Saved a semantic concept",
content = {@Content(
mediaType = "application/json",
schema = @Schema(implementation = ConceptDto.class))}),
})
public ResponseEntity<ConceptDto> saveConcept(@NotNull @Valid @RequestBody ConceptSaveDto data) {
- log.debug("endpoint save or update concept, data={}", data);
+ log.debug("endpoint save concept, data={}", data);
final ConceptDto dto = ontologyMapper.tableColumnConceptToConceptDto(semanticService.saveConcept(data));
- log.trace("save or update concept resulted in dto {}", dto);
- return ResponseEntity.ok()
- .body(dto);
- }
-
- @PutMapping("/concept")
- @Transactional
- @PreAuthorize("hasAuthority('create-semantic-concept')")
- @Timed(value = "semantics.concept.save", description = "Time needed to create or update a semantic concept")
- @Operation(summary = "Create or update a semantic concept", security = @SecurityRequirement(name = "bearerAuth"))
- @ApiResponses(value = {
- @ApiResponse(responseCode = "202",
- description = "Created or updated a semantic concept",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ConceptDto.class))}),
- })
- public ResponseEntity<ConceptDto> saveConcept(@NotNull @Valid @RequestBody ConceptSaveDto data) {
- log.debug("endpoint save or update concept, data={}", data);
- final ConceptDto dto = ontologyMapper.tableColumnConceptToConceptDto(semanticService.saveConcept(data));
- log.trace("save or update concept resulted in dto {}", dto);
+ log.trace("save concept resulted in dto {}", dto);
return ResponseEntity.ok()
.body(dto);
}
@@ -129,11 +106,11 @@ public class SemanticsEndpoint {
@PostMapping("/unit")
@Transactional
@PreAuthorize("hasAuthority('create-semantic-unit')")
- @Timed(value = "semantics.unit.save", description = "Time needed to create or update a semantic unit")
- @Operation(summary = "Create or update a semantic unit", security = @SecurityRequirement(name = "bearerAuth"))
+ @Timed(value = "semantics.unit.save", description = "Time needed to save a semantic unit")
+ @Operation(summary = "Save a semantic unit", security = @SecurityRequirement(name = "bearerAuth"))
@ApiResponses(value = {
@ApiResponse(responseCode = "202",
- description = "Created or updated a semantic unit",
+ description = "Saved a semantic unit",
content = {@Content(
mediaType = "application/json",
schema = @Schema(implementation = UnitDto.class))}),
@@ -141,7 +118,7 @@ public class SemanticsEndpoint {
public ResponseEntity<UnitDto> saveConcept(@NotNull @Valid @RequestBody UnitSaveDto data) {
log.debug("endpoint save or update unit, data={}", data);
final UnitDto dto = ontologyMapper.tableColumnUnitToUnitDto(semanticService.saveUnit(data));
- log.trace("save or update unit resulted in dto {}", dto);
+ log.trace("save unit resulted in dto {}", dto);
return ResponseEntity.accepted()
.body(dto);
}
diff --git a/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java b/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
index f9581b2993..cc3689fded 100644
--- a/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
+++ b/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
@@ -95,7 +95,7 @@ public class TableEndpoint {
@NotNull @PathVariable("tableId") Long tableId,
@NotNull @PathVariable("columnId") Long columnId)
throws QueryMalformedException, TableColumnNotFoundException {
- log.debug("endpoint analyse table semantics, databaseId={}, tableId={}, columnId={}", databaseId, tableId, columnId);
+ log.debug("endpoint analyse table column semantics, databaseId={}, tableId={}, columnId={}", databaseId, tableId, columnId);
final List<TableColumnEntityDto> dtos = tableService.suggestTableColumnSemantics(databaseId, tableId, columnId);
log.trace("analyse table semantics resulted in dtos {}", dtos);
return ResponseEntity.ok()
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/mapper/OntologyMapper.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/mapper/OntologyMapper.java
index 7268311727..aeec69284c 100644
--- a/dbrepo-semantics-service/services/src/main/java/at/tuwien/mapper/OntologyMapper.java
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/mapper/OntologyMapper.java
@@ -1,9 +1,6 @@
package at.tuwien.mapper;
-import at.tuwien.api.database.table.columns.concepts.ConceptDto;
-import at.tuwien.api.database.table.columns.concepts.ConceptSaveDto;
-import at.tuwien.api.database.table.columns.concepts.UnitDto;
-import at.tuwien.api.database.table.columns.concepts.UnitSaveDto;
+import at.tuwien.api.database.table.columns.concepts.*;
import at.tuwien.api.semantics.OntologyBriefDto;
import at.tuwien.api.semantics.OntologyCreateDto;
import at.tuwien.api.semantics.OntologyDto;
@@ -14,6 +11,8 @@ import org.mapstruct.Mapper;
import org.mapstruct.Mapping;
import org.mapstruct.Mappings;
+import java.util.List;
+
@Mapper(componentModel = "spring")
public interface OntologyMapper {
@@ -42,57 +41,79 @@ public interface OntologyMapper {
TableColumnConcept conceptSaveDtoToTableColumnConcept(ConceptSaveDto data);
- default String ontologyToFindByLabelQuery(Ontology ontology, String label, Integer limit) {
+ default String defaultNamespaces(List<Ontology> data) {
+ return String.join("\n",
+ data.stream()
+ .map(o -> "PREFIX " + o.getPrefix() + ": <" + o.getUri() + ">")
+ .toList());
+ }
+
+ default String ontologyToFindByLabelQuery(List<Ontology> ontologies, Ontology ontology, String label, Integer limit) {
if (ontology.getSparqlEndpoint() != null) {
/* prefer SPARQL endpoint over rdf */
return String.join("\n",
- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
+ defaultNamespaces(ontologies),
"SELECT * {",
" SERVICE <" + ontology.getSparqlEndpoint() + "> {",
- " SELECT ?o ?label ?comment {",
- " ?o rdfs:label \"" + label.replace("\"", "") + "\"@en .",
- " ?o rdfs:label ?label .",
- " OPTIONAL {?o rdfs:comment ?comment} .",
- " FILTER (langMatches(lang(?label), \"EN\" ) )",
- " FILTER (langMatches(lang(?comment), \"EN\" ) )",
- " } LIMIT " + limit,
+ " SELECT ?o ?label ?description {",
+ " OPTIONAL {",
+ " ?o rdfs:label ?label",
+ " FILTER (LANG(?label) = 'en')",
+ " }",
+ " OPTIONAL {",
+ " ?o schema:description ?description",
+ " FILTER (LANG(?description) = 'en')",
+ " }",
+ " } LIMIT " + limit,
" }",
"}");
}
return String.join("\n",
- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
+ defaultNamespaces(ontologies),
"SELECT ?o ?label ?comment {",
" ?o rdfs:label \"" + label.replace("\"", "") + "\"@en .",
- " ?o rdfs:label ?label .",
- " OPTIONAL {?o rdfs:comment ?comment} .",
- " FILTER (langMatches(lang(?label), \"EN\" ) )",
- " FILTER (langMatches(lang(?comment), \"EN\" ) )",
+ " OPTIONAL {",
+ " ?o rdfs:label ?label",
+ " FILTER (LANG(?label) = 'en')",
+ " }",
+ " OPTIONAL {",
+ " ?o schema:description ?description",
+ " FILTER (LANG(?description) = 'en')",
+ " }",
"} LIMIT " + limit);
