org.molgenis.dataexplorer.controller

Class DataExplorerController

java.lang.Object

org.molgenis.framework.ui.MolgenisPluginController

org.molgenis.dataexplorer.controller.DataExplorerController

@Controller
 @RequestMapping(value="/plugin/dataexplorer")
 @SessionAttributes(value={"galaxyUrl","galaxyApiKey"})
public class DataExplorerController
extends MolgenisPluginController

Controller class for the data explorer.

Field Summary

Fields

Modifier and Type	Field and Description
static String	AGGREGATES_NORESULTS_MESSAGE
static String	BROWSERLINKS
static String	CHAINS
static String	COORDSYSTEM
static String	DEFAULT_AGGREGATES_NORESULTS_MESSAGE
static boolean	DEFAULT_VAL_AGGREGATES_DISTINCT_HIDE
static String	DEFAULT_VAL_HEADER_ABBREVIATE
static boolean	DEFAULT_VAL_SHOW_WIZARD_ONINIT
static String	HIGHLIGHTREGION
static String	ID
static String	INITLOCATION
static String	KEY_DATAEXPLORER_EDITABLE
static String	KEY_DATAEXPLORER_ROW_CLICKABLE
static String	KEY_GALAXY_ENABLED
static String	KEY_GALAXY_URL
static String	KEY_HEADER_ABBREVIATE
static String	KEY_HIDE_ITEM_SELECTION
static String	KEY_HIDE_SEARCH_BOX
static String	KEY_MOD_AGGREGATES
static String	KEY_MOD_AGGREGATES_DISTINCT_HIDE
static String	KEY_MOD_AGGREGATES_DISTINCT_OVERRIDE
static String	KEY_MOD_ANNOTATORS
static String	KEY_MOD_CHARTS
static String	KEY_MOD_DATA
static String	KEY_MOD_DISEASEMATCHER
static String	KEY_MOD_ENTITIESREPORT
static String	KEY_SHOW_WIZARD_ONINIT
static String	SOURCES
static String	URI

Fields inherited from class org.molgenis.framework.ui.MolgenisPluginController

PLUGIN_URI_PREFIX

Constructor Summary

Constructors

Constructor and Description
DataExplorerController()

Method Summary

Modifier and Type	Method and Description
AggregateResult	aggregate(AggregateRequest request)
void	download(String dataRequestStr, javax.servlet.http.HttpServletResponse response)
void	exportToGalaxy(GalaxyDataExportRequest galaxyDataExportRequest, org.springframework.ui.Model model)
String	getModule(String moduleId, String entityName, org.springframework.ui.Model model)
ModulesConfigResponse	getModules(String entityName) Returns modules configuration for this entity based on current user permissions.
Map<String,String>	getSettings(String keyStartsWith)
ErrorMessageResponse	handleGalaxyDataExportException(GalaxyDataExportException e)
ErrorMessageResponse	handleRuntimeException(RuntimeException e)
String	init(String selectedEntityName, String searchTerm, org.springframework.ui.Model model) Show the explorer page
String	viewEntityDetails(String entityName, String entityId, org.springframework.ui.Model model) Builds a model containing one entity and returns the entityReport ftl view

Methods inherited from class org.molgenis.framework.ui.MolgenisPluginController

getId, 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

KEY_MOD_AGGREGATES

public static final String KEY_MOD_AGGREGATES

See Also:

Constant Field Values

KEY_MOD_ANNOTATORS

public static final String KEY_MOD_ANNOTATORS

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Constant Field Values

KEY_MOD_CHARTS

public static final String KEY_MOD_CHARTS

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Constant Field Values

KEY_MOD_DATA

public static final String KEY_MOD_DATA

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Constant Field Values

KEY_MOD_DISEASEMATCHER

public static final String KEY_MOD_DISEASEMATCHER

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Constant Field Values

KEY_GALAXY_ENABLED

public static final String KEY_GALAXY_ENABLED

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Constant Field Values

KEY_GALAXY_URL

public static final String KEY_GALAXY_URL

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Constant Field Values

KEY_SHOW_WIZARD_ONINIT

public static final String KEY_SHOW_WIZARD_ONINIT

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Constant Field Values

KEY_HEADER_ABBREVIATE

public static final String KEY_HEADER_ABBREVIATE

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Constant Field Values

KEY_HIDE_SEARCH_BOX

public static final String KEY_HIDE_SEARCH_BOX

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Constant Field Values

KEY_HIDE_ITEM_SELECTION

public static final String KEY_HIDE_ITEM_SELECTION

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Constant Field Values

KEY_MOD_AGGREGATES_DISTINCT_HIDE

public static final String KEY_MOD_AGGREGATES_DISTINCT_HIDE

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Constant Field Values

KEY_MOD_AGGREGATES_DISTINCT_OVERRIDE

public static final String KEY_MOD_AGGREGATES_DISTINCT_OVERRIDE

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Constant Field Values

KEY_MOD_ENTITIESREPORT

public static final String KEY_MOD_ENTITIESREPORT

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Constant Field Values

DEFAULT_VAL_SHOW_WIZARD_ONINIT

public static final boolean DEFAULT_VAL_SHOW_WIZARD_ONINIT

See Also:

Constant Field Values

DEFAULT_VAL_AGGREGATES_DISTINCT_HIDE

public static final boolean DEFAULT_VAL_AGGREGATES_DISTINCT_HIDE

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Constant Field Values

DEFAULT_VAL_HEADER_ABBREVIATE

public static final String DEFAULT_VAL_HEADER_ABBREVIATE

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Constant Field Values

DEFAULT_AGGREGATES_NORESULTS_MESSAGE

public static final String DEFAULT_AGGREGATES_NORESULTS_MESSAGE

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Constant Field Values

INITLOCATION

public static final String INITLOCATION

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Constant Field Values

COORDSYSTEM

public static final String COORDSYSTEM

See Also:

Constant Field Values

CHAINS

public static final String CHAINS

See Also:

Constant Field Values

SOURCES

public static final String SOURCES

See Also:

Constant Field Values

BROWSERLINKS

public static final String BROWSERLINKS

See Also:

Constant Field Values

AGGREGATES_NORESULTS_MESSAGE

public static final String AGGREGATES_NORESULTS_MESSAGE

See Also:

Constant Field Values

HIGHLIGHTREGION

public static final String HIGHLIGHTREGION

See Also:

Constant Field Values

KEY_DATAEXPLORER_EDITABLE

public static final String KEY_DATAEXPLORER_EDITABLE

See Also:

Constant Field Values

KEY_DATAEXPLORER_ROW_CLICKABLE

public static final String KEY_DATAEXPLORER_ROW_CLICKABLE

See Also:

Constant Field Values

Constructor Detail

DataExplorerController

public DataExplorerController()

Method Detail

init

@RequestMapping(method=GET)
public String init(@RequestParam(value="entity",required=false)
                                               String selectedEntityName,
                                               @RequestParam(value="searchTerm",required=false)
                                               String searchTerm,
                                               org.springframework.ui.Model model)
                                        throws Exception

Show the explorer page

Parameters:

model -

Returns:

the view name

Throws:

Exception

getModule

@RequestMapping(value="/module/{moduleId}",
                method=GET)
public String getModule(@PathVariable(value="moduleId")
                                                                                                String moduleId,
                                                                                                @RequestParam(value="entity")
                                                                                                String entityName,
                                                                                                org.springframework.ui.Model model)

getModules

@RequestMapping(value="/modules",
                method=GET)
 @ResponseBody
public ModulesConfigResponse getModules(@RequestParam(value="entity")
                                                                                                                     String entityName)

Returns modules configuration for this entity based on current user permissions.

Parameters:

entityName -

Returns:

download

@RequestMapping(value="/download",
                method=POST)
public void download(@RequestParam(value="dataRequest")
                                                                                     String dataRequestStr,
                                                                                     javax.servlet.http.HttpServletResponse response)
                                                                              throws IOException

Throws:

IOException

exportToGalaxy

@RequestMapping(value="/galaxy/export",
                method=POST)
 @ResponseStatus(value=OK)
public void exportToGalaxy(@RequestBody
                                                                                                                           GalaxyDataExportRequest galaxyDataExportRequest,
                                                                                                                           org.springframework.ui.Model model)
                                                                                                                    throws IOException

Throws:

IOException

aggregate

@RequestMapping(value="/aggregate",
                method=POST,
                produces="application/json",
                consumes="application/json")
 @ResponseBody
public AggregateResult aggregate(@RequestBody
                                                                                                                                                                                                           AggregateRequest request)

viewEntityDetails

@RequestMapping(value="/details",
                method=POST)
public String viewEntityDetails(@RequestParam(value="entityName")
                                                                                               String entityName,
                                                                                               @RequestParam(value="entityId")
                                                                                               String entityId,
                                                                                               org.springframework.ui.Model model)
                                                                                        throws Exception

Builds a model containing one entity and returns the entityReport ftl view

Parameters:

entityName -

entityId -

model -

Returns:

entity report view

Throws:

Exception - if an entity name or id is not found

getSettings

@RequestMapping(value="/settings",
                method=GET)
 @ResponseBody
public Map<String,String> getSettings(@RequestParam(required=false)
                                                                                                                    String keyStartsWith)

handleGalaxyDataExportException

@ExceptionHandler(value=GalaxyDataExportException.class)
 @ResponseBody
 @ResponseStatus(value=BAD_REQUEST)
public ErrorMessageResponse handleGalaxyDataExportException(GalaxyDataExportException e)

handleRuntimeException

@ExceptionHandler(value=java.lang.RuntimeException.class)
 @ResponseBody
 @ResponseStatus(value=INTERNAL_SERVER_ERROR)
public ErrorMessageResponse handleRuntimeException(RuntimeException e)