Broken build

it/src/main/scala/org/mbari/oni/endpoints/HistoryEndpointsSuite.scala

@@ -1,3 +1,19 @@
+/*
+ * Copyright 2024 Monterey Bay Aquarium Research Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package org.mbari.oni.endpoints
 
 import org.mbari.oni.domain.ExtendedHistory

oni/src/main/java/org/mbari/oni/jpa/entities/UserAccountEntity.java

@@ -87,7 +87,7 @@ public class UserAccountEntity implements Serializable, IPersistentObject {
         nullable = false,
         length = 50
     )
-    String password;
+    String encryptedPassword;
 
     @Column(
         name = "Role",
@@ -109,7 +109,7 @@ public class UserAccountEntity implements Serializable, IPersistentObject {
     String userName;
 
     public boolean authenticate(String unencryptedPassword) {
-        return (new BasicPasswordEncryptor()).checkPassword(unencryptedPassword, password);
+        return (new BasicPasswordEncryptor()).checkPassword(unencryptedPassword, encryptedPassword);
     }
 
     @Override
@@ -150,8 +150,8 @@ public String getLastName() {
         return lastName;
     }
 
-    public String getPassword() {
-        return password;
+    public String getEncryptedPassword() {
+        return encryptedPassword;
     }
 
     public String getRole() {
@@ -202,8 +202,12 @@ public void setLastName(String lastName) {
         this.lastName = lastName;
     }
 
-    public void setPassword(String unencryptedPassword) {
-        this.password = (new BasicPasswordEncryptor()).encryptPassword(unencryptedPassword);
+    public void setEncryptedPassword(String encryptedPassword) {
+        this.encryptedPassword = encryptedPassword;
+    }
+
+    public void setPassword(String password) {
+        this.encryptedPassword = (new BasicPasswordEncryptor()).encryptPassword(password);
     }
 
     public void setRole(String role) {

oni/src/main/java/org/mbari/oni/jpa/repositories/PrefNodeRepository.java

@@ -0,0 +1,54 @@
+/*
+ * Copyright (c) Monterey Bay Aquarium Research Institute 2024
+ *
+ * oni code is non-public software. Unauthorized copying of this file,
+ * via any medium is strictly prohibited. Proprietary and confidential. 
+ */
+
+package org.mbari.oni.jpa.repositories;
+
+import jakarta.persistence.EntityManager;
+import org.mbari.oni.jpa.entities.PreferenceNodeEntity;
+
+import java.util.List;
+import java.util.Optional;
+
+public class PrefNodeRepository extends Repository {
+
+    public PrefNodeRepository(EntityManager entityManager) {
+        super(entityManager);
+    }
+
+    public Optional<PreferenceNodeEntity> findByNodeNameAndPrefKey(String name, String key) {
+        return findByNamedQuery("PreferenceNode.findByNodeNameAndPrefKey", Map.of("nodeName", name, "prefKey", key))
+                .stream()
+                .findFirst();
+    }
+
+    public PreferenceNodeEntity create(String name, String key, String value) {
+        var prefNode = new PreferenceNodeEntity();
+        prefNode.setName(name);
+        prefNode.setKey(key);
+        prefNode.setValue(value);
+        return entityManager.persist(prefNode);
+    }
+
+    public Optional<PreferenceNodeEntity> update(String name, String key, String value) {
+        var prefNode = findByNodeNameAndPrefKey(name, key);
+        prefNode.setValue(value);
+        return entityManager.merge(prefNode);
+    }
+
+    public void delete(String name, String key) {
+        var opt = findByNodeNameAndPrefKey(name, key);
+        opt.ifPresent(prefNode -> entityManager.remove(prefNode));
+    }
+
+    public List<PreferenceNodeEntity> findByNodeName(String name) {
+        return findByNamedQuery("PreferenceNode.findAllByNodeName", Map.of("nodeName", name));
+    }
+
+    public List<PreferenceNodeEntity> findByNodeNameLike(String name) {
+        return findByNamedQuery("PreferenceNode.findAllLikeNodeName", Map.of("nodeName", name + '%'));
+    }
+}

oni/src/main/java/org/mbari/oni/jpa/repositories/Repository.java

@@ -50,6 +50,13 @@ public void delete(Object object) {
         entityManager.remove(object);
     }
 
+    public void create(Object object) {
+        entityManager.persist(object);
+    }
+
+    public void update(Object object) {
+        entityManager.merge(object);
+    }
 
     public <T> List<T> findByNamedQuery(String name) {
         Query query = entityManager.createNamedQuery(name);
@@ -75,4 +82,6 @@ public <T> Optional<T> findByPrimaryKey(Class<T> clazz, Object primaryKey) {
     }
 
 
+
+
 }

oni/src/main/scala/org/mbari/oni/Endpoints.scala

@@ -26,7 +26,6 @@ object Endpoints:
     val historyEndpoints: HistoryEndpoints               = HistoryEndpoints(entityMangerFactory)
     val phylogenyEndpoints: PhylogenyEndpoints           = PhylogenyEndpoints(entityMangerFactory)
 
