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alex-odysseusjcnamendiOdysseusoleg-odysseuschrisknoll
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Tools module functionality (#2389)
- adding permissions to sec_permission, sec_role_permission (migration script) - distinguishing the Tools listing logic for administrators and the other users - replacing PermissionManager usage with UserRepository when appropriate to avoid exceptions when there is no security enabled --------- Co-authored-by: Juan Carlos Namendi Pineda <[email protected]> Co-authored-by: oleg-odysseus <[email protected]> Co-authored-by: Chris Knoll <[email protected]>
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13 files changed

+564
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‎src/main/java/org/ohdsi/webapi/security/model/EntityType.java

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import org.ohdsi.webapi.reusable.domain.Reusable;
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import org.ohdsi.webapi.source.Source;
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import org.ohdsi.webapi.tag.domain.Tag;
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import org.ohdsi.webapi.tool.Tool;
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public enum EntityType {
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COHORT_DEFINITION(CohortDefinition.class),
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PREDICTION(PredictionAnalysis.class),
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COHORT_SAMPLE(CohortSample.class),
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TAG(Tag.class),
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TOOL(Tool.class),
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REUSABLE(Reusable.class);
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private final Class<? extends CommonEntity> entityClass;
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‎src/main/java/org/ohdsi/webapi/security/model/ToolPermissionSchema.java

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package org.ohdsi.webapi.security.model;
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import org.springframework.stereotype.Component;
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import java.util.HashMap;
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import java.util.Map;
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@Component
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public class ToolPermissionSchema extends EntityPermissionSchema {
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private static Map<String, String> writePermissions = new HashMap<String, String>() {{
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put("tool:%s:delete", "Delete Tool with id = %s");
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}};
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private static Map<String, String> readPermissions = new HashMap<String, String>() {
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{
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put("tool:%s:get", "View Tool with id = %s");
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}
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};
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public ToolPermissionSchema() {
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super(EntityType.TOOL, readPermissions, writePermissions);
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}
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}

‎src/main/java/org/ohdsi/webapi/tool/Tool.java

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package org.ohdsi.webapi.tool;
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import org.hibernate.annotations.GenericGenerator;
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import org.hibernate.annotations.Parameter;
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import org.ohdsi.webapi.model.CommonEntity;
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import javax.persistence.Entity;
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import javax.persistence.Table;
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import javax.persistence.Id;
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import javax.persistence.GeneratedValue;
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import javax.persistence.Column;
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import java.util.Objects;
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@Entity
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@Table(name = "tool")
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public class Tool extends CommonEntity<Integer> {
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@Id
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@GenericGenerator(
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name = "tool_generator",
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strategy = "org.hibernate.id.enhanced.SequenceStyleGenerator",
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parameters = {
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@Parameter(name = "sequence_name", value = "tool_seq"),
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@Parameter(name = "increment_size", value = "1")
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}
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)
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@GeneratedValue(generator = "tool_generator")
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private Integer id;
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@Column(name = "name")
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private String name;
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@Column(name = "url")
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private String url;
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@Column(name = "description")
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private String description;
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@Column(name = "is_enabled")
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private Boolean enabled;
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@Override
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public Integer getId() {
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return id;
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}
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public void setId(Integer id) {
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this.id = id;
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}
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public String getName() {
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return name;
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}
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public void setName(String name) {
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this.name = name;
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}
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public String getUrl() {
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return url;
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}
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public void setUrl(String url) {
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this.url = url;
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}
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public String getDescription() {
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return description;
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}
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public void setDescription(String description) {
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this.description = description;
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}
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public Boolean getEnabled() {
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return enabled;
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}
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public void setEnabled(Boolean enabled) {
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this.enabled = enabled;
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}
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@Override
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public boolean equals(Object o) {
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if (this == o) return true;
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if (o == null || getClass() != o.getClass()) return false;
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Tool tool = (Tool) o;
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return Objects.equals(name, tool.name);
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}
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@Override
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public int hashCode() {
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return Objects.hash(name);
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}
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}

‎src/main/java/org/ohdsi/webapi/tool/ToolController.java

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package org.ohdsi.webapi.tool;
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import org.ohdsi.webapi.tool.dto.ToolDTO;
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import org.springframework.stereotype.Controller;
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import javax.ws.rs.Consumes;
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import javax.ws.rs.DELETE;
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import javax.ws.rs.GET;
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import javax.ws.rs.POST;
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import javax.ws.rs.PUT;
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import javax.ws.rs.Path;
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import javax.ws.rs.PathParam;
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import javax.ws.rs.Produces;
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import javax.ws.rs.core.MediaType;
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import java.util.List;
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@Controller
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@Path("/tool")
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public class ToolController {
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private final ToolServiceImpl service;
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public ToolController(ToolServiceImpl service) {
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this.service = service;
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}
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@GET
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@Path("")
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@Produces(MediaType.APPLICATION_JSON)
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public List<ToolDTO> getTools() {
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return service.getTools();
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}
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@GET
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@Path("/{id}")
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@Produces(MediaType.APPLICATION_JSON)
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public ToolDTO getToolById(@PathParam("id") Integer id) {
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return service.getById(id);
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}
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@POST
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@Path("")
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@Produces(MediaType.APPLICATION_JSON)
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@Consumes(MediaType.APPLICATION_JSON)
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public ToolDTO createTool(ToolDTO dto) {
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return service.saveTool(dto);
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}
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@DELETE
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@Path("/{id}")
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@Produces(MediaType.APPLICATION_JSON)
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public void delete(@PathParam("id") Integer id) {
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service.delete(id);
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}
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@PUT
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@Path("")
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@Produces(MediaType.APPLICATION_JSON)
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@Consumes(MediaType.APPLICATION_JSON)
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public ToolDTO updateTool(ToolDTO toolDTO) {
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return service.saveTool(toolDTO);
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}
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}