}
- default String ontologyToFindByUriQuery(Ontology ontology, String uri) {
+ default String ontologyToFindByUriQuery(List<Ontology> ontologies, Ontology ontology, String uri) {
if (ontology.getSparqlEndpoint() != null) {
/* prefer SPARQL endpoint over rdf */
return String.join("\n",
- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
+ defaultNamespaces(ontologies),
"SELECT * {",
" SERVICE <" + ontology.getSparqlEndpoint() + "> {",
- " SELECT ?label ?comment {",
- " <" + uri + "> rdfs:label ?label .",
- " OPTIONAL {<" + uri + "> rdfs:comment ?comment} .",
- " FILTER (langMatches(lang(?label), \"EN\" ) )",
- " FILTER (langMatches(lang(?comment), \"EN\" ) )",
+ " SELECT ?label ?description {",
+ " OPTIONAL {",
+ " <" + uri + "> rdfs:label ?label",
+ " FILTER (LANG(?label) = 'en')",
+ " }",
+ " OPTIONAL {",
+ " <" + uri + "> schema:description ?description",
+ " FILTER (LANG(?description) = 'en')",
+ " }",
" } LIMIT 1",
" }",
"}");
}
return String.join("\n",
- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
- "SELECT ?label ?comment {",
- " <" + uri + "> rdfs:label ?label .",
- " OPTIONAL {<" + uri + "> rdfs:comment ?comment} .",
- " FILTER (langMatches(lang(?label), \"EN\" ) )",
- " FILTER (langMatches(lang(?comment), \"EN\" ) )",
+ defaultNamespaces(ontologies),
+ "SELECT ?label ?description {",
+ " OPTIONAL {",
+ " <" + uri + "> rdfs:label ?label",
+ " FILTER (LANG(?label) = 'en')",
+ " }",
+ " OPTIONAL {",
+ " <" + uri + "> schema:description ?description",
+ " FILTER (LANG(?description) = 'en')",
+ " }",
"} LIMIT 1");
}
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/QueryServiceImpl.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/QueryServiceImpl.java
index 68e9d93e2a..5b51cfdf8c 100644
--- a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/QueryServiceImpl.java
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/QueryServiceImpl.java
@@ -30,10 +30,13 @@ public class QueryServiceImpl implements QueryService {
private final Dataset dataset;
private final OntologyMapper ontologyMapper;
+ private final OntologyRepository ontologyRepository;
@Autowired
- public QueryServiceImpl(OntologyRepository ontologyRepository, OntologyMapper ontologyMapper) {
+ public QueryServiceImpl(OntologyRepository ontologyRepository, OntologyMapper ontologyMapper,
+ OntologyRepository ontologyRepository1) {
this.ontologyMapper = ontologyMapper;
+ this.ontologyRepository = ontologyRepository1;
final Context context = ARQ.getContext().copy();
this.dataset = DatasetFactory.create();
/* registry */
@@ -62,17 +65,19 @@ public class QueryServiceImpl implements QueryService {
@Override
public List<EntityDto> findByLabel(Ontology ontology, String label, Integer limit) throws QueryMalformedException {
- final String statement = ontologyMapper.ontologyToFindByLabelQuery(ontology, label, limit);
+ final List<Ontology> ontologies = ontologyRepository.findAll();
+ final String statement = ontologyMapper.ontologyToFindByLabelQuery(ontologies, ontology, label, limit);
+ log.trace("execute sparql query:\n{}", statement);
final List<EntityDto> results = new LinkedList<>();
try (QueryExecution execution = QueryExecutionFactory.create(statement, this.dataset.getDefaultModel())) {
final Iterator<QuerySolution> resultSet = execution.execSelect();
while (resultSet.hasNext()) {
final QuerySolution solution = resultSet.next();
- final RDFNode comment = solution.get("comment");
+ final RDFNode description = solution.get("description");
final EntityDto entity = EntityDto.builder()
.uri(solution.get("o").toString())
.label(label)
- .comment(comment != null ? comment.asLiteral().getLexicalForm() : null)
+ .description(description != null ? description.asLiteral().getLexicalForm() : null)
.build();
results.add(entity);
}
@@ -85,18 +90,20 @@ public class QueryServiceImpl implements QueryService {
@Override
public List<EntityDto> findByUri(Ontology ontology, String uri) throws QueryMalformedException {
- final String statement = ontologyMapper.ontologyToFindByUriQuery(ontology, uri);
+ final List<Ontology> ontologies = ontologyRepository.findAll();
+ final String statement = ontologyMapper.ontologyToFindByUriQuery(ontologies, ontology, uri);
+ log.trace("execute sparql query:\n{}", statement);
try (QueryExecution execution = QueryExecutionFactory.create(statement, this.dataset.getDefaultModel())) {
final Iterator<QuerySolution> resultSet = execution.execSelect();
final List<EntityDto> results = new LinkedList<>();
while (resultSet.hasNext()) {
final QuerySolution solution = resultSet.next();
final RDFNode label = solution.get("label");
- final RDFNode comment = solution.get("comment");
+ final RDFNode description = solution.get("description");
final EntityDto entity = EntityDto.builder()
.uri(uri)
.label(label != null ? label.asLiteral().getLexicalForm() : null)
- .comment(comment != null ? comment.asLiteral().getLexicalForm() : null)
+ .description(description != null ? description.asLiteral().getLexicalForm() : null)
.build();
results.add(entity);
}
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/SemanticServiceImpl.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/SemanticServiceImpl.java
index 8c8cab0469..94a55ee511 100644
--- a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/SemanticServiceImpl.java
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/SemanticServiceImpl.java
@@ -34,15 +34,13 @@ public class SemanticServiceImpl implements SemanticService {
@Override
@Transactional(readOnly = true)
public List<TableColumnConcept> findAllConcepts() {
- final List<TableColumnConcept> concepts = tableColumnConceptRepository.findAll();
- return concepts;
+ return tableColumnConceptRepository.findAll();
}
@Override
@Transactional(readOnly = true)
public List<TableColumnUnit> findAllUnits() {
- final List<TableColumnUnit> units = tableColumnUnitRepository.findAll();
- return units;
+ return tableColumnUnitRepository.findAll();
}
@Override
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
index d51df7fcf1..8f58625094 100644
--- a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
@@ -88,7 +88,7 @@ public class TableServiceImpl implements TableService {
.columnId(optional.get().getId())
.label(e.getLabel())
.uri(e.getUri())
- .comment(e.getComment())
+ .description(e.getDescription())
.build())
.toList());
}
diff --git a/dbrepo-table-service/rest-service/src/main/java/at/tuwien/endpoints/TableColumnEndpoint.java b/dbrepo-table-service/rest-service/src/main/java/at/tuwien/endpoints/TableColumnEndpoint.java
index 82d41b6d86..5d025939ba 100644
--- a/dbrepo-table-service/rest-service/src/main/java/at/tuwien/endpoints/TableColumnEndpoint.java
+++ b/dbrepo-table-service/rest-service/src/main/java/at/tuwien/endpoints/TableColumnEndpoint.java
