/**
* Show the explorer page
*
* @param model
* @return the view name
*/
@RequestMapping(method = RequestMethod.GET)
public String init(
@RequestParam(value = "dataset", required = false) String selectedEntityName,
@RequestParam(value = "wizard", required = false) Boolean wizard,
Model model)
throws Exception {
// set entityExplorer URL for link to EntityExplorer for x/mrefs, but only if the user has
// permission to see the
// plugin
if (molgenisPermissionService.hasPermissionOnPlugin(
EntityExplorerController.ID, Permission.READ)
|| molgenisPermissionService.hasPermissionOnPlugin(
EntityExplorerController.ID, Permission.WRITE)) {
model.addAttribute("entityExplorerUrl", EntityExplorerController.ID);
}
Iterable<EntityMetaData> entitiesMeta =
Iterables.transform(
dataService.getEntityNames(),
new Function<String, EntityMetaData>() {
@Override
public EntityMetaData apply(String entityName) {
return dataService.getEntityMetaData(entityName);
}
});
model.addAttribute("entitiesMeta", entitiesMeta);
if (selectedEntityName == null) {
selectedEntityName = entitiesMeta.iterator().next().getName();
}
model.addAttribute("selectedEntityName", selectedEntityName);
model.addAttribute("wizard", (wizard != null) && wizard.booleanValue());
// Init genome browser
model.addAttribute("genomeBrowserSets", getGenomeBrowserSetsToModel());
String appHrefCss = molgenisSettings.getProperty(KEY_APP_HREF_CSS);
if (appHrefCss != null) model.addAttribute(KEY_APP_HREF_CSS.replaceAll("\\.", "_"), appHrefCss);
// including/excluding charts
Boolean appIncludeCharts =
molgenisSettings.getBooleanProperty(KEY_APP_INCLUDE_CHARTS, INCLUDE_CHARTS_MODULE);
model.addAttribute(MODEL_APP_INCLUDE_CHARTS, appIncludeCharts);
model.addAttribute(INITLOCATION, molgenisSettings.getProperty(INITLOCATION));
model.addAttribute(COORDSYSTEM, molgenisSettings.getProperty(COORDSYSTEM));
model.addAttribute(CHAINS, molgenisSettings.getProperty(CHAINS));
model.addAttribute(SOURCES, molgenisSettings.getProperty(SOURCES));
model.addAttribute(BROWSERLINKS, molgenisSettings.getProperty(BROWSERLINKS));
model.addAttribute(SEARCHENDPOINT, molgenisSettings.getProperty(SEARCHENDPOINT));
model.addAttribute(KARYOTYPEENDPOINT, molgenisSettings.getProperty(KARYOTYPEENDPOINT));
model.addAttribute(GENOMEBROWSERTABLE, molgenisSettings.getProperty(GENOMEBROWSERTABLE));
return "view-dataexplorer";
}
/**
* @param meta
* @param attributesSet set of lowercase attribute names to include in response
* @param attributeExpandsSet set of lowercase attribute names to expand in response
*/
public EntityMetaDataResponse(
EntityMetaData meta,
Set<String> attributesSet,
Map<String, Set<String>> attributeExpandsSet,
MolgenisPermissionService permissionService,
DataService dataService) {
String name = meta.getName();
this.href = Href.concatMetaEntityHref(RestController.BASE_URI, name);
this.hrefCollection =
String.format("%s/%s", RestController.BASE_URI, name); // FIXME apply Href escaping fix
if (attributesSet == null || attributesSet.contains("name".toLowerCase())) {
this.name = name;
} else this.name = null;
if (attributesSet == null || attributesSet.contains("description".toLowerCase())) {
this.description = meta.getDescription();
} else this.description = null;
if (attributesSet == null || attributesSet.contains("label".toLowerCase())) {
label = meta.getLabel();
} else this.label = null;
if (attributesSet == null || attributesSet.contains("attributes".toLowerCase())) {
this.attributes = new LinkedHashMap<String, Object>();
for (AttributeMetaData attr : meta.getAttributes()) {
if (!attr.getName().equals("__Type")) {
if (attributeExpandsSet != null
&& attributeExpandsSet.containsKey("attributes".toLowerCase())) {
Set<String> subAttributesSet = attributeExpandsSet.get("attributes".toLowerCase());
this.attributes.put(
attr.getName(),
new AttributeMetaDataResponse(
name,
attr,
subAttributesSet,
Collections.singletonMap(
"refEntity".toLowerCase(), Sets.newHashSet("idattribute")),
permissionService,
dataService));
} else {
String attrHref =
Href.concatMetaAttributeHref(RestController.BASE_URI, name, attr.getName());
this.attributes.put(attr.getName(), Collections.singletonMap("href", attrHref));
}
}
}
} else this.attributes = null;
if (attributesSet == null || attributesSet.contains("labelAttribute".toLowerCase())) {
AttributeMetaData labelAttribute = meta.getLabelAttribute();
this.labelAttribute = labelAttribute != null ? labelAttribute.getName() : null;
} else this.labelAttribute = null;
if (attributesSet == null || attributesSet.contains("idAttribute".toLowerCase())) {
AttributeMetaData idAttribute = meta.getIdAttribute();
this.idAttribute = idAttribute != null ? idAttribute.getName() : null;
} else this.idAttribute = null;
if (attributesSet == null || attributesSet.contains("lookupAttributes".toLowerCase())) {
Iterable<AttributeMetaData> lookupAttributes = meta.getLookupAttributes();
this.lookupAttributes =
lookupAttributes != null
? Lists.newArrayList(
Iterables.transform(
lookupAttributes,
new Function<AttributeMetaData, String>() {
@Override
public String apply(AttributeMetaData attribute) {
return attribute.getName();
}
}))
: null;
} else this.lookupAttributes = null;
if (attributesSet == null || attributesSet.contains("abstract".toLowerCase())) {
isAbstract = meta.isAbstract();
} else this.isAbstract = null;
this.writable =
permissionService.hasPermissionOnEntity(name, Permission.WRITE)
&& dataService.getCapabilities(name).contains(RepositoryCapability.WRITABLE);
}