gCubeSystem
/
grsf-publisher-ws
16
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

minor fixes to csv 

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/grsf-publisher-ws@157715 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Costantino Perciante 2017-10-27 14:04:47 +00:00
parent 3c10c7467c
commit 4d9c4888b2
6 changed files with 78 additions and 78 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/others/TimeSeriesBean.java
View File

@ -82,7 +82,7 @@ public class TimeSeriesBean<T, T1> implements Comparable<TimeSeriesBean<T, T1>>{
}
public void setYear(Long year) {
this.year = year;
this.year = year == null? -1 : year;
}
public T1 getUnit() {
@ -132,7 +132,7 @@ public class TimeSeriesBean<T, T1> implements Comparable<TimeSeriesBean<T, T1>>{
@Override
public int compareTo(TimeSeriesBean<T, T1> o) {
return (int) (this.year - o.year); // ascending.. low to highest
return Long.compare(this.year, o.year);
}
@Override
@ -142,7 +142,7 @@ public class TimeSeriesBean<T, T1> implements Comparable<TimeSeriesBean<T, T1>>{
String unit = (this.unit != null ? " " + this.unit : "");
String databaseSource = (this.databaseSource != null ? " (" + this.databaseSource + ")" : "");
String dataOwner = (this.dataOwner != null ? " " + this.dataOwner : "");
String referenceYear = " Ref. Year " + year;
String referenceYear = year >= 0 ? " Ref. Year " + year : "";
String reportingYearOrAssessment = (assessment != null ? " and Rep. Year or Assessment Id " + assessment + "" : "");
return value + unit + databaseSource + dataOwner + referenceYear + reportingYearOrAssessment;

122
src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherFisheryService.java
View File