@@ -85,8 +85,8 @@ public class TableColumnEndpoint {
@NotNull Principal principal,
@NotNull @RequestHeader("Authorization") String authorization)
throws TableNotFoundException, TableMalformedException, DatabaseNotFoundException,
- ContainerNotFoundException, UnitNotFoundException, ConceptNotFoundException, NotAllowedException,
- SemanticEntityPersistException {
+ ContainerNotFoundException, NotAllowedException, SemanticEntityPersistException,
+ SemanticEntityNotFoundException {
log.debug("endpoint update table, containerId={}, databaseId={}, tableId={}, principal={}", containerId,
databaseId, tableId, principal);
if (!User.hasRole(principal, "modify-foreign-table-column-semantics")) {
diff --git a/dbrepo-table-service/rest-service/src/test/java/at/tuwien/endpoint/TableColumnEndpointUnitTest.java b/dbrepo-table-service/rest-service/src/test/java/at/tuwien/endpoint/TableColumnEndpointUnitTest.java
index 38f3e9547f..2dd1a03a5a 100644
--- a/dbrepo-table-service/rest-service/src/test/java/at/tuwien/endpoint/TableColumnEndpointUnitTest.java
+++ b/dbrepo-table-service/rest-service/src/test/java/at/tuwien/endpoint/TableColumnEndpointUnitTest.java
@@ -101,7 +101,9 @@ public class TableColumnEndpointUnitTest extends BaseUnitTest {
@Test
@WithMockUser(username = USER_1_USERNAME, authorities = {"modify-table-column-semantics"})
- public void update_publicHasRoleHasOwnWriteAccess_succeeds() throws TableNotFoundException, NotAllowedException, TableMalformedException, UnitNotFoundException, DatabaseNotFoundException, ConceptNotFoundException, ContainerNotFoundException, SemanticEntityPersistException {
+ public void update_publicHasRoleHasOwnWriteAccess_succeeds() throws TableNotFoundException, NotAllowedException,
+ TableMalformedException, DatabaseNotFoundException, ContainerNotFoundException,
+ SemanticEntityPersistException, SemanticEntityNotFoundException {
/* test */
generic_update(CONTAINER_3_ID, DATABASE_3_ID, TABLE_8_ID, COLUMN_1_1_ID, DATABASE_3, TABLE_8, COLUMN_8_2_WITH_SEMANTICS, COLUMN_8_2_SEMANTICS_UPDATE_DTO, USER_1_USERNAME, USER_1_PRINCIPAL, DATABASE_3_USER_1_WRITE_OWN_ACCESS);
@@ -140,8 +142,8 @@ public class TableColumnEndpointUnitTest extends BaseUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"modify-table-column-semantics"})
public void update_publicHasRoleForeignHasAllWriteAccess_succeeds() throws TableNotFoundException,
- NotAllowedException, TableMalformedException, UnitNotFoundException, DatabaseNotFoundException,
- ConceptNotFoundException, ContainerNotFoundException, SemanticEntityPersistException {
+ NotAllowedException, TableMalformedException, DatabaseNotFoundException,
+ ContainerNotFoundException, SemanticEntityPersistException, SemanticEntityNotFoundException {
/* test */
generic_update(CONTAINER_3_ID, DATABASE_3_ID, TABLE_8_ID, COLUMN_1_1_ID, DATABASE_3, TABLE_8, COLUMN_8_2_WITH_SEMANTICS, COLUMN_8_2_SEMANTICS_UPDATE_DTO, USER_2_USERNAME, USER_2_PRINCIPAL, DATABASE_3_USER_2_WRITE_ALL_ACCESS);
@@ -183,7 +185,9 @@ public class TableColumnEndpointUnitTest extends BaseUnitTest {
@Test
@WithMockUser(username = USER_1_USERNAME, authorities = {"modify-table-column-semantics"})
- public void update_privateHasRoleHasOwnWriteAccess_succeeds() throws TableNotFoundException, NotAllowedException, TableMalformedException, UnitNotFoundException, DatabaseNotFoundException, ConceptNotFoundException, ContainerNotFoundException, SemanticEntityPersistException {
+ public void update_privateHasRoleHasOwnWriteAccess_succeeds() throws TableNotFoundException, NotAllowedException,
+ TableMalformedException, DatabaseNotFoundException, ContainerNotFoundException,
+ SemanticEntityPersistException, SemanticEntityNotFoundException {
/* test */
generic_update(CONTAINER_1_ID, DATABASE_1_ID, TABLE_1_ID, COLUMN_1_1_ID, DATABASE_1, TABLE_1, COLUMN_1_4_WITH_SEMANTICS, COLUMN_1_4_SEMANTICS_UPDATE_DTO, USER_1_USERNAME, USER_1_PRINCIPAL, DATABASE_1_USER_1_WRITE_OWN_ACCESS);
@@ -222,8 +226,8 @@ public class TableColumnEndpointUnitTest extends BaseUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"modify-table-column-semantics"})
public void update_privateHasRoleForeignHasAllWriteAccess_succeeds() throws TableNotFoundException,
- NotAllowedException, TableMalformedException, UnitNotFoundException, DatabaseNotFoundException,
- ConceptNotFoundException, ContainerNotFoundException, SemanticEntityPersistException {
+ NotAllowedException, TableMalformedException, DatabaseNotFoundException,
+ ContainerNotFoundException, SemanticEntityPersistException, SemanticEntityNotFoundException {
/* test */
generic_update(CONTAINER_1_ID, DATABASE_1_ID, TABLE_1_ID, COLUMN_1_1_ID, DATABASE_1, TABLE_1, COLUMN_1_4_WITH_SEMANTICS, COLUMN_1_4_SEMANTICS_UPDATE_DTO, USER_2_USERNAME, USER_2_PRINCIPAL, DATABASE_1_USER_2_WRITE_ALL_ACCESS);
@@ -238,7 +242,7 @@ public class TableColumnEndpointUnitTest extends BaseUnitTest {
ColumnSemanticsUpdateDto data, String username,
Principal principal, DatabaseAccess access)
throws DatabaseNotFoundException, NotAllowedException, TableNotFoundException, TableMalformedException,
- UnitNotFoundException, ConceptNotFoundException, ContainerNotFoundException, SemanticEntityPersistException {
+ ContainerNotFoundException, SemanticEntityPersistException, SemanticEntityNotFoundException {
/* mock */
if (database != null) {
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/exception/SemanticEntityNotFoundException.java b/dbrepo-table-service/services/src/main/java/at/tuwien/exception/SemanticEntityNotFoundException.java
new file mode 100644
index 0000000000..70098f61da
--- /dev/null
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/exception/SemanticEntityNotFoundException.java
@@ -0,0 +1,21 @@
+package at.tuwien.exception;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(code = HttpStatus.NOT_FOUND)
+public class SemanticEntityNotFoundException extends Exception {
+
+ public SemanticEntityNotFoundException(String msg) {
+ super(msg);
+ }
+
+ public SemanticEntityNotFoundException(String msg, Throwable thr) {
+ super(msg, thr);
+ }
+
+ public SemanticEntityNotFoundException(Throwable thr) {
+ super(thr);
+ }
+
+}
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/gateway/SemanticServiceGateway.java b/dbrepo-table-service/services/src/main/java/at/tuwien/gateway/SemanticServiceGateway.java
new file mode 100644
index 0000000000..df54e70226
--- /dev/null
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/gateway/SemanticServiceGateway.java
@@ -0,0 +1,8 @@
+package at.tuwien.gateway;
+
+import at.tuwien.api.semantics.EntityDto;
+import at.tuwien.exception.SemanticEntityNotFoundException;
+
+public interface SemanticServiceGateway {
+ EntityDto getEntity(Long ontologyId, String uri, String authorization) throws SemanticEntityNotFoundException;
