ref 20971: ShortLink - Check for obsolete short urls

https://support.d4science.org/issues/20971

Fixed ShortLink urls.

CHANGELOG.md

@@ -1,5 +1,15 @@
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+# Changelog for "ecological-engine-smart-executor"
+
+## [v1.6.6] - 2021-05-31
+
+### Fixes
+
+- Fixed obsolete short urls [#20971]
+
+
 
-# Changelog
 ## [v1.6.5] - 2021-01-20
 
 ### Features
@@ -64,4 +74,3 @@
 
 
 
-This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

README.md

@@ -35,12 +35,4 @@ open-source software toolkit used for building and operating Hybrid Data
 Infrastructures enabling the dynamic deployment of Virtual Research Environments
 by favouring the realisation of reuse oriented policies.
  
-The projects leading to this software have received funding from a series of European Union programmes including:
+The projects leading to this software have received funding from a series of European Union programmes see [FUNDING.md](FUNDING.md)
-
-- the Sixth Framework Programme for Research and Technological Development
-    - DILIGENT (grant no. 004260);
-- the Seventh Framework Programme for research, technological development and demonstration 
-    - D4Science (grant no. 212488), D4Science-II (grant no.239019), ENVRI (grant no. 283465), EUBrazilOpenBio (grant no. 288754), iMarine(grant no. 283644);
-- the H2020 research and innovation programme 
-    - BlueBRIDGE (grant no. 675680), EGIEngage (grant no. 654142), ENVRIplus (grant no. 654182), Parthenos (grant no. 654119), SoBigData (grant no. 654024),DESIRA (grant no. 818194), ARIADNEplus (grant no. 823914), RISIS2 (grant no. 824091), PerformFish (grant no. 727610), AGINFRAplus (grant no. 731001);
-    

changelog.xml

@@ -1,5 +1,16 @@
 <ReleaseNotes xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:noNamespaceSchemaLocation="xsd/changelog.xsd">
+	<Changeset
+		component="org.gcube.data-analysis.ecological-engine-smart-executor.1-6-6"
+		date="2021-05-31">
+		<Change>Fixed obsolete short urls [#20971]</Change>
+	</Changeset>
+	<Changeset
+		component="org.gcube.data-analysis.ecological-engine-smart-executor.1-6-5"
+		date="2021-01-20">
+		<Change>Added commons-io-2.6 dependency</Change>
+		<Change>Update ecological-engine lower bound range</Change>
+	</Changeset>
 	<Changeset
 		component="org.gcube.data-analysis.ecological-engine-smart-executor.1-6-4"
 		date="2020-10-15">

descriptor.xml

@@ -15,7 +15,7 @@
 				<include>README.md</include>
 				<include>LICENSE.md</include>
 				<include>CHANGELOG.md</include>
-				<include>changelog.xml</include>
+				<include>FUNDING.md</include>
 				<include>profile.xml</include>
 			</includes>
 			<fileMode>755</fileMode>

pom.xml

@@ -9,7 +9,7 @@
 	</parent>
 	<groupId>org.gcube.dataanalysis</groupId>
 	<artifactId>ecological-engine-smart-executor</artifactId>
-	<version>1.6.5</version>
+	<version>1.6.6-SNAPSHOT</version>
 	<name>ecological-engine-smart-executor</name>
 	<description>Smart Ecological Engine Executor library</description>
 

src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/CMSY.java

@@ -53,8 +53,8 @@ public class CMSY extends ActorNode {
 		
 		List<StatisticalType> parameters = new ArrayList<StatisticalType>();
 		