‎src/main/java/org/ohdsi/webapi/tool/ToolRepository.java

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package org.ohdsi.webapi.tool;
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import java.util.List;
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import org.springframework.data.jpa.repository.JpaRepository;
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import org.springframework.stereotype.Repository;
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@Repository
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public interface ToolRepository extends JpaRepository<Tool, Integer> {
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List<Tool> findAllByEnabled(boolean enabled);
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}

‎src/main/java/org/ohdsi/webapi/tool/ToolService.java

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package org.ohdsi.webapi.tool;
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import org.ohdsi.webapi.tool.dto.ToolDTO;
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import java.util.List;
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public interface ToolService {
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List<ToolDTO> getTools();
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ToolDTO saveTool(ToolDTO toolDTO);
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ToolDTO getById(Integer id);
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void delete(Integer id);
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}

‎src/main/java/org/ohdsi/webapi/tool/ToolServiceImpl.java

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package org.ohdsi.webapi.tool;
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import java.text.SimpleDateFormat;
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import java.time.Instant;
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import java.util.Date;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.shiro.SecurityUtils;
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import org.ohdsi.webapi.service.AbstractDaoService;
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import org.ohdsi.webapi.shiro.Entities.UserEntity;
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import org.ohdsi.webapi.tool.dto.ToolDTO;
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import org.springframework.stereotype.Service;
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@Service
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public class ToolServiceImpl extends AbstractDaoService implements ToolService {
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private static final String DATE_TIME_FORMAT = "yyyy-MM-dd HH:mm:ss";
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private final ToolRepository toolRepository;
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public ToolServiceImpl(ToolRepository toolRepository) {
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this.toolRepository = toolRepository;
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}
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@Override
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public List<ToolDTO> getTools() {
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List<Tool> tools = (isAdmin() || canManageTools()) ? toolRepository.findAll() : toolRepository.findAllByEnabled(true);
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return tools.stream()
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.map(this::toDTO).collect(Collectors.toList());
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}
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@Override
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public ToolDTO saveTool(ToolDTO toolDTO) {
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Tool tool = saveToolFromDTO(toolDTO, getCurrentUser());
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return toDTO(toolRepository.saveAndFlush(tool));
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}
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private Tool saveToolFromDTO(ToolDTO toolDTO, UserEntity currentUser) {
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Tool tool = toEntity(toolDTO);
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if (toolDTO.getId() == null) {
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tool.setCreatedBy(currentUser);
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}
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tool.setModifiedBy(currentUser);
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return tool;
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}
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@Override
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public ToolDTO getById(Integer id) {
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return toDTO(toolRepository.findOne(id));
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}
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@Override
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public void delete(Integer id) {
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toolRepository.delete(id);
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}
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private boolean canManageTools() {
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return Stream.of("tool:put", "tool:post", "tool:*:delete")
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.allMatch(permission -> SecurityUtils.getSubject().isPermitted(permission));
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}
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Tool toEntity(ToolDTO toolDTO) {
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boolean isNewTool = toolDTO.getId() == null;
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Tool tool = isNewTool ? new Tool() : toolRepository.findOne(toolDTO.getId());
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Instant currentInstant = Instant.now();
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if (isNewTool) {
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setCreationDetails(tool, currentInstant);
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} else {
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setModificationDetails(tool, currentInstant);
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}
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updateToolFromDTO(tool, toolDTO);
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return tool;
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}
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private void setCreationDetails(Tool tool, Instant currentInstant) {
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tool.setCreatedDate(Date.from(currentInstant));
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tool.setCreatedBy(getCurrentUser());
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}
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private void setModificationDetails(Tool tool, Instant currentInstant) {
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tool.setModifiedDate(Date.from(currentInstant));
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tool.setModifiedBy(getCurrentUser());
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}
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private void updateToolFromDTO(Tool tool, ToolDTO toolDTO) {
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Optional.ofNullable(toolDTO.getName()).ifPresent(tool::setName);
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Optional.ofNullable(toolDTO.getUrl()).ifPresent(tool::setUrl);
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Optional.ofNullable(toolDTO.getDescription()).ifPresent(tool::setDescription);
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Optional.ofNullable(toolDTO.getEnabled()).ifPresent(tool::setEnabled);
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}
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ToolDTO toDTO(Tool tool) {
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return Optional.ofNullable(tool)
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.map(t -> {
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ToolDTO toolDTO = new ToolDTO();
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toolDTO.setId(t.getId());
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toolDTO.setName(t.getName());
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toolDTO.setUrl(t.getUrl());
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toolDTO.setDescription(t.getDescription());
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Optional.ofNullable(tool.getCreatedBy())
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.map(UserEntity::getId)
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.map(userRepository::findOne)
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.map(UserEntity::getName)
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.ifPresent(toolDTO::setCreatedByName);
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Optional.ofNullable(tool.getModifiedBy())
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.map(UserEntity::getId)
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.map(userRepository::findOne)
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.map(UserEntity::getName)
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.ifPresent(toolDTO::setModifiedByName);
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toolDTO.setCreatedDate(t.getCreatedDate() != null ? new SimpleDateFormat(DATE_TIME_FORMAT).format(t.getCreatedDate()) : null);
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toolDTO.setModifiedDate(t.getModifiedDate() != null ? new SimpleDateFormat(DATE_TIME_FORMAT).format(t.getModifiedDate()) : null);
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toolDTO.setEnabled(t.getEnabled());
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return toolDTO;
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})
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.orElse(null);
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}
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}

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