+}
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/gateway/impl/SemanticServiceGatewayImpl.java b/dbrepo-table-service/services/src/main/java/at/tuwien/gateway/impl/SemanticServiceGatewayImpl.java
new file mode 100644
index 0000000000..7b4f839984
--- /dev/null
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/gateway/impl/SemanticServiceGatewayImpl.java
@@ -0,0 +1,49 @@
+package at.tuwien.gateway.impl;
+
+import at.tuwien.api.semantics.EntityDto;
+import at.tuwien.exception.SemanticEntityNotFoundException;
+import at.tuwien.gateway.SemanticServiceGateway;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.*;
+import org.springframework.stereotype.Service;
+import org.springframework.web.client.RestTemplate;
+
+import java.net.URI;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
+
+@Slf4j
+@Service
+public class SemanticServiceGatewayImpl implements SemanticServiceGateway {
+
+ private final RestTemplate restTemplate;
+
+ @Autowired
+ public SemanticServiceGatewayImpl(RestTemplate restTemplate) {
+ this.restTemplate = restTemplate;
+ }
+
+ @Override
+ public EntityDto getEntity(Long ontologyId, String uri, String authorization) throws SemanticEntityNotFoundException {
+ final String url = "/api/semantic/ontology/" + ontologyId + "/entity?uri=" + uri;
+ final HttpHeaders headers = new HttpHeaders();
+ headers.set("Authorization", authorization);
+ final ResponseEntity<EntityDto[]> response = restTemplate.exchange(url, HttpMethod.GET,
+ new HttpEntity<>(null, headers), EntityDto[].class);
+ if (!response.getStatusCode().equals(HttpStatus.OK) || response.getBody() == null) {
+ log.error("Failed to get semantic entity for uri {}", uri);
+ throw new SemanticEntityNotFoundException("Failed to get concept for uri " + uri);
+ }
+ if (response.getBody().length != 1) {
+ log.error("None or multiple entities found for uri {}", uri);
+ throw new SemanticEntityNotFoundException("None or multiple entities found for uri " + uri);
+ }
+ return response.getBody()[0];
+ }
+
+ private String urlEncode(String value) {
+ return URLEncoder.encode(value, StandardCharsets.UTF_8);
+ }
+
+}
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java b/dbrepo-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java
index 5dd576ce0f..688e44c832 100644
--- a/dbrepo-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/mapper/TableMapper.java
@@ -14,6 +14,7 @@ import at.tuwien.api.database.table.constraints.ConstraintsCreateDto;
import at.tuwien.api.database.table.constraints.foreignKey.ForeignKeyCreateDto;
import at.tuwien.api.database.table.constraints.foreignKey.ForeignKeyDto;
import at.tuwien.api.database.table.constraints.foreignKey.ReferenceTypeDto;
+import at.tuwien.api.semantics.EntityDto;
import at.tuwien.entities.database.Database;
import at.tuwien.entities.database.table.Table;
import at.tuwien.entities.database.table.columns.TableColumn;
@@ -85,14 +86,14 @@ public interface TableMapper {
Table tableCreateDtoToTable(TableCreateDto data);
@Mappings({
- @Mapping(source = "conceptUri", target = "uri")
+ @Mapping(source = "label", target = "name")
})
- TableColumnConcept columnSemanticsUpdateDtoToTableColumnConcept(ColumnSemanticsUpdateDto data);
+ TableColumnConcept entityDtoToTableColumnConcept(EntityDto data);
@Mappings({
- @Mapping(source = "unitUri", target = "uri")
+ @Mapping(source = "label", target = "name")
})
- TableColumnUnit columnSemanticsUpdateDtoToTableColumnUnit(ColumnSemanticsUpdateDto data);
+ TableColumnUnit entityDtoToTableColumnUnit(EntityDto data);
default TableColumn columnNameToTableColumn(Table table, String name) throws TableMalformedException {
String internalName = nameToInternalName(name);
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/repository/jpa/OntologyRepository.java b/dbrepo-table-service/services/src/main/java/at/tuwien/repository/jpa/OntologyRepository.java
new file mode 100644
index 0000000000..75c296f527
--- /dev/null
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/repository/jpa/OntologyRepository.java
@@ -0,0 +1,10 @@
+package at.tuwien.repository.jpa;
+
+import at.tuwien.entities.semantics.Ontology;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+
+@Repository
+public interface OntologyRepository extends JpaRepository<Ontology, Long> {
+
+}
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/service/SemanticService.java b/dbrepo-table-service/services/src/main/java/at/tuwien/service/SemanticService.java
new file mode 100644
index 0000000000..343a27347d
--- /dev/null
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/service/SemanticService.java
@@ -0,0 +1,32 @@
+package at.tuwien.service;
+
+import at.tuwien.entities.database.table.columns.TableColumnConcept;
+import at.tuwien.entities.database.table.columns.TableColumnUnit;
+import at.tuwien.exception.ConceptNotFoundException;
+import at.tuwien.exception.SemanticEntityNotFoundException;
+import at.tuwien.exception.UnitNotFoundException;
+
+public interface SemanticService {
+
+ /**
+ * Finds a ColumnConcept with given uri
+ *
+ * @param uri The uri.
+ * @return The concept, if successful.
+ * @throws ConceptNotFoundException The ColumnConcept was not found in the metadata database.
+ */
+ TableColumnConcept findConcept(String uri) throws ConceptNotFoundException;
+
+ /**
+ * Finds a unit with given uri
+ *
+ * @param uri The uri.
+ * @return The unit, if successful.
+ * @throws UnitNotFoundException The unit was not found in the metadata database.
+ */
+ TableColumnUnit findUnit(String uri) throws UnitNotFoundException;
+
+ TableColumnConcept saveConcept(String uri, String authorization) throws SemanticEntityNotFoundException;
+
+ TableColumnUnit saveUnit(String uri, String authorization) throws SemanticEntityNotFoundException;
+}
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/service/TableService.java b/dbrepo-table-service/services/src/main/java/at/tuwien/service/TableService.java
index dae9cb07f6..3bc0a73af5 100644
--- a/dbrepo-table-service/services/src/main/java/at/tuwien/service/TableService.java
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/service/TableService.java
@@ -78,16 +78,14 @@ public interface TableService {
* @param tableId The table id.
* @param columnId The column id.
* @param updateDto The update data containing unit and concept uris.
- * @return The updated table column.
- * @throws TableNotFoundException
+ * @return The updated table column, if successful.
+ * @throws TableNotFoundException The table was not found in the metadata database.
* @throws DatabaseNotFoundException The database was not found in the metadata database.
* @throws ContainerNotFoundException The container was not found.
* @throws TableMalformedException The table seems malformed by the mapper.
- * @throws UnitNotFoundException
- * @throws ConceptNotFoundException
*/
TableColumn update(Long containerId, Long databaseId, Long tableId, Long columnId,
ColumnSemanticsUpdateDto updateDto, String authorization)
throws TableNotFoundException, DatabaseNotFoundException, ContainerNotFoundException,
- TableMalformedException, UnitNotFoundException, ConceptNotFoundException, SemanticEntityPersistException;
+ TableMalformedException, SemanticEntityPersistException, SemanticEntityNotFoundException;
}
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/service/impl/SemanticServiceImpl.java b/dbrepo-table-service/services/src/main/java/at/tuwien/service/impl/SemanticServiceImpl.java
new file mode 100644
index 0000000000..94cd509ae8
--- /dev/null
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/service/impl/SemanticServiceImpl.java
@@ -0,0 +1,107 @@
+package at.tuwien.service.impl;
+
+import at.tuwien.entities.database.table.columns.TableColumnConcept;
+import at.tuwien.entities.database.table.columns.TableColumnUnit;
+import at.tuwien.entities.semantics.Ontology;
+import at.tuwien.exception.ConceptNotFoundException;
+import at.tuwien.exception.SemanticEntityNotFoundException;
+import at.tuwien.exception.UnitNotFoundException;
+import at.tuwien.gateway.SemanticServiceGateway;
+import at.tuwien.mapper.TableMapper;
+import at.tuwien.repository.jpa.ConceptRepository;
+import at.tuwien.repository.jpa.OntologyRepository;
+import at.tuwien.repository.jpa.UnitRepository;
+import at.tuwien.service.SemanticService;
+import lombok.extern.log4j.Log4j2;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+import java.util.Optional;
+
+@Log4j2
+@Service
+public class SemanticServiceImpl implements SemanticService {
+
+ private final TableMapper tableMapper;
+ private final UnitRepository unitRepository;
+ private final ConceptRepository conceptRepository;
+ private final OntologyRepository ontologyRepository;
+ private final SemanticServiceGateway semanticServiceGateway;
+
+ @Autowired
+ public SemanticServiceImpl(TableMapper tableMapper, UnitRepository unitRepository, ConceptRepository conceptRepository,
+ OntologyRepository ontologyRepository, SemanticServiceGateway semanticServiceGateway) {
+ this.tableMapper = tableMapper;
+ this.unitRepository = unitRepository;
+ this.conceptRepository = conceptRepository;
+ this.ontologyRepository = ontologyRepository;
+ this.semanticServiceGateway = semanticServiceGateway;
+ }
+
+ @Override
+ public TableColumnConcept findConcept(String uri) throws ConceptNotFoundException {
+ final Optional<TableColumnConcept> optional = conceptRepository.findById(uri);
+ if (optional.isEmpty()) {
+ log.error("Failed to find column concept with uri {}", uri);
+ throw new ConceptNotFoundException("Failed to find concept with uri " + uri);
+ }
+ return optional.get();
+ }
+
+ @Override
+ public TableColumnUnit findUnit(String uri) throws UnitNotFoundException {
+ final Optional<TableColumnUnit> optional = unitRepository.findById(uri);
+ if (optional.isEmpty()) {
+ log.error("Failed to find unit with uri {}", uri);
+ throw new UnitNotFoundException("Failed to find unit");
+ }
+ return optional.get();
+ }
+
+ @Override
+ public TableColumnConcept saveConcept(String uri, String authorization) throws SemanticEntityNotFoundException {
+ /* check compatible ontologies */
+ final Ontology ontology = getCompatibleOntology(uri);
+ if (ontology == null) {
+ return TableColumnConcept.builder()
+ .uri(uri)
+ .build();
+ }
+ final TableColumnConcept entity = tableMapper.entityDtoToTableColumnConcept(semanticServiceGateway.getEntity(ontology.getId(), uri, authorization));
+ final TableColumnConcept concept = conceptRepository.save(entity);
+ log.debug("saved concept with uri {}", concept.getUri());
+ log.trace("saved concept {}", concept.getUri());
+ return concept;
+ }
+
+ @Override
+ public TableColumnUnit saveUnit(String uri, String authorization) throws SemanticEntityNotFoundException {
+ final Ontology ontology = getCompatibleOntology(uri);
+ if (ontology == null) {
+ return TableColumnUnit.builder()
+ .uri(uri)
+ .build();
+ }
+ final TableColumnUnit entity = tableMapper.entityDtoToTableColumnUnit(semanticServiceGateway.getEntity(ontology.getId(), uri, authorization));
+ final TableColumnUnit unit = unitRepository.save(entity);
+ log.debug("saved unit with uri {}", unit.getUri());
+ log.trace("saved unit {}", unit.getUri());
+ return unit;
+ }
+
+ private Ontology getCompatibleOntology(String uri) {
+ final List<Ontology> ontologies = ontologyRepository.findAll()
+ .stream()
+ .filter(o -> uri.startsWith(o.getUri()))
+ .toList();
+ if (ontologies.size() != 1) {
+ log.warn("Failed to find registered ontology for entity with uri {}", uri);
+ return null;
+ }
+ final Ontology ontology = ontologies.get(0);
+ log.debug("found available compatible ontology with id {}", ontology.getId());
+ return ontology;
+ }
+
+}
diff --git a/dbrepo-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java b/dbrepo-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
index 9f46855a19..c0b1681e8b 100644
--- a/dbrepo-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
+++ b/dbrepo-table-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
@@ -7,21 +7,14 @@ import at.tuwien.entities.container.Container;
import at.tuwien.entities.database.Database;
import at.tuwien.entities.database.table.Table;
import at.tuwien.entities.database.table.columns.TableColumn;
-import at.tuwien.entities.database.table.columns.TableColumnConcept;
-import at.tuwien.entities.database.table.columns.TableColumnUnit;
import at.tuwien.entities.user.User;
import at.tuwien.exception.*;
import at.tuwien.mapper.TableMapper;
import at.tuwien.repository.elastic.TableColumnIdxRepository;
import at.tuwien.repository.elastic.TableIdxRepository;
-import at.tuwien.repository.jpa.ConceptRepository;
import at.tuwien.repository.jpa.TableColumnRepository;
import at.tuwien.repository.jpa.TableRepository;
-import at.tuwien.repository.jpa.UnitRepository;
-import at.tuwien.service.ContainerService;
-import at.tuwien.service.DatabaseService;
-import at.tuwien.service.TableService;
-import at.tuwien.service.UserService;
+import at.tuwien.service.*;
import com.mchange.v2.c3p0.ComboPooledDataSource;
import lombok.extern.log4j.Log4j2;
import org.springframework.beans.factory.annotation.Autowired;
@@ -41,28 +34,26 @@ public class TableServiceImpl extends HibernateConnector implements TableService
private final TableMapper tableMapper;
private final UserService userService;
- private final UnitRepository unitRepository;
- private final TableRepository tableRepository;
private final DatabaseService databaseService;
+ private final SemanticService semanticService;
+ private final TableRepository tableRepository;
private final ContainerService containerService;
- private final ConceptRepository conceptRepository;
private final TableIdxRepository tableIdxRepository;
private final TableColumnRepository tableColumnRepository;
private final TableColumnIdxRepository tableColumnIdxRepository;
@Autowired
- public TableServiceImpl(TableMapper tableMapper, UserService userService, UnitRepository unitRepository,
+ public TableServiceImpl(TableMapper tableMapper, UserService userService, SemanticService semanticService,
TableRepository tableRepository, DatabaseService databaseService,
- ContainerService containerService, ConceptRepository conceptRepository,
- TableIdxRepository tableIdxRepository, TableColumnRepository tableColumnRepository,
+ ContainerService containerService, TableIdxRepository tableIdxRepository,
+ TableColumnRepository tableColumnRepository,
TableColumnIdxRepository tableColumnIdxRepository) {
this.tableMapper = tableMapper;
this.userService = userService;
- this.unitRepository = unitRepository;
+ this.semanticService = semanticService;
this.tableRepository = tableRepository;
this.databaseService = databaseService;
this.containerService = containerService;
- this.conceptRepository = conceptRepository;
this.tableIdxRepository = tableIdxRepository;
this.tableColumnRepository = tableColumnRepository;
this.tableColumnIdxRepository = tableColumnIdxRepository;
@@ -214,24 +205,28 @@ public class TableServiceImpl extends HibernateConnector implements TableService
public TableColumn update(Long containerId, Long databaseId, Long tableId, Long columnId,
ColumnSemanticsUpdateDto updateDto, String authorization)
throws TableNotFoundException, DatabaseNotFoundException, ContainerNotFoundException,
- TableMalformedException, UnitNotFoundException, ConceptNotFoundException {
+ TableMalformedException, SemanticEntityNotFoundException {
final Table table = findById(containerId, databaseId, tableId);
final TableColumn column = findColumn(table, columnId);
/* assign */
if (updateDto.getUnitUri() != null) {
- unitRepository.save(tableMapper.columnSemanticsUpdateDtoToTableColumnUnit(updateDto));
- final TableColumnUnit unit = findUnit(updateDto.getUnitUri());
- column.setUnit(unit);
- log.debug("update unit of column, unit={}, column={}", unit, column);
+ try {
+ column.setUnit(semanticService.findUnit(updateDto.getUnitUri()));
+ } catch (UnitNotFoundException e) {
+ log.warn("Unit with uri {} not found in metadata database", updateDto.getUnitUri());
+ column.setUnit(semanticService.saveUnit(updateDto.getUnitUri(), authorization));
+ }
} else {
column.setUnit(null);
log.debug("remove unit of column, column={}", column);
}
if (updateDto.getConceptUri() != null) {
- conceptRepository.save(tableMapper.columnSemanticsUpdateDtoToTableColumnConcept(updateDto));
- final TableColumnConcept concept = findConcept(updateDto.getConceptUri());
- column.setConcept(concept);
- log.debug("update ColumnConcept of column, concept={}, column={}", concept, column);
+ try {
+ column.setConcept(semanticService.findConcept(updateDto.getConceptUri()));
+ } catch (ConceptNotFoundException e) {
+ log.warn("Concept with uri {} not found in metadata database", updateDto.getConceptUri());
+ column.setConcept(semanticService.saveConcept(updateDto.getConceptUri(), authorization));
+ }
} else {
column.setConcept(null);
log.debug("remove ColumnConcept of column, column={}", column);
@@ -267,36 +262,4 @@ public class TableServiceImpl extends HibernateConnector implements TableService
return optional.get();
}
- /**
- * Finds a ColumnConcept with given uri
- *
- * @param uri The uri.