-		IOHelper.addStringInput(parameters, idsFile, "Http link to a file containing prior information about the stocks, in WKLife IV format. Example: http://goo.gl/9rg3qK", "");
+		IOHelper.addStringInput(parameters, idsFile, "Http link to a file containing prior information about the stocks, in WKLife IV format.", "");
-		IOHelper.addStringInput(parameters, stocksFile, "Http link to a file containing catch and biomass (or CPUE) trends , in WKLife IV format. Example: http://goo.gl/Mp2ZLY", "");
+		IOHelper.addStringInput(parameters, stocksFile, "Http link to a file containing catch and biomass (or CPUE) trends , in WKLife IV format.", "");
 		IOHelper.addStringInput(parameters,stock,"The stock on which the procedure has to focus e.g. HLH_M07","" );
 				
 		return parameters;

src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java

@@ -44,7 +44,7 @@ public class FAOMSY extends ActorNode {
 				"Estimates the Maximum Sustainable Yield (MSY) of a stock, based on a catch trend. " +
 				"The algorithm has been developed by the Resource Use and Conservation Division of the FAO Fisheries and Aquaculture Department (contact: Yimin Ye, yimin.ye@fao.org). " +
 				"It is applicable to a CSV file containing metadata and catch statistics for a set of marine species and produces MSY estimates for each species. " +
-				"The CSV must follow a FAO-defined format (e.g. http://goo.gl/g6YtVx). " +
+				"The CSV must follow a FAO-defined format. " +
 				"The output is made up of two (optional) files: one for sucessfully processed species and another one for species that could not be processed because data were not sufficient to estimate MSY.";
 	}
 
@@ -58,7 +58,7 @@ public class FAOMSY extends ActorNode {
 	public List<StatisticalType> getInputParameters() {
 		
 		List<StatisticalType> parameters = new ArrayList<StatisticalType>();
-		IOHelper.addStringInput(parameters, stocksFile, "Http link to a file containing catch statistics for a group of species. Example: http://goo.gl/g6YtVx", "");
+		IOHelper.addStringInput(parameters, stocksFile, "Http link to a file containing catch statistics for a group of species.", "");
 		return parameters;
 	}
 

src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java

@@ -24,19 +24,19 @@ public abstract class YasmeenMatcher implements Matcher {
 
 	protected static HashMap<String, String> createReferenceMap() {
 		HashMap<String, String> urlsMaps = new HashMap<String, String>();
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.ASFIS.name(), "http://goo.gl/qfeTp7");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.ASFIS.name(), "https://data.d4science.org/shub/E_Z3g0Vm9MMDZBYld4MEMySUdET0hzWnd5R1NYUG1PcXZaU21DU2tLd0xmaCtBWk9sWHUzVmNJMTNhblBXV0F0VQ==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.FISHBASE.name(), "http://goo.gl/FcnUc0");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.FISHBASE.name(), "https://data.d4science.org/shub/E_c0pLQ2ZSZGd2ZFNLTFozNWM1eEZvc25CdFdibysvVVd1dVZDb3p1T0ZJb1pJT3g5YXNFY0lmbUFHMVFHaXdwZA==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS.name(), "http://goo.gl/AUcUXt");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS.name(), "https://data.d4science.org/shub/E_UFdIK2IxOEtoODAyTUNxY1BjTGJNclpQMDhkaEdHYXVNMUxmK3B2OFlNNDE3OWg3d0d1cm5JSHhCTDNYaGhSNw==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ANIMALIA.name(), "http://goo.gl/mW1fvb");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ANIMALIA.name(), "https://data.d4science.org/shub/E_ZUExS3FlU25NTURycXRUODVkZXdMZWJsR1dYMVpnVW42RDNHTHNkaGJtZjFaL2VGQklkTGUrUVdVa05uWnVZag==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_CNIDARIA.name(), "http://goo.gl/N6vCq8");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_CNIDARIA.name(), "https://data.d4science.org/shub/E_SHBjWnp1TTcrblVrMHJqZDZTTlN1bGJKVWxJV0FKUC8wYVpRZkFPMkZLbWJUMHlSRjBCQjNSVjFjalI0UWx5cQ==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ECHINODERMATA.name(), "http://goo.gl/2qQThI");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ECHINODERMATA.name(), "https://data.d4science.org/shub/E_R1ZYbEdHKzBtYlBPbzB6T3NWRDgrdlNHbWlPdHJRZVJDUmtEVitLQk11Unl4ZkE4aGhxNTFGZWxTV3lkZm9kOA==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_PLATYHELMINTHES.name(), "http://goo.gl/RLmCn2");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_PLATYHELMINTHES.name(), "https://data.d4science.org/shub/E_R25wUVFRSGJwK0xJL1MzZFdmeWNzZlNKNFFKQXRwL0JrZXBjYTJvRnE0a2Z2dm16L2VqZlI4ZUd0bldJV3h1Uw==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_FULL.name(), "http://goo.gl/fJ9feg");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_FULL.name(), "https://data.d4science.org/shub/E_NUJlVVhKak9NeWpIekdFdUU1Ty96UHA2QkpCZ0xISVNrdnN4VlBvRnRQZnhLcW1CUXVVMGMzbU5Dekpkcm5HaA==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_CHORDATA.name(), "http://goo.gl/11upZC");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_CHORDATA.name(), "https://data.d4science.org/shub/E_L3hTNzdrWFRQLzJYaVRGR0ZhWVhwSmluNFNvdkNKN3lWNEQ1Z0orZXBqSUdWYUJPaTFPMXdZWW1LYzg0UUtHUQ==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_MAMMALIA.name(), "http://goo.gl/J4fga6");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_MAMMALIA.name(), "https://data.d4science.org/shub/E_dHh4akNxazViQUVNTFNDd0E4RldnTDVlSUZ5b1lLdDluKzV2R21sSHZWTXBIaGVKbDNnZmUrNWVtUjZZUmthaA==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.IRMNG_ACTINOPTERYGII.name(), "http://goo.gl/Z8eRly");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.IRMNG_ACTINOPTERYGII.name(), "https://data.d4science.org/shub/E_bzZtY2xUeFZNSTA1WThMQjNLWWNrc1piSjRPZnk5REUrTUt6bVU3QjRIRWorUTBJUWZPNEdHOWdSYyt0RGFLVg==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_ANIMALIA.name(), "http://goo.gl/XRMWgr");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_ANIMALIA.name(), "https://data.d4science.org/shub/E_czVkaEtpeGxJTHJ5ZUNJanZBMzJmb3Q2VFhyNkZCZzlNTTk4KzRMcFQ5UlcrQlU0NEFJVEwzNmIxVmR2Vkt1YQ==");
-		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_PISCES.name(), "http://goo.gl/OdPRiA");
+		urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_PISCES.name(), "https://data.d4science.org/shub/E_Ylg2azNMMTBPOFIwNlRwMFZVSUM2WlFOSGZZUll0MVk4OXI2bmYrM2Y2OGlLYk5DZ3lqTlVPRUNKcnpITG1aRw==");
 
 		return urlsMaps;
 	}

src/main/java/org/gcube/dataanalysis/executor/rscripts/KnitrCompiler.java

@@ -20,7 +20,7 @@ public class KnitrCompiler extends GenericRScript {
 	
 	protected void initVariables(){
 		mainScriptName="IRDTunaAtlas-master/report/knitr/compileKnitR_CNR.R";
-		packageURL="http://goo.gl/T7V8LV";
+		packageURL="https://data.d4science.net/LP5L";
 		
 		environmentalvariables = new ArrayList<String>();
 		inputvariables.add("zipfile");

src/main/java/org/gcube/dataanalysis/executor/rscripts/SGVMS_Interpolation.java

@@ -26,7 +26,7 @@ public class SGVMS_Interpolation extends StandardLocalInfraAlgorithm {
 	@Override
 	public String getDescription() {
 		return "An interpolation method relying on the implementation by the Study Group on VMS (SGVMS). The method uses two interpolation approached to simulate vessels points at a certain temporal resolution. The input is a file in TACSAT format uploaded on the Statistical Manager. The output is another TACSAT file containing interpolated points." +
-				"The underlying R code has been extracted from the SGVM VMSTools framework. This algorithm comes after a feasibility study (http://goo.gl/risQre) which clarifies the features an e-Infrastructure adds to the original scripts. " +
+				"The underlying R code has been extracted from the SGVM VMSTools framework. This algorithm comes after a feasibility study which clarifies the features an e-Infrastructure adds to the original scripts. " +
 				"Limitation: the input will be processed up to "+maxPoints+" vessels trajectory points. " +
 				"Credits: Hintzen, N. T., Bastardie, F., Beare, D., Piet, G. J., Ulrich, C., Deporte, N., Egekvist, J., et al. 2012. VMStools: Open-source software for the processing, analysis and visualisation of fisheries logbook and VMS data. Fisheries Research, 115-116: 31-43. " +
 				"Hintzen, N. T., Piet, G. J., and Brunel, T. 2010. Improved estimation of trawling tracks using cubic Hermite spline interpolation of position registration data. Fisheries Research, 101: 108-115. " +
@@ -87,7 +87,7 @@ public class SGVMS_Interpolation extends StandardLocalInfraAlgorithm {
 	@Override
 	protected void setInputParameters() {
 		//declare the input parameters the user will set: they will basically correspond to the R context
-		inputs.add(new PrimitiveType(File.class.getName(), null, PrimitiveTypes.FILE, "InputFile", "Input file in TACSAT format. E.g. http://goo.gl/i16kPw"));
+		inputs.add(new PrimitiveType(File.class.getName(), null, PrimitiveTypes.FILE, "InputFile", "Input file in TACSAT format."));
 		addIntegerInput("npoints", "The number of pings or positions required between each real or actual vessel position or ping", "10");
 		addIntegerInput("interval", "Average time in minutes between two adjacent datapoints", "120");
 		addIntegerInput("margin", "Maximum deviation from specified interval to find adjacent datapoints (tolerance)", "10");

src/main/java/org/gcube/dataanalysis/executor/rscripts/TemplateRScripts.java

@@ -23,7 +23,7 @@ public class TemplateRScripts extends GenericRScript {
 	
 	protected void initVariables(){
 		mainScriptName="IRDTunaAtlas-master/report/knitr/compileKnitR_CNR.R";
-		packageURL="http://goo.gl/T7V8LV";
+		packageURL="https://data.d4science.net/LP5L";
 		
 		environmentalvariables = new ArrayList<String>();
 		inputvariables.add("zipfile");

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java

@@ -53,10 +53,7 @@ public static AlgorithmConfiguration getConfig() {
 		config.setParam("IDsFile","https://dl.dropboxusercontent.com/u/12809149/WKLIFE4ID.csv");
 		config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/WKLIFE4Stocks.csv");
 		
-		//config.setParam("IDsFile","http://goo.gl/9rg3qK");
+	
-		//		config.setParam("StocksFile","http://goo.gl/Mp2ZLY");
-//		config.setParam("StocksFile","http://goo.gl/btuIIe");
-//		config.setParam("SelectedStock","Pan_bor_1");
 		config.setParam("SelectedStock","HLH_M08");
 		
 		return config;

src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java

@@ -53,20 +53,7 @@ public static AlgorithmConfiguration getConfig() {
 		config.setParam("ServiceUserName", "gianpaolo.coro");
 		
 		D4ScienceDistributedProcessing.maxMessagesAllowedPerJob=2;
-		// http://goo.gl/FV95FP //1000 sp
+	
-			
-		config.setParam("StocksFile","http://goo.gl/dQKq75"); // 2 species
-//		config.setParam("StocksFile","http://goo.gl/n1bKOg"); // 1 species non processed type
-//		config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short1.csv");
-//		config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Short2.csv");
-		//config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_Longtest.csv");
-//		config.setParam("StocksFile","https://dl.dropboxusercontent.com/u/12809149/FAOMSY_1000sptest.csv");
-//		config.setParam("StocksFile","http://goo.gl/B09ZL0"); //50species
-		//config.setParam("IDsFile","http://goo.gl/9rg3qK");
-		//		config.setParam("StocksFile","http://goo.gl/Mp2ZLY");
-//		config.setParam("StocksFile","http://goo.gl/btuIIe");
-//		config.setParam("SelectedStock","Pan_bor_1");
-//		config.setParam("SelectedStock","HLH_M08");
 		
 		return config;
 	}