[ALS-4736] Add named dataset (#146)

* Add table and API for naming a dataset id (#132)
* Adds named_dataset sql table for saving named dataset ids.
* Adds a SecurityContext class to persist authenticated user information for the entire request.
* Updates JWTFilter class to add the new SecurityContext to the context object.
* Adds classes for new service, entity, and endpoints needed.
* Add metadata column to named_dataset table to extend in the future. (#135)
* Update migration file name. (#143)

pic-sure-api-data/pom.xml

@@ -37,5 +37,10 @@
 			<groupId>org.hibernate</groupId>
 			<artifactId>hibernate-core</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>io.swagger.core.v3</groupId>
+			<artifactId>swagger-annotations</artifactId>
+			<version>2.2.8</version>
+		</dependency>
 	</dependencies>
 </project>

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/AuthUser.java

@@ -0,0 +1,69 @@
+package edu.harvard.dbmi.avillach.data.entity;
+
+import java.security.Principal;
+
+import javax.json.Json;
+
+/*
+ * This class is used to mirror the User object from the auth DB to maintain schema separation. - nc
+ */
+public class AuthUser extends BaseEntity implements Principal {
+    private String userId;
+
+    private String subject;
+
+    private String roles;
+
+    private String email;
+
+    public String getUserId() {
+        return userId;
+    }
+
+    public AuthUser setUserId(String userId) {
+        this.userId = userId;
+        return this;
+    }
+
+    public String getSubject() {
+        return subject;
+    }
+
+    public AuthUser setSubject(String subject) {
+        this.subject = subject;
+        return this;
+    }
+
+    public String getRoles() {
+        return roles;
+    }
+
+    public AuthUser setRoles(String roles) {
+        this.roles = roles;
+        return this;
+    }
+
+    public String getEmail(){
+        return email;
+    }
+
+    public AuthUser setEmail(String email){
+        this.email = email;
+        return this;
+    }
+
+    @Override // Principal method
+    public String getName() {
+        return getEmail();
+    }
+
+    @Override
+    public String toString() {
+        return Json.createObjectBuilder()
+            .add("userId", userId)
+            .add("subject", subject)
+            .add("email", email)
+            .add("roles", roles)
+            .build().toString();
+    }
+}

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/NamedDataset.java

@@ -0,0 +1,101 @@
+package edu.harvard.dbmi.avillach.data.entity;
+
+import java.util.Map;
+
+import javax.json.Json;
+import javax.persistence.Column;
+import javax.persistence.Convert;
+import javax.persistence.Entity;
+import javax.persistence.JoinColumn;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import io.swagger.v3.oas.annotations.media.Schema;
+
+import edu.harvard.dbmi.avillach.data.entity.convert.JsonConverter;
+
+@Schema(description = "A NamedDataset object containing query, name, user, and archived status.")
+@Entity(name = "named_dataset")
+@Table(uniqueConstraints = { 
+    @UniqueConstraint(name = "unique_queryId_user", columnNames = { "queryId", "user" })
+})
+public class NamedDataset extends BaseEntity {
+    @Schema(description = "The associated Query")
+    @OneToOne
+    @JoinColumn(name = "queryId")
+    private Query query;
+
+    @Schema(description = "The user identifier")
+    @Column(length = 255)
+    private String user;
+
+    @Schema(description = "The name user has assigned to this dataset")
+    @Column(length = 255)
+    private String name;
+
+    @Schema(description = "The archived state")
+    private Boolean archived = false;
+
+    @Schema(description = "A json string object containing override specific values")
+    @Column(length = 8192)
+    @Convert(converter = JsonConverter.class)
+    private Map<String, Object> metadata;
+
+    public NamedDataset setName(String name) {
+        this.name = name;
+        return this;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public NamedDataset setArchived(Boolean archived) {
+        this.archived = archived;
+        return this;
+    }
+
+    public Boolean getArchived() {
+        return archived;
+    }
+
+    public NamedDataset setQuery(Query query) {
+        this.query = query;
+        return this;
+    }
+
+    public Query getQuery(){
+        return query;
+    }
+
+    public NamedDataset setUser(String user) {
+        this.user = user;
+        return this;
+    }
+
+    public String getUser(){
+        return user;
+    }
+
+    public Map<String, Object> getMetadata(){
+        return metadata;
+    }
+
+    public NamedDataset setMetadata(Map<String, Object> metadata){
+        this.metadata = metadata;
+        return this;
+    }
+
+    @Override
+    public String toString() {
+        return Json.createObjectBuilder()
+            .add("uuid", uuid.toString())
+            .add("name", name)
+            .add("archived", archived)
+            .add("queryId", query.getUuid().toString())
+            .add("user", user)
+            .add("metadata", metadata.toString())
+            .build().toString();
+    }
+}