- * @return The concept, if successful.
- * @throws ConceptNotFoundException The ColumnConcept was not found in the metadata database.
- */
- protected TableColumnConcept findConcept(String uri) throws ConceptNotFoundException {
- final Optional<TableColumnConcept> optional = conceptRepository.findById(uri);
- if (optional.isEmpty()) {
- log.error("Failed to find column concept with uri {}", uri);
- throw new ConceptNotFoundException("Failed to find concept with uri " + uri);
- }
- return optional.get();
- }
-
- /**
- * Finds a unit with given uri
- *
- * @param uri The uri.
- * @return The unit, if successful.
- * @throws UnitNotFoundException The unit was not found in the metadata database.
- */
- protected TableColumnUnit findUnit(String uri) throws UnitNotFoundException {
- final Optional<TableColumnUnit> optional = unitRepository.findById(uri);
- if (optional.isEmpty()) {
- log.error("Failed to find unit with uri {}", uri);
- throw new UnitNotFoundException("Failed to find unit");
- }
- return optional.get();
- }
-
}
diff --git a/dbrepo-ui/.env.example b/dbrepo-ui/.env.example
index 53a7f375f5..c6d247fe18 100644
--- a/dbrepo-ui/.env.example
+++ b/dbrepo-ui/.env.example
@@ -13,3 +13,4 @@ SANDBOX=false
SHARED_FILESYSTEM="/tmp"
TITLE="Database Repository"
VERSION="latest"
+GIT_HASH="deadbeef"
diff --git a/dbrepo-ui/Dockerfile b/dbrepo-ui/Dockerfile
index 582126fc3e..f3b107c8d8 100644
--- a/dbrepo-ui/Dockerfile
+++ b/dbrepo-ui/Dockerfile
@@ -57,6 +57,7 @@ ENV VERSION="${TAG}"
ENV TITLE="Database Repository"
ENV ICON="/favicon.ico"
ENV DBREPO_CLIENT_SECRET="client-secret"
+ENV GIT_HASH="deadbeef"
WORKDIR /app
diff --git a/dbrepo-ui/api/semantic.service.js b/dbrepo-ui/api/semantic.service.js
index 0c9f01b7db..01b8b021a3 100644
--- a/dbrepo-ui/api/semantic.service.js
+++ b/dbrepo-ui/api/semantic.service.js
@@ -36,6 +36,23 @@ class SemanticService {
})
}
+ updateConcept (data) {
+ return new Promise((resolve, reject) => {
+ api.put('/api/semantic/concept', data, { headers: { Accept: 'application/json' } })
+ .then((response) => {
+ const concept = response.data
+ console.debug('response concept', concept)
+ resolve(concept)
+ })
+ .catch((error) => {
+ const { code, message } = error
+ console.error('Failed to update concept', error)
+ Vue.$toast.error(`[${code}] Failed to update concept: ${message}`)
+ reject(error)
+ })
+ })
+ }
+
findAllUnits () {
return new Promise((resolve, reject) => {
api.get('/api/semantic/unit', { headers: { Accept: 'application/json' } })
@@ -53,6 +70,23 @@ class SemanticService {
})
}
+ updateUnit (data) {
+ return new Promise((resolve, reject) => {
+ api.put('/api/semantic/unit', data, { headers: { Accept: 'application/json' } })
+ .then((response) => {
+ const unit = response.data
+ console.debug('response unit', unit)
+ resolve(unit)
+ })
+ .catch((error) => {
+ const { code, message } = error
+ console.error('Failed to update unit', error)
+ Vue.$toast.error(`[${code}] Failed to update unit: ${message}`)
+ reject(error)
+ })
+ })
+ }
+
findOntology (id) {
return new Promise((resolve, reject) => {
api.get(`/api/semantic/ontology/${id}`, { headers: { Accept: 'application/json' } })
diff --git a/dbrepo-ui/components/dialogs/EditSemantics.vue b/dbrepo-ui/components/dialogs/EditSemantics.vue
deleted file mode 100644
index 5debbc5840..0000000000
--- a/dbrepo-ui/components/dialogs/EditSemantics.vue
+++ /dev/null
@@ -1,96 +0,0 @@
-<template>
- <div>
- <v-card>
- <v-card-title>Edit</v-card-title>
- <v-card-text>
- <v-form ref="form" v-model="valid" autocomplete="off" @submit.prevent="submit">
- <v-row>
- <v-col>
- <v-text-field
- v-model="semanticDto.name"
- clearable
- label="Name" />
- </v-col>
- </v-row>
- <v-row>
- <v-col>
- <v-text-field
- v-model="semanticDto.uri"
- clearable
- label="URI"
- :rules="[v => !!v || $t('Required')]"
- required />
- </v-col>
- </v-row>
- </v-form>
- </v-card-text>
- <v-card-actions>
- <v-spacer />
- <v-btn
- class="mb-2"
- @click="cancel">
- Cancel
- </v-btn>
- <v-btn
- color="primary"
- class="mb-2 mr-2"
- :disabled="!valid"
- :loading="loadingSave"
- @click="save">
- Save
- </v-btn>
- </v-card-actions>
- </v-card>
- </div>
-</template>
-
-<script>
-import SemanticService from '@/api/semantic.service'
-
-export default {
- props: {
- entity: {
- type: Object,
- default () {
- return {}
- }
- }
- },
- data () {
- return {
- valid: false,
- localEntity: null,
- loadingSave: false,
- semanticDto: {
- name: null,
- uri: null
- }
- }
- },
- computed: {
- },
- watch: {
- entity () {
- this.semanticDto.name = this.entity.name
- this.semanticDto.uri = this.entity.uri
- }
- },
- mounted () {
- this.semanticDto.name = this.entity.name
- this.semanticDto.uri = this.entity.uri
- },
- methods: {
- cancel () {
- this.$emit('close', { success: false, action: 'cancel' })
- },
- save () {
- SemanticService.u
- },
- submit () {
- this.$refs.form.validate()
- }
- }
-}
-</script>
-<style scoped>
-</style>
diff --git a/dbrepo-ui/components/dialogs/Semantics.vue b/dbrepo-ui/components/dialogs/Semantics.vue
index 97910f2690..caf5908002 100644
--- a/dbrepo-ui/components/dialogs/Semantics.vue
+++ b/dbrepo-ui/components/dialogs/Semantics.vue
@@ -1,37 +1,61 @@
<template>
<div>
<v-card>
- <v-card-title>Assign Semantic Information</v-card-title>
- <v-card-subtitle v-if="!loadingSemantics">
- Recommend <strong v-text="recommendations.length" /> {{ recommendations.length === 1 ? 'entity' : 'entities' }} that matches the column name
- </v-card-subtitle>
+ <v-progress-linear
+ v-if="loadingSemantics"
+ color="primary"
+ indeterminate />
+ <v-card-title v-text="column.name" />
+ <v-card-subtitle v-if="loadingSemantics && !semanticEntity">Loading semantic recommendations ...</v-card-subtitle>
+ <v-card-text>
+ <v-alert
+ v-if="!entity"
+ border="left"
+ color="info"
+ dark
+ icon="mdi-share-variant"
+ class="pl-6">
+ <p>
+ The following ontologies automatically will query the fields <code>rdfs:label</code> and
+ <code>schema:description</code> and store it for this column. You can still use other URIs that are not
+ matching these ontologies, the URI will be displayed instead.