@ -49,7 +49,7 @@ import eu.trentorise.opendata.jackan.model.CkanDataset;
* Fishery web service methods.
* @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
*/
@Path("{source:firms|FIRMS|ram|RAM|grsf|GRSF|FishSource|fishsource}/fishery/")
@Path("{source:firms|FIRMS|grsf|GRSF|FishSource|fishsource}/fishery/")
public class GrsfPublisherFisheryService {
// the context
@ -108,9 +108,9 @@ public class GrsfPublisherFisheryService {
}else{
String apiKey = catalogue.getApiKeyFromUsername(username);
String organization = HelperMethods.retrieveOrgNameFromScope(context); //"grsf_admin";
String organization = HelperMethods.retrieveOrgNameFromScope(context);
CommonServiceUtils.hasAdminRole(username, catalogue, apiKey, organization);
// extend this role to the other organizations in this context
CommonServiceUtils.extendRoleToOtherOrganizations(username, catalogue, organization, RolesCkanGroupOrOrg.ADMIN);
@ -136,7 +136,19 @@ public class GrsfPublisherFisheryService {
List<ResourceBean> resources = record.getExtrasResources();
// validate end set sources
CommonServiceUtils.validateRecordAndMapFields(apiKey, context, contextServlet, sourceInPath, record, Product_Type.FISHERY, tags, customFields, groups, resources, username, futureTitle);
CommonServiceUtils.validateRecordAndMapFields(
apiKey,
context,
contextServlet,
sourceInPath,
record,
Product_Type.FISHERY,
tags,
customFields,
groups,
resources,
username,
futureTitle);
// check the license id
String license = null;
@ -145,7 +157,8 @@ public class GrsfPublisherFisheryService {
else
if(HelperMethods.existsLicenseId(record.getLicense(), catalogue))
license = record.getLicense();
else throw new Exception("Please check the license id!");
else
throw new Exception("Please check the license id!");
long version = record.getVersion() == null ? 1 : record.getVersion();
@ -159,7 +172,7 @@ public class GrsfPublisherFisheryService {
throw new Exception("Failed to retrieve the namespaces for the key fields!");
customFields = HelperMethods.replaceFieldsKey(customFields, namespaces, !sourceInPath.equals(Sources.GRSF));
String publishInOrganization = CommonServiceUtils.evaluateOrganization(organization, sourceInPath);
logger.info("Invoking create method..");
@ -186,16 +199,16 @@ public class GrsfPublisherFisheryService {
if(id != null){
logger.info("Created record with identifier " + id);
String description = "Short Name: " + record.getShortName() + "\n";
String description = Constants.SHORT_NAME_CUSTOM_KEY + ": " + record.getShortName() + "\n";
if(sourceInPath.equals(Sources.GRSF))
description += ", GRSF Semantic Identifier: " + record.getFisheryId() + "\n";
description += ", " + Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY + ": " + record.getFisheryId() + "\n";
CommonServiceUtils.actionsPostCreateOrUpdate(
id, futureName, record, apiKey, username, organization,
null, responseBean, catalogue, namespaces, groups, context, token, futureTitle, authorFullname,
contextServlet, false, description);
status = Status.CREATED;
}else{
@ -261,10 +274,6 @@ public class GrsfPublisherFisheryService {
status = Status.OK;
responseBean.setId(fisheryInCkan.getId());
}
else{
status = Status.INTERNAL_SERVER_ERROR;
throw new Exception("Request failed, sorry. Unable to delete/purge the fishery");
}
}else{
status = Status.BAD_REQUEST;
throw new Exception("The id you are using doesn't belong to a Fishery item having source " + source + "!");
@ -394,7 +403,7 @@ public class GrsfPublisherFisheryService {
if(catalogId == null || catalogId.isEmpty()){
status = Status.BAD_REQUEST;
throw new Exception("Please specify the 'catalog_id' property");
throw new Exception("Please specify the '" + Constants.CATALOG_ID + "' property");
}
DataCatalogue catalogue = HelperMethods.getDataCatalogueRunningInstance(context);
@ -419,13 +428,12 @@ public class GrsfPublisherFisheryService {
throw new Exception("Sorry but there was not possible to retrieve your fullname/email!");
}
String organization = HelperMethods.retrieveOrgNameFromScope(context); //"grsf_admin";
String organization = HelperMethods.retrieveOrgNameFromScope(context);
// check he/she has admin role
CommonServiceUtils.hasAdminRole(username, catalogue, apiKey, organization);
// name, title, product url and are going to remain unchanged (so we keep them from the publisher record);
// name, title, product url and are going to remain unchanged (so we keep them from the already published record);
String name = recordPublished.getName();
String title = recordPublished.getTitle();
@ -467,62 +475,58 @@ public class GrsfPublisherFisheryService {
// set the visibility of the datatest according the context
boolean publicDataset = context.equals((String)contextServlet.getInitParameter(HelperMethods.PUBLIC_CONTEX_KEY));
// add the SYSTEM_TYPE
customFields.put(Constants.SYSTEM_TYPE_CUSTOM_KEY, Arrays.asList(sourceInPath.getOrigName()));
// convert extras' keys to keys with namespace
Map<String, String> namespaces = HelperMethods.getFieldToFieldNameSpaceMapping(Constants.GENERIC_RESOURCE_NAME_MAP_KEY_NAMESPACES_FISHERY);
if(namespaces == null)
throw new Exception("Failed to retrieve the namespaces for the key fields!");
// retrieve the url
// retrieve the already generated url
String modifiedUUIDKey = namespaces.containsKey(Constants.ITEM_URL_FIELD) ?
namespaces.get(Constants.ITEM_URL_FIELD) :
Constants.ITEM_URL_FIELD;
String itemUrl = recordPublished.getExtrasAsHashMap().get(modifiedUUIDKey);
customFields.put(Constants.ITEM_URL_FIELD, Arrays.asList(itemUrl));
String itemUrl = recordPublished.getExtrasAsHashMap().get(modifiedUUIDKey);
customFields.put(Constants.ITEM_URL_FIELD, Arrays.asList(itemUrl));
// replace fields
customFields = HelperMethods.replaceFieldsKey(customFields, namespaces, !sourceInPath.equals(Sources.GRSF));
String publishInOrganization = CommonServiceUtils.evaluateOrganization(organization, sourceInPath);
// replace fields
customFields = HelperMethods.replaceFieldsKey(customFields, namespaces, !sourceInPath.equals(Sources.GRSF));
logger.info("Invoking update method..");
String publishInOrganization = CommonServiceUtils.evaluateOrganization(organization, sourceInPath);
// update the product
String id = catalogue.updateCKanDataset(
apiKey,
catalogId,
title, name,
publishInOrganization,
authorFullname,
authorMail,
record.getMaintainer(),
record.getMaintainerContact(),
version,
HelperMethods.removeHTML(record.getDescription()),
license,
new ArrayList<String>(tags),
null, // remove any previous group
customFields,
resources,
publicDataset);
logger.info("Invoking update method..");
if(id != null){
logger.info("Item updated!");
CommonServiceUtils.actionsPostCreateOrUpdate(
id, name, record, apiKey, username, organization,
itemUrl, responseBean, catalogue, namespaces, groups, context, token, title, authorFullname,
contextServlet, false, null);
status = Status.OK;
}else{
throw new Exception("There was an error during the item updated, sorry");
}
// update the product
String id = catalogue.updateCKanDataset(
apiKey,
catalogId,
title, name,
publishInOrganization,
authorFullname,
authorMail,
record.getMaintainer(),
record.getMaintainerContact(),
version,
HelperMethods.removeHTML(record.getDescription()),
license,
new ArrayList<String>(tags),
null, // remove any previous group
customFields,
resources,
publicDataset);
if(id != null){
logger.info("Item updated!");
CommonServiceUtils.actionsPostCreateOrUpdate(
id, name, record, apiKey, username, organization,
itemUrl, responseBean, catalogue, namespaces, groups, context, token, title, authorFullname,
contextServlet, false, null);
status = Status.OK;
}else{
throw new Exception("There was an error during the item updated, sorry");
}
}
}catch(Exception e){
logger.error("Failed to update fishery record" + e);
status = Status.INTERNAL_SERVER_ERROR;
responseBean.setError(e.getMessage());
}
return Response.status(status).entity(responseBean).build();

10
src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherStockService.java
View File

@ -200,15 +200,16 @@ public class GrsfPublisherStockService {
if(id != null){
logger.info("Product created! Id is " + id);
String description = "Short Name: " + record.getShortName() + "\n";
String description = Constants.SHORT_NAME_CUSTOM_KEY + ": " + record.getShortName() + "\n";
if(sourceInPath.equals(Sources.GRSF))
description += ", GRSF Semantic Identifier: " + record.getStockId() + "\n";
description += ", " + Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY + ": " + record.getStockId() + "\n";
CommonServiceUtils.actionsPostCreateOrUpdate(
id, futureName, record, apiKey, username, organization, null,
responseBean, catalogue, namespaces, groups, context, token,
futureTitle, authorFullname, contextServlet, false, description);
status = Status.CREATED;
}else
@ -323,7 +324,6 @@ public class GrsfPublisherStockService {
for (String id : fullGroupListIds) {
CkanDataset dataset = catalogue.getDataset(id, catalogue.getApiKeyFromUsername(username));
if(dataset != null){
String type = dataset.getExtrasAsHashMap().get(Constants.DOMAIN_CUSTOM_KEY);
if(Product_Type.STOCK.getOrigName().equals(type))
datasetsIds.add(id);
@ -474,9 +474,6 @@ public class GrsfPublisherStockService {
// set the visibility of the datatest according the context
boolean publicDataset = context.equals((String)contextServlet.getInitParameter(HelperMethods.PUBLIC_CONTEX_KEY));
// add the SYSTEM_TYPE
customFields.put(Constants.SYSTEM_TYPE_CUSTOM_KEY, Arrays.asList(sourceInPath.getOrigName()));
// convert extras' keys to keys with namespace
Map<String, String> namespaces = HelperMethods.getFieldToFieldNameSpaceMapping(Constants.GENERIC_RESOURCE_NAME_MAP_KEY_NAMESPACES_STOCK);
@ -529,7 +526,6 @@ public class GrsfPublisherStockService {
}
}catch(Exception e){
logger.error("Failed to update stock record", e);
status = Status.INTERNAL_SERVER_ERROR;
responseBean.setError(e.getMessage());
}
return Response.status(status).entity(responseBean).build();

3
src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/CommonServiceUtils.java
View File

@ -61,7 +61,6 @@ public class CommonServiceUtils {
licenses = HelperMethods.getLicenses(HelperMethods.getDataCatalogueRunningInstance(ScopeProvider.instance.get()));
}catch(Exception e){
logger.error("Failed to retrieve the list of licenses");
return null;
}
return licenses;
}
@ -583,7 +582,7 @@ public class CommonServiceUtils {
}
/**
* Evaluate in which organization a record has to be published. The only expcetion is when grsf_admin is involved.
* Evaluate in which organization a record has to be published. The only exception is when grsf_admin is involved.
* @param organization
* @param sourceInPath
* @return

6
src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/GcoreEndPointReaderSocial.java
View File

@ -41,17 +41,17 @@ public class GcoreEndPointReaderSocial {
query.addCondition("$resource/Profile/DeploymentData/Status/text() eq 'ready'");
query.addCondition(String.format("$resource/Profile/ServiceName/text() eq '%s'",serviceName));
query.setResult("$resource/Profile/AccessPoint/RunningInstanceInterfaces//Endpoint[@EntryName/string() eq \""+resource+"\"]/text()");
DiscoveryClient<String> client = client();
List<String> endpoints = client.submit(query);
if (endpoints == null || endpoints.isEmpty()) throw new Exception("Cannot retrieve the GCoreEndpoint serviceName: "+serviceName +", serviceClass: " +serviceClass +", in scope: "+context);
if (endpoints == null || endpoints.isEmpty())
throw new Exception("Cannot retrieve the GCoreEndpoint serviceName: "+serviceName +", serviceClass: " +serviceClass +", in scope: "+context);
this.basePath = endpoints.get(0);
if(basePath==null)
throw new Exception("Endpoint:"+resource+", is null for serviceName: "+serviceName +", serviceClass: " +serviceClass +", in scope: "+context);
logger.info("found entyname "+basePath+" for ckanResource: "+resource);
}catch(Exception e){
logger.error("Unable to retrieve such service endpoint information!", e);

9
src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/csv/CSVUtils.java
View File

@ -108,7 +108,7 @@ public class CSVUtils {
for (TimeSeriesBean<T, T1> bean : timeSeries)
{
StringBuffer oneLine = new StringBuffer();
oneLine.append(bean.getYear());
oneLine.append(bean.getYear() > 0 ? bean.getYear() : "");
if(isValuePresent){
oneLine.append(CSV_SEPARATOR);
@ -144,9 +144,6 @@ public class CSVUtils {
bw.close();
// file created
logger.debug("CSV file created correctly on this machine!");
// Add names of the sources to the file's name
for (String source : sources) {
relevantSources[0] += source + "_";
@ -155,6 +152,10 @@ public class CSVUtils {
// on exit delete it...
file.deleteOnExit();
// file created
logger.debug("CSV file created correctly on this machine!");
return file;
}
catch(Exception e){