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/convert/JsonConverter.java

@@ -0,0 +1,50 @@
+package edu.harvard.dbmi.avillach.data.entity.convert;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.persistence.AttributeConverter;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+public class JsonConverter implements AttributeConverter<Map<String, Object>, String> {
+    private final Logger logger = LoggerFactory.getLogger(JsonConverter.class);
+
+    @Override
+    public String convertToDatabaseColumn(Map<String, Object> objectData) {
+        if (objectData == null) {
+            return "{}";
+        }
+
+        String jsonData = null;
+        try {
+            jsonData = new ObjectMapper().writeValueAsString(objectData);
+        } catch (final JsonProcessingException e) {
+            logger.error("JSON writing error", e);
+        }
+
+        return jsonData;
+    }
+
+    @Override
+    public Map<String, Object> convertToEntityAttribute(String jsonData) {
+        if (jsonData == null) {
+            return new HashMap<String, Object>();
+        }
+
+        Map<String, Object> objectData = null;
+        try {
+            objectData = new ObjectMapper().readValue(jsonData, new TypeReference<HashMap<String, Object>>() {});
+        } catch (final IOException e) {
+            logger.error("JSON reading error", e);
+        }
+
+        return objectData;
+    }
+}

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/NamedDatasetRepository.java

@@ -0,0 +1,13 @@
+package edu.harvard.dbmi.avillach.data.repository;
+
+import edu.harvard.dbmi.avillach.data.entity.NamedDataset;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.transaction.Transactional;
+import java.util.UUID;
+
+@Transactional
+@ApplicationScoped
+public class NamedDatasetRepository extends BaseRepository<NamedDataset, UUID>{
+    protected NamedDatasetRepository() {super(NamedDataset.class);}
+}

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/request/NamedDatasetRequest.java

@@ -0,0 +1,64 @@
+package edu.harvard.dbmi.avillach.data.request;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.UUID;
+
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Pattern;
+
+import io.swagger.v3.oas.annotations.media.Schema;
+
+@Schema(
+    description = "Request to add or update a named dataset.",
+    example = "{\n" + //
+        "    \"queryId\": \"ec780aeb-d981-432a-b72b-51d4ecb3fd53\",\n" + //
+        "    \"name\": \"My first Query\",\n" + //
+        "    \"archived\": false\n" + //
+        "    \"metadata\": {}\n" + //
+        "}"
+)
+public class NamedDatasetRequest {
+    @NotNull
+    private UUID queryId;
+
+    @NotNull
+    @Pattern(regexp = "^[\\w\\d \\-\\\\/?+=\\[\\].():\"']+$")
+    private String name;
+
+    private Boolean archived = false;
+
+    private Map<String, Object> metadata = new HashMap<String, Object>();
+
+    public UUID getQueryId() {
+        return queryId;
+    }
+
+    public void setQueryId(UUID query) {
+        this.queryId = query;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public Boolean getArchived(){
+        return archived;
+    }
+
+    public void setArchived(Boolean archived) {
+        this.archived = archived;
+    }
+
+    public Map<String, Object> getMetadata(){
+        return metadata;
+    }
+
+    public void setMetadata(Map<String, Object> metadata){
+        this.metadata = metadata;
+    }
+}

pic-sure-api-data/src/main/resources/db/sql/V5__ADD_NAMED_DATASET_TABLE.sql

@@ -0,0 +1,13 @@
+USE `picsure`;
+
+CREATE TABLE `named_dataset` (
+    `uuid` binary(16) NOT NULL,
+    `queryId` binary(16) NOT NULL,
+    `user` varchar(255) COLLATE utf8_bin DEFAULT NULL,
+    `name` varchar(255) COLLATE utf8_bin DEFAULT NULL,
+    `archived` bit(1) NOT NULL DEFAULT FALSE,
+    `metadata` TEXT,
+    PRIMARY KEY (`uuid`),
+    CONSTRAINT `foreign_queryId` FOREIGN KEY (`queryId`) REFERENCES `query` (`uuid`),
+    CONSTRAINT `unique_queryId_user` UNIQUE (`queryId`, `user`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin;