From 04d69356f005576690a4aa5b23fea2737905653a Mon Sep 17 00:00:00 2001 From: Giancarlo Panichi Date: Mon, 31 May 2021 12:58:05 +0200 Subject: [PATCH] ref 20971: ShortLink - Check for obsolete short urls https://support.d4science.org/issues/20971 Fixed ShortLink urls. --- CHANGELOG.md | 13 ++++++++-- README.md | 10 +------ changelog.xml | 11 ++++++++ descriptor.xml | 2 +- pom.xml | 2 +- .../executor/nodes/algorithms/CMSY.java | 4 +-- .../executor/nodes/algorithms/FAOMSY.java | 4 +-- .../bionym/abstracts/YasmeenMatcher.java | 26 +++++++++---------- .../executor/rscripts/KnitrCompiler.java | 2 +- .../rscripts/SGVMS_Interpolation.java | 4 +-- .../executor/rscripts/TemplateRScripts.java | 2 +- .../executor/tests/RegressionTestCMSY.java | 5 +--- .../executor/tests/RegressionTestFAOMSY.java | 15 +---------- 13 files changed, 48 insertions(+), 52 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 904f645..b2e5fa2 100644 --- a/CHANGELOG.md +++ b/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). diff --git a/README.md b/README.md index 0ec90ed..73f933e 100644 --- a/README.md +++ b/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 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); - \ No newline at end of file +The projects leading to this software have received funding from a series of European Union programmes see [FUNDING.md](FUNDING.md) \ No newline at end of file diff --git a/changelog.xml b/changelog.xml index ad38a3f..dc1a488 100644 --- a/changelog.xml +++ b/changelog.xml @@ -1,5 +1,16 @@ + + Fixed obsolete short urls [#20971] + + + Added commons-io-2.6 dependency + Update ecological-engine lower bound range + diff --git a/descriptor.xml b/descriptor.xml index 12df762..e87081c 100644 --- a/descriptor.xml +++ b/descriptor.xml @@ -15,7 +15,7 @@ README.md LICENSE.md CHANGELOG.md - changelog.xml + FUNDING.md profile.xml 755 diff --git a/pom.xml b/pom.xml index bf3b18c..2d23891 100644 --- a/pom.xml +++ b/pom.xml @@ -9,7 +9,7 @@ org.gcube.dataanalysis ecological-engine-smart-executor - 1.6.5 + 1.6.6-SNAPSHOT ecological-engine-smart-executor Smart Ecological Engine Executor library diff --git a/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/CMSY.java b/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/CMSY.java index fe21a89..a9c100f 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/CMSY.java +++ b/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/CMSY.java @@ -53,8 +53,8 @@ public class CMSY extends ActorNode { List parameters = new ArrayList(); - 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, 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, 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.", ""); IOHelper.addStringInput(parameters,stock,"The stock on which the procedure has to focus e.g. HLH_M07","" ); return parameters; diff --git a/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java b/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java index ccda547..5334b20 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/nodes/algorithms/FAOMSY.java +++ b/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 getInputParameters() { List parameters = new ArrayList(); - 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; } diff --git a/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java b/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java index 044e284..6496aa7 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java +++ b/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 createReferenceMap() { HashMap urlsMaps = new HashMap(); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.ASFIS.name(), "http://goo.gl/qfeTp7"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.FISHBASE.name(), "http://goo.gl/FcnUc0"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS.name(), "http://goo.gl/AUcUXt"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ANIMALIA.name(), "http://goo.gl/mW1fvb"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_CNIDARIA.name(), "http://goo.gl/N6vCq8"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ECHINODERMATA.name(), "http://goo.gl/2qQThI"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_PLATYHELMINTHES.name(), "http://goo.gl/RLmCn2"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_FULL.name(), "http://goo.gl/fJ9feg"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_CHORDATA.name(), "http://goo.gl/11upZC"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_MAMMALIA.name(), "http://goo.gl/J4fga6"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.IRMNG_ACTINOPTERYGII.name(), "http://goo.gl/Z8eRly"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_ANIMALIA.name(), "http://goo.gl/XRMWgr"); - urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_PISCES.name(), "http://goo.gl/OdPRiA"); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.ASFIS.name(), "https://data.d4science.org/shub/E_Z3g0Vm9MMDZBYld4MEMySUdET0hzWnd5R1NYUG1PcXZaU21DU2tLd0xmaCtBWk9sWHUzVmNJMTNhblBXV0F0VQ=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.FISHBASE.name(), "https://data.d4science.org/shub/E_c0pLQ2ZSZGd2ZFNLTFozNWM1eEZvc25CdFdibysvVVd1dVZDb3p1T0ZJb1pJT3g5YXNFY0lmbUFHMVFHaXdwZA=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS.name(), "https://data.d4science.org/shub/E_UFdIK2IxOEtoODAyTUNxY1BjTGJNclpQMDhkaEdHYXVNMUxmK3B2OFlNNDE3OWg3d0d1cm5JSHhCTDNYaGhSNw=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ANIMALIA.name(), "https://data.d4science.org/shub/E_ZUExS3FlU25NTURycXRUODVkZXdMZWJsR1dYMVpnVW42RDNHTHNkaGJtZjFaL2VGQklkTGUrUVdVa05uWnVZag=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_CNIDARIA.name(), "https://data.d4science.org/shub/E_SHBjWnp1TTcrblVrMHJqZDZTTlN1bGJKVWxJV0FKUC8wYVpRZkFPMkZLbWJUMHlSRjBCQjNSVjFjalI0UWx5cQ=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_ECHINODERMATA.name(), "https://data.d4science.org/shub/E_R1ZYbEdHKzBtYlBPbzB6T3NWRDgrdlNHbWlPdHJRZVJDUmtEVitLQk11Unl4ZkE4aGhxNTFGZWxTV3lkZm9kOA=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.OBIS_PLATYHELMINTHES.name(), "https://data.d4science.org/shub/E_R25wUVFRSGJwK0xJL1MzZFdmeWNzZlNKNFFKQXRwL0JrZXBjYTJvRnE0a2Z2dm16L2VqZlI4ZUd0bldJV3h1Uw=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_FULL.name(), "https://data.d4science.org/shub/E_NUJlVVhKak9NeWpIekdFdUU1Ty96UHA2QkpCZ0xISVNrdnN4VlBvRnRQZnhLcW1CUXVVMGMzbU5Dekpkcm5HaA=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_CHORDATA.name(), "https://data.d4science.org/shub/E_L3hTNzdrWFRQLzJYaVRGR0ZhWVhwSmluNFNvdkNKN3lWNEQ1Z0orZXBqSUdWYUJPaTFPMXdZWW1LYzg0UUtHUQ=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.COL_MAMMALIA.name(), "https://data.d4science.org/shub/E_dHh4akNxazViQUVNTFNDd0E4RldnTDVlSUZ5b1lLdDluKzV2R21sSHZWTXBIaGVKbDNnZmUrNWVtUjZZUmthaA=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.IRMNG_ACTINOPTERYGII.name(), "https://data.d4science.org/shub/E_bzZtY2xUeFZNSTA1WThMQjNLWWNrc1piSjRPZnk5REUrTUt6bVU3QjRIRWorUTBJUWZPNEdHOWdSYyt0RGFLVg=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_ANIMALIA.name(), "https://data.d4science.org/shub/E_czVkaEtpeGxJTHJ5ZUNJanZBMzJmb3Q2VFhyNkZCZzlNTTk4KzRMcFQ5UlcrQlU0NEFJVEwzNmIxVmR2Vkt1YQ=="); + urlsMaps.put(YasmeenGlobalParameters.BuiltinDataSources.WORMS_PISCES.name(), "https://data.d4science.org/shub/E_Ylg2azNMMTBPOFIwNlRwMFZVSUM2WlFOSGZZUll0MVk4OXI2bmYrM2Y2OGlLYk5DZ3lqTlVPRUNKcnpITG1aRw=="); return urlsMaps; } diff --git a/src/main/java/org/gcube/dataanalysis/executor/rscripts/KnitrCompiler.java b/src/main/java/org/gcube/dataanalysis/executor/rscripts/KnitrCompiler.java index 7906913..103f262 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/rscripts/KnitrCompiler.java +++ b/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(); inputvariables.add("zipfile"); diff --git a/src/main/java/org/gcube/dataanalysis/executor/rscripts/SGVMS_Interpolation.java b/src/main/java/org/gcube/dataanalysis/executor/rscripts/SGVMS_Interpolation.java index 739c5e1..aa21415 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/rscripts/SGVMS_Interpolation.java +++ b/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"); diff --git a/src/main/java/org/gcube/dataanalysis/executor/rscripts/TemplateRScripts.java b/src/main/java/org/gcube/dataanalysis/executor/rscripts/TemplateRScripts.java index 248b5be..76f8981 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/rscripts/TemplateRScripts.java +++ b/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(); inputvariables.add("zipfile"); diff --git a/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java index 3356db3..d9b042e 100644 --- a/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java +++ b/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; diff --git a/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java index 74b234b..2f13057 100644 --- a/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java +++ b/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; }