org.molgenis.semanticmapper.controller

Class MappingServiceController

java.lang.Object

org.molgenis.web.PluginController

org.molgenis.semanticmapper.controller.MappingServiceController

@Controller
 @RequestMapping(value="/plugin/mappingservice")
public class MappingServiceController
extends PluginController

Field Summary

Fields

Modifier and Type	Field and Description
static String	ID
static String	URI

Fields inherited from class org.molgenis.web.PluginController

PLUGIN_URI_PREFIX

Constructor Summary

Constructors

Constructor and Description

MappingServiceController(AlgorithmService algorithmService, MappingService mappingService, DataService dataService, OntologyTagService ontologyTagService, SemanticSearchService semanticSearchService, org.molgenis.core.ui.menu.MenuReaderService menuReaderService, MappingJobExecutionFactory mappingJobExecutionFactory, org.molgenis.security.user.UserAccountService userAccountService, org.molgenis.jobs.JobExecutor jobExecutor, org.molgenis.core.ui.jobs.JobsController jobsController)

Method Summary

Modifier and Type	Method and Description
String	addEntityMapping(String mappingProjectId, String target, String source) Adds a new EntityMapping to an existing MappingTarget
String	addMappingProject(String name, String targetEntity) Adds a new mapping project.
String	advancedMappingEditor(String mappingProjectId, String target, String source, String targetAttribute, String sourceAttribute, String algorithm, org.springframework.ui.Model model) Returns a view that allows the user to edit mappings involving xrefs / categoricals / strings
String	attributeMappingFeedback(String mappingProjectId, String target, String source, String targetAttribute, String algorithm, org.springframework.ui.Model model)
String	cloneMappingProject(String mappingProjectId)
String	createIntegratedEntity(String mappingProjectId, String targetEntityTypeId, String label, String packageId, Boolean addSourceAttribute) Creates the integrated entity for a mapping project's target
String	deleteMappingProject(String mappingProjectId) Removes a mapping project
FirstAttributeMappingInfo	getFirstAttributeMappingInfo(String mappingProjectId, String target, List<AttributeMapping.AlgorithmState> skipAlgorithmStates, org.springframework.ui.Model model) Find the firstattributeMapping skip the the algorithmStates that are given in the AttributeMapping to an EntityMapping.
List<ExplainedAttributeDto>	getSemanticSearchAttributeMapping(Map<String,String> requestBody) This controller will first of all check if the user-defined search terms exist.
String	getSuggestedAlgorithm(GenerateAlgorithmRequest generateAlgorithmRequest)
boolean	isNewEntity(String targetEntityTypeId) Checks if an entityTypeID already exists.
String	removeAttributeMapping(String mappingProjectId, String target, String source, String attribute) Removes a attribute mapping
String	removeEntityMapping(String mappingProjectId, String target, String source) Removes entity mapping
String	saveAttributeMapping(String mappingProjectId, String target, String source, String targetAttribute, String algorithm, AttributeMapping.AlgorithmState algorithmState) Adds a new AttributeMapping to an EntityMapping.
void	saveCategoryMapping(String mappingProjectId, String target, String source, String targetAttribute, String algorithm)
org.springframework.http.ResponseEntity<String>	scheduleMappingJob(String mappingProjectId, String targetEntityTypeId, String label, String packageId, Boolean addSourceAttribute) Schedules a MappingJobExecution.
Map<String,Object>	testScript(MappingServiceRequest mappingServiceRequest) Tests an algoritm by computing it for all entities in the source repository.
org.molgenis.semanticmapper.controller.MappingServiceController.AttributeMappingValidationReport	validateAttributeMapping(@Valid MappingServiceRequest mappingServiceRequest)
String	viewAttributeMapping(String mappingProjectId, String target, String source, String targetAttribute, org.springframework.ui.Model model) Displays an AttributeMapping
String	viewMappingProject(String identifier, org.springframework.ui.Model model) Displays a mapping project.
String	viewMappingProjects(org.springframework.ui.Model model) Initializes the model with all mapping projects and all entities to the model.

Methods inherited from class org.molgenis.web.PluginController

getId, getPluginSettings, getUri

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ID

public static final String ID

See Also:

Constant Field Values

URI

public static final String URI

See Also:

Constant Field Values

Constructor Detail

MappingServiceController

public MappingServiceController(AlgorithmService algorithmService,
                                MappingService mappingService,
                                DataService dataService,
                                OntologyTagService ontologyTagService,
                                SemanticSearchService semanticSearchService,
                                org.molgenis.core.ui.menu.MenuReaderService menuReaderService,
                                MappingJobExecutionFactory mappingJobExecutionFactory,
                                org.molgenis.security.user.UserAccountService userAccountService,
                                org.molgenis.jobs.JobExecutor jobExecutor,
                                org.molgenis.core.ui.jobs.JobsController jobsController)

Method Detail

viewMappingProjects

@GetMapping
public String viewMappingProjects(org.springframework.ui.Model model)

Initializes the model with all mapping projects and all entities to the model.