-
     val authorizationEndpoints: AuthorizationEndpoints = AuthorizationEndpoints()
     val healthEndpoints: HealthEndpoints               = HealthEndpoints()
 

oni/src/main/scala/org/mbari/oni/domain/ConceptMetadata.scala

@@ -29,12 +29,10 @@ object ConceptMetadata:
     def from(concept: ConceptEntity): ConceptMetadata =
         val name = concept.getPrimaryConceptName.getName
 
-        val alternateNames = concept
-            .getConceptNames
+        val alternateNames = concept.getAlternativeConceptNames
             .asScala
-            .filter(_.getNameType != ConceptNameTypes.PRIMARY.getType)
-            .toSet
             .map(_.getName)
+            .toSet
 
         val media = concept
             .getConceptMetadata

oni/src/main/scala/org/mbari/oni/domain/PrefNode.scala

@@ -0,0 +1,25 @@
+/*
+ * Copyright (c) Monterey Bay Aquarium Research Institute 2024
+ *
+ * oni code is non-public software. Unauthorized copying of this file,
+ * via any medium is strictly prohibited. Proprietary and confidential. 
+ */
+
+package org.mbari.oni.domain
+
+import org.mbari.oni.jpa.entities.PreferenceNodeEntity
+
+case class PrefNode(name: String, key: String, value: String):
+    def toEntity: PreferenceNodeEntity =
+        val entity = new PreferenceNodeEntity()
+        entity.setNodeName(name)
+        entity.setPrefKey(key)
+        entity.setPrefValue(value)
+        entity
+
+object PrefNode:
+    def from(entity: PreferenceNodeEntity): PrefNode = PrefNode(
+        entity.getNodeName,
+        entity.getPrefKey,
+        entity.getPrefValue
+    )

oni/src/main/scala/org/mbari/oni/domain/UserAccount.scala

@@ -0,0 +1,59 @@
+/*
+ * Copyright (c) Monterey Bay Aquarium Research Institute 2024
+ *
+ * oni code is non-public software. Unauthorized copying of this file,
+ * via any medium is strictly prohibited. Proprietary and confidential. 
+ */
+
+package org.mbari.oni.domain
+
+import org.jasypt.util.password.BasicPasswordEncryptor
+import org.mbari.oni.jpa.entities.UserAccountEntity
+import org.mbari.oni.etc.jdk.Numbers.given
+
+case class UserAccount(
+                   username: String,
+                   password: String,
+                   role: String = "ReadOnly",
+                   affiliation: Option[String] = None,
+                   firstName: Option[String] = None,
+                   lastName: Option[String] = None,
+                   email: Option[String] = None,
+                   id: Option[Long] = None,
+                   isEncrypted: Option[Boolean] = None
+               ) {
+
+    def toEntity: UserAccountEntity = {
+        val entity = new UserAccountEntity()
+        entity.setUserName(username)
+        // If the password is not encrypted, then encrypt it
+        if (isEncrypted.getOrElse(false))
+            entity.setEncryptedPassword(password)
+        else
+            entity.setPassword(password)
+        entity.setRole(role)
+        entity.setAffiliation(affiliation.orNull)
+        entity.setFirstName(firstName.orNull)
+        entity.setLastName(lastName.orNull)
+        entity.setEmail(email.orNull)
+        entity.setId(id.map(_.asInstanceOf[java.lang.Long]).orNull)
+        entity
+    }
+
+}
+
+object UserAccount {
+
+    def from(userAccount: UserAccountEntity): UserAccount = UserAccount(
+        userAccount.getUserName,
+        userAccount.getEncryptedPassword,
+        userAccount.getRole,
+        Option(userAccount.getAffiliation),
+        Option(userAccount.getFirstName),
+        Option(userAccount.getLastName),
+        Option(userAccount.getEmail),
+        Option(userAccount.getPrimaryKey).map(_.asInstanceOf[Long]),
+        Some(true)
+    )
+
+}

oni/src/main/scala/org/mbari/oni/domain/UserAccountUpdate.scala

@@ -0,0 +1,20 @@
+/*
+ * Copyright (c) Monterey Bay Aquarium Research Institute 2024
+ *
+ * oni code is non-public software. Unauthorized copying of this file,
+ * via any medium is strictly prohibited. Proprietary and confidential. 
+ */
+
+package org.mbari.oni.domain
+
+case class UserAccountUpdate(username: String,
+                             password: Option[String] = None,
+                             role: Option[String] = None,
+                             affiliation: Option[String] = None,
+                             firstName: Option[String] = None,
+                             lastName: Option[String] = None,
+                             email: Option[String] = None,
+                            ) {
+
+
+}

oni/src/main/scala/org/mbari/oni/endpoints/HistoryEndpoints.scala

@@ -1,3 +1,10 @@
+/*
+ * Copyright (c) Monterey Bay Aquarium Research Institute 2024
+ *
+ * oni code is non-public software. Unauthorized copying of this file,
+ * via any medium is strictly prohibited. Proprietary and confidential. 
+ */
+
 package org.mbari.oni.endpoints
 
 import jakarta.persistence.EntityManagerFactory

oni/src/main/scala/org/mbari/oni/endpoints/LinkEndpoints.scala

@@ -0,0 +1,91 @@
+/*
+ * Copyright (c) Monterey Bay Aquarium Research Institute 2024
+ *
+ * oni code is non-public software. Unauthorized copying of this file,
+ * via any medium is strictly prohibited. Proprietary and confidential. 
+ */
+
+package org.mbari.oni.endpoints
+
+import jakarta.persistence.EntityManagerFactory
+import org.mbari.oni.domain.{ErrorMsg, Link}
+import org.mbari.oni.services.LinkService
+import sttp.tapir.*
+import sttp.tapir.Endpoint
+import sttp.tapir.json.circe.*
+import sttp.tapir.server.ServerEndpoint
+import sttp.tapir.server.nima.Id
+import org.mbari.oni.etc.circe.CirceCodecs.given
+
+class LinkEndpoints(entityManagerFactory: EntityManagerFactory) extends Endpoints {
+
+    private val service = LinkService(entityManagerFactory)
+    private val base = "links"
+    private val tag = "Links"
+    // get all links
+
+    val allLinksEndpoint: Endpoint[Unit, Unit, ErrorMsg, Seq[Link], Any] = openEndpoint
+        .get
+        .in(base)
+        .out(jsonBody[Seq[Link]])
+        .name("links")
+        .description("Get all links")
+        .tag(tag)
+
+    val allLinksEndpointImpl: ServerEndpoint[Any, Id] = allLinksEndpoint.serverLogic {
+        _ => handleErrors(service.findAllLinkTemplates())
+    }
+
+    // get links for a concept
+    val linksForConceptEndpoint: Endpoint[Unit, String, ErrorMsg, Seq[Link], Any] = openEndpoint
+        .get
+        .in(base / path[String]("name"))
+        .out(jsonBody[Seq[Link]])
+        .name("linksForConcept")
+        .description("Get all link templates applicable to a concept")
+        .tag(tag)
+
+    val linksForConceptEndpointImpl: ServerEndpoint[Any, Id] = linksForConceptEndpoint.serverLogic { name =>
+        handleErrors(service.findAllLinkTemplatesForConcept(name))
+    }
+
+    // get links for a concept and linkname
+    val linksForConceptAndLinkNameEndpoint: Endpoint[Unit, (String, String), ErrorMsg, Seq[Link], Any] = openEndpoint
+        .get
+        .in(base / path[String]("name") / "using" / path[String]("linkName"))
+        .out(jsonBody[Seq[Link]])
+        .name("linksForConceptAndLinkName")
+        .description("Get all link templates applicable to a concept and link name")
+        .tag(tag)
+
+    val linksForConceptAndLinkNameEndpointImpl: ServerEndpoint[Any, Id] = linksForConceptAndLinkNameEndpoint.serverLogic { (name, linkName) =>
+        handleErrors(service.findLinkTemplatesByNameForConcept(name, linkName))
+    }
+
+    // get link realizations for a concept
+    val linkRealizationsEndpoint: Endpoint[Unit, String, ErrorMsg, Seq[Link], Any] = openEndpoint
+        .get
+        .in(base / "query" / "linkrealizations" / path[String]("linkName"))
+        .out(jsonBody[Seq[Link]])
+        .name("linkRealizations")
+        .description("Get all link realizations for a link name")
+        .tag(tag)
+
+    val linkRealizationsEndpointImpl: ServerEndpoint[Any, Id] = linkRealizationsEndpoint.serverLogic { linkName =>
+        handleErrors(service.findLinkRealizationsByLinkName(linkName))
+    }
+
+    override def all: List[Endpoint[_, _, _, _, _]] = List (
+        linkRealizationsEndpoint,
+        linksForConceptAndLinkNameEndpoint,
+        linksForConceptEndpoint, // TODO verify this order works
+        allLinksEndpoint,
+    )
+
+    override def allImpl: List[ServerEndpoint[Any, Id]] = List(
+        linkRealizationsEndpointImpl,
+        linksForConceptAndLinkNameEndpointImpl,
+        linksForConceptEndpointImpl,
+        allLinksEndpointImpl,
+    )
+}

oni/src/main/scala/org/mbari/oni/endpoints/RawEndpoints.scala

@@ -0,0 +1,12 @@
+/*
+ * Copyright (c) Monterey Bay Aquarium Research Institute 2024
+ *
+ * oni code is non-public software. Unauthorized copying of this file,
+ * via any medium is strictly prohibited. Proprietary and confidential. 
+ */
+
+package org.mbari.oni.endpoints
+
+class RawEndpoints {
+
+}