+ </p>
+ <div v-for="(item,idx) in ontologies" :key="idx">
+ <a :href="item.uri" target="_blank" v-text="item.uri" />
+ </div>
+ </v-alert>
+ <v-alert
+ v-if="entity"
+ border="left"
+ color="primary"
+ dark
+ icon="mdi-share-variant"
+ class="pl-6">
+ <div>
+ <a :href="entity.uri" class="white--text" target="_blank" v-text="entity.name ? entity.name : entity.uri" />
+ </div>
+ <div v-text="entity.description" />
+ </v-alert>
+ </v-card-text>
<v-card-text>
<v-form ref="form" v-model="valid" autocomplete="off" @submit.prevent="submit">
- <v-row>
- <v-col>
- <v-progress-linear
- v-if="loadingSemantics"
- color="secondary"
- indeterminate />
- <v-list-item-group v-if="!loadingSemantics" v-model="recommendation">
- <v-list-item v-for="(item,idx) in recommendations" :key="idx" three-line>
- <template v-slot:default="{ active, }">
- <v-list-item-action>
- <v-checkbox
- :input-value="active"
- color="primary" />
- </v-list-item-action>
- <v-list-item-content>
- <v-list-item-title v-text="item.label" />
- <v-list-item-subtitle v-text="item.uri" />
- <v-list-item-subtitle class="mt-1" v-text="item.comment" />
- </v-list-item-content>
- </template>
- </v-list-item>
- </v-list-item-group>
- </v-col>
- </v-row>
- <v-row>
+ <v-list-item-group v-if="!loadingSemantics" v-model="recommendation">
+ <v-list-item v-for="(item,idx) in recommendations" :key="idx" three-line>
+ <template v-slot:default="{ active, }">
+ <v-list-item-action>
+ <v-checkbox
+ :input-value="active"
+ color="primary" />
+ </v-list-item-action>
+ <v-list-item-content>
+ <v-list-item-title v-text="item.label" />
+ <v-list-item-subtitle v-text="item.uri" />
+ <v-list-item-subtitle class="mt-1" v-text="item.description" />
+ </v-list-item-content>
+ </template>
+ </v-list-item>
+ </v-list-item-group>
+ <v-row dense>
<v-col>
<v-text-field
v-model="uri"
@@ -99,24 +123,26 @@ export default {
valid: false,
loading: false,
loadingOntologies: false,
- loadingSemantics: false,
- ontologies: []
+ loadingSemantics: false
}
},
computed: {
+ ontologies () {
+ return this.$store.state.ontologies
+ },
+ entity () {
+ if (!this.column[this.mode]) {
+ return null
+ }
+ return this.column[this.mode]
+ }
},
watch: {
column () {
- this.loadSemantics()
- if (this.column.unit && this.mode === 'unit') {
- this.uri = this.column.unit.uri
- return
- }
- if (this.column.concept && this.mode === 'concept') {
- this.uri = this.column.concept.uri
- return
+ if (!this.column[this.mode]) {
+ this.recommendSemantics()
}
- this.uri = null
+ this.init()
},
recommendation (index) {
if (!this.recommendations[index] || !('uri' in this.recommendations[index])) {
@@ -127,8 +153,10 @@ export default {
}
},
mounted () {
- this.loadOntologies()
- this.loadSemantics()
+ this.init()
+ if (!this.column[this.mode]) {
+ this.recommendSemantics()
+ }
},
methods: {
cancel () {
@@ -153,17 +181,7 @@ export default {
this.loadingSave = false
})
},
- loadOntologies () {
- this.loadingOntologies = true
- SemanticService.findAllOntologies()
- .then((ontologies) => {
- this.ontologies = ontologies
- })
- .finally(() => {
- this.loadingOntologies = false
- })
- },
- loadSemantics () {
+ recommendSemantics () {
this.loadingSemantics = true
SemanticService.suggestTableColumn(this.database.id, this.tableId, this.column.id)
.then((recommendations) => {
@@ -179,6 +197,17 @@ export default {
}
return str.match(/https?:\/\//g)
},
+ init () {
+ if (this.column.unit && this.mode === 'unit') {
+ this.uri = this.column.unit.uri
+ return
+ }
+ if (this.column.concept && this.mode === 'concept') {
+ this.uri = this.column.concept.uri
+ return
+ }
+ this.uri = null
+ },
submit () {
this.$refs.form.validate()
}
diff --git a/dbrepo-ui/components/dialogs/ViewSemanticEntity.vue b/dbrepo-ui/components/dialogs/ViewSemanticEntity.vue
new file mode 100644
index 0000000000..6830ae76f4
--- /dev/null
+++ b/dbrepo-ui/components/dialogs/ViewSemanticEntity.vue
@@ -0,0 +1,72 @@
+<template>
+ <div>
+ <v-card>
+ <v-card-title v-text="entity.name" />
+ <v-card-subtitle>
+ <a :href="entity.uri" target="_blank" v-text="entity.uri" />
+ </v-card-subtitle>
+ <v-card-text>
+ <p v-text="description" />
+ </v-card-text>
+ <div v-for="(item,idx) in entity.columns" :key="idx">
+ <v-list-item-group>
+ <v-list-item two-line :to="link(item)">
+ <v-list-item-content>
+ <v-list-item-title v-text="item.name" />
+ <v-list-item-subtitle class="mt-2" v-text="link(item)" />
+ </v-list-item-content>
+ </v-list-item>
+ </v-list-item-group>
+ </div>
+ <v-card-actions class="mt-2">
+ <v-spacer />
+ <v-btn
+ class="mb-2"
+ @click="cancel">
+ Cancel
+ </v-btn>
+ </v-card-actions>
+ </v-card>
+ </div>
+</template>
+
+<script>
+export default {
+ props: {
+ mode: {
+ type: String,
+ default () {
+ return 'unit'
+ }
+ },
+ entity: {
+ type: Object,
+ default () {
+ return {}
+ }
+ }
+ },
+ data () {
+ return {
+ }
+ },
+ computed: {
+ description () {
+ if (!this.entity.description) {
+ return '(no description)'
+ }
+ return this.entity.description
+ }
+ },
+ methods: {
+ cancel () {
+ this.$emit('close', { success: false, action: 'cancel' })
+ },
+ link (item) {
+ return `/container/${item.database_id}/database/${item.database_id}/table/${item.table_id}/schema`
+ }
+ }
+}
+</script>
+<style scoped>
+</style>
diff --git a/dbrepo-ui/config.js b/dbrepo-ui/config.js
index d0222abf07..bc199503b7 100644
--- a/dbrepo-ui/config.js
+++ b/dbrepo-ui/config.js
@@ -17,5 +17,6 @@ config.elasticPassword = process.env.ELASTIC_PASSWORD || 'elastic'
config.clientSecret = process.env.DBREPO_CLIENT_SECRET || 'MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG'