Parameters:

model - the model to initialized

Returns:

view name of the mapping projects list

addMappingProject

@PostMapping(value="/addMappingProject")
public String addMappingProject(@RequestParam(value="mapping-project-name")
                                                                         String name,
                                                                         @RequestParam(value="target-entity")
                                                                         String targetEntity)

Adds a new mapping project.

Parameters:

name - name of the mapping project

targetEntity - name of the project's first MappingTarget's target entity

Returns:

redirect URL for the newly created mapping project

deleteMappingProject

@PostMapping(value="/removeMappingProject")
public String deleteMappingProject(@RequestParam
                                                                               String mappingProjectId)

Removes a mapping project

Parameters:

mappingProjectId - the ID of the mapping project

Returns:

redirect url to the same page to force a refresh

removeAttributeMapping

@PostMapping(value="/removeAttributeMapping")
public String removeAttributeMapping(@RequestParam
                                                                                   String mappingProjectId,
                                                                                   @RequestParam
                                                                                   String target,
                                                                                   @RequestParam
                                                                                   String source,
                                                                                   @RequestParam
                                                                                   String attribute)

Removes a attribute mapping

Parameters:

mappingProjectId - the ID of the mapping project

target - the target entity

source - the source entity

attribute - the attribute that is mapped

addEntityMapping

@PostMapping(value="/addEntityMapping")
public String addEntityMapping(@RequestParam
                                                                       String mappingProjectId,
                                                                       String target,
                                                                       String source)

Adds a new EntityMapping to an existing MappingTarget

Parameters:

target - the name of the MappingTarget's entity to add a source entity to

source - the name of the source entity of the newly added EntityMapping

mappingProjectId - the ID of the MappingTarget's MappingProject

Returns:

redirect URL for the mapping project

removeEntityMapping

@PostMapping(value="/removeEntityMapping")
public String removeEntityMapping(@RequestParam
                                                                             String mappingProjectId,
                                                                             String target,
                                                                             String source)

Removes entity mapping

Parameters:

mappingProjectId - ID of the mapping project to remove entity mapping from

target - entity name of the mapping target

source - entity name of the mapping source

Returns:

redirect url of the mapping project's page

validateAttributeMapping

@PostMapping(value="/validateAttrMapping")
 @ResponseBody
public org.molgenis.semanticmapper.controller.MappingServiceController.AttributeMappingValidationReport validateAttributeMapping(@Valid @RequestBody
                                                                                                                                                                                           @Valid MappingServiceRequest mappingServiceRequest)

saveAttributeMapping

@PostMapping(value="/saveattributemapping")
public String saveAttributeMapping(@RequestParam
                                                                               String mappingProjectId,
                                                                               @RequestParam
                                                                               String target,
                                                                               @RequestParam
                                                                               String source,
                                                                               @RequestParam
                                                                               String targetAttribute,
                                                                               @RequestParam
                                                                               String algorithm,
                                                                               @RequestParam
                                                                               AttributeMapping.AlgorithmState algorithmState)

Adds a new AttributeMapping to an EntityMapping.

Parameters:

mappingProjectId - ID of the mapping project

target - name of the target entity

source - name of the source entity

targetAttribute - name of the target attribute

algorithm - the mapping algorithm

Returns:

redirect URL for the attributemapping

getFirstAttributeMappingInfo

@PostMapping(value="/firstattributemapping")
 @ResponseBody
public FirstAttributeMappingInfo getFirstAttributeMappingInfo(@RequestParam
                                                                                                                          String mappingProjectId,
                                                                                                                          @RequestParam
                                                                                                                          String target,
                                                                                                                          @RequestParam(value="skipAlgorithmStates[]")
                                                                                                                          List<AttributeMapping.AlgorithmState> skipAlgorithmStates,
                                                                                                                          org.springframework.ui.Model model)

Find the firstattributeMapping skip the the algorithmStates that are given in the AttributeMapping to an EntityMapping.

Parameters:

mappingProjectId - ID of the mapping project

target - name of the target entity

skipAlgorithmStates - the mapping algorithm states that should skip

viewMappingProject

@GetMapping(value="/mappingproject/{id}")
public String viewMappingProject(@PathVariable(value="id")
                                                                           String identifier,
                                                                           org.springframework.ui.Model model)

Displays a mapping project.

Parameters:

identifier - identifier of the MappingProject

model - the model

Returns:

View name for a single mapping project

cloneMappingProject

@PostMapping(value="/mappingproject/clone")
public String cloneMappingProject(@RequestParam(value="mappingProjectId")
                                                                              String mappingProjectId)

getSemanticSearchAttributeMapping

@PostMapping(value="/attributeMapping/semanticsearch",
             consumes="application/json")
 @ResponseBody
public List<ExplainedAttributeDto> getSemanticSearchAttributeMapping(@RequestBody
                                                                                                                                                                                     Map<String,String> requestBody)

This controller will first of all check if the user-defined search terms exist. If so, the searchTerms will be used directly in the SemanticSearchService. If the searchTerms are not defined by users, it will use the ontologyTermTags in the SemantiSearchService. If neither of the searchTerms and the OntologyTermTags exist, it will use the information from the targetAttribute in the SemanticSearchService

If string terms are sent to the SemanticSearchService, they will be first of all converted to the ontologyTerms using findTag method

getSuggestedAlgorithm

@PostMapping(value="/attributemapping/algorithm",
             consumes="application/json")
 @ResponseBody
public String getSuggestedAlgorithm(@RequestBody
                                                                                                                                               GenerateAlgorithmRequest generateAlgorithmRequest)

isNewEntity

@GetMapping(value="/isNewEntity")
 @ResponseBody
public boolean isNewEntity(@RequestParam
                                                                            String targetEntityTypeId)

Checks if an entityTypeID already exists. Used to validate ID field in the "New dataset" tab when creating a new integrated dataset.

createIntegratedEntity

@RequestMapping(value="/createIntegratedEntity")
public String createIntegratedEntity(@RequestParam
                                                                                      String mappingProjectId,
                                                                                      @RequestParam
                                                                                      String targetEntityTypeId,
                                                                                      @RequestParam(required=false)
                                                                                      String label,
                                                                                      @RequestParam(required=false,name="package")
                                                                                      String packageId,
                                                                                      @RequestParam(required=false)
                                                                                      Boolean addSourceAttribute)

Creates the integrated entity for a mapping project's target

Parameters:

mappingProjectId - ID of the mapping project

targetEntityTypeId - ID of the target entity to create or update

label - label of the target entity to create

packageId - ID of the package to put the newly created entity in

Returns:

redirect URL to the data explorer displaying the newly generated entity

scheduleMappingJob

@PostMapping(value="/map",
             produces="text/plain")
public org.springframework.http.ResponseEntity<String> scheduleMappingJob(@RequestParam
                                                                                                                                         String mappingProjectId,
                                                                                                                                         @RequestParam
                                                                                                                                         String targetEntityTypeId,
                                                                                                                                         @RequestParam(required=false)
                                                                                                                                         String label,
                                                                                                                                         @RequestParam(required=false,name="package")
                                                                                                                                         String packageId,
                                                                                                                                         @RequestParam(required=false)
                                                                                                                                         Boolean addSourceAttribute)
                                                                                                                                  throws URISyntaxException

Schedules a MappingJobExecution.

Parameters:

mappingProjectId - ID of the mapping project

targetEntityTypeId - ID of the target entity to create or update

label - label of the target entity to create

packageId - ID of the package to put the newly created entity in

Returns:

the href of the created MappingJobExecution

Throws:

URISyntaxException

viewAttributeMapping

@GetMapping(value="/attributeMapping")
public String viewAttributeMapping(@RequestParam
                                                                          String mappingProjectId,
                                                                          @RequestParam
                                                                          String target,
                                                                          @RequestParam
                                                                          String source,
                                                                          @RequestParam
                                                                          String targetAttribute,
                                                                          org.springframework.ui.Model model)

Displays an AttributeMapping

Parameters:

mappingProjectId - ID of the MappingProject

target - name of the target entity

source - name of the source entity

targetAttribute - name of the target attribute

attributeMappingFeedback

@PostMapping(value="/attributemappingfeedback")
public String attributeMappingFeedback(@RequestParam
                                                                                       String mappingProjectId,
                                                                                       @RequestParam
                                                                                       String target,
                                                                                       @RequestParam
                                                                                       String source,
                                                                                       @RequestParam
                                                                                       String targetAttribute,
                                                                                       @RequestParam
                                                                                       String algorithm,
                                                                                       org.springframework.ui.Model model)

advancedMappingEditor

@PostMapping(value="/advancedmappingeditor")
public String advancedMappingEditor(@RequestParam
                                                                                 String mappingProjectId,
                                                                                 @RequestParam
                                                                                 String target,
                                                                                 @RequestParam
                                                                                 String source,
                                                                                 @RequestParam
                                                                                 String targetAttribute,
                                                                                 @RequestParam
                                                                                 String sourceAttribute,
                                                                                 @RequestParam
                                                                                 String algorithm,
                                                                                 org.springframework.ui.Model model)

Returns a view that allows the user to edit mappings involving xrefs / categoricals / strings

saveCategoryMapping

@PostMapping(value="/savecategorymapping")
 @ResponseBody
public void saveCategoryMapping(@RequestParam
                                                                                          String mappingProjectId,
                                                                                          @RequestParam
                                                                                          String target,
                                                                                          @RequestParam
                                                                                          String source,
                                                                                          @RequestParam
                                                                                          String targetAttribute,
                                                                                          @RequestParam
                                                                                          String algorithm)

testScript

@PostMapping(value="/mappingattribute/testscript",
             consumes="application/json",
             produces="application/json")
 @ResponseBody
public Map<String,Object> testScript(@RequestBody
                                                                                                                                                                                           MappingServiceRequest mappingServiceRequest)

Tests an algoritm by computing it for all entities in the source repository.

Parameters:

mappingServiceRequest - the MappingServiceRequest sent by the client

Returns:

Map with the results and size of the source