config.defaultPublisher = process.env.DEFAULT_PID_PUBLISHER || 'Technische Universität Wien'
config.doiUrl = process.env.DOI_URL || 'https://doi.org'
+config.gitHash = process.env.GIT_HASH || 'deadbeef'
module.exports = config
diff --git a/dbrepo-ui/layouts/default.vue b/dbrepo-ui/layouts/default.vue
index 75eaccafae..30596e71b7 100644
--- a/dbrepo-ui/layouts/default.vue
+++ b/dbrepo-ui/layouts/default.vue
@@ -10,7 +10,7 @@
<v-list-item class="mt-2">
<v-list-item-content>
<v-list-item-subtitle>
- {{ version }}
+ {{ version }} ({{ gitHash }})
</v-list-item-subtitle>
<v-list-item-title class="text-h6">
Database Repository
@@ -183,6 +183,9 @@ export default {
version () {
return this.$config.version
},
+ gitHash () {
+ return this.$config.gitHash
+ },
canListOntologies () {
if (!this.roles) {
return false
diff --git a/dbrepo-ui/nuxt.config.js b/dbrepo-ui/nuxt.config.js
index 9db2e6dc80..fee9bcc801 100644
--- a/dbrepo-ui/nuxt.config.js
+++ b/dbrepo-ui/nuxt.config.js
@@ -1,6 +1,6 @@
import path from 'path'
import colors from 'vuetify/es5/util/colors'
-import { api, icon, search, clientSecret, title, sandbox, logo, version, defaultPublisher, doiUrl, baseUrl } from './config'
+import { api, icon, search, clientSecret, title, sandbox, logo, version, defaultPublisher, doiUrl, baseUrl, gitHash } from './config'
const proxy = {}
@@ -94,7 +94,8 @@ export default {
clientSecret,
defaultPublisher,
doiUrl,
- baseUrl
+ baseUrl,
+ gitHash
},
serverMiddleware: [
diff --git a/dbrepo-ui/pages/semantic/index.vue b/dbrepo-ui/pages/semantic/index.vue
index a9362fb6d3..63353bb5ab 100644
--- a/dbrepo-ui/pages/semantic/index.vue
+++ b/dbrepo-ui/pages/semantic/index.vue
@@ -25,39 +25,39 @@
<a :href="item.uri" target="_blank" v-text="item.uri" />
</template>
<template v-slot:item.action="{ item }">
- <v-btn small @click="edit(item)">
- Edit
+ <v-btn small :disabled="disabled(item)" @click="view(item)">
+ Usages
</v-btn>
</template>
</v-data-table>
</v-card-text>
</v-card>
<v-dialog
- v-model="editSemanticDialog"
- persistent
+ v-model="viewSemanticEntityDialog"
max-width="640">
- <EditSemantics :entity="entity" @close="close" />
+ <ViewSemanticEntity :mode="mode" :entity="entity" @close="close" />
</v-dialog>
<v-breadcrumbs :items="items" class="pa-0 mt-2" />
</div>
</template>
<script>
import SemanticService from '@/api/semantic.service'
-import EditSemantics from '@/components/dialogs/EditSemantics.vue'
+import ViewSemanticEntity from '@/components/dialogs/ViewSemanticEntity.vue'
export default {
components: {
- EditSemantics
+ ViewSemanticEntity
},
data () {
return {
loadingConcepts: false,
loadingUnits: false,
entity: null,
- editSemanticDialog: false,
+ viewSemanticEntityDialog: false,
headers: [
- { text: 'Name', value: 'name' },
{ text: 'URI', value: 'uri' },
+ { text: 'Name', value: 'name' },
+ { text: 'Description', value: 'description' },
{ text: 'Usages', value: 'usages' },
{ text: null, value: 'action' }
],
@@ -97,6 +97,9 @@ export default {
rows () {
return this.tab === 0 ? this.concepts : this.units
},
+ mode () {
+ return this.tab === 0 ? 'concept' : 'unit'
+ },
canListOntologies () {
if (!this.roles) {
return false
@@ -137,12 +140,20 @@ export default {
this.loadingUnits = false
})
},
- edit (entity) {
+ disabled (item) {
+ return !item.usages || this.usages === 0
+ },
+ view (entity) {
this.entity = entity
- this.editSemanticDialog = true
+ this.viewSemanticEntityDialog = true
},
close (event) {
- this.editSemanticDialog = false
+ if (this.mode === 'unit') {
+ this.loadUnits()
+ } else if (this.mode === 'concept') {
+ this.loadConcepts()
+ }
+ this.viewSemanticEntityDialog = false
}
}
}
diff --git a/dbrepo-ui/pages/semantic/ontology/_ontology_id/index.vue b/dbrepo-ui/pages/semantic/ontology/_ontology_id/index.vue
index f8e486420b..a9b4422d3a 100644
--- a/dbrepo-ui/pages/semantic/ontology/_ontology_id/index.vue
+++ b/dbrepo-ui/pages/semantic/ontology/_ontology_id/index.vue
@@ -1,9 +1,16 @@
<template>
<div v-if="canListOntologies">
<v-toolbar flat>
+ <v-toolbar-title>
+ <v-btn id="back-btn" plain class="mr-2" to="/semantic/ontology">
+ <v-icon left>mdi-arrow-left</v-icon>
+ </v-btn>
+ </v-toolbar-title>
<v-toolbar-title>
<v-skeleton-loader v-if="loading" type="text" class="skeleton-small" />
- <span v-if="!loading" v-text="title" />
+ <span v-if="!loading">
+ Ontology <a v-if="ontology" :href="ontology.uri" target="_blank" v-text="ontology.uri" />
+ </span>
</v-toolbar-title>
<v-spacer />
<v-toolbar-title>
@@ -117,12 +124,6 @@ export default {
ontologies () {
return this.$store.state.ontologies
},
- title () {
- if (!this.ontology) {
- return 'Ontology'
- }
- return `Ontology ${this.ontology.prefix}`
- },
canListOntologies () {
if (!this.roles) {
return false
@@ -156,7 +157,7 @@ export default {
SemanticService.unregisterOntology(this.$route.params.ontology_id)
.then(async () => {
await this.$store.dispatch('reloadOntologies')
- await this.$router.push('/ontology')
+ await this.$router.push('/semantic/ontology')
})
.finally(() => {
this.loadingDelete = false
diff --git a/dbrepo-ui/pages/semantic/ontology/index.vue b/dbrepo-ui/pages/semantic/ontology/index.vue
index dcb79ccc92..b39800ec41 100644
--- a/dbrepo-ui/pages/semantic/ontology/index.vue
+++ b/dbrepo-ui/pages/semantic/ontology/index.vue
@@ -1,6 +1,11 @@
<template>
<div v-if="canListOntologies">
<v-toolbar flat>
+ <v-toolbar-title>
+ <v-btn id="back-btn" plain class="mr-2" to="/semantic">
+ <v-icon left>mdi-arrow-left</v-icon>
+ </v-btn>
+ </v-toolbar-title>
<v-toolbar-title>{{ ontologies.length }} {{ $t('layout.ontologies', { name: 'vue-i18n' }) }}</v-toolbar-title>
<v-spacer />
<v-toolbar-title>
--
